FlatCAM/camlib.py

# ########################################################## ##
# FlatCAM: 2D Post-processing for Manufacturing               #
# http://flatcam.org                                          #
# Author: Juan Pablo Caram (c)                                #
# Date: 2/5/2014                                              #
# MIT Licence                                                 #
# ########################################################## ##


from PyQt5 import QtWidgets, QtCore
from io import StringIO

import numpy as np
from numpy.linalg import solve, norm

import platform
from copy import deepcopy

import traceback
from decimal import Decimal

from rtree import index as rtindex
from lxml import etree as ET

# See: http://toblerity.org/shapely/manual.html
from shapely.geometry import Polygon, LineString, Point, LinearRing, MultiLineString, MultiPoint, MultiPolygon

from shapely.geometry import box as shply_box
from shapely.ops import cascaded_union, unary_union, polygonize
import shapely.affinity as affinity
from shapely.wkt import loads as sloads
from shapely.wkt import dumps as sdumps
from shapely.geometry.base import BaseGeometry
from shapely.geometry import shape

# needed for legacy mode
# Used for solid polygons in Matplotlib
from descartes.patch import PolygonPatch

import collections
from collections import Iterable

import rasterio
from rasterio.features import shapes
import ezdxf

# TODO: Commented for FlatCAM packaging with cx_freeze
# from scipy.spatial import KDTree, Delaunay
# from scipy.spatial import Delaunay

from flatcamParsers.ParseSVG import *
from flatcamParsers.ParseDXF import *

if platform.architecture()[0] == '64bit':
    from ortools.constraint_solver import pywrapcp
    from ortools.constraint_solver import routing_enums_pb2

import logging
import FlatCAMApp
import gettext
import FlatCAMTranslation as fcTranslate
import builtins

fcTranslate.apply_language('strings')

log = logging.getLogger('base2')
log.setLevel(logging.DEBUG)

formatter = logging.Formatter('[%(levelname)s] %(message)s')
handler = logging.StreamHandler()
handler.setFormatter(formatter)
log.addHandler(handler)

if '_' not in builtins.__dict__:
    _ = gettext.gettext


class ParseError(Exception):
    pass


class ApertureMacro:
    """
    Syntax of aperture macros.

    <AM command>:           AM<Aperture macro name>*<Macro content>
    <Macro content>:        {{<Variable definition>*}{<Primitive>*}}
    <Variable definition>:  $K=<Arithmetic expression>
    <Primitive>:            <Primitive code>,<Modifier>{,<Modifier>}|<Comment>
    <Modifier>:             $M|< Arithmetic expression>
    <Comment>:              0 <Text>
    """

    # ## Regular expressions
    am1_re = re.compile(r'^%AM([^\*]+)\*(.+)?(%)?$')
    am2_re = re.compile(r'(.*)%$')
    amcomm_re = re.compile(r'^0(.*)')
    amprim_re = re.compile(r'^[1-9].*')
    amvar_re = re.compile(r'^\$([0-9a-zA-z]+)=(.*)')

    def __init__(self, name=None):
        self.name = name
        self.raw = ""

        # ## These below are recomputed for every aperture
        # ## definition, in other words, are temporary variables.
        self.primitives = []
        self.locvars = {}
        self.geometry = None

    def to_dict(self):
        """
        Returns the object in a serializable form. Only the name and
        raw are required.

        :return: Dictionary representing the object. JSON ready.
        :rtype: dict
        """

        return {
            'name': self.name,
            'raw': self.raw
        }

    def from_dict(self, d):
        """
        Populates the object from a serial representation created
        with ``self.to_dict()``.

        :param d: Serial representation of an ApertureMacro object.
        :return: None
        """
        for attr in ['name', 'raw']:
            setattr(self, attr, d[attr])

    def parse_content(self):
        """
        Creates numerical lists for all primitives in the aperture
        macro (in ``self.raw``) by replacing all variables by their
        values iteratively and evaluating expressions. Results
        are stored in ``self.primitives``.

        :return: None
        """
        # Cleanup
        self.raw = self.raw.replace('\n', '').replace('\r', '').strip(" *")
        self.primitives = []

        # Separate parts
        parts = self.raw.split('*')

        # ### Every part in the macro ####
        for part in parts:
            # ## Comments. Ignored.
            match = ApertureMacro.amcomm_re.search(part)
            if match:
                continue

            # ## Variables
            # These are variables defined locally inside the macro. They can be
            # numerical constant or defined in terms of previously define
            # variables, which can be defined locally or in an aperture
            # definition. All replacements occur here.
            match = ApertureMacro.amvar_re.search(part)
            if match:
                var = match.group(1)
                val = match.group(2)

                # Replace variables in value
                for v in self.locvars:
                    # replaced the following line with the next to fix Mentor custom apertures not parsed OK
                    # val = re.sub((r'\$'+str(v)+r'(?![0-9a-zA-Z])'), str(self.locvars[v]), val)
                    val = val.replace('$' + str(v), str(self.locvars[v]))

                # Make all others 0
                val = re.sub(r'\$[0-9a-zA-Z](?![0-9a-zA-Z])', "0", val)
                # Change x with *
                val = re.sub(r'[xX]', "*", val)

                # Eval() and store.
                self.locvars[var] = eval(val)
                continue

            # ## Primitives
            # Each is an array. The first identifies the primitive, while the
            # rest depend on the primitive. All are strings representing a
            # number and may contain variable definition. The values of these
            # variables are defined in an aperture definition.
            match = ApertureMacro.amprim_re.search(part)
            if match:
                # ## Replace all variables
                for v in self.locvars:
                    # replaced the following line with the next to fix Mentor custom apertures not parsed OK
                    # part = re.sub(r'\$' + str(v) + r'(?![0-9a-zA-Z])', str(self.locvars[v]), part)
                    part = part.replace('$' + str(v), str(self.locvars[v]))

                # Make all others 0
                part = re.sub(r'\$[0-9a-zA-Z](?![0-9a-zA-Z])', "0", part)

                # Change x with *
                part = re.sub(r'[xX]', "*", part)

                # ## Store
                elements = part.split(",")
                self.primitives.append([eval(x) for x in elements])
                continue

            log.warning("Unknown syntax of aperture macro part: %s" % str(part))

    def append(self, data):
        """
        Appends a string to the raw macro.

        :param data: Part of the macro.
        :type data: str
        :return: None
        """
        self.raw += data

    @staticmethod
    def default2zero(n, mods):
        """
        Pads the ``mods`` list with zeros resulting in an
        list of length n.

        :param n: Length of the resulting list.
        :type n: int
        :param mods: List to be padded.
        :type mods: list
        :return: Zero-padded list.
        :rtype: list
        """
        x = [0.0] * n
        na = len(mods)
        x[0:na] = mods
        return x

    @staticmethod
    def make_circle(mods):
        """

        :param mods: (Exposure 0/1, Diameter >=0, X-coord, Y-coord)
        :return:
        """

        pol, dia, x, y = ApertureMacro.default2zero(4, mods)

        return {"pol": int(pol), "geometry": Point(x, y).buffer(dia/2)}

    @staticmethod
    def make_vectorline(mods):
        """

        :param mods: (Exposure 0/1, Line width >= 0, X-start, Y-start, X-end, Y-end,
            rotation angle around origin in degrees)
        :return:
        """
        pol, width, xs, ys, xe, ye, angle = ApertureMacro.default2zero(7, mods)

        line = LineString([(xs, ys), (xe, ye)])
        box = line.buffer(width/2, cap_style=2)
        box_rotated = affinity.rotate(box, angle, origin=(0, 0))

        return {"pol": int(pol), "geometry": box_rotated}

    @staticmethod
    def make_centerline(mods):
        """

        :param mods: (Exposure 0/1, width >=0, height >=0, x-center, y-center,
            rotation angle around origin in degrees)
        :return:
        """

        pol, width, height, x, y, angle = ApertureMacro.default2zero(6, mods)

        box = shply_box(x-width/2, y-height/2, x+width/2, y+height/2)
        box_rotated = affinity.rotate(box, angle, origin=(0, 0))

        return {"pol": int(pol), "geometry": box_rotated}

    @staticmethod
    def make_lowerleftline(mods):
        """

        :param mods: (exposure 0/1, width >=0, height >=0, x-lowerleft, y-lowerleft,
            rotation angle around origin in degrees)
        :return:
        """

        pol, width, height, x, y, angle = ApertureMacro.default2zero(6, mods)

        box = shply_box(x, y, x+width, y+height)
        box_rotated = affinity.rotate(box, angle, origin=(0, 0))

        return {"pol": int(pol), "geometry": box_rotated}

    @staticmethod
    def make_outline(mods):
        """

        :param mods:
        :return:
        """

        pol = mods[0]
        n = mods[1]
        points = [(0, 0)]*(n+1)

        for i in range(n+1):
            points[i] = mods[2*i + 2:2*i + 4]

        angle = mods[2*n + 4]

        poly = Polygon(points)
        poly_rotated = affinity.rotate(poly, angle, origin=(0, 0))

        return {"pol": int(pol), "geometry": poly_rotated}

    @staticmethod
    def make_polygon(mods):
        """
        Note: Specs indicate that rotation is only allowed if the center
        (x, y) == (0, 0). I will tolerate breaking this rule.

        :param mods: (exposure 0/1, n_verts 3<=n<=12, x-center, y-center,
            diameter of circumscribed circle >=0, rotation angle around origin)
        :return:
        """

        pol, nverts, x, y, dia, angle = ApertureMacro.default2zero(6, mods)
        points = [(0, 0)]*nverts

        for i in range(nverts):
            points[i] = (x + 0.5 * dia * np.cos(2*np.pi * i/nverts),
                         y + 0.5 * dia * np.sin(2*np.pi * i/nverts))

        poly = Polygon(points)
        poly_rotated = affinity.rotate(poly, angle, origin=(0, 0))

        return {"pol": int(pol), "geometry": poly_rotated}

    @staticmethod
    def make_moire(mods):
        """
        Note: Specs indicate that rotation is only allowed if the center
        (x, y) == (0, 0). I will tolerate breaking this rule.

        :param mods: (x-center, y-center, outer_dia_outer_ring, ring thickness,
            gap, max_rings, crosshair_thickness, crosshair_len, rotation
            angle around origin in degrees)
        :return:
        """

        x, y, dia, thickness, gap, nrings, cross_th, cross_len, angle = ApertureMacro.default2zero(9, mods)

        r = dia/2 - thickness/2
        result = Point((x, y)).buffer(r).exterior.buffer(thickness/2.0)
        ring = Point((x, y)).buffer(r).exterior.buffer(thickness/2.0)  # Need a copy!

        i = 1  # Number of rings created so far

        # ## If the ring does not have an interior it means that it is
        # ## a disk. Then stop.
        while len(ring.interiors) > 0 and i < nrings:
            r -= thickness + gap
            if r <= 0:
                break
            ring = Point((x, y)).buffer(r).exterior.buffer(thickness/2.0)
            result = cascaded_union([result, ring])
            i += 1

        # ## Crosshair
        hor = LineString([(x - cross_len, y), (x + cross_len, y)]).buffer(cross_th/2.0, cap_style=2)
        ver = LineString([(x, y-cross_len), (x, y + cross_len)]).buffer(cross_th/2.0, cap_style=2)
        result = cascaded_union([result, hor, ver])

        return {"pol": 1, "geometry": result}

    @staticmethod
    def make_thermal(mods):
        """
        Note: Specs indicate that rotation is only allowed if the center
        (x, y) == (0, 0). I will tolerate breaking this rule.

        :param mods: [x-center, y-center, diameter-outside, diameter-inside,
            gap-thickness, rotation angle around origin]
        :return:
        """

        x, y, dout, din, t, angle = ApertureMacro.default2zero(6, mods)

        ring = Point((x, y)).buffer(dout/2.0).difference(Point((x, y)).buffer(din/2.0))
        hline = LineString([(x - dout/2.0, y), (x + dout/2.0, y)]).buffer(t/2.0, cap_style=3)
        vline = LineString([(x, y - dout/2.0), (x, y + dout/2.0)]).buffer(t/2.0, cap_style=3)
        thermal = ring.difference(hline.union(vline))

        return {"pol": 1, "geometry": thermal}

    def make_geometry(self, modifiers):
        """
        Runs the macro for the given modifiers and generates
        the corresponding geometry.

        :param modifiers: Modifiers (parameters) for this macro
        :type modifiers: list
        :return: Shapely geometry
        :rtype: shapely.geometry.polygon
        """

        # ## Primitive makers
        makers = {
            "1": ApertureMacro.make_circle,
            "2": ApertureMacro.make_vectorline,
            "20": ApertureMacro.make_vectorline,
            "21": ApertureMacro.make_centerline,
            "22": ApertureMacro.make_lowerleftline,
            "4": ApertureMacro.make_outline,
            "5": ApertureMacro.make_polygon,
            "6": ApertureMacro.make_moire,
            "7": ApertureMacro.make_thermal
        }

        # ## Store modifiers as local variables
        modifiers = modifiers or []
        modifiers = [float(m) for m in modifiers]
        self.locvars = {}
        for i in range(0, len(modifiers)):
            self.locvars[str(i + 1)] = modifiers[i]

        # ## Parse
        self.primitives = []  # Cleanup
        self.geometry = Polygon()
        self.parse_content()

        # ## Make the geometry
        for primitive in self.primitives:
            # Make the primitive
            prim_geo = makers[str(int(primitive[0]))](primitive[1:])

            # Add it (according to polarity)
            # if self.geometry is None and prim_geo['pol'] == 1:
            #     self.geometry = prim_geo['geometry']
            #     continue
            if prim_geo['pol'] == 1:
                self.geometry = self.geometry.union(prim_geo['geometry'])
                continue
            if prim_geo['pol'] == 0:
                self.geometry = self.geometry.difference(prim_geo['geometry'])
                continue

        return self.geometry


class Geometry(object):
    """
    Base geometry class.
    """

    defaults = {
        "units": 'mm',
        # "geo_steps_per_circle": 128
    }

    def __init__(self, geo_steps_per_circle=None):
        # Units (in or mm)
        self.units = self.app.defaults["units"]
        self.decimals = self.app.decimals

        # Final geometry: MultiPolygon or list (of geometry constructs)
        self.solid_geometry = None

        # Final geometry: MultiLineString or list (of LineString or Points)
        self.follow_geometry = None

        # Attributes to be included in serialization
        self.ser_attrs = ["units", 'solid_geometry', 'follow_geometry']

        # Flattened geometry (list of paths only)
        self.flat_geometry = []

        # this is the calculated conversion factor when the file units are different than the ones in the app
        self.file_units_factor = 1

        # Index
        self.index = None

        self.geo_steps_per_circle = geo_steps_per_circle

        # variables to display the percentage of work done
        self.geo_len = 0
        self.old_disp_number = 0
        self.el_count = 0

        if self.app.is_legacy is False:
            self.temp_shapes = self.app.plotcanvas.new_shape_group()
        else:
            from flatcamGUI.PlotCanvasLegacy import ShapeCollectionLegacy
            self.temp_shapes = ShapeCollectionLegacy(obj=self, app=self.app, name='camlib.geometry')

    def plot_temp_shapes(self, element, color='red'):

        try:
            for sub_el in element:
                self.plot_temp_shapes(sub_el)
        except TypeError:  # Element is not iterable...
            # self.add_shape(shape=element, color=color, visible=visible, layer=0)
            self.temp_shapes.add(tolerance=float(self.app.defaults["global_tolerance"]),
                                 shape=element, color=color, visible=True, layer=0)

    def make_index(self):
        self.flatten()
        self.index = FlatCAMRTree()

        for i, g in enumerate(self.flat_geometry):
            self.index.insert(i, g)

    def add_circle(self, origin, radius):
        """
        Adds a circle to the object.

        :param origin: Center of the circle.
        :param radius: Radius of the circle.
        :return: None
        """

        if self.solid_geometry is None:
            self.solid_geometry = []

        if type(self.solid_geometry) is list:
            self.solid_geometry.append(Point(origin).buffer(radius, int(self.geo_steps_per_circle)))
            return

        try:
            self.solid_geometry = self.solid_geometry.union(
                Point(origin).buffer(radius, int(self.geo_steps_per_circle))
            )
        except Exception as e:
            log.error("Failed to run union on polygons. %s" % str(e))
            return

    def add_polygon(self, points):
        """
        Adds a polygon to the object (by union)

        :param points: The vertices of the polygon.
        :return: None
        """
        if self.solid_geometry is None:
            self.solid_geometry = []

        if type(self.solid_geometry) is list:
            self.solid_geometry.append(Polygon(points))
            return

        try:
            self.solid_geometry = self.solid_geometry.union(Polygon(points))
        except Exception as e:
            log.error("Failed to run union on polygons. %s" % str(e))
            return

    def add_polyline(self, points):
        """
        Adds a polyline to the object (by union)

        :param points: The vertices of the polyline.
        :return: None
        """
        if self.solid_geometry is None:
            self.solid_geometry = []

        if type(self.solid_geometry) is list:
            self.solid_geometry.append(LineString(points))
            return

        try:
            self.solid_geometry = self.solid_geometry.union(LineString(points))
        except Exception as e:
            log.error("Failed to run union on polylines. %s" % str(e))
            return

    def is_empty(self):
        if isinstance(self.solid_geometry, BaseGeometry):
            return self.solid_geometry.is_empty

        if isinstance(self.solid_geometry, list):
            return len(self.solid_geometry) == 0

        self.app.inform.emit('[ERROR_NOTCL] %s' %
                             _("self.solid_geometry is neither BaseGeometry or list."))
        return

    def subtract_polygon(self, points):
        """
        Subtract polygon from the given object. This only operates on the paths in the original geometry,
        i.e. it converts polygons into paths.

        :param points: The vertices of the polygon.
        :return: none
        """
        if self.solid_geometry is None:
            self.solid_geometry = []

        # pathonly should be allways True, otherwise polygons are not subtracted
        flat_geometry = self.flatten(pathonly=True)
        log.debug("%d paths" % len(flat_geometry))
        polygon = Polygon(points)
        toolgeo = cascaded_union(polygon)
        diffs = []
        for target in flat_geometry:
            if type(target) == LineString or type(target) == LinearRing:
                diffs.append(target.difference(toolgeo))
            else:
                log.warning("Not implemented.")
        self.solid_geometry = cascaded_union(diffs)

    def bounds(self):
        """
        Returns coordinates of rectangular bounds
        of geometry: (xmin, ymin, xmax, ymax).
        """
        # fixed issue of getting bounds only for one level lists of objects
        # now it can get bounds for nested lists of objects

        log.debug("camlib.Geometry.bounds()")

        if self.solid_geometry is None:
            log.debug("solid_geometry is None")
            return 0, 0, 0, 0

        def bounds_rec(obj):
            if type(obj) is list:
                minx = np.Inf
                miny = np.Inf
                maxx = -np.Inf
                maxy = -np.Inf

                for k in obj:
                    if type(k) is dict:
                        for key in k:
                            minx_, miny_, maxx_, maxy_ = bounds_rec(k[key])
                            minx = min(minx, minx_)
                            miny = min(miny, miny_)
                            maxx = max(maxx, maxx_)
                            maxy = max(maxy, maxy_)
                    else:
                        minx_, miny_, maxx_, maxy_ = bounds_rec(k)
                        minx = min(minx, minx_)
                        miny = min(miny, miny_)
                        maxx = max(maxx, maxx_)
                        maxy = max(maxy, maxy_)
                return minx, miny, maxx, maxy
            else:
                # it's a Shapely object, return it's bounds
                return obj.bounds

        if self.multigeo is True:
            minx_list = []
            miny_list = []
            maxx_list = []
            maxy_list = []

            for tool in self.tools:
                minx, miny, maxx, maxy = bounds_rec(self.tools[tool]['solid_geometry'])
                minx_list.append(minx)
                miny_list.append(miny)
                maxx_list.append(maxx)
                maxy_list.append(maxy)

            return(min(minx_list), min(miny_list), max(maxx_list), max(maxy_list))
        else:
            bounds_coords = bounds_rec(self.solid_geometry)
            return bounds_coords

        # try:
        #     # from here: http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
        #     def flatten(l, ltypes=(list, tuple)):
        #         ltype = type(l)
        #         l = list(l)
        #         i = 0
        #         while i < len(l):
        #             while isinstance(l[i], ltypes):
        #                 if not l[i]:
        #                     l.pop(i)
        #                     i -= 1
        #                     break
        #                 else:
        #                     l[i:i + 1] = l[i]
        #             i += 1
        #         return ltype(l)
        #
        #     log.debug("Geometry->bounds()")
        #     if self.solid_geometry is None:
        #         log.debug("solid_geometry is None")
        #         return 0, 0, 0, 0
        #
        #     if type(self.solid_geometry) is list:
        #         # TODO: This can be done faster. See comment from Shapely mailing lists.
        #         if len(self.solid_geometry) == 0:
        #             log.debug('solid_geometry is empty []')
        #             return 0, 0, 0, 0
        #         return cascaded_union(flatten(self.solid_geometry)).bounds
        #     else:
        #         return self.solid_geometry.bounds
        # except Exception as e:
        #     self.app.inform.emit("[ERROR_NOTCL] Error cause: %s" % str(e))

        # log.debug("Geometry->bounds()")
        # if self.solid_geometry is None:
        #     log.debug("solid_geometry is None")
        #     return 0, 0, 0, 0
        #
        # if type(self.solid_geometry) is list:
        #     # TODO: This can be done faster. See comment from Shapely mailing lists.
        #     if len(self.solid_geometry) == 0:
        #         log.debug('solid_geometry is empty []')
        #         return 0, 0, 0, 0
        #     return cascaded_union(self.solid_geometry).bounds
        # else:
        #     return self.solid_geometry.bounds

    def find_polygon(self, point, geoset=None):
        """
        Find an object that object.contains(Point(point)) in
        poly, which can can be iterable, contain iterable of, or
        be itself an implementer of .contains().

        :param point: See description
        :param geoset: a polygon or list of polygons where to find if the param point is contained
        :return: Polygon containing point or None.
        """

        if geoset is None:
            geoset = self.solid_geometry

        try:  # Iterable
            for sub_geo in geoset:
                p = self.find_polygon(point, geoset=sub_geo)
                if p is not None:
                    return p
        except TypeError:  # Non-iterable
            try:  # Implements .contains()
                if isinstance(geoset, LinearRing):
                    geoset = Polygon(geoset)
                if geoset.contains(Point(point)):
                    return geoset
            except AttributeError:  # Does not implement .contains()
                return None

        return None

    def get_interiors(self, geometry=None):

        interiors = []

        if geometry is None:
            geometry = self.solid_geometry

        # ## If iterable, expand recursively.
        try:
            for geo in geometry:
                interiors.extend(self.get_interiors(geometry=geo))

        # ## Not iterable, get the interiors if polygon.
        except TypeError:
            if type(geometry) == Polygon:
                interiors.extend(geometry.interiors)

        return interiors

    def get_exteriors(self, geometry=None):
        """
        Returns all exteriors of polygons in geometry. Uses
        ``self.solid_geometry`` if geometry is not provided.

        :param geometry: Shapely type or list or list of list of such.
        :return: List of paths constituting the exteriors
           of polygons in geometry.
        """

        exteriors = []

        if geometry is None:
            geometry = self.solid_geometry

        # ## If iterable, expand recursively.
        try:
            for geo in geometry:
                exteriors.extend(self.get_exteriors(geometry=geo))

        # ## Not iterable, get the exterior if polygon.
        except TypeError:
            if type(geometry) == Polygon:
                exteriors.append(geometry.exterior)

        return exteriors

    def flatten(self, geometry=None, reset=True, pathonly=False):
        """
        Creates a list of non-iterable linear geometry objects.
        Polygons are expanded into its exterior and interiors if specified.

        Results are placed in self.flat_geometry

        :param geometry: Shapely type or list or list of list of such.
        :param reset: Clears the contents of self.flat_geometry.
        :param pathonly: Expands polygons into linear elements.
        """

        if geometry is None:
            geometry = self.solid_geometry

        if reset:
            self.flat_geometry = []

        # ## If iterable, expand recursively.
        try:
            for geo in geometry:
                if geo is not None:
                    self.flatten(geometry=geo,
                                 reset=False,
                                 pathonly=pathonly)

        # ## Not iterable, do the actual indexing and add.
        except TypeError:
            if pathonly and type(geometry) == Polygon:
                self.flat_geometry.append(geometry.exterior)
                self.flatten(geometry=geometry.interiors,
                             reset=False,
                             pathonly=True)
            else:
                self.flat_geometry.append(geometry)

        return self.flat_geometry

    # def make2Dstorage(self):
    #
    #     self.flatten()
    #
    #     def get_pts(o):
    #         pts = []
    #         if type(o) == Polygon:
    #             g = o.exterior
    #             pts += list(g.coords)
    #             for i in o.interiors:
    #                 pts += list(i.coords)
    #         else:
    #             pts += list(o.coords)
    #         return pts
    #
    #     storage = FlatCAMRTreeStorage()
    #     storage.get_points = get_pts
    #     for shape in self.flat_geometry:
    #         storage.insert(shape)
    #     return storage

    # def flatten_to_paths(self, geometry=None, reset=True):
    #     """
    #     Creates a list of non-iterable linear geometry elements and
    #     indexes them in rtree.
    #
    #     :param geometry: Iterable geometry
    #     :param reset: Wether to clear (True) or append (False) to self.flat_geometry
    #     :return: self.flat_geometry, self.flat_geometry_rtree
    #     """
    #
    #     if geometry is None:
    #         geometry = self.solid_geometry
    #
    #     if reset:
    #         self.flat_geometry = []
    #
    #     # ## If iterable, expand recursively.
    #     try:
    #         for geo in geometry:
    #             self.flatten_to_paths(geometry=geo, reset=False)
    #
    #     # ## Not iterable, do the actual indexing and add.
    #     except TypeError:
    #         if type(geometry) == Polygon:
    #             g = geometry.exterior
    #             self.flat_geometry.append(g)
    #
    #             # ## Add first and last points of the path to the index.
    #             self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[0])
    #             self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[-1])
    #
    #             for interior in geometry.interiors:
    #                 g = interior
    #                 self.flat_geometry.append(g)
    #                 self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[0])
    #                 self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[-1])
    #         else:
    #             g = geometry
    #             self.flat_geometry.append(g)
    #             self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[0])
    #             self.flat_geometry_rtree.insert(len(self.flat_geometry) - 1, g.coords[-1])
    #
    #     return self.flat_geometry, self.flat_geometry_rtree

    def isolation_geometry(self, offset, geometry=None, iso_type=2, corner=None, follow=None, passes=0):
        """
        Creates contours around geometry at a given
        offset distance.

        :param offset: Offset distance.
        :type offset: float
        :param iso_type: type of isolation, can be 0 = exteriors or 1 = interiors or 2 = both (complete)
        :param corner: type of corner for the isolation: 0 = round; 1 = square; 2= beveled (line that connects the ends)
        :param follow: whether the geometry to be isolated is a follow_geometry
        :param passes: current pass out of possible multiple passes for which the isolation is done
        :return: The buffered geometry.
        :rtype: Shapely.MultiPolygon or Shapely.Polygon
        """

        if self.app.abort_flag:
            # graceful abort requested by the user
            raise FlatCAMApp.GracefulException

        geo_iso = list()

        if follow:
            return geometry

        if geometry:
            working_geo = geometry
        else:
            working_geo = self.solid_geometry

        try:
            geo_len = len(working_geo)
        except TypeError:
            geo_len = 1

        old_disp_number = 0
        pol_nr = 0
        # yet, it can be done by issuing an unary_union in the end, thus getting rid of the overlapping geo
        try:
            for pol in working_geo:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException
                if offset == 0:
                    geo_iso.append(pol)
                else:
                    corner_type = 1 if corner is None else corner
                    geo_iso.append(pol.buffer(offset, int(self.geo_steps_per_circle), join_style=corner_type))
                pol_nr += 1
                disp_number = int(np.interp(pol_nr, [0, geo_len], [0, 100]))

                if  old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %s %d: %d%%' %
                                                             (_("Pass"), int(passes + 1), int(disp_number)))
                    old_disp_number = disp_number
        except TypeError:
            # taking care of the case when the self.solid_geometry is just a single Polygon, not a list or a
            # MultiPolygon (not an iterable)
            if offset == 0:
                geo_iso.append(working_geo)
            else:
                corner_type = 1 if corner is None else corner
                geo_iso.append(working_geo.buffer(offset, int(self.geo_steps_per_circle), join_style=corner_type))

        self.app.proc_container.update_view_text(' %s' % _("Buffering"))
        geo_iso = unary_union(geo_iso)

        self.app.proc_container.update_view_text('')
        # end of replaced block

        if iso_type == 2:
            return geo_iso
        elif iso_type == 0:
            self.app.proc_container.update_view_text(' %s' % _("Get Exteriors"))
            return self.get_exteriors(geo_iso)
        elif iso_type == 1:
            self.app.proc_container.update_view_text(' %s' % _("Get Interiors"))
            return self.get_interiors(geo_iso)
        else:
            log.debug("Geometry.isolation_geometry() --> Type of isolation not supported")
            return "fail"

    def flatten_list(self, list):
        for item in list:
            if isinstance(item, Iterable) and not isinstance(item, (str, bytes)):
                yield from self.flatten_list(item)
            else:
                yield item

    def import_svg(self, filename, object_type=None, flip=True, units='MM'):
        """
        Imports shapes from an SVG file into the object's geometry.

        :param filename: Path to the SVG file.
        :type filename: str
        :param object_type: parameter passed further along
        :param flip: Flip the vertically.
        :type flip: bool
        :param units: FlatCAM units
        :return: None
        """

        log.debug("camlib.Geometry.import_svg()")

        # Parse into list of shapely objects
        svg_tree = ET.parse(filename)
        svg_root = svg_tree.getroot()

        # Change origin to bottom left
        # h = float(svg_root.get('height'))
        # w = float(svg_root.get('width'))
        h = svgparselength(svg_root.get('height'))[0]  # TODO: No units support yet

        geos = getsvggeo(svg_root, object_type)
        if flip:
            geos = [translate(scale(g, 1.0, -1.0, origin=(0, 0)), yoff=h) for g in geos]

        # Add to object
        if self.solid_geometry is None:
            self.solid_geometry = list()

        if type(self.solid_geometry) is list:
            if type(geos) is list:
                self.solid_geometry += geos
            else:
                self.solid_geometry.append(geos)
        else:  # It's shapely geometry
            self.solid_geometry = [self.solid_geometry, geos]

        # flatten the self.solid_geometry list for import_svg() to import SVG as Gerber
        self.solid_geometry = list(self.flatten_list(self.solid_geometry))

        geos_text = getsvgtext(svg_root, object_type, units=units)
        if geos_text is not None:
            geos_text_f = list()
            if flip:
                # Change origin to bottom left
                for i in geos_text:
                    _, minimy, _, maximy = i.bounds
                    h2 = (maximy - minimy) * 0.5
                    geos_text_f.append(translate(scale(i, 1.0, -1.0, origin=(0, 0)), yoff=(h + h2)))
            if geos_text_f:
                self.solid_geometry = self.solid_geometry + geos_text_f

    def import_dxf(self, filename, object_type=None, units='MM'):
        """
        Imports shapes from an DXF file into the object's geometry.

        :param filename: Path to the DXF file.
        :type filename: str
        :param units: Application units
        :type flip: str
        :return: None
        """

        # Parse into list of shapely objects
        dxf = ezdxf.readfile(filename)
        geos = getdxfgeo(dxf)

        # Add to object
        if self.solid_geometry is None:
            self.solid_geometry = []

        if type(self.solid_geometry) is list:
            if type(geos) is list:
                self.solid_geometry += geos
            else:
                self.solid_geometry.append(geos)
        else:  # It's shapely geometry
            self.solid_geometry = [self.solid_geometry, geos]

        # flatten the self.solid_geometry list for import_dxf() to import DXF as Gerber
        self.solid_geometry = list(self.flatten_list(self.solid_geometry))
        if self.solid_geometry is not None:
            self.solid_geometry = cascaded_union(self.solid_geometry)
        else:
            return

        # commented until this function is ready
        # geos_text = getdxftext(dxf, object_type, units=units)
        # if geos_text is not None:
        #     geos_text_f = []
        #     self.solid_geometry = [self.solid_geometry, geos_text_f]

    def import_image(self, filename, flip=True, units='MM', dpi=96, mode='black', mask=None):
        """
        Imports shapes from an IMAGE file into the object's geometry.

        :param filename: Path to the IMAGE file.
        :type filename: str
        :param flip: Flip the object vertically.
        :type flip: bool
        :param units: FlatCAM units
        :param dpi: dots per inch on the imported image
        :param mode: how to import the image: as 'black' or 'color'
        :param mask: level of detail for the import
        :return: None
        """
        if mask is None:
            mask = [128, 128, 128, 128]

        scale_factor = 25.4 / dpi if units.lower() == 'mm' else 1 / dpi

        geos = list()
        unscaled_geos = list()

        with rasterio.open(filename) as src:
            # if filename.lower().rpartition('.')[-1] == 'bmp':
            #     red = green = blue = src.read(1)
            #     print("BMP")
            # elif filename.lower().rpartition('.')[-1] == 'png':
            #     red, green, blue, alpha = src.read()
            # elif filename.lower().rpartition('.')[-1] == 'jpg':
            #     red, green, blue = src.read()

            red = green = blue = src.read(1)

            try:
                green = src.read(2)
            except Exception:
                pass

            try:
                blue = src.read(3)
            except Exception:
                pass

        if mode == 'black':
            mask_setting = red <= mask[0]
            total = red
            log.debug("Image import as monochrome.")
        else:
            mask_setting = (red <= mask[1]) + (green <= mask[2]) + (blue <= mask[3])
            total = np.zeros(red.shape, dtype=np.float32)
            for band in red, green, blue:
                total += band
            total /= 3
            log.debug("Image import as colored. Thresholds are: R = %s , G = %s, B = %s" %
                      (str(mask[1]), str(mask[2]), str(mask[3])))

        for geom, val in shapes(total, mask=mask_setting):
            unscaled_geos.append(shape(geom))

        for g in unscaled_geos:
            geos.append(scale(g, scale_factor, scale_factor, origin=(0, 0)))

        if flip:
            geos = [translate(scale(g, 1.0, -1.0, origin=(0, 0))) for g in geos]

        # Add to object
        if self.solid_geometry is None:
            self.solid_geometry = list()

        if type(self.solid_geometry) is list:
            # self.solid_geometry.append(cascaded_union(geos))
            if type(geos) is list:
                self.solid_geometry += geos
            else:
                self.solid_geometry.append(geos)
        else:  # It's shapely geometry
            self.solid_geometry = [self.solid_geometry, geos]

        # flatten the self.solid_geometry list for import_svg() to import SVG as Gerber
        self.solid_geometry = list(self.flatten_list(self.solid_geometry))
        self.solid_geometry = cascaded_union(self.solid_geometry)

        # self.solid_geometry = MultiPolygon(self.solid_geometry)
        # self.solid_geometry = self.solid_geometry.buffer(0.00000001)
        # self.solid_geometry = self.solid_geometry.buffer(-0.00000001)

    def size(self):
        """
        Returns (width, height) of rectangular
        bounds of geometry.
        """
        if self.solid_geometry is None:
            log.warning("Solid_geometry not computed yet.")
            return 0
        bounds = self.bounds()
        return bounds[2] - bounds[0], bounds[3] - bounds[1]
        
    def get_empty_area(self, boundary=None):
        """
        Returns the complement of self.solid_geometry within
        the given boundary polygon. If not specified, it defaults to
        the rectangular bounding box of self.solid_geometry.
        """
        if boundary is None:
            boundary = self.solid_geometry.envelope
        return boundary.difference(self.solid_geometry)
        

    def clear_polygon(self, polygon, tooldia, steps_per_circle, overlap=0.15, connect=True, contour=True,
                      prog_plot=False):
        """
        Creates geometry inside a polygon for a tool to cover
        the whole area.

        This algorithm shrinks the edges of the polygon and takes
        the resulting edges as toolpaths.

        :param polygon: Polygon to clear.
        :param tooldia: Diameter of the tool.
        :param steps_per_circle: number of linear segments to be used to approximate a circle
        :param overlap: Overlap of toolpasses.
        :param connect: Draw lines between disjoint segments to
                        minimize tool lifts.
        :param contour: Paint around the edges. Inconsequential in
                        this painting method.
        :param prog_plot: boolean; if Ture use the progressive plotting
        :return:
        """

        # log.debug("camlib.clear_polygon()")
        assert type(polygon) == Polygon or type(polygon) == MultiPolygon, \
            "Expected a Polygon or MultiPolygon, got %s" % type(polygon)

        # ## The toolpaths
        # Index first and last points in paths
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        geoms = FlatCAMRTreeStorage()
        geoms.get_points = get_pts

        # Can only result in a Polygon or MultiPolygon
        # NOTE: The resulting polygon can be "empty".
        current = polygon.buffer((-tooldia / 1.999999), int(steps_per_circle))
        if current.area == 0:
            # Otherwise, trying to to insert current.exterior == None
            # into the FlatCAMStorage will fail.
            # print("Area is None")
            return None

        # current can be a MultiPolygon
        try:
            for p in current:
                geoms.insert(p.exterior)
                for i in p.interiors:
                    geoms.insert(i)

        # Not a Multipolygon. Must be a Polygon
        except TypeError:
            geoms.insert(current.exterior)
            for i in current.interiors:
                geoms.insert(i)

        while True:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            # provide the app with a way to process the GUI events when in a blocking loop
            QtWidgets.QApplication.processEvents()

            # Can only result in a Polygon or MultiPolygon
            current = current.buffer(-tooldia * (1 - overlap), int(steps_per_circle))
            if current.area > 0:

                # current can be a MultiPolygon
                try:
                    for p in current:
                        geoms.insert(p.exterior)
                        for i in p.interiors:
                            geoms.insert(i)
                            if prog_plot:
                                self.plot_temp_shapes(p)

                # Not a Multipolygon. Must be a Polygon
                except TypeError:
                    geoms.insert(current.exterior)
                    if prog_plot:
                        self.plot_temp_shapes(current.exterior)
                    for i in current.interiors:
                        geoms.insert(i)
                        if prog_plot:
                            self.plot_temp_shapes(i)
            else:
                log.debug("camlib.Geometry.clear_polygon() --> Current Area is zero")
                break

        if prog_plot:
            self.temp_shapes.redraw()

        # Optimization: Reduce lifts
        if connect:
            # log.debug("Reducing tool lifts...")
            geoms = Geometry.paint_connect(geoms, polygon, tooldia, int(steps_per_circle))

        return geoms

    def clear_polygon2(self, polygon_to_clear, tooldia, steps_per_circle, seedpoint=None, overlap=0.15,
                       connect=True, contour=True, prog_plot=False):
        """
        Creates geometry inside a polygon for a tool to cover
        the whole area.

        This algorithm starts with a seed point inside the polygon
        and draws circles around it. Arcs inside the polygons are
        valid cuts. Finalizes by cutting around the inside edge of
        the polygon.

        :param polygon_to_clear: Shapely.geometry.Polygon
        :param steps_per_circle: how many linear segments to use to approximate a circle
        :param tooldia: Diameter of the tool
        :param seedpoint: Shapely.geometry.Point or None
        :param overlap: Tool fraction overlap bewteen passes
        :param connect: Connect disjoint segment to minumize tool lifts
        :param contour: Cut countour inside the polygon.
        :return: List of toolpaths covering polygon.
        :rtype: FlatCAMRTreeStorage | None
        :param prog_plot: boolean; if True use the progressive plotting
        """

        # log.debug("camlib.clear_polygon2()")

        # Current buffer radius
        radius = tooldia / 2 * (1 - overlap)

        # ## The toolpaths
        # Index first and last points in paths
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        geoms = FlatCAMRTreeStorage()
        geoms.get_points = get_pts

        # Path margin
        path_margin = polygon_to_clear.buffer(-tooldia / 2, int(steps_per_circle))

        if path_margin.is_empty or path_margin is None:
            return

        # Estimate good seedpoint if not provided.
        if seedpoint is None:
            seedpoint = path_margin.representative_point()

        # Grow from seed until outside the box. The polygons will
        # never have an interior, so take the exterior LinearRing.
        while True:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            # provide the app with a way to process the GUI events when in a blocking loop
            QtWidgets.QApplication.processEvents()

            path = Point(seedpoint).buffer(radius, int(steps_per_circle)).exterior
            path = path.intersection(path_margin)

            # Touches polygon?
            if path.is_empty:
                break
            else:
                # geoms.append(path)
                # geoms.insert(path)
                # path can be a collection of paths.
                try:
                    for p in path:
                        geoms.insert(p)
                        if prog_plot:
                            self.plot_temp_shapes(p)
                except TypeError:
                    geoms.insert(path)
                    if prog_plot:
                        self.plot_temp_shapes(path)

                if prog_plot:
                    self.temp_shapes.redraw()

            radius += tooldia * (1 - overlap)

        # Clean inside edges (contours) of the original polygon
        if contour:
            outer_edges = [
                x.exterior for x in autolist(polygon_to_clear.buffer(-tooldia / 2, int(steps_per_circle)))
            ]
            inner_edges = []
            # Over resulting polygons
            for x in autolist(polygon_to_clear.buffer(-tooldia / 2, int(steps_per_circle))):
                for y in x.interiors:  # Over interiors of each polygon
                    inner_edges.append(y)
            # geoms += outer_edges + inner_edges
            for g in outer_edges + inner_edges:
                if g and not g.is_empty:
                    geoms.insert(g)
                    if prog_plot:
                        self.plot_temp_shapes(g)

        if prog_plot:
            self.temp_shapes.redraw()

        # Optimization connect touching paths
        # log.debug("Connecting paths...")
        # geoms = Geometry.path_connect(geoms)

        # Optimization: Reduce lifts
        if connect:
            # log.debug("Reducing tool lifts...")
            geoms_conn = Geometry.paint_connect(geoms, polygon_to_clear, tooldia, steps_per_circle)
            if geoms_conn:
                return geoms_conn

        return geoms

    def clear_polygon3(self, polygon, tooldia, steps_per_circle, overlap=0.15, connect=True, contour=True,
                       prog_plot=False):
        """
        Creates geometry inside a polygon for a tool to cover
        the whole area.

        This algorithm draws horizontal lines inside the polygon.

        :param polygon: The polygon being painted.
        :type polygon: shapely.geometry.Polygon
        :param tooldia: Tool diameter.
        :param steps_per_circle: how many linear segments to use to approximate a circle
        :param overlap: Tool path overlap percentage.
        :param connect: Connect lines to avoid tool lifts.
        :param contour: Paint around the edges.
        :param prog_plot: boolean; if to use the progressive plotting
        :return:
        """

        # log.debug("camlib.clear_polygon3()")
        if not isinstance(polygon, Polygon):
            log.debug("camlib.Geometry.clear_polygon3() --> Not a Polygon but %s" % str(type(polygon)))
            return None

        # ## The toolpaths
        # Index first and last points in paths
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        geoms = FlatCAMRTreeStorage()
        geoms.get_points = get_pts

        lines_trimmed = []

        # Bounding box
        left, bot, right, top = polygon.bounds

        try:
            margin_poly = polygon.buffer(-tooldia / 1.99999999, (int(steps_per_circle)))
        except Exception as e:
            log.debug("camlib.Geometry.clear_polygon3() --> Could not buffer the Polygon")
            return None

        # First line
        try:
            y = top - tooldia / 1.99999999
            while y > bot + tooldia / 1.999999999:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException

                # provide the app with a way to process the GUI events when in a blocking loop
                QtWidgets.QApplication.processEvents()

                line = LineString([(left, y), (right, y)])
                line = line.intersection(margin_poly)
                lines_trimmed.append(line)
                y -= tooldia * (1 - overlap)
                if prog_plot:
                    self.plot_temp_shapes(line)
                    self.temp_shapes.redraw()

            # Last line
            y = bot + tooldia / 2
            line = LineString([(left, y), (right, y)])
            line = line.intersection(margin_poly)

            for ll in line:
                lines_trimmed.append(ll)
                if prog_plot:
                    self.plot_temp_shapes(line)
        except Exception as e:
            log.debug('camlib.Geometry.clear_polygon3() Processing poly --> %s' % str(e))
            return None

        if prog_plot:
            self.temp_shapes.redraw()

        lines_trimmed = unary_union(lines_trimmed)

        # Add lines to storage
        try:
            for line in lines_trimmed:
                if isinstance(line, LineString) or isinstance(line, LinearRing):
                    geoms.insert(line)
                else:
                    log.debug("camlib.Geometry.clear_polygon3(). Not a line: %s" % str(type(line)))
        except TypeError:
            # in case lines_trimmed are not iterable (Linestring, LinearRing)
            geoms.insert(lines_trimmed)

        # Add margin (contour) to storage
        if contour:
            try:
                for poly in margin_poly:
                    if isinstance(poly, Polygon) and not poly.is_empty:
                        geoms.insert(poly.exterior)
                        if prog_plot:
                            self.plot_temp_shapes(poly.exterior)
                        for ints in poly.interiors:
                            geoms.insert(ints)
                            if prog_plot:
                                self.plot_temp_shapes(ints)
            except TypeError:
                if isinstance(margin_poly, Polygon) and not margin_poly.is_empty:
                    marg_ext = margin_poly.exterior
                    geoms.insert(marg_ext)
                    if prog_plot:
                        self.plot_temp_shapes(margin_poly.exterior)
                    for ints in margin_poly.interiors:
                        geoms.insert(ints)
                        if prog_plot:
                            self.plot_temp_shapes(ints)

        if prog_plot:
            self.temp_shapes.redraw()

        # Optimization: Reduce lifts
        if connect:
            # log.debug("Reducing tool lifts...")
            geoms_conn = Geometry.paint_connect(geoms, polygon, tooldia, steps_per_circle)
            if geoms_conn:
                return geoms_conn

        return geoms

    def scale(self, xfactor, yfactor, point=None):
        """
        Scales all of the object's geometry by a given factor. Override
        this method.
        :param xfactor: Number by which to scale on X axis.
        :type xfactor: float
        :param yfactor: Number by which to scale on Y axis.
        :type yfactor: float
        :param point: point to be used as reference for scaling; a tuple
        :return: None
        :rtype: None
        """
        return

    def offset(self, vect):
        """
        Offset the geometry by the given vector. Override this method.

        :param vect: (x, y) vector by which to offset the object.
        :type vect: tuple
        :return: None
        """
        return

    @staticmethod
    def paint_connect(storage, boundary, tooldia, steps_per_circle, max_walk=None):
        """
        Connects paths that results in a connection segment that is
        within the paint area. This avoids unnecessary tool lifting.

        :param storage: Geometry to be optimized.
        :type storage: FlatCAMRTreeStorage
        :param boundary: Polygon defining the limits of the paintable area.
        :type boundary: Polygon
        :param tooldia: Tool diameter.
        :rtype tooldia: float
        :param steps_per_circle: how many linear segments to use to approximate a circle
        :param max_walk: Maximum allowable distance without lifting tool.
        :type max_walk: float or None
        :return: Optimized geometry.
        :rtype: FlatCAMRTreeStorage
        """

        # If max_walk is not specified, the maximum allowed is
        # 10 times the tool diameter
        max_walk = max_walk or 10 * tooldia

        # Assuming geolist is a flat list of flat elements

        # ## Index first and last points in paths
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        # storage = FlatCAMRTreeStorage()
        # storage.get_points = get_pts
        #
        # for shape in geolist:
        #     if shape is not None:  # TODO: This shouldn't have happened.
        #         # Make LlinearRings into linestrings otherwise
        #         # When chaining the coordinates path is messed up.
        #         storage.insert(LineString(shape))
        #         #storage.insert(shape)

        # ## Iterate over geometry paths getting the nearest each time.
        #optimized_paths = []
        optimized_paths = FlatCAMRTreeStorage()
        optimized_paths.get_points = get_pts
        path_count = 0
        current_pt = (0, 0)
        try:
            pt, geo = storage.nearest(current_pt)
        except StopIteration:
            log.debug("camlib.Geometry.paint_connect(). Storage empty")
            return None

        storage.remove(geo)

        geo = LineString(geo)
        current_pt = geo.coords[-1]
        try:
            while True:
                path_count += 1
                # log.debug("Path %d" % path_count)

                pt, candidate = storage.nearest(current_pt)
                storage.remove(candidate)

                candidate = LineString(candidate)

                # If last point in geometry is the nearest
                # then reverse coordinates.
                # but prefer the first one if last == first
                if pt != candidate.coords[0] and pt == candidate.coords[-1]:
                    candidate.coords = list(candidate.coords)[::-1]

                # Straight line from current_pt to pt.
                # Is the toolpath inside the geometry?
                walk_path = LineString([current_pt, pt])
                walk_cut = walk_path.buffer(tooldia / 2, int(steps_per_circle))

                if walk_cut.within(boundary) and walk_path.length < max_walk:
                    # log.debug("Walk to path #%d is inside. Joining." % path_count)

                    # Completely inside. Append...
                    geo.coords = list(geo.coords) + list(candidate.coords)
                    # try:
                    #     last = optimized_paths[-1]
                    #     last.coords = list(last.coords) + list(geo.coords)
                    # except IndexError:
                    #     optimized_paths.append(geo)

                else:

                    # Have to lift tool. End path.
                    # log.debug("Path #%d not within boundary. Next." % path_count)
                    # optimized_paths.append(geo)
                    optimized_paths.insert(geo)
                    geo = candidate

                current_pt = geo.coords[-1]

                # Next
                # pt, geo = storage.nearest(current_pt)

        except StopIteration:  # Nothing left in storage.
            # pass
            optimized_paths.insert(geo)

        return optimized_paths

    @staticmethod
    def path_connect(storage, origin=(0, 0)):
        """
        Simplifies paths in the FlatCAMRTreeStorage storage by
        connecting paths that touch on their enpoints.

        :param storage: Storage containing the initial paths.
        :rtype storage: FlatCAMRTreeStorage
        :return: Simplified storage.
        :rtype: FlatCAMRTreeStorage
        """

        log.debug("path_connect()")

        # ## Index first and last points in paths
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]
        #
        # storage = FlatCAMRTreeStorage()
        # storage.get_points = get_pts
        #
        # for shape in pathlist:
        #     if shape is not None:  # TODO: This shouldn't have happened.
        #         storage.insert(shape)

        path_count = 0
        pt, geo = storage.nearest(origin)
        storage.remove(geo)
        # optimized_geometry = [geo]
        optimized_geometry = FlatCAMRTreeStorage()
        optimized_geometry.get_points = get_pts
        # optimized_geometry.insert(geo)
        try:
            while True:
                path_count += 1
                _, left = storage.nearest(geo.coords[0])

                # If left touches geo, remove left from original
                # storage and append to geo.
                if type(left) == LineString:
                    if left.coords[0] == geo.coords[0]:
                        storage.remove(left)
                        geo.coords = list(geo.coords)[::-1] + list(left.coords)
                        continue

                    if left.coords[-1] == geo.coords[0]:
                        storage.remove(left)
                        geo.coords = list(left.coords) + list(geo.coords)
                        continue

                    if left.coords[0] == geo.coords[-1]:
                        storage.remove(left)
                        geo.coords = list(geo.coords) + list(left.coords)
                        continue

                    if left.coords[-1] == geo.coords[-1]:
                        storage.remove(left)
                        geo.coords = list(geo.coords) + list(left.coords)[::-1]
                        continue

                _, right = storage.nearest(geo.coords[-1])

                # If right touches geo, remove left from original
                # storage and append to geo.
                if type(right) == LineString:
                    if right.coords[0] == geo.coords[-1]:
                        storage.remove(right)
                        geo.coords = list(geo.coords) + list(right.coords)
                        continue

                    if right.coords[-1] == geo.coords[-1]:
                        storage.remove(right)
                        geo.coords = list(geo.coords) + list(right.coords)[::-1]
                        continue

                    if right.coords[0] == geo.coords[0]:
                        storage.remove(right)
                        geo.coords = list(geo.coords)[::-1] + list(right.coords)
                        continue

                    if right.coords[-1] == geo.coords[0]:
                        storage.remove(right)
                        geo.coords = list(left.coords) + list(geo.coords)
                        continue

                # right is either a LinearRing or it does not connect
                # to geo (nothing left to connect to geo), so we continue
                # with right as geo.
                storage.remove(right)

                if type(right) == LinearRing:
                    optimized_geometry.insert(right)
                else:
                    # Cannot extend geo any further. Put it away.
                    optimized_geometry.insert(geo)

                    # Continue with right.
                    geo = right

        except StopIteration:  # Nothing found in storage.
            optimized_geometry.insert(geo)

        # print path_count
        log.debug("path_count = %d" % path_count)

        return optimized_geometry

    def convert_units(self, obj_units):
        """
        Converts the units of the object to ``units`` by scaling all
        the geometry appropriately. This call ``scale()``. Don't call
        it again in descendents.

        :param units: "IN" or "MM"
        :type units: str
        :return: Scaling factor resulting from unit change.
        :rtype: float
        """

        if obj_units.upper() == self.units.upper():
            log.debug("camlib.Geometry.convert_units() --> Factor: 1")
            return 1.0

        if obj_units.upper() == "MM":
            factor = 25.4
            log.debug("camlib.Geometry.convert_units() --> Factor: 25.4")
        elif obj_units.upper() == "IN":
            factor = 1 / 25.4
            log.debug("camlib.Geometry.convert_units() --> Factor: %s" % str(1 / 25.4))
        else:
            log.error("Unsupported units: %s" % str(obj_units))
            log.debug("camlib.Geometry.convert_units() --> Factor: 1")
            return 1.0

        self.units = obj_units
        self.scale(factor, factor)
        self.file_units_factor = factor
        return factor

    def to_dict(self):
        """
        Returns a representation of the object as a dictionary.
        Attributes to include are listed in ``self.ser_attrs``.

        :return: A dictionary-encoded copy of the object.
        :rtype: dict
        """
        d = {}
        for attr in self.ser_attrs:
            d[attr] = getattr(self, attr)
        return d

    def from_dict(self, d):
        """
        Sets object's attributes from a dictionary.
        Attributes to include are listed in ``self.ser_attrs``.
        This method will look only for only and all the
        attributes in ``self.ser_attrs``. They must all
        be present. Use only for deserializing saved
        objects.

        :param d: Dictionary of attributes to set in the object.
        :type d: dict
        :return: None
        """
        for attr in self.ser_attrs:
            setattr(self, attr, d[attr])

    def union(self):
        """
        Runs a cascaded union on the list of objects in
        solid_geometry.

        :return: None
        """
        self.solid_geometry = [cascaded_union(self.solid_geometry)]

    def export_svg(self, scale_stroke_factor=0.00,
                   scale_factor_x=None, scale_factor_y=None,
                   skew_factor_x=None, skew_factor_y=None,
                   skew_reference='center',
                   mirror=None):
        """
        Exports the Geometry Object as a SVG Element

        :return: SVG Element
        """

        # Make sure we see a Shapely Geometry class and not a list
        if self.kind.lower() == 'geometry':
            flat_geo = []
            if self.multigeo:
                for tool in self.tools:
                    flat_geo += self.flatten(self.tools[tool]['solid_geometry'])
                geom_svg = cascaded_union(flat_geo)
            else:
                geom_svg = cascaded_union(self.flatten())
        else:
            geom_svg = cascaded_union(self.flatten())

        skew_ref = 'center'
        if skew_reference != 'center':
            xmin, ymin, xmax, ymax = geom_svg.bounds
            if skew_reference == 'topleft':
                skew_ref = (xmin, ymax)
            elif skew_reference == 'bottomleft':
                skew_ref = (xmin, ymin)
            elif skew_reference == 'topright':
                skew_ref = (xmax, ymax)
            elif skew_reference == 'bottomright':
                skew_ref = (xmax, ymin)

        geom = geom_svg

        if scale_factor_x:
            geom = affinity.scale(geom_svg, scale_factor_x, 1.0)
        if scale_factor_y:
            geom = affinity.scale(geom_svg, 1.0, scale_factor_y)
        if skew_factor_x:
            geom = affinity.skew(geom_svg, skew_factor_x, 0.0, origin=skew_ref)
        if skew_factor_y:
            geom = affinity.skew(geom_svg, 0.0, skew_factor_y, origin=skew_ref)
        if mirror:
            if mirror == 'x':
                geom = affinity.scale(geom_svg, 1.0, -1.0)
            if mirror == 'y':
                geom = affinity.scale(geom_svg, -1.0, 1.0)
            if mirror == 'both':
                geom = affinity.scale(geom_svg, -1.0, -1.0)

        # scale_factor is a multiplication factor for the SVG stroke-width used within shapely's svg export
        # If 0 or less which is invalid then default to 0.01
        # This value appears to work for zooming, and getting the output svg line width
        # to match that viewed on screen with FlatCam
        # MS: I choose a factor of 0.01 so the scale is right for PCB UV film
        if scale_stroke_factor <= 0:
            scale_stroke_factor = 0.01

        # Convert to a SVG
        svg_elem = geom.svg(scale_factor=scale_stroke_factor)
        return svg_elem

    def mirror(self, axis, point):
        """
        Mirrors the object around a specified axis passign through
        the given point.

        :param axis: "X" or "Y" indicates around which axis to mirror.
        :type axis: str
        :param point: [x, y] point belonging to the mirror axis.
        :type point: list
        :return: None
        """
        log.debug("camlib.Geometry.mirror()")

        px, py = point
        xscale, yscale = {"X": (1.0, -1.0), "Y": (-1.0, 1.0)}[axis]

        def mirror_geom(obj):
            if type(obj) is list:
                new_obj = []
                for g in obj:
                    new_obj.append(mirror_geom(g))
                return new_obj
            else:
                try:
                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                    return affinity.scale(obj, xscale, yscale, origin=(px, py))
                except AttributeError:
                    return obj

        try:
            if self.multigeo is True:
                for tool in self.tools:
                    # variables to display the percentage of work done
                    self.geo_len = 0
                    try:
                        for g in self.tools[tool]['solid_geometry']:
                            self.geo_len += 1
                    except TypeError:
                        self.geo_len = 1
                    self.old_disp_number = 0
                    self.el_count = 0

                    self.tools[tool]['solid_geometry'] = mirror_geom(self.tools[tool]['solid_geometry'])
            else:
                # variables to display the percentage of work done
                self.geo_len = 0
                try:
                    for g in self.solid_geometry:
                        self.geo_len += 1
                except TypeError:
                    self.geo_len = 1
                self.old_disp_number = 0
                self.el_count = 0

                self.solid_geometry = mirror_geom(self.solid_geometry)
            self.app.inform.emit('[success] %s...' %
                                 _('Object was mirrored'))
        except AttributeError:
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _("Failed to mirror. No object selected"))

        self.app.proc_container.new_text = ''

    def rotate(self, angle, point):
        """
        Rotate an object by an angle (in degrees) around the provided coordinates.

        Parameters
        ----------
        The angle of rotation are specified in degrees (default). Positive angles are
        counter-clockwise and negative are clockwise rotations.

        The point of origin can be a keyword 'center' for the bounding box
        center (default), 'centroid' for the geometry's centroid, a Point object
        or a coordinate tuple (x0, y0).

        See shapely manual for more information:
        http://toblerity.org/shapely/manual.html#affine-transformations
        """
        log.debug("camlib.Geometry.rotate()")

        px, py = point

        def rotate_geom(obj):
            if type(obj) is list:
                new_obj = []
                for g in obj:
                    new_obj.append(rotate_geom(g))
                return new_obj
            else:
                try:
                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                    return affinity.rotate(obj, angle, origin=(px, py))
                except AttributeError:
                    return obj

        try:
            if self.multigeo is True:
                for tool in self.tools:
                    # variables to display the percentage of work done
                    self.geo_len = 0
                    try:
                        for g in self.tools[tool]['solid_geometry']:
                            self.geo_len += 1
                    except TypeError:
                        self.geo_len = 1
                    self.old_disp_number = 0
                    self.el_count = 0

                    self.tools[tool]['solid_geometry'] = rotate_geom(self.tools[tool]['solid_geometry'])
            else:
                # variables to display the percentage of work done
                self.geo_len = 0
                try:
                    for g in self.solid_geometry:
                        self.geo_len += 1
                except TypeError:
                    self.geo_len = 1
                self.old_disp_number = 0
                self.el_count = 0

                self.solid_geometry = rotate_geom(self.solid_geometry)
            self.app.inform.emit('[success] %s...' %
                                 _('Object was rotated'))
        except AttributeError:
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _("Failed to rotate. No object selected"))

        self.app.proc_container.new_text = ''

    def skew(self, angle_x, angle_y, point):
        """
        Shear/Skew the geometries of an object by angles along x and y dimensions.

        Parameters
        ----------
        angle_x, angle_y : float, float
            The shear angle(s) for the x and y axes respectively. These can be
            specified in either degrees (default) or radians by setting
            use_radians=True.
        point: tuple of coordinates (x,y)

        See shapely manual for more information:
        http://toblerity.org/shapely/manual.html#affine-transformations
        """
        log.debug("camlib.Geometry.skew()")

        px, py = point

        def skew_geom(obj):
            if type(obj) is list:
                new_obj = []
                for g in obj:
                    new_obj.append(skew_geom(g))
                return new_obj
            else:
                try:
                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                    return affinity.skew(obj, angle_x, angle_y, origin=(px, py))
                except AttributeError:
                    return obj

        try:
            if self.multigeo is True:
                for tool in self.tools:
                    # variables to display the percentage of work done
                    self.geo_len = 0
                    try:
                        for g in self.tools[tool]['solid_geometry']:
                            self.geo_len += 1
                    except TypeError:
                        self.geo_len = 1
                    self.old_disp_number = 0
                    self.el_count = 0

                    self.tools[tool]['solid_geometry'] = skew_geom(self.tools[tool]['solid_geometry'])
            else:
                # variables to display the percentage of work done
                self.geo_len = 0
                try:
                    for g in self.solid_geometry:
                        self.geo_len += 1
                except TypeError:
                    self.geo_len = 1
                self.old_disp_number = 0
                self.el_count = 0

                self.solid_geometry = skew_geom(self.solid_geometry)
            self.app.inform.emit('[success] %s...' %
                                 _('Object was skewed'))
        except AttributeError:
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _("Failed to skew. No object selected"))

        self.app.proc_container.new_text = ''

        # if type(self.solid_geometry) == list:
        #     self.solid_geometry = [affinity.skew(g, angle_x, angle_y, origin=(px, py))
        #                            for g in self.solid_geometry]
        # else:
        #     self.solid_geometry = affinity.skew(self.solid_geometry, angle_x, angle_y,
        #                                         origin=(px, py))

    def buffer(self, distance, join, factor):
        """

        :param distance: if 'factor' is True then distance is the factor
        :param factor: True or False (None)
        :return:
        """

        log.debug("camlib.Geometry.buffer()")

        if distance == 0:
            return

        def buffer_geom(obj):
            if type(obj) is list:
                new_obj = []
                for g in obj:
                    new_obj.append(buffer_geom(g))
                return new_obj
            else:
                try:
                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                    if factor is None:
                        return obj.buffer(distance, resolution=self.geo_steps_per_circle, join_style=join)
                    else:
                        return affinity.scale(obj, xfact=distance, yfact=distance, origin='center')
                except AttributeError:
                    return obj

        try:
            if self.multigeo is True:
                for tool in self.tools:
                    # variables to display the percentage of work done
                    self.geo_len = 0
                    try:
                        self.geo_len += len(self.tools[tool]['solid_geometry'])
                    except TypeError:
                        self.geo_len += 1
                    self.old_disp_number = 0
                    self.el_count = 0

                    res = buffer_geom(self.tools[tool]['solid_geometry'])
                    try:
                        __ = iter(res)
                        self.tools[tool]['solid_geometry'] = res
                    except TypeError:
                        self.tools[tool]['solid_geometry'] = [res]

            # variables to display the percentage of work done
            self.geo_len = 0
            try:
                self.geo_len = len(self.solid_geometry)
            except TypeError:
                self.geo_len = 1
            self.old_disp_number = 0
            self.el_count = 0

            self.solid_geometry = buffer_geom(self.solid_geometry)

            self.app.inform.emit('[success] %s...' %  _('Object was buffered'))
        except AttributeError:
            self.app.inform.emit('[ERROR_NOTCL] %s' % _("Failed to buffer. No object selected"))

        self.app.proc_container.new_text = ''


class AttrDict(dict):
    def __init__(self, *args, **kwargs):
        super(AttrDict, self).__init__(*args, **kwargs)
        self.__dict__ = self


class CNCjob(Geometry):
    """
    Represents work to be done by a CNC machine.

    *ATTRIBUTES*

    * ``gcode_parsed`` (list): Each is a dictionary:

    =====================  =========================================
    Key                    Value
    =====================  =========================================
    geom                   (Shapely.LineString) Tool path (XY plane)
    kind                   (string) "AB", A is "T" (travel) or
                           "C" (cut). B is "F" (fast) or "S" (slow).
    =====================  =========================================
    """

    defaults = {
        "global_zdownrate": None,
        "pp_geometry_name":'default',
        "pp_excellon_name":'default',
        "excellon_optimization_type": "B",
    }

    settings = QtCore.QSettings("Open Source", "FlatCAM")
    if settings.contains("machinist"):
        machinist_setting = settings.value('machinist', type=int)
    else:
        machinist_setting = 0

    def __init__(self,
                 units="in", kind="generic", tooldia=0.0,
                 z_cut=-0.002, z_move=0.1,
                 feedrate=3.0, feedrate_z=3.0, feedrate_rapid=3.0, feedrate_probe=3.0,
                 pp_geometry_name='default', pp_excellon_name='default',
                 depthpercut=0.1,z_pdepth=-0.02,
                 spindlespeed=None, spindledir='CW', dwell=True, dwelltime=1000,
                 toolchangez=0.787402, toolchange_xy=[0.0, 0.0],
                 endz=2.0,
                 segx=None,
                 segy=None,
                 steps_per_circle=None):

        self.decimals = self.app.decimals

        # Used when parsing G-code arcs
        self.steps_per_circle = int(self.app.defaults['cncjob_steps_per_circle'])

        Geometry.__init__(self, geo_steps_per_circle=self.steps_per_circle)

        self.kind = kind

        self.units = units

        self.z_cut = z_cut
        self.tool_offset = dict()

        self.z_move = z_move

        self.feedrate = feedrate
        self.z_feedrate = feedrate_z
        self.feedrate_rapid = feedrate_rapid

        self.tooldia = tooldia
        self.z_toolchange = toolchangez
        self.xy_toolchange = toolchange_xy
        self.toolchange_xy_type = None

        self.toolC = tooldia

        self.z_end = endz
        self.z_depthpercut = depthpercut

        self.unitcode = {"IN": "G20", "MM": "G21"}

        self.feedminutecode = "G94"
        # self.absolutecode = "G90"
        # self.incrementalcode = "G91"
        self.coordinates_type = self.app.defaults["cncjob_coords_type"]

        self.gcode = ""
        self.gcode_parsed = None

        self.pp_geometry_name = pp_geometry_name
        self.pp_geometry = self.app.preprocessors[self.pp_geometry_name]

        self.pp_excellon_name = pp_excellon_name
        self.pp_excellon = self.app.preprocessors[self.pp_excellon_name]

        self.pp_solderpaste_name = None

        # Controls if the move from Z_Toolchange to Z_Move is done fast with G0 or normally with G1
        self.f_plunge = None

        # Controls if the move from Z_Cutto Z_Move is done fast with G0 or G1 until zero and then G0 to Z_move
        self.f_retract = None

        # how much depth the probe can probe before error
        self.z_pdepth = z_pdepth if z_pdepth else None

        # the feedrate(speed) with which the probel travel while probing
        self.feedrate_probe = feedrate_probe if feedrate_probe else None

        self.spindlespeed = spindlespeed
        self.spindledir = spindledir
        self.dwell = dwell
        self.dwelltime = dwelltime

        self.segx = float(segx) if segx is not None else 0.0
        self.segy = float(segy) if segy is not None else 0.0

        self.input_geometry_bounds = None

        self.oldx = None
        self.oldy = None

        self.tool = 0.0

        # here store the travelled distance
        self.travel_distance = 0.0
        # here store the routing time
        self.routing_time = 0.0

        # used for creating drill CCode geometry; will be updated in the generate_from_excellon_by_tool()
        self.exc_drills = None
        self.exc_tools = None

        # search for toolchange parameters in the Toolchange Custom Code
        self.re_toolchange_custom = re.compile(r'(%[a-zA-Z0-9\-_]+%)')

        # search for toolchange code: M6
        self.re_toolchange = re.compile(r'^\s*(M6)$')

        # Attributes to be included in serialization
        # Always append to it because it carries contents
        # from Geometry.
        self.ser_attrs += ['kind', 'z_cut', 'z_move', 'z_toolchange', 'feedrate', 'z_feedrate', 'feedrate_rapid',
                           'tooldia', 'gcode', 'input_geometry_bounds', 'gcode_parsed', 'steps_per_circle',
                           'z_depthpercut', 'spindlespeed', 'dwell', 'dwelltime']

    @property
    def postdata(self):
        return self.__dict__

    def convert_units(self, units):
        log.debug("camlib.CNCJob.convert_units()")

        factor = Geometry.convert_units(self, units)

        self.z_cut = float(self.z_cut) * factor
        self.z_move *= factor
        self.feedrate *= factor
        self.z_feedrate *= factor
        self.feedrate_rapid *= factor
        self.tooldia *= factor
        self.z_toolchange *= factor
        self.z_end *= factor
        self.z_depthpercut = float(self.z_depthpercut) * factor

        return factor

    def doformat(self, fun, **kwargs):
        return self.doformat2(fun, **kwargs) + "\n"

    def doformat2(self, fun, **kwargs):
        attributes = AttrDict()
        attributes.update(self.postdata)
        attributes.update(kwargs)
        try:
            returnvalue = fun(attributes)
            return returnvalue
        except Exception:
            self.app.log.error('Exception occurred within a preprocessor: ' + traceback.format_exc())
            return ''

    def parse_custom_toolchange_code(self, data):
        text = data
        match_list = self.re_toolchange_custom.findall(text)

        if match_list:
            for match in match_list:
                command = match.strip('%')
                try:
                    value = getattr(self, command)
                except AttributeError:
                    self.app.inform.emit('[ERROR] %s: %s' %
                                         (_("There is no such parameter"), str(match)))
                    log.debug("CNCJob.parse_custom_toolchange_code() --> AttributeError ")
                    return 'fail'
                text = text.replace(match, str(value))
            return text

    def optimized_travelling_salesman(self, points, start=None):
        """
        As solving the problem in the brute force way is too slow,
        this function implements a simple heuristic: always
        go to the nearest city.

        Even if this algorithm is extremely simple, it works pretty well
        giving a solution only about 25%% longer than the optimal one (cit. Wikipedia),
        and runs very fast in O(N^2) time complexity.

        >>> optimized_travelling_salesman([[i,j] for i in range(5) for j in range(5)])
        [[0, 0], [0, 1], [0, 2], [0, 3], [0, 4], [1, 4], [1, 3], [1, 2], [1, 1], [1, 0], [2, 0], [2, 1], [2, 2],
        [2, 3], [2, 4], [3, 4], [3, 3], [3, 2], [3, 1], [3, 0], [4, 0], [4, 1], [4, 2], [4, 3], [4, 4]]
        >>> optimized_travelling_salesman([[0,0],[10,0],[6,0]])
        [[0, 0], [6, 0], [10, 0]]
        """

        if start is None:
            start = points[0]
        must_visit = points
        path = [start]
        # must_visit.remove(start)
        while must_visit:
            nearest = min(must_visit, key=lambda x: distance(path[-1], x))
            path.append(nearest)
            must_visit.remove(nearest)
        return path

    def generate_from_excellon_by_tool(self, exobj, tools="all", drillz = 3.0, toolchange=False, toolchangez=0.1,
                                       toolchangexy='', endz=2.0, startz=None, excellon_optimization_type='B'):
        """
        Creates gcode for this object from an Excellon object
        for the specified tools.

        :param exobj: Excellon object to process
        :type exobj: Excellon
        :param tools: Comma separated tool names
        :type: tools: str
        :param drillz: drill Z depth
        :type drillz: float
        :param toolchange: Use tool change sequence between tools.
        :type toolchange: bool
        :param toolchangez: Height at which to perform the tool change.
        :type toolchangez: float
        :param toolchangexy: Toolchange X,Y position
        :type toolchangexy: String containing 2 floats separated by comma
        :param startz: Z position just before starting the job
        :type startz: float
        :param endz: final Z position to move to at the end of the CNC job
        :type endz: float
        :param excellon_optimization_type: Single character that defines which drill re-ordering optimisation algorithm
        is to be used: 'M' for meta-heuristic and 'B' for basic
        :type excellon_optimization_type: string
        :return: None
        :rtype: None
        """

        # create a local copy of the exobj.drills so it can be used for creating drill CCode geometry
        self.exc_drills = deepcopy(exobj.drills)
        self.exc_tools = deepcopy(exobj.tools)

        self.z_cut = deepcopy(drillz)
        old_zcut = deepcopy(drillz)

        if self.machinist_setting == 0:
            if drillz > 0:
                self.app.inform.emit('[WARNING] %s' %
                                     _("The Cut Z parameter has positive value. "
                                       "It is the depth value to drill into material.\n"
                                       "The Cut Z parameter needs to have a negative value, assuming it is a typo "
                                       "therefore the app will convert the value to negative. "
                                       "Check the resulting CNC code (Gcode etc)."))
                self.z_cut = -drillz
            elif drillz == 0:
                self.app.inform.emit('[WARNING] %s: %s' %
                                     (_("The Cut Z parameter is zero. There will be no cut, skipping file"),
                                      exobj.options['name']))
                return 'fail'

        self.z_toolchange = toolchangez

        try:
            if toolchangexy == '':
                self.xy_toolchange = None
            else:
                self.xy_toolchange = [float(eval(a)) for a in toolchangexy.split(",")]
                if len(self.xy_toolchange) < 2:
                    self.app.inform.emit('[ERROR]%s' %
                                         _("The Toolchange X,Y field in Edit -> Preferences has to be "
                                           "in the format (x, y) \nbut now there is only one value, not two. "))
                    return 'fail'
        except Exception as e:
            log.debug("camlib.CNCJob.generate_from_excellon_by_tool() --> %s" % str(e))
            pass

        self.startz = startz
        self.z_end = endz

        self.pp_excellon = self.app.preprocessors[self.pp_excellon_name]
        p = self.pp_excellon

        log.debug("Creating CNC Job from Excellon...")

        # Tools
        
        # sort the tools list by the second item in tuple (here we have a dict with diameter of the tool)
        # so we actually are sorting the tools by diameter
        # sorted_tools = sorted(exobj.tools.items(), key=lambda t1: t1['C'])

        sort = []
        for k, v in list(exobj.tools.items()):
            sort.append((k, v.get('C')))
        sorted_tools = sorted(sort,key=lambda t1: t1[1])

        if tools == "all":
            tools = [i[0] for i in sorted_tools]   # we get a array of ordered tools
            log.debug("Tools 'all' and sorted are: %s" % str(tools))
        else:
            selected_tools = [x.strip() for x in tools.split(",")]  # we strip spaces and also separate the tools by ','
            selected_tools = [t1 for t1 in selected_tools if t1 in selected_tools]

            # Create a sorted list of selected tools from the sorted_tools list
            tools = [i for i, j in sorted_tools for k in selected_tools if i == k]
            log.debug("Tools selected and sorted are: %s" % str(tools))

        # build a self.options['Tools_in_use'] list from scratch if we don't have one like in the case of
        # running this method from a Tcl Command
        build_tools_in_use_list = False
        if 'Tools_in_use' not in self.options:
            self.options['Tools_in_use'] = list()

        # if the list is empty (either we just added the key or it was already there but empty) signal to build it
        if not self.options['Tools_in_use']:
            build_tools_in_use_list = True

        # fill the data into the self.exc_cnc_tools dictionary
        for it in sorted_tools:
            for to_ol in tools:
                if to_ol == it[0]:
                    drill_no = 0
                    sol_geo = list()
                    for dr in exobj.drills:
                        if dr['tool'] == it[0]:
                            drill_no += 1
                            sol_geo.append(dr['point'])
                    slot_no = 0
                    for dr in exobj.slots:
                        if dr['tool'] == it[0]:
                            slot_no += 1
                            start = (dr['start'].x, dr['start'].y)
                            stop = (dr['stop'].x, dr['stop'].y)
                            sol_geo.append(
                                LineString([start, stop]).buffer((it[1] / 2.0), resolution=self.geo_steps_per_circle)
                            )

                    try:
                        z_off = float(self.tool_offset[it[1]]) * (-1)
                    except KeyError:
                        z_off = 0

                    default_data = dict()
                    for k, v in list(self.options.items()):
                        default_data[k] = deepcopy(v)

                    self.exc_cnc_tools[it[1]] = dict()
                    self.exc_cnc_tools[it[1]]['tool'] = it[0]
                    self.exc_cnc_tools[it[1]]['nr_drills'] = drill_no
                    self.exc_cnc_tools[it[1]]['nr_slots'] = slot_no
                    self.exc_cnc_tools[it[1]]['offset_z'] = z_off
                    self.exc_cnc_tools[it[1]]['data'] = default_data
                    self.exc_cnc_tools[it[1]]['solid_geometry'] = deepcopy(sol_geo)

                    # build a self.options['Tools_in_use'] list from scratch if we don't have one like in the case of
                    # running this method from a Tcl Command
                    if build_tools_in_use_list is True:
                        self.options['Tools_in_use'].append(
                            [it[0], it[1], drill_no, slot_no]
                        )

        print(self.options['Tools_in_use'])

        self.app.inform.emit(_("Creating a list of points to drill..."))
        # Points (Group by tool)
        points = dict()
        for drill in exobj.drills:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if drill['tool'] in tools:
                try:
                    points[drill['tool']].append(drill['point'])
                except KeyError:
                    points[drill['tool']] = [drill['point']]

        # log.debug("Found %d drills." % len(points))

        self.gcode = list()

        self.f_plunge = self.app.defaults["excellon_f_plunge"]
        self.f_retract = self.app.defaults["excellon_f_retract"]

        # Initialization
        gcode = self.doformat(p.start_code)
        gcode += self.doformat(p.feedrate_code)

        if toolchange is False:
            if self.xy_toolchange is not None:
                gcode += self.doformat(p.lift_code, x=self.xy_toolchange[0], y=self.xy_toolchange[1])
                gcode += self.doformat(p.startz_code, x=self.xy_toolchange[0], y=self.xy_toolchange[1])
            else:
                gcode += self.doformat(p.lift_code, x=0.0, y=0.0)
                gcode += self.doformat(p.startz_code, x=0.0, y=0.0)

        # Distance callback
        class CreateDistanceCallback(object):
            """Create callback to calculate distances between points."""

            def __init__(self):
                """Initialize distance array."""
                locations = create_data_array()
                size = len(locations)
                self.matrix = {}

                for from_node in range(size):
                    self.matrix[from_node] = {}
                    for to_node in range(size):
                        if from_node == to_node:
                            self.matrix[from_node][to_node] = 0
                        else:
                            x1 = locations[from_node][0]
                            y1 = locations[from_node][1]
                            x2 = locations[to_node][0]
                            y2 = locations[to_node][1]
                            self.matrix[from_node][to_node] = distance_euclidian(x1, y1, x2, y2)

            # def Distance(self, from_node, to_node):
            #     return int(self.matrix[from_node][to_node])
            def Distance(self, from_index, to_index):
                # Convert from routing variable Index to distance matrix NodeIndex.
                from_node = manager.IndexToNode(from_index)
                to_node = manager.IndexToNode(to_index)
                return self.matrix[from_node][to_node]

        # Create the data.
        def create_data_array():
            locations = []
            for point in points[tool]:
                locations.append((point.coords.xy[0][0], point.coords.xy[1][0]))
            return locations

        if self.xy_toolchange is not None:
            self.oldx = self.xy_toolchange[0]
            self.oldy = self.xy_toolchange[1]
        else:
            self.oldx = 0.0
            self.oldy = 0.0

        measured_distance = 0.0
        measured_down_distance = 0.0
        measured_up_to_zero_distance = 0.0
        measured_lift_distance = 0.0

        self.app.inform.emit('%s...' % _("Starting G-Code"))

        current_platform = platform.architecture()[0]
        if current_platform == '64bit':
            used_excellon_optimization_type = excellon_optimization_type
            if used_excellon_optimization_type == 'M':
                log.debug("Using OR-Tools Metaheuristic Guided Local Search drill path optimization.")
                if exobj.drills:
                    for tool in tools:
                        self.tool=tool
                        self.postdata['toolC'] = exobj.tools[tool]["C"]
                        self.tooldia = exobj.tools[tool]["C"]

                        if self.app.abort_flag:
                            # graceful abort requested by the user
                            raise FlatCAMApp.GracefulException

                        # ###############################################
                        # ############ Create the data. #################
                        # ###############################################

                        node_list = []
                        locations = create_data_array()
                        tsp_size = len(locations)
                        num_routes = 1  # The number of routes, which is 1 in the TSP.
                        # Nodes are indexed from 0 to tsp_size - 1. The depot is the starting node of the route.
                        depot = 0
                        # Create routing model.
                        if tsp_size > 0:
                            manager = pywrapcp.RoutingIndexManager(tsp_size, num_routes, depot)
                            routing = pywrapcp.RoutingModel(manager)
                            search_parameters = pywrapcp.DefaultRoutingSearchParameters()
                            search_parameters.local_search_metaheuristic = (
                                routing_enums_pb2.LocalSearchMetaheuristic.GUIDED_LOCAL_SEARCH)

                            # Set search time limit in milliseconds.
                            if float(self.app.defaults["excellon_search_time"]) != 0:
                                search_parameters.time_limit.seconds = int(
                                    float(self.app.defaults["excellon_search_time"]))
                            else:
                                search_parameters.time_limit.seconds = 3

                            # Callback to the distance function. The callback takes two
                            # arguments (the from and to node indices) and returns the distance between them.
                            dist_between_locations = CreateDistanceCallback()
                            dist_callback = dist_between_locations.Distance
                            transit_callback_index = routing.RegisterTransitCallback(dist_callback)
                            routing.SetArcCostEvaluatorOfAllVehicles(transit_callback_index)

                            # Solve, returns a solution if any.
                            assignment = routing.SolveWithParameters(search_parameters)

                            if assignment:
                                # Solution cost.
                                log.info("Total distance: " + str(assignment.ObjectiveValue()))

                                # Inspect solution.
                                # Only one route here; otherwise iterate from 0 to routing.vehicles() - 1.
                                route_number = 0
                                node = routing.Start(route_number)
                                start_node = node

                                while not routing.IsEnd(node):
                                    if self.app.abort_flag:
                                        # graceful abort requested by the user
                                        raise FlatCAMApp.GracefulException

                                    node_list.append(node)
                                    node = assignment.Value(routing.NextVar(node))
                            else:
                                log.warning('No solution found.')
                        else:
                            log.warning('Specify an instance greater than 0.')
                        # ############################################# ##

                        # Only if tool has points.
                        if tool in points:
                            if self.app.abort_flag:
                                # graceful abort requested by the user
                                raise FlatCAMApp.GracefulException

                            # Tool change sequence (optional)
                            if toolchange:
                                gcode += self.doformat(p.toolchange_code, toolchangexy=(self.oldx, self.oldy))
                                gcode += self.doformat(p.spindle_code)  # Spindle start
                                if self.dwell is True:
                                    gcode += self.doformat(p.dwell_code)  # Dwell time
                            else:
                                gcode += self.doformat(p.spindle_code)
                                if self.dwell is True:
                                    gcode += self.doformat(p.dwell_code)  # Dwell time

                            current_tooldia = float('%.*f' % (self.decimals, float(exobj.tools[tool]["C"])))

                            self.app.inform.emit(
                                '%s: %s%s.' % (_("Starting G-Code for tool with diameter"),
                                               str(current_tooldia),
                                               str(self.units))
                            )

                            # TODO apply offset only when using the GUI, for TclCommand this will create an error
                            # because the values for Z offset are created in build_ui()
                            try:
                                z_offset = float(self.tool_offset[current_tooldia]) * (-1)
                            except KeyError:
                                z_offset = 0
                            self.z_cut = z_offset + old_zcut

                            self.coordinates_type = self.app.defaults["cncjob_coords_type"]
                            if self.coordinates_type == "G90":
                                # Drillling! for Absolute coordinates type G90
                                # variables to display the percentage of work done
                                geo_len = len(node_list)

                                old_disp_number = 0
                                log.warning("Number of drills for which to generate GCode: %s" % str(geo_len))

                                loc_nr = 0
                                for k in node_list:
                                    if self.app.abort_flag:
                                        # graceful abort requested by the user
                                        raise FlatCAMApp.GracefulException

                                    locx = locations[k][0]
                                    locy = locations[k][1]

                                    gcode += self.doformat(p.rapid_code, x=locx, y=locy)
                                    gcode += self.doformat(p.down_code, x=locx, y=locy)

                                    measured_down_distance += abs(self.z_cut) + abs(self.z_move)

                                    if self.f_retract is False:
                                        gcode += self.doformat(p.up_to_zero_code, x=locx, y=locy)
                                        measured_up_to_zero_distance += abs(self.z_cut)
                                        measured_lift_distance += abs(self.z_move)
                                    else:
                                        measured_lift_distance += abs(self.z_cut) + abs(self.z_move)

                                    gcode += self.doformat(p.lift_code, x=locx, y=locy)
                                    measured_distance += abs(distance_euclidian(locx, locy, self.oldx, self.oldy))
                                    self.oldx = locx
                                    self.oldy = locy

                                    loc_nr += 1
                                    disp_number = int(np.interp(loc_nr, [0, geo_len], [0, 100]))

                                    if old_disp_number < disp_number <= 100:
                                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                                        old_disp_number = disp_number

                            else:
                                self.app.inform.emit('[ERROR_NOTCL] %s...' % _('G91 coordinates not implemented'))
                                return 'fail'
                        self.z_cut = deepcopy(old_zcut)
                else:
                    log.debug("camlib.CNCJob.generate_from_excellon_by_tool() --> "
                              "The loaded Excellon file has no drills ...")
                    self.app.inform.emit('[ERROR_NOTCL] %s...' % _('The loaded Excellon file has no drills'))
                    return 'fail'

                log.debug("The total travel distance with OR-TOOLS Metaheuristics is: %s" % str(measured_distance))

            if used_excellon_optimization_type == 'B':
                log.debug("Using OR-Tools Basic drill path optimization.")
                if exobj.drills:
                    for tool in tools:
                        if self.app.abort_flag:
                            # graceful abort requested by the user
                            raise FlatCAMApp.GracefulException

                        self.tool=tool
                        self.postdata['toolC']=exobj.tools[tool]["C"]
                        self.tooldia = exobj.tools[tool]["C"]

                        # ############################################# ##
                        node_list = []
                        locations = create_data_array()
                        tsp_size = len(locations)
                        num_routes = 1  # The number of routes, which is 1 in the TSP.

                        # Nodes are indexed from 0 to tsp_size - 1. The depot is the starting node of the route.
                        depot = 0

                        # Create routing model.
                        if tsp_size > 0:
                            manager = pywrapcp.RoutingIndexManager(tsp_size, num_routes, depot)
                            routing = pywrapcp.RoutingModel(manager)
                            search_parameters = pywrapcp.DefaultRoutingSearchParameters()

                            # Callback to the distance function. The callback takes two
                            # arguments (the from and to node indices) and returns the distance between them.
                            dist_between_locations = CreateDistanceCallback()
                            dist_callback = dist_between_locations.Distance
                            transit_callback_index = routing.RegisterTransitCallback(dist_callback)
                            routing.SetArcCostEvaluatorOfAllVehicles(transit_callback_index)

                            # Solve, returns a solution if any.
                            assignment = routing.SolveWithParameters(search_parameters)

                            if assignment:
                                # Solution cost.
                                log.info("Total distance: " + str(assignment.ObjectiveValue()))

                                # Inspect solution.
                                # Only one route here; otherwise iterate from 0 to routing.vehicles() - 1.
                                route_number = 0
                                node = routing.Start(route_number)
                                start_node = node

                                while not routing.IsEnd(node):
                                    node_list.append(node)
                                    node = assignment.Value(routing.NextVar(node))
                            else:
                                log.warning('No solution found.')
                        else:
                            log.warning('Specify an instance greater than 0.')
                        # ############################################# ##

                        # Only if tool has points.
                        if tool in points:
                            if self.app.abort_flag:
                                # graceful abort requested by the user
                                raise FlatCAMApp.GracefulException

                            # Tool change sequence (optional)
                            if toolchange:
                                gcode += self.doformat(p.toolchange_code, toolchangexy=(self.oldx, self.oldy))
                                gcode += self.doformat(p.spindle_code)  # Spindle start)
                                if self.dwell is True:
                                    gcode += self.doformat(p.dwell_code)  # Dwell time
                            else:
                                gcode += self.doformat(p.spindle_code)
                                if self.dwell is True:
                                    gcode += self.doformat(p.dwell_code)  # Dwell time

                            current_tooldia = float('%.*f' % (self.decimals, float(exobj.tools[tool]["C"])))

                            self.app.inform.emit(
                                '%s: %s%s.' % (_("Starting G-Code for tool with diameter"),
                                               str(current_tooldia),
                                               str(self.units))
                            )

                            # TODO apply offset only when using the GUI, for TclCommand this will create an error
                            # because the values for Z offset are created in build_ui()
                            try:
                                z_offset = float(self.tool_offset[current_tooldia]) * (-1)
                            except KeyError:
                                z_offset = 0
                            self.z_cut = z_offset + old_zcut

                            self.coordinates_type = self.app.defaults["cncjob_coords_type"]
                            if self.coordinates_type == "G90":
                                # Drillling! for Absolute coordinates type G90
                                # variables to display the percentage of work done
                                geo_len = len(node_list)
                                disp_number = 0
                                old_disp_number = 0
                                log.warning("Number of drills for which to generate GCode: %s" % str(geo_len))

                                loc_nr = 0
                                for k in node_list:
                                    if self.app.abort_flag:
                                        # graceful abort requested by the user
                                        raise FlatCAMApp.GracefulException

                                    locx = locations[k][0]
                                    locy = locations[k][1]

                                    gcode += self.doformat(p.rapid_code, x=locx, y=locy)
                                    gcode += self.doformat(p.down_code, x=locx, y=locy)

                                    measured_down_distance += abs(self.z_cut) + abs(self.z_move)

                                    if self.f_retract is False:
                                        gcode += self.doformat(p.up_to_zero_code, x=locx, y=locy)
                                        measured_up_to_zero_distance += abs(self.z_cut)
                                        measured_lift_distance += abs(self.z_move)
                                    else:
                                        measured_lift_distance += abs(self.z_cut) + abs(self.z_move)

                                    gcode += self.doformat(p.lift_code, x=locx, y=locy)
                                    measured_distance += abs(distance_euclidian(locx, locy, self.oldx, self.oldy))
                                    self.oldx = locx
                                    self.oldy = locy

                                    loc_nr += 1
                                    disp_number = int(np.interp(loc_nr, [0, geo_len], [0, 100]))

                                    if old_disp_number < disp_number <= 100:
                                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                                        old_disp_number = disp_number

                            else:
                                self.app.inform.emit('[ERROR_NOTCL] %s...' % _('G91 coordinates not implemented'))
                                return 'fail'
                        self.z_cut = deepcopy(old_zcut)
                else:
                    log.debug("camlib.CNCJob.generate_from_excellon_by_tool() --> "
                              "The loaded Excellon file has no drills ...")
                    self.app.inform.emit('[ERROR_NOTCL] %s...' %
                                         _('The loaded Excellon file has no drills'))
                    return 'fail'

                log.debug("The total travel distance with OR-TOOLS Basic Algorithm is: %s" % str(measured_distance))
        else:
            used_excellon_optimization_type = 'T'

        if used_excellon_optimization_type == 'T':
            log.debug("Using Travelling Salesman drill path optimization.")
            for tool in tools:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException

                if exobj.drills:
                    self.tool = tool
                    self.postdata['toolC'] = exobj.tools[tool]["C"]
                    self.tooldia = exobj.tools[tool]["C"]

                    # Only if tool has points.
                    if tool in points:
                        if self.app.abort_flag:
                            # graceful abort requested by the user
                            raise FlatCAMApp.GracefulException

                        # Tool change sequence (optional)
                        if toolchange:
                            gcode += self.doformat(p.toolchange_code, toolchangexy=(self.oldx, self.oldy))
                            gcode += self.doformat(p.spindle_code)  # Spindle start)
                            if self.dwell is True:
                                gcode += self.doformat(p.dwell_code)  # Dwell time
                        else:
                            gcode += self.doformat(p.spindle_code)
                            if self.dwell is True:
                                gcode += self.doformat(p.dwell_code)  # Dwell time

                        current_tooldia = float('%.*f' % (self.decimals, float(exobj.tools[tool]["C"])))

                        self.app.inform.emit(
                            '%s: %s%s.' % (_("Starting G-Code for tool with diameter"),
                                           str(current_tooldia),
                                           str(self.units))
                        )

                        # TODO apply offset only when using the GUI, for TclCommand this will create an error
                        # because the values for Z offset are created in build_ui()
                        try:
                            z_offset = float(self.tool_offset[current_tooldia]) * (-1)
                        except KeyError:
                            z_offset = 0
                        self.z_cut = z_offset + old_zcut

                        self.coordinates_type = self.app.defaults["cncjob_coords_type"]
                        if self.coordinates_type == "G90":
                            # Drillling! for Absolute coordinates type G90
                            altPoints = []
                            for point in points[tool]:
                                altPoints.append((point.coords.xy[0][0], point.coords.xy[1][0]))

                            node_list = self.optimized_travelling_salesman(altPoints)
                            # variables to display the percentage of work done
                            geo_len = len(node_list)
                            disp_number = 0
                            old_disp_number = 0
                            log.warning("Number of drills for which to generate GCode: %s" % str(geo_len))

                            loc_nr = 0
                            for point in node_list:
                                if self.app.abort_flag:
                                    # graceful abort requested by the user
                                    raise FlatCAMApp.GracefulException

                                gcode += self.doformat(p.rapid_code, x=point[0], y=point[1])
                                gcode += self.doformat(p.down_code, x=point[0], y=point[1])

                                measured_down_distance += abs(self.z_cut) + abs(self.z_move)

                                if self.f_retract is False:
                                    gcode += self.doformat(p.up_to_zero_code, x=point[0], y=point[1])
                                    measured_up_to_zero_distance += abs(self.z_cut)
                                    measured_lift_distance += abs(self.z_move)
                                else:
                                    measured_lift_distance += abs(self.z_cut) + abs(self.z_move)

                                gcode += self.doformat(p.lift_code, x=point[0], y=point[1])
                                measured_distance += abs(distance_euclidian(point[0], point[1], self.oldx, self.oldy))
                                self.oldx = point[0]
                                self.oldy = point[1]

                                loc_nr += 1
                                disp_number = int(np.interp(loc_nr, [0, geo_len], [0, 100]))

                                if old_disp_number < disp_number <= 100:
                                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                                    old_disp_number = disp_number
                        else:
                            self.app.inform.emit('[ERROR_NOTCL] %s...' %  _('G91 coordinates not implemented'))
                            return 'fail'
                    else:
                        log.debug("camlib.CNCJob.generate_from_excellon_by_tool() --> "
                                  "The loaded Excellon file has no drills ...")
                        self.app.inform.emit('[ERROR_NOTCL] %s...' %
                                             _('The loaded Excellon file has no drills'))
                        return 'fail'
                self.z_cut = deepcopy(old_zcut)
            log.debug("The total travel distance with Travelling Salesman Algorithm is: %s" % str(measured_distance))

        gcode += self.doformat(p.spindle_stop_code)  # Spindle stop
        gcode += self.doformat(p.end_code, x=0, y=0)

        measured_distance += abs(distance_euclidian(self.oldx, self.oldy, 0, 0))
        log.debug("The total travel distance including travel to end position is: %s" %
                  str(measured_distance) + '\n')
        self.travel_distance = measured_distance

        # I use the value of self.feedrate_rapid for the feadrate in case of the measure_lift_distance and for
        # traveled_time because it is not always possible to determine the feedrate that the CNC machine uses
        # for G0 move (the fastest speed available to the CNC router). Although self.feedrate_rapids is used only with
        # Marlin preprocessor and derivatives.
        self.routing_time = (measured_down_distance + measured_up_to_zero_distance) / self.feedrate
        lift_time = measured_lift_distance / self.feedrate_rapid
        traveled_time = measured_distance / self.feedrate_rapid
        self.routing_time += lift_time + traveled_time

        self.gcode = gcode
        self.app.inform.emit(_("Finished G-Code generation..."))
        return 'OK'

    def generate_from_multitool_geometry(
            self, geometry, append=True,
            tooldia=None, offset=0.0, tolerance=0, z_cut=1.0, z_move=2.0,
            feedrate=2.0, feedrate_z=2.0, feedrate_rapid=30,
            spindlespeed=None, spindledir='CW', dwell=False, dwelltime=1.0,
            multidepth=False, depthpercut=None,
            toolchange=False, toolchangez=1.0, toolchangexy="0.0, 0.0", extracut=False, extracut_length=0.2,
            startz=None, endz=2.0, pp_geometry_name=None, tool_no=1):
        """
        Algorithm to generate from multitool Geometry.

        Algorithm description:
        ----------------------
        Uses RTree to find the nearest path to follow.

        :param geometry:
        :param append:
        :param tooldia:
        :param offset:
        :param tolerance:
        :param z_cut:
        :param z_move:
        :param feedrate:
        :param feedrate_z:
        :param feedrate_rapid:
        :param spindlespeed:
        :param spindledir:          Direction of rotation for the spindle. If using GRBL laser mode will
        adjust the laser mode

        :param dwell:
        :param dwelltime:
        :param multidepth:          If True, use multiple passes to reach the desired depth.
        :param depthpercut:         Maximum depth in each pass.
        :param toolchange:
        :param toolchangez:
        :param toolchangexy:
        :param extracut:            Adds (or not) an extra cut at the end of each path overlapping the
                                    first point in path to ensure complete copper removal
        :param extracut_length:     Extra cut legth at the end of the path
        :param startz:
        :param endz:
        :param pp_geometry_name:
        :param tool_no:
        :return:                    GCode - string
        """

        log.debug("Generate_from_multitool_geometry()")

        temp_solid_geometry = []
        if offset != 0.0:
            for it in geometry:
                # if the geometry is a closed shape then create a Polygon out of it
                if isinstance(it, LineString):
                    c = it.coords
                    if c[0] == c[-1]:
                        it = Polygon(it)
                temp_solid_geometry.append(it.buffer(offset, join_style=2))
        else:
            temp_solid_geometry = geometry

        # ## Flatten the geometry. Only linear elements (no polygons) remain.
        flat_geometry = self.flatten(temp_solid_geometry, pathonly=True)
        log.debug("%d paths" % len(flat_geometry))

        self.tooldia = float(tooldia) if tooldia else None
        self.z_cut = float(z_cut) if z_cut else None
        self.z_move = float(z_move) if z_move is not None else None

        self.feedrate = float(feedrate) if feedrate else None
        self.z_feedrate = float(feedrate_z) if feedrate_z is not None else None
        self.feedrate_rapid = float(feedrate_rapid) if feedrate_rapid else None

        self.spindlespeed = int(spindlespeed) if spindlespeed != 0 else None
        self.spindledir = spindledir
        self.dwell = dwell
        self.dwelltime = float(dwelltime) if dwelltime else None

        self.startz = float(startz) if startz is not None else None
        self.z_end = float(endz) if endz is not None else None

        self.z_depthpercut = float(depthpercut) if depthpercut else None
        self.multidepth = multidepth

        self.z_toolchange = float(toolchangez) if toolchangez is not None else None

        # it servers in the preprocessor file
        self.tool = tool_no

        try:
            if toolchangexy == '':
                self.xy_toolchange = None
            else:
                self.xy_toolchange = [float(eval(a)) for a in toolchangexy.split(",")]
                if len(self.xy_toolchange) < 2:
                    self.app.inform.emit('[ERROR]  %s' % _("The Toolchange X,Y field in Edit -> Preferences has to be "
                                                           "in the format (x, y) \n"
                                                           "but now there is only one value, not two."))
                    return 'fail'
        except Exception as e:
            log.debug("camlib.CNCJob.generate_from_multitool_geometry() --> %s" % str(e))
            pass

        self.pp_geometry_name = pp_geometry_name if pp_geometry_name else 'default'
        self.f_plunge = self.app.defaults["geometry_f_plunge"]

        if self.z_cut is None:
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _("Cut_Z parameter is None or zero. Most likely a bad combinations of "
                                   "other parameters."))
            return 'fail'

        if self.machinist_setting == 0:
            if self.z_cut > 0:
                self.app.inform.emit('[WARNING] %s' %
                                     _("The Cut Z parameter has positive value. "
                                       "It is the depth value to cut into material.\n"
                                       "The Cut Z parameter needs to have a negative value, assuming it is a typo "
                                       "therefore the app will convert the value to negative."
                                       "Check the resulting CNC code (Gcode etc)."))
                self.z_cut = -self.z_cut
            elif self.z_cut == 0:
                self.app.inform.emit('[WARNING] %s: %s' %
                                     (_("The Cut Z parameter is zero. There will be no cut, skipping file"),
                                      self.options['name']))
                return 'fail'

            if self.z_move is None:
                self.app.inform.emit('[ERROR_NOTCL] %s' % _("Travel Z parameter is None or zero."))
                return 'fail'

            if self.z_move < 0:
                self.app.inform.emit('[WARNING] %s' %
                                     _("The Travel Z parameter has negative value. "
                                       "It is the height value to travel between cuts.\n"
                                       "The Z Travel parameter needs to have a positive value, assuming it is a typo "
                                       "therefore the app will convert the value to positive."
                                       "Check the resulting CNC code (Gcode etc)."))
                self.z_move = -self.z_move
            elif self.z_move == 0:
                self.app.inform.emit('[WARNING] %s: %s' %
                                     (_("The Z Travel parameter is zero. This is dangerous, skipping file"),
                                      self.options['name']))
                return 'fail'

        # made sure that depth_per_cut is no more then the z_cut
        if abs(self.z_cut) < self.z_depthpercut:
            self.z_depthpercut = abs(self.z_cut)

        # ## Index first and last points in paths
        # What points to index.
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        # Create the indexed storage.
        storage = FlatCAMRTreeStorage()
        storage.get_points = get_pts

        # Store the geometry
        log.debug("Indexing geometry before generating G-Code...")
        self.app.inform.emit(_("Indexing geometry before generating G-Code..."))

        for shape in flat_geometry:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if shape is not None:  # TODO: This shouldn't have happened.
                storage.insert(shape)

        # self.input_geometry_bounds = geometry.bounds()

        if not append:
            self.gcode = ""

        # tell preprocessor the number of tool (for toolchange)
        self.tool = tool_no

        # this is the tool diameter, it is used as such to accommodate the preprocessor who need the tool diameter
        # given under the name 'toolC'
        self.postdata['toolC'] = self.tooldia

        # Initial G-Code
        self.pp_geometry = self.app.preprocessors[self.pp_geometry_name]
        p = self.pp_geometry

        self.gcode = self.doformat(p.start_code)

        self.gcode += self.doformat(p.feedrate_code)        # sets the feed rate

        if toolchange is False:
            self.gcode += self.doformat(p.lift_code, x=0, y=0)  # Move (up) to travel height
            self.gcode += self.doformat(p.startz_code, x=0, y=0)

        if toolchange:
            # if "line_xyz" in self.pp_geometry_name:
            #     self.gcode += self.doformat(p.toolchange_code, x=self.xy_toolchange[0], y=self.xy_toolchange[1])
            # else:
            #     self.gcode += self.doformat(p.toolchange_code)
            self.gcode += self.doformat(p.toolchange_code)

            if 'laser' not in self.pp_geometry_name:
                self.gcode += self.doformat(p.spindle_code)     # Spindle start
            else:
                # for laser this will disable the laser
                self.gcode += self.doformat(p.lift_code, x=self.oldx, y=self.oldy)  # Move (up) to travel height

            if self.dwell is True:
                self.gcode += self.doformat(p.dwell_code)   # Dwell time
        else:
            if 'laser' not in self.pp_geometry_name:
                self.gcode += self.doformat(p.spindle_code)  # Spindle start

            if self.dwell is True:
                self.gcode += self.doformat(p.dwell_code)   # Dwell time

        total_travel = 0.0
        total_cut = 0.0

        # ## Iterate over geometry paths getting the nearest each time.
        log.debug("Starting G-Code...")
        self.app.inform.emit('%s...' % _("Starting G-Code"))

        path_count = 0
        current_pt = (0, 0)

        # variables to display the percentage of work done
        geo_len = len(flat_geometry)

        old_disp_number = 0
        log.warning("Number of paths for which to generate GCode: %s" % str(geo_len))

        current_tooldia = float('%.*f' % (self.decimals, float(self.tooldia)))

        self.app.inform.emit( '%s: %s%s.' % (_("Starting G-Code for tool with diameter"),
                                             str(current_tooldia),
                                             str(self.units)))

        pt, geo = storage.nearest(current_pt)

        try:
            while True:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException

                path_count += 1

                # Remove before modifying, otherwise deletion will fail.
                storage.remove(geo)

                # If last point in geometry is the nearest but prefer the first one if last point == first point
                # then reverse coordinates.
                if pt != geo.coords[0] and pt == geo.coords[-1]:
                    geo.coords = list(geo.coords)[::-1]

                # ---------- Single depth/pass --------
                if not multidepth:
                    # calculate the cut distance
                    total_cut = total_cut + geo.length

                    self.gcode += self.create_gcode_single_pass(geo, extracut, extracut_length, tolerance,
                                                                old_point=current_pt)

                # --------- Multi-pass ---------
                else:
                    # calculate the cut distance
                    # due of the number of cuts (multi depth) it has to multiplied by the number of cuts
                    nr_cuts = 0
                    depth = abs(self.z_cut)
                    while depth > 0:
                        nr_cuts += 1
                        depth -= float(self.z_depthpercut)

                    total_cut += (geo.length * nr_cuts)

                    self.gcode += self.create_gcode_multi_pass(geo, extracut, extracut_length, tolerance,
                                                               postproc=p, old_point=current_pt)

                # calculate the total distance
                total_travel = total_travel + abs(distance(pt1=current_pt, pt2=pt))
                current_pt = geo.coords[-1]

                pt, geo = storage.nearest(current_pt)   # Next

                disp_number = int(np.interp(path_count, [0, geo_len], [0, 100]))
                if old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                    old_disp_number = disp_number
        except StopIteration:  # Nothing found in storage.
            pass

        log.debug("Finished G-Code... %s paths traced." % path_count)

        # add move to end position
        total_travel += abs(distance_euclidian(current_pt[0], current_pt[1], 0, 0))
        self.travel_distance += total_travel + total_cut
        self.routing_time += total_cut / self.feedrate

        # Finish
        self.gcode += self.doformat(p.spindle_stop_code)
        self.gcode += self.doformat(p.lift_code, x=current_pt[0], y=current_pt[1])
        self.gcode += self.doformat(p.end_code, x=0, y=0)
        self.app.inform.emit(
            '%s... %s %s.' % (_("Finished G-Code generation"), str(path_count), _("paths traced"))
        )
        return self.gcode

    def generate_from_geometry_2(
            self, geometry, append=True, tooldia=None, offset=0.0, tolerance=0, z_cut=None, z_move=None,
            feedrate=None, feedrate_z=None, feedrate_rapid=None,
            spindlespeed=None, spindledir='CW', dwell=False, dwelltime=None,
            multidepth=False, depthpercut=None,
            toolchange=False, toolchangez=None, toolchangexy="0.0, 0.0",
            extracut=False, extracut_length=None, startz=None, endz=None,
            pp_geometry_name=None, tool_no=1):
        """
        Second algorithm to generate from Geometry.

        Algorithm description:
        ----------------------
        Uses RTree to find the nearest path to follow.

        :param geometry:
        :param append:
        :param tooldia:
        :param tolerance:
        :param multidepth: If True, use multiple passes to reach
           the desired depth.
        :param depthpercut: Maximum depth in each pass.
        :param extracut: Adds (or not) an extra cut at the end of each path
            overlapping the first point in path to ensure complete copper removal
        :param extracut_length: The extra cut length
        :return: None
        """

        if not isinstance(geometry, Geometry):
            self.app.inform.emit('[ERROR] %s: %s' % (_("Expected a Geometry, got"), type(geometry)))
            return 'fail'
        log.debug("Executing camlib.CNCJob.generate_from_geometry_2()")

        # if solid_geometry is empty raise an exception
        if not geometry.solid_geometry:
            self.app.inform.emit(
                '[ERROR_NOTCL] %s' % _("Trying to generate a CNC Job from a Geometry object without solid_geometry.")
            )

        temp_solid_geometry = list()

        def bounds_rec(obj):
            if type(obj) is list:
                minx = np.Inf
                miny = np.Inf
                maxx = -np.Inf
                maxy = -np.Inf

                for k in obj:
                    if type(k) is dict:
                        for key in k:
                            minx_, miny_, maxx_, maxy_ = bounds_rec(k[key])
                            minx = min(minx, minx_)
                            miny = min(miny, miny_)
                            maxx = max(maxx, maxx_)
                            maxy = max(maxy, maxy_)
                    else:
                        minx_, miny_, maxx_, maxy_ = bounds_rec(k)
                        minx = min(minx, minx_)
                        miny = min(miny, miny_)
                        maxx = max(maxx, maxx_)
                        maxy = max(maxy, maxy_)
                return minx, miny, maxx, maxy
            else:
                # it's a Shapely object, return it's bounds
                return obj.bounds

        if offset != 0.0:
            offset_for_use = offset

            if offset < 0:
                a, b, c, d = bounds_rec(geometry.solid_geometry)
                # if the offset is less than half of the total length or less than half of the total width of the
                # solid geometry it's obvious we can't do the offset
                if -offset > ((c - a) / 2) or -offset > ((d - b) / 2):
                    self.app.inform.emit(
                        '[ERROR_NOTCL] %s' %
                        _("The Tool Offset value is too negative to use for the current_geometry.\n"
                          "Raise the value (in module) and try again.")
                    )
                    return 'fail'
                # hack: make offset smaller by 0.0000000001 which is insignificant difference but allow the job
                # to continue
                elif -offset == ((c - a) / 2) or -offset == ((d - b) / 2):
                    offset_for_use = offset - 0.0000000001

            for it in geometry.solid_geometry:
                # if the geometry is a closed shape then create a Polygon out of it
                if isinstance(it, LineString):
                    c = it.coords
                    if c[0] == c[-1]:
                        it = Polygon(it)
                temp_solid_geometry.append(it.buffer(offset_for_use, join_style=2))
        else:
            temp_solid_geometry = geometry.solid_geometry

        # ## Flatten the geometry. Only linear elements (no polygons) remain.
        flat_geometry = self.flatten(temp_solid_geometry, pathonly=True)
        log.debug("%d paths" % len(flat_geometry))

        default_dia = 0.01
        if isinstance(self.app.defaults["geometry_cnctooldia"], float):
            default_dia = self.app.defaults["geometry_cnctooldia"]
        else:
            try:
                tools_string = self.app.defaults["geometry_cnctooldia"].split(",")
                tools_diameters = [eval(a) for a in tools_string if a != '']
                default_dia = tools_diameters[0] if tools_diameters else 0.0
            except Exception as e:
                self.app.log.debug("camlib.CNCJob.generate_from_geometry_2() --> %s" % str(e))

        try:
            self.tooldia = float(tooldia) if tooldia else default_dia
        except ValueError:
            self.tooldia = [float(el) for el in tooldia.split(',') if el != ''] if tooldia is not None else default_dia

        self.z_cut = float(z_cut) if z_cut is not None else self.app.defaults["geometry_cutz"]
        self.z_move = float(z_move) if z_move is not None else self.app.defaults["geometry_travelz"]

        self.feedrate = float(feedrate) if feedrate is not None else self.app.defaults["geometry_feedrate"]
        self.z_feedrate = float(feedrate_z) if feedrate_z is not None else self.app.defaults["geometry_feedrate_z"]
        self.feedrate_rapid = float(feedrate_rapid) if feedrate_rapid is not None else \
            self.app.defaults["geometry_feedrate_rapid"]

        self.spindlespeed = int(spindlespeed) if spindlespeed != 0 else None
        self.spindledir = spindledir
        self.dwell = dwell
        self.dwelltime = float(dwelltime) if dwelltime is not None else self.app.defaults["geometry_dwelltime"]

        self.startz = float(startz) if startz is not None else self.app.defaults["geometry_startz"]
        self.z_end = float(endz) if endz is not None else self.app.defaults["geometry_endz"]
        self.z_depthpercut = float(depthpercut) if depthpercut is not None else 0.0
        self.multidepth = multidepth
        self.z_toolchange = float(toolchangez) if toolchangez is not None else self.app.defaults["geometry_toolchangez"]
        self.extracut_length = float(extracut_length) if extracut_length is not None else \
            self.app.defaults["geometry_extracut_length"]

        try:
            if toolchangexy == '':
                self.xy_toolchange = None
            else:
                self.xy_toolchange = [float(eval(a)) for a in toolchangexy.split(",")]
                if len(self.xy_toolchange) < 2:
                    self.app.inform.emit(
                        '[ERROR] %s' %
                        _("The Toolchange X,Y field in Edit -> Preferences has to be in the format (x, y) \n"
                          "but now there is only one value, not two. ")
                    )
                    return 'fail'
        except Exception as e:
            log.debug("camlib.CNCJob.generate_from_geometry_2() --> %s" % str(e))
            pass

        self.pp_geometry_name = pp_geometry_name if pp_geometry_name else 'default'
        self.f_plunge = self.app.defaults["geometry_f_plunge"]

        if self.machinist_setting == 0:
            if self.z_cut is None:
                self.app.inform.emit(
                    '[ERROR_NOTCL] %s' % _("Cut_Z parameter is None or zero. Most likely a bad combinations of "
                                           "other parameters.")
                )
                return 'fail'

            if self.z_cut > 0:
                self.app.inform.emit('[WARNING] %s' %
                                     _("The Cut Z parameter has positive value. "
                                       "It is the depth value to cut into material.\n"
                                       "The Cut Z parameter needs to have a negative value, assuming it is a typo "
                                       "therefore the app will convert the value to negative."
                                       "Check the resulting CNC code (Gcode etc)."))
                self.z_cut = -self.z_cut
            elif self.z_cut == 0:
                self.app.inform.emit(
                    '[WARNING] %s: %s' % (_("The Cut Z parameter is zero. There will be no cut, skipping file"),
                                          geometry.options['name'])
                )
                return 'fail'

            if self.z_move is None:
                self.app.inform.emit('[ERROR_NOTCL] %s' % _("Travel Z parameter is None or zero."))
                return 'fail'

            if self.z_move < 0:
                self.app.inform.emit('[WARNING] %s' %
                                     _("The Travel Z parameter has negative value. "
                                       "It is the height value to travel between cuts.\n"
                                       "The Z Travel parameter needs to have a positive value, assuming it is a typo "
                                       "therefore the app will convert the value to positive."
                                       "Check the resulting CNC code (Gcode etc)."))
                self.z_move = -self.z_move
            elif self.z_move == 0:
                self.app.inform.emit(
                    '[WARNING] %s: %s' % (_("The Z Travel parameter is zero. This is dangerous, skipping file"),
                                          self.options['name'])
                )
                return 'fail'

        # made sure that depth_per_cut is no more then the z_cut
        try:
            if abs(self.z_cut) < self.z_depthpercut:
                self.z_depthpercut = abs(self.z_cut)
        except TypeError:
            self.z_depthpercut = abs(self.z_cut)

        # ## Index first and last points in paths
        # What points to index.
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        # Create the indexed storage.
        storage = FlatCAMRTreeStorage()
        storage.get_points = get_pts

        # Store the geometry
        log.debug("Indexing geometry before generating G-Code...")
        self.app.inform.emit(_("Indexing geometry before generating G-Code..."))

        for shape in flat_geometry:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if shape is not None:  # TODO: This shouldn't have happened.
                storage.insert(shape)

        if not append:
            self.gcode = ""

        # tell preprocessor the number of tool (for toolchange)
        self.tool = tool_no

        # this is the tool diameter, it is used as such to accommodate the preprocessor who need the tool diameter
        # given under the name 'toolC'
        self.postdata['toolC'] = self.tooldia

        # Initial G-Code
        self.pp_geometry = self.app.preprocessors[self.pp_geometry_name]
        p = self.pp_geometry

        self.oldx = 0.0
        self.oldy = 0.0

        self.gcode = self.doformat(p.start_code)

        self.gcode += self.doformat(p.feedrate_code)        # sets the feed rate

        if toolchange is False:
            self.gcode += self.doformat(p.lift_code, x=self.oldx , y=self.oldy )  # Move (up) to travel height
            self.gcode += self.doformat(p.startz_code, x=self.oldx , y=self.oldy )

        if toolchange:
            # if "line_xyz" in self.pp_geometry_name:
            #     self.gcode += self.doformat(p.toolchange_code, x=self.xy_toolchange[0], y=self.xy_toolchange[1])
            # else:
            #     self.gcode += self.doformat(p.toolchange_code)
            self.gcode += self.doformat(p.toolchange_code)

            if 'laser' not in self.pp_geometry_name:
                self.gcode += self.doformat(p.spindle_code)     # Spindle start
            else:
                # for laser this will disable the laser
                self.gcode += self.doformat(p.lift_code, x=self.oldx, y=self.oldy)  # Move (up) to travel height

            if self.dwell is True:
                self.gcode += self.doformat(p.dwell_code)   # Dwell time
        else:
            if 'laser' not in self.pp_geometry_name:
                self.gcode += self.doformat(p.spindle_code)  # Spindle start

            if self.dwell is True:
                self.gcode += self.doformat(p.dwell_code)   # Dwell time

        total_travel = 0.0
        total_cut = 0.0

        # Iterate over geometry paths getting the nearest each time.
        log.debug("Starting G-Code...")
        self.app.inform.emit('%s...' % _("Starting G-Code"))

        # variables to display the percentage of work done
        geo_len = len(flat_geometry)

        old_disp_number = 0
        log.warning("Number of paths for which to generate GCode: %s" % str(geo_len))

        current_tooldia = float('%.*f' % (self.decimals, float(self.tooldia)))

        self.app.inform.emit(
            '%s: %s%s.' % (_("Starting G-Code for tool with diameter"), str(current_tooldia), str(self.units))
        )

        path_count = 0
        current_pt = (0, 0)
        pt, geo = storage.nearest(current_pt)
        try:
            while True:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException

                path_count += 1

                # Remove before modifying, otherwise deletion will fail.
                storage.remove(geo)

                # If last point in geometry is the nearest but prefer the first one if last point == first point
                # then reverse coordinates.
                if pt != geo.coords[0] and pt == geo.coords[-1]:
                    geo.coords = list(geo.coords)[::-1]

                # ---------- Single depth/pass --------
                if not multidepth:
                    # calculate the cut distance
                    total_cut += geo.length
                    self.gcode += self.create_gcode_single_pass(geo, extracut, self.extracut_length, tolerance,
                                                                old_point=current_pt)

                # --------- Multi-pass ---------
                else:
                    # calculate the cut distance
                    # due of the number of cuts (multi depth) it has to multiplied by the number of cuts
                    nr_cuts = 0
                    depth = abs(self.z_cut)
                    while depth > 0:
                        nr_cuts += 1
                        depth -= float(self.z_depthpercut)

                    total_cut += (geo.length * nr_cuts)

                    self.gcode += self.create_gcode_multi_pass(geo, extracut, self.extracut_length, tolerance,
                                                               postproc=p, old_point=current_pt)

                # calculate the travel distance
                total_travel += abs(distance(pt1=current_pt, pt2=pt))
                current_pt = geo.coords[-1]

                pt, geo = storage.nearest(current_pt) # Next

                disp_number = int(np.interp(path_count, [0, geo_len], [0, 100]))
                if old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                    old_disp_number = disp_number
        except StopIteration:  # Nothing found in storage.
            pass

        log.debug("Finishing G-Code... %s paths traced." % path_count)

        # add move to end position
        total_travel += abs(distance_euclidian(current_pt[0], current_pt[1], 0, 0))
        self.travel_distance += total_travel + total_cut
        self.routing_time += total_cut / self.feedrate

        # Finish
        self.gcode += self.doformat(p.spindle_stop_code)
        self.gcode += self.doformat(p.lift_code, x=current_pt[0], y=current_pt[1])
        self.gcode += self.doformat(p.end_code, x=0, y=0)
        self.app.inform.emit(
            '%s... %s %s' % (_("Finished G-Code generation"), str(path_count), _(" paths traced."))
        )

        return self.gcode

    def generate_gcode_from_solderpaste_geo(self, **kwargs):
        """
               Algorithm to generate from multitool Geometry.

               Algorithm description:
               ----------------------
               Uses RTree to find the nearest path to follow.

               :return: Gcode string
               """

        log.debug("Generate_from_solderpaste_geometry()")

        # ## Index first and last points in paths
        # What points to index.
        def get_pts(o):
            return [o.coords[0], o.coords[-1]]

        self.gcode = ""

        if not kwargs:
            log.debug("camlib.generate_from_solderpaste_geo() --> No tool in the solderpaste geometry.")
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _("There is no tool data in the SolderPaste geometry."))


        # this is the tool diameter, it is used as such to accommodate the preprocessor who need the tool diameter
        # given under the name 'toolC'

        self.postdata['z_start'] = kwargs['data']['tools_solderpaste_z_start']
        self.postdata['z_dispense'] = kwargs['data']['tools_solderpaste_z_dispense']
        self.postdata['z_stop'] = kwargs['data']['tools_solderpaste_z_stop']
        self.postdata['z_travel'] = kwargs['data']['tools_solderpaste_z_travel']
        self.postdata['z_toolchange'] = kwargs['data']['tools_solderpaste_z_toolchange']
        self.postdata['xy_toolchange'] = kwargs['data']['tools_solderpaste_xy_toolchange']
        self.postdata['frxy'] = kwargs['data']['tools_solderpaste_frxy']
        self.postdata['frz'] = kwargs['data']['tools_solderpaste_frz']
        self.postdata['frz_dispense'] = kwargs['data']['tools_solderpaste_frz_dispense']
        self.postdata['speedfwd'] = kwargs['data']['tools_solderpaste_speedfwd']
        self.postdata['dwellfwd'] = kwargs['data']['tools_solderpaste_dwellfwd']
        self.postdata['speedrev'] = kwargs['data']['tools_solderpaste_speedrev']
        self.postdata['dwellrev'] = kwargs['data']['tools_solderpaste_dwellrev']
        self.postdata['pp_solderpaste_name'] = kwargs['data']['tools_solderpaste_pp']

        self.postdata['toolC'] = kwargs['tooldia']

        self.pp_solderpaste_name = kwargs['data']['tools_solderpaste_pp'] if kwargs['data']['tools_solderpaste_pp'] \
            else self.app.defaults['tools_solderpaste_pp']
        p = self.app.preprocessors[self.pp_solderpaste_name]

        # ## Flatten the geometry. Only linear elements (no polygons) remain.
        flat_geometry = self.flatten(kwargs['solid_geometry'], pathonly=True)
        log.debug("%d paths" % len(flat_geometry))

        # Create the indexed storage.
        storage = FlatCAMRTreeStorage()
        storage.get_points = get_pts

        # Store the geometry
        log.debug("Indexing geometry before generating G-Code...")
        for shape in flat_geometry:
            if shape is not None:
                storage.insert(shape)

        # Initial G-Code
        self.gcode = self.doformat(p.start_code)
        self.gcode += self.doformat(p.spindle_off_code)
        self.gcode += self.doformat(p.toolchange_code)

        # ## Iterate over geometry paths getting the nearest each time.
        log.debug("Starting SolderPaste G-Code...")
        path_count = 0
        current_pt = (0, 0)

        # variables to display the percentage of work done
        geo_len = len(flat_geometry)
        disp_number = 0
        old_disp_number = 0

        pt, geo = storage.nearest(current_pt)

        try:
            while True:
                if self.app.abort_flag:
                    # graceful abort requested by the user
                    raise FlatCAMApp.GracefulException

                path_count += 1

                # Remove before modifying, otherwise deletion will fail.
                storage.remove(geo)

                # If last point in geometry is the nearest but prefer the first one if last point == first point
                # then reverse coordinates.
                if pt != geo.coords[0] and pt == geo.coords[-1]:
                    geo.coords = list(geo.coords)[::-1]

                self.gcode += self.create_soldepaste_gcode(geo, p=p, old_point=current_pt)
                current_pt = geo.coords[-1]
                pt, geo = storage.nearest(current_pt)  # Next

                disp_number = int(np.interp(path_count, [0, geo_len], [0, 100]))
                if old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                    old_disp_number = disp_number
        except StopIteration:  # Nothing found in storage.
            pass

        log.debug("Finishing SolderPste G-Code... %s paths traced." % path_count)
        self.app.inform.emit(
            '%s... %s %s' % (_("Finished SolderPste G-Code generation"), str(path_count), _("paths traced."))
        )

        # Finish
        self.gcode += self.doformat(p.lift_code)
        self.gcode += self.doformat(p.end_code)

        return self.gcode

    def create_soldepaste_gcode(self, geometry, p, old_point=(0, 0)):
        gcode = ''
        path = geometry.coords

        self.coordinates_type = self.app.defaults["cncjob_coords_type"]
        if self.coordinates_type == "G90":
            # For Absolute coordinates type G90
            first_x = path[0][0]
            first_y = path[0][1]
        else:
            # For Incremental coordinates type G91
            first_x = path[0][0] - old_point[0]
            first_y = path[0][1] - old_point[1]

        if type(geometry) == LineString or type(geometry) == LinearRing:
            # Move fast to 1st point
            gcode += self.doformat(p.rapid_code, x=first_x, y=first_y)  # Move to first point

            # Move down to cutting depth
            gcode += self.doformat(p.z_feedrate_code)
            gcode += self.doformat(p.down_z_start_code)
            gcode += self.doformat(p.spindle_fwd_code) # Start dispensing
            gcode += self.doformat(p.dwell_fwd_code)
            gcode += self.doformat(p.feedrate_z_dispense_code)
            gcode += self.doformat(p.lift_z_dispense_code)
            gcode += self.doformat(p.feedrate_xy_code)

            # Cutting...
            prev_x = first_x
            prev_y = first_y
            for pt in path[1:]:
                if self.coordinates_type == "G90":
                    # For Absolute coordinates type G90
                    next_x = pt[0]
                    next_y = pt[1]
                else:
                    # For Incremental coordinates type G91
                    next_x = pt[0] - prev_x
                    next_y = pt[1] - prev_y
                gcode += self.doformat(p.linear_code, x=next_x, y=next_y)  # Linear motion to point
                prev_x = next_x
                prev_y = next_y

            # Up to travelling height.
            gcode += self.doformat(p.spindle_off_code) # Stop dispensing
            gcode += self.doformat(p.spindle_rev_code)
            gcode += self.doformat(p.down_z_stop_code)
            gcode += self.doformat(p.spindle_off_code)
            gcode += self.doformat(p.dwell_rev_code)
            gcode += self.doformat(p.z_feedrate_code)
            gcode += self.doformat(p.lift_code)
        elif type(geometry) == Point:
            gcode += self.doformat(p.linear_code, x=first_x, y=first_y)  # Move to first point

            gcode += self.doformat(p.feedrate_z_dispense_code)
            gcode += self.doformat(p.down_z_start_code)
            gcode += self.doformat(p.spindle_fwd_code) # Start dispensing
            gcode += self.doformat(p.dwell_fwd_code)
            gcode += self.doformat(p.lift_z_dispense_code)

            gcode += self.doformat(p.spindle_off_code)  # Stop dispensing
            gcode += self.doformat(p.spindle_rev_code)
            gcode += self.doformat(p.spindle_off_code)
            gcode += self.doformat(p.down_z_stop_code)
            gcode += self.doformat(p.dwell_rev_code)
            gcode += self.doformat(p.z_feedrate_code)
            gcode += self.doformat(p.lift_code)
        return gcode

    def create_gcode_single_pass(self, geometry, extracut, extracut_length, tolerance, old_point=(0, 0)):
        # G-code. Note: self.linear2gcode() and self.point2gcode() will lower and raise the tool every time.
        gcode_single_pass = ''

        if type(geometry) == LineString or type(geometry) == LinearRing:
            if extracut is False:
                gcode_single_pass = self.linear2gcode(geometry, tolerance=tolerance, old_point=old_point)
            else:
                if geometry.is_ring:
                    gcode_single_pass = self.linear2gcode_extra(geometry, extracut_length, tolerance=tolerance,
                                                                old_point=old_point)
                else:
                    gcode_single_pass = self.linear2gcode(geometry, tolerance=tolerance, old_point=old_point)
        elif type(geometry) == Point:
            gcode_single_pass = self.point2gcode(geometry)
        else:
            log.warning("G-code generation not implemented for %s" % (str(type(geometry))))
            return

        return gcode_single_pass

    def create_gcode_multi_pass(self, geometry, extracut, extracut_length, tolerance, postproc, old_point=(0, 0)):

        gcode_multi_pass = ''

        if isinstance(self.z_cut, Decimal):
            z_cut = self.z_cut
        else:
            z_cut = Decimal(self.z_cut).quantize(Decimal('0.000000001'))

        if self.z_depthpercut is None:
            self.z_depthpercut = z_cut
        elif not isinstance(self.z_depthpercut, Decimal):
            self.z_depthpercut = Decimal(self.z_depthpercut).quantize(Decimal('0.000000001'))

        depth = 0
        reverse = False
        while depth > z_cut:

            # Increase depth. Limit to z_cut.
            depth -= self.z_depthpercut
            if depth < z_cut:
                depth = z_cut

            # Cut at specific depth and do not lift the tool.
            # Note: linear2gcode() will use G00 to move to the first point in the path, but it should be already
            # at the first point if the tool is down (in the material).  So, an extra G00 should show up but
            # is inconsequential.
            if type(geometry) == LineString or type(geometry) == LinearRing:
                if extracut is False:
                    gcode_multi_pass += self.linear2gcode(geometry, tolerance=tolerance, z_cut=depth, up=False,
                                                          old_point=old_point)
                else:
                    if geometry.is_ring:
                        gcode_multi_pass += self.linear2gcode_extra(geometry, extracut_length, tolerance=tolerance,
                                                                    z_cut=depth, up=False, old_point=old_point)
                    else:
                        gcode_multi_pass += self.linear2gcode(geometry, tolerance=tolerance, z_cut=depth, up=False,
                                                              old_point=old_point)

            # Ignore multi-pass for points.
            elif type(geometry) == Point:
                gcode_multi_pass += self.point2gcode(geometry, old_point=old_point)
                break  # Ignoring ...
            else:
                log.warning("G-code generation not implemented for %s" % (str(type(geometry))))

            # Reverse coordinates if not a loop so we can continue cutting without returning to the beginning.
            if type(geometry) == LineString:
                geometry.coords = list(geometry.coords)[::-1]
                reverse = True

        # If geometry is reversed, revert.
        if reverse:
            if type(geometry) == LineString:
                geometry.coords = list(geometry.coords)[::-1]

        # Lift the tool
        gcode_multi_pass += self.doformat(postproc.lift_code, x=old_point[0], y=old_point[1])
        return gcode_multi_pass

    def codes_split(self, gline):
        """
        Parses a line of G-Code such as "G01 X1234 Y987" into
        a dictionary: {'G': 1.0, 'X': 1234.0, 'Y': 987.0}

        :param gline: G-Code line string
        :return: Dictionary with parsed line.
        """

        command = {}

        if 'Roland' in self.pp_excellon_name or 'Roland' in self.pp_geometry_name:
            match_z = re.search(r"^Z(\s*-?\d+\.\d+?),(\s*\s*-?\d+\.\d+?),(\s*\s*-?\d+\.\d+?)*;$", gline)
            if match_z:
                command['G'] = 0
                command['X'] = float(match_z.group(1).replace(" ", "")) * 0.025
                command['Y'] = float(match_z.group(2).replace(" ", "")) * 0.025
                command['Z'] = float(match_z.group(3).replace(" ", "")) * 0.025

        elif 'hpgl' in self.pp_excellon_name or 'hpgl' in self.pp_geometry_name:
            match_pa = re.search(r"^PA(\s*-?\d+\.\d+?),(\s*\s*-?\d+\.\d+?)*;$", gline)
            if match_pa:
                command['G'] = 0
                command['X'] = float(match_pa.group(1).replace(" ", "")) / 40
                command['Y'] = float(match_pa.group(2).replace(" ", "")) / 40
            match_pen = re.search(r"^(P[U|D])", gline)
            if match_pen:
                if match_pen.group(1) == 'PU':
                    # the value does not matter, only that it is positive so the gcode_parse() know it is > 0,
                    # therefore the move is of kind T (travel)
                    command['Z'] = 1
                else:
                    command['Z'] = 0

        elif 'laser' in self.pp_excellon_name.lower() or 'laser' in self.pp_geometry_name.lower() or \
                (self.pp_solderpaste_name is not None and 'paste' in self.pp_solderpaste_name.lower()):
            match_lsr = re.search(r"X([\+-]?\d+.[\+-]?\d+)\s*Y([\+-]?\d+.[\+-]?\d+)", gline)
            if match_lsr:
                command['X'] = float(match_lsr.group(1).replace(" ", ""))
                command['Y'] = float(match_lsr.group(2).replace(" ", ""))

            match_lsr_pos = re.search(r"^(M0?[3-5])", gline)
            if match_lsr_pos:
                if 'M05' in match_lsr_pos.group(1) or 'M5' in match_lsr_pos.group(1):
                    # the value does not matter, only that it is positive so the gcode_parse() know it is > 0,
                    # therefore the move is of kind T (travel)
                    command['Z'] = 1
                else:
                    command['Z'] = 0

            match_lsr_pos_2 = re.search(r"^(M10[6|7])", gline)
            if match_lsr_pos_2:
                if 'M107' in match_lsr_pos_2.group(1):
                    command['Z'] = 1
                else:
                    command['Z'] = 0
        elif self.pp_solderpaste_name is not None:
            if 'Paste' in self.pp_solderpaste_name:
                match_paste = re.search(r"X([\+-]?\d+.[\+-]?\d+)\s*Y([\+-]?\d+.[\+-]?\d+)", gline)
                if match_paste:
                    command['X'] = float(match_paste.group(1).replace(" ", ""))
                    command['Y'] = float(match_paste.group(2).replace(" ", ""))
        else:
            match = re.search(r'^\s*([A-Z])\s*([\+\-\.\d\s]+)', gline)
            while match:
                command[match.group(1)] = float(match.group(2).replace(" ", ""))
                gline = gline[match.end():]
                match = re.search(r'^\s*([A-Z])\s*([\+\-\.\d\s]+)', gline)
        return command

    def gcode_parse(self, force_parsing=None):
        """
        G-Code parser (from self.gcode). Generates dictionary with
        single-segment LineString's and "kind" indicating cut or travel,
        fast or feedrate speed.
        """

        kind = ["C", "F"]  # T=travel, C=cut, F=fast, S=slow

        # Results go here
        geometry = []        

        # Last known instruction
        current = {'X': 0.0, 'Y': 0.0, 'Z': 0.0, 'G': 0}

        # Current path: temporary storage until tool is
        # lifted or lowered.
        if self.toolchange_xy_type == "excellon":
            if self.app.defaults["excellon_toolchangexy"] == '':
                pos_xy = (0, 0)
            else:
                pos_xy = [float(eval(a)) for a in self.app.defaults["excellon_toolchangexy"].split(",")]
        else:
            if self.app.defaults["geometry_toolchangexy"] == '':
                pos_xy = (0, 0)
            else:
                pos_xy = [float(eval(a)) for a in self.app.defaults["geometry_toolchangexy"].split(",")]

        path = [pos_xy]
        # path = [(0, 0)]

        gcode_lines_list = self.gcode.splitlines()
        self.app.inform.emit('%s: %d' % (_("Parsing GCode file. Number of lines"), len(gcode_lines_list)))

        # Process every instruction
        for line in gcode_lines_list:
            if force_parsing is False or force_parsing is None:
                if '%MO' in line or '%' in line or 'MOIN' in line or 'MOMM' in line:
                    return "fail"

            gobj = self.codes_split(line)

            # ## Units
            if 'G' in gobj and (gobj['G'] == 20.0 or gobj['G'] == 21.0):
                self.units = {20.0: "IN", 21.0: "MM"}[gobj['G']]
                continue

            # TODO take into consideration the tools and update the travel line thickness
            if 'T' in gobj:
                pass

            # ## Changing height
            if 'Z' in gobj:
                if 'Roland' in self.pp_excellon_name or 'Roland' in self.pp_geometry_name:
                    pass
                elif 'hpgl' in self.pp_excellon_name or 'hpgl' in self.pp_geometry_name:
                    pass
                elif 'laser' in self.pp_excellon_name or 'laser' in self.pp_geometry_name:
                    pass
                elif ('X' in gobj or 'Y' in gobj) and gobj['Z'] != current['Z']:
                    if self.pp_geometry_name == 'line_xyz' or self.pp_excellon_name == 'line_xyz':
                        pass
                    else:
                        log.warning("Non-orthogonal motion: From %s" % str(current))
                        log.warning("  To: %s" % str(gobj))

                current['Z'] = gobj['Z']
                # Store the path into geometry and reset path
                if len(path) > 1:
                    geometry.append({"geom": LineString(path),
                                     "kind": kind})
                    path = [path[-1]]  # Start with the last point of last path.

                # create the geometry for the holes created when drilling Excellon drills
                if self.origin_kind == 'excellon':
                    if current['Z'] < 0:
                        current_drill_point_coords = (
                            float('%.*f' % (self.decimals, current['X'])),
                            float('%.*f' % (self.decimals, current['Y']))
                        )

                        # find the drill diameter knowing the drill coordinates
                        for pt_dict in self.exc_drills:
                            point_in_dict_coords = (
                                float('%.*f' % (self.decimals, pt_dict['point'].x)),
                                float('%.*f' % (self.decimals, pt_dict['point'].y))
                            )
                            if point_in_dict_coords == current_drill_point_coords:
                                tool = pt_dict['tool']
                                dia = self.exc_tools[tool]['C']
                                kind = ['C', 'F']
                                geometry.append(
                                    {
                                        "geom": Point(current_drill_point_coords).buffer(dia/2.0).exterior,
                                        "kind": kind
                                    }
                                )
                                break

            if 'G' in gobj:
                current['G'] = int(gobj['G'])
                
            if 'X' in gobj or 'Y' in gobj:
                if 'X' in gobj:
                    x = gobj['X']
                    # current['X'] = x
                else:
                    x = current['X']
                
                if 'Y' in gobj:
                    y = gobj['Y']
                else:
                    y = current['Y']

                kind = ["C", "F"]  # T=travel, C=cut, F=fast, S=slow

                if current['Z'] > 0:
                    kind[0] = 'T'
                if current['G'] > 0:
                    kind[1] = 'S'

                if current['G'] in [0, 1]:  # line
                    path.append((x, y))

                arcdir = [None, None, "cw", "ccw"]
                if current['G'] in [2, 3]:  # arc
                    center = [gobj['I'] + current['X'], gobj['J'] + current['Y']]
                    radius = np.sqrt(gobj['I']**2 + gobj['J']**2)
                    start = np.arctan2(-gobj['J'], -gobj['I'])
                    stop = np.arctan2(-center[1] + y, -center[0] + x)
                    path += arc(center, radius, start, stop, arcdir[current['G']], int(self.steps_per_circle))

                current['X'] = x
                current['Y'] = y

            # Update current instruction
            for code in gobj:
                current[code] = gobj[code]

        self.app.inform.emit('%s...' % _("Creating Geometry from the parsed GCode file. "))
        # There might not be a change in height at the
        # end, therefore, see here too if there is
        # a final path.
        if len(path) > 1:
            geometry.append(
                {
                    "geom": LineString(path),
                    "kind": kind
                }
            )

        self.gcode_parsed = geometry
        return geometry

    # def plot(self, tooldia=None, dpi=75, margin=0.1,
    #          color={"T": ["#F0E24D", "#B5AB3A"], "C": ["#5E6CFF", "#4650BD"]},
    #          alpha={"T": 0.3, "C": 1.0}):
    #     """
    #     Creates a Matplotlib figure with a plot of the
    #     G-code job.
    #     """
    #     if tooldia is None:
    #         tooldia = self.tooldia
    #
    #     fig = Figure(dpi=dpi)
    #     ax = fig.add_subplot(111)
    #     ax.set_aspect(1)
    #     xmin, ymin, xmax, ymax = self.input_geometry_bounds
    #     ax.set_xlim(xmin-margin, xmax+margin)
    #     ax.set_ylim(ymin-margin, ymax+margin)
    #
    #     if tooldia == 0:
    #         for geo in self.gcode_parsed:
    #             linespec = '--'
    #             linecolor = color[geo['kind'][0]][1]
    #             if geo['kind'][0] == 'C':
    #                 linespec = 'k-'
    #             x, y = geo['geom'].coords.xy
    #             ax.plot(x, y, linespec, color=linecolor)
    #     else:
    #         for geo in self.gcode_parsed:
    #             poly = geo['geom'].buffer(tooldia/2.0)
    #             patch = PolygonPatch(poly, facecolor=color[geo['kind'][0]][0],
    #                                  edgecolor=color[geo['kind'][0]][1],
    #                                  alpha=alpha[geo['kind'][0]], zorder=2)
    #             ax.add_patch(patch)
    #
    #     return fig

    def plot2(self, tooldia=None, dpi=75, margin=0.1, gcode_parsed=None,
              color=None, alpha={"T": 0.3, "C": 1.0}, tool_tolerance=0.0005, obj=None, visible=False, kind='all'):
        """
        Plots the G-code job onto the given axes.

        :param tooldia: Tool diameter.
        :param dpi: Not used!
        :param margin: Not used!
        :param color: Color specification.
        :param alpha: Transparency specification.
        :param tool_tolerance: Tolerance when drawing the toolshape.
        :param obj
        :param visible
        :param kind
        :return: None
        """
        # units = self.app.ui.general_defaults_form.general_app_group.units_radio.get_value().upper()

        if color is None:
            color = {
                "T": [self.app.defaults["cncjob_travel_fill"], self.app.defaults["cncjob_travel_line"]],
                "C": [self.app.defaults["cncjob_plot_fill"], self.app.defaults["cncjob_plot_line"]]
            }

        gcode_parsed = gcode_parsed if gcode_parsed else self.gcode_parsed
        path_num = 0

        if tooldia is None:
            tooldia = self.tooldia

        # this should be unlikely unless when upstream the tooldia is a tuple made by one dia and a comma like (2.4,)
        if isinstance(tooldia, list):
            tooldia = tooldia[0] if tooldia[0] is not None else self.tooldia

        if tooldia == 0:
            for geo in gcode_parsed:
                if kind == 'all':
                    obj.add_shape(shape=geo['geom'], color=color[geo['kind'][0]][1], visible=visible)
                elif kind == 'travel':
                    if geo['kind'][0] == 'T':
                        obj.add_shape(shape=geo['geom'], color=color['T'][1], visible=visible)
                elif kind == 'cut':
                    if geo['kind'][0] == 'C':
                        obj.add_shape(shape=geo['geom'], color=color['C'][1], visible=visible)
        else:
            text = []
            pos = []
            self.coordinates_type = self.app.defaults["cncjob_coords_type"]
            if self.coordinates_type == "G90":
                # For Absolute coordinates type G90
                for geo in gcode_parsed:
                    if geo['kind'][0] == 'T':
                        current_position = geo['geom'].coords[0]
                        if current_position not in pos:
                            pos.append(current_position)
                            path_num += 1
                            text.append(str(path_num))

                        current_position = geo['geom'].coords[-1]
                        if current_position not in pos:
                            pos.append(current_position)
                            path_num += 1
                            text.append(str(path_num))

                    # plot the geometry of Excellon objects
                    if self.origin_kind == 'excellon':
                        try:
                            poly = Polygon(geo['geom'])
                        except ValueError:
                            # if the geos are travel lines it will enter into Exception
                            poly = geo['geom'].buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                            poly = poly.simplify(tool_tolerance)
                    else:
                        # plot the geometry of any objects other than Excellon
                        poly = geo['geom'].buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                        poly = poly.simplify(tool_tolerance)

                    if kind == 'all':
                        obj.add_shape(shape=poly, color=color[geo['kind'][0]][1], face_color=color[geo['kind'][0]][0],
                                      visible=visible, layer=1 if geo['kind'][0] == 'C' else 2)
                    elif kind == 'travel':
                        if geo['kind'][0] == 'T':
                            obj.add_shape(shape=poly, color=color['T'][1], face_color=color['T'][0],
                                          visible=visible, layer=2)
                    elif kind == 'cut':
                        if geo['kind'][0] == 'C':
                            obj.add_shape(shape=poly, color=color['C'][1], face_color=color['C'][0],
                                          visible=visible, layer=1)
            else:
                # For Incremental coordinates type G91
                self.app.inform.emit('[ERROR_NOTCL] %s' % _('G91 coordinates not implemented ...'))
                for geo in gcode_parsed:
                    if geo['kind'][0] == 'T':
                        current_position = geo['geom'].coords[0]
                        if current_position not in pos:
                            pos.append(current_position)
                            path_num += 1
                            text.append(str(path_num))

                        current_position = geo['geom'].coords[-1]
                        if current_position not in pos:
                            pos.append(current_position)
                            path_num += 1
                            text.append(str(path_num))

                    # plot the geometry of Excellon objects
                    if self.origin_kind == 'excellon':
                        try:
                            poly = Polygon(geo['geom'])
                        except ValueError:
                            # if the geos are travel lines it will enter into Exception
                            poly = geo['geom'].buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                            poly = poly.simplify(tool_tolerance)
                    else:
                        # plot the geometry of any objects other than Excellon
                        poly = geo['geom'].buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                        poly = poly.simplify(tool_tolerance)

                    if kind == 'all':
                        obj.add_shape(shape=poly, color=color[geo['kind'][0]][1], face_color=color[geo['kind'][0]][0],
                                      visible=visible, layer=1 if geo['kind'][0] == 'C' else 2)
                    elif kind == 'travel':
                        if geo['kind'][0] == 'T':
                            obj.add_shape(shape=poly, color=color['T'][1], face_color=color['T'][0],
                                          visible=visible, layer=2)
                    elif kind == 'cut':
                        if geo['kind'][0] == 'C':
                            obj.add_shape(shape=poly, color=color['C'][1], face_color=color['C'][0],
                                          visible=visible, layer=1)
                # current_x = gcode_parsed[0]['geom'].coords[0][0]
                # current_y = gcode_parsed[0]['geom'].coords[0][1]
                # old_pos = (
                #     current_x,
                #     current_y
                # )
                #
                # for geo in gcode_parsed:
                #     if geo['kind'][0] == 'T':
                #         current_position = (
                #             geo['geom'].coords[0][0] + old_pos[0],
                #             geo['geom'].coords[0][1] + old_pos[1]
                #         )
                #         if current_position not in pos:
                #             pos.append(current_position)
                #             path_num += 1
                #             text.append(str(path_num))
                #
                #         delta = (
                #             geo['geom'].coords[-1][0] - geo['geom'].coords[0][0],
                #             geo['geom'].coords[-1][1] - geo['geom'].coords[0][1]
                #         )
                #         current_position = (
                #             current_position[0] + geo['geom'].coords[-1][0],
                #             current_position[1] + geo['geom'].coords[-1][1]
                #         )
                #         if current_position not in pos:
                #             pos.append(current_position)
                #             path_num += 1
                #             text.append(str(path_num))
                #
                #     # plot the geometry of Excellon objects
                #     if self.origin_kind == 'excellon':
                #         if isinstance(geo['geom'], Point):
                #             # if geo is Point
                #             current_position = (
                #                 current_position[0] + geo['geom'].x,
                #                 current_position[1] + geo['geom'].y
                #             )
                #             poly = Polygon(Point(current_position))
                #         elif isinstance(geo['geom'], LineString):
                #             # if the geos are travel lines (LineStrings)
                #             new_line_pts = []
                #             old_line_pos = deepcopy(current_position)
                #             for p in list(geo['geom'].coords):
                #                 current_position = (
                #                     current_position[0] + p[0],
                #                     current_position[1] + p[1]
                #                 )
                #                 new_line_pts.append(current_position)
                #                 old_line_pos = p
                #             new_line = LineString(new_line_pts)
                #
                #             poly = new_line.buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                #             poly = poly.simplify(tool_tolerance)
                #     else:
                #         # plot the geometry of any objects other than Excellon
                #         new_line_pts = []
                #         old_line_pos = deepcopy(current_position)
                #         for p in list(geo['geom'].coords):
                #             current_position = (
                #                 current_position[0] + p[0],
                #                 current_position[1] + p[1]
                #             )
                #             new_line_pts.append(current_position)
                #             old_line_pos = p
                #         new_line = LineString(new_line_pts)
                #
                #         poly = new_line.buffer(distance=(tooldia / 1.99999999), resolution=self.steps_per_circle)
                #         poly = poly.simplify(tool_tolerance)
                #
                #     old_pos = deepcopy(current_position)
                #
                #     if kind == 'all':
                #         obj.add_shape(shape=poly, color=color[geo['kind'][0]][1], face_color=color[geo['kind'][0]][0],
                #                       visible=visible, layer=1 if geo['kind'][0] == 'C' else 2)
                #     elif kind == 'travel':
                #         if geo['kind'][0] == 'T':
                #             obj.add_shape(shape=poly, color=color['T'][1], face_color=color['T'][0],
                #                           visible=visible, layer=2)
                #     elif kind == 'cut':
                #         if geo['kind'][0] == 'C':
                #             obj.add_shape(shape=poly, color=color['C'][1], face_color=color['C'][0],
                #                           visible=visible, layer=1)

            try:
                obj.annotation.set(text=text, pos=pos, visible=obj.options['plot'],
                                   font_size=self.app.defaults["cncjob_annotation_fontsize"],
                                   color=self.app.defaults["cncjob_annotation_fontcolor"])
            except Exception:
                pass

    def create_geometry(self):
        self.app.inform.emit('%s: %s' % (_("Unifying Geometry from parsed Geometry segments"),
                                         str(len(self.gcode_parsed))))
        # TODO: This takes forever. Too much data?
        # self.solid_geometry = cascaded_union([geo['geom'] for geo in self.gcode_parsed])

        # This is much faster but not so nice to look at as you can see different segments of the geometry
        self.solid_geometry = [geo['geom'] for geo in self.gcode_parsed]

        return self.solid_geometry

    # code snippet added by Lei Zheng in a rejected pull request on FlatCAM https://bitbucket.org/realthunder/
    def segment(self, coords):
        """
        break long linear lines to make it more auto level friendly
        """

        if len(coords) < 2 or self.segx <= 0 and self.segy <= 0:
            return list(coords)

        path = [coords[0]]

        # break the line in either x or y dimension only
        def linebreak_single(line, dim, dmax):
            if dmax <= 0:
                return None

            if line[1][dim] > line[0][dim]:
                sign = 1.0
                d = line[1][dim] - line[0][dim]
            else:
                sign = -1.0
                d = line[0][dim] - line[1][dim]
            if d > dmax:
                # make sure we don't make any new lines too short
                if d > dmax * 2:
                    dd = dmax
                else:
                    dd = d / 2
                other = dim ^ 1
                return (line[0][dim] + dd * sign, line[0][other] + \
                        dd * (line[1][other] - line[0][other]) / d)
            return None

        # recursively breaks down a given line until it is within the
        # required step size
        def linebreak(line):
            pt_new = linebreak_single(line, 0, self.segx)
            if pt_new is None:
                pt_new2 = linebreak_single(line, 1, self.segy)
            else:
                pt_new2 = linebreak_single((line[0], pt_new), 1, self.segy)
            if pt_new2 is not None:
                pt_new = pt_new2[::-1]

            if pt_new is None:
                path.append(line[1])
            else:
                path.append(pt_new)
                linebreak((pt_new, line[1]))

        for pt in coords[1:]:
            linebreak((path[-1], pt))

        return path

    def linear2gcode(self, linear, tolerance=0, down=True, up=True,
                     z_cut=None, z_move=None, zdownrate=None,
                     feedrate=None, feedrate_z=None, feedrate_rapid=None, cont=False, old_point=(0, 0)):
        """
        Generates G-code to cut along the linear feature.

        :param linear: The path to cut along.
        :type: Shapely.LinearRing or Shapely.Linear String
        :param tolerance: All points in the simplified object will be within the
            tolerance distance of the original geometry.
        :type tolerance: float
        :param feedrate: speed for cut on X - Y plane
        :param feedrate_z: speed for cut on Z plane
        :param feedrate_rapid: speed to move between cuts; usually is G0 but some CNC require to specify it
        :return: G-code to cut along the linear feature.
        :rtype: str
        """

        if z_cut is None:
            z_cut = self.z_cut

        if z_move is None:
            z_move = self.z_move
        #
        # if zdownrate is None:
        #     zdownrate = self.zdownrate

        if feedrate is None:
            feedrate = self.feedrate

        if feedrate_z is None:
            feedrate_z = self.z_feedrate

        if feedrate_rapid is None:
            feedrate_rapid = self.feedrate_rapid

        # Simplify paths?
        if tolerance > 0:
            target_linear = linear.simplify(tolerance)
        else:
            target_linear = linear

        gcode = ""

        # path = list(target_linear.coords)
        path = self.segment(target_linear.coords)

        p = self.pp_geometry

        self.coordinates_type = self.app.defaults["cncjob_coords_type"]
        if self.coordinates_type == "G90":
            # For Absolute coordinates type G90
            first_x = path[0][0]
            first_y = path[0][1]
        else:
            # For Incremental coordinates type G91
            first_x = path[0][0] - old_point[0]
            first_y = path[0][1] - old_point[1]

        # Move fast to 1st point
        if not cont:
            gcode += self.doformat(p.rapid_code, x=first_x, y=first_y)  # Move to first point

        # Move down to cutting depth
        if down:
            # Different feedrate for vertical cut?
            gcode += self.doformat(p.z_feedrate_code)
            # gcode += self.doformat(p.feedrate_code)
            gcode += self.doformat(p.down_code, x=first_x, y=first_y, z_cut=z_cut)
            gcode += self.doformat(p.feedrate_code, feedrate=feedrate)

        # Cutting...
        prev_x = first_x
        prev_y = first_y
        for pt in path[1:]:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if self.coordinates_type == "G90":
                # For Absolute coordinates type G90
                next_x = pt[0]
                next_y = pt[1]
            else:
                # For Incremental coordinates type G91
                # next_x = pt[0] - prev_x
                # next_y = pt[1] - prev_y
                self.app.inform.emit('[ERROR_NOTCL] %s' %
                                     _('G91 coordinates not implemented ...'))
                next_x = pt[0]
                next_y = pt[1]

            gcode += self.doformat(p.linear_code, x=next_x, y=next_y, z=z_cut)  # Linear motion to point
            prev_x = pt[0]
            prev_y = pt[1]

        # Up to travelling height.
        if up:
            gcode += self.doformat(p.lift_code, x=prev_x, y=prev_y, z_move=z_move)  # Stop cutting
        return gcode

    def linear2gcode_extra(self, linear, extracut_length, tolerance=0, down=True, up=True,
                     z_cut=None, z_move=None, zdownrate=None,
                     feedrate=None, feedrate_z=None, feedrate_rapid=None, cont=False, old_point=(0, 0)):
        """
        Generates G-code to cut along the linear feature.

        :param linear: The path to cut along.
        :param extracut_length: how much to cut extra over the first point at the end of the path
        :type: Shapely.LinearRing or Shapely.Linear String
        :param tolerance: All points in the simplified object will be within the
            tolerance distance of the original geometry.
        :type tolerance: float
        :param feedrate: speed for cut on X - Y plane
        :param feedrate_z: speed for cut on Z plane
        :param feedrate_rapid: speed to move between cuts; usually is G0 but some CNC require to specify it
        :return: G-code to cut along the linear feature.
        :rtype: str
        """

        if z_cut is None:
            z_cut = self.z_cut

        if z_move is None:
            z_move = self.z_move
        #
        # if zdownrate is None:
        #     zdownrate = self.zdownrate

        if feedrate is None:
            feedrate = self.feedrate

        if feedrate_z is None:
            feedrate_z = self.z_feedrate

        if feedrate_rapid is None:
            feedrate_rapid = self.feedrate_rapid

        # Simplify paths?
        if tolerance > 0:
            target_linear = linear.simplify(tolerance)
        else:
            target_linear = linear

        gcode = ""

        path = list(target_linear.coords)
        p = self.pp_geometry

        self.coordinates_type = self.app.defaults["cncjob_coords_type"]
        if self.coordinates_type == "G90":
            # For Absolute coordinates type G90
            first_x = path[0][0]
            first_y = path[0][1]
        else:
            # For Incremental coordinates type G91
            first_x = path[0][0] - old_point[0]
            first_y = path[0][1] - old_point[1]

        # Move fast to 1st point
        if not cont:
            gcode += self.doformat(p.rapid_code, x=first_x, y=first_y)  # Move to first point

        # Move down to cutting depth
        if down:
            # Different feedrate for vertical cut?
            if self.z_feedrate is not None:
                gcode += self.doformat(p.z_feedrate_code)
                # gcode += self.doformat(p.feedrate_code)
                gcode += self.doformat(p.down_code, x=first_x, y=first_y, z_cut=z_cut)
                gcode += self.doformat(p.feedrate_code, feedrate=feedrate)
            else:
                gcode += self.doformat(p.down_code, x=first_x, y=first_y, z_cut=z_cut)  # Start cutting

        # Cutting...
        prev_x = first_x
        prev_y = first_y
        for pt in path[1:]:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if self.coordinates_type == "G90":
                # For Absolute coordinates type G90
                next_x = pt[0]
                next_y = pt[1]
            else:
                # For Incremental coordinates type G91
                # For Incremental coordinates type G91
                # next_x = pt[0] - prev_x
                # next_y = pt[1] - prev_y
                self.app.inform.emit('[ERROR_NOTCL] %s' % _('G91 coordinates not implemented ...'))
                next_x = pt[0]
                next_y = pt[1]

            gcode += self.doformat(p.linear_code, x=next_x, y=next_y, z=z_cut)  # Linear motion to point
            prev_x = pt[0]
            prev_y = pt[1]

        # this line is added to create an extra cut over the first point in patch
        # to make sure that we remove the copper leftovers
        # Linear motion to the 1st point in the cut path
        # if self.coordinates_type == "G90":
        #     # For Absolute coordinates type G90
        #     last_x = path[1][0]
        #     last_y = path[1][1]
        # else:
        #     # For Incremental coordinates type G91
        #     last_x = path[1][0] - first_x
        #     last_y = path[1][1] - first_y
        # gcode += self.doformat(p.linear_code, x=last_x, y=last_y)

        # the first point for extracut is always mandatory if the extracut is enabled. But if the length of distance
        # between point 0 and point 1 is more than the distance we set for the extra cut then make an interpolation
        # along the path and find the point at the distance extracut_length

        if extracut_length == 0.0:
            gcode += self.doformat(p.linear_code, x=path[1][0], y=path[1][1])
            last_pt = path[1]
        else:
            if abs(distance(path[1], path[0])) > extracut_length:
                i_point = LineString([path[0], path[1]]).interpolate(extracut_length)
                gcode += self.doformat(p.linear_code, x=i_point.x, y=i_point.y)
                last_pt = (i_point.x, i_point.y)
            else:
                last_pt = path[0]
                for pt in path[1:]:
                    extracut_distance = abs(distance(pt, last_pt))
                    if extracut_distance <= extracut_length:
                        gcode += self.doformat(p.linear_code, x=pt[0], y=pt[1])
                        last_pt = pt
                    else:
                        break

        # Up to travelling height.
        if up:
            gcode += self.doformat(p.lift_code, x=last_pt[0], y=last_pt[1], z_move=z_move)  # Stop cutting

        return gcode

    def point2gcode(self, point, old_point=(0, 0)):
        gcode = ""

        if self.app.abort_flag:
            # graceful abort requested by the user
            raise FlatCAMApp.GracefulException

        path = list(point.coords)
        p = self.pp_geometry

        self.coordinates_type = self.app.defaults["cncjob_coords_type"]
        if self.coordinates_type == "G90":
            # For Absolute coordinates type G90
            first_x = path[0][0]
            first_y = path[0][1]
        else:
            # For Incremental coordinates type G91
            # first_x = path[0][0] - old_point[0]
            # first_y = path[0][1] - old_point[1]
            self.app.inform.emit('[ERROR_NOTCL] %s' %
                                 _('G91 coordinates not implemented ...'))
            first_x = path[0][0]
            first_y = path[0][1]

        gcode += self.doformat(p.linear_code, x=first_x, y=first_y)  # Move to first point

        if self.z_feedrate is not None:
            gcode += self.doformat(p.z_feedrate_code)
            gcode += self.doformat(p.down_code, x=first_x, y=first_y, z_cut = self.z_cut)
            gcode += self.doformat(p.feedrate_code)
        else:
            gcode += self.doformat(p.down_code, x=first_x, y=first_y, z_cut = self.z_cut)  # Start cutting

        gcode += self.doformat(p.lift_code, x=first_x, y=first_y)  # Stop cutting
        return gcode

    def export_svg(self, scale_stroke_factor=0.00):
        """
        Exports the CNC Job as a SVG Element

        :scale_factor: float
        :return: SVG Element string
        """
        # scale_factor is a multiplication factor for the SVG stroke-width used within shapely's svg export
        # If not specified then try and use the tool diameter
        # This way what is on screen will match what is outputed for the svg
        # This is quite a useful feature for svg's used with visicut

        if scale_stroke_factor <= 0:
            scale_stroke_factor = self.options['tooldia'] / 2

        # If still 0 then default to 0.05
        # This value appears to work for zooming, and getting the output svg line width
        # to match that viewed on screen with FlatCam
        if scale_stroke_factor == 0:
            scale_stroke_factor = 0.01

        # Separate the list of cuts and travels into 2 distinct lists
        # This way we can add different formatting / colors to both
        cuts = []
        travels = []
        for g in self.gcode_parsed:
            if self.app.abort_flag:
                # graceful abort requested by the user
                raise FlatCAMApp.GracefulException

            if g['kind'][0] == 'C': cuts.append(g)
            if g['kind'][0] == 'T': travels.append(g)

        # Used to determine the overall board size
        self.solid_geometry = cascaded_union([geo['geom'] for geo in self.gcode_parsed])

        # Convert the cuts and travels into single geometry objects we can render as svg xml
        if travels:
            travelsgeom = cascaded_union([geo['geom'] for geo in travels])

        if self.app.abort_flag:
            # graceful abort requested by the user
            raise FlatCAMApp.GracefulException

        if cuts:
            cutsgeom = cascaded_union([geo['geom'] for geo in cuts])

        # Render the SVG Xml
        # The scale factor affects the size of the lines, and the stroke color adds different formatting for each set
        # It's better to have the travels sitting underneath the cuts for visicut
        svg_elem = ""
        if travels:
            svg_elem = travelsgeom.svg(scale_factor=scale_stroke_factor, stroke_color="#F0E24D")
        if cuts:
            svg_elem += cutsgeom.svg(scale_factor=scale_stroke_factor, stroke_color="#5E6CFF")

        return svg_elem

    def bounds(self):
        """
        Returns coordinates of rectangular bounds
        of geometry: (xmin, ymin, xmax, ymax).
        """
        # fixed issue of getting bounds only for one level lists of objects
        # now it can get bounds for nested lists of objects

        log.debug("camlib.CNCJob.bounds()")

        def bounds_rec(obj):
            if type(obj) is list:
                minx = np.Inf
                miny = np.Inf
                maxx = -np.Inf
                maxy = -np.Inf

                for k in obj:
                    if type(k) is dict:
                        for key in k:
                            minx_, miny_, maxx_, maxy_ = bounds_rec(k[key])
                            minx = min(minx, minx_)
                            miny = min(miny, miny_)
                            maxx = max(maxx, maxx_)
                            maxy = max(maxy, maxy_)
                    else:
                        minx_, miny_, maxx_, maxy_ = bounds_rec(k)
                        minx = min(minx, minx_)
                        miny = min(miny, miny_)
                        maxx = max(maxx, maxx_)
                        maxy = max(maxy, maxy_)
                return minx, miny, maxx, maxy
            else:
                # it's a Shapely object, return it's bounds
                return obj.bounds

        if self.multitool is False:
            log.debug("CNCJob->bounds()")
            if self.solid_geometry is None:
                log.debug("solid_geometry is None")
                return 0, 0, 0, 0

            bounds_coords = bounds_rec(self.solid_geometry)
        else:
            minx = np.Inf
            miny = np.Inf
            maxx = -np.Inf
            maxy = -np.Inf
            for k, v in self.cnc_tools.items():
                minx = np.Inf
                miny = np.Inf
                maxx = -np.Inf
                maxy = -np.Inf
                try:
                    for k in v['solid_geometry']:
                        minx_, miny_, maxx_, maxy_ = bounds_rec(k)
                        minx = min(minx, minx_)
                        miny = min(miny, miny_)
                        maxx = max(maxx, maxx_)
                        maxy = max(maxy, maxy_)
                except TypeError:
                    minx_, miny_, maxx_, maxy_ = bounds_rec(v['solid_geometry'])
                    minx = min(minx, minx_)
                    miny = min(miny, miny_)
                    maxx = max(maxx, maxx_)
                    maxy = max(maxy, maxy_)

            bounds_coords = minx, miny, maxx, maxy
        return bounds_coords

    # TODO This function should be replaced at some point with a "real" function. Until then it's an ugly hack ...
    def scale(self, xfactor, yfactor=None, point=None):
        """
        Scales all the geometry on the XY plane in the object by the
        given factor. Tool sizes, feedrates, or Z-axis dimensions are
        not altered.

        :param factor: Number by which to scale the object.
        :type factor: float
        :param point: the (x,y) coords for the point of origin of scale
        :type tuple of floats
        :return: None
        :rtype: None
        """
        log.debug("camlib.CNCJob.scale()")

        if yfactor is None:
            yfactor = xfactor

        if point is None:
            px = 0
            py = 0
        else:
            px, py = point

        def scale_g(g):
            """

            :param g: 'g' parameter it's a gcode string
            :return:  scaled gcode string
            """

            temp_gcode = ''
            header_start = False
            header_stop = False
            units = self.app.defaults['units'].upper()

            lines = StringIO(g)
            for line in lines:

                # this changes the GCODE header ---- UGLY HACK
                if "TOOL DIAMETER" in line or "Feedrate:" in line:
                    header_start = True

                if "G20" in line or "G21" in line:
                    header_start = False
                    header_stop = True

                if header_start is True:
                    header_stop = False
                    if "in" in line:
                        if units == 'MM':
                            line = line.replace("in", "mm")
                    if "mm" in line:
                        if units == 'IN':
                            line = line.replace("mm", "in")

                    # find any float number in header (even multiple on the same line) and convert it
                    numbers_in_header = re.findall(self.g_nr_re, line)
                    if numbers_in_header:
                        for nr in numbers_in_header:
                            new_nr = float(nr) * xfactor
                            # replace the updated string
                            line = line.replace(nr, ('%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_nr))
                            )

                # this scales all the X and Y and Z and F values and also the Tool Dia in the toolchange message
                if header_stop is True:
                    if "G20" in line:
                        if units == 'MM':
                            line = line.replace("G20", "G21")
                    if "G21" in line:
                        if units == 'IN':
                            line = line.replace("G21", "G20")

                    # find the X group
                    match_x = self.g_x_re.search(line)
                    if match_x:
                        if match_x.group(1) is not None:
                            new_x = float(match_x.group(1)[1:]) * xfactor
                            # replace the updated string
                            line = line.replace(
                                match_x.group(1),
                                'X%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_x)
                            )
                    # find the Y group
                    match_y = self.g_y_re.search(line)
                    if match_y:
                        if match_y.group(1) is not None:
                            new_y = float(match_y.group(1)[1:]) * yfactor
                            line = line.replace(
                                match_y.group(1),
                                'Y%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_y)
                            )
                    # find the Z group
                    match_z = self.g_z_re.search(line)
                    if match_z:
                        if match_z.group(1) is not None:
                            new_z = float(match_z.group(1)[1:]) * xfactor
                            line = line.replace(
                                match_z.group(1),
                                'Z%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_z)
                            )

                    # find the F group
                    match_f = self.g_f_re.search(line)
                    if match_f:
                        if match_f.group(1) is not None:
                            new_f = float(match_f.group(1)[1:]) * xfactor
                            line = line.replace(
                                match_f.group(1),
                                'F%.*f' % (self.app.defaults["cncjob_fr_decimals"], new_f)
                            )
                    # find the T group (tool dia on toolchange)
                    match_t = self.g_t_re.search(line)
                    if match_t:
                        if match_t.group(1) is not None:
                            new_t = float(match_t.group(1)[1:]) * xfactor
                            line = line.replace(
                                match_t.group(1),
                                '= %.*f' % (self.app.defaults["cncjob_coords_decimals"], new_t)
                            )

                temp_gcode += line
            lines.close()
            header_stop = False
            return temp_gcode

        if self.multitool is False:
            # offset Gcode
            self.gcode = scale_g(self.gcode)

            # variables to display the percentage of work done
            self.geo_len = 0
            try:
                for g in self.gcode_parsed:
                    self.geo_len += 1
            except TypeError:
                self.geo_len = 1
            self.old_disp_number = 0
            self.el_count = 0

            # scale geometry
            for g in self.gcode_parsed:
                try:
                    g['geom'] = affinity.scale(g['geom'], xfactor, yfactor, origin=(px, py))
                except AttributeError:
                    return g['geom']

                self.el_count += 1
                disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                if self.old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                    self.old_disp_number = disp_number

            self.create_geometry()
        else:
            for k, v in self.cnc_tools.items():
                # scale Gcode
                v['gcode'] = scale_g(v['gcode'])

                # variables to display the percentage of work done
                self.geo_len = 0
                try:
                    for g in v['gcode_parsed']:
                        self.geo_len += 1
                except TypeError:
                    self.geo_len = 1
                self.old_disp_number = 0
                self.el_count = 0

                # scale gcode_parsed
                for g in v['gcode_parsed']:
                    try:
                        g['geom'] = affinity.scale(g['geom'], xfactor, yfactor, origin=(px, py))
                    except AttributeError:
                        return g['geom']

                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                v['solid_geometry'] = cascaded_union([geo['geom'] for geo in v['gcode_parsed']])
        self.create_geometry()
        self.app.proc_container.new_text = ''

    def offset(self, vect):
        """
        Offsets all the geometry on the XY plane in the object by the
        given vector.
        Offsets all the GCODE on the XY plane in the object by the
        given vector.

        g_offsetx_re, g_offsety_re, multitool, cnnc_tools are attributes of FlatCAMCNCJob class in camlib

        :param vect: (x, y) offset vector.
        :type vect: tuple
        :return: None
        """
        log.debug("camlib.CNCJob.offset()")

        dx, dy = vect

        def offset_g(g):
            """

            :param g: 'g' parameter it's a gcode string
            :return:  offseted gcode string
            """

            temp_gcode = ''
            lines = StringIO(g)
            for line in lines:
                # find the X group
                match_x = self.g_x_re.search(line)
                if match_x:
                    if match_x.group(1) is not None:
                        # get the coordinate and add X offset
                        new_x = float(match_x.group(1)[1:]) + dx
                        # replace the updated string
                        line = line.replace(
                            match_x.group(1),
                            'X%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_x)
                        )
                match_y = self.g_y_re.search(line)
                if match_y:
                    if match_y.group(1) is not None:
                        new_y = float(match_y.group(1)[1:]) + dy
                        line = line.replace(
                            match_y.group(1),
                            'Y%.*f' % (self.app.defaults["cncjob_coords_decimals"], new_y)
                        )
                temp_gcode += line
            lines.close()
            return temp_gcode

        if self.multitool is False:
            # offset Gcode
            self.gcode = offset_g(self.gcode)

            # variables to display the percentage of work done
            self.geo_len = 0
            try:
                for g in self.gcode_parsed:
                    self.geo_len += 1
            except TypeError:
                self.geo_len = 1
            self.old_disp_number = 0
            self.el_count = 0

            # offset geometry
            for g in self.gcode_parsed:
                try:
                    g['geom'] = affinity.translate(g['geom'], xoff=dx, yoff=dy)
                except AttributeError:
                    return g['geom']

                self.el_count += 1
                disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                if self.old_disp_number < disp_number <= 100:
                    self.app.proc_container.update_view_text(' %d%%' % disp_number)
                    self.old_disp_number = disp_number

            self.create_geometry()
        else:
            for k, v in self.cnc_tools.items():
                # offset Gcode
                v['gcode'] = offset_g(v['gcode'])

                # variables to display the percentage of work done
                self.geo_len = 0
                try:
                    for g in v['gcode_parsed']:
                        self.geo_len += 1
                except TypeError:
                    self.geo_len = 1
                self.old_disp_number = 0
                self.el_count = 0

                # offset gcode_parsed
                for g in v['gcode_parsed']:
                    try:
                        g['geom'] = affinity.translate(g['geom'], xoff=dx, yoff=dy)
                    except AttributeError:
                        return g['geom']

                    self.el_count += 1
                    disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
                    if self.old_disp_number < disp_number <= 100:
                        self.app.proc_container.update_view_text(' %d%%' % disp_number)
                        self.old_disp_number = disp_number

                # for the bounding box
                v['solid_geometry'] = cascaded_union([geo['geom'] for geo in v['gcode_parsed']])

        self.app.proc_container.new_text = ''

    def mirror(self, axis, point):
        """
        Mirror the geometrys of an object by an given axis around the coordinates of the 'point'
        :param angle:
        :param point: tupple of coordinates (x,y)
        :return:
        """
        log.debug("camlib.CNCJob.mirror()")

        px, py = point
        xscale, yscale = {"X": (1.0, -1.0), "Y": (-1.0, 1.0)}[axis]

        # variables to display the percentage of work done
        self.geo_len = 0
        try:
            for g in self.gcode_parsed:
                self.geo_len += 1
        except TypeError:
            self.geo_len = 1
        self.old_disp_number = 0
        self.el_count = 0

        for g in self.gcode_parsed:
            try:
                g['geom'] = affinity.scale(g['geom'], xscale, yscale, origin=(px, py))
            except AttributeError:
                return g['geom']

            self.el_count += 1
            disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
            if self.old_disp_number < disp_number <= 100:
                self.app.proc_container.update_view_text(' %d%%' % disp_number)
                self.old_disp_number = disp_number

        self.create_geometry()
        self.app.proc_container.new_text = ''

    def skew(self, angle_x, angle_y, point):
        """
        Shear/Skew the geometries of an object by angles along x and y dimensions.

        Parameters
        ----------
        angle_x, angle_y : float, float
            The shear angle(s) for the x and y axes respectively. These can be
            specified in either degrees (default) or radians by setting
            use_radians=True.
        point: tupple of coordinates (x,y)

        See shapely manual for more information:
        http://toblerity.org/shapely/manual.html#affine-transformations
        """
        log.debug("camlib.CNCJob.skew()")

        px, py = point

        # variables to display the percentage of work done
        self.geo_len = 0
        try:
            for g in self.gcode_parsed:
                self.geo_len += 1
        except TypeError:
            self.geo_len = 1
        self.old_disp_number = 0
        self.el_count = 0

        for g in self.gcode_parsed:
            try:
                g['geom'] = affinity.skew(g['geom'], angle_x, angle_y, origin=(px, py))
            except AttributeError:
                return g['geom']

            self.el_count += 1
            disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
            if self.old_disp_number < disp_number <= 100:
                self.app.proc_container.update_view_text(' %d%%' % disp_number)
                self.old_disp_number = disp_number

        self.create_geometry()
        self.app.proc_container.new_text = ''

    def rotate(self, angle, point):
        """
        Rotate the geometrys of an object by an given angle around the coordinates of the 'point'
        :param angle:
        :param point: tupple of coordinates (x,y)
        :return:
        """
        log.debug("camlib.CNCJob.rotate()")

        px, py = point

        # variables to display the percentage of work done
        self.geo_len = 0
        try:
            for g in self.gcode_parsed:
                self.geo_len += 1
        except TypeError:
            self.geo_len = 1
        self.old_disp_number = 0
        self.el_count = 0

        for g in self.gcode_parsed:
            try:
                g['geom'] = affinity.rotate(g['geom'], angle, origin=(px, py))
            except AttributeError:
                return g['geom']

            self.el_count += 1
            disp_number = int(np.interp(self.el_count, [0, self.geo_len], [0, 100]))
            if self.old_disp_number < disp_number <= 100:
                self.app.proc_container.update_view_text(' %d%%' % disp_number)
                self.old_disp_number = disp_number

        self.create_geometry()
        self.app.proc_container.new_text = ''


def get_bounds(geometry_list):
    xmin = np.Inf
    ymin = np.Inf
    xmax = -np.Inf
    ymax = -np.Inf

    for gs in geometry_list:
        try:
            gxmin, gymin, gxmax, gymax = gs.bounds()
            xmin = min([xmin, gxmin])
            ymin = min([ymin, gymin])
            xmax = max([xmax, gxmax])
            ymax = max([ymax, gymax])
        except Exception:
            log.warning("DEVELOPMENT: Tried to get bounds of empty geometry.")

    return [xmin, ymin, xmax, ymax]


def arc(center, radius, start, stop, direction, steps_per_circ):
    """
    Creates a list of point along the specified arc.

    :param center: Coordinates of the center [x, y]
    :type center: list
    :param radius: Radius of the arc.
    :type radius: float
    :param start: Starting angle in radians
    :type start: float
    :param stop: End angle in radians
    :type stop: float
    :param direction: Orientation of the arc, "CW" or "CCW"
    :type direction: string
    :param steps_per_circ: Number of straight line segments to
        represent a circle.
    :type steps_per_circ: int
    :return: The desired arc, as list of tuples
    :rtype: list
    """
    # TODO: Resolution should be established by maximum error from the exact arc.

    da_sign = {"cw": -1.0, "ccw": 1.0}
    points = []
    if direction == "ccw" and stop <= start:
        stop += 2 * np.pi
    if direction == "cw" and stop >= start:
        stop -= 2 * np.pi
    
    angle = abs(stop - start)
        
    # angle = stop-start
    steps = max([int(np.ceil(angle / (2 * np.pi) * steps_per_circ)), 2])
    delta_angle = da_sign[direction] * angle * 1.0 / steps
    for i in range(steps + 1):
        theta = start + delta_angle * i
        points.append((center[0] + radius * np.cos(theta), center[1] + radius * np.sin(theta)))
    return points


def arc2(p1, p2, center, direction, steps_per_circ):
    r = np.sqrt((center[0] - p1[0]) ** 2 + (center[1] - p1[1]) ** 2)
    start = np.arctan2(p1[1] - center[1], p1[0] - center[0])
    stop = np.arctan2(p2[1] - center[1], p2[0] - center[0])
    return arc(center, r, start, stop, direction, steps_per_circ)


def arc_angle(start, stop, direction):
    if direction == "ccw" and stop <= start:
        stop += 2 * np.pi
    if direction == "cw" and stop >= start:
        stop -= 2 * np.pi

    angle = abs(stop - start)
    return angle


# def find_polygon(poly, point):
#     """
#     Find an object that object.contains(Point(point)) in
#     poly, which can can be iterable, contain iterable of, or
#     be itself an implementer of .contains().
#
#     :param poly: See description
#     :return: Polygon containing point or None.
#     """
#
#     if poly is None:
#         return None
#
#     try:
#         for sub_poly in poly:
#             p = find_polygon(sub_poly, point)
#             if p is not None:
#                 return p
#     except TypeError:
#         try:
#             if poly.contains(Point(point)):
#                 return poly
#         except AttributeError:
#             return None
#
#     return None


def to_dict(obj):
    """
    Makes the following types into serializable form:

    * ApertureMacro
    * BaseGeometry

    :param obj: Shapely geometry.
    :type obj: BaseGeometry
    :return: Dictionary with serializable form if ``obj`` was
        BaseGeometry or ApertureMacro, otherwise returns ``obj``.
    """
    if isinstance(obj, ApertureMacro):
        return {
            "__class__": "ApertureMacro",
            "__inst__": obj.to_dict()
        }
    if isinstance(obj, BaseGeometry):
        return {
            "__class__": "Shply",
            "__inst__": sdumps(obj)
        }
    return obj


def dict2obj(d):
    """
    Default deserializer.

    :param d:  Serializable dictionary representation of an object
        to be reconstructed.
    :return: Reconstructed object.
    """
    if '__class__' in d and '__inst__' in d:
        if d['__class__'] == "Shply":
            return sloads(d['__inst__'])
        if d['__class__'] == "ApertureMacro":
            am = ApertureMacro()
            am.from_dict(d['__inst__'])
            return am
        return d
    else:
        return d


# def plotg(geo, solid_poly=False, color="black"):
#     try:
#         __ = iter(geo)
#     except:
#         geo = [geo]
#
#     for g in geo:
#         if type(g) == Polygon:
#             if solid_poly:
#                 patch = PolygonPatch(g,
#                                      facecolor="#BBF268",
#                                      edgecolor="#006E20",
#                                      alpha=0.75,
#                                      zorder=2)
#                 ax = subplot(111)
#                 ax.add_patch(patch)
#             else:
#                 x, y = g.exterior.coords.xy
#                 plot(x, y, color=color)
#                 for ints in g.interiors:
#                     x, y = ints.coords.xy
#                     plot(x, y, color=color)
#                 continue
#
#         if type(g) == LineString or type(g) == LinearRing:
#             x, y = g.coords.xy
#             plot(x, y, color=color)
#             continue
#
#         if type(g) == Point:
#             x, y = g.coords.xy
#             plot(x, y, 'o')
#             continue
#
#         try:
#             __ = iter(g)
#             plotg(g, color=color)
#         except:
#             log.error("Cannot plot: " + str(type(g)))
#             continue

# def alpha_shape(points, alpha):
#     """
#     Compute the alpha shape (concave hull) of a set of points.
#
#     @param points: Iterable container of points.
#     @param alpha: alpha value to influence the gooeyness of the border. Smaller
#                   numbers don't fall inward as much as larger numbers. Too large,
#                   and you lose everything!
#     """
#     if len(points) < 4:
#         # When you have a triangle, there is no sense in computing an alpha
#         # shape.
#         return MultiPoint(list(points)).convex_hull
#
#     def add_edge(edges, edge_points, coords, i, j):
#         """Add a line between the i-th and j-th points, if not in the list already"""
#         if (i, j) in edges or (j, i) in edges:
#             # already added
#             return
#         edges.add( (i, j) )
#         edge_points.append(coords[ [i, j] ])
#
#     coords = np.array([point.coords[0] for point in points])
#
#     tri = Delaunay(coords)
#     edges = set()
#     edge_points = []
#     # loop over triangles:
#     # ia, ib, ic = indices of corner points of the triangle
#     for ia, ib, ic in tri.vertices:
#         pa = coords[ia]
#         pb = coords[ib]
#         pc = coords[ic]
#
#         # Lengths of sides of triangle
#         a = math.sqrt((pa[0]-pb[0])**2 + (pa[1]-pb[1])**2)
#         b = math.sqrt((pb[0]-pc[0])**2 + (pb[1]-pc[1])**2)
#         c = math.sqrt((pc[0]-pa[0])**2 + (pc[1]-pa[1])**2)
#
#         # Semiperimeter of triangle
#         s = (a + b + c)/2.0
#
#         # Area of triangle by Heron's formula
#         area = math.sqrt(s*(s-a)*(s-b)*(s-c))
#         circum_r = a*b*c/(4.0*area)
#
#         # Here's the radius filter.
#         #print circum_r
#         if circum_r < 1.0/alpha:
#             add_edge(edges, edge_points, coords, ia, ib)
#             add_edge(edges, edge_points, coords, ib, ic)
#             add_edge(edges, edge_points, coords, ic, ia)
#
#     m = MultiLineString(edge_points)
#     triangles = list(polygonize(m))
#     return cascaded_union(triangles), edge_points

# def voronoi(P):
#     """
#     Returns a list of all edges of the voronoi diagram for the given input points.
#     """
#     delauny = Delaunay(P)
#     triangles = delauny.points[delauny.vertices]
#
#     circum_centers = np.array([triangle_csc(tri) for tri in triangles])
#     long_lines_endpoints = []
#
#     lineIndices = []
#     for i, triangle in enumerate(triangles):
#         circum_center = circum_centers[i]
#         for j, neighbor in enumerate(delauny.neighbors[i]):
#             if neighbor != -1:
#                 lineIndices.append((i, neighbor))
#             else:
#                 ps = triangle[(j+1)%3] - triangle[(j-1)%3]
#                 ps = np.array((ps[1], -ps[0]))
#
#                 middle = (triangle[(j+1)%3] + triangle[(j-1)%3]) * 0.5
#                 di = middle - triangle[j]
#
#                 ps /= np.linalg.norm(ps)
#                 di /= np.linalg.norm(di)
#
#                 if np.dot(di, ps) < 0.0:
#                     ps *= -1000.0
#                 else:
#                     ps *= 1000.0
#
#                 long_lines_endpoints.append(circum_center + ps)
#                 lineIndices.append((i, len(circum_centers) + len(long_lines_endpoints)-1))
#
#     vertices = np.vstack((circum_centers, long_lines_endpoints))
#
#     # filter out any duplicate lines
#     lineIndicesSorted = np.sort(lineIndices) # make (1,2) and (2,1) both (1,2)
#     lineIndicesTupled = [tuple(row) for row in lineIndicesSorted]
#     lineIndicesUnique = np.unique(lineIndicesTupled)
#
#     return vertices, lineIndicesUnique
#
#
# def triangle_csc(pts):
#     rows, cols = pts.shape
#
#     A = np.bmat([[2 * np.dot(pts, pts.T), np.ones((rows, 1))],
#                  [np.ones((1, rows)), np.zeros((1, 1))]])
#
#     b = np.hstack((np.sum(pts * pts, axis=1), np.ones((1))))
#     x = np.linalg.solve(A,b)
#     bary_coords = x[:-1]
#     return np.sum(pts * np.tile(bary_coords.reshape((pts.shape[0], 1)), (1, pts.shape[1])), axis=0)
#
#
# def voronoi_cell_lines(points, vertices, lineIndices):
#     """
#     Returns a mapping from a voronoi cell to its edges.
#
#     :param points: shape (m,2)
#     :param vertices: shape (n,2)
#     :param lineIndices: shape (o,2)
#     :rtype: dict point index -> list of shape (n,2) with vertex indices
#     """
#     kd = KDTree(points)
#
#     cells = collections.defaultdict(list)
#     for i1, i2 in lineIndices:
#         v1, v2 = vertices[i1], vertices[i2]
#         mid = (v1+v2)/2
#         _, (p1Idx, p2Idx) = kd.query(mid, 2)
#         cells[p1Idx].append((i1, i2))
#         cells[p2Idx].append((i1, i2))
#
#     return cells
#
#
# def voronoi_edges2polygons(cells):
#     """
#     Transforms cell edges into polygons.
#
#     :param cells: as returned from voronoi_cell_lines
#     :rtype: dict point index -> list of vertex indices which form a polygon
#     """
#
#     # first, close the outer cells
#     for pIdx, lineIndices_ in cells.items():
#         dangling_lines = []
#         for i1, i2 in lineIndices_:
#             p = (i1, i2)
#             connections = filter(lambda k: p != k and
#             (p[0] == k[0] or p[0] == k[1] or p[1] == k[0] or p[1] == k[1]), lineIndices_)
#             # connections = filter(lambda (i1_, i2_): (i1, i2) != (i1_, i2_) and
#             (i1 == i1_ or i1 == i2_ or i2 == i1_ or i2 == i2_), lineIndices_)
#             assert 1 <= len(connections) <= 2
#             if len(connections) == 1:
#                 dangling_lines.append((i1, i2))
#         assert len(dangling_lines) in [0, 2]
#         if len(dangling_lines) == 2:
#             (i11, i12), (i21, i22) = dangling_lines
#             s = (i11, i12)
#             t = (i21, i22)
#
#             # determine which line ends are unconnected
#             connected = filter(lambda k: k != s and (k[0] == s[0] or k[1] == s[0]), lineIndices_)
#             # connected = filter(lambda (i1,i2): (i1,i2) != (i11,i12) and (i1 == i11 or i2 == i11), lineIndices_)
#             i11Unconnected = len(connected) == 0
#
#             connected = filter(lambda k: k != t and (k[0] == t[0] or k[1] == t[0]), lineIndices_)
#             # connected = filter(lambda (i1,i2): (i1,i2) != (i21,i22) and (i1 == i21 or i2 == i21), lineIndices_)
#             i21Unconnected = len(connected) == 0
#
#             startIdx = i11 if i11Unconnected else i12
#             endIdx = i21 if i21Unconnected else i22
#
#             cells[pIdx].append((startIdx, endIdx))
#
#     # then, form polygons by storing vertex indices in (counter-)clockwise order
#     polys = dict()
#     for pIdx, lineIndices_ in cells.items():
#         # get a directed graph which contains both directions and arbitrarily follow one of both
#         directedGraph = lineIndices_ + [(i2, i1) for (i1, i2) in lineIndices_]
#         directedGraphMap = collections.defaultdict(list)
#         for (i1, i2) in directedGraph:
#             directedGraphMap[i1].append(i2)
#         orderedEdges = []
#         currentEdge = directedGraph[0]
#         while len(orderedEdges) < len(lineIndices_):
#             i1 = currentEdge[1]
#             i2 = directedGraphMap[i1][0] if directedGraphMap[i1][0] != currentEdge[0] else directedGraphMap[i1][1]
#             nextEdge = (i1, i2)
#             orderedEdges.append(nextEdge)
#             currentEdge = nextEdge
#
#         polys[pIdx] = [i1 for (i1, i2) in orderedEdges]
#
#     return polys
#
#
# def voronoi_polygons(points):
#     """
#     Returns the voronoi polygon for each input point.
#
#     :param points: shape (n,2)
#     :rtype: list of n polygons where each polygon is an array of vertices
#     """
#     vertices, lineIndices = voronoi(points)
#     cells = voronoi_cell_lines(points, vertices, lineIndices)
#     polys = voronoi_edges2polygons(cells)
#     polylist = []
#     for i in range(len(points)):
#         poly = vertices[np.asarray(polys[i])]
#         polylist.append(poly)
#     return polylist
#
#
# class Zprofile:
#     def __init__(self):
#
#         # data contains lists of [x, y, z]
#         self.data = []
#
#         # Computed voronoi polygons (shapely)
#         self.polygons = []
#         pass
#
#     # def plot_polygons(self):
#     #     axes = plt.subplot(1, 1, 1)
#     #
#     #     plt.axis([-0.05, 1.05, -0.05, 1.05])
#     #
#     #     for poly in self.polygons:
#     #         p = PolygonPatch(poly, facecolor=np.random.rand(3, 1), alpha=0.3)
#     #         axes.add_patch(p)
#
#     def init_from_csv(self, filename):
#         pass
#
#     def init_from_string(self, zpstring):
#         pass
#
#     def init_from_list(self, zplist):
#         self.data = zplist
#
#     def generate_polygons(self):
#         self.polygons = [Polygon(p) for p in voronoi_polygons(array([[x[0], x[1]] for x in self.data]))]
#
#     def normalize(self, origin):
#         pass
#
#     def paste(self, path):
#         """
#         Return a list of dictionaries containing the parts of the original
#         path and their z-axis offset.
#         """
#
#         # At most one region/polygon will contain the path
#         containing = [i for i in range(len(self.polygons)) if self.polygons[i].contains(path)]
#
#         if len(containing) > 0:
#             return [{"path": path, "z": self.data[containing[0]][2]}]
#
#         # All region indexes that intersect with the path
#         crossing = [i for i in range(len(self.polygons)) if self.polygons[i].intersects(path)]
#
#         return [{"path": path.intersection(self.polygons[i]),
#                  "z": self.data[i][2]} for i in crossing]


def autolist(obj):
    try:
        __ = iter(obj)
        return obj
    except TypeError:
        return [obj]


def three_point_circle(p1, p2, p3):
    """
    Computes the center and radius of a circle from
    3 points on its circumference.

    :param p1: Point 1
    :param p2: Point 2
    :param p3: Point 3
    :return: center, radius
    """
    # Midpoints
    a1 = (p1 + p2) / 2.0
    a2 = (p2 + p3) / 2.0

    # Normals
    b1 = np.dot((p2 - p1), np.array([[0, -1], [1, 0]], dtype=np.float32))
    b2 = np.dot((p3 - p2), np.array([[0, 1], [-1, 0]], dtype=np.float32))

    # Params
    try:
        T = solve(np.transpose(np.array([-b1, b2])), a1 - a2)
    except Exception as e:
        log.debug("camlib.three_point_circle() --> %s" % str(e))
        return

    # Center
    center = a1 + b1 * T[0]

    # Radius
    radius = np.linalg.norm(center - p1)

    return center, radius, T[0]


def distance(pt1, pt2):
    return np.sqrt((pt1[0] - pt2[0]) ** 2 + (pt1[1] - pt2[1]) ** 2)


def distance_euclidian(x1, y1, x2, y2):
    return np.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2)


class FlatCAMRTree(object):
    """
    Indexes geometry (Any object with "cooords" property containing
    a list of tuples with x, y values). Objects are indexed by
    all their points by default. To index by arbitrary points,
    override self.points2obj.
    """

    def __init__(self):
        # Python RTree Index
        self.rti = rtindex.Index()

        # ## Track object-point relationship
        # Each is list of points in object.
        self.obj2points = []

        # Index is index in rtree, value is index of
        # object in obj2points.
        self.points2obj = []

        self.get_points = lambda go: go.coords

    def grow_obj2points(self, idx):
        """
        Increases the size of self.obj2points to fit
        idx + 1 items.

        :param idx: Index to fit into list.
        :return: None
        """
        if len(self.obj2points) > idx:
            # len == 2, idx == 1, ok.
            return
        else:
            # len == 2, idx == 2, need 1 more.
            # range(2, 3)
            for i in range(len(self.obj2points), idx + 1):
                self.obj2points.append([])

    def insert(self, objid, obj):
        self.grow_obj2points(objid)
        self.obj2points[objid] = []

        for pt in self.get_points(obj):
            self.rti.insert(len(self.points2obj), (pt[0], pt[1], pt[0], pt[1]), obj=objid)
            self.obj2points[objid].append(len(self.points2obj))
            self.points2obj.append(objid)

    def remove_obj(self, objid, obj):
        # Use all ptids to delete from index
        for i, pt in enumerate(self.get_points(obj)):
            try:
                self.rti.delete(self.obj2points[objid][i], (pt[0], pt[1], pt[0], pt[1]))
            except IndexError:
                pass

    def nearest(self, pt):
        """
        Will raise StopIteration if no items are found.

        :param pt:
        :return:
        """
        return next(self.rti.nearest(pt, objects=True))


class FlatCAMRTreeStorage(FlatCAMRTree):
    """
    Just like FlatCAMRTree it indexes geometry, but also serves
    as storage for the geometry.
    """

    def __init__(self):
        # super(FlatCAMRTreeStorage, self).__init__()
        super().__init__()

        self.objects = []

        # Optimization attempt!
        self.indexes = {}

    def insert(self, obj):
        self.objects.append(obj)
        idx = len(self.objects) - 1

        # Note: Shapely objects are not hashable any more, although
        # there seem to be plans to re-introduce the feature in
        # version 2.0. For now, we will index using the object's id,
        # but it's important to remember that shapely geometry is
        # mutable, ie. it can be modified to a totally different shape
        # and continue to have the same id.
        # self.indexes[obj] = idx
        self.indexes[id(obj)] = idx

        # super(FlatCAMRTreeStorage, self).insert(idx, obj)
        super().insert(idx, obj)

    # @profile
    def remove(self, obj):
        # See note about self.indexes in insert().
        # objidx = self.indexes[obj]
        objidx = self.indexes[id(obj)]

        # Remove from list
        self.objects[objidx] = None

        # Remove from index
        self.remove_obj(objidx, obj)

    def get_objects(self):
        return (o for o in self.objects if o is not None)

    def nearest(self, pt):
        """
        Returns the nearest matching points and the object
        it belongs to.

        :param pt: Query point.
        :return: (match_x, match_y), Object owner of
          matching point.
        :rtype: tuple
        """
        tidx = super(FlatCAMRTreeStorage, self).nearest(pt)
        return (tidx.bbox[0], tidx.bbox[1]), self.objects[tidx.object]


# class myO:
#     def __init__(self, coords):
#         self.coords = coords
#
#
# def test_rti():
#
#     o1 = myO([(0, 0), (0, 1), (1, 1)])
#     o2 = myO([(2, 0), (2, 1), (2, 1)])
#     o3 = myO([(2, 0), (2, 1), (3, 1)])
#
#     os = [o1, o2]
#
#     idx = FlatCAMRTree()
#
#     for o in range(len(os)):
#         idx.insert(o, os[o])
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]
#
#     idx.remove_obj(0, o1)
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]
#
#     idx.remove_obj(1, o2)
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]
#
#
# def test_rtis():
#
#     o1 = myO([(0, 0), (0, 1), (1, 1)])
#     o2 = myO([(2, 0), (2, 1), (2, 1)])
#     o3 = myO([(2, 0), (2, 1), (3, 1)])
#
#     os = [o1, o2]
#
#     idx = FlatCAMRTreeStorage()
#
#     for o in range(len(os)):
#         idx.insert(os[o])
#
#     #os = None
#     #o1 = None
#     #o2 = None
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]
#
#     idx.remove(idx.nearest((2,0))[1])
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]
#
#     idx.remove(idx.nearest((0,0))[1])
#
#     print [x.bbox for x in idx.rti.nearest((0, 0), num_results=20, objects=True)]