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epi_pre.py
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# -*- coding: utf-8 -*-
# Copyright (C) 2017 - Universitat Pompeu Fabra
# Author - Guillermo Jimenez-Perez <guillermo.jim.per@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
from os import system
from os import mkdir
from os.path import isfile
from os.path import isdir
from os.path import split
from os.path import splitext
from os.path import join
from numpy import int
from numpy import dtype
from numpy.matlib import repmat
from scipy import zeros
from scipy import array
from scipy import asarray
from scipy import mean
from scipy import sqrt
from scipy import pi
from scipy import sin
from scipy import cos
from scipy import tan
from scipy import arccos
from scipy import cumsum
from scipy import where
from scipy import flipud
from scipy import roll
from scipy import dot
from scipy import cross
from scipy.linalg import norm
from scipy.sparse import csr_matrix
from scipy.sparse import spdiags
from scipy.sparse import find
from vtk import vtkPolyDataReader
from vtk import vtkPolyData
from vtk import vtkPolyDataWriter
from vtk import vtkPoints
from vtk import vtkIdList
from vtk import vtkPlane
from vtk import vtkClipPolyData
from scipy.sparse.linalg import spsolve
from mvpoly.rbf import RBFThinPlateSpline
from PointPicker import PointSelector
import utils
class EpiQCM(object):
__path = None
__polydata = None
__points = None
__polygons = None
__boundary = None
__anterior = None
__posterior = None
__apex = None
__LV_laplacian = None
__LV_boundary = None
__LV_polydata = None
__LV_homeomorphism = None
__LV_apex = None
__LV_anterior = None
__LV_posterior = None
__RV_boundary = None
__RV_laplacian = None
__RV_polydata = None
__RV_homeomorphism = None
__RV_apex = None
__RV_anterior = None
__RV_posterior = None
__output_path = None
def __init__(self, path, anterior=None, posterior=None, apex=None, output_path=None):
""" """
print("TO-DO: DOCUMENTATION")
self.__anterior = anterior
self.__posterior = posterior
self.__apex = apex
# Reading the input VTK file
if self.polydata is None:
self.__polydata = utils.polydataReader(path)
# Establishing an output path
if output_path is None:
self.__output_path = self.path
else:
if output_path is self.path:
print(" * Output path provided coincides with input path.\n"+
" Overwriting the input file is not permitted.\n"+
" Writing in the default location...\n")
self.__output_path = self.path
else:
self.__output_path = output_path
######################################################################
# ¿¿ELIMINAR??
######################################################################
# # Exporting VTK points to numpy for a more efficient manipulation
# pointVector = self.polydata.GetPoints()
# try:
# rows = len(pointVector.GetPoint(0))
# cols = pointVector.GetNumberOfPoints()
# points = zeros((rows,cols))
# except:
# raise Exception("The VTK file provided does not contain any points")
# if pointVector:
# for i in range(0, pointVector.GetNumberOfPoints()):
# point_tuple = pointVector.GetPoint(i)
# points[0,i] = point_tuple[0]
# points[1,i] = point_tuple[1]
# points[2,i] = point_tuple[2]
######################################################################
# ¿¿ELIMINAR??
######################################################################
# Exporting VTK triangles to numpy for a more efficient manipulation
# polygons = None
# for i in xrange(self.polydata.GetNumberOfCells()):
# pointIds = self.polydata.GetCell(i).GetPointIds()
# if polygons is None:
# try:
# rows = pointIds.GetNumberOfIds()
# cols = self.polydata.GetNumberOfCells()
# polygons = zeros((rows,cols), dtype=int)
# except:
# raise Exception("The VTK file provided does not contain a triangulation")
# polygons[0,i] = pointIds.GetId(0)
# polygons[1,i] = pointIds.GetId(1)
# polygons[2,i] = pointIds.GetId(2)
# self.__points = points
# self.__points = polygons
self.__points = utils.vtkPointsToNumpy(self.polydata)
self.__polygons = utils.vtkCellsToNumpy(self.polydata)
# Calculate landmarks if not provided
self.__calc_landmarks()
self.__closest_boundary_point()
self.__calc_boundary()
self.__rearrange()
self.__calc_laplacian()
self.__calc_homeomorphism()
self.__calc_thin_plate_splines()
self.__write_output()
@property
def path(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__path
@property
def output_path(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__output_path
@property
def polydata(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__polydata
@property
def points(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__points
@property
def polygons(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__polygons
##########################################################################
# ¿¿ELIMINAR??
##########################################################################
@output_path.setter
def output_path(self, output_path):
""" """
print("TO-DO: DOCUMENTATION")
if output_path is self.path:
print(" * Warning! Overwriting the input file is not permitted.\n"
" Aborting...\n")
return
else:
if self.output_path == self.path:
print(" * Warning! The file written to the default location will *not*\n"
" be deleted\n")
else:
print(" * Warning! The file written to the previous working location will \n"
" *not* be deleted\n")
self.__output_path = output_path
self.__write_output()
##########################################################################
# ¿¿ELIMINAR??
##########################################################################
@property
def anterior(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__anterior
@property
def posterior(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__posterior
@property
def apex(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__apex
##########################################################################
# ¿¿ELIMINAR??
##########################################################################
@apex.setter
def apex(self, apex):
""" """
print("TO-DO: DOCUMENTATION")
if apex >= self.polydata.GetNumberOfPoints():
raise RuntimeError("Apical point provided is out of bounds")
self.__apex = apex
self.__calc_homeomorphism()
self.__write_output()
##########################################################################
# ¿¿ELIMINAR??
##########################################################################
@property
def laplacian(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__laplacian
@property
def boundary(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__boundary
@property
def boundary_points(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.points[:, self.boundary]
@property
def homeomorphism(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__homeomorphism
@property
def output_polydata(self):
""" """
print("TO-DO: DOCUMENTATION")
return self.__output_polydata
##########################################################################
##########################################################################
def __calc_landmarks(self):
""" """
print("TO-DO: DOCUMENTATION")
print("TO-DO: DESCRIPTORS TO KNOW HOW TO INTRODUCE LANDMARKS")
selected = False
while(not selected):
if self.anterior is None:
if self.posterior is None:
if self.apex is None:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 3:
selected = True
self.__anterior = ps.GetSelectedPointIds().GetId(0)
self.__apex = ps.GetSelectedPointIds().GetId(1)
self.__posterior = ps.GetSelectedPointIds().GetId(2)
else:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 2:
selected = True
self.__anterior = ps.GetSelectedPointIds().GetId(0)
self.__posterior = ps.GetSelectedPointIds().GetId(1)
else:
if self.apex is None:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 2:
selected = True
self.__anterior = ps.GetSelectedPointIds().GetId(0)
self.__apex = ps.GetSelectedPointIds().GetId(1)
else:
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 1:
selected = True
self.__anterior = ps.GetSelectedPointIds().GetId(0)
else:
if self.posterior is None:
if self.apex is None:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 2:
selected = True
self.__apex = ps.GetSelectedPointIds().GetId(0)
self.__posterior = ps.GetSelectedPointIds().GetId(1)
else:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 1:
selected = True
self.__posterior = ps.GetSelectedPointIds().GetId(0)
else:
if self.apex is None:
# print("DESCRIPTION")
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 1:
selected = True
self.__apex = ps.GetSelectedPointIds().GetId(0)
else:
selected = True
##########################################################################
## CLOSEST BOUNDARY FUNCTION
##########################################################################
def __closest_boundary_point(self, point):
""" """
print("TO-DO: DOCUMENTATION")
##########################################################################
## CLOSEST BOUNDARY FUNCTION
##########################################################################
def __divide(self):
""" """
print("TO-DO: DOCUMENTATION")
print("TO-DO: COMPROBAR LV Y RV, QUE SEAN ESAS LAS PARTES DEL CLIPPING PLANE")
# if self.anterior is None or self.posterior is None or self.apex is None:
# self.__calc_landmarks()
clip = vtk.vtkClipPolyData()
plane = vtk.vtkPlane()
anterior = self.anterior
posterior = self.posterior
apex = self.apex
O = asarray(self.polydata.GetPoint(self.apex))
A = asarray(self.polydata.GetPoint(self.anterior))
B = asarray(self.polydata.GetPoint(self.posterior))
OA = A - O
OB = B - O
# Clipping plane 1
normal = cross(OA,OB)/norm(cross(OA,OB))
plane.SetOrigin(self.polydata.GetPoint(self.apex))
plane.SetNormal((normal[0], normal[1], normal[2]))
clip.SetClipFunction(plane)
clip.SetInputData(self.polydata)
clip.Update()
self.__RV_polydata = clip.GetOutput()
# Clipping plane 2
normal = cross(OB,OA)/norm(cross(OB,OA))
plane.SetOrigin(self.polydata.GetPoint(self.apex))
plane.SetNormal((normal[0], normal[1], normal[2]))
clip.SetClipFunction(plane)
clip.SetInputData(self.polydata)
clip.Update()
self.__LV_polydata = clip.GetOutput()
def __calc_boundary(self):
""" """
print("TO-DO: DOCUMENTATION")
startingPoint = None
currentPoint = None
foundBoundary = False
cellId = None
boundary = []
visitedEdges = []
visitedBoundaryEdges = []
for cellId in xrange(self.polydata.GetNumberOfCells()):
cellPointIdList = vtkIdList()
cellEdges = []
self.polydata.GetCellPoints(cellId, cellPointIdList)
cellEdges = [[cellPointIdList.GetId(0),
cellPointIdList.GetId(1)],
[cellPointIdList.GetId(1),
cellPointIdList.GetId(2)],
[cellPointIdList.GetId(2),
cellPointIdList.GetId(0)]]
for i in xrange(len(cellEdges)):
if (cellEdges[i] in visitedEdges) == False:
visitedEdges.append(cellEdges[i])
edgeIdList = vtkIdList()
edgeIdList.InsertNextId(cellEdges[i][0])
edgeIdList.InsertNextId(cellEdges[i][1])
singleCellEdgeNeighborIds = vtkIdList()
self.polydata.GetCellEdgeNeighbors(cellId, cellEdges[i][0], cellEdges[i][1], singleCellEdgeNeighborIds)
if singleCellEdgeNeighborIds.GetNumberOfIds() == 0:
foundBoundary = True
startingPoint = cellEdges[i][0]
currentPoint = cellEdges[i][1]
boundary.append(cellEdges[i][0])
boundary.append(cellEdges[i][1])
visitedBoundaryEdges.append([currentPoint,startingPoint])
visitedBoundaryEdges.append([startingPoint,currentPoint])
if foundBoundary == True:
break
if foundBoundary == False:
raise Exception("The mesh provided has no boundary not possible to do Quasi-Conformal Mapping on this dataset.")
while currentPoint != startingPoint:
neighboringCells = vtkIdList()
self.polydata.GetPointCells(currentPoint, neighboringCells)
for i in xrange(neighboringCells.GetNumberOfIds()):
cell = neighboringCells.GetId(i)
triangle = self.polydata.GetCell(cell)
for j in xrange(triangle.GetNumberOfPoints()):
if triangle.GetPointId(j) == currentPoint:
j1 = (j + 1) % 3
j2 = (j + 2) % 3
edge1 = [triangle.GetPointId(j),
triangle.GetPointId(j1)]
edge2 = [triangle.GetPointId(j),
triangle.GetPointId(j2)]
edgeNeighbors1 = vtkIdList()
edgeNeighbors2 = vtkIdList()
self.polydata.GetCellEdgeNeighbors(cell, edge1[0], edge1[1], edgeNeighbors1)
self.polydata.GetCellEdgeNeighbors(cell, edge2[0], edge2[1], edgeNeighbors2)
if edgeNeighbors1.GetNumberOfIds() == 0:
if ([edge1[1], edge1[0]] in visitedBoundaryEdges) == False:
if (edge1[1] in boundary) == False:
boundary.append(edge1[1])
visitedBoundaryEdges.append([edge1[0], edge1[1]])
visitedBoundaryEdges.append([edge1[1], edge1[0]])
currentPoint = edge1[1]
break
if edgeNeighbors2.GetNumberOfIds() == 0:
if ([edge2[1], edge2[0]] in visitedBoundaryEdges) == False:
if (edge2[1] in boundary) == False:
boundary.append(edge2[1])
visitedBoundaryEdges.append([edge2[0], edge2[1]])
visitedBoundaryEdges.append([edge2[1], edge2[0]])
currentPoint = edge2[1]
break
boundary = asarray(boundary, dtype=int)
center = mean(self.points[:,boundary], axis=1)
vector1 = asarray(self.points[:,boundary[0]] - center)
vector2 = asarray(self.points[:,boundary[1]] - center)
vectorNormal= cross(vector1, vector2)
vectorApex = self.points[:, self.apex] - center
if len(center.shape) is not 1:
if center.shape[0] is not 3:
raise Exception("Something went wrong. Probably forgot to transpose this. Contact maintainer.")
if dot(vectorApex, vectorNormal) < 0:
boundary = flipud(boundary)
boundary = roll(boundary, 1)
self.__boundary = boundary
def __calc_laplacian(self):
""" """
print("TO-DO: DOCUMENTATION")
numPoints = self.polydata.GetNumberOfPoints()
numPolygons = self.polydata.GetNumberOfPolys()
numDims = self.polydata.GetPoints().GetData().GetNumberOfComponents()
sparseMatrix = csr_matrix((numPoints, numPoints))
for i in range(0, numDims):
i1 = (i + 0)%3
i2 = (i + 1)%3
i3 = (i + 2)%3
vectP2P1 = (self.points[:, self.polygons[i2, :]]
- self.points[:, self.polygons[i1, :]])
vectP3P1 = (self.points[:, self.polygons[i3, :]]
- self.points[:, self.polygons[i1, :]])
vectP2P1 = vectP2P1 / repmat(sqrt((vectP2P1**2).sum(0)),
numDims, 1)
vectP3P1 = vectP3P1 / repmat(sqrt((vectP3P1**2).sum(0)),
numDims, 1)
angles = arccos((vectP2P1 * vectP3P1).sum(0))
iterData1 = csr_matrix((1/tan(angles), (self.polygons[i2,:],
self.polygons[i3,:])),
shape=(numPoints, numPoints))
iterData2 = csr_matrix((1/tan(angles), (self.polygons[i3,:],
self.polygons[i2,:])),
shape=(numPoints, numPoints))
sparseMatrix = sparseMatrix + iterData1 + iterData2
# diagonal = sparseMatrix.sum(0)
# diagonalSparse = spdiags(diagonal, 0, numPoints, numPoints)
# self.__laplacian = diagonalSparse - sparseMatrix
self.__laplacian = sparseMatrix
def __calc_homeomorphism(self):
""" """
print("TO-DO: DOCUMENTATION")
if (self.laplacian is not None) and (self.boundary is not None):
numPoints = self.polydata.GetNumberOfPoints()
diagonal = self.laplacian.sum(0)
diagonalSparse = spdiags(diagonal, 0, numPoints, numPoints)
homeomorphism_laplacian = diagonalSparse - self.laplacian
# Finds non-zero elements in the laplacian matrix
(nzi, nzj) = find(self.laplacian)[0:2]
for point in self.boundary:
positions = where(nzi==point)[0]
homeomorphism_laplacian[nzi[positions], nzj[positions]] = 0
homeomorphism_laplacian[point, point] = 1
# Finds a distribution of the boundary points around a circle
boundaryNext = roll(self.boundary, -1)
boundaryNextPoints = self.points[:, boundaryNext]
distanceToNext = boundaryNextPoints - self.points[:, self.boundary]
euclideanNorm = sqrt((distanceToNext**2).sum(0))
perimeter = euclideanNorm.sum()
fraction = euclideanNorm/perimeter
angles = cumsum(2*pi*fraction)
angles = roll(angles, 1)
angles[0] = 0
# Creates the constrain for the homeomorphism
Z = zeros((2, angles.size))
Z[0,:] = cos(angles)
Z[1,:] = sin(angles)
boundaryConstrain = zeros((2, self.polydata.GetNumberOfPoints()))
boundaryConstrain[:, self.boundary] = Z
self.__homeomorphism = spsolve(homeomorphism_laplacian,
boundaryConstrain.transpose()).transpose()
def __calc_thin_plate_splines(self):
""" """
print("TO-DO: DOCUMENTATION")
if (self.homeomorphism is not None) and (self.apex is not None):
boundaryPoints = self.homeomorphism[:,self.boundary]
source = zeros((boundaryPoints.shape[0],
boundaryPoints.shape[1] + 1))
destination = zeros((boundaryPoints.shape[0],
boundaryPoints.shape[1] + 1))
source[:, 0:source.shape[1] - 1] = boundaryPoints
source[:, source.shape[1] - 1] = self.homeomorphism[:, self.apex]
destination[:, 0:source.shape[1] - 1] = boundaryPoints
destination[:, 0:source.shape[1] - 1] = boundaryPoints
# For a faster calculation, the mvpoly package has been used. The
# Thin Plate Splines has been calculated using the X coordinate of
# the points in the real part of a complex number and the Y
# coordinate of the point as the imaginary part. After the
# interpolation, the separate real and imaginary parts have been
# recovered, encoding the new (X,Y) positions after the relaxation.
x = source[0,:]
y = source[1,:]
d = destination[0,:] + 1j*destination[1,:]
thinPlateInterpolation = RBFThinPlateSpline(x,y,d)
result = thinPlateInterpolation(self.homeomorphism[0,:], self.homeomorphism[1,:])
self.__homeomorphism[0,:] = result.real
self.__homeomorphism[1,:] = result.imag
def flip_boundary(self):
""" """
print("TO-DO: DOCUMENTATION")
self.__boundary = flipud(self.boundary)
self.__boundary = roll(self.boundary, 1)
##########################################################################
##########################################################################
def __closest_point(self, objectivePoint):
""" """
print("TO-DO: DOCUMENTATION")
try:
dimensions = len(anterior)
except:
dimensions = 0
if objectivePoint == self.septum:
return
if objectivePoint in self.boundary:
septalIndex = objectivePoint
closestPoint = objectivePoint
closestPointIndex = where(self.boundary==objectivePoint)
if len(closestPointIndex) == 1:
if len(closestPointIndex[0]) == 1:
closestPointIndex = closestPointIndex[0][0]
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
else:
print(" * Provided point not found in the boundary. Selecting \n"
" closest point available...")
try:
searched_point = self.points[:, objectivePoint]
except:
raise Exception("Septal point provided out of data bounds the point does not exist (it is out of bounds) or a point identifier beyond the total amount of points has been provided. Check input.")
if len(self.boundary.shape) == 1:
searched_point = repmat(searched_point, self.boundary.size, 1)
searched_point = searched_point.transpose()
else:
raise Exception("It seems you have multiple boundaries. Contact the package maintainer.")
distanceToObjectivePoint = (self.points[:, self.boundary] - searched_point)
distanceToObjectivePoint = sqrt((distanceToObjectivePoint**2).sum(0))
closestPointIndex = where(distanceToObjectivePoint == distanceToObjectivePoint.min())
if len(closestPointIndex) == 1:
if len(closestPointIndex[0]) == 1:
closestPointIndex = closestPointIndex[0][0]
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
septalIndex = self.boundary[closestPointIndex]
self.__boundary = roll(self.boundary, -closestPointIndex)
center = asarray([0, 0]) # The center of the disk will always be a
vector1 = asarray([1, 0]) # point (0,0) and the septum a vector (1,0),
# as induced by the boundary conditions
vector2 = self.homeomorphism[:, septalIndex] - center
angle = arccos(dot(vector1, vector2)/(norm(vector1)*norm(vector2)))
# If the y coordinate of the vector w.r.t. the rotation will take place
# is negative, the rotation must be done counterclock-wise
if vector2[1] > 0:
angle = -angle
rotation_matrix = asarray([[cos(angle), -sin(angle)],
[sin(angle), cos(angle)]])
self.__septum = septalIndex
self.__homeomorphism = rotation_matrix.dot(self.homeomorphism)
self.__write_output()
##########################################################################
##########################################################################
def __rearrange(self, objectivePoint=None):
""" """
print("TO-DO: DOCUMENTATION")
septalIndex = None
septalPoint = None
closestPoint = None
if objectivePoint is None:
if self.septum is None:
raise Exception("No septal point provided in function call and no septal point provided in constructor. Aborting arrangement. ")
else:
septalIndex = self.septum
else:
print(" * Using provided septal point as rearranging point.")
self.__septum = objectivePoint
septalIndex = objectivePoint
if septalIndex in self.boundary:
closestPoint = septalIndex
closestPointIndex = where(self.boundary==septalIndex)
if len(closestPointIndex) == 1:
if len(closestPointIndex[0]) == 1:
closestPointIndex = closestPointIndex[0][0]
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
self.__boundary = roll(self.boundary, -closestPointIndex)
else:
try:
septalPoint = self.points[:, septalIndex]
except:
raise Exception("Septal point provided out of data bounds the point does not exist (it is out of bounds) or a point identifier beyond the total amount of points has been provided. Check input.")
if len(self.boundary.shape) == 1:
septalPoint = repmat(septalPoint,
self.boundary.size, 1)
septalPoint = septalPoint .transpose()
else:
raise Exception("It seems you have multiple boundaries. Contact the package maintainer.")
distanceToObjectivePoint = (self.points[:, self.boundary] - septalPoint)
distanceToObjectivePoint = sqrt((distanceToObjectivePoint**2).sum(0))
closestPointIndex = where(distanceToObjectivePoint == distanceToObjectivePoint.min())
if len(closestPointIndex) == 1:
if len(closestPointIndex[0]) == 1:
closestPointIndex = closestPointIndex[0][0]
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
else:
raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
self.__boundary = roll(self.boundary, -closestPointIndex)
# def rearrange_boundary(self, objectivePoint):
# """Rearranges the boundary aroung a new point identifier
# """
# old_septum = self.septum
# septalIndex = None
# closestPoint = None
# if objectivePoint == self.septum:
# return
# if objectivePoint in self.boundary:
# septalIndex = objectivePoint
# closestPoint = objectivePoint
# closestPointIndex = where(self.boundary==objectivePoint)
# if len(closestPointIndex) == 1:
# if len(closestPointIndex[0]) == 1:
# closestPointIndex = closestPointIndex[0][0]
# else:
# raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
# else:
# raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
# else:
# print(" * Provided point not found in the boundary. Selecting \n"
# " closest point available...")
# try:
# searched_point = self.points[:, objectivePoint]
# except:
# raise Exception("Septal point provided out of data bounds the point does not exist (it is out of bounds) or a point identifier beyond the total amount of points has been provided. Check input.")
# if len(self.boundary.shape) == 1:
# searched_point = repmat(searched_point, self.boundary.size, 1)
# searched_point = searched_point.transpose()
# else:
# raise Exception("It seems you have multiple boundaries. Contact the package maintainer.")
# distanceToObjectivePoint = (self.points[:, self.boundary] - searched_point)
# distanceToObjectivePoint = sqrt((distanceToObjectivePoint**2).sum(0))
# closestPointIndex = where(distanceToObjectivePoint == distanceToObjectivePoint.min())
# if len(closestPointIndex) == 1:
# if len(closestPointIndex[0]) == 1:
# closestPointIndex = closestPointIndex[0][0]
# else:
# raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
# else:
# raise Exception("It seems your vtk file has more than one point ID associated to the objective point. Check your input data or contact the maintainer.")
# septalIndex = self.boundary[closestPointIndex]
# self.__boundary = roll(self.boundary, -closestPointIndex)
# center = asarray([0, 0]) # The center of the disk will always be a
# vector1 = asarray([1, 0]) # point (0,0) and the septum a vector (1,0),
# # as induced by the boundary conditions
# vector2 = self.homeomorphism[:, septalIndex] - center
# angle = arccos(dot(vector1, vector2)/(norm(vector1)*norm(vector2)))
# # If the y coordinate of the vector w.r.t. the rotation will take place
# # is negative, the rotation must be done counterclock-wise
# if vector2[1] > 0:
# angle = -angle
# rotation_matrix = asarray([[cos(angle), -sin(angle)],
# [sin(angle), cos(angle)]])
# self.__septum = septalIndex
# self.__homeomorphism = rotation_matrix.dot(self.homeomorphism)
# self.__write_output()
def closest_boundary_point(self, objectivePoint=None):
""" """
print("TO-DO: DOCUMENTATION")
if objectivePoint is None:
selected = True
while(selected):
ps = PointSelector()
ps.DoSelection(self.polydata)
if ps.GetSelectedPoints().GetNumberOfPoints() == 1:
selected = False
objectivePoint = ps.GetSelectedPointIds().GetId(0)
output_point = None
if objectivePoint in self.boundary:
output_point = where(self.boundary==objectivePoint)