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CCSegPipeSeg.py
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CCSegPipeSeg.py
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#!/usr/bin/env python3
import tempfile
import os
import scipy
import cv2
import math
import numpy
import nibabel
import matplotlib.pyplot as plt
import h5py
import shutil
import CCSegUtils
import Otsu
import skimage.morphology
import skimage.segmentation
import skimage.feature
import skimage.color
# My Lucas-Kanade tracker
import LKTracker
from matplotlib.font_manager import FontProperties
import errno
import scipy.ndimage
from joblib import Parallel, delayed
def watershedTransformSeg(IMG, Seg, penaltyIMG = None):
watershedMask = scipy.ndimage.morphology.binary_dilation(Seg, structure = radialStrel(7))
segEroded = scipy.ndimage.morphology.binary_erosion(Seg, structure = numpy.ones((3, 3)))
#segEroded = numpy.array(Seg)
watershedMaskEroded = scipy.ndimage.morphology.binary_erosion(watershedMask, structure = numpy.ones((3, 3)))
outerMarker = numpy.logical_and(numpy.logical_not(watershedMaskEroded), watershedMask)
if penaltyIMG is None:
gaussianDerivFilter = numpy.atleast_2d(numpy.array([0.0021, 0.4319, 0, -0.4319, -0.0021]))
#print gaussianDerivFilter
#print gaussianDerivFilter.T
FX = scipy.ndimage.filters.convolve(IMG, gaussianDerivFilter, mode = 'nearest')
FY = scipy.ndimage.filters.convolve(IMG, gaussianDerivFilter.T, mode = 'nearest')
edgeMAG = numpy.sqrt(FX * FX + FY * FY)
edgeMAG[numpy.logical_not(watershedMask)] = 0
penaltyIMG = numpy.array(edgeMAG)
#peak_local_max(-edgeMAG, indices = False, footprint = numpy.ones((3, 3)), labels=image)
#SE = numpy.ones((3, 3))
#T = scipy.ndimage.morphology.grey_erosion(edgeMAG, footprint = SE)
#localMin = numpy.logical_and(T == edgeMAG, edgeMAG > 0)
#watershedMarkers = numpy.logical_or(localMin, Seg)
watershedMarkers = numpy.logical_or(segEroded, outerMarker)
watershedMarkers = scipy.ndimage.measurements.label(numpy.uint16(watershedMarkers), structure = numpy.ones([3, 3]))[0]
#
# print watershedMarkers[segEroded]
# plt.clf()
# plt.subplot(2, 2, 1)
# CCSegUtils.showIMG(watershedMarkers)
# plt.subplot(2, 2, 2)
# CCSegUtils.showIMG(outerMarker)
# plt.subplot(2, 2, 3)
# CCSegUtils.showIMG(segEroded)
#
# plt.gcf().set_size_inches((20, 10), forward = True)
# plt.show()
#
watershedSegLabels = numpy.unique(watershedMarkers[segEroded])
#print I
#I = watershedMarkers[segEroded]
#print watershedSegLabels
#watershedSegLabels = I[0]
watershedTransform = skimage.segmentation.watershed(penaltyIMG, numpy.uint16(watershedMarkers), mask = watershedMask)
#watershedAreas = regionProps(watershedTransform, ['area'])
#I = numpy.argmax(watershedAreas['area'])
#watershedSeg = (watershedTransform == I + 1)
#watershedSeg = (watershedTransform == watershedSegLabel)
#watershedSeg, junk = CCSegUtils.ismember(watershedTransform, watershedSegLabels)
watershedSeg = numpy.in1d(numpy.ravel(watershedTransform), numpy.ravel(watershedSegLabels))
#print watershedSeg
#print watershedSegLabels
watershedSeg = numpy.reshape(watershedSeg, watershedTransform.shape)
#print watershedSeg.shape
return (watershedSeg, watershedMarkers, watershedTransform, penaltyIMG)
# implements imfill(BW, 'holes')
def bwFillHoles(BW):
assert(isinstance(BW, numpy.ndarray) and BW.dtype == numpy.bool)
mask = numpy.pad(numpy.logical_not(BW), 1, mode='constant', constant_values = 1)
marker = numpy.pad(numpy.zeros(BW.shape, dtype=numpy.bool), 1, mode='constant', constant_values = 1)
numDilations = 0
while True:
oldMarker = numpy.array(marker)
marker = numpy.logical_and(mask, scipy.ndimage.morphology.binary_dilation(marker, structure = numpy.ones((3, 3), dtype=numpy.bool)))
if numpy.array_equal(oldMarker, marker):
break;
numDilations = numDilations + 1
del oldMarker
print(("bwFillHoles finished with " + str(numDilations) + " dilations"))
marker = numpy.take(marker, numpy.arange(1, marker.shape[0] - 1), axis = 0)
marker = numpy.take(marker, numpy.arange(1, marker.shape[1] - 1), axis = 1)
#plt.subplot(1, 2, 1); CCSegUtils.showIMG(marker);
#plt.subplot(1, 2, 2); CCSegUtils.showIMG(BW);
return numpy.logical_not(marker)
#return numpy.logical_or(BW, numpy.logical_not(marker))
# bwselect using masks
# label the Mask
# extract all values in the labeled Mask under the marker
# retain only labels that overlap with the marker
def bwSelectWithMask(mask, marker):
outIMG = numpy.zeros(marker.shape, dtype = numpy.bool)
if not numpy.any(marker):
return outIMG
else:
BWLabels, numLabels = scipy.ndimage.measurements.label(mask, structure = numpy.ones([3, 3]))
labelsUnderMarker = BWLabels[marker]
labelsUnderMarker = labelsUnderMarker[labelsUnderMarker.nonzero()]
labelsUnderMarker = numpy.unique(labelsUnderMarker)
#print "labelsUnderMarker: " + str(labelsUnderMarker)
for z in range(numpy.size(labelsUnderMarker)):
outIMG = numpy.logical_or(outIMG, BWLabels == labelsUnderMarker[z])
return outIMG
def dicesCoefficient(A, B):
return 2.0 * numpy.sum(numpy.logical_and(A, B)) / (numpy.sum(A) + numpy.sum(B))
def bwAreaOpen(BW, areaThresh):
outIMG = numpy.zeros(BW.shape, dtype=numpy.bool)
BWLabels, numLabels = scipy.ndimage.measurements.label(BW, structure = numpy.ones([3, 3]))
if numLabels >= 1:
BWRegionProps = CCSegUtils.regionProps(BWLabels, ['Area'])
I = numpy.where(BWRegionProps['area'] > areaThresh)[0]
for z in range(numpy.size(I)):
outIMG = numpy.logical_or(outIMG, BWLabels == I[z] + 1)
return outIMG
def imMatchHist(inputIMG, targetIMG):
# performs histogram matching so that the intensities of InputIMG are remapped to correspond to the histogram of TargetIMG
#targetIMGBins, binSpacing = numpy.linspace(numpy.min(targetIMG), numpy.max(targetIMG), num = numBins - 2, retstep = True)
numBins = 10000
targetIMGHist, targetIMGBins = numpy.histogram(numpy.ravel(targetIMG), bins = numBins, density = False)
targetIMGHist = numpy.double(targetIMGHist)
# density doesnt normalize to 1, so do that
targetIMGHist = targetIMGHist / numpy.sum(targetIMGHist)
targetIMGHistCDF = numpy.cumsum(targetIMGHist)
# make the bins centres, not edges
targetIMGBins = targetIMGBins[:-1] + numpy.diff(targetIMGBins) / 2
#print targetIMGBins
# remove zero count bins
I = numpy.nonzero(targetIMGHist)
targetIMGBins = targetIMGBins[I]
targetIMGHistCDF = targetIMGHistCDF[I]
inputIMGHist, inputIMGBins = numpy.histogram(numpy.ravel(inputIMG), bins = numBins, density = False)
inputIMGHist = numpy.double(inputIMGHist)
inputIMGHist = inputIMGHist / numpy.sum(inputIMGHist)
inputIMGHistCDF = numpy.cumsum(inputIMGHist)
inputIMGBins = inputIMGBins[:-1] + numpy.diff(inputIMGBins) / 2
# remove zero-count bins
I = numpy.nonzero(inputIMGHist)
inputIMGBins = inputIMGBins[I]
inputIMGHistCDF = inputIMGHistCDF[I]
#plt.subplot(1, 2, 1)
#plt.plot(inputIMGBins, inputIMGHistCDF, 'b-', targetIMGBins, targetIMGHistCDF, 'g-')
#plt.show()
# find the point on the CDF of the input image of each of the input pixels
CDFOfInputIMG = numpy.interp(numpy.ravel(inputIMG), inputIMGBins, inputIMGHistCDF)
# find the bins that are the same point on the CDF of the target image
matchedIMG = numpy.interp(CDFOfInputIMG, targetIMGHistCDF, targetIMGBins)
matchedIMG = numpy.reshape(matchedIMG, inputIMG.shape)
return matchedIMG
#plt.plot(targetIMGBins[:-1] + numpy.diff(targetIMGBins) / 2, targetIMGHist)
#plt.show()
#print targetIMGHist.shape
#print targetIMGBins.shape
#% get the CDFs of the histogram of the target image
# [TargetIMGHist, TargetIMGBins] = hist(TargetIMG(:), TargetIMGBins);
# TargetIMGHist = TargetIMGHist ./ sum(TargetIMGHist);
# TargetIMGHistCDF = cumsum(TargetIMGHist);
# % get the CDFs of the histogram of the matched filter
#
# InputIMGBins = linspace(min(InputIMG(:)), max(InputIMG(:)), NumBins - 2);
# S = InputIMGBins(2) - InputIMGBins(1);
# InputIMGBins = [InputIMGBins(1) - S, InputIMGBins, InputIMGBins(end) + S];
# clear S;
# [InputIMGHist, InputIMGBins] = hist(InputIMG(:), InputIMGBins);
# InputIMGHist = InputIMGHist ./ sum(InputIMGHist);
# InputIMGHistCDF = cumsum(InputIMGHist);
#
# % use unique to create a CDF with no repeated elements
# [UInputIMGHistCDF, I] = unique(InputIMGHistCDF);
# UInputIMGHistCDFBins = InputIMGBins(I);
#
# [UTargetIMGHistCDF, I] = unique(TargetIMGHistCDF);
# UTargetIMGHistCDFBins = TargetIMGBins(I);
# clear I J;
#
# CDFInputIMGPixels = interp1(UInputIMGHistCDFBins, UInputIMGHistCDF, InputIMG(:));
# MatchedIMG = interp1(UTargetIMGHistCDF, UTargetIMGHistCDFBins, CDFInputIMGPixels);
#
# MatchedIMG = reshape(MatchedIMG, size(InputIMG));
#function [InitialResampledAVW, ...
# MatchedFilterRemapped, ...
# LKParameters, LKCost, ...
# TX, TY, InterpX, InterpY, ...
# TemplateLKIMG, TemplateProbLKIMG, FornixProbLKIMG, ...
# ResampledGroundCropped, ResampledAVWCropped, ...
# TemplateProbLKIMGCropped, FornixProbLKIMGCropped, ...
# OriginalOtsuMask, OtsuMask, ...
# TemplateOverlap, OtsuSEG] = do_lk_and_otsu(ResampledAVW, MatchedFilter, MatchedFilterProb, MatchedFilterFornixProb, ResampledGroundAVW, real_total_offset, DoLK)
#plt.show()
#plt.imshow(RW, origin = 'lower')
#print numpy.array([ normXCorrCenterI, normXCorrCenterJ])
#plt.imshow(resampledAVW, origin = 'lower')
#plt.plot(normXCorrCenterJ, normXCorrCenterI, marker='o', markerfacecolor='blue', markersize=12)
#plt.plot(I[1], I[0], marker='o', markerfacecolor='red', markersize=3, linestyle='none')
#plt.plot([centreXCorrMaxJ, centreXCorrMaxJ + croppedTemplateAVW.shape[1]], [centreXCorrMaxI, centreXCorrMaxI])
#plt.plot([centreXCorrMaxJ, centreXCorrMaxJ + croppedTemplateAVW.shape[1]], [centreXCorrMaxI + croppedTemplateAVW.shape[0], centreXCorrMaxI + croppedTemplateAVW.shape[0]])
#plt.plot([centreXCorrMaxJ, centreXCorrMaxJ], [centreXCorrMaxI, centreXCorrMaxI + croppedTemplateAVW.shape[0]])
#plt.plot([centreXCorrMaxJ + croppedTemplateAVW.shape[1], centreXCorrMaxJ + croppedTemplateAVW.shape[1]], [centreXCorrMaxI, centreXCorrMaxI + croppedTemplateAVW.shape[0]])
def segCCLKandOtsu(IMG, templateIMG, templateCCProbIMG, templateFornixProbIMG, groundIMG, initialTranslation, DoLK = True, targetIMGMask = None):
#print "Initial translation: " + str(initialTranslation)
#print "IMG size: " + str(IMG.shape)
#print "Template size: " + str(templateIMG.shape)
#print numpy.arange(initialTranslation[1], initialTranslation[1] + templateIMG.shape[1])
croppedIMG = numpy.take(IMG, numpy.arange(initialTranslation[0], initialTranslation[0] + templateIMG.shape[1]), axis = 1)
#print croppedIMG.shape
croppedIMG = numpy.take(croppedIMG, numpy.arange(initialTranslation[1], initialTranslation[1] + templateIMG.shape[0]), axis = 0)
remappedTemplateIMG = imMatchHist(templateIMG, croppedIMG)
#remappedTemplateIMGHist, remappedTemplateIMGBins = numpy.histogram(numpy.ravel(remappedTemplateIMG), bins = 100, density = True)
#remappedTemplateIMGBins = remappedTemplateIMGBins[:-1] + numpy.diff(remappedTemplateIMGBins)
#croppedIMGHist, croppedIMGBins = numpy.histogram(numpy.ravel(croppedIMG), bins = 100, density = True)
#croppedIMGBins = croppedIMGBins[:-1] + numpy.diff(croppedIMGBins)
#plt.plot(croppedIMGBins, croppedIMGHist)
#plt.plot(remappedTemplateIMGBins, remappedTemplateIMGHist)
#plt.show()
if DoLK == True:
numLKIterations = 100
else:
numLKIterations = 0
LKParameters, LKCost = LKTracker.weightedAffineInvComp(IMG, remappedTemplateIMG, templateIMG / numpy.max(templateIMG), numpy.array([0, 0, 0, 0, initialTranslation[0], initialTranslation[1]]), numLKIterations, targetIMGMask = targetIMGMask)
# [TX, TY, InterpX, InterpY] = coords_template_lk_img(LKParameters, ResampledAVW, MatchedFilter);
# find the coordinates of the template after the warp onto the target image
TX, TY, interpX, interpY = LKTracker.coordsOfAffineWarpedTemplate(LKParameters, IMG, templateIMG)
#plt.subplot(2, 2, 1); CCSegUtils.showIMG(TX);
#plt.subplot(2, 2, 2); CCSegUtils.showIMG(TY);
#plt.subplot(2, 2, 3); CCSegUtils.showIMG(InterpX);
#plt.subplot(2, 2, 4); CCSegUtils.showIMG(InterpY);
#plt.show()
#quit()
# resample the template in the image space
templateLKIMG = CCSegUtils.interp2q(numpy.arange(1, templateIMG.shape[1] + 1), numpy.arange(1, templateIMG.shape[0] + 1), templateIMG, interpX, interpY, extrapval = numpy.nan)
templateCCProbLKIMG = CCSegUtils.interp2q(numpy.arange(1, templateIMG.shape[1] + 1), numpy.arange(1, templateIMG.shape[0] + 1), templateCCProbIMG, interpX, interpY, extrapval = 0)
templateFornixProbLKIMG = CCSegUtils.interp2q(numpy.arange(1, templateIMG.shape[1] + 1), numpy.arange(1, templateIMG.shape[0] + 1), templateFornixProbIMG, interpX, interpY, extrapval = 0)
#plt.subplot(2, 2, 1); CCSegUtils.showIMG(templateLKIMG);
#plt.subplot(2, 2, 2); CCSegUtils.showIMG(templateCCProbLKIMG);
#plt.subplot(2, 2, 3); CCSegUtils.showIMG(templateFornixProbLKIMG);
#plt.subplot(2, 2, 4); CCSegUtils.showIMG(numpy.isnan(templateLKIMG));
#plt.show()
#quit()
# find the valid bounding box of the template in the image space
I = numpy.where(numpy.logical_not(numpy.isnan(templateLKIMG)))
cropRows = numpy.arange(numpy.min(I[0]), numpy.max(I[0]) + 1)
cropCols = numpy.arange(numpy.min(I[1]), numpy.max(I[1]) + 1)
del I
# crop the warped images
croppedIMG = IMG.take(cropRows, axis = 0).take(cropCols, axis = 1)
croppedTemplateLKIMG = templateLKIMG.take(cropRows, axis = 0).take(cropCols, axis = 1)
croppedTemplateCCProbLKIMG = templateCCProbLKIMG.take(cropRows, axis = 0).take(cropCols, axis = 1)
croppedTemplateFornixProbLKIMG = templateFornixProbLKIMG.take(cropRows, axis = 0).take(cropCols, axis = 1)
if not groundIMG == None:
croppedGroundIMG = groundIMG.take(cropRows, axis = 0).take(cropCols, axis = 1)
else:
croppedGroundIMG = None
# reset the NaN values in the warped template to zero
croppedTemplateLKIMG[numpy.where(numpy.isnan(croppedTemplateLKIMG))] = 0
# [THRESH, OtsuSEG] = robust_otsu2(ResampledAVWCropped, [0.05, 0.98]);
# OtsuSEG(ResampledAVWCropped > THRESH(end)) = 3;
# OtsuMask = (OtsuSEG == 3);
otsuSeg = Otsu.robustOtsu(croppedIMG, [0.05, 0.98], NumberClasses=3, maskOutZeros = True)
otsuSegWM = (otsuSeg == 3)
origOtsuSegWM = numpy.array(otsuSegWM)
#plt.subplot(1, 2, 1); CCSegUtils.showIMG(origOtsuSegWM);
#plt.subplot(1, 2, 2); CCSegUtils.showIMG(croppedIMG);
#plt.show()
#quit()
del otsuSeg
templateFornixMask = (croppedTemplateFornixProbLKIMG > 0.01)
# FornixMaskIdx = find((FornixProbLKIMGCropped * 50) > 0.5);
# OtsuMaskCC = bwconncomp(OtsuMask);
# OtsuMaskL = labelmatrix(OtsuMaskCC);
# OtsuMaskR = regionprops(OtsuMaskCC, 'Area', 'PixelIdxList');
otsuSegWMLabels, numLabels = scipy.ndimage.measurements.label(otsuSegWM, structure = numpy.ones([3, 3]))
otsuSegWMRegionProps = CCSegUtils.regionProps(otsuSegWMLabels, ['Area', 'Mask'])
#plt.subplot(1, 2, 1); CCSegUtils.showIMG(otsuSegWMLabels);
#plt.show()
#quit()
# TemplateOverlap = zeros(length(OtsuMaskR), 1);
# % keep all regions that have high overlap with template or big area
# for z = 1:length(OtsuMaskR)
# IDX = setdiff(OtsuMaskR(z).PixelIdxList, FornixMaskIdx);
# TemplateOverlap(z) = sum(TemplateProbLKIMGCropped(IDX)) ./ length(IDX);
# clear IDX;
# end
templateOverlap = numpy.zeros((numLabels))
J = numpy.argmax(otsuSegWMRegionProps['area'])
for z in range(numLabels):
M = numpy.logical_and(otsuSegWMRegionProps['mask'][z], numpy.logical_not(templateFornixMask))
# if z == J:
# #print J
# #print otsuSegWMRegionProps['area']
# SR = 1
# SC = 3
# plt.subplot(SR, SC, 1)
# CCSegUtils.showIMG(otsuSegWMRegionProps['mask'][z])
# plt.subplot(SR, SC, 2)
# CCSegUtils.showIMG(templateFornixMask)
# plt.subplot(SR, SC, 3)
# CCSegUtils.showIMG(croppedTemplateCCProbLKIMG)
#
# plt.gcf().set_size_inches((20, 10), forward = True)
# plt.show()
# quit()
#
if numpy.any(M):
#print numpy.sum(M)
templateOverlap[z] = numpy.sum(croppedTemplateCCProbLKIMG[M]) / numpy.sum(M)
del M
#rint templateOverlap
largeTemplateOverlapIDX = numpy.where(templateOverlap > 0.01)[0]
#print otsuSegWMRegionProps['area'][largeTemplateOverlapIDX]
#print templateOverlap[largeTemplateOverlapIDX]
#quit()
#print templateOverlap
#print largeTemplateOverlapIDX
#print otsuSegWMRegionProps['area']
#print otsuSegWMRegionProps['area'][largeTemplateOverlapIDX]
otsuSegCC = numpy.zeros(otsuSegWM.shape, dtype=numpy.bool)
if numpy.size(largeTemplateOverlapIDX) > 0:
I = numpy.where(otsuSegWMRegionProps['area'][largeTemplateOverlapIDX] >= 200)[0]
if numpy.size(I) == 0:
# select the region with the highest overlap
I = numpy.argmax(templateOverlap)
otsuSegCC = numpy.array(otsuSegWMRegionProps['mask'][I])
#CCSegUtils.showIMG(otsuSegCC)
# SR = 2
# SC = 2
# plt.subplot(SR, SC, 1)
# CCSegUtils.showIMG(otsuSegWMLabels == largeTemplateOverlapIDX[J] + 1)
#
# plt.subplot(SR, SC, 2)
# CCSegUtils.showIMG(croppedTemplateCCProbLKIMG)
#
# for z in range(numpy.size(largeTemplateOverlapIDX)):
# otsuSegCC = numpy.logical_or(otsuSegCC, otsuSegWMLabels == largeTemplateOverlapIDX[z] + 1)
#
# plt.subplot(SR, SC, 3)
# CCSegUtils.showIMG(otsuSegCC)
#
# plt.subplot(SR, SC, 4)
#
# I = numpy.argmax(otsuSegWMRegionProps['area'])
#
# CCSegUtils.showIMG(otsuSegWMLabels == I + 1)
#
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#quit()
else:
#print I
for z in range(numpy.size(I)):
otsuSegCC = numpy.logical_or(otsuSegCC, otsuSegWMRegionProps['mask'][largeTemplateOverlapIDX[I[z]]])#otsuSegWMLabels == largeTemplateOverlapIDX[I[z]] + 1)
return (TX, TY, interpX, interpY, croppedIMG, croppedTemplateLKIMG, croppedTemplateCCProbLKIMG, croppedTemplateFornixProbLKIMG, croppedGroundIMG, otsuSegCC, cropRows, cropCols, LKCost)
#plt.subplot(2, 2, 1); CCSegUtils.showIMG(croppedTemplateLKIMG);
#plt.subplot(2, 2, 2); CCSegUtils.showIMG(croppedTemplateCCProbLKIMG);
#plt.subplot(2, 2, 3); CCSegUtils.showIMG(croppedTemplateFornixProbLKIMG);
#plt.subplot(2, 2, 4); CCSegUtils.showIMG(otsuSegCC);
#plt.show()
#quit()
# I = find(TemplateOverlap > 0.01);
# if(~isempty(I))
# OtsuMask = ismember(OtsuMaskL, I);
# OtsuMask = bwareaopen(OtsuMask, 200);
# clear Junk OtsuMaskL OtsuMaskR I;
# else
# disp('Current XCORR and LK failed');
# OtsuMask = false(size(OtsuMaskL));
# end
def nearestAnglesDistances(templateSegMask, estSegMask):
if numpy.all(templateSegMask == False) or numpy.all(estSegMask == False):
return (None, None)
templateSegContours, hierarchy = CCSegUtils.findContours(numpy.uint8(templateSegMask), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
#assert(len(templateSegContours) == 1),"Template CC seg has multiple contours, this should never happen"
if(not (len(templateSegContours) == 1)):
return (None, None)
smoothingFilter = numpy.array([1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0])
smoothingFilter = numpy.atleast_2d(smoothingFilter)
tangentFilter = numpy.array([1, 0, -1])
tangentFilter = numpy.atleast_2d(tangentFilter)
templateSegContour = numpy.squeeze(templateSegContours[0]).T
#print smoothingFilter.shape
#print templateSegContour.shape
smoothedTemplateSegContour = scipy.ndimage.filters.convolve(numpy.double(templateSegContour), smoothingFilter, mode = 'wrap')
tangentTemplateSegContour = scipy.ndimage.filters.convolve(numpy.double(smoothedTemplateSegContour), tangentFilter, mode = 'wrap')
# normalise the tangents to unit magnitude, numpy does the broadcasting for us so we just need to divide by the magnitudes
#print tangentTemplateSegContour
#print numpy.sqrt(numpy.sum(tangentTemplateSegContour * tangentTemplateSegContour, axis = 0))
T = numpy.sqrt(numpy.sum(tangentTemplateSegContour * tangentTemplateSegContour, axis = 0))
T[numpy.where(T == 0)] = 1
tangentTemplateSegContour = tangentTemplateSegContour / T
del T
#print templateSegContour[0]
#print smoothedTemplateSegContour[0]
#print smoothedTemplateSegContour[0].shape
#print numpy.concatenate([smoothedTemplateSegContour[0], numpy.array([smoothedTemplateSegContour[0, 0]])])
#print smoothedTemplateSegContour.shape
#CCSegUtils.showIMG(templateSegMask); CCSegUtils.plotContour(smoothedTemplateSegContour);
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#quit()
estSegContoursFirst, hierarchy = CCSegUtils.findContours(numpy.uint8(estSegMask), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
del hierarchy
estSegContours = list()
for z in range(len(estSegContoursFirst)):
estSegContours.append(numpy.atleast_2d(numpy.squeeze(estSegContoursFirst[z]).T))
del estSegContoursFirst
smoothedEstSegContours = list()
tangentEstSegContours = list()
#CCSegUtils.showIMG(allSegMasks)
#CCSegUtils.plotContour(smoothedTemplateSegContour)
for z in range(len(estSegContours)):
if estSegContours[z].shape[0] == 2:
smoothedEstSegContours.append(scipy.ndimage.filters.convolve(numpy.double(estSegContours[z]), smoothingFilter, mode = 'wrap'))
tangentEstSegContours.append(scipy.ndimage.filters.convolve(numpy.double(smoothedEstSegContours[-1]), tangentFilter, mode = 'wrap'))
#print smoothedEstSegContours[z].shape
#CCSegUtils.plotContour(smoothedEstSegContours[z])
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#quit()
allSmoothedEstSegContours = numpy.concatenate(smoothedEstSegContours, axis = 1)
allTangentEstSegContours = numpy.concatenate(tangentEstSegContours, axis = 1)
#print smoothedEstSegContours[z]
allTangentEstSegContoursMAG = numpy.sqrt(numpy.sum(allTangentEstSegContours * allTangentEstSegContours, axis = 0))
I = numpy.where(allTangentEstSegContoursMAG == 0)[0]
if numpy.size(I) > 0:
IDXToDelete = numpy.concatenate((I, numpy.mod(I + 1, numpy.size(allTangentEstSegContoursMAG))))
#CCSegUtils.showIMG(estSegMask)
#CCSegUtils.plotContour(allSmoothedEstSegContours)
#plt.plot(allSmoothedEstSegContours[0, IDXToDelete], allSmoothedEstSegContours[1, IDXToDelete], 'g*')
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#quit()
allSmoothedEstSegContours = numpy.delete(allSmoothedEstSegContours, I, axis = 1)
allTangentEstSegContours = scipy.ndimage.filters.convolve(allSmoothedEstSegContours, tangentFilter, mode = 'wrap')
#allTangentEstSegContoursMAG =
#rint allSmoothedEstSegContours.shape
del smoothedEstSegContours
del tangentEstSegContours
# find the indices of the closest points on the estimated contours for each of the template points
# put the tempate coordinates along the X axis, estimated coordinates along the Y axis
# so therefore to evaluate distances for each template coordinate use axis = 0, to process each column
smoothedTemplateSegContourX, allSmoothedEstSegContoursX = numpy.meshgrid(numpy.atleast_2d(smoothedTemplateSegContour[0]), numpy.atleast_2d(allSmoothedEstSegContours[0]))
smoothedTemplateSegContourY, allSmoothedEstSegContoursY = numpy.meshgrid(numpy.atleast_2d(smoothedTemplateSegContour[1]), numpy.atleast_2d(allSmoothedEstSegContours[1]))
D = numpy.sqrt((smoothedTemplateSegContourX - allSmoothedEstSegContoursX) * (smoothedTemplateSegContourX - allSmoothedEstSegContoursX) + (smoothedTemplateSegContourY - allSmoothedEstSegContoursY) * (smoothedTemplateSegContourY - allSmoothedEstSegContoursY))
closestIDX = numpy.argmin(D, axis = 0)
closestDistances = D[(closestIDX, numpy.arange(D.shape[1]))]
del D
del smoothedTemplateSegContourX; del allSmoothedEstSegContoursX;
del smoothedTemplateSegContourY; del allSmoothedEstSegContoursY;
# normalise the tangents to unit magnitude, numpy does the broadcasting for us so we just need to divide by the magnitudes
#print allTangentEstSegContours
allTangentEstSegContours = allTangentEstSegContours / numpy.sqrt(numpy.sum(allTangentEstSegContours * allTangentEstSegContours, axis = 0))
# compute the dot product between template tangent vectors and those in the closest indices in the EstSegContours
dotProducts = numpy.minimum(numpy.abs(numpy.sum(numpy.take(allTangentEstSegContours, closestIDX, axis = 1) * tangentTemplateSegContour, axis = 0)), 1.0)
# clip to [0, 1]
#dotProducts = numpy.abs(dotProducts)
#dotProducts = numpy.minimum(dotProducts, 1)
return (closestDistances, dotProducts)
#dotProduct = numpy.maximum(dotProduct, -1)
#CCSegUtils.showIMG(D)
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#allSegMasks = numpy.zeros(estSegMask.shape)
#allSegMasks[numpy.where(numpy.logical_and(numpy.logical_not(templateSegMask), estSegMask))] = 1
#allSegMasks[numpy.where(numpy.logical_and(templateSegMask, numpy.logical_not(estSegMask)))] = 2
#allSegMasks[numpy.where(numpy.logical_and(templateSegMask, estSegMask))] = 3
#quit()
def bwJoinMSTBoundaries(BW):
assert(isinstance(BW, numpy.ndarray) and BW.dtype == numpy.bool)
# [B] = bwboundaries(BW, 8);
firstcontours, hierarchy = CCSegUtils.findContours(numpy.uint8(BW), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
del hierarchy
if len(firstcontours) == 1:
return numpy.zeros(BW.shape, dtype = numpy.bool)
else:
contours = list()
for curContour in range(len(firstcontours)):
T = numpy.atleast_2d(numpy.array(numpy.squeeze(firstcontours[curContour])))
if T.shape[0] > 1:
contours.append(T)
del firstcontours
# contourDistances contains the minimum distances contourDistances[I, J] = minimum distance between contours A and B
contourDistances = numpy.zeros((len(contours), len(contours)))
# contourMinIDXI[I, J] and contourMinIDXJ[I, J] are the indices of the elements in contours I and J, respectively that form the distance contourDistances[I, J]
contourMinIDXI = numpy.zeros((len(contours), len(contours)), dtype = numpy.uint32)
contourMinIDXJ = numpy.zeros((len(contours), len(contours)), dtype = numpy.uint32)
for contourI in range(len(contours) - 1):
for contourJ in range(contourI + 1, len(contours)):
#print contours[contourI]
#print contours[contourJ]
XI, XJ = numpy.meshgrid(numpy.take(contours[contourI], [0], axis = 1), numpy.take(contours[contourJ], [0], axis = 1))
YI, YJ = numpy.meshgrid(numpy.take(contours[contourI], [1], axis = 1), numpy.take(contours[contourJ], [1], axis = 1))
D = numpy.double((XI - XJ) * (XI - XJ) + (YI - YJ) * (YI - YJ))
I = numpy.argmin(numpy.sqrt(D))
H = numpy.unravel_index(I, XI.shape)
contourDistances[contourI, contourJ] = D[H[0], H[1]]
contourMinIDXI[contourI, contourJ] = H[1]
contourMinIDXJ[contourI, contourJ] = H[0]
del H
del XI
del XJ
del YI
del YJ
del I
del D
# CCSegUtils.showIMG(BW)
# plt.plot(numpy.take(contours[contourI], [0], axis = 1), numpy.take(contours[contourI], [1], axis = 1), 'r')
# plt.plot(numpy.take(contours[contourJ], [0], axis = 1), numpy.take(contours[contourJ], [1], axis = 1), 'b')
# plt.plot(contours[contourI][H[1], 0], contours[contourI][H[1], 1], 'm*')
# plt.plot(contours[contourJ][H[0], 0], contours[contourJ][H[0], 1], 'm*')
# plt.show()
#print D[H[1], H[0]]
# quit()
#for contourJ in range(contourI + 1, len(contours)):
#for contourI in range(len(contours) - 1):
#contourDistances = contourDistances + contourDistances.T
#contourMinIDXI = numpy.uint32(contourMinIDXI + contourMinIDXI.T)
#contourMinIDXJ = numpy.uint32(contourMinIDXJ + contourMinIDXJ.T)
#CCSegUtils.showIMG(BW)
#contourI = 0
#contourJ = 1
#plt.plot(numpy.take(contours[contourI], [0], axis = 1), numpy.take(contours[contourI], [1], axis = 1), 'r')
#plt.plot(numpy.take(contours[contourJ], [0], axis = 1), numpy.take(contours[contourJ], [1], axis = 1), 'b')
# plt.plot(AX, AY, 'm-')
# plt.show()
if len(contours) == 2:
edges = numpy.atleast_2d(numpy.array([0, 1], dtype=numpy.uint32))
else:
# minimum spanning tree
#print contourDistances
C = scipy.sparse.csr_matrix(contourDistances, dtype = numpy.double)
MSP = scipy.sparse.csgraph.minimum_spanning_tree(C)
edges = MSP.nonzero()
edges = numpy.concatenate((numpy.atleast_2d(edges[0]), numpy.atleast_2d(edges[1])), axis = 0).T
edges = numpy.uint32(edges)
#edges = numpy.atleast_2d(numpy.array([0, 1], dtype=numpy.uint32))
#print edges
del C; del MSP;
#quit()
joiningSegments = numpy.zeros(BW.shape, dtype=numpy.bool)
# print edges.dtype
# print contourMinIDXI.dtype
for curEdge in range(edges.shape[0]):
contourI = edges[curEdge, 0]
contourJ = edges[curEdge, 1]
AX = numpy.array([contours[contourI][contourMinIDXI[contourI, contourJ], 0], contours[contourJ][contourMinIDXJ[contourI, contourJ], 0]])
AY = numpy.array([contours[contourI][contourMinIDXI[contourI, contourJ], 1], contours[contourJ][contourMinIDXJ[contourI, contourJ], 1]])
arcLength = numpy.sqrt((AX[0] - AX[1]) * (AX[0] - AX[1]) + (AY[0] - AY[1]) * (AY[0] - AY[1]))
n = numpy.ceil(arcLength * numpy.sqrt(2.0))
IX = numpy.linspace(AX[0], AX[1], n)
IY = numpy.linspace(AY[0], AY[1], n)
IX = numpy.uint32(numpy.round(IX))
IY = numpy.uint32(numpy.round(IY))
T = numpy.zeros_like(joiningSegments)
T[(IY, IX)] = True
del IX; del IY;
del n
del arcLength
del contourI; del contourJ;
Angle = numpy.arctan2(AY[1] - AY[0], AX[1] - AX[0]);
Angle = numpy.mod(Angle + 2 * numpy.pi, 2 * numpy.pi);
R = numpy.array([5, 5]) + 7 * numpy.abs(numpy.array([numpy.cos(Angle), numpy.sin(Angle)]))
AngleWeighting = -0.9 * numpy.cos(2 * (Angle + 45 * numpy.pi / 180));
SQ = numpy.sqrt(R[0] * R[1]) * AngleWeighting;
SIGMA = numpy.array([[R[0], SQ], [SQ, R[1]]])
F, FWHM = CCSegUtils.gaussianFWHM2D(SIGMA)
joiningSegments = numpy.logical_or(joiningSegments, scipy.ndimage.morphology.binary_dilation(T, structure = (F > FWHM)))
del F; del FWHM; del Angle; del R; del SQ; del SIGMA;
# [F, HalfMaximum] = gaussian_fwhm2d(SIGMA);
del AX; del AY;
#
# JoiningSegments = imdilate(T, double(F > HalfMaximum));
#
#CCSegUtils.showIMG(joiningSegments)
#plt.show()
return joiningSegments
#quit()
# if(length(B) == 1)
# JoiningSegments = false(size(BW));
# else
#
# Distances = zeros(length(B));
# DistancesMinI = zeros(length(B));
# DistancesMinJ = zeros(length(B));
#
# for BoundaryI = 1:length(B) - 1
# for BoundaryJ = BoundaryI + 1:length(B)
# XC = bsxfun(@minus, B{BoundaryI}(:, 1), B{BoundaryJ}(:, 1)');
# YC = bsxfun(@minus, B{BoundaryI}(:, 2), B{BoundaryJ}(:, 2)');
# SZ = size(XC);
# XC = XC(:);
# YC = YC(:);
# [Distances(BoundaryI, BoundaryJ), I] = min(sqrt(XC .* XC + YC .* YC));
# [DistancesMinI(BoundaryI, BoundaryJ), DistancesMinJ(BoundaryI, BoundaryJ)] = ind2sub(SZ, I);
# end
# end
# Distances = Distances + Distances';
# DistancesMinI = DistancesMinI + DistancesMinI';
# DistancesMinJ = DistancesMinJ + DistancesMinJ';
# if(length(B) > 2)
# edges = prim(Distances);
# % this is because we calculate the distances based on increasing indices of edges
# % if the edges are returned with a greater index on the left it
# % will create errors downstream, so sort them
# edges = sort(edges, 2);
# else
# edges = [1, 2];
# end
#
# for z = 1:size(edges, 1)
# StartX = B{edges(z, 1)}(DistancesMinI(edges(z, 1), edges(z, 2)), 2);
# EndX = B{edges(z, 2)}(DistancesMinJ(edges(z, 1), edges(z, 2)), 2);
# StartY = B{edges(z, 1)}(DistancesMinI(edges(z, 1), edges(z, 2)), 1);
# EndY = B{edges(z, 2)}(DistancesMinJ(edges(z, 1), edges(z, 2)), 1);
#
# ArcLength = sqrt((StartX - EndX) * (StartX - EndX) + (StartY - EndY) * (StartY - EndY));
# n = ceil(ArcLength * sqrt(2)); % make sure we cover all pixels
#
# IX = linspace(StartX, EndX, n);
# IY = linspace(StartY, EndY, n);
# IX = round(IX);
# IY = round(IY);
# I = sub2ind(size(BW), IY, IX);
# I = unique(I);
# T = false(size(BW));
# T(I) = 1;
# Angle = atan2(EndY - StartY, EndX - StartX);
# Angle = mod(Angle + 2 * pi, 2 * pi);
#
# R = [5, 5] + 7 * abs([cos(Angle), sin(Angle)]);
#
# AngleWeighting = -0.9 * cos(2 * (Angle + 45 * pi / 180));
#
# SQ = sqrt(R(1) * R(2)) * AngleWeighting;
# SIGMA = [R(1), SQ; SQ, R(2)];
# [F, HalfMaximum] = gaussian_fwhm2d(SIGMA);
#
# JoiningSegments = imdilate(T, double(F > HalfMaximum));
#
# clear I IX IY n ArcLength EndY StartY EndX StartX F T HalfMaximum SQ Angle AngleWeighting R;
# end
# end
#
def radialStrel(R):
X, Y = numpy.meshgrid(numpy.arange(-R, R + 1), numpy.arange(-R, R + 1))
S = numpy.sqrt(X * X + Y * Y)
return (S <= R)
# retain largest component
def segCC(outputBase, groundTruthFile = None, doLK = True, doGraphics = False, segNoAuto = False, segChooseFirst = False, segGridInitPoints = False):
(outputDir, subjectID) = os.path.split(outputBase)
PNGDirectory = os.path.join(outputDir, "seg")
if doGraphics:
CCSegUtils.mkdirSafe(PNGDirectory)
# bwFillHoles test
#A = numpy.zeros((100, 100), dtype=numpy.bool)
#A[24:75, 24:75] = True
#A[39:51, 39:51] = False
#bwFillHoles(A)
#CCSegUtils.showIMG(A);
#plt.gcf().set_size_inches((20, 10), forward = True)
#plt.show()
#quit()
# testing interp2
#xx = numpy.arange(1, 5)
#yy = numpy.arange(1, 6)
#V = numpy.random.normal(0, 1, (yy.size, xx.size))
#xi = numpy.array([0, 1, xx[-1]])
#yi = numpy.array([0, 1, yy[-1]])
#rint V.shape
#rint xx.shape
#rint yy.shape
#F = interp2q(xx, yy, V, xi, yi)
#print F
#quit()
midSagMATFile = outputBase + "_midsag.hdf5"
assert(os.path.isfile(midSagMATFile)),"midsag hdf5 file not found"
FID = h5py.File(midSagMATFile, 'r')
NIIPixdims = numpy.array(FID['NIIPixdims'])
midSagAVW = numpy.array(FID['midSagAVW'])
#skullCrop = numpy.array(FID["skullCrop"]) # the initial cropping indices of the background
#originalOrientationString = str(numpy.array(FID['originalOrientationString']))
#originalNativeFile = str(numpy.array(FID['originalNativeFile']))
#originalNativeCroppedFile = str(numpy.array(FID['originalNativeCroppedFile']))
try:
flirtTemplateFile = str(numpy.array(FID['flirtTemplateFile']))
flirtMAT = numpy.array(FID["flirtMAT"]) # the transformation between originalNativeCroppedFile -> flirtTemplateFile
except Exception:
flirtTemplateFile = None
flirtMAT = None
#flirtCropZerosRows = numpy.array(FID["flirtCropZerosRows"])
#flirtCropZerosCols = numpy.array(FID["flirtCropZerosCols"])
#try:
# parasagittalSlices = numpy.array(FID['parasagittalSlices'])
# parasagittalFX = numpy.array(FID['parasagittalFX'])
# parasagittalFY = numpy.array(FID['parasagittalFY'])
# parasagittalFZ = numpy.array(FID['parasagittalFZ'])
#except Exception:
symNII = nibabel.load(outputBase + "_native_midsag_sym.nii.gz")
parasagittalSlices, parasagittalFX, parasagittalFY, parasagittalFZ = CCSegUtils.parasagittalSlicesAndGradients(symNII.get_data(), symNII.header.get_zooms(), numSlices = 3)
del symNII
#parasagittalSlices = None
#parasagittalFX = None
#parasagittalFY = None
#parasagittalFZ = None
#MSPMethod = str(numpy.array(FID['MSPMethod']))
midSagAVWBrainMask = numpy.logical_not(numpy.isnan(midSagAVW))
# dilate this a bit
midSagAVW[numpy.where(numpy.logical_not(midSagAVWBrainMask))] = 0
midSagAVWBrainMask = numpy.double(midSagAVWBrainMask)
#midSagAVW = midSagAVW[:, ::-1]
#midSagAVW = numpy.rot90(midSagAVW, -1)
FID.close()
del FID
# FID = h5py.File(midSagMATFile, 'w')
#
# FID.create_dataset("NIIPixdims", data=NIIPixdims, compression = 'gzip')
# FID.create_dataset("midSagAVW", data=midSagAVW, compression = 'gzip')
# FID.create_dataset("MSPMethod", data=MSPMethod)
#
# FID.close()
# return
#rint "NIIPixdims = " + str(NIIPixdims)
#CCSegUtils.showIMG(midSagAVW)
#plt.show()
#quit()
if not groundTruthFile == None:
assert(os.path.isfile(groundTruthFile)),"Ground truth file was given, but it does not exist: " + groundTruthFile
groundTruthNII = nibabel.load(groundTruthFile)
groundTruthAVW = GroundTruthNII.get_data()
groundTruthAVW = numpy.rot90(GroundTruthAVW, 1)
#if not groundTruthFile == None:
# load atlases
scriptPath = os.path.realpath(__file__)
(scriptDir, tail) = os.path.split(scriptPath)
atlasDir = os.path.join(scriptDir, 'data')
fornixProbNII = nibabel.load(os.path.join(atlasDir, 'all_fornix_dilated_prob.nii.gz'))
fornixProbAVW = numpy.rot90(numpy.squeeze(fornixProbNII.get_data()), 1)
CCProbNII = nibabel.load(os.path.join(atlasDir, 'all_cc_prob.nii.gz'))
CCProbAVW = numpy.rot90(numpy.squeeze(CCProbNII.get_data()), 1)
templateNII = nibabel.load(os.path.join(atlasDir, 'all_msp_mean.nii.gz'))
templateAVW = numpy.rot90(numpy.squeeze(templateNII.get_data()), 1)
del atlasDir
templatePixdims = templateNII.header.get_zooms()[1:]
#print "midSagAVW.shape = " + str(midSagAVW.shape)
# resample to the space of the template
midSagAVWxx = numpy.arange(0, midSagAVW.shape[1]) * NIIPixdims[0]
midSagAVWxx = midSagAVWxx - numpy.mean(midSagAVWxx)
midSagAVWyy = numpy.arange(0, midSagAVW.shape[0]) * NIIPixdims[1]
midSagAVWyy = midSagAVWyy - numpy.mean(midSagAVWyy)
midSagAVWX, midSagAVWY = numpy.meshgrid(midSagAVWxx, midSagAVWyy)
templatexx = numpy.arange(0, templateAVW.shape[1]) * templatePixdims[0]
templatexx = templatexx - numpy.mean(templatexx)
templateyy = numpy.arange(0, templateAVW.shape[0]) * templatePixdims[1]
templateyy = templateyy - numpy.mean(templateyy)
# compute overlap box of midSagAVWxx, midSagAVWyy, templatexx, templateyy
lowX = numpy.maximum(midSagAVWxx[ 0], templatexx[ 0])
lowY = numpy.maximum(midSagAVWyy[ 0], templateyy[ 0])
highX = numpy.minimum(midSagAVWxx[-1], templatexx[-1])
highY = numpy.minimum(midSagAVWyy[-1], templateyy[-1])
resamplexx = numpy.arange(lowX, highX + templatePixdims[0], templatePixdims[0])
resampleyy = numpy.arange(lowY, highY + templatePixdims[1], templatePixdims[1])
#$del lowX; del lowY; del highX; del highY;
#resampleX, resampleY = numpy.meshgrid(numpy.arange(lowX, highX + templatePixdims[0], templatePixdims[0]), numpy.arange(lowY, highY + templatePixdims[1], templatePixdims[1]))
resampleX, resampleY = numpy.meshgrid(resamplexx, resampleyy)
# set up the interpolator as a function
#midSagAVWInterpolator = scipy.interpolate.interp2d(midSagAVWxx, midSagAVWyy, midSagAVW, fill_value=0)
#resampledAVW = midSagAVWInterpolator(resamplexx, resampleyy)
resampledAVW = CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, midSagAVW, resampleX, resampleY, interpmethod = 'linear', extrapval = 0)
resampledAVWBrainMask = CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, midSagAVWBrainMask, resampleX, resampleY, interpmethod = 'linear', extrapval = 0)
if not parasagittalSlices is None:
resampledSlices = list()
resampledFX = list()
resampledFY = list()
resampledFZ = list()
for z in range(parasagittalSlices.shape[2]):
resampledSlices.append(CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, parasagittalSlices[:, :, z], resampleX, resampleY, interpmethod = 'linear', extrapval = 0))
resampledFX.append(CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, parasagittalFX[:, :, z], resampleX, resampleY, interpmethod = 'linear', extrapval = 0))
resampledFY.append(CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, parasagittalFY[:, :, z], resampleX, resampleY, interpmethod = 'linear', extrapval = 0))
resampledFZ.append(CCSegUtils.interp2q(midSagAVWxx, midSagAVWyy, parasagittalFZ[:, :, z], resampleX, resampleY, interpmethod = 'linear', extrapval = 0))
parasagittalSlices = numpy.stack(resampledSlices, axis = 2)
parasagittalFX = numpy.stack(resampledFX, axis = 2)