def weightedAffineInvCompWarpCost(targetIMG, templateIMG, templateWeight, curParameters, displayStuff, targetIMGMask = None):
#function [ImageWarpedToTemplate, TX, TY, ErrorIMG, CostValue] = lk_weighted_run_affine_inv_comp_warpcost(targetIMG, templateIMG, TemplateW, CurParameters, displayStuff)
# [ImageWarpedToTemplate, TX, TY] = lk_warp_image_affine(targetIMG, size(templateIMG), CurParameters);
targetIMGToTemplate, TX, TY = warpImageAffine(targetIMG, templateIMG.shape, curParameters)
if displayStuff == True:
pylab.subplot(4, 3, 5); CCSegUtils.showIMG(targetIMGToTemplate); pylab.title('template coordinates warped to image');
pylab.subplot2grid((4, 3), (1, 2), rowspan = 2, colspan = 1); pylab.cla(); CCSegUtils.showIMG(targetIMG);
pylab.plot(TX[:, 0], TY[:, 0], 'b-')
pylab.plot(TX[0, :], TY[0, :], 'b-')
pylab.plot(TX[:, -1], TY[:, -1], 'b-')
pylab.plot(TX[-1, :], TY[-1, :], 'b-')
pylab.title('Coordinates on target')
#print "oiajfdoijadsf"
errorIMG = targetIMGToTemplate - templateIMG
LKCost = numpy.sum(errorIMG * templateWeight * errorIMG)
# find out if any coordinates are not in the mask
if targetIMGMask != None:
T = CCSegUtils.interp2q(numpy.arange(1, targetIMG.shape[1] + 1), numpy.arange(1, targetIMG.shape[0] + 1), targetIMGMask, TX, TY, extrapval = 0)
if numpy.any(T == 0):
LKCost = numpy.inf
return (targetIMGToTemplate, TX, TY, errorIMG, LKCost)
def warpImageAffine(targetIMG, templateIMGSize, affineParameters):
#
#function [WarpedIMG, TX, TY] = lk_warp_image_affine(targetIMG, TemplateIMGSize, Parameters)
#
#% [WarpedImage] = lk_warp_image_affine(targetIMG, TemplateIMGSize, Parameters)
#%
#% DESCRIPTION
#% Warps an image onto a template using the affine parameters
#% Parameters = [p1, p2, p3, p4, p5, p6];
#% Assumes that the template coordinates are [1:size(TemplateIMGSize(2)), 1:size(TemplateIMGSize(1))]
#%
#% PARAMETERS
#% targetIMG [InputM, InputN]: the input image
#% TemplateIMGSize [2]: [M, N] the size of the template
#%
#% RETURNS
#% WarpedImage [M, N]: the portion of the warped image that was in the boundary of the template
#%
#% In the algorithm, the template is the input and the TemplateIMGSize comes
#% from the I dont know
#%
#% Copyright 2013, Chris Adamson, Murdoch Childrens Research Institute
#% See LICENSE for full license information.
#%
#
#if(numel(Parameters) ~= 6)
# error('Parameters should have 6 elements');
#end
assert(numpy.size(affineParameters) == 6),"Affine parameters should have 6 elements"
#[TemplateX, TemplateY] = meshgrid(1:TemplateIMGSize(2), 1:TemplateIMGSize(1));
templateX, templateY = numpy.meshgrid(numpy.arange(1, templateIMGSize[1] + 1), numpy.arange(1, templateIMGSize[0] + 1))
#XY = cat(1, TemplateX(:)', TemplateY(:)', ones(1, prod(TemplateIMGSize)));
XY = numpy.concatenate((numpy.atleast_2d(numpy.ravel(templateX)), numpy.atleast_2d(numpy.ravel(templateY)), numpy.ones([1, numpy.prod(templateIMGSize)])), axis = 0)
transformMatrix = numpy.matrix([[1 + affineParameters[0], affineParameters[2], affineParameters[4]], [affineParameters[1], 1 + affineParameters[3], affineParameters[5]], [0, 0, 1]])
TXY = transformMatrix * XY
#TXY = numpy.take(TXY, [0, 1], axis = 0)
TX = numpy.array(numpy.reshape(numpy.take(TXY, [0], axis = 0), templateIMGSize))
TY = numpy.array(numpy.reshape(numpy.take(TXY, [1], axis = 0), templateIMGSize))
warpedIMG = CCSegUtils.interp2q(numpy.arange(1, targetIMG.shape[1] + 1), numpy.arange(1, targetIMG.shape[0] + 1), targetIMG, TX, TY, extrapval = 0)
return (warpedIMG, TX, TY)
def thicknessCC(outputBase, groundTruthFile = None, numThicknessNodes = 100, doGraphics = False):
assert(isinstance(numThicknessNodes, int) and numThicknessNodes > 0),"number of thickness nodes must be non-zero, positive and of type int"
segMATFile = outputBase + "_seg.hdf5"
segManeditMATFile = outputBase + "_seg_manedit.hdf5"
assert(os.path.isfile(segMATFile)),"Seg mat file not found: " + segMATFile
(outputDir, tail) = os.path.split(outputBase)
subjectID = tail
FID = h5py.File(segMATFile, 'r')
seg = dict()
seg['IMG'] = numpy.array(FID['IMG']);
#seg['initialSeg'] = numpy.array(FID['initialSeg']) > 0
seg['finalSeg'] = numpy.array(FID['finalSeg']) > 0
seg['finalSegNoArtefacts'] = numpy.array(FID['finalSegNoArtefacts']) > 0 # the greater than 0 is to convert it to a boolean array
seg['templatePixdims'] = numpy.array(FID['templatePixdims'])
#print seg['templatePixdims']
FID.close()
#print seg['IMG'].dtype
#pylab.subplot(1, 4, 1); CCSegUtils.showIMG(seg['initialSeg'])
#pylab.subplot(1, 4, 2); CCSegUtils.showIMG(seg['finalSeg'])
#pylab.subplot(1, 4, 3); CCSegUtils.showIMG(seg['finalSegNoArtefacts'])
#pylab.subplot(1, 4, 4); CCSegUtils.showIMG(seg['IMG'])
#pylab.gcf().set_size_inches((20, 10), forward = True)
#pylab.show()
#quit()
if os.path.isfile(segManeditMATFile):
print "using man edit seg"
FID = h5py.File(segManeditMATFile, 'r')
finalSeg = numpy.array(FID['finalSegManEdit']) > 0
FID.close()
else:
finalSeg = numpy.array(seg['finalSeg'])
if doGraphics:
outputPNG = os.path.join(outputDir, 'endpoint', subjectID + "_endpoints.png")
else:
outputPNG = None
try:
finalContours = LaplaceThicknessMethod.endpointsFind(finalSeg, outputPNG = outputPNG)
except Exception as e:
raise(e)
#return
xx, yy, scaledContours, streamlines, validStreamlines, solvedImage = LaplaceThicknessMethod.laplaceEquation2DContours(finalContours['xi'], finalContours['yi'], finalContours['xo'][::-1], finalContours['yo'][::-1], seg['templatePixdims'][0], seg['templatePixdims'][1], 1.0 / numpy.min(seg['templatePixdims']), 100, redoFactorisation = True)
startV = numpy.zeros((2, numThicknessNodes))
# make start points for each streamline
for z in range(numThicknessNodes):
D = numpy.diff(streamlines[z], axis = 1)
cumArcLength = numpy.cumsum(numpy.sqrt(numpy.sum(D * D, axis = 0)))
cumArcLength = cumArcLength / cumArcLength[-1]
cumArcLength = numpy.concatenate((numpy.array([0]), cumArcLength))
startV[0, z] = numpy.interp(0.5, cumArcLength, streamlines[z][0])
startV[1, z] = numpy.interp(0.5, cumArcLength, streamlines[z][1])
thicknessProfile = numpy.zeros((numThicknessNodes))
for z in range(numThicknessNodes):
D = numpy.diff(streamlines[z], axis = 1)
thicknessProfile[z] = numpy.sum(numpy.sqrt(numpy.sum(D * D, axis = 0)))
# here, we need to scale if we are using the longitudinal method
FID = h5py.File(outputBase + "_midsag.hdf5", 'r')
MSPMethod = FID['MSPMethod'].value
if MSPMethod == 'long':
flirtMAT = numpy.matrix(numpy.array(FID['flirtMAT']))
(rotmat, skew, scales, transl, angles) = FLIRT.fsl_decomp_aff(flirtMAT)
scales = numpy.diag(scales)
D = numpy.abs(scales[0] - scales)
if numpy.any(D > 1e-5):
print "Scaling constants are not equal, this should not happen, using mean anyway"
globalScale = numpy.mean(scales)
print "global scale: " + str(globalScale)
thicknessProfile = thicknessProfile / globalScale
FID.close()
thicknessProfile[numpy.logical_not(validStreamlines)] = 0
registeredThicknessProfile = registerProfile(thicknessProfile)
if doGraphics:
PNGDirectory = os.path.join(outputDir, "thickness")
try:
os.makedirs(PNGDirectory)
except OSError as exc: # Python >2.5
if exc.errno == errno.EEXIST and os.path.isdir(PNGDirectory):
pass
else:
raise Exception
outputPNG = os.path.join(PNGDirectory, subjectID + "_thickness.png")
pylab.clf()
pylab.subplot(2, 1, 1)
for z in range(len(streamlines)):
if validStreamlines[z] == True:
lineProps = {'color': 'b', 'linewidth': 2}
else:
lineProps = {'color': 'm', 'linewidth': 2}
CCSegUtils.plotContour(streamlines[z], closed = False, lineProps = lineProps)
if numpy.mod(z, 5) == 0:
#pylab.text(streamlines[z][0, 0], streamlines[z][1, 0], str(z))startV[0, z], startV[1, z]
pylab.text(startV[0, z], startV[1, z], str(z), horizontalalignment='center', verticalalignment='center', backgroundcolor='w')
#CCSegUtils.plotContour(streamlinesOuter[z], closed = False)
#CCSegUtils.plotContour(streamlinesInner[z], closed = False)
lineProps = {'color': 'g', 'linewidth': 2}
pylab.plot(scaledContours['inner'][0], scaledContours['inner'][1], **lineProps)
lineProps = {'color': 'r', 'linewidth': 2}
pylab.plot(scaledContours['outer'][0], scaledContours['outer'][1], **lineProps)
pylab.gca().invert_yaxis()
pylab.gca().get_xaxis().set_ticks([])
pylab.gca().get_yaxis().set_ticks([])
pylab.title('Streamlines')
pylab.subplot(2, 1, 2)
thicknessProfilePlot, = pylab.plot(thicknessProfile)
registeredThicknessProfilePlot, = pylab.plot(registeredThicknessProfile)
pylab.legend([thicknessProfilePlot, registeredThicknessProfilePlot], ['Original thickness profile', 'Registered thickness profile'], loc = 9)
pylab.title('Thickness profile')
pylab.xlabel('Node')
pylab.ylabel('Thickness (mm)')
#pylab.subplot(1, 2, 2); CCSegUtils.showIMG(FY, extent = [xx[0], xx[-1], yy[0], yy[-1]], ticks = True);
#for z in range(numpy.size(sxi)):
# CCSegUtils.plotContour(streamlinesOuter[z], closed = False)
# CCSegUtils.plotContour(streamlinesInner[z], closed = False)
#pylab.plot(scaledxi[0], scaledyi[0])
#pylab.plot(scaledxo[0], scaledyo[0])
#print scaledxi
#print scaledyi
# CCSegUtils.showIMG(FX)
#print outputPNG
pylab.savefig(outputPNG)
CCSegUtils.cropAutoWhitePNG(outputPNG)
#pylab.gcf().set_size_inches((20, 10), forward = True)
#pylab.show()
#quit()
# perform Witelson and "Hofer and Frahm" parcellations on the CCs, output parcellations of the streamlines
#../witelson_hoferfrahm_parcellation_schemes.png
# first, get the leftmost and rightmost pixels
maskClosed = numpy.isfinite(solvedImage)
I = numpy.where(maskClosed)
minCol = numpy.min(I[1])
maxCol = numpy.max(I[1])
minColRow = numpy.mean(I[0][numpy.where(I[1] == minCol)])
maxColRow = numpy.mean(I[0][numpy.where(I[1] == maxCol)])
pylab.clf()
minColX = xx[minCol]
minColY = yy[minColRow]
maxColX = xx[maxCol]
maxColY = yy[maxColRow]
# get the slope of the line, rise over run
cropLineM = (maxColY - minColY) / (maxColX - minColX)
# get the Y intercept
cropLineC = minColY - (minColX * cropLineM)
#print str(cropLineM) + " * X + " + str(cropLineC)
X, Y = numpy.meshgrid(xx, yy)
midLineCross = Y - (cropLineM * X + cropLineC)
#midLineCross = numpy.sign(midLineCross)
witelsonLabels = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
hoferFrahmLabels = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
emsellLabels = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
I = numpy.where(maskClosed)
midLineCrossInMask = midLineCross[I]
midLineCrossInMaskIMG = numpy.array(midLineCross)
midLineCrossInMaskIMG[numpy.logical_not(maskClosed)] = numpy.nan
validX = X[I]
validY = Y[I]
# according to the witelson and HoferFrahm parcellations, the lines of division are perpendicular to the line that cuts the CC
# find the scalar projection of the vector go)ing from (minColX, minColY) to (validX, validY) on (minColX, minColY) -> (maxColX, maxColY)
# construct vectors A and B, the scalar projection is A . B / |B|^2
AX = validX - minColX
AY = validY - minColY
BX = maxColX - minColX
BY = maxColY - minColY
antPostProportion = (AX * BX + AY * BY) / (BX * BX + BY * BY)
del AX
del AY
del BX
del BY
# because our images are posterior to anterior, we need to invert the direction, i.e.:
antPostProportion = 1.0 - antPostProportion
witelsonI = numpy.zeros(validX.shape, dtype = numpy.uint8)
witelsonI[numpy.where(antPostProportion < (1.0 / 3.0))] = 1
witelsonI[numpy.where(numpy.logical_and(antPostProportion < (1.0 / 2.0), witelsonI == 0))] = 2
witelsonI[numpy.where(numpy.logical_and(antPostProportion < (2.0 / 3.0), witelsonI == 0))] = 3
witelsonI[numpy.where(numpy.logical_and(antPostProportion < (4.0 / 5.0), witelsonI == 0))] = 4
witelsonI[numpy.where(witelsonI == 0)] = 5
witelsonI[midLineCrossInMask > 0] = 0
#SIMG = numpy.zeros(maskClosed.shape)
#SIMG[I] = witelsonI
witelsonLabels[I] = witelsonI
hoferFrahmI = numpy.zeros(validX.shape, dtype = numpy.uint8)
hoferFrahmI[numpy.where(antPostProportion < (1.0 / 6.0))] = 1
hoferFrahmI[numpy.where(numpy.logical_and(antPostProportion < (1.0 / 2.0), hoferFrahmI == 0))] = 2
hoferFrahmI[numpy.where(numpy.logical_and(antPostProportion < (2.0 / 3.0), hoferFrahmI == 0))] = 3
hoferFrahmI[numpy.where(numpy.logical_and(antPostProportion < (3.0 / 4.0), hoferFrahmI == 0))] = 4
hoferFrahmI[numpy.where(hoferFrahmI == 0)] = 5
hoferFrahmI[midLineCrossInMask > 0] = 0
hoferFrahmLabels[I] = hoferFrahmI
emsellI = numpy.zeros(validX.shape, dtype = numpy.uint8)
emsellI[numpy.where(antPostProportion < (1.0 / 6.0))] = 2
emsellI[numpy.where(numpy.logical_and(antPostProportion < (1.0 / 3.0), numpy.logical_and(emsellI == 0, midLineCrossInMask <= 0)))] = 3
emsellI[numpy.where(numpy.logical_and(antPostProportion < (1.0 / 2.0), numpy.logical_and(emsellI == 0, midLineCrossInMask <= 0)))] = 4
emsellI[numpy.where(numpy.logical_and(antPostProportion < (2.0 / 3.0), numpy.logical_and(emsellI == 0, midLineCrossInMask <= 0)))] = 5
emsellI[numpy.where(numpy.logical_and(antPostProportion < (4.0 / 5.0), numpy.logical_and(emsellI == 0, midLineCrossInMask <= 0)))] = 6
emsellI[numpy.where(numpy.logical_and(emsellI == 0, midLineCrossInMask <= 0))] = 7
emsellI[numpy.where(numpy.logical_and(emsellI == 0, antPostProportion > (1.0 / 2.0)))] = 8
# we need to find the apex of the genu
# it is the pixel closest to the rightmost element of the inferior boundary
# firstly find out which contour is the inferior contour
# it is the contour whose minimum y coordinate is greatest
if numpy.min(scaledContours['inner'][1]) > numpy.min(scaledContours['outer'][1]):
inferiorContourXY = numpy.array(scaledContours['inner'])
else:
inferiorContourXY = numpy.array(scaledContours['outer'])
#print scaledContours
# find the rightmost point
rightMostInnerXY = numpy.take(inferiorContourXY, [numpy.argmax(inferiorContourXY[0])], axis = 1)
# get the anterior-posterior proportion that is closest to this point
rightMostInnerXYClosestIDX = numpy.argmin(numpy.abs(rightMostInnerXY[0] - validX) + numpy.abs(rightMostInnerXY[1] - validY))
antPostProportionClosest = antPostProportion[rightMostInnerXYClosestIDX]
midLineCrossInMaskClosest = midLineCrossInMask[rightMostInnerXYClosestIDX]
emsellI[numpy.where(numpy.logical_and(numpy.logical_and(antPostProportion > antPostProportionClosest, antPostProportion < (1.0 / 2.0)), midLineCrossInMask > midLineCrossInMaskClosest))] = 1
################### THIS DOESNT ALWAYS WORK ######################## NEW METHOD ABOVE
# it is the pixel with the highest S value in the right half on the 0 contour of midLineCrossInMask
# if pixels on 0 contour of midLineCrossInMask
# make midLineCrossInMask image
#midLineCrossInMaskIMG = numpy.zeros(maskClosed.shape)
#midLineCrossInMaskIMG.fill(numpy.inf)
# make SIMG
#IMG = numpy.zeros(maskClosed.shape)
#IMG.fill(numpy.nan)
#midLineCrossInMaskIMG[I] = midLineCrossInMask
#IMG[I] = S
# the roll shifts elements down one row, so this says pixelsAtSignChangeIMG[I, J] = midLineCrossInMaskIMG[I, J] == 1 && midLineCrossInMaskIMG[I - 1, J] == -1
#pixelsAtSignChangeIMG = numpy.logical_and(midLineCrossInMaskIMG == 1, numpy.roll(midLineCrossInMaskIMG, 1, axis = 0) < 1)
#pixelsAtSignChange = pixelsAtSignChangeIMG[I]
# find highest S in the right half
#SAtPixelsAtSignChange = S[pixelsAtSignChange]
#R = 1
#SC = 1
#pylab.subplot(SR, SC, 1)
#CCSegUtils.showIMG(FY, extent = [xx[0], xx[-1], yy[0], yy[-1]], ticks = True);
#CCSegUtils.showIMG(midLineCrossInMaskIMG, extent = [xx[0], xx[-1], yy[0], yy[-1]], ticks = True)
#pylab.plot(inferiorContourXY[0, rightMostIDX], inferiorContourXY[1, rightMostIDX], 'r*')
# pylab.colorbar()
# pylab.subplot(SR, SC, 2)
# CCSegUtils.showIMG(midLineCrossInMaskIMG == 1)
#
# pylab.subplot(SR, SC, 3)
# CCSegUtils.showIMG(pixelsAtSignChangeIMG)
#
#pylab.gcf().set_size_inches((20, 10), forward = True)
#pylab.show()
#quit()
#
# try:
# SAtApex = numpy.max(SAtPixelsAtSignChange[SAtPixelsAtSignChange < (1.0 / 2.0)])
# print "Proportion at rostrum apex: " + str(SAtApex)
# emsellI[numpy.where(numpy.logical_and(numpy.logical_and(S > SAtApex, S < (1.0 / 2.0)), midLineCrossInMask > 0))] = 1
# except Exception:
# print "Rostrum apex not found, region 1 will be empty"
#
emsellLabels[I] = emsellI
# make RGB images
witelsonRGB = numpy.tile(numpy.atleast_3d(numpy.double(maskClosed)), (1, 1, 3))
hoferFrahmRGB = numpy.tile(numpy.atleast_3d(numpy.double(maskClosed)), (1, 1, 3))
emsellRGB = numpy.tile(numpy.atleast_3d(numpy.double(maskClosed)), (1, 1, 3))
#witelsonIMG = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
#hoferFrahmIMG = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
#emsellIMG = numpy.zeros(maskClosed.shape, dtype = numpy.uint8)
#witelsonIMG[I] = witelsonLabels
#hoferFrahmIMG[I] = hoferFrahmLabels
#emsellIMG[I] = emsellLabels
CMAP = numpy.array([[1, 1, 1], [1, 0, 0], [0, 0.5, 0], [0, 0, 1], [1, 1, 0], [1, 0, 1], [0.5, 0, 0], [0, 1, 1], [1, 0, 0.5]])
#emsellLabels = numpy.mod(emsellLabels, CMAP.shape[0])
for z in range(3):
T = witelsonRGB[:, :, z]
T[I] = CMAP[witelsonLabels[I], z]
witelsonRGB[:, :, z] = T
T = hoferFrahmRGB[:, :, z]
T[I] = CMAP[hoferFrahmLabels[I], z]
hoferFrahmRGB[:, :, z] = T
T = emsellRGB[:, :, z]
T[I] = CMAP[emsellLabels[I], z]
emsellRGB[:, :, z] = T
del T
del I
del witelsonI
del hoferFrahmI
del emsellI
#CCSegUtils.showIMG(maskClosed, extent = [xx[0], xx[-1], yy[0], yy[-1]])
#pylab.subplot(2, 1, 1)
#CCSegUtils.showIMG(witelsonRGB, extent = [xx[0], xx[-1], yy[0], yy[-1]])
#pylab.title('Witelson parcellation')
#pylab.subplot(2, 1, 2)
#CCSegUtils.showIMG(hoferFrahmRGB, extent = [xx[0], xx[-1], yy[0], yy[-1]])
#pylab.title('Hofer and Frahm parcellation')
#pylab.plot(xx, cropLineM * xx + cropLineC, 'b-')
#pylab.plot(minColX, minColY, 'g*')
#pylab.plot(maxColX, maxColY, 'r*')
#pylab.gcf().set_size_inches((20, 10), forward = True)
#pylab.show()
#pylab.savefig(outputPNG)
witelsonNodeLabels = CCSegUtils.interp2q(xx, yy, numpy.double(witelsonLabels), startV[0], startV[1], interpmethod = 'nearest')
witelsonNodeLabels = numpy.uint8(witelsonNodeLabels)
hoferFrahmNodeLabels = CCSegUtils.interp2q(xx, yy, numpy.double(hoferFrahmLabels), startV[0], startV[1], interpmethod = 'nearest')
hoferFrahmNodeLabels = numpy.uint8(hoferFrahmNodeLabels)
emsellNodeLabels = CCSegUtils.interp2q(xx, yy, numpy.double(emsellLabels), startV[0], startV[1], interpmethod = 'nearest')
emsellNodeLabels = numpy.uint8(emsellNodeLabels)
if doGraphics:
pylab.clf()
lineProps = {'color': 'y', 'linewidth': 2}
SR = 3
SC = 1
pylab.subplot(SR, SC, 1)
CCSegUtils.showIMG(witelsonRGB, extent = [xx[0], xx[-1], yy[0], yy[-1]])
for z in range(numThicknessNodes):
pylab.text(startV[0, z], startV[1, z], str(witelsonNodeLabels[z]), horizontalalignment='center', verticalalignment='center')
CCSegUtils.plotStreamlines(streamlines, lineProps = lineProps)
pylab.title('Witelson parcellation')
pylab.subplot(SR, SC, 2)
CCSegUtils.showIMG(hoferFrahmRGB, extent = [xx[0], xx[-1], yy[0], yy[-1]])
for z in range(numThicknessNodes):
pylab.text(startV[0, z], startV[1, z], str(hoferFrahmNodeLabels[z]), horizontalalignment='center', verticalalignment='center')
CCSegUtils.plotStreamlines(streamlines, lineProps = lineProps)
pylab.title('Hofer and Frahm parcellation')
pylab.subplot(SR, SC, 3)
CCSegUtils.showIMG(emsellRGB, extent = [xx[0], xx[-1], yy[0], yy[-1]])
for z in range(numThicknessNodes):
pylab.text(startV[0, z], startV[1, z], str(emsellNodeLabels[z]), horizontalalignment='center', verticalalignment='center')
CCSegUtils.plotStreamlines(streamlines, lineProps = lineProps)
pylab.title('Emsell parcellation')
parcellationPNGDirectory = os.path.join(outputDir, "parcellations")
try:
os.makedirs(parcellationPNGDirectory)
except OSError as exc: # Python >2.5
if exc.errno == errno.EEXIST and os.path.isdir(parcellationPNGDirectory):
pass
else:
raise Exception
outputPNG = os.path.join(parcellationPNGDirectory, subjectID + "_parcellations.png")
pylab.gcf().set_size_inches((20, 10), forward = True)
#pylab.show()
#quit()
pylab.savefig(outputPNG)
CCSegUtils.cropAutoWhitePNG(outputPNG)
pixelArea = (xx[1] - xx[0]) * (yy[1] - yy[0])
# now do the stats
witelsonStats = CCSegUtils.parcellationStats(witelsonLabels, pixelArea, thicknessProfile, witelsonNodeLabels)
hoferFrahmStats = CCSegUtils.parcellationStats(hoferFrahmLabels, pixelArea, thicknessProfile, hoferFrahmNodeLabels)
emsellStats = CCSegUtils.parcellationStats(emsellLabels, pixelArea, thicknessProfile, emsellNodeLabels)
#print witelsonStats
#print hoferFrahmStats
#quit()
outputMAT = outputBase + "_thickness.hdf5"
FID = h5py.File(outputMAT, 'w')
FID.create_dataset("xx", data = xx, compression = 'gzip')
FID.create_dataset("yy", data = yy, compression = 'gzip')
finalContoursGroup = FID.create_group("finalContours")
finalContoursGroup.create_dataset("inner", data = scaledContours['inner'], compression = 'gzip')
finalContoursGroup.create_dataset("outer", data = scaledContours['outer'], compression = 'gzip')
#FID.create_dataset("startV", data = startV, compression = 'gzip')
FID.create_dataset("validStreamlines", data = numpy.uint8(validStreamlines), compression = 'gzip')
FID.create_dataset("thicknessProfile", data = thicknessProfile, compression = 'gzip')
FID.create_dataset("registeredThicknessProfile", data = registeredThicknessProfile, compression = 'gzip')
streamlinesGroup = FID.create_group("streamlines")
for z in range(numThicknessNodes):
streamlinesGroup.create_dataset(str(z), data = streamlines[z], compression = 'gzip')
FID.create_dataset("solvedImage", data = solvedImage, compression = 'gzip')
FID.create_dataset("witelsonLabels", data = witelsonLabels, compression = 'gzip')
FID.create_dataset("witelsonNodeLabels", data = witelsonNodeLabels, compression = 'gzip')
witelsonGroup = FID.create_group("witelsonStats")
for curKey in witelsonStats.iterkeys():
witelsonGroup.create_dataset(curKey, data = witelsonStats[curKey], compression = 'gzip')
FID.create_dataset("hoferFrahmLabels", data = hoferFrahmLabels, compression = 'gzip')
FID.create_dataset("hoferFrahmNodeLabels", data = hoferFrahmNodeLabels, compression = 'gzip')
hoferFrahmGroup = FID.create_group("hoferFrahmStats")
for curKey in hoferFrahmStats.iterkeys():
hoferFrahmGroup.create_dataset(curKey, data = hoferFrahmStats[curKey], compression = 'gzip')
FID.create_dataset("emsellLabels", data = emsellLabels, compression = 'gzip')
FID.create_dataset("emsellNodeLabels", data = emsellNodeLabels, compression = 'gzip')
emsellGroup = FID.create_group("emsellStats")
for curKey in emsellStats.iterkeys():
emsellGroup.create_dataset(curKey, data = emsellStats[curKey], compression = 'gzip')
FID.create_dataset("startV", data = startV, compression = 'gzip')
#FID.create_dataset("maskClosed", data = maskClosed, compression = 'gzip')
FID.close()
def segCCToNativeOneFile(segIMG, outputBase, midSagMATFile, segMATFile, dilateToParaSag = False, flirtInterpType = 'trilinear'): FID = h5py.File(segMATFile, 'r') resampledAVWShape = numpy.array(FID['resampledAVWShape']) LKCropRows = numpy.array(FID['LKCropRows']) LKCropCols = numpy.array(FID['LKCropCols']) midSagAVWxx = numpy.array(FID['midSagAVWxx']) midSagAVWyy = numpy.array(FID['midSagAVWyy']) resamplexx = numpy.array(FID['resamplexx']) resampleyy = numpy.array(FID['resampleyy']) #print seg['templatePixdims'] FID.close() #print seg['IMG'].dtype FID = h5py.File(midSagMATFile, 'r') MSPMethod = str(numpy.array(FID['MSPMethod'])) FID.close() 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'])) flirtTemplateFile = str(numpy.array(FID['flirtTemplateFile'])) if flirtTemplateFile == "***": flirtTemplateFile = CCSegUtils.MNI152FLIRTTemplate() flirtMAT = numpy.array(FID["flirtMAT"]) # the transformation between originalNativeCroppedFile -> flirtTemplateFile flirtCropZerosRows = numpy.array(FID["flirtCropZerosRows"]) flirtCropZerosCols = numpy.array(FID["flirtCropZerosCols"]) #midSagAVW = midSagAVW[:, ::-1] #midSagAVW = numpy.rot90(midSagAVW, -1) FID.close() if not numpy.array_equal(flirtMAT.shape, (4, 4)): print "the flirt matrix should be a 4x4 array, it is not" return del FID #pylab.subplot(1, 4, 1); CCSegUtils.showIMG(seg['initialSeg']) #pylab.subplot(1, 4, 2); CCSegUtils.showIMG(seg['finalSeg']) #pylab.subplot(1, 4, 3); CCSegUtils.showIMG(seg['finalSegNoArtefacts']) #pylab.subplot(1, 4, 4); CCSegUtils.showIMG(seg['IMG']) finalSegResampledAVWSpace = numpy.zeros(resampledAVWShape, dtype = numpy.uint8) #finalSegResampledAVWSpace[LKOutput['cropRows'], LKOutput['cropCols']] = finalSeg finalSegResampledAVWSpace[LKCropRows[0]:(LKCropRows[1] + 1), LKCropCols[0]:(LKCropCols[1] + 1)] = segIMG midSagAVWX, midSagAVWY = numpy.meshgrid(midSagAVWxx, midSagAVWyy) finalSegMidSagAVWSpace = CCSegUtils.interp2q(resamplexx, resampleyy, numpy.double(finalSegResampledAVWSpace), midSagAVWX, midSagAVWY, interpmethod = 'nearest', extrapval = 0) flirtTemplateNII = nibabel.load(flirtTemplateFile) #print finalSegMidSagAVWSpace.shape finalSegTemplateSpace = numpy.zeros((flirtTemplateNII.shape[2], flirtTemplateNII.shape[1]), dtype = numpy.uint8) #print finalSegTemplateSpace.shape finalSegTemplateSpace[flirtCropZerosRows[0]:(flirtCropZerosRows[-1] + 1), flirtCropZerosCols[0]:(flirtCropZerosCols[-1] + 1)] = finalSegMidSagAVWSpace finalSegTemplateSpaceNIIData = numpy.zeros((flirtTemplateNII.shape[1], flirtTemplateNII.shape[0], flirtTemplateNII.shape[2]), dtype = numpy.uint8) #NIIData = flirtTemplateNII.get_data() #NIIData = numpy.rot90(NIIData, 1) #print "flirt template: " + flirtTemplateFile T = math.floor(flirtTemplateNII.shape[0] / 2) #print flirtTemplateNII #print finalSegTemplateSpaceNIIData.shape #print finalSegTemplateSpace.shape finalSegTemplateSpaceNIIData[:, T] = numpy.rot90(finalSegTemplateSpace[:, ::-1], -1) if dilateToParaSag == True: finalSegTemplateSpaceNIIData[:, T - 1] = numpy.rot90(finalSegTemplateSpace[:, ::-1], -1) finalSegTemplateSpaceNIIData[:, T + 1] = numpy.rot90(finalSegTemplateSpace[:, ::-1], -1) finalSegTemplateSpaceNIIData = numpy.uint8(numpy.rot90(finalSegTemplateSpaceNIIData, -1)) newNII = nibabel.Nifti1Image(finalSegTemplateSpaceNIIData, flirtTemplateNII.get_affine()) NIITempDir = tempfile.mkdtemp() nibabel.save(newNII, os.path.join(NIITempDir, 'test.nii.gz')) invFlirtMAT = numpy.linalg.inv(flirtMAT) numpy.savetxt(os.path.join(NIITempDir, 'test.mat'), invFlirtMAT, fmt = '%.18f') # run flirt to project the segmentation to native space CommandString = os.environ['FSLDIR'] + '/bin/flirt -in ' + os.path.join(NIITempDir, 'test') + ' -ref ' + originalNativeCroppedFile + ' -applyxfm -init ' + os.path.join(NIITempDir, 'test.mat') + ' -interp ' + flirtInterpType + ' -out ' + (outputBase + "_native_axial_cropped.nii.gz") #print CommandString os.system(CommandString) segNativeCroppedNII = nibabel.load((outputBase + "_native_axial_cropped.nii.gz")) originalNativeNII = nibabel.load(originalNativeFile) finalSegNativeNIIData = numpy.zeros(originalNativeNII.shape, dtype = segNativeCroppedNII.get_data().dtype) finalSegNativeNIIData = numpy.rot90(finalSegNativeNIIData, 1) finalSegNativeNIIData[skullCrop[0, 0]:(skullCrop[0, 1] + 1), skullCrop[1, 0]:(skullCrop[1, 1] + 1), skullCrop[2, 0]:(skullCrop[2, 1] + 1)] = numpy.rot90(segNativeCroppedNII.get_data(), 1) finalSegNativeNIIData = numpy.rot90(finalSegNativeNIIData, -1) #print skullCrop finalSegNativeSpaceNII = nibabel.Nifti1Image(finalSegNativeNIIData, originalNativeNII.get_affine()) nibabel.save(finalSegNativeSpaceNII, (outputBase + "_native_axial.nii.gz")) os.system(os.environ['FSLDIR'] + '/bin/fslswapdim ' + (outputBase + "_native_axial.nii.gz") + ' ' + originalOrientationString + ' ' + (outputBase + "_native.nii.gz")) shutil.rmtree(NIITempDir) del newNII del T
def segCCToNative(outputBase, doGraphics = False, dilateToParaSag = False): midSagMATFile = outputBase + "_midsag.hdf5" assert(os.path.isfile(midSagMATFile)),"midsag hdf5 file not found" segMATFile = outputBase + "_seg.hdf5" segManeditMATFile = outputBase + "_seg_manedit.hdf5" #finalSeg = numpy.array(seg['finalSeg']) assert(os.path.isfile(segMATFile)),"Seg mat file not found: " + segMATFile FID = h5py.File(segMATFile, 'r') autoFinalSeg = numpy.array(FID['finalSegNoArtefacts']) templatePixdims = numpy.array(FID['templatePixdims']) #print seg['templatePixdims'] FID.close() #print seg['IMG'].dtype #pylab.subplot(1, 4, 1); CCSegUtils.showIMG(seg['initialSeg']) #pylab.subplot(1, 4, 2); CCSegUtils.showIMG(seg['finalSeg']) #pylab.subplot(1, 4, 3); CCSegUtils.showIMG(seg['finalSegNoArtefacts']) #pylab.subplot(1, 4, 4); CCSegUtils.showIMG(seg['IMG']) #pylab.gcf().set_size_inches((20, 10), forward = True) #pylab.show() #quit() if os.path.isfile(segManeditMATFile): FID = h5py.File(segManeditMATFile, 'r') finalSeg = numpy.array(FID['finalSegManEdit']) > 0 FID.close() else: finalSeg = numpy.array(autoFinalSeg) segCCToNativeOneFile(numpy.uint8(finalSeg), outputBase + "_seg", midSagMATFile, segMATFile, dilateToParaSag = dilateToParaSag) #print finalSeg.shape thicknessMATFile = outputBase + "_thickness.hdf5" if os.path.isfile(thicknessMATFile): finalSegxx = numpy.arange(finalSeg.shape[1]) finalSegyy = numpy.arange(finalSeg.shape[0]) finalSegX, finalSegY = numpy.meshgrid(finalSegxx, finalSegyy) FID = h5py.File(thicknessMATFile, 'r') labelNames = ['witelson', 'hoferFrahm', 'emsell'] for curLabels in labelNames: curLabelIMG = numpy.array(FID[curLabels + 'Labels']) # for the parcellations, we need to get the parcellation images in the same space as the segmentation images # so we resample the parcellation image using the grid of the segmentation image, we need to reverse a scaling that was performed in the thickness part: curLabelIMG = CCSegUtils.interp2q(numpy.array(FID['xx']) / templatePixdims[0], numpy.array(FID['yy']) / templatePixdims[1], numpy.double(curLabelIMG), finalSegX, finalSegY, interpmethod = 'nearest', extrapval = 0) #SR = 1 #SC = 3 #pylab.subplot(SR, SC, 1); CCSegUtils.showIMG(finalSeg) #pylab.subplot(SR, SC, 2); CCSegUtils.showIMG(curLabelIMG) #pylab.subplot(SR, SC, 3); CCSegUtils.showIMG(T) #pylab.gcf().set_size_inches((20, 10), forward = True) #pylab.show() #quit() segCCToNativeOneFile(numpy.uint8(curLabelIMG), outputBase + "_parcellation_" + curLabels.lower(), midSagMATFile, segMATFile, flirtInterpType = 'nearestneighbour', dilateToParaSag = dilateToParaSag) FID.close()
