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 steepestDescentImagesAffineDisplay(SDImages, IMGSize): IMG = list() for z in range(SDImages.shape[1]): IMG.append(numpy.reshape(numpy.take(SDImages, [z], axis = 1), IMGSize)) IMG = numpy.concatenate(IMG, axis = 1) CCSegUtils.showIMG(IMG);
def jacobianAffineDisplay(jacobian, IMGSize): #% Displays the jacobian as an image in the current plot using imshow #IMG = cell(2, 6); # list of two empty lists IMG = list() IMG.append([]) IMG.append([]) for z in range(len(jacobian)): #for CurParameter = 1:6 IMG[0].append(numpy.reshape(jacobian[z][0, :], IMGSize)) IMG[1].append(numpy.reshape(jacobian[z][1, :], IMGSize)) IMG = numpy.concatenate((numpy.concatenate(IMG[0], axis = 1), numpy.concatenate(IMG[1], axis = 1)), axis = 0) #IMG = cell2mat(IMG); CCSegUtils.showIMG(IMG)
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 selectSubjectsFromOpts(inputDirectory, opts = None):
singleSubject = None
subjectsIncludeFile = None
subjectsExcludeFile = None
subjectsIncludeListArg = None
subjectsExcludeListArg = None
for o, a in opts:
if o == '--subjects-include':
subjectsIncludeListArg = a.split(',')
if o == '--subjects-exclude':
subjectsExcludeListArg = a.split(',')
if o == '--subjects-include-file':
subjectsIncludeFile = a
if o == '--subjects-exclude-file':
subjectsExcludeFile = a
if o == '--single-subject':
singleSubject = a
#print "inputDirectory"
#print inputDirectory
#print "subjectsIncludeFile"
#print subjectsIncludeFile
#print "subjectsExcludeFile"
#print subjectsExcludeFile
#print "subjectsIncludeListArg"
#print subjectsIncludeListArg
#print "subjectsExcludeListArg"
#print subjectsExcludeListArg
#print "singleSubject"
#print singleSubject
subjectsInclude = None
if subjectsIncludeFile != None:
print "using include file: " + subjectsIncludeFile
if not os.path.isfile(subjectsIncludeFile):
criticalError("The subjects include file was given, but the file was not found")
fp = open(subjectsIncludeFile, 'r')
subjectsInclude = fp.readlines()
subjectsInclude = map(lambda s: s.strip(), subjectsInclude)
fp.close()
subjectsExclude = None
if subjectsExcludeFile != None:
print "using exclude file: " + subjectsExcludeFile
if not os.path.isfile(subjectsExcludeFile):
criticalError("The subjects exclude file was given, but the file was not found")
fp = open(subjectsExcludeFile, 'r')
subjectsExclude = fp.readlines()
subjectsExclude = map(lambda s: s.strip(), subjectsExclude)
fp.close()
if subjectsIncludeListArg != None:
if subjectsInclude != None:
for curSubject in subjectsIncludeListArg:
if curSubject in subjectsInclude:
subjectsInclude.append(curSubject)
else:
subjectsInclude = subjectsIncludeListArg[:]
if subjectsExcludeListArg != None:
if subjectsExclude != None:
for curSubject in subjectsExcludeListArg:
if not curSubject in subjectsExclude:
subjectsExclude.append(curSubject)
else:
subjectsExclude = subjectsExcludeListArg[:]
#print "subjectsInclude = "
#print subjectsInclude
#print "subjectsExclude = "
#print subjectsExclude
# if we are using an include AND exclude lists, remove all elements of the include list that are in the exclude list
if subjectsInclude != None and subjectsExclude != None:
print "Warning, using both include and exclude lists, removing excluded subjects from include list"
subjectsInclude = [x for x in subjectsInclude if not x in subjectsExclude]
# get a list of nifti files in the input directory
inputDirectoryFileList = os.listdir(inputDirectory)
# contains a list of nifti file prefixes for all nii.gz files found in inputDirectory
#inputNIFTIFiles = [x for x in sorted(inputDirectoryFileList) if x.endswith(".nii.gz")]
# remove the .nii.gz
#inputNIFTIFiles = map(lambda s: s[:-7], inputNIFTIFiles)
inputDirectoryFileList = [os.path.join(inputDirectory, x) for x in inputDirectoryFileList]
inputNIFTIFiles = CCSegUtils.imglob(inputDirectoryFileList)
# remove None elements
inputNIFTIFiles = [x for x in inputNIFTIFiles if x != None]
#print "inputNIFTIFiles = "
#print inputNIFTIFiles
# strip the input directory
for z in range(len(inputNIFTIFiles)):
(head, tail) = os.path.split(inputNIFTIFiles[z])
inputNIFTIFiles[z] = tail
del tail
del head
#inputNIFTIFiles = map(lambda s: s[:-7], inputNIFTIFiles)
# replace with CCSegUtils.imglob
if subjectsInclude != None:
inputNIFTIFiles = [x for x in inputNIFTIFiles if x in subjectsInclude]
if subjectsExclude != None:
inputNIFTIFiles = [x for x in inputNIFTIFiles if x not in subjectsExclude]
if singleSubject != None:
if singleSubject in inputNIFTIFiles:
actualInputFiles = [singleSubject]
print "processing single subject: " + singleSubject
else:
criticalError("Single subject was given as: " + singleSubject + ", but the NIFTI file was not found in input directory")
else:
actualInputFiles = inputNIFTIFiles[:]
return sorted(actualInputFiles)
def weightedAffineInvComp(targetIMG, templateIMG, templateWeight, initialParameters, numIterations, targetIMGMask = None):
# Python port of lk_run_affine_for_comp
#% [varargout] = lk_run_affine_for_comp(targetIMG, templateIMG, InitialParameters, NumIterations)
#%
#% LUCAS-KANADE algorithm Inverse Compositional method, affine
#% transformation
#% Registers the image to the template, using composition to update the
#% parameters
#%
#% PARAMETERS
#% targetIMG [M, N]: the input image
#% templateIMG [TM, TN]: the target image
#% InitialParameters [6, 1]: the initial transformation
#% NumIterations [1]: the number of iterations to perform
#%
#% Copyright 2013, Chris Adamson, Murdoch Childrens Research Institute
#% See LICENSE for full license information.
#%
displayStuff = False
if displayStuff == True:
pylab.clf()
pylab.subplot(4, 3, 1); CCSegUtils.showIMG(targetIMG); pylab.title("Image");
pylab.subplot(4, 3, 2); CCSegUtils.showIMG(templateIMG); pylab.title("Template");
FY, FX = numpy.gradient(templateIMG)
templateJacobian = jacobianAffine(templateIMG.shape)
if displayStuff == True:
pylab.subplot(4, 3, 3); CCSegUtils.showIMG(numpy.concatenate((FX, FY), axis = 1)); pylab.title('Template gradients');
pylab.subplot(4, 3, 4); jacobianAffineDisplay(templateJacobian, templateIMG.shape); pylab.title('Template Jacobian');
# % compute steepest descent images
#[SDImages] = lk_sd_images_affine(FX, FY, Jacobian);
SDImages = steepestDescentImagesAffine(FX, FY, templateJacobian)
# TemplateWMatrix = spdiags(TemplateW(:), 0, numel(TemplateW), numel(TemplateW));
templateWeightMatrix = scipy.sparse.spdiags(numpy.ravel(templateWeight), numpy.array([0]), numpy.size(templateWeight), numpy.size(templateWeight))
# H = full(SDImages' * TemplateWMatrix * SDImages);
Hessian = numpy.matrix(SDImages).T * templateWeightMatrix * numpy.matrix(SDImages)
#print Hessian
# SDImages = full(TemplateWMatrix * SDImages);
SDImages = templateWeightMatrix * numpy.matrix(SDImages)
#rint templateWeightMatrix
if displayStuff == True:
pylab.subplot(4, 3, 8); steepestDescentImagesAffineDisplay(SDImages, templateIMG.shape); pylab.title('Steepest descent images');
pylab.subplot(4, 3, 10); CCSegUtils.showIMG(Hessian); pylab.title('Hessian');
curParameters = initialParameters
(targetIMGToTemplate, TX, TY, errorIMG, LKCost) = weightedAffineInvCompWarpCost(targetIMG, templateIMG, templateWeight, curParameters, displayStuff, targetIMGMask = targetIMGMask)
if numpy.isinf(LKCost):
return (curParameters, LKCost)
del targetIMGToTemplate; del TX; del TY;
#[~, ~, ~, ErrorIMG, CostValue] = lk_weighted_run_affine_inv_comp_warpcost(targetIMG, templateIMG, TemplateW, CurParameters, displayStuf f);
# for CurIter = 1:NumIterations
for curIter in range(numIterations):
if(displayStuff == True):
pylab.subplot(4, 3, 7);
CCSegUtils.showIMG(errorIMG); pylab.title('Error Image');
SDUpdate = scipy.linalg.solve(Hessian, numpy.matrix(SDImages).T * numpy.matrix(numpy.atleast_2d(numpy.ravel(errorIMG))).T)
if(displayStuff == True):
pylab.subplot(4, 3, 11);
pylab.cla()
pylab.bar(numpy.arange(0, numpy.size(SDUpdate)), SDUpdate); pylab.title('SD Updates');
# compose the new warp
# make the transformation matrix used to transform the coordinates
curParametersMatrix = numpy.concatenate((numpy.reshape(curParameters, (2, 3), order='F'), numpy.matrix([0, 0, 1])), axis = 0)
curParametersMatrix[0, 0] = curParametersMatrix[0, 0] + 1.0
curParametersMatrix[1, 1] = curParametersMatrix[1, 1] + 1.0
# CurParametersMatrix = [reshape(CurParameters, 2, 3); 0 0 1];
# CurParametersMatrix(1, 1) = CurParametersMatrix(1, 1) + 1;
# CurParametersMatrix(2, 2) = CurParametersMatrix(2, 2) + 1;
SDUpdateMatrix = numpy.concatenate((numpy.reshape(SDUpdate, (2, 3), order = 'F'), numpy.matrix([0, 0, 1])), axis = 0)
SDUpdateMatrix[0, 0] = SDUpdateMatrix[0, 0] + 1.0
SDUpdateMatrix[1, 1] = SDUpdateMatrix[1, 1] + 1.0
#print curParameters
#print curParametersMatrix
#print "SDUpdateMatrix"
#print SDUpdateMatrix
# matrix division, solve composedMatrix * SDUpdateMatrix = curParametersMatrix for composedMatrix
# numpy has no equivalent, so solve for
# SDUpdateMatrix^T * composedMatrix^T = curParametersMatrix
# then traspose the result
composedMatrix = scipy.linalg.solve(SDUpdateMatrix.T, curParametersMatrix.T).T
composedMatrix[0, 0] = composedMatrix[0, 0] - 1.0
composedMatrix[1, 1] = composedMatrix[1, 1] - 1.0
#print "Composed Matrix"
#print composedMatrix
composedMatrix = numpy.take(composedMatrix, [0, 1], axis = 0)
curParameters = numpy.ravel(composedMatrix, order = 'F')
#print curParameters
if(displayStuff == True):
pylab.subplot(4, 3, 12)
pylab.cla()
pylab.bar(numpy.arange(0, numpy.size(curParameters)), curParameters); pylab.title('Parameters');
F = pylab.gcf()
F.set_size_inches((20, 10), forward = True)
(targetIMGToTemplate, TX, TY, errorIMG, LKCost) = weightedAffineInvCompWarpCost(targetIMG, templateIMG, templateWeight, curParameters, displayStuff, targetIMGMask = targetIMGMask)
if numpy.isinf(LKCost):
#print "InfCost"
return (curParameters, LKCost)
if displayStuff == True:
pylab.draw()
pylab.show(block = False)
#quit()
#composedMatrix = curParametersMatrix
# SDUpdateMatrix = [reshape(SDUpdate, 2, 3); 0 0 1];
# SDUpdateMatrix(1, 1) = SDUpdateMatrix(1, 1) + 1;
# SDUpdateMatrix(2, 2) = SDUpdateMatrix(2, 2) + 1;
# %SDUpdateMatrix = inv(SDUpdateMatrix);
#
# %ComposedMatrix = CurParametersMatrix * SDUpdateMatrix;
# ComposedMatrix = CurParametersMatrix / SDUpdateMatrix;
# ComposedMatrix = ComposedMatrix(1:2, :);
# CurParameters = ComposedMatrix(:);
# CurParameters(1) = CurParameters(1) - 1;
# CurParameters(4) = CurParameters(4) - 1;
# %CurParameters = CurParameters + SDUpdate;
#
# ParameterHistory(:, CurIter) = CurParameters;
#
# if(displayStuff == true)
# subplot(4, 3, 12);
# bar(CurParameters); title('Parameters');
# drawnow;
# end
# %disp([num2str(CurIter) ': ' num2str(ObjectiveFunction(CurIter))]);
# %urParameters
# %keyboard;
# [~, ~, ~, ErrorIMG, CostValue] = lk_weighted_run_affine_inv_comp_warpcost(targetIMG, templateIMG, TemplateW, CurParameters, displayStuff);
# end
#
#pylab.show()
return (curParameters, LKCost)
def midsagExtract(inputBase, outputBase, MSPMethod, doGraphics = False):
# check for the presence of FSLDIR in the enviornment variables
assert('FSLDIR' in os.environ),"FSLDIR not set, FSL must be set up"
NIFTIFileName = CCSegUtils.findNIFTIFromPrefix(inputBase)
if NIFTIFileName == None:
print("Something went wrong, the NIFTI file doesnt exist")
quit()
NII = nibabel.load(NIFTIFileName)
#print NII
#print inputBase
# find out if we have a 2D or a 3D image
NIISize = NII.get_shape()
assert(len(NIISize) == 2 or len(NIISize) == 3),"The input NIFTI file is not 2D or 3D: " + inputBase
if len(NIISize) == 2:
#FID.create_dataset("NIIPixdims", data=NIIPixdims, compression = 'gzip')
#FID.create_dataset("midSagAVW", data=midSagAVW, compression = 'gzip')
#FID.create_dataset("MSPMethod", data=MSPMethod)
#FID.create_dataset("originalOrientationString", data=origOrientationString)
#FID.create_dataset("originalNativeFile", data=(outputBase + "_native.nii.gz"))
#FID.create_dataset("skullCrop", data=skullCrop)
#FID.create_dataset("originalNativeCroppedFile", data=(outputBase + "_native_cropped.nii.gz"))
#FID.create_dataset("flirtMAT", data=flirtMAT)
#FID.create_dataset("flirtTemplateFile", data=flirtTemplateFile)
#FID.create_dataset("flirtCropZerosRows", data=flirtCropZerosRows)
#FID.create_dataset("flirtCropZerosCols", data=flirtCropZerosCols)
print "2D input not supported yet"
quit()
# 2D image, so it is already the midsagittal plane
else:
# 3D image
outputMAT = outputBase + "_midsag.hdf5"
(head, tail) = os.path.split(outputBase)
if doGraphics:
PNGDirectory = os.path.join(head, "midsag")
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, tail + "_midsag.png")
del head; del tail;
# use FSLORIENT to get the RADIOLOGICAL/NEUROLOGICAL orientation of the image
# we may not need this
NIIPixdims = NII.get_header().get_zooms()[1:3]
if MSPMethod == 'long':
# testing
(head, subjectID) = os.path.split(outputBase)
stdMat = os.path.join(head, subjectID + "_to_std.mat")
assert(os.path.isfile(stdMat)),"FLIRT MAT file not found, need to run CCSegLongPreprocess: " + stdMat
flirtTemplateFile = CCSegUtils.MNI152FLIRTTemplate()
flirtTemplateFileBrainMask = flirtTemplateFile[:-7] + "_brain_mask.nii.gz"
NIITempDir = tempfile.mkdtemp()
toStdNII = os.path.join(NIITempDir, subjectID + "_to_std.nii.gz")
flirtInterp = 'trilinear'
commandString = [os.path.join(os.environ['FSLDIR'], 'bin', 'flirt'), '-interp', flirtInterp, '-applyxfm', '-init', stdMat, '-ref', flirtTemplateFile, '-out', toStdNII, '-in', NIFTIFileName]
#print " ".join(commandString)
subprocess.call(commandString)
flirtMAT = numpy.loadtxt(stdMat)
#toStdNII = CCSegUtils.findNIFTIFromPrefix(os.path.join(head, subjectID + "_to_std"))
#assert(toStdNII != None),"standard image not found, need to run CCSegLongPreprocess: " + os.path.join(head, subjectID + "_to_std")
NIIBrainMask = nibabel.load(flirtTemplateFileBrainMask)
NII = nibabel.load(toStdNII)
NIIPixdims = NII.get_header().get_zooms()[1:3]
NIISize = NII.get_shape()
NIIData = numpy.rot90(NII.get_data(), 1)
NIIBrainMaskData = numpy.rot90(NIIBrainMask.get_data(), 1)
T = math.floor(NIIData.shape[1] / 2)
# extract the midsagittal slice
if (NIIData.shape[1] % 2 == 0):
# even number of slices
midSagAVW = (numpy.double(NIIData[:, T - 1]) + numpy.double(NIIData[:, T])) / 2.0
midSagAVWBrainMask = (numpy.double(NIIBrainMaskData[:, T - 1]) + numpy.double(NIIBrainMaskData[:, T])) / 2.0
else:
# odd number of slices
midSagAVW = numpy.double(NIIData[:, T])
midSagAVWBrainMask = numpy.double(NIIBrainMaskData[:, T])
midSagAVW[numpy.where(midSagAVWBrainMask < 0.5)] = numpy.nan
midSagAVW = numpy.rot90(midSagAVW, 1)
midSagAVW = numpy.array(midSagAVW[:, ::-1])
shutil.rmtree(NIITempDir)
else:
Transform = NII.get_sform(coded=True)
if Transform[0] == None:
print "Trying qform in " + inputBase
Transform = NII.get_qform(coded=True)
assert(Transform[0] != None),"No transformation information in NIFTI file" + inputBase
det = numpy.linalg.det(Transform[0][0:3, 0:3])
(icode, jcode, kcode) = niftiOrientations(Transform[0])
del Transform
if numpy.abs(det) < 1e-12:
OrientationString = None
elif det < 0.0:
OrientationString = "RL PA IS"
else:
OrientationString = "LR PA IS"
origOrientationString = list()
pat = re.compile("NIFTI_([LRASIP])2([LRASIP])")
mat = pat.match(icode)
if mat != None:
origOrientationString.append(mat.group(1) + mat.group(2))
mat = pat.match(jcode)
if mat != None:
origOrientationString.append(mat.group(1) + mat.group(2))
mat = pat.match(kcode)
if mat != None:
origOrientationString.append(mat.group(1) + mat.group(2))
origOrientationString = " ".join(origOrientationString)
#print icode + " " + jcode + " " + kcode
#assert(not (icode == "NIFTI_INVALID" or jcode == "NIFTI_INVALID" or kcode == "NIFTI_INVALID")),"Invalid NIFTI orientations in " + inputBase
# if icode == "NIFTI_L2R" or jcode == "NIFTI_L2R" or kcode == "NIFTI_L2R":
# OrientationString = "LR PA IS"
# elif icode == "NIFTI_R2L" or jcode == "NIFTI_R2L" or kcode == "NIFTI_R2L":
# OrientationString = "RL PA IS"
# else:
# OrientationString = None
# del icode
# del jcode
# del kcode
#
assert(OrientationString != None),"Could not find RADIOLOGICAL/NEUROLOGICAL orientation in " + inputBase
#print "OrientationString = " + OrientationString
NIITempDir = tempfile.mkdtemp()
#print NIITempDir
NIIFileForMidSag = os.path.join(NIITempDir, 'in.nii.gz')
os.system(os.environ['FSLDIR'] + '/bin/fslswapdim ' + inputBase + ' ' + OrientationString + ' ' + NIIFileForMidSag)
NII = nibabel.load(NIIFileForMidSag)
shutil.copyfile(NIIFileForMidSag, outputBase + "_native.nii.gz")
NIIData = numpy.array(NII.get_data())
NIIData = numpy.rot90(NIIData, 1)
NIIPixdims = NII.get_header().get_zooms()
#print "pixdims: " + str(NIIPixdims)
#print NII
# perform 3-class otsu thresholding
#print numpy.min(NIIData)
#print numpy.max(NIIData)
OtsuSeg = Otsu.robustOtsu(NIIData, [0.02, 0.98], NumberClasses = 2)
L, NumLabels = scipy.ndimage.measurements.label(OtsuSeg, structure = numpy.ones([3, 3, 3]))
LAreas = scipy.ndimage.measurements.labeled_comprehension(OtsuSeg, L, numpy.arange(1, NumLabels + 1), numpy.size, numpy.uint32, 0)
MaxLabel = numpy.argmax(LAreas) + 1
OtsuSeg[numpy.where(L != MaxLabel)] = 0
del L; del MaxLabel; del NumLabels
# cut off the neck, find the bounding box
I = numpy.nonzero(OtsuSeg)
minI = numpy.min(I[0]); maxI = numpy.max(I[0]);
minJ = numpy.min(I[1]); maxJ = numpy.max(I[1]);
minK = numpy.min(I[2]); maxK = numpy.max(I[2]);
minK = numpy.int32(numpy.maximum(numpy.floor(maxK - 180 / NIIPixdims[2]), 0))
skullCrop = numpy.array([[minI, maxI], [minJ, maxJ], [minK, maxK]])
#print str(minI) + " " + str(maxI) + ", " + str(minJ) + " " + str(maxJ) + ", " + str(minK) + " " + str(maxK)
NIIData = numpy.take(NIIData, numpy.arange(minI, maxI + 1), axis=0)
NIIData = numpy.take(NIIData, numpy.arange(minJ, maxJ + 1), axis=1)
NIIData = numpy.take(NIIData, numpy.arange(minK, maxK + 1), axis=2)
if numpy.max(NIIData) > 32767:
NIIData = numpy.double(NIIData)
NIIData = (NIIData - numpy.min(NIIData)) / (numpy.max(NIIData) - numpy.min(NIIData))
NIIData = numpy.round(NIIData * 1000.0)
NIIData = numpy.int16(NIIData)
NIIData = numpy.rot90(NIIData, -1)
NIISaving = nibabel.Nifti1Image(NIIData, NII.get_affine(), NII.get_header())
NIISaving.set_data_dtype(numpy.int16)
NIIFileForART = os.path.join(NIITempDir, 'in_art.nii')
NIIFileForARTOutput = os.path.join(NIITempDir, 'in_art_output.nii')
nibabel.save(NIISaving, NIIFileForART)
nibabel.save(NIISaving, outputBase + "_native_cropped.nii.gz")
del NIISaving
if MSPMethod == 'acpcdetect':
scriptPath = os.path.realpath(__file__)
(head, tail) = os.path.split(scriptPath)
CommandString = 'ARTHOME=' + os.path.join(head, 'ART') + " " + os.path.join(head, 'ART', 'acpcdetect') + ' -i ' + NIIFileForART + ' -o ' + NIIFileForARTOutput
print CommandString
os.system(CommandString)
inF = file(NIIFileForARTOutput, 'rb')
s = inF.read()
inF.close()
outF = gzip.GzipFile(NIIFileForARTOutput + ".gz", 'wb')
outF.write(s)
outF.close()
os.unlink(NIIFileForARTOutput)
flirtTemplateFile = outputBase + "_template.nii.gz"
shutil.copyfile(NIIFileForARTOutput + ".gz", flirtTemplateFile)
# get the aligned image and register the original image to it to get the transformation
flirtOutputFile = None
elif MSPMethod == 'flirt':
flirtTemplateFile = '***'
flirtOutputFile = NIIFileForARTOutput
flirtCost = 'mutualinfo'
flirtInterp = 'trilinear'
NIIFileARTOutputAffineMat = os.path.join(NIITempDir, 'in_art_output.mat')
D = 15
if flirtTemplateFile == "***":
realFlirtTemplateFile = CCSegUtils.MNI152FLIRTTemplate()
else:
realFlirtTemplateFile = flirtTemplateFile
CommandString = os.environ['FSLDIR'] + '/bin/flirt -in ' + NIIFileForART + ' -ref ' + realFlirtTemplateFile + ' -dof 6 -searchrx ' + str(-D) + ' ' + str(D) + ' -searchry ' + str(-D) + ' ' + str(D) + ' -searchrz ' + str(-D) + ' ' + str(D) + ' -omat ' + NIIFileARTOutputAffineMat + ' -cost ' + flirtCost + " -interp " + flirtInterp
# interpTypes = ['trilinear', 'nearestneighbour']
# costFns = ['mutualinfo','corratio','normcorr','normmi','leastsq']
#
# for flirtInterp in interpTypes:
# for flirtCost in costFns:
# CommandString = os.environ['FSLDIR'] + '/bin/flirt -in ' + NIIFileForART + ' -ref ' + flirtTemplateFile + ' -dof 6 -searchrx ' + str(-D) + ' ' + str(D) + ' -searchry ' + str(-D) + ' ' + str(D) + ' -searchrz ' + str(-D) + ' ' + str(D) + ' -omat ' + NIIFileARTOutputAffineMat + ' -cost ' + flirtCost + ' -interp ' + flirtInterp
#
# start_time = time.time()
# os.system(CommandString)
# elapsed_time = time.time() - start_time
# print "interp: " + flirtInterp + ", cost: " + flirtCost + ", time: " + str(elapsed_time)
# quit()
if flirtOutputFile != None:
CommandString = CommandString + " -out " + NIIFileForARTOutput
del D
#print CommandString
os.system(CommandString)
shutil.copyfile(NIIFileForARTOutput + ".gz", outputBase + "_native_cropped_to_template.nii.gz")
#flirtMAT = open(NIIFileARTOutputAffineMat, 'r')
flirtMAT = numpy.loadtxt(NIIFileARTOutputAffineMat)
shutil.copyfile(NIIFileARTOutputAffineMat, outputBase + "_native_cropped_to_template.mat")
# find out whether the output file is a nifti or compressed nifti
#print NIIFileForARTOutput
NII = nibabel.load(NIIFileForARTOutput + ".gz")
NIIData = NII.get_data()
NIIData = numpy.rot90(NIIData, 1)
T = math.floor(NIIData.shape[1] / 2)
# extract the midsagittal slice
if (NIIData.shape[1] % 2 == 0):
# even number of slices
midSagAVW = (numpy.double(NIIData[:, T - 1]) + numpy.double(NIIData[:, T])) / 2.0
else:
# odd number of slices
midSagAVW = numpy.double(NIIData[:, T])
midSagAVW = numpy.rot90(midSagAVW, 1)
midSagAVW = numpy.array(midSagAVW[:, ::-1])
# crop out the zeros, sometimes FLIRT shrinks the image, causes problems downstream with the registration
I = numpy.nonzero(midSagAVW)
flirtCropZerosRows = numpy.arange(numpy.min(I[0]), numpy.max(I[0]) + 1)
flirtCropZerosCols = numpy.arange(numpy.min(I[1]), numpy.max(I[1]) + 1)
midSagAVW = numpy.take(midSagAVW, flirtCropZerosRows, axis=0)
midSagAVW = numpy.take(midSagAVW, flirtCropZerosCols, axis=1)
#print "flirtCropZerosRows: " + str(flirtCropZerosRows[0]) + " " + str(flirtCropZerosRows[-1])
#print "flirtCropZerosCols: " + str(flirtCropZerosCols[0]) + " " + str(flirtCropZerosCols[-1])
del I
shutil.rmtree(NIITempDir)
if MSPMethod != 'long':
FID = h5py.File(outputMAT, 'w')
FID.create_dataset("NIIPixdims", data=NIIPixdims, compression = 'gzip')
FID.create_dataset("midSagAVW", data=midSagAVW, compression = 'gzip')
FID.create_dataset("MSPMethod", data=MSPMethod)
FID.create_dataset("originalOrientationString", data=origOrientationString)
FID.create_dataset("originalNativeFile", data=(outputBase + "_native.nii.gz"))
FID.create_dataset("skullCrop", data=skullCrop)
FID.create_dataset("originalNativeCroppedFile", data=(outputBase + "_native_cropped.nii.gz"))
FID.create_dataset("flirtMAT", data=flirtMAT)
FID.create_dataset("flirtTemplateFile", data=flirtTemplateFile)
FID.create_dataset("flirtCropZerosRows", data=flirtCropZerosRows)
FID.create_dataset("flirtCropZerosCols", data=flirtCropZerosCols)
FID.close()
else:
FID = h5py.File(outputMAT, 'w')
FID.create_dataset("NIIPixdims", data=NIIPixdims, compression = 'gzip')
FID.create_dataset("midSagAVW", data=midSagAVW, compression = 'gzip')
FID.create_dataset("MSPMethod", data=MSPMethod)
FID.create_dataset("flirtMAT", data=flirtMAT)
FID.create_dataset("flirtTemplateFile", data=flirtTemplateFile)
FID.close()
#print NII.get_header().get_zooms()
#print NIIPixdims
#ylab.imshow(midSagAVW)
#pylab.set_cmap(pylab.cm.gray)
#pylab.show()
#if len(NIISize) == 2:
if doGraphics:
T = numpy.double(midSagAVW)
T = (T - numpy.min(T)) / (numpy.max(T) - numpy.min(T))
T = numpy.uint8(numpy.round(T * 255))
scipy.misc.imsave(outputPNG, T)
del T
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()