def removeParticles(fp, removeList, comm, size, rank):
[row, col, numFrames, frameList] = misc.getVitals(fp)
particleList = fp.attrs['particleList']
zfillVal = fp.attrs['zfillVal']
procFrameList = numpy.array_split(frameList, size)
for frame in procFrameList[rank]:
labelImg = fp['/segmentation/labelStack/' +
str(frame).zfill(zfillVal)].value
for r in removeList:
labelImg[labelImg == r] = 0
numpy.save(str(frame).zfill(zfillVal) + '.npy', labelImg)
comm.Barrier()
if (rank == 0):
for frame in frameList:
labelImg = numpy.load(str(frame).zfill(zfillVal) + '.npy')
fileIO.writeH5Dataset(
fp, '/segmentation/labelStack/' + str(frame).zfill(zfillVal),
labelImg)
fileIO.delete(str(frame).zfill(zfillVal) + '.npy')
for r in removeList:
fp.attrs['particleList'] = numpy.delete(
fp.attrs['particleList'],
numpy.where(fp.attrs['particleList'] == r))
comm.Barrier()
return 0
def globalRelabelParticles(fp, correctionList, comm, size, rank):
[row, col, numFrames, frameList] = misc.getVitals(fp)
particleList = fp.attrs['particleList']
zfillVal = fp.attrs['zfillVal']
procFrameList = numpy.array_split(frameList, size)
for frame in procFrameList[rank]:
labelImg = fp['/segmentation/labelStack/' +
str(frame).zfill(zfillVal)].value
for i in range(len(correctionList)):
for j in range(len(correctionList[i]) - 1):
labelImg[labelImg == correctionList[i]
[j]] = correctionList[i][-1]
numpy.save(str(frame).zfill(zfillVal) + '.npy', labelImg)
comm.Barrier()
if (rank == 0):
for frame in frameList:
labelImg = numpy.load(str(frame).zfill(zfillVal) + '.npy')
fileIO.writeH5Dataset(
fp, '/segmentation/labelStack/' + str(frame).zfill(zfillVal),
labelImg)
fileIO.delete(str(frame).zfill(zfillVal) + '.npy')
particleInFrame = numpy.unique(labelImg)[1:]
if (frame == frameList[0]):
particleList = particleInFrame.copy()
else:
particleList = numpy.unique(
numpy.append(particleList, particleInFrame))
fp.attrs['particleList'] = particleList
comm.Barrier()
return 0
def relabelParticles(fp, comm, size, rank):
[row, col, numFrames, frameList] = misc.getVitals(fp)
particleList = fp.attrs['particleList']
zfillVal = fp.attrs['zfillVal']
procFrameList = numpy.array_split(frameList, size)
maxLabel = numpy.max(particleList) + 1
counter = 1
newLabels = {}
for particle in particleList:
newLabels[particle] = []
for frame in frameList:
particlesInFrame = numpy.unique(
fp['/segmentation/labelStack/' +
str(frame).zfill(zfillVal)].value)[1:]
for p in particlesInFrame:
if not newLabels[p]:
newLabels[p] = [maxLabel, counter]
maxLabel += 1
counter += 1
for frame in procFrameList[rank]:
labelImg = fp['/segmentation/labelStack/' +
str(frame).zfill(zfillVal)].value
for key in newLabels.keys():
labelImg[labelImg == key] = newLabels[key][0]
for key in newLabels.keys():
labelImg[labelImg == newLabels[key][0]] = newLabels[key][1]
numpy.save(str(frame).zfill(zfillVal) + '.npy', labelImg)
comm.Barrier()
if (rank == 0):
for frame in frameList:
labelImg = numpy.load(str(frame).zfill(zfillVal) + '.npy')
if (counter < 256):
labelImg = labelImg.astype('uint8')
elif (counter < 65536):
labelImg = labelImg.astype('uint16')
else:
labelImg = labelImg.astype('uint32')
fileIO.writeH5Dataset(
fp, '/segmentation/labelStack/' + str(frame).zfill(zfillVal),
labelImg)
fileIO.delete(str(frame).zfill(zfillVal) + '.npy')
particleInFrame = numpy.unique(labelImg)[1:]
if (frame == frameList[0]):
particleList = particleInFrame.copy()
else:
particleList = numpy.unique(
numpy.append(particleList, particleInFrame))
fp.attrs['particleList'] = particleList
comm.Barrier()
return 0
def framewiseRelabelParticles(fp, frameWiseCorrectionList, comm, size, rank):
[row, col, numFrames, frameList] = misc.getVitals(fp)
particleList = fp.attrs['particleList']
zfillVal = fp.attrs['zfillVal']
procFrameList = numpy.array_split(frameList, size)
for frame in procFrameList[rank]:
labelImg = fp['/segmentation/labelStack/' +
str(frame).zfill(zfillVal)].value
for frameWiseCorrection in frameWiseCorrectionList:
subFrameList, subCorrectionList = frameWiseCorrection[
0], frameWiseCorrection[1]
for subFrame in subFrameList:
if (frame == subFrame):
newLabel = subCorrectionList[-1]
for oldLabel in subCorrectionList[:-1]:
labelImg[labelImg == oldLabel] = newLabel
numpy.save(str(frame).zfill(zfillVal) + '.npy', labelImg)
comm.Barrier()
if (rank == 0):
for frame in frameList:
labelImg = numpy.load(str(frame).zfill(zfillVal) + '.npy')
fileIO.writeH5Dataset(
fp, '/segmentation/labelStack/' + str(frame).zfill(zfillVal),
labelImg)
fileIO.delete(str(frame).zfill(zfillVal) + '.npy')
particleInFrame = numpy.unique(labelImg)[1:]
if (frame == frameList[0]):
particleList = particleInFrame.copy()
else:
particleList = numpy.unique(
numpy.append(particleList, particleInFrame))
fp.attrs['particleList'] = particleList
comm.Barrier()
return 0
'.png', finalImg)
outFile.close()
fp.flush(), fp.close()
comm.Barrier()
if (rank == 0):
for r in range(size):
if (r == 0):
measures = numpy.loadtxt(outputDir + '/segmentation_' + str(r) +
'.dat')
else:
measures = numpy.row_stack(
(measures,
numpy.loadtxt(outputDir + '/segmentation_' + str(r) +
'.dat')))
fileIO.delete(outputDir + '/segmentation_' + str(r) + '.dat')
numpy.savetxt(outputDir + '/segmentation.dat', measures, fmt='%.6f')
comm.Barrier()
#######################################################################
#######################################################################
# CREATE BINARY IMAGES INTO HDF5 FILE
#######################################################################
if (rank == 0):
print "Creating binary images from segmented images"
if (rank == 0):
fp = h5py.File(outputFile, 'r+')
else:
fp = h5py.File(outputFile, 'r')
[row, col, numFrames, frameList] = misc.getVitals(fp)
'.png', finalImg)
outFile.close()
fp.flush(), fp.close()
comm.Barrier()
if (rank == 0):
for r in range(size):
if (r == 0):
measures = numpy.loadtxt(outputDir + '/segmentation_' + str(r) +
'.dat')
else:
measures = numpy.row_stack(
(measures,
numpy.loadtxt(outputDir + '/segmentation_' + str(r) +
'.dat')))
fileIO.delete(outputDir + '/segmentation_' + str(r) + '.dat')
numpy.savetxt(outputDir + '/segmentation.dat', measures, fmt='%.6f')
comm.Barrier()
#######################################################################
#######################################################################
# CREATE BINARY IMAGES INTO HDF5 FILE
#######################################################################
#if (rank==0):
#print "Creating binary images from segmented images"
#if (rank==0):
#fp = h5py.File(outputFile, 'r+')
#else:
#fp = h5py.File(outputFile, 'r')
#[row,col,numFrames,frameList] = misc.getVitals(fp)