def fill_holes(imp, is3d=False):
if not is3d:
# 2D fill holes
stack = imp.getStack() # get the stack within the ImagePlus
nslices = stack.getSize() # get the number of slices
for index in range(1, nslices + 1):
ip = stack.getProcessor(index)
ip.invert()
# Reconstruction.fillHoles(imp.getProcessor())
Reconstruction.fillHoles(ip)
ip.invert()
#if not is3d:
# # 2D fill holes
# stack = imp.getStack() # get the stack within the ImagePlus
# nslices = stack.getSize() # get the number of slices
# for index in range(1, nslices + 1):
# ip = stack.getProcessor(index)
#
# # Reconstruction.fillHoles(imp.getProcessor())
# Reconstruction.fillHoles(ip)
if is3d:
# 3D fill holes
imp = Reconstruction3D.fillHoles(imp.getImageStack())
return imp
def fill_holes(imp):
numZ = imp.getNSlices()
if numZ == 1:
# 2D fill holes
Reconstruction.fillHoles(imp.getProcessor())
if numZ > 1:
# 3D fill holes
imp = Reconstruction3D.fillHoles(imp.getImageStack())
return imp
def run(imagefile):
# Opening the image
log.log(LogLevel.INFO, 'Opening Image: ' + imagefile)
# open image file and get a specific series
imp, MetaInfo = ImportTools.openfile(imagefile)
log.log(LogLevel.INFO, 'File Extension : ' + MetaInfo['Extension'])
if 'ResolutionCount' in MetaInfo:
log.log(LogLevel.INFO,
'Resolution Count : ' + str(MetaInfo['ResolutionCount']))
if 'SeriesCount' in MetaInfo:
log.log(LogLevel.INFO,
'SeriesCount : ' + str(MetaInfo['SeriesCount']))
if 'SizeC' in MetaInfo:
log.log(LogLevel.INFO, 'Channel Count : ' + str(MetaInfo['SizeC']))
# do the processing
log.log(LogLevel.INFO, 'Start Processing ...')
if EXTRACT_CHANNEL:
# get the correct channel
if MetaInfo['SizeC'] > 1:
log.log(LogLevel.INFO, 'Extract Channel : ' + str(CHINDEX))
imps = ChannelSplitter.split(imp)
imp = imps[CHINDEX - 1]
# correct background using rolling ball
if CORRECT_BACKGROUND:
log.log(LogLevel.INFO, 'Rolling Ball Background subtraction...')
imp = FilterTools.apply_rollingball(imp,
radius=RB_RADIUS,
createBackground=CREATEBACKGROUND,
lightBackground=LIGHTBACKGROUND,
useParaboloid=USEPARABOLOID,
doPresmooth=DOPRESMOOTH,
correctCorners=CORRECTCORNERS)
if FILTERDIM == '2D':
if RANKFILTER != 'NONE':
# apply filter
log.log(LogLevel.INFO, 'Apply 2D Filter : ' + RANKFILTER)
imp = FilterTools.apply_filter(imp,
radius=RADIUS,
filtertype=RANKFILTER)
if FILTERDIM == '3D':
if FILTER3D != 'NONE':
# apply filter
log.log(LogLevel.INFO, 'Apply 3D Filter : ' + FILTER3D)
imp = FilterTools.apply_filter3d(imp,
radiusx=RADIUSX,
radiusy=RADIUSY,
radiusz=RADIUSZ,
filtertype=FILTER3D)
if THRESHOLD != 'NONE':
# apply threshold
log.log(LogLevel.INFO, 'Apply Threshold : ' + THRESHOLD)
log.log(LogLevel.INFO, 'Correction Factor : ' + str(CORRFACTOR))
imp = ThresholdTools.apply_threshold(imp,
method=THRESHOLD,
background_threshold='dark',
stackopt=TH_STACKOPT,
corrf=CORRFACTOR)
# imp_t = imp.duplicate()
# imp_t.show("Threshold")
if FILL_HOLES:
# 3D fill holes
log.log(LogLevel.INFO, '3D Fill Holes ...')
imp = Reconstruction3D.fillHoles(imp.getImageStack())
if not FILL_HOLES:
imp = imp.getImageStack()
if WATERSHED:
# run watershed on stack
weights = ChamferWeights3D.BORGEFORS.getFloatWeights()
normalize = True
dynamic = 2
connectivity = LABEL_CONNECT
log.log(LogLevel.INFO, 'Run Watershed to separate particles ...')
#dist = BinaryImages.distanceMap(imp.getImageStack(), weights, normalize)
dist = BinaryImages.distanceMap(imp, weights, normalize)
Images3D.invert(dist)
#imp = ExtendedMinimaWatershed.extendedMinimaWatershed(dist, imp.getImageStack(), dynamic, connectivity, 32, False )
imp = ExtendedMinimaWatershed.extendedMinimaWatershed(
dist, imp, dynamic, connectivity, 32, False)
# extend borders
log.log(LogLevel.INFO, 'Border Extension ...')
# create BorderManager and add Zeros in all dimensions
bmType = BorderManager3D.Type.fromLabel("BLACK")
bm = bmType.createBorderManager(imp)
#bm = bmType.createBorderManager(imp.getStack())
BorderExt = ExtendBordersPlugin()
# extend border by always exb
#imp = BorderExt.process(imp.getStack(), EXB, EXB, EXB, EXB, EXB, EXB, bm)
imp = BorderExt.process(imp, EXB, EXB, EXB, EXB, EXB, EXB, bm)
# convert back to ImgPlus
pastack = ImagePlus('Particles', imp)
# check for pixel in 3d by size
log.log(LogLevel.INFO,
'Filtering VoxelSize - Minimum : ' + str(MINVOXSIZE))
pastack = BinaryImages.volumeOpening(pastack.getStack(), MINVOXSIZE)
imp = ImagePlus('Particles Filtered', pastack)
pastack = BinaryImages.componentsLabeling(imp, LABEL_CONNECT,
LABEL_BITDEPTH)
# get the labels
labels = LabelImages.findAllLabels(pastack)
log.log(LogLevel.INFO, 'Labels Filtered : ' + str(len(labels)))
# run 3D particle analysis
log.log(LogLevel.INFO, '3D Particle Analysis ...')
PA3d = ParticleAnalysis3DPlugin()
results = PA3d.process(pastack)
# colorize the labels
if LABEL_COLORIZE:
log.log(LogLevel.INFO, 'Colorize Lables ...')
#maxLabel = 255
maxLabel = len(labels)
bgColor = Color.BLACK
shuffleLut = True
lutName = CommonLabelMaps.GOLDEN_ANGLE.getLabel()
# Create a new LUT from info in dialog
lut = CommonLabelMaps.fromLabel(lutName).computeLut(
maxLabel, shuffleLut)
# Create a new RGB image from index image and LUT options
pastack_rgb = LabelImages.labelToRgb(pastack, lut, bgColor)
# convert to rgb color
IJ.run(pastack_rgb, "RGB Color", "slices")
if LABEL_COLORIZE:
return pastack_rgb, results, labels
elif not LABEL_COLORIZE:
return pastack, results, labels
def run(imagefile):
# Opening the image
log.info('Opening Image: ' + imagefile)
# open image file and get a specific series
imp, MetaInfo = ImportTools.openfile(imagefile)
log.info('File Extension : ' + MetaInfo['Extension'])
if 'ResolutionCount' in MetaInfo:
log.info('Resolution Count : ' + str(MetaInfo['ResolutionCount']))
if 'SeriesCount' in MetaInfo:
log.info('SeriesCount : ' + str(MetaInfo['SeriesCount']))
if 'SizeC' in MetaInfo:
log.info('Channel Count : ' + str(MetaInfo['SizeC']))
# do the processing
log.info('Start Processing ...')
# get the correct channel
if MetaInfo['SizeC'] > 1:
log.info('Extract Channel : ' + str(MetaInfo['ChannelCount']))
imps = ChannelSplitter.split(imp)
imp = imps[CHINDEX - 1]
# convert to 8bit grayscale
ic = ImageConverter(imp)
ic.convertToGray8()
if FILL_HOLES:
# 3D fill holes
log.info('3D Fill Holes ...')
imp = Reconstruction3D.fillHoles(imp.getImageStack())
if not FILL_HOLES:
imp = imp.getImageStack()
# run watershed on stack
weights = ChamferWeights3D.BORGEFORS.getFloatWeights()
normalize = True
dynamic = 2
connectivity = LABEL_CONNECT
log.info('Applying Run Watershed to separate particles ...')
#dist = BinaryImages.distanceMap(imp.getImageStack(), weights, normalize)
dist = BinaryImages.distanceMap(imp, weights, normalize)
Images3D.invert(dist)
#imp = ExtendedMinimaWatershed.extendedMinimaWatershed(dist, imp.getImageStack(), dynamic, connectivity, 32, False )
imp = ExtendedMinimaWatershed.extendedMinimaWatershed(
dist, imp, dynamic, connectivity, 32, False)
# extend borders
log.info('Applying Border Extension ...')
# create BorderManager and add Zeros in all dimensions
bmType = BorderManager3D.Type.fromLabel("BLACK")
bm = bmType.createBorderManager(imp)
#bm = bmType.createBorderManager(imp.getStack())
BorderExt = ExtendBordersPlugin()
# extend border by always exb
#imp = BorderExt.process(imp.getStack(), EXB, EXB, EXB, EXB, EXB, EXB, bm)
imp = BorderExt.process(imp, EXB, EXB, EXB, EXB, EXB, EXB, bm)
# convert back to ImgPlus
pastack = ImagePlus('Particles', imp)
# check for pixel in 3d by size
log.info('Filtering VoxelSize - Minimum : ' + str(MINVOXSIZE))
pastack = BinaryImages.volumeOpening(pastack.getStack(), MINVOXSIZE)
imp = ImagePlus('Particles Filtered', pastack)
pastack = BinaryImages.componentsLabeling(imp, LABEL_CONNECT,
LABEL_BITDEPTH)
# get the labels
labels = LabelImages.findAllLabels(pastack)
log.info('Labels Filtered : ' + str(len(labels)))
# run 3D particle analysis
log.info('3D Particle Analysis ...')
PA3d = ParticleAnalysis3DPlugin()
results = PA3d.process(pastack)
# colorize the labels
if LABEL_COLORIZE:
log.info('Colorize Lables ...')
#maxLabel = 255
maxLabel = len(labels)
bgColor = Color.BLACK
shuffleLut = True
lutName = CommonLabelMaps.GOLDEN_ANGLE.getLabel()
# Create a new LUT from info in dialog
lut = CommonLabelMaps.fromLabel(lutName).computeLut(
maxLabel, shuffleLut)
# Create a new RGB image from index image and LUT options
pastack_rgb = LabelImages.labelToRgb(pastack, lut, bgColor)
# convert to rgb color
IJ.run(pastack_rgb, "RGB Color", "slices")
if LABEL_COLORIZE:
return pastack_rgb, results, labels
elif not LABEL_COLORIZE:
return pastack, results, labels