def select_images():
"""
Returns two ImagePlus objects that can be used by the drift correction.
If more than two images are available a dialog is used for selection.
"""
if WindowManager.getImageCount() > 0:
imp = WindowManager.getCurrentImage()
if imp.getImageStackSize() == 2:
dup = Duplicator()
img1 = dup.run(imp, 1, 1)
img1.setTitle("Slice1")
img2 = dup.run(imp, 2, 2)
img2.setTitle("Slice2")
elif WindowManager.getImageCount() == 2:
img1, img2 = [WindowManager.getImage(id) for id in WindowManager.getIDList()]
elif WindowManager.getImageCount() > 2:
image_ids = WindowManager.getIDList()
image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
try:
sel1, sel2 = dialogs.create_selection_dialog(image_titles, range(2))
except TypeError:
return(None, None)
img1 = WindowManager.getImage(image_ids[sel1])
img2 = WindowManager.getImage(image_ids[sel2])
else:
IJ.error("You need two images to run the script.")
return(None, None)
else:
IJ.error("You need two images to run the script.")
return(None, None)
return (img1, img2)
def crop(self):
self.imp.setRoi(self.outlineRoi)
duplicator = Duplicator()
self.imp.setHideOverlay(True)
self.impCrop = duplicator.run(self.imp)
self.impCrop.show()
self.imp.setHideOverlay(False)
def creating_vor_roi(self):
"""
runs voronoi on cell to create vor_rois
"""
rm = RoiManager.getRoiManager()
rm.reset()
d = Duplicator()
nuc_bin_copy = d.run(self.hseg.nuc_bin())
nuc_bin_copy.show()
IJ.run(nuc_bin_copy, "Make Binary", "")
nuc_bin_copy.setRoi(self.roi())
IJ.run(nuc_bin_copy, "Clear Outside", "")
# 1/0
IJ.run(nuc_bin_copy, "Voronoi", "")
nuc_bin_copy.setRoi(None)
ip = nuc_bin_copy.getProcessor()
ip.setMinAndMax(0, 1)
IJ.run(nuc_bin_copy, "Apply LUT", "")
nuc_bin_copy.setRoi(self.roi())
IJ.run(nuc_bin_copy, "Analyze Particles...", "add")
vor_rois = rm.getRoisAsArray()
# self.hseg.raw_stack().show()
# 10/0
futils.force_close(nuc_bin_copy)
return vor_rois
def process(self, image, seeds=None):
self.objects = None
self.labelImage = None
duplicator = Duplicator()
spots = duplicator.run(image)
IJ.setMinAndMax(spots, 0, 1)
IJ.run(spots, "16-bit", "")
spot3DImage = ImageHandler.wrap(spots)
if seeds != None:
seed3DImage = ImageHandler.wrap(seeds)
else:
seed3DImage = self.__computeSeeds(spots)
algorithm = Segment3DSpots(spot3DImage, seed3DImage)
algorithm.show = False
algorithm.setSeedsThreshold(self.seedsThreshold)
algorithm.setLocalThreshold(self.localBackground)
algorithm.setWatershed(self.watershed)
algorithm.setVolumeMin(self.volumeMin)
algorithm.setVolumeMax(self.volumeMax)
algorithm.setMethodLocal(Segment3DSpots.LOCAL_CONSTANT)
algorithm.setMethodSeg(Segment3DSpots.SEG_MAX)
algorithm.segmentAll()
self.objects = algorithm.getObjects()
self.labelImage = ImagePlus("OM_" + spots.getTitle(), algorithm.getLabelImage().getImageStack())
return self.labelImage
def vor_cell(nuc_bin_imp, cell):
"""creates the voronoi for one cell, cell is assumed to have nucs"""
rm = RoiManager.getRoiManager()
rm.reset()
d = Duplicator()
nuc_bin_copy = d.run(nuc_bin_imp)
IJ.run(nuc_bin_copy, "Make Binary", "")
nuc_bin_copy.setRoi(cell.roi)
IJ.run(nuc_bin_copy, "Clear Outside", "")
IJ.run(nuc_bin_copy, "Voronoi", "")
nuc_bin_copy.setRoi(None)
ip = nuc_bin_copy.getProcessor()
ip.setMinAndMax(0, 1)
IJ.run(nuc_bin_copy, "Apply LUT", "")
IJ.run(nuc_bin_copy, "Invert", "")
nuc_bin_copy.setRoi(cell.roi)
IJ.run(nuc_bin_copy, "Analyze Particles...", "add")
vor_rois = rm.getRoisAsArray()
nuc_inds = [x for x in range(len(cell.nucs))]
for vor_roi in vor_rois:
temp = None
for i, nuc_ind in enumerate(nuc_inds):
nuc_roi = cell.nucs[nuc_ind].roi
nuc_cent = roi_cent(nuc_roi, integer=True)
if vor_roi.contains(*nuc_cent):
cell.nucs[nuc_ind].vor_roi = vor_roi
## I don't think I need to do this, I could just use i outside of loop but it feels so insecure or something
temp = i
break
else:
IJ.log('cell: {}, issue with voronoi nuc match up'.format(
cell.name))
rm.reset()
for i, nuc in enumerate(cell.nucs):
x = int(nuc.roi.getXBase())
y = int(nuc.roi.getYBase())
IJ.log('{}. ({},{})'.format(i, x, y))
add_roi(Roi(x, y, 10, 10), str(i))
IJ.log(str(nuc_inds))
add_roi(vor_roi, "vor_roi")
## raise RuntimeError('cell: {}, issue with voronoi nuc match up'.format(cell.name))
if temp is not None:
del nuc_inds[temp]
force_close(nuc_bin_copy)
def runSimulation(options, image):
print "Testing segmentation with blur" + \
" x=" + "%f" % options['gaussXY'] + \
" y=" + "%f" % options['gaussXY'] + \
" z=" + "%f" % options['gaussZ'] + \
" localBackground=" + "%i" % options['localBackground'] + \
" seedRadius=" + "%i" % options['seedRadius']
duplicator = Duplicator()
inputPM = duplicator.run(image)
inputPM.setTitle("Gauss_segment_input")
inputName = image.getTitle()
inputName = inputName[:inputName.rfind('.')]
### Blur nuclei probability map to smoothen segmentation
IJ.run(inputPM, "Gaussian Blur 3D...",
" x=" + "%f" % options['gaussXY'] + \
" y=" + "%f" % options['gaussXY'] + \
" z=" + "%f" % options['gaussZ'])
### Segment image using nuclear probability map
print ">>> Segmenting image..."
segmentator = Segmentator(options, "Segmented")
segmentedImage = segmentator.process(inputPM)
outputName = "OM_XY" + ("%f" % options['gaussXY']) + "_Z" + ("%f" % options['gaussZ']) + \
"_TH" + ("%i" % options['localBackground']) + \
"_SR" + ("%i" % options['seedRadius']) + \
"_" + inputName
segmentator.save(segmentedImage, outputName)
### Get object measurements
print ">>> Measuring objects..."
results = {'all':0, '0':0, '250':0, '500':0, '750':0, '1000':0, '1500':0, 'edge':0}
analyzer = Analyzer(options, segmentator.objects, "Results")
segmented = ImageInt.wrap(segmentedImage)
for objectV in analyzer.objects.getObjectsList():
if (options['edgeXY'] and options['edgeZ']) or \
(not objectV.edgeImage(segmented, not options['edgeXY'], not options['edgeZ'])):
results['all'] = results['all'] + 1
volume = objectV.getVolumePixels()
if volume <= 250:
results['0'] = results['0'] + 1
elif volume > 250 and volume <= 500:
results['250'] = results['250'] + 1
elif volume > 500 and volume <= 750:
results['500'] = results['500'] + 1
elif volume > 750 and volume <= 1000:
results['750'] = results['750'] + 1
elif volume > 1000 and volume <= 1500:
results['1000'] = results['1000'] + 1
else:
results['1500'] = results['1500'] + 1
else:
results['edge'] = results['edge'] + 1
return results
def getMask(imp, chan): dup = Duplicator() mask = dup.run(imp, chan, chan, 1,1, 1,1) sigma = 0.2 IJ.run(mask, "Gaussian Blur...", "sigma="+str(sigma)+" scaled") if chan==1: method = "Otsu" else: method = "MaxEntropy" IJ.setAutoThreshold(mask, method+" dark") Prefs.blackBackground = True IJ.run(mask, "Convert to Mask", "") IJ.run(mask, "Close-", "") IJ.run(mask, "Watershed", "") return mask
def make_and_clean_binary(imp, threshold_method):
"""convert the membrane identification channel into binary for segmentation"""
if "Local: " in threshold_method:
dup = Duplicator()
imp1 = dup.run(imp)
imp2 = dup.run(imp)
imp.changes = False
imp.close()
threshold_method = threshold_method.split("Local: ")[1]
IJ.run(imp1, "8-bit", "")
IJ.run(
imp1, "Auto Local Threshold", "method=" + threshold_method +
" radius=15 parameter_1=0 parameter_2=0 white stack")
IJ.run(imp2, "Make Binary",
"method=MinError background=Dark calculate")
ic = ImageCalculator()
imp = ic.run("AND create stack", imp1, imp2)
IJ.run(imp, "Invert", "stack")
IJ.run(imp, "Make Binary",
"method=Default background=Default calculate")
elif "Edge" in threshold_method:
IJ.run(imp, "Find Edges", "stack")
IJ.run(imp, "Make Binary", "method=Mean background=Dark calculate")
else:
IJ.run(imp, "Make Binary",
"method=" + threshold_method + " background=Dark calculate")
# "calculate" ensures that threshold is calculated image-wise
IJ.run(imp, "Open", "stack")
IJ.run(imp, "Close-", "stack")
IJ.run(imp, "Close-", "stack")
IJ.run(imp, "Open", "stack")
IJ.run(imp, "Fill Holes", "stack")
IJ.run(imp, "Erode", "stack")
IJ.run(imp, "Erode", "stack")
keep_largest_blob(imp)
IJ.run(imp, "Dilate", "stack")
IJ.run(imp, "Dilate", "stack")
IJ.run(imp, "Open", "stack")
if "Edge" in threshold_method:
IJ.run(imp, "Erode", "stack")
IJ.run(imp, "Erode", "stack")
return imp
def poreDetectionUV(inputImp, inputDataset, inputRoi, ops, data, display, detectionParameters):
title = inputImp.getTitle()
title=title.replace('UV', 'SD')
print title
#trueColorImp= WindowManager.getImage(title)
#print type( trueColorImp)
# calculate are of roi
stats=inputImp.getStatistics()
inputRoiArea=stats.area
print inputRoi
# get the bounding box of the active roi
inputRec = inputRoi.getBounds()
x1=long(inputRec.getX())
y1=long(inputRec.getY())
x2=x1+long(inputRec.getWidth())-1
y2=y1+long(inputRec.getHeight())-1
print x1
print y1
print x2
print y2
# crop the roi
interval=FinalInterval( array([x1, y1 ,0], 'l'), array([x2, y2, 2], 'l') )
cropped=ops.crop(interval, None, inputDataset.getImgPlus() )
datacropped=data.create(cropped)
display.createDisplay("cropped", datacropped)
croppedPlus=IJ.getImage()
duplicator=Duplicator()
substackMaker=SubstackMaker()
# duplicate the roi
duplicate=duplicator.run(croppedPlus)
#duplicate.show()
# convert duplicate of roi to HSB and get brightness
IJ.run(duplicate, "HSB Stack", "");
brightnessPlus=substackMaker.makeSubstack(duplicate, "3-3")
brightness=ImgPlus(ImageJFunctions.wrapByte(brightnessPlus))
brightnessPlus.setTitle("Brightness")
#brightnessPlus.show()
# make another duplicate, split channels and get red
duplicate=duplicator.run(croppedPlus)
channels=ChannelSplitter().split(duplicate)
redPlus=channels[0]
red=ImgPlus(ImageJFunctions.wrapByte(redPlus))
redPlus.show()
# convert to lab
IJ.run(croppedPlus, "Color Transformer", "colour=Lab")
IJ.selectWindow('Lab')
labPlus=IJ.getImage()
# get the A channel
APlus=substackMaker.makeSubstack(labPlus, "2-2")
APlus.setTitle('A')
APlus.show()
APlus.getProcessor().resetMinAndMax()
APlus.updateAndDraw()
AThresholded=threshold(APlus, -10, 50)
# get the B channel
BPlus=substackMaker.makeSubstack(labPlus, "3-3")
BPlus.setTitle('B')
BPlus.show()
BPlus.getProcessor().resetMinAndMax()
BPlus.updateAndDraw()
BThresholded=threshold(BPlus, -10, 50)
# AND the Athreshold and Bthreshold to get a map of the red pixels
ic = ImageCalculator();
redMask = ic.run("AND create", AThresholded, BThresholded);
IJ.run(redMask, "Divide...", "value=255");
#redMask.show()
labPlus.close()
# threshold the spots from the red channel
thresholdedred=SpotDetectionGray(red, data, display, ops, False)
display.createDisplay("thresholdedred", data.create(thresholdedred))
impthresholdedred = ImageJFunctions.wrap(thresholdedred, "wrapped")
# threshold the spots from the brightness channel
thresholded=SpotDetectionGray(brightness, data, display, ops, False)
display.createDisplay("thresholded", data.create(thresholded))
impthresholded=ImageJFunctions.wrap(thresholded, "wrapped")
# or the thresholding results from red and brightness channel
impthresholded = ic.run("OR create", impthresholded, impthresholdedred);
# convert to mask
Prefs.blackBackground = True
IJ.run(impthresholded, "Convert to Mask", "")
# clear the region outside the roi
clone=inputRoi.clone()
clone.setLocation(0,0)
Utility.clearOutsideRoi(impthresholded, clone)
# create a hidden roi manager
roim = RoiManager(True)
# count the particlesimp.getProcessor().setColor(Color.green)
countParticles(impthresholded, roim, detectionParameters.minSize, detectionParameters.maxSize, detectionParameters.minCircularity, detectionParameters.maxCircularity)
# define a function to determine the percentage of pixels that are foreground in a binary image
# inputs:
# imp: binary image, 0=background, 1=foreground
# roi: an roi
def isRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean>detectionParameters.redPercentage): return True
else: return False
def notRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean>detectionParameters.redPercentage): return False
else: return True
allList=[]
for roi in roim.getRoisAsArray():
allList.append(roi.clone())
# count particles that are red
redList=CountParticles.filterParticlesWithFunction(redMask, allList, isRed)
# count particles that are red
blueList=CountParticles.filterParticlesWithFunction(redMask, allList, notRed)
print "Total particles: "+str(len(allList))
print "Filtered particles: "+str(len(redList))
# for each roi add the offset such that the roi is positioned in the correct location for the
# original image
[roi.setLocation(roi.getXBase()+x1, roi.getYBase()+y1) for roi in allList]
# create an overlay and add the rois
overlay1=Overlay()
inputRoi.setStrokeColor(Color.green)
overlay1.add(inputRoi)
[CountParticles.addParticleToOverlay(roi, overlay1, Color.red) for roi in redList]
[CountParticles.addParticleToOverlay(roi, overlay1, Color.cyan) for roi in blueList]
def drawAllRoisOnImage(imp, mainRoi, redList, blueList):
imp.getProcessor().setColor(Color.green)
IJ.run(imp, "Line Width...", "line=3");
imp.getProcessor().draw(inputRoi)
imp.updateAndDraw()
IJ.run(imp, "Line Width...", "line=1");
[CountParticles.drawParticleOnImage(imp, roi, Color.magenta) for roi in redList]
[CountParticles.drawParticleOnImage(imp, roi, Color.green) for roi in blueList]
imp.updateAndDraw()
drawAllRoisOnImage(inputImp, inputRoi, redList, blueList)
#drawAllRoisOnImage(trueColorImp, inputRoi, redList, blueList)
# draw overlay
#inputImp.setOverlay(overlay1)
#inputImp.updateAndDraw()
statsdict=CountParticles.calculateParticleStats(APlus, BPlus, redMask, roim.getRoisAsArray())
print inputRoiArea
areas=statsdict['Areas']
poreArea=0
for area in areas:
poreArea=poreArea+area
ATotal=0
ALevels=statsdict['ALevel']
for A in ALevels:
ATotal=ATotal+A
AAverage=ATotal/len(ALevels)
BTotal=0
BLevels=statsdict['BLevel']
for B in BLevels:
BTotal=BTotal+B
BAverage=BTotal/len(BLevels)
redTotal=0
redPercentages=statsdict['redPercentage']
for red in redPercentages:
redTotal=redTotal+red
redAverage=redTotal/len(redPercentages)
pixwidth=inputImp.getCalibration().pixelWidth
inputRoiArea=inputRoiArea/(pixwidth*pixwidth)
print str(len(allList))+" "+str(len(redList))+" "+str(len(blueList))+" "+str(poreArea/inputRoiArea)+" "+str(redAverage)
Nuclei.close()
imp2.changes = False
imp2.close()
if automatic_save_results:
dataname = imp1.getTitle()
filename = dataname + ".csv"
#files = glob.glob(savepath+"/"+dataname+"*.csv")
savename = savepath + "/" + filename
ort.saveAs(savename)
else:
print "not saving"
if filenum == 0:
dup = Duplicator()
stack1 = dup.run(imp1)
print "first round"
else:
try:
dup = Duplicator()
stack2 = dup.run(imp1)
stack1 = concat.run(stack1, stack2)
stack1.setTitle(directory)
print "making stack"
except NameError:
dup = Duplicator()
stack1 = dup.run(imp1)
print "first image was empty"
imp1.changes = False
imp1.close()
def poreDetectionUV(inputImp, inputDataset, inputRoi, ops, data, display, detectionParameters):
# set calibration
detectionParameters.setCalibration(inputImp);
# calculate area of roi
stats=inputImp.getStatistics()
inputRoiArea=stats.area
# get the bounding box of the active roi
inputRec = inputRoi.getBounds()
x1=long(inputRec.getX())
y1=long(inputRec.getY())
x2=x1+long(inputRec.getWidth())-1
y2=y1+long(inputRec.getHeight())-1
# crop the roi
interval=FinalInterval( array([x1, y1 ,0], 'l'), array([x2, y2, 2], 'l') )
#cropped=ops.image().crop(interval, None, inputDataset.getImgPlus() )
cropped=ops.image().crop(inputDataset.getImgPlus() , interval)
datacropped=data.create(cropped)
display.createDisplay("cropped", datacropped)
croppedPlus=IJ.getImage()
# instantiate the duplicator and the substackmaker classes
duplicator=Duplicator()
substackMaker=SubstackMaker()
# duplicate the roi
duplicate=duplicator.run(croppedPlus)
# convert duplicate of roi to HSB and get brightness
IJ.run(duplicate, "HSB Stack", "");
brightnessPlus=substackMaker.makeSubstack(duplicate, "3-3")
brightness=ImgPlus(ImageJFunctions.wrapByte(brightnessPlus))
brightnessPlus.setTitle("Brightness")
#brightnessPlus.show()
# make another duplicate, split channels and get red
duplicate=duplicator.run(croppedPlus)
channels=ChannelSplitter().split(duplicate)
redPlus=channels[0]
red=ImgPlus(ImageJFunctions.wrapByte(redPlus))
# convert to lab
IJ.run(croppedPlus, "Color Transformer", "colour=Lab")
IJ.selectWindow('Lab')
labPlus=IJ.getImage()
croppedPlus.changes=False
croppedPlus.close()
# get the A channel
APlus=substackMaker.makeSubstack(labPlus, "2-2")
APlus.setTitle('A')
#APlus.show()
APlus.getProcessor().resetMinAndMax()
#APlus.updateAndDraw()
AThresholded=threshold(APlus, -10, 50)
# get the B channel
BPlus=substackMaker.makeSubstack(labPlus, "3-3")
BPlus.setTitle('B')
#BPlus.show()
BPlus.getProcessor().resetMinAndMax()
#BPlus.updateAndDraw()
BThresholded=threshold(BPlus, -10, 50)
# AND the Athreshold and Bthreshold to get a map of the red pixels
ic = ImageCalculator();
redMask = ic.run("AND create", AThresholded, BThresholded);
IJ.run(redMask, "Divide...", "value=255");
labPlus.close()
fast=True
# threshold the spots from the red channel
if (fast==False):
thresholdedred=SpotDetectionGray(red, data, display, ops, "triangle")
impthresholdedred = ImageJFunctions.wrap(thresholdedred, "wrapped")
else:
impthresholdedred=SpotDetection2(redPlus)
# threshold the spots from the brightness channel
if (fast==False):
thresholded=SpotDetectionGray(brightness, data, display, ops, "triangle")
impthresholded=ImageJFunctions.wrap(thresholded, "wrapped")
else:
impthresholded=SpotDetection2(brightnessPlus)
# or the thresholding results from red and brightness channel
impthresholded = ic.run("OR create", impthresholded, impthresholdedred);
roim=RoiManager(True)
# convert to mask
Prefs.blackBackground = True
IJ.run(impthresholded, "Convert to Mask", "")
def isRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean>detectionParameters.porphyrinRedPercentage): return True
else: return False
def notRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean>detectionParameters.porphyrinRedPercentage): return False
else: return True
roiClone=inputRoi.clone()
roiClone.setLocation(0,0)
Utility.clearOutsideRoi(impthresholded, roiClone)
impthresholded.show()
countParticles(impthresholded, roim, detectionParameters.porphyrinMinSize, detectionParameters.porphyrinMaxSize, \
detectionParameters.porphyrinMinCircularity, detectionParameters.porphyrinMaxCircularity)
uvPoreList=[]
for roi in roim.getRoisAsArray():
uvPoreList.append(roi.clone())
#allList=uvPoreList+closedPoresList+openPoresList
# count particles that are porphyrins (red)
porphyrinList=CountParticles.filterParticlesWithFunction(redMask, uvPoreList, isRed)
# count particles that are visible on uv but not porphyrins
sebumList=CountParticles.filterParticlesWithFunction(redMask, uvPoreList, notRed)
# for each roi add the offset such that the roi is positioned in the correct location for the
# original image
[roi.setLocation(roi.getXBase()+x1, roi.getYBase()+y1) for roi in uvPoreList]
# draw the ROIs on to the image
inputImp.getProcessor().setColor(Color.green)
IJ.run(inputImp, "Line Width...", "line=3");
inputImp.getProcessor().draw(inputRoi)
IJ.run(inputImp, "Line Width...", "line=1");
[CountParticles.drawParticleOnImage(inputImp, roi, Color.magenta) for roi in porphyrinList]
[CountParticles.drawParticleOnImage(inputImp, roi, Color.green) for roi in sebumList]
inputImp.updateAndDraw()
# calculate stats for the UV visible particles
detectionParameters.setCalibration(APlus)
statsDictUV=CountParticles.calculateParticleStatsUV(APlus, BPlus, redMask, roim.getRoisAsArray())
totalUVPoreArea=0
for area in statsDictUV['Areas']:
totalUVPoreArea=totalUVPoreArea+area
averageUVPoreArea=totalUVPoreArea/len(statsDictUV['Areas'])
poreDiameter=0
for diameter in statsDictUV['Diameters']:
poreDiameter=poreDiameter+diameter
poreDiameter=poreDiameter/len(statsDictUV['Diameters'])
redTotal=0
for red in statsDictUV['redPercentage']:
redTotal=redTotal+red
redAverage=redTotal/len(statsDictUV['redPercentage'])
statslist=[len(porphyrinList), 100*redAverage];
statsheader=[Messages.Porphyrins, Messages.PercentageRedPixels]
print("Roi Area: "+str(inputRoiArea))
print("Total Pore Area: "+str(totalUVPoreArea))
print("Average Pore Area: "+str(averageUVPoreArea))
print str(len(uvPoreList))+" "+str(len(porphyrinList))+" "+str(len(sebumList))+" "+str(100*totalUVPoreArea/inputRoiArea)+" "+str(100*redAverage)
print "cp min circularity"+str(detectionParameters.closedPoresMinCircularity)+":"+str(detectionParameters.closedPoresMinSize)
# close the thresholded image
impthresholded.changes=False
impthresholded.close()
return uvPoreList, statslist, statsheader
def duplicate_channel(imp, start_slice, end_slice, channel):
d = Duplicator()
new_imp = d.run(imp, channel, channel, start_slice, end_slice, 1, 1)
return new_imp
def NND(imp, mapC, compareC):
cal = imp.getCalibration()
title = imp.getTitle()
impZ = imp.getNSlices()
dup = Duplicator()
compare = dup.run(imp, compareC, compareC, 1, impZ, 1, 1)
compare = reslice(compare, cal.pixelWidth)
IJ.run(compare, "Gaussian Blur 3D...", "x=3 y=3 z=3")
Z = compare.getNSlices()
IJ.setAutoThreshold(compare, THRESHOLD + " dark stack")
Prefs.blackBackground = True
IJ.run(compare, "Convert to Mask",
"method=" + THRESHOLD + " background=Dark black")
IJ.run(compare, "Exact Signed Euclidean Distance Transform (3D)", "")
edtcompare = WindowManager.getImage("EDT")
edtcompare.getWindow().setVisible(False)
mapp = dup.run(imp, mapC, mapC, 1, impZ, 1, 1)
mapp = reslice(mapp, cal.pixelWidth)
IJ.run(mapp, "Gaussian Blur 3D...", "x=3 y=3 z=3")
IJ.setAutoThreshold(mapp, THRESHOLD + " dark stack")
Prefs.blackBackground = True
IJ.run(mapp, "Convert to Mask",
"method=" + THRESHOLD + " background=Dark black")
dists = []
rt = ResultsTable()
ol = Overlay()
row = 0
for z in range(Z):
mapp.setPosition(z + 1)
IJ.run(mapp, "Create Selection", "")
if mapp.getStatistics().mean == 0:
IJ.run(mapp, "Make Inverse", "")
roi = mapp.getRoi()
if roi is None:
continue
edtcompare.setPosition(z + 1)
edtcompare.setRoi(roi)
IJ.setBackgroundColor(0, 0, 0)
IJ.run(edtcompare, "Clear Outside", "slice")
ip = edtcompare.getProcessor()
roiList = ShapeRoi(roi).getRois() #split roi to limit bounds
for sr in roiList:
bounds = sr.getBounds()
for y in range(0, bounds.height):
for x in range(0, bounds.width):
if sr.contains(bounds.x + x, bounds.y + y):
d = ip.getf(bounds.x + x,
bounds.y + y) * cal.pixelWidth * 1000
rt.setValue("C" + str(mapC) + " X", row,
(bounds.x + x) * cal.pixelWidth)
rt.setValue("C" + str(mapC) + " Y", row,
(bounds.y + y) * cal.pixelHeight)
rt.setValue("C" + str(mapC) + " Z", row,
z * cal.pixelDepth)
rt.setValue("Distance to C" + str(compareC) + " (nm)",
row, d)
row += 1
histD = d
if histD >= 0: #set all overlapping voxel distances to 0
histD = 0
dists.append(
-histD) #invert to positive for outside distance
posZ = int(((z + 1) / float(Z)) * impZ) + 1
roi.setPosition(0, posZ, 1)
roi.setStrokeColor(Colour.MAGENTA)
ol.add(roi)
compare.setPosition(z + 1)
IJ.run(compare, "Create Selection", "")
if compare.getStatistics().mean == 0:
IJ.run(compare, "Make Inverse", "")
compareRoi = compare.getRoi()
if compareRoi is not None:
compareRoi.setPosition(0, posZ, 1)
compareRoi.setStrokeColor(Colour.CYAN)
ol.add(compareRoi)
edtcompare.killRoi()
histogram(title + " C" + str(mapC) + "-C" + str(compareC) + " Distance",
dists)
rt.show(title + " C" + str(mapC) + "-C" + str(compareC) + " Distance")
imp.setOverlay(ol)
compare.close()
edtcompare.changes = False
edtcompare.close()
mapp.close()
def getThreshold(self, imp, method): thresholder = Auto_Threshold() duplicator = Duplicator() tmp = duplicator.run(imp) return thresholder.exec(tmp, method, False, False, True, False, False, True)
def poreDetectionUV(inputImp, inputDataset, inputRoi, ops, data, display,
detectionParameters):
# set calibration
detectionParameters.setCalibration(inputImp)
# calculate area of roi
stats = inputImp.getStatistics()
inputRoiArea = stats.area
# get the bounding box of the active roi
inputRec = inputRoi.getBounds()
x1 = long(inputRec.getX())
y1 = long(inputRec.getY())
x2 = x1 + long(inputRec.getWidth()) - 1
y2 = y1 + long(inputRec.getHeight()) - 1
# crop the roi
interval = FinalInterval(array([x1, y1, 0], 'l'), array([x2, y2, 2], 'l'))
#cropped=ops.image().crop(interval, None, inputDataset.getImgPlus() )
cropped = ops.image().crop(inputDataset.getImgPlus(), interval)
datacropped = data.create(cropped)
display.createDisplay("cropped", datacropped)
croppedPlus = IJ.getImage()
# instantiate the duplicator and the substackmaker classes
duplicator = Duplicator()
substackMaker = SubstackMaker()
# duplicate the roi
duplicate = duplicator.run(croppedPlus)
# convert duplicate of roi to HSB and get brightness
IJ.run(duplicate, "HSB Stack", "")
brightnessPlus = substackMaker.makeSubstack(duplicate, "3-3")
brightness = ImgPlus(ImageJFunctions.wrapByte(brightnessPlus))
brightnessPlus.setTitle("Brightness")
#brightnessPlus.show()
# make another duplicate, split channels and get red
duplicate = duplicator.run(croppedPlus)
channels = ChannelSplitter().split(duplicate)
redPlus = channels[0]
red = ImgPlus(ImageJFunctions.wrapByte(redPlus))
# convert to lab
IJ.run(croppedPlus, "Color Transformer", "colour=Lab")
IJ.selectWindow('Lab')
labPlus = IJ.getImage()
croppedPlus.changes = False
croppedPlus.close()
# get the A channel
APlus = substackMaker.makeSubstack(labPlus, "2-2")
APlus.setTitle('A')
#APlus.show()
APlus.getProcessor().resetMinAndMax()
#APlus.updateAndDraw()
AThresholded = threshold(APlus, -10, 50)
# get the B channel
BPlus = substackMaker.makeSubstack(labPlus, "3-3")
BPlus.setTitle('B')
#BPlus.show()
BPlus.getProcessor().resetMinAndMax()
#BPlus.updateAndDraw()
BThresholded = threshold(BPlus, -10, 50)
# AND the Athreshold and Bthreshold to get a map of the red pixels
ic = ImageCalculator()
redMask = ic.run("AND create", AThresholded, BThresholded)
IJ.run(redMask, "Divide...", "value=255")
labPlus.close()
fast = True
# threshold the spots from the red channel
if (fast == False):
thresholdedred = SpotDetectionGray(red, data, display, ops, "triangle")
impthresholdedred = ImageJFunctions.wrap(thresholdedred, "wrapped")
else:
impthresholdedred = SpotDetection2(redPlus)
# threshold the spots from the brightness channel
if (fast == False):
thresholded = SpotDetectionGray(brightness, data, display, ops,
"triangle")
impthresholded = ImageJFunctions.wrap(thresholded, "wrapped")
else:
impthresholded = SpotDetection2(brightnessPlus)
# or the thresholding results from red and brightness channel
impthresholded = ic.run("OR create", impthresholded, impthresholdedred)
roim = RoiManager(True)
# convert to mask
Prefs.blackBackground = True
IJ.run(impthresholded, "Convert to Mask", "")
def isRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean > detectionParameters.porphyrinRedPercentage):
return True
else:
return False
def notRed(imp, roi):
stats = imp.getStatistics()
if (stats.mean > detectionParameters.porphyrinRedPercentage):
return False
else:
return True
roiClone = inputRoi.clone()
roiClone.setLocation(0, 0)
Utility.clearOutsideRoi(impthresholded, roiClone)
impthresholded.show()
countParticles(impthresholded, roim, detectionParameters.porphyrinMinSize, detectionParameters.porphyrinMaxSize, \
detectionParameters.porphyrinMinCircularity, detectionParameters.porphyrinMaxCircularity)
uvPoreList = []
for roi in roim.getRoisAsArray():
uvPoreList.append(roi.clone())
#allList=uvPoreList+closedPoresList+openPoresList
# count particles that are porphyrins (red)
porphyrinList = CountParticles.filterParticlesWithFunction(
redMask, uvPoreList, isRed)
# count particles that are visible on uv but not porphyrins
sebumList = CountParticles.filterParticlesWithFunction(
redMask, uvPoreList, notRed)
# for each roi add the offset such that the roi is positioned in the correct location for the
# original image
[
roi.setLocation(roi.getXBase() + x1,
roi.getYBase() + y1) for roi in uvPoreList
]
# draw the ROIs on to the image
inputImp.getProcessor().setColor(Color.green)
IJ.run(inputImp, "Line Width...", "line=3")
inputImp.getProcessor().draw(inputRoi)
IJ.run(inputImp, "Line Width...", "line=1")
[
CountParticles.drawParticleOnImage(inputImp, roi, Color.magenta)
for roi in porphyrinList
]
[
CountParticles.drawParticleOnImage(inputImp, roi, Color.green)
for roi in sebumList
]
inputImp.updateAndDraw()
# calculate stats for the UV visible particles
detectionParameters.setCalibration(APlus)
statsDictUV = CountParticles.calculateParticleStatsUV(
APlus, BPlus, redMask, roim.getRoisAsArray())
totalUVPoreArea = 0
for area in statsDictUV['Areas']:
totalUVPoreArea = totalUVPoreArea + area
averageUVPoreArea = totalUVPoreArea / len(statsDictUV['Areas'])
poreDiameter = 0
for diameter in statsDictUV['Diameters']:
poreDiameter = poreDiameter + diameter
poreDiameter = poreDiameter / len(statsDictUV['Diameters'])
redTotal = 0
for red in statsDictUV['redPercentage']:
redTotal = redTotal + red
redAverage = redTotal / len(statsDictUV['redPercentage'])
statslist = [len(porphyrinList), 100 * redAverage]
statsheader = [Messages.Porphyrins, Messages.PercentageRedPixels]
print("Roi Area: " + str(inputRoiArea))
print("Total Pore Area: " + str(totalUVPoreArea))
print("Average Pore Area: " + str(averageUVPoreArea))
print str(len(uvPoreList)) + " " + str(len(porphyrinList)) + " " + str(
len(sebumList)) + " " + str(
100 * totalUVPoreArea / inputRoiArea) + " " + str(100 * redAverage)
print "cp min circularity" + str(
detectionParameters.closedPoresMinCircularity) + ":" + str(
detectionParameters.closedPoresMinSize)
# close the thresholded image
impthresholded.changes = False
impthresholded.close()
return uvPoreList, statslist, statsheader
def poreDetectionTrueColor(inputImp, inputDataset, inputRoi, ops, data, display, detectionParameters):
detectionParameters.setCalibration(inputImp);
# calculate area of roi
stats=inputImp.getStatistics()
inputRoiArea=stats.area
# get the bounding box of the active roi
inputRec = inputRoi.getBounds()
x1=long(inputRec.getX())
y1=long(inputRec.getY())
x2=x1+long(inputRec.getWidth())-1
y2=y1+long(inputRec.getHeight())-1
# crop the roi
interval=FinalInterval( array([x1, y1 ,0], 'l'), array([x2, y2, 2], 'l') )
cropped=ops.image().crop(inputDataset.getImgPlus(), interval )
datacropped=data.create(cropped)
display.createDisplay("cropped", datacropped)
croppedPlus=IJ.getImage()
# instantiate the duplicator and the substackmaker classes
duplicator=Duplicator()
substackMaker=SubstackMaker()
# duplicate the roi
duplicate=duplicator.run(croppedPlus)
# separate into RGB and get the blue channel
IJ.run(duplicate, "RGB Stack", "")
bluePlus=substackMaker.makeSubstack(duplicate, "3-3")
blue=ImgPlus(ImageJFunctions.wrapByte(bluePlus))
bluePlus.setTitle("Blue")
# duplicate and look for bright spots
thresholdedLight=SpotDetection2(bluePlus)
# duplicate and look for dark spots
thresholdedDark=SpotDetection3(bluePlus, True)
# convert to mask
Prefs.blackBackground = True
#IJ.run(thresholdedDark, "Convert to Mask", "")substackMaker
# clear the region outside the roi
clone=inputRoi.clone()
clone.setLocation(0,0)
Utility.clearOutsideRoi(thresholdedLight, clone)
Utility.clearOutsideRoi(thresholdedDark, clone)
roimClosedPores = RoiManager(True)
detectionParameters.setCalibration(thresholdedDark)
countParticles(thresholdedDark, roimClosedPores, detectionParameters.closedPoresMinSize, detectionParameters.closedPoresMaxSize, \
detectionParameters.closedPoresMinCircularity, detectionParameters.closedPoresMaxCircularity)
# count number of open pores
roimOpenPores = RoiManager(True)
detectionParameters.setCalibration(thresholdedDark)
countParticles(thresholdedDark, roimOpenPores, detectionParameters.openPoresMinSize, detectionParameters.openPoresMaxSize, \
detectionParameters.openPoresMinCircularity, detectionParameters.openPoresMaxCircularity)
# count number of sebum
roimSebum = RoiManager(True)
detectionParameters.setCalibration(thresholdedLight)
countParticles(thresholdedLight, roimSebum, detectionParameters.sebumMinSize, detectionParameters.sebumMaxSize, \
detectionParameters.sebumMinCircularity, detectionParameters.sebumMaxCircularity)
# create lists for open and closed pores
closedPoresList=[]
for roi in roimClosedPores.getRoisAsArray():
closedPoresList.append(roi.clone())
openPoresList=[]
for roi in roimOpenPores.getRoisAsArray():
openPoresList.append(roi.clone())
# create lists for sebum
sebumsList=[]
for roi in roimSebum.getRoisAsArray():
sebumsList.append(roi.clone())
# a list of all pores
allList=closedPoresList+openPoresList+sebumsList
# calculate the stats for all pores
detectionParameters.setCalibration(bluePlus)
statsDict=CountParticles.calculateParticleStats(bluePlus, allList)
poresTotalArea=0
for area in statsDict['Areas']:
poresTotalArea=poresTotalArea+area
print area
poresAverageArea=poresTotalArea/len(statsDict['Areas'])
# for each roi add the offset such that the roi is positioned in the correct location for the
# original image
[roi.setLocation(roi.getXBase()+x1, roi.getYBase()+y1) for roi in allList]
# draw the rois on the image
inputImp.getProcessor().setColor(Color.green)
IJ.run(inputImp, "Line Width...", "line=3");
inputImp.getProcessor().draw(inputRoi)
IJ.run(inputImp, "Line Width...", "line=1");
[CountParticles.drawParticleOnImage(inputImp, roi, Color.red) for roi in closedPoresList]
[CountParticles.drawParticleOnImage(inputImp, roi, Color.magenta) for roi in openPoresList]
[CountParticles.drawParticleOnImage(inputImp, roi, Color.green) for roi in sebumsList]
inputImp.updateAndDraw()
# close images that represent intermediate steps
croppedPlus.changes=False
croppedPlus.close()
bluePlus.changes=False
bluePlus.close()
print "Total ROI Area: "+str(inputRoiArea)
print "Num closed pores: "+str(len(closedPoresList))
print "Num open pores: "+str(len(openPoresList))
print "Num sebums: "+str(len(sebumsList))
print "Total particles: "+str(len(allList))+ " total area: "+str(poresTotalArea)
statslist=[inputRoiArea, len(allList), len(closedPoresList), len(openPoresList), len(sebumsList), poresAverageArea, 100*poresTotalArea/inputRoiArea]
header=[Messages.TotalAreaMask, Messages.TotalDetectedPores, Messages.ClosedPores, Messages.OpenPores, Messages.Sebum, Messages.PoresAverageArea, Messages.PoresFractionalArea]
return header,statslist
def poreDetectionTrueColor(inputImp, inputDataset, inputRoi, ops, data,
display, detectionParameters):
detectionParameters.setCalibration(inputImp)
# calculate area of roi
stats = inputImp.getStatistics()
inputRoiArea = stats.area
# get the bounding box of the active roi
inputRec = inputRoi.getBounds()
x1 = long(inputRec.getX())
y1 = long(inputRec.getY())
x2 = x1 + long(inputRec.getWidth()) - 1
y2 = y1 + long(inputRec.getHeight()) - 1
# crop the roi
interval = FinalInterval(array([x1, y1, 0], 'l'), array([x2, y2, 2], 'l'))
cropped = ops.crop(interval, None, inputDataset.getImgPlus())
datacropped = data.create(cropped)
display.createDisplay("cropped", datacropped)
croppedPlus = IJ.getImage()
duplicator = Duplicator()
substackMaker = SubstackMaker()
# duplicate the roi
duplicate = duplicator.run(croppedPlus)
# separate into RGB and get the blue channel
IJ.run(duplicate, "RGB Stack", "")
bluePlus = substackMaker.makeSubstack(duplicate, "3-3")
blue = ImgPlus(ImageJFunctions.wrapByte(bluePlus))
bluePlus.setTitle("Blue")
# duplicate and look for bright spots
thresholdedLight = SpotDetection2(bluePlus)
# duplicate and look for dark spots
thresholdedDark = SpotDetection3(bluePlus, True)
# convert to mask
Prefs.blackBackground = True
#IJ.run(thresholdedDark, "Convert to Mask", "")
# clear the region outside the roi
clone = inputRoi.clone()
clone.setLocation(0, 0)
Utility.clearOutsideRoi(thresholdedLight, clone)
Utility.clearOutsideRoi(thresholdedDark, clone)
roimClosedPores = RoiManager(True)
detectionParameters.setCalibration(thresholdedDark)
countParticles(thresholdedDark, roimClosedPores, detectionParameters.closedPoresMinSize, detectionParameters.closedPoresMaxSize, \
detectionParameters.closedPoresMinCircularity, detectionParameters.closedPoresMaxCircularity)
# count number of open pores
roimOpenPores = RoiManager(True)
detectionParameters.setCalibration(thresholdedDark)
countParticles(thresholdedDark, roimOpenPores, detectionParameters.openPoresMinSize, detectionParameters.openPoresMaxSize, \
detectionParameters.openPoresMinCircularity, detectionParameters.openPoresMaxCircularity)
# count number of sebum
roimSebum = RoiManager(True)
detectionParameters.setCalibration(thresholdedLight)
countParticles(thresholdedLight, roimSebum, detectionParameters.sebumMinSize, detectionParameters.sebumMaxSize, \
detectionParameters.sebumMinCircularity, detectionParameters.sebumMaxCircularity)
# create lists for open and closed pores
closedPoresList = []
for roi in roimClosedPores.getRoisAsArray():
closedPoresList.append(roi.clone())
openPoresList = []
for roi in roimOpenPores.getRoisAsArray():
openPoresList.append(roi.clone())
# create lists for sebum
sebumsList = []
for roi in roimSebum.getRoisAsArray():
sebumsList.append(roi.clone())
# a list of all pores
allList = closedPoresList + openPoresList + sebumsList
# calculate the stats for all pores
detectionParameters.setCalibration(bluePlus)
statsDict = CountParticles.calculateParticleStats(bluePlus, allList)
poresTotalArea = 0
for area in statsDict['Areas']:
poresTotalArea = poresTotalArea + area
print area
poresAverageArea = poresTotalArea / len(statsDict['Areas'])
# for each roi add the offset such that the roi is positioned in the correct location for the
# original image
[
roi.setLocation(roi.getXBase() + x1,
roi.getYBase() + y1) for roi in allList
]
# draw the rois on the image
inputImp.getProcessor().setColor(Color.green)
IJ.run(inputImp, "Line Width...", "line=3")
inputImp.getProcessor().draw(inputRoi)
IJ.run(inputImp, "Line Width...", "line=1")
[
CountParticles.drawParticleOnImage(inputImp, roi, Color.red)
for roi in closedPoresList
]
[
CountParticles.drawParticleOnImage(inputImp, roi, Color.magenta)
for roi in openPoresList
]
[
CountParticles.drawParticleOnImage(inputImp, roi, Color.green)
for roi in sebumsList
]
inputImp.updateAndDraw()
# close images that represent intermediate steps
croppedPlus.changes = False
croppedPlus.close()
bluePlus.changes = False
bluePlus.close()
print "Total ROI Area: " + str(inputRoiArea)
print "Num closed pores: " + str(len(closedPoresList))
print "Num open pores: " + str(len(openPoresList))
print "Num sebums: " + str(len(sebumsList))
print "Total particles: " + str(
len(allList)) + " total area: " + str(poresTotalArea)
statslist = [
inputRoiArea,
len(allList),
len(closedPoresList),
len(openPoresList),
len(sebumsList), poresAverageArea, 100 * poresTotalArea / inputRoiArea
]
header = [
Messages.TotalAreaMask, Messages.TotalDetectedPores,
Messages.ClosedPores, Messages.OpenPores, Messages.Sebum,
Messages.PoresAverageArea, Messages.PoresFractionalArea
]
return header, statslist
