def resetpressed(event):
self.__ranges.clear()
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#rm.runCommand("Show All")
#rm.runCommand("Select All")
#rm.runCommand("Set Color", "blue")
IJ.resetThreshold(self.__image)
keys=self.__slidersDict.keys()
for k in keys:
if k.endswith("min"):
self.__slidersDict[k].setValue(0)
self.__slidersDict[k].repaint()
else:
self.__slidersDict[k].setValue(self.__slidersDict[k].getMaximum())
self.__slidersDict[k].repaint()
def getFlipArray(maskPAImgPlus):
"""Given the PA-aligned mask image, return a list of booleans, indicating whether or not we should flip the corresponding index"""
maskPAImgPlus.show()
# IJ.run(maskPAImgPlus, "Shape Smoothing", "relative_proportion_fds=15 absolute_number_fds=2 keep=[Relative_proportion of FDs] stack");
IJ.run("Set Measurements...", "shape")
IJ.setThreshold(maskPAImgPlus, 1, 1000, "No Update")
stk = maskPAImgPlus.getStack()
tableLeft = ResultsTable()
PA.setResultsTable(tableLeft)
IJ.makeRectangle(0, 0,
maskPAImgPlus.getWidth() / 2 - 5,
maskPAImgPlus.getHeight())
IJ.run(maskPAImgPlus, "Analyze Particles...", "stack")
tableRight = ResultsTable()
PA.setResultsTable(tableRight)
IJ.makeRectangle(maskPAImgPlus.getWidth() / 2 - 5, 0,
maskPAImgPlus.getWidth() / 2 + 5,
maskPAImgPlus.getHeight())
IJ.run(maskPAImgPlus, "Analyze Particles...", "stack")
maskPAImgPlus.hide()
IJ.resetThreshold(maskPAImgPlus)
leftCirc = [tableLeft.getValue("Circ.", i) for i in range(stk.getSize())]
rightCirc = [tableRight.getValue("Circ.", i) for i in range(stk.getSize())]
return [leftCirc[i] < rightCirc[i] for i in range(len(leftCirc))]
def get_threshold(imp, method):
# from ij.process import AutoThresholder
# from ij.process import ImageStatistics
# thresholder = AutoThresholder()
# stats = imp.getProcessor().getStatistics()
# value = thresholder.getThreshold(method, stats.histogram)
arg = "%s dark" % method
IJ.setAutoThreshold(imp, arg)
value = imp.getProcessor().getMinThreshold()
IJ.resetThreshold(imp)
return value
def updatepressed(event):
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.run("Threshold...")
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rt.show("tempRT")
areas=rt.getColumn(ResultsTable.AREA)
means=rt.getColumn(ResultsTable.MEAN)
majors=rt.getColumn(ResultsTable.MAJOR)
minors=rt.getColumn(ResultsTable.MINOR)
#print 0
if self.__slidersDict["Area_max"].getMaximum() < int(max(areas)+1):
# print 1
self.__slidersDict["Area_max"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Area_min"].getMaximum() < int(max(areas)+1):
# print 2
self.__slidersDict["Area_min"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Mean_max"].getMaximum() < int(max(means)+1):
# print 3
self.__slidersDict["Mean_max"].setMaximum(int(max(means))+1)
if self.__slidersDict["Mean_min"].getMaximum() < int(max(means)+1):
# print 4
self.__slidersDict["Mean_min"].setMaximum(int(max(means))+1)
if self.__slidersDict["Major_max"].getMaximum() < int(max(majors)):
# print 5
self.__slidersDict["Major_max"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Major_min"].getMaximum() < int(max(majors)+1):
# print 6
self.__slidersDict["Major_min"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Minor_max"].getMaximum() < int(max(minors)+1):
# print 7
self.__slidersDict["Minor_max"].setMaximum(int(max(minors))+1)
if self.__slidersDict["Minor_min"].getMaximum() < int(max(minors)+1):
# print 8
self.__slidersDict["Minor_min"].setMaximum(int(max(minors))+1)
if self.__slidersDict["AR_max"].getMaximum() < int((max(majors)+1)/min(minors)+1):
# print 9
self.__slidersDict["AR_max"].setMaximum(int((max(majors)+1)/(min(minors))))
if self.__slidersDict["AR_min"].getMaximum() < int((max(majors)+1)/min(minors)):
# print 10
self.__slidersDict["AR_min"].setMaximum(int((max(majors)+1)/(min(minors))))
#print 11
for sb in self.__slidersDict.values():
sb.repaint()
#rm.runCommand("reset")
#temprois=self.getIncludeRois()
#IJ.run(self.__image, "Remove Overlay", "")
#o=Overlay()
#for roi in temprois:
# o.addElement(roi)
#self.__image.killRoi()
#self.__image.setOverlay(o)
self.__image.updateAndDraw()
def showSettingsDialog(self):
if self.__image.getOverlay() is not None : self.__image.getOverlay().clear()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
#rm.runCommand("Deselect")
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rm.runCommand("Show All")
self.__ranges.clear()
#areas, means, majors, minors=[],[],[],[]
#for roi in self.__roisArray:
# m=Morph(self.__image, roi)
# areas.append(m.Area)
# means.append(m.Mean)
# majors.append(m.Major)
# minors.append(m.Minor)
#maxarea=max(areas)*1000
#maxint=max(means)*10
#maxline=max(majors)*100
#maxminline=max(minors)*100
#minline=min(minors)
#namemeasures=["Area", "Mean", "Angle", "Major", "Minor", "Solidity", "AR", "Round", "Circ"]
#maxmeasures=[maxarea, maxint, 180*10, maxline, maxminline, 1*1000, (maxline/minline), 1*1000, 1*1000]
#set1000=Set(["Solidity", "Round", "Circ"])
#set10=Set(["Angle"])
def buttonPressed(event):
temprois=self.getIncludeRois()
for roi in temprois:
m=Morph(self.__image, roi)
IJ.log("----------------------------------")
IJ.log(roi.getName())
for r in self.__ranges.values():
IJ.log(r[0]+" min= "+str(r[1])+" < val="+str(m.__getattribute__(r[0]))+" < max= "+str(r[2]))
IJ.run(self.__image, "Remove Overlay", "")
o=Overlay()
for roi in temprois:
o.addElement(roi)
self.__image.killRoi()
self.__image.setOverlay(o)
self.__image.updateAndDraw()
def updatepressed(event):
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.run("Threshold...")
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rt.show("tempRT")
areas=rt.getColumn(ResultsTable.AREA)
means=rt.getColumn(ResultsTable.MEAN)
majors=rt.getColumn(ResultsTable.MAJOR)
minors=rt.getColumn(ResultsTable.MINOR)
#print 0
if self.__slidersDict["Area_max"].getMaximum() < int(max(areas)+1):
# print 1
self.__slidersDict["Area_max"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Area_min"].getMaximum() < int(max(areas)+1):
# print 2
self.__slidersDict["Area_min"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Mean_max"].getMaximum() < int(max(means)+1):
# print 3
self.__slidersDict["Mean_max"].setMaximum(int(max(means))+1)
if self.__slidersDict["Mean_min"].getMaximum() < int(max(means)+1):
# print 4
self.__slidersDict["Mean_min"].setMaximum(int(max(means))+1)
if self.__slidersDict["Major_max"].getMaximum() < int(max(majors)):
# print 5
self.__slidersDict["Major_max"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Major_min"].getMaximum() < int(max(majors)+1):
# print 6
self.__slidersDict["Major_min"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Minor_max"].getMaximum() < int(max(minors)+1):
# print 7
self.__slidersDict["Minor_max"].setMaximum(int(max(minors))+1)
if self.__slidersDict["Minor_min"].getMaximum() < int(max(minors)+1):
# print 8
self.__slidersDict["Minor_min"].setMaximum(int(max(minors))+1)
if self.__slidersDict["AR_max"].getMaximum() < int((max(majors)+1)/min(minors)+1):
# print 9
self.__slidersDict["AR_max"].setMaximum(int((max(majors)+1)/(min(minors))))
if self.__slidersDict["AR_min"].getMaximum() < int((max(majors)+1)/min(minors)):
# print 10
self.__slidersDict["AR_min"].setMaximum(int((max(majors)+1)/(min(minors))))
#print 11
for sb in self.__slidersDict.values():
sb.repaint()
#rm.runCommand("reset")
#temprois=self.getIncludeRois()
#IJ.run(self.__image, "Remove Overlay", "")
#o=Overlay()
#for roi in temprois:
# o.addElement(roi)
#self.__image.killRoi()
#self.__image.setOverlay(o)
self.__image.updateAndDraw()
def resetpressed(event):
self.__ranges.clear()
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#rm.runCommand("Show All")
#rm.runCommand("Select All")
#rm.runCommand("Set Color", "blue")
IJ.resetThreshold(self.__image)
keys=self.__slidersDict.keys()
for k in keys:
if k.endswith("min"):
self.__slidersDict[k].setValue(0)
self.__slidersDict[k].repaint()
else:
self.__slidersDict[k].setValue(self.__slidersDict[k].getMaximum())
self.__slidersDict[k].repaint()
def valueChanged(event):
name=event.getSource().getName()
names=name.split("_")
factor=1
if names[0] in self.__set1000: factor=0.001
if names[0] in self.__set10:factor=0.1
value=event.getSource().getValue()*factor
if names[1]=="min":
self.__ranges[names[0]]=(names[0], value, self.__slidersDict[names[0]+"_max"].getValue()*factor, self.__boxesDict[names[0]].getState())
#self.__ranges[names[0]]=(names[0], value, self.__slidersDict[names[0]+"_max"].getValue()*factor)
else: self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, value, self.__boxesDict[names[0]].getState())
#self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, value)
temprois=self.getIncludeRois()
IJ.run(self.__image, "Remove Overlay", "")
o=Overlay()
for roi in temprois:
o.addElement(roi)
self.__image.killRoi()
self.__image.setOverlay(o)
self.__image.updateAndDraw()
def selectAll(event):
name=event.getSource().getLabel()
names=name.split("_")
factor=1
if names[0] in self.__set1000: factor=0.001
if names[0] in self.__set10:factor=0.1
name=event.getSource().getLabel()
names=name.split("_")
value=event.getSource().getState()
self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, self.__slidersDict[names[0]+"_max"].getValue()*factor, value)
gd0=NonBlockingGenericDialog("settings")
gd0.setResizable(True)
gd0.setFont(Font("Courrier", 1, 8))
count=0
self.__slidersDict={}
self.__boxesDict={}
self.__boxesDict.clear()
self.__slidersDict.clear()
for i in range(len(self.__namemeasures)):
gd0.setInsets(-10,0,0)
gd0.addSlider("Min"+self.__namemeasures[i], 0, self.__maxmeasures[i], 0)
gd0.getSliders().get(count).adjustmentValueChanged = valueChanged
gd0.getSliders().get(count).setName(self.__namemeasures[i]+"_min")
self.__slidersDict[self.__namemeasures[i]+"_min"]=gd0.getSliders().get(count)
gd0.addSlider("Max"+self.__namemeasures[i], 0, self.__maxmeasures[i], self.__maxmeasures[i])
gd0.getSliders().get(count+1).adjustmentValueChanged = valueChanged
gd0.getSliders().get(count+1).setName(self.__namemeasures[i]+"_max")
self.__slidersDict[self.__namemeasures[i]+"_max"]=gd0.getSliders().get(count+1)
gd0.addCheckbox("all", True)
gd0.getCheckboxes().get(i).itemStateChanged = selectAll
gd0.getCheckboxes().get(i).setLabel(self.__namemeasures[i]+"_all")
self.__boxesDict[self.__namemeasures[i]]=gd0.getCheckboxes().get(i)
gd0.setInsets(-10,0,0)
#gd0.addMessage("...........................................................................")
count=count+2
panel0=Panel()
#trybutton=Button("Try")
#trybutton.setActionCommand("DrawOverlay")
#trybutton.actionPerformed = buttonPressed
#updatebutton=Button("Update")
#updatebutton.setActionCommand("Update")
#updatebutton.actionPerformed = updatepressed
#resetbutton=Button("Reset")
#resetbutton.setActionCommand("Reset")
#resetbutton.actionPerformed = resetpressed
#panel0.add(trybutton)
#panel0.add(updatebutton)
#panel0.add(resetbutton)
#gd0.addPanel(panel0)
gd0.setResizable(True)
gd0.showDialog()
#self.__image.setSlice(self.__firstslice)
#self.__image.updateAndDraw()
if gd0.wasOKed():
#for key in self.__ranges.keys(): IJ.log("Measure : "+str(self.__ranges[key][0])+" min = "+str(self.__ranges[key][1])+" max = "+str(self.__ranges[key][2]))
return self.__ranges
def reduceZ():
imp = IJ.getImage() #get the standardtack
title_1 = imp.getTitle()
title = title_1.split(' - ')[1]
print(title)
dimentions = imp.getDimensions()
numZ, numChannels, numframes = dimentions[3], dimentions[2], dimentions[4]
print(numChannels)
IJ.run(imp, "Set Measurements...", "kurtosis redirect=None decimal=3")
kurtTotal = []
for time in range(numframes):
print(time)
time = time + 1
imp.setPosition(1, 1, time)
kurt = []
for z in range(numZ):
z = z + 1
imp.setPosition(1, z, time)
imp.setRoi(70, 40, 437, 459)
IJ.setAutoThreshold(imp, "MaxEntropy dark")
IJ.run(imp, "Measure", "")
IJ.resetThreshold(imp)
rt = ResultsTable()
t = rt.getResultsTable()
kurt.append(t.getValueAsDouble(23, z - 1)) # 23 = kurtosis
kurtTotal.append(kurt.index(max(kurt)) + 1)
IJ.run(imp, "Clear Results", "")
print(kurtTotal)
IJ.run(imp, "Select All", "")
imp2 = IJ.createImage("GFP", "16-bit black", dimentions[0], dimentions[1],
numframes)
imp2 = HyperStackConverter.toHyperStack(imp2, 1, 1, numframes, "Color")
print(' ------------')
print(numframes)
channel = 1
i = 0
for time in range(numframes):
time = time + 1
imp.setPosition(channel, kurtTotal[i], time)
imp.copy()
imp2.setPosition(channel, 1, time)
imp2.paste()
print(time)
i = i + 1
IJ.run(imp2, "Delete Slice", "delete=slice")
imp2.show()
imp4 = IJ.createImage("RFP", "16-bit black", dimentions[0], dimentions[1],
numframes)
imp4 = HyperStackConverter.toHyperStack(imp4, 1, 1, numframes, "Color")
print(' ------------')
channel = 2
i = 0
for time in range(numframes):
time = time + 1
imp.setPosition(channel, kurtTotal[i], time)
imp.copy()
print(imp.title)
imp4.setPosition(channel, 1, time)
imp4.paste()
i = i + 1
IJ.run(imp4, "Delete Slice", "delete=slice")
imp4.show()
IJ.selectWindow(title_1)
IJ.run("Close")
imp5 = ImagePlus()
IJ.run(imp5, "Merge Channels...", "c1=RFP c2=GFP create")
imp5 = IJ.getImage()
IJ.run(
imp5, "Bio-Formats Exporter",
"save=/home/rickettsia/Desktop/data/Clamydial_Image_Analysis/EMS_BMEC_20X_01192020/Zreduced/"
+ title + ".ome.tif export compression=LZW")
IJ.selectWindow('Merged')
IJ.run("Close")
######### open image using dialogue box
#imp = IJ.getImage()
original = IJ.openImage(getFile())
original.show()
########## Use thresholding and selection to define UFOV ###################################################################################
#IJ.run("ROI Manager...", "") # not sure if I need this
IJ.setRawThreshold(
original, 1, 255,
'') # background pixels have value 0. See IMAGE>ADJUST>THRESHOLD
IJ.run(original, "Create Selection",
"") # add bounding box. See EDIT>SELECTION
IJ.run(original, "To Bounding Box",
"") # this box defines the UFOV. See EDIT>SELECTION
IJ.resetThreshold(
original) # get back original now UFOV is definedthresholding
UFOV = Duplicator().run(
original) # duplicate the original image, only the CFOV
UFOV.setTitle("UFOV")
UFOV.show()
CFOV_fraction = 0.75 # choose the fraction of the UFOV that defines the CFOV
IJ.run(original, "Scale... ", "x=" + str(CFOV_fraction) + " y=" +
str(CFOV_fraction) + " centered") # rescale bounding box to get CFOV
CFOV = Duplicator().run(
original) # duplicate the original image, only the CFOV
CFOV.setTitle("CFOV")
CFOV.show()
gd.showDialog()
Pixel_size = gd.getNextNumber() #6.4 # ENTER mm, remember tolerance is +/-30%
return Pixel_size
######### open image using dialogue box
#imp = IJ.getImage()
original = IJ.openImage(getFile())
original.show()
########## Use thresholding and selection to define UFOV ###################################################################################
#IJ.run("ROI Manager...", "") # not sure if I need this
IJ.setRawThreshold(original, 1, 255,'') # background pixels have value 0. See IMAGE>ADJUST>THRESHOLD
IJ.run(original, "Create Selection", "") # add bounding box. See EDIT>SELECTION
IJ.run(original,"To Bounding Box", "") # this box defines the UFOV. See EDIT>SELECTION
IJ.resetThreshold(original) # get back original now UFOV is definedthresholding
UFOV = Duplicator().run(original) # duplicate the original image, only the CFOV
UFOV.setTitle("UFOV")
UFOV.show()
CFOV_fraction = 0.75 # choose the fraction of the UFOV that defines the CFOV
IJ.run(original,"Scale... ", "x="+str(CFOV_fraction)+" y="+str(CFOV_fraction)+" centered") # rescale bounding box to get CFOV
CFOV = Duplicator().run(original) # duplicate the original image, only the CFOV
CFOV.setTitle("CFOV")
CFOV.show()
######### Nema process including Re-bin image to larger pixels ################################################################################
desired_pixel_width = getPixel() # 6.4 mm default, remember tolerance is +/-30%
