def runPoreDetection():
'''roiManager=RoiManager(False)
roiManager.runCommand("open", roiname)
roiHash=roiManager.getROIs()
roi=roiHash.get("Right")
print roi'''
imageList = Utility.GetOpenImageList()
nbgd = NonBlockingGenericDialog(Messages.AddRoi)
nbgd.addMessage(Messages.ChooseImage)
if (imageList == None):
IJ.showMessage(Messages.noOpenImages)
return
nbgd.addChoice("Image1:", imageList, imageList[0])
nbgd.showDialog()
name = nbgd.getNextChoice()
inputImp = WindowManager.getImage(name)
inputDataset = Utility.getDatasetByName(data, name)
detectionParameters = DetectionParameters(10, 200, 0.5, 1.0, 0.3)
#inputImp.setRoi(roi)
nbgd2 = NonBlockingGenericDialog(Messages.PositionRoi)
nbgd2.addMessage(Messages.PositionRoiAndPressOK)
nbgd2.showDialog()
poreDetectionUV(inputImp, inputDataset,
inputImp.getRoi().clone(), ops, data, display,
detectionParameters)
def runPoreDetection():
'''roiManager=RoiManager(False)
roiManager.runCommand("open", roiname)
roiHash=roiManager.getROIs()
roi=roiHash.get("Right")
print roi'''
imageList=Utility.GetOpenImageList()
nbgd=NonBlockingGenericDialog(Messages.AddRoi)
nbgd.addMessage(Messages.ChooseImage)
if (imageList==None):
IJ.showMessage(Messages.noOpenImages)
return;
nbgd.addChoice("Image1:", imageList, imageList[0]);
nbgd.showDialog()
name = nbgd.getNextChoice()
inputImp = WindowManager.getImage(name)
inputDataset=Utility.getDatasetByName(data, name)
detectionParameters=DetectionParameters(10, 200, 0.5, 1.0, 0.3)
#inputImp.setRoi(roi)
nbgd2=NonBlockingGenericDialog(Messages.PositionRoi)
nbgd2.addMessage(Messages.PositionRoiAndPressOK)
nbgd2.showDialog()
poreDetectionUV(inputImp, inputDataset, inputImp.getRoi().clone(), ops, data, display, detectionParameters)
def apply_thresh_overlay(overlay):
''' Clear outside rois in overlay '''
# --- Dialog -----------------------------------
wlist = WindowManager.getImageTitles()
gd = NonBlockingGenericDialog('Apply Mask to')
gd.setCancelLabel('Exit')
gd.addChoice('Select Movie', wlist, wlist[0])
gd.addCheckbox('Duplicate', True)
gd.showDialog() # dialog is open
if gd.wasCanceled():
return False
sel_win = gd.getNextChoice()
do_duplicate = gd.getNextBoolean()
# --- Dialog End ------------------------------
win_name = IJ.selectWindow(sel_win)
movie = IJ.getImage()
movie = slices_to_frames(movie)
C = movie.getC()
S = movie.getSlice()
if do_duplicate:
IJ.log('duplicating ' + movie.shortTitle)
movie = movie.duplicate()
NFrames = movie.getNFrames()
if overlay.size() != NFrames: # one roi for each frame!
display_msg(
'Mask count mismatch!', 'Mask count mismatch!\nGot ' + str(Nrois) +
' masks and ' + str(NFrames) + ' frames.. !')
for frame in range(1, NFrames + 1):
movie.setPosition(C, S, frame)
mask_roi = overlay.get(frame - 1)
ip = movie.getProcessor()
ip.setValue(0)
ip.setRoi(mask_roi)
ip.fillOutside(mask_roi)
movie.show()
return True
def __selectMeasureStack(self) :
# We allow the user to choose what to measure in the stack, and on which stack.
gd1=NonBlockingGenericDialog("Stack Choice for measures")
idimages=WindowManager.getIDList()
images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
imagesnames=[img.getTitle() for img in images]
activindex=0
for i in range(len(imagesnames)) :
if imagesnames[i] == self.__activeTitle :
activindex=i
gd1.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
gd1.showDialog()
chosenstack=gd1.getNextChoice()
self.__img=WindowManager.getImage(chosenstack)
IJ.selectWindow(self.__img.getID())
if gd1.wasOKed() : return True
else : return False
def __selectTrackStack(self) :
gd0=NonBlockingGenericDialog("Stack Choice")
idimages=WindowManager.getIDList()
#images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
images=[WindowManager.getImage(imgID) for imgID in idimages]
imagesnames=[img.getTitle() for img in images]
for i in range(len(imagesnames)) :
if imagesnames[i] == self.__activeTitle : activindex=i
gd0.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
gd0.showDialog()
chosenstack=gd0.getNextChoice()
self.__img = WindowManager.getImage(chosenstack)
self.__maxLife = self.__img.getImageStackSize()
IJ.selectWindow(self.__img.getID())
self.__activeTitle=self.__img.getTitle()
self.__imagesnames[:]=[]
#self.__imagesnames.append("image1")
self.__imagesnames.append(self.__activeTitle)
if gd0.wasOKed() : return True
else : return False
def __settings(self, imgName, flag) :
"""
Allows the user to choose several parameters for the tracking.
"""
#fenetre=JFrame("Import")
#optionpane=JOptionPane("Do you want to import previous preferences ?",JOptionPane.QUESTION_MESSAGE ,JOptionPane.YES_NO_OPTION )
#optionpane.setVisible(True)
#dialog = optionpane.createDialog(fenetre, "Import")
#dialog.show()
#choice = optionpane.getValue()
#if choice==JOptionPane.YES_OPTION : self.__ImportPref()
image=self.__dictImages[imgName]
def outputpath(event) :
macrodir=IJ.getDirectory("macros")
frame = Frame("Select the macro file")
fd = FileDialog(frame)
fd.setDirectory(macrodir)
fd.show()
macrodir = fd.getDirectory()
self.__macropath = fd.getFile()
self.__text.setText(self.__macropath)
print self.__macropath
#self.__macropath=IJ.getDirectory("macros")
#self.__macropath=IJ.getDirectory("")
#self.__text.setText(self.__macropath)
panel0=Panel()
pathbutton=Button("Select macro file", actionPerformed = outputpath)
#pathbutton.actionPerformed = outputpath
self.__text = TextField(self.__macropath)
panel0.add(pathbutton)
panel0.add(self.__text)
# -------- start batch mode --------- #
if self.__batch :
pass
#self.__ImportPref(flag)
image.hide()
else :
image.show()
IJ.selectWindow(image.getID())
gd0=NonBlockingGenericDialog("Settings")
gd0.setFont(Font("Courrier", 1, 10))
gd0.addMessage("---------------- PRE-PROCESSING OPTIONS -------------------")
gd0.addCheckbox("Substract Background",self.__subback) #box 1 subback
gd0.addNumericField("Radius",self.__radius,0)
gd0.addCheckbox("Run a macro for pre processing",self.__runmacro) #box 2 runmacro
gd0.addPanel(panel0)
gd0.addMessage("-------------------------------------------")
gd0.addMessage("Tracking parameters")
gd0.addMessage("Coeffs modulate de weight of each parameter")
gd0.addMessage("Max delta set the maximum allowed change in absolute units")
gd0.addMessage(" ")
gd0.addNumericField("Coeff Area : ",self.__distparam[0],0)
gd0.addNumericField("Max deltaArea : ",self.__distparam[1],self.__nbdigits,6,"x times")
gd0.addNumericField("Coeff Angle : ",self.__distparam[2],0)
gd0.addNumericField("Max deltaAngle : ",self.__distparam[3],self.__nbdigits,6,"degrees")
gd0.addNumericField("Coeff Feret : ",self.__distparam[4],0)
gd0.addNumericField("Max deltaFeret : ",self.__distparam[5],self.__nbdigits,6,"x times")
gd0.addNumericField("Coeff PositionX : ",self.__distparam[6],0)
gd0.addNumericField("Max deltaPositionX : ",self.__distparam[7],self.__nbdigits,6,"pixels")
gd0.addNumericField("Coeff PositionY : ",self.__distparam[8],0)
gd0.addNumericField("Max deltaPositionY : ",self.__distparam[9],self.__nbdigits,6,"pixels")
gd0.addMessage("-------------------------------------------")
automethods=AutoThresholder.getMethods()
gd0.addCheckbox("Manual Threshold",self.__manthresh) #box 3 manthresh
gd0.addChoice("Threshol Method : ",automethods,self.__thresMethod)
gd0.addMessage("-------------------------------------------")
#gd0.addCheckbox("Symmetry Around 0-180",self.__optionAngle)
#gd0.addMessage("-------------------------------------------")
#gd0.addCheckbox("Save cell files", self.__optionSave)
#gd0.addMessage("-------------------------------------------")
gd0.addCheckbox("Track new cells", self.__optionNewCells) #box 4 newcells
gd0.addMessage("-------------------------------------------")
gd0.addCheckbox("Generate time list with follow time lapse interval ?", self.__optionTimelapse) #box 5 timelapse
gd0.addNumericField("Estimated time lapse : ",self.__timelapse,self.__nbdigits,6,"seconds")
#gd0.hideCancelButton()
gd0.showDialog()
if gd0.wasCanceled() : return False
#chosenstack=gd0.getNextChoice()
#self.__img=WindowManager.getImage(chosenstack)
self.__subback=gd0.getNextBoolean() #box 1 subback
self.__radius=gd0.getNextNumber()
self.__runmacro=gd0.getNextBoolean() #box 2 runmacro
for i in range(10) : self.__distparam[i]=gd0.getNextNumber()
#self.__distmethod=gd0.getNextChoice()
self.__manthresh=gd0.getNextBoolean() #box 3 manthresh
self.__thresMethod=gd0.getNextChoice()
#self.__optionAngle=gd0.getNextBoolean()
#self.__optionSave=gd0.getNextBoolean()
self.__optionNewCells=gd0.getNextBoolean() #box 4 newcells
self.__optionTimelapse=gd0.getNextBoolean() #box 5 timelapse
self.__timelapse=int(gd0.getNextNumber())
# -------- start end batch mode --------- #
if self.__optionTimelapse :
self.__dictTimeStack[imgName]=range(0,image.getImageStackSize()*self.__timelapse, self.__timelapse)
if not self.__optionTimelapse and self.__source=="image" :
self.__dictTimeStack[imgName]=range(0,image.getImageStackSize())
#if option_import==True :
# temparray=
#else : temparray=self.__calRois("image1", 1)
#imp=self.__dictImages["image1"]
if self.__manthresh :
ip=image.getProcessor()
self.__maxthr=ip.getMaxThreshold()
self.__minthr=ip.getMinThreshold()
temparray=self.__calRois(image, 1)
self.__rr=RangeRois(temparray, image)
if (not self.__batch) :
image.show()
self.__params=self.__rr.showSettingsDialog().values()
if self.__batch : image.hide()
return True
sourceImages = []
if theImage.getNChannels() == 1:
IJ.run("8-bit")
sourceImages.append(theImage)
else:
sourceImages = ChannelSplitter.split(theImage)
sourceNames = []
for im in sourceImages:
im.show()
sourceNames.append(im.getTitle())
gd0 = NonBlockingGenericDialog("Select source image...")
gd0.addChoice("Source image",sourceNames,sourceNames[0])
gd0.showDialog()
if (gd0.wasOKed()):
chosenImage = gd0.getNextChoice()
theImage = WindowManager.getImage(chosenImage)
IJ.selectWindow(chosenImage)
else:
theImage = sourceImages[0]
IJ.selectWindow(sourceNames[0])
gd = NonBlockingGenericDialog("Set slice params...")
gd.addNumericField("Slice start:",1,0)
gd.addNumericField("Slice end:",theImage.getNSlices(),0)
gd.showDialog()
if (gd.wasOKed()):
## Selecting the ROI over the stack
startSlice = int(gd.getNextNumber())
endSlice = gd.getNextNumber()
