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()