def ER_points(all_x, all_y, overlay, ER_measurements): imp = IJ.getImage() overlay = Overlay() overlay = imp.getOverlay() ## gets points added to overlay, and extracts a list of x & y values. list length must be three ### try: roi_points = overlay.toArray() except AttributeError as error: nbgd = NonBlockingGenericDialog("Select three Roi's") nbgd.hideCancelButton() nbgd.showDialog() overlay = imp.getOverlay() roi_points = overlay.toArray() pass for i in range(overlay.size()): roi = overlay.get(i) p = roi_points[i].getPolygon() all_x.append(p.xpoints[0]) all_y.append(p.ypoints[0]) while len(all_x) != 3: if len(all_x) < 3: nbgd = NonBlockingGenericDialog("Must Select three Roi's") nbgd.setCancelLabel("Roi Reset") nbgd.showDialog() if nbgd.wasCanceled(): IJ.run("Remove Overlay", "") ER_points(all_x, all_y, overlay, ER_measurements) if len(all_x) > 3: all_x.pop(0) all_y.pop(0) overlay.clear()
def measure_gd(src_folder,file_names): from javax.swing import JButton gd = NonBlockingGenericDialog("Loci to compartment") gd.setResizable(True) gd.pack() gd.addMessage("Draw a freehand ROI aound loci and closest \n compartment(e.g. speckle) and press 0 on keyboard.") gd.addMessage("To load next image press Next Image button.") next_imp_bt = JButton('Next Image', actionPerformed=load_next_image) gd.add(next_imp_bt) gd.setLocation(10,10) gd.setAlwaysOnTop(True) gd.hideCancelButton() gd.showDialog() # if gd.wasOKed(): IJ.log( "Measurement done! You're welcome!")
def measure_gd(): # Dialouge box for measurements. # It from javax.swing import JButton gd = NonBlockingGenericDialog("Loci to compartment") gd.setResizable(True) gd.pack() gd.addMessage( "Draw a freehand ROI around the loci and closest \ncompartment(e.g. speckle) and press 0 on keyboard." ) next_imp_bt = JButton('Analyze active image', actionPerformed=analyze_image) gd.add(next_imp_bt) gd.setLocation(10, 10) gd.setAlwaysOnTop(True) gd.hideCancelButton() gd.showDialog() # if gd.wasOKed(): IJ.log("Measurement done! Happy FISHing")
def __settings(self, imgName) : """ Lets the user to choose different measures to make, and displays it following the choice of the user. """ try : dico=self.__dictCells[imgName] except KeyError : try : dico=self.__dictCells[imgName[:-4]] except KeyError : return False else : imgName=imgName[:-4] dico=self.__dictCells[imgName] for cellname in dico.keys() : self.__dictMeasures[dico[cellname]]={} # Represents the datas on a diagram def diagrambuttonPressed(event) : IJ.showMessage("Push 'Auto' button each time you want to see the diagram") x1=10 y1=20 x2=100 y2=50 x3=60 y3=30 xr=10 yr=20 wr=20 hr=20 rect=Rectangle(xr,yr,wr,hr) #img=IJ.getImage() #nbslices=self.__img.getImageStackSize() nbslices=self.__maxLife IJ.run("Hyperstack...", "title=Diagram type=32-bit display=Color width="+str(x2+(nbslices+1)*x3)+" height="+str(y2+y3*len(dico))+" channels=1 slices="+str(len(self.__measures))+" frames=1") im=IJ.getImage() ip=im.getProcessor() for i in range(len(self.__measures)) : indiceligne=0 maxvalue=0 minvalue=1000000 im.setPosition(1,i+1,1) for cellname in self.__listcellname : indiceligne+=1 for indicecolonne in range(1,nbslices+1): rect.setLocation(x2+indicecolonne*x3+int(x3/6),(y1+indiceligne*y3-int(y3/2))) # we create at the first iteration a dictionary with the rectangles (for a future use) if i==0 : self.__gridrectangle[(indiceligne,indicecolonne)]=Rectangle(rect) im.setRoi(rect) ipr=im.getProcessor() # we find the min and max values of the datas for a measure given. if self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]>maxvalue : maxvalue=self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1] if self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]<minvalue : minvalue=self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1] # we fill the rectangle with the value of the measure ipr.setValue(self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]) ipr.fill() # we write the names and the n of slices on the image with the maxvalue. ip.setValue(maxvalue) ip.moveTo(x1,y1) ip.drawString(self.__measures[i]) for j in range(1,nbslices+1) : ip.moveTo(x2+j*x3,y1) ip.drawString("Slice "+str(j)) j=0 for cellname in self.__listcellname : ip.moveTo(x1,y2+j*y3) ip.drawString(cellname) j+=1 im.killRoi() im=IJ.run(im,"Fire","") IJ.run("Brightness/Contrast...", "") #im.setMinAndMax(minvalue,maxvalue) #im.updateImage() #we add a mouse listener in order to be able to show the roi corresponding to a rectangle when the user clicks on it. listener = ML() listener.name=imgName for imp in map(WindowManager.getImage, WindowManager.getIDList()): if imp.getTitle().startswith("Diagram") : win = imp.getWindow() if win is None: continue win.getCanvas().addMouseListener(listener) # Represents the datas on a series of graphs. def graphbuttonPressed(event) : colors=[] #img=IJ.getImage() #nbslices=self.__img.getImageStackSize() nbslices=self.__maxLife acell=dico.values()[0] if self.__useTime : x = acell.getListTimes() namex="Time sec" else : x = range(1,nbslices+1) namex = "Frame" maxx=max(x) minx=min(x) #x=[i for i in range(1,nbslices+1)] font=Font("new", Font.BOLD, 14) tempname = WindowManager.getUniqueName(self.__img.getShortTitle()) for i in range(len(self.__measures)) : #print "i", i, self.__measures[i] yarray=[] flag=True miny=10000000000 maxy=-1000000000 #we find the min and max values in order to set the scale. for cellname in self.__listcellname : colors.append(dico[cellname].getColor()) yarray.append(self.__dictMeasures[dico[cellname]][self.__measures[i]]) #for meas in self.__dictMeasures[dico[cellname]][self.__measures[i]] : for meas in yarray[-1] : if (meas<miny) and (Double.isNaN(meas)==False) : miny=meas if max(yarray[-1])>maxy : maxy=max(yarray[-1]) miny-=0.1*miny maxy+=0.1*maxy count=0.05 for j in range(len(yarray)) : if j==0 : if len(self.__measures)>1 : plot=Plot("Plots-"+str(self.__measures[i]),namex,str(self.__measures[i]),x,yarray[j]) else : plot=Plot("Plot-"+tempname,namex,str(self.__measures[i]),x,yarray[j]) plot.setLimits(minx,maxx,miny,maxy) plot.setColor(colors[j]) plot.changeFont(font) plot.addLabel(0.05, count, self.__listcellname[j]) else : plot.setColor(colors[j]) plot.setLineWidth(3) plot.addPoints(x,yarray[j],Plot.LINE) plot.addLabel(0.05, count, self.__listcellname[j]) count+=0.05 plot.setColor(colors[0]) plot.show() if len(self.__measures)>1 : IJ.run("Images to Stack", "name="+tempname+"-plots title=Plots- use") #def histbuttonPressed(event) : # # pass # Represents the values in a tab. def tabbuttonPressed(event) : tab="\t" headings=[] measures=[] #img=IJ.getImage() #for i in range(self.__img.getImageStackSize()+1) : for i in range(self.__maxLife+1) : headings.append("Slice "+str(i)) headings[0]=WindowManager.getUniqueName(self.__img.getShortTitle()) #for m in self.__measurescompl : for m in self.__dictMeasures[dico[self.__listcellname[0]]].keys() : headstring="" for head in headings: headstring+=head+tab tw=TextWindow(self.__listfiles[0]+"-"+m,headstring,"",800,600) tp=tw.getTextPanel() #for cellname in dico.keys() : for cellname in self.__listcellname : line=[] line=[str(meas)+tab for meas in self.__dictMeasures[dico[cellname]][m]] line.insert(0, cellname+tab) linestr="" for s in line: linestr+=s tp.appendLine(linestr) tp.updateDisplay() if self.__measuresparambool_global[0] : tw=TextWindow("Latency","cell\tLatency", "",800,600) tp=tw.getTextPanel() for i in range(len(self.__listcellname)) : #if latencies[i][0] : line=self.__listcellname[i]+"\t"+str(latencies[i][1]) #else : line=self.__listcellname[i]+"\t"+"NaN" line=self.__listcellname[i]+"\t"+str(latencies[i][1]) tp.appendLine(line) tp.updateDisplay() def helpbuttonPressed(event) : IJ.showMessage("TO DO") def newsetPressed(event) : gd0.dispose() self.__settings() def alignbuttonPressed(event) : IJ.showMessage("TO DO") def mergebuttonPressed(event) : IJ.showMessage("TO DO") def saveResults() : #if len(self.__listcellname) == 0 : nbslices=self.__maxLife acell=dico.values()[0] if self.__useTime : x = acell.getListTimes() namex="Time_sec" else : x = range(1,nbslices+1) namex = "Frame" if not path.exists(self.__rootpath+"Results"+os.path.sep) : os.makedirs(self.__rootpath+os.path.sep+"Results"+os.path.sep, mode=0777) tab="\t" nl="\n" measures=[] headstring="" #if self.__savemode : mode = "a" #else : mode ="w" mode = "a" #for i in range(1, self.__maxLife+1) :headstring += "Slice_"+str(i)+tab for i in range(self.__maxLife) :headstring += str(x[i])+tab #for m in self.__measurescompl : for m in self.__dictMeasures[dico[self.__listcellname[0]]].keys() : f = open(self.__rootpath+"Results"+os.path.sep+m+".txt", mode) #f.write(m+nl) f.write(imgName+"-"+self.__time+"-"+m+"-"+namex+tab+headstring+nl) if len(self.__listcellname) == 0 : f.write("no cells") else : for cellname in self.__listcellname : linestr=cellname+tab for measure in self.__dictMeasures[dico[cellname]][m] : #print m, cellname, measure linestr += str(measure)+tab linestr+=nl f.write(linestr) f.close() if self.__measuresparambool_global[0] : m = "Latency" f = open(self.__rootpath+"Results"+os.path.sep+m+".txt", mode) f.write(imgName+"-"+self.__time+"-"+m+nl) for i in range(len(self.__listcellname)) : #if latencies[i][0] : line=self.__listcellname[i]+"\t"+str(latencies[i][1]) #else : line=self.__listcellname[i]+"\t"+"NaN" line=self.__listcellname[i]+"\t"+str(latencies[i][1]) line+=nl f.write(line) f.close() # # ----------- main measures dialog ------------------------- # # Allows the user to choose the measures to make, etc.. measureslabels_indep=["MaxFeret","MinFeret","AngleFeret","XFeret","YFeret","Area","Angle","Major","Minor","Solidity","AR","Round","Circ","XC","YC","FerCoord","FerAxis","MidAxis"] measureslabels_dep=["Mean","StdDev","IntDen","Kurt","Skew","XM","YM","Fprofil","MidProfil","NFoci","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"] measureslabels_global=["Latency", "velocity", "cumulatedDist"] measureslabels_dep_tabonly=set(["MidAxis","FerCoord","FerAxis","Fprofil","MidProfil","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"]) ens_measures_global=set(measureslabels_global) ens_measures_indep=set(measureslabels_indep) ens_measures_dep=set(measureslabels_dep) measureslabels=[] for label in measureslabels_indep : measureslabels.append(label) for label in measureslabels_dep : measureslabels.append(label) #self.__defaultmeasures=[False for i in range(len(measureslabels))] #self.__defaultmeasures_global=[False for i in range(len(measureslabels_global))] gdmeasures=NonBlockingGenericDialog("MeasuresChoice") gdmeasures.setFont(Font("Courrier", 1, 10)) gdmeasures.addMessage("******* TIME SETTINGS *******") gdmeasures.addCheckbox("Only starting at begining :", self.__onlystart) # 1 only start gdmeasures.addNumericField("Minimal Lifetime : ",self.__minLife,0) gdmeasures.addNumericField("Maximal Lifetime : ",self.__maxLife,0) #gdmeasures.addNumericField("Maximal Lifetime : ",self.__img.getImageStackSize(),0) gdmeasures.addCheckbox("x axis in seconds", self.__useTime) # 2 use time gdmeasures.addMessage("") gdmeasures.addMessage("") gdmeasures.addMessage("Choose the measures to make on the cells : ") gdmeasures.addMessage("******* TIME MEASURES *******") gdmeasures.addCheckboxGroup(4,8,measureslabels,self.__defaultmeasures) gdmeasures.addMessage("") gdmeasures.addMessage("******* GLOBAL MEASURES *******") gdmeasures.addMessage("PLEASE : If you have selected movement parameters you MUST to select XC and YC !") gdmeasures.addCheckboxGroup(3,1,measureslabels_global,self.__defaultmeasures_global) gdmeasures.addNumericField("Noise value for maxima finder: ",self.__noise,0) gdmeasures.addMessage("") gdmeasures.addMessage("******* OPTIONS *******") gdmeasures.addCheckbox("Select the cells in next dialog ?", self.__onlyselect) # 3 only select gdmeasures.addCheckbox("Save results to text files ?", self.__savetables) # 4 save files #gdmeasures.addCheckbox("Append mode ?", self.__savemode) # 5 append mode gdmeasures.addCheckbox("Analyse in batch mode ?", self.__batchanalyse) # 6 analysis batch mode gdmeasures.addCheckbox("Update overlay ?", self.__updateoverlay) # 7 update overlay gdmeasures.addMessage("") gdmeasures.addMessage("") help_panel=Panel() helpbutton=Button("HELP") helpbutton.actionPerformed = helpbuttonPressed help_panel.add(helpbutton) gdmeasures.addPanel(help_panel) gdmeasures.hideCancelButton() if not self.__batchanalyse : gdmeasures.showDialog() self.__onlystart=gdmeasures.getNextBoolean() # 1 only start self.__minLife=gdmeasures.getNextNumber() self.__maxLife=gdmeasures.getNextNumber() self.__useTime=gdmeasures.getNextBoolean() # 2 use time self.__measuresparambool=[] self.__measuresparambool_global=[] for i in range(len(measureslabels)) : self.__measuresparambool.append(gdmeasures.getNextBoolean()) self.__defaultmeasures[i]=self.__measuresparambool[-1] for i in range(len(measureslabels_global)) : self.__measuresparambool_global.append(gdmeasures.getNextBoolean()) self.__defaultmeasures_global[i] = self.__measuresparambool_global[i] self.__noise=gdmeasures.getNextNumber() self.__onlyselect=gdmeasures.getNextBoolean() # 3 only select self.__savetables = gdmeasures.getNextBoolean() # 4 save files #self.__savemode = gdmeasures.getNextBoolean() # 5 append mode self.__batchanalyse = gdmeasures.getNextBoolean() # 6 analyse mode self.__updateoverlay = gdmeasures.getNextBoolean() # 7 update overlay # we update a list of all cells that have a lifetime corresponding to what the user chose. if len (self.__allcells) == 0 : for cellname in dico.keys() : if dico[cellname].getLifeTime()>=self.__minLife : #and dico[cellname].getLifeTime()<=self.__maxLife : if self.__onlystart : if dico[cellname].getSlideInit()<2 : self.__allcells.append(cellname) else : self.__allcells.append(cellname) if self.__noise == 0 : self.__noise = None if self.__batchanalyse : self.__onlyselect = False if self.__onlyselect : try : self.__gw except AttributeError : if not path.exists(self.__pathdir+"Selected-Cells"+os.path.sep) : os.makedirs(self.__pathdir+os.path.sep+"Selected-Cells"+os.path.sep, mode=0777) self.__gw = CellsSelection() self.__gw.setTitle(imgName) self.__gw.run(self.__allcells, self.__pathdir+"ROIs"+os.path.sep) self.__gw.show() self.__gw.setSelected(self.__allcells) while not self.__gw.oked and self.__gw.isShowing() : self.__gw.setLabel("Validate selection with OK !!") self.__listcellname = list(self.__gw.getSelected()) self.__gw.resetok() self.__gw.setLabel("...") self.__gw.hide() else : if self.__gw.getTitle() == imgName : self.__gw.show() self.__gw.setSelected(self.__listcellname) self.__listcellname[:]=[] while not self.__gw.oked and self.__gw.isShowing() : self.__gw.setLabel("Validate selection with OK !!") self.__listcellname = list(self.__gw.getSelected()) self.__gw.resetok() self.__gw.setLabel("...") self.__gw.hide() else : self.__gw.dispose() if not path.exists(self.__pathdir+"Selected-Cells"+os.path.sep) : os.makedirs(self.__pathdir+os.path.sep+"Selected-Cells"+os.path.sep, mode=0777) self.__gw = CellsSelection() self.__gw.setTitle(imgName) self.__gw.run(self.__allcells, self.__pathdir+"ROIs"+os.path.sep) self.__gw.show() self.__gw.setSelected(self.__allcells) self.__listcellname[:]=[] while not self.__gw.oked and self.__gw.isShowing() : self.__gw.setLabel("Validate selection with OK !!") self.__listcellname = list(self.__gw.getSelected()) self.__gw.resetok() self.__gw.setLabel("...") self.__gw.hide() filestodelet=glob.glob(self.__pathdir+"Selected-Cells"+os.path.sep+"*.cell") for f in filestodelet : os.remove(f) for cell in self.__listcellname : sourcestr = self.__pathdir+"Cells"+os.path.sep+cell+".cell" deststr = self.__pathdir+"Selected-Cells"+os.path.sep+cell+".cell" #os.system("copy "+sourcestr+", "+deststr) #shutil.copy(self.__pathdir+"Cells"+os.path.sep+cell+".cell",self.__pathdir+"Selected-Cells"+os.path.sep+cell+".cell") shutil.copy(sourcestr,deststr) self.__dictNcells[imgName] = len(self.__listcellname) else : self.__listcellname = list(self.__allcells) self.__dictNcells[imgName] = len(self.__listcellname) if len(self.__listcellname) == 0 : self.__dictNcells[imgName] = 0 return False self.__img.hide() # we make the measures. for i in range(len(measureslabels)) : IJ.showProgress(i, len(measureslabels)) if self.__measuresparambool[i]==True : self.__measurescompl.append(measureslabels[i]) if (measureslabels[i] in measureslabels_dep_tabonly)==False : self.__measures.append(measureslabels[i]) if (i<18) and (measureslabels[i] in ens_measures_indep) : self.__measureAll(self.__img,measureslabels[i],False, imgName, self.__noise) ens_measures_indep.discard(measureslabels[i]) if i>=18 : self.__measureAll(self.__img,measureslabels[i],True, imgName, self.__noise) if self.__measuresparambool_global[0] : # calculate latency latencies=[] for i in range(len(self.__listcellname)) : IJ.showProgress(i, len(self.__listcellname)) latencies.append(self.latencie(self.__listcellname[i], self.__img, imgName, self.__useTime)) if self.__measuresparambool_global[1] : # calculate velocity self.__measures.append("velocity") #velocities=[] for i in range(len(self.__listcellname)) : IJ.showProgress(i, len(self.__listcellname)) self.__measureVelocity(self.__img,imgName) if self.__measuresparambool_global[2] : # calculate cumulatedDistance self.__measures.append("cumulatedDist") #velocities=[] for i in range(len(self.__listcellname)) : IJ.showProgress(i, len(self.__listcellname)) self.__measurecumulDist(self.__img,imgName) self.__img.show() self.__img.getProcessor().resetThreshold() if self.__updateoverlay : if self.__img.getOverlay() is not None : self.__img.getOverlay().clear() outputrois=[] cellnames=[] self.__img.hide() for cellname in self.__listcellname : for r in dico[cellname].getListRoi(): if isinstance(r,Roi) : pos=r.getPosition() #print "MC overlay", cellname, r.getName(), pos #r.setPosition(0) #overlay.add(r) outputrois.append(r) if "cell" in r.getName() : cellnames.append(r.getName()) else : cellnames.append(str(pos)+"-"+cellname) #print cellnames[-1] rm = RoiManager.getInstance() if (rm==None): rm = RoiManager() rm.show() self.__img.show() IJ.selectWindow(self.__img.getTitle()) rm.runCommand("reset") for i in range(len(outputrois)) : outputrois[i].setName(cellnames[i]) rm.addRoi(outputrois[i]) rm.select(rm.getCount()-1) rm.runCommand("Rename", cellnames[i]) IJ.run("Show Overlay", "") rm.runCommand("UseNames", "true") rm.runCommand("Associate", "true") IJ.run(self.__img, "Labels...", "color=red font=12 show use") IJ.run(self.__img, "From ROI Manager", "") rm.runCommand("Show None") rm.runCommand("Show All") # ----------- batch analyse ------------------------ if self.__batchanalyse : if self.__savetables : saveResults() self.__dictMeasures.clear() self.__allcells[:]=[] self.__measurescompl[:]=[] self.__measures[:]=[] return False # ---------- display methodes dialog ---------------- # Allows the user to choose how to see the results of the measures. gd0=NonBlockingGenericDialog("Display") gd0.addMessage("How do you want to see the results ?") panel0=Panel() diagrambutton=Button("Diagram") diagrambutton.actionPerformed = diagrambuttonPressed panel0.add(diagrambutton) graphbutton=Button("Graph") graphbutton.actionPerformed = graphbuttonPressed panel0.add(graphbutton) tabbutton=Button("Tab") tabbutton.actionPerformed = tabbuttonPressed panel0.add(tabbutton) gd0.addPanel(panel0) gd0.addCheckbox("Analyse next stack ?", self.__nextstack) gd0.hideCancelButton() gd0.showDialog() self.__nextstack = gd0.getNextBoolean() # ---------- save tables --------------------------- if self.__savetables : saveResults() # --------- re-start analysis ------------------- self.__dictMeasures.clear() #self.__listcellname[:]=[] self.__allcells[:]=[] self.__measurescompl[:]=[] self.__measures[:]=[] if self.__nextstack : return False else : return True
IJ.setForegroundColor(255, 255, 255) IJ.setBackgroundColor(1, 1, 1) imp2 = IJ.getImage() IJ.run(imp2, "Draw", "slice") IJ.run("Select None") if always_auto is True: to_transport_channel() average_max = high(bit_depth) if always_auto is False: if always_select is False: nbgd = NonBlockingGenericDialog("Golgi_selection") Methods = ['Automatic Selection', 'Manual Selection'] nbgd.addRadioButtonGroup("Methods", Methods, 2, 1, Methods[0]) nbgd.hideCancelButton() nbgd.showDialog() golgi_method = nbgd.getNextRadioButton() if golgi_method == Methods[0]: average_max = high(bit_depth) elif golgi_method == Methods[1]: to_golgi_channel() IJ.setTool("polygon") region = 'Select Golgi' selection(region) to_transport_channel() average_max = high(bit_depth) IJ.setForegroundColor(255, 255, 255) IJ.setBackgroundColor(1, 1, 1) imp2 = IJ.getImage() IJ.run(imp2, "Draw", "slice")