Python WindowManager.getIDList方法代码示例

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
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)

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_images(ids):
    """
    Returns a list of ImagePlus objects.
    :param ids: The ids of the ImagePlus objects to return.
    """
    image_ids = WindowManager.getIDList()
    return [WindowManager.getImage(image_ids[id]) for id in ids]

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_image_titles():
    """
    Returns the titles of all open image windows as a list.
    """
    image_ids = WindowManager.getIDList()
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    return image_titles

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_setup():
    ''' Returns the drift correction mode and three image.
    The order of return values is drift detection mode, pre-edge 1, pre-edge 2, post-edge.
    '''
    options = drift.get_options()
    modes = drift.get_modes()
    dialog = GenericDialog('3-window-method setup')
    dialog.addMessage('Select the mode  for drift correction\n' +
                      'and the images to process.')
    dialog.addChoice('Mode:', options, options[0])
    image_ids = WindowManager.getIDList()
    if not image_ids or len(image_ids) < 2:
        return [None]*4
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    dialog.addMessage('Post-edge is divided by the pre-edge.')
    dialog.addChoice('Pre-edge 1', image_titles, image_titles[0])
    dialog.addChoice('Pre-edge 2', image_titles, image_titles[1])
    dialog.addChoice('Post-edge', image_titles, image_titles[2])
    dialog.showDialog()
    if dialog.wasCanceled():
        return [None]*4
    mode = modes[dialog.getNextChoiceIndex()]
    img1 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    img2 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    img3 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    return mode, img1, img2, img3

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_images(minimum=0, maximum=None, exact=None):
    ''' Returns a list of ImagePlus objects or None if it failed.
    Passing None as parameter will trigger a dialog to show up to enter the exact number of images.
    :param minimum: The minimum number of images to select (default: 0).
    :param maximum: The maximum number of images to select (default: None).
    :param exact: Set this to get an exact number of images (default: None).
    '''
    if not (minimum or maximum or exact):
        exact = int(IJ.getNumber("How many images do you want to process?", 3))
    def check_count(count):
        '''Returns True if the count of images is as required.'''
        # print count, exact, minimum, maximum
        if exact:
            if not count == exact:
                return False
        else:
            if minimum:
                if count < minimum:
                    return False
            if maximum:
                if count > maximum:
                    return False
        return True

    # Option 1: The selected image is a stack and has the demanded size.
    if check_count(WindowManager.getCurrentImage().getStackSize()):
        return stack_to_list_of_imp(WindowManager.getCurrentImage())

    # Option 2: The count of open images matches the demanded number.
    image_ids = WindowManager.getIDList()
    if exact:
        if len(image_ids) < exact:
            return None
        if len(image_ids) == exact:
            return [WindowManager.getImage(img_id) for img_id in image_ids]

    # Option 3: The user can select the images from a list.
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    img_count = len(image_ids)
    if exact:
        img_count = exact
    elif maximum:
        img_count = maximum
        image_titles.append('None')
    images_selected = dialogs.create_selection_dialog(image_titles,
                                                      range(img_count),
                                                      'Select images for drift correction'
                                                     )
    # dialogs.create_selection_dialog() returns None if canceled
    if not images_selected:
        return None
    # This is only true if 'None has been appended to image_titles and the user selected it.
    if len(image_ids) in images_selected:
        images_selected.remove(len(image_ids))
    if not check_count(len(images_selected)):
        return None
    image_list = [WindowManager.getImage(image_ids[selection]) for selection in images_selected]
    return image_list

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def run_script():
    while WindowManager.getImageCount() < 10:
        create_test_image()
     
    image_titles = [WindowManager.getImage(id).getTitle() for id in WindowManager.getIDList()]
    # range(3) will create the list [0, 1, 2].
    selected_indices = create_selection_dialog(image_titles, range(3))
    # The script stops if the dialog has ben canceld (None was returned from create_selection_dialog).
    if selected_indices is None:
        print('Script was canceld.')
        return
    # We have to get the corresponding IMagePlus objects.
    selected_imps = [WindowManager.getImage(id) for id in [WindowManager.getIDList()[index] for index in selected_indices]]
    # The previous line can be split into 2 lines:
    # selected_ids = [WindowManager.getIDList()[index] for index in selected_indices]
    # selected_imps = [WindowManager.getImage(id) for id in selected_ids]
     
    for imp in selected_imps:
        # Strings can be formated using the % operator:
        # http://www.learnpython.org/en/String_Formatting
        IJ.log('The image \'%s\' has been selected.' % imp.getTitle())

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
	def ShowRoi(self,imp,point, name):
		for indices in self.__gridrectangle.keys() :
			if self.__gridrectangle[indices].contains(point) :
				roitemp=self.__dictCells[name][self.__listcellname[indices[0]-1]].getRoi(indices[1]-1)
		if isinstance(roitemp,Roi) :
			idimages=WindowManager.getIDList()
			for i in range(len(idimages)) :
				if idimages[i]==self.__img.getID() :
					IJ.selectWindow(self.__img.getID())	
			rm = RoiManager.getInstance()
			for i in range(rm.getCount()) :
				if rm.getName(str(i))==roitemp.getName() :
					rm.select(i)
					selectroi=self.__img.getRoi()
					#col=rm.getSelectedRoisAsArray().getStrokeColor()
					selectroi.setStrokeColor(Color.red)
					selectroi.setStrokeWidth(3)
					self.__img.updateAndDraw()
					break

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
	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

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_setup():
    '''Returns two ImagePlus objects and a dictionary of properties to copy.'''
    dialog = GenericDialog('Copy Properties setup')
    dialog.addMessage('Select the source and target image and the properties to copy.')
    image_ids = WindowManager.getIDList()
    if not image_ids or len(image_ids) < 2:
        IJ.showMessage('Two or more images are necessary to use this plugin.')
        return [None]*3
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    dialog.addChoice('Source', image_titles, image_titles[0])
    dialog.addChoice('Target', image_titles, image_titles[1])
    dialog.addCheckbox('Copy Calibration', True)
    dialog.addCheckbox('Copy Slice Labels', False)
    dialog.showDialog()
    if dialog.wasCanceled():
        return [None]*3
    source = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    target = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    choices = {'cal': dialog.getNextBoolean(),
               'labels': dialog.getNextBoolean()
              }
    return source, target, choices

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def get_setup():
    ''' Returns the drift correction mode and two image.'''
    options = drift.get_options()
    modes = drift.get_modes()
    dialog = GenericDialog('Jump-ratio setup')
    dialog.addMessage('Select the mode  for drift correction\n' +
                      'and the images to process.')
    dialog.addChoice('Mode:', options, options[0])
    image_ids = WindowManager.getIDList()
    if not image_ids or len(image_ids) < 2:
        return [None]*3
    image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
    dialog.addMessage('Post-edge is divided by the pre-edge.')
    dialog.addChoice('Pre-edge', image_titles, image_titles[0])
    dialog.addChoice('Post-edge', image_titles, image_titles[1])
    dialog.showDialog()
    if dialog.wasCanceled():
        return [None]*3
    mode = modes[dialog.getNextChoiceIndex()]
    img1 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    img2 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
    return mode, img1, img2

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
	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

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
	
	# Performs scaling
	if (gd.wasOKed()):
		anchorTiles = range(startTile,finishTile+1,stepSize)
		print anchorTiles
		for i in anchorTiles:
			if (i+stepSize-1 > finishTile):
				lastAnchorTile = finishTile
			else:
				lastAnchorTile = i+stepSize-1
			
			iterTiles = range(i,lastAnchorTile+1)
			params = "open=[" + theFilePath + "] color_mode=Default view=Hyperstack stack_order=XYCZT series_list=" + str(i) + "-" + str(lastAnchorTile)
			print params
			IJ.run("Bio-Formats Importer", params)
			imageIDList = WindowManager.getIDList()
			if (len(imageIDList) == len(iterTiles)):
				count = 0
				for j in imageIDList:
					theImage = WindowManager.getImage(j)
					print theImage.getTitle()
					params2 = "x=" + str(ratio) + " y=" + str(ratio) + " z=1.0 interpolation=Bilinear average create title=doggie"
					IJ.run(theImage,"Scale...",params2)
					theImage.close()
					saveImage = WindowManager.getImage("doggie")
					IJ.saveAsTiff(saveImage,theDirectory+baseName+"_resized/tile_"+str(iterTiles[count])+".tif")
					saveImage.close()
					count = count + 1
			else:
				print "Open image count does not match tile count!"	

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
def run_combine(filePath):
	basePath,baseName = os.path.split(filePath)
	imagePrefix = os.path.splitext(baseName)[0]
	resizeName = basePath + "/" + baseName + "_tiles/resized/"
	checkName = basePath + "/" + baseName + "_tiles/resized/" + imagePrefix + "_seq/"
	activeName = basePath + "/" + baseName + "_tiles"
	outputName = basePath + "/stitched/" + imagePrefix + "/"
	IJ.log("Combining " + filePath + "...")
	if (not os.path.isdir(outputName)):
		try:
			os.makedirs(outputName)
			if (not os.path.isdir(checkName)):
				raise ValueError("Stitched image directory not found")
			for dirpath, dirnames, files in os.walk(checkName):
				if not files:
					raise ValueError("Stitched image directory is empty")
			IJ.run("Bio-Formats Importer", "open=["+ activeName +"/tile_1.ome.tif] color_mode=Default view=Hyperstack stack_order=XYCZT");
			tileImage = WindowManager.getImage("tile_1.ome.tif")
			nChannels = tileImage.getNChannels()
			tileImage.close()
			options = "open=[" + checkName + "] starting=1 increment=1 scale=100 file=[] sort"
			IJ.run("Image Sequence...", options)
			theImage = IJ.getImage()
			for i in range(1,nChannels+1):
				params = "slices=" + str(i) + "-" + str(theImage.getNSlices()) + "-" + str(nChannels)
				IJ.run(theImage,"Make Substack...",params)
			theImage.close()
			wList = WindowManager.getIDList()
			for i in range(len(wList)):
				currImage = WindowManager.getImage(wList[i])
				currImage.setTitle("image"+str(i+1))
				IJ.save(currImage,outputName+imagePrefix+"_ch"+str(i+1)+".tif")
			if nChannels > 1 and not os.path.isfile(outputName+imagePrefix+"_composite.tif"):
				if nChannels == 2:
					params = ("c1=" + WindowManager.getImage(wList[0]).getTitle() + 
							" c4=" + WindowManager.getImage(wList[1]).getTitle() + " create ignore")
				elif nChannels == 3:
					params = ("c1=" + WindowManager.getImage(wList[1]).getTitle() +
							" c2=" + WindowManager.getImage(wList[0]).getTitle() +
							" c4=" + WindowManager.getImage(wList[2]).getTitle() + " create ignore")
				elif nChannels == 4:
					params = ("c1=" + WindowManager.getImage(wList[1]).getTitle() +
							" c2=" + WindowManager.getImage(wList[2]).getTitle() +
							" c3=" + WindowManager.getImage(wList[0]).getTitle() +
							" c4=" + WindowManager.getImage(wList[3]).getTitle() + " create ignore")
				elif nChannels == 5:
					params = ("c1=" + WindowManager.getImage(wList[1]).getTitle() +
							" c2=" + WindowManager.getImage(wList[2]).getTitle() +
							" c3=" + WindowManager.getImage(wList[0]).getTitle() +
							" c4=" + WindowManager.getImage(wList[4]).getTitle() + 
							" c7=" + WindowManager.getImage(wList[3]).getTitle() +
							" create ignore")
				else:
					IJ.log("No composite image created due to excess channels (>4)")
				IJ.run("Merge Channels...", params)
				compositeImage = IJ.getImage()
				IJ.save(compositeImage,outputName+imagePrefix+"_composite.tif")			
			wList = WindowManager.getIDList()
			for i in range(len(wList)):
				currImage = WindowManager.getImage(wList[i])						
				currImage.close()
			IJ.log("succeeded")
			returnVal = 0
		except:
			IJ.log("failed")
			os.rmdir(outputName)
			wList = WindowManager.getIDList()
			for i in range(len(wList)):
				currImage = WindowManager.getImage(wList[i])
				currImage.close()
			returnVal = 1
	else:
		IJ.log("skipped")
		returnVal = 2

	return returnVal

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
 def check_existence(title):
     if WindowManager.getIDList() is None:
         return False
     image_titles = (WindowManager.getImage(id).getTitle() for id in WindowManager.getIDList())
     return title in image_titles

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getIDList [as 别名]
		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)