コード例 #1
0
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)
コード例 #2
0
ファイル: CellCropper_V4.py プロジェクト: schiklen/DotObjects
    def __init__(self, p):
        self.cellCounter = 1
        self.olay = Overlay()
        self.position = p
        print p.getRoiPath()
        if p.getRoiPath() != None:         # check if there is an existing overlay file and load it!
            p.loadRois()

        self.frame = JFrame("CellCropper", size=(200,200))
        self.frame.setLocation(20,120)
        self.Panel = JPanel(GridLayout(0,1))
        self.frame.add(self.Panel)
        #self.nameField = JTextField("p" + "_c",15)
        self.nameField = JTextField("p" + str(self.position.getID()) + "_c",15)
        self.Panel.add(self.nameField)
        self.cutoutButton = JButton("Cut out cell",actionPerformed=cut)
        self.Panel.add(self.cutoutButton)
        self.delOlButton = JButton("Delete Overlay",actionPerformed=delOverlay)
        self.Panel.add(self.delOlButton)
        self.saveOlButton = JButton("Save Overlay",actionPerformed=saveOverlay)
        self.Panel.add(self.saveOlButton) 
        self.quitButton = JButton("Quit script",actionPerformed=quit)
        self.Panel.add(self.quitButton)
        self.frame.pack()
        WindowManager.addWindow(self.frame)
        self.show()
コード例 #3
0
ファイル: HelperDialogs.py プロジェクト: m-entrup/EFTEMj
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]
コード例 #4
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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
コード例 #5
0
ファイル: HelperDialogs.py プロジェクト: m-entrup/EFTEMj
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
コード例 #6
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ファイル: CellCropper_V4.py プロジェクト: schiklen/DotObjects
 def close(self):
     if self.olay != None:
         yncd = YesNoCancelDialog(self.frame, "Save overlay?", "Save overlay?") #frame, title, message
         if yncd.yesPressed():
             self.saveOverlay()
     WindowManager.removeWindow(self.frame)
     self.frame.dispose()
コード例 #7
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def watershed_3d(imp, radius):
  imp.show() # one needs to display it, otherwise below function cannot find it
  IJ.run("3D Watershed Split", "binary=%s seeds=Automatic radius=%s" % (imp.getTitle(), radius))
  imp.hide()
  # get the output image
  imp_out = IJ.getImage()
  imp_out.hide()
  # remove the EDT image, which is also displayed
  WindowManager.getImage("EDT").close()
  return imp_out
コード例 #8
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def close_all_image_windows():
  # forcefully closes all open images windows
  ids = WindowManager.getIDList();
  if (ids==None):
    return
  for i in ids:
     imp = WindowManager.getImage(i)
     if (imp!=None):
       win = imp.getWindow()
       if (win!=None):
         imp.changes = False # avoids the "save changes" dialog
         win.close()
コード例 #9
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def objects_counter_3d(imp_bw, imp_intens, measurements, threshold, vol_min, vol_max):
  # set options
  options = "%s dots_size=5 font_size=10 show_numbers white_numbers redirect_to=%s" % (measurements, imp_intens.getTitle())
  IJ.run("3D OC Options", options);
  # make sure the output image does not exist already as this leasds to weird behaviors....
  outlines_title = "Surface map of %s redirect to %s" % (imp_bw.getTitle(),imp_intens.getTitle())
  if WindowManager.getImage(outlines_title) != None: 
    WindowManager.getImage(outlines_title).close()
  # analyze
  imp_bw.show(); imp_intens.show();
  IJ.run(imp_bw, "3D Objects Counter", "threshold=%s min.=%s max.=%s exclude_objects_on_edges surfaces statistics" % (threshold, vol_min, vol_max))
  imp_out = IJ.getImage(); imp_out.setTitle("outlines"); imp_out.hide()
  return imp_out
コード例 #10
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ファイル: Convert_to_HDF5.py プロジェクト: fzadow/tileserver
def getImage():
    """Get first open image or open Bio-Formats importer if no image is
	available."""
    imp = WindowManager.getCurrentImage()
    if not imp:
        # Show bio formats open dialog
        IJ.run("Bio-Formats")
        imp = WindowManager.getCurrentImage()
        print("Start")
    if not imp:
        IJ.noImage()
        raise ValueError("Need image")
    return imp
コード例 #11
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def draw_roi_on_full_res_tile(containing_tiles_dict,subupcoords_dict):
	masterXs = []
	masterYs = []
	for key in containing_tiles_dict.keys():
		if (len(containing_tiles_dict.keys())>1):
			active_image = WindowManager.getImage("Fused")
		else:
			active_image = WindowManager.getImage("tile_"+key+".ome.tif")
		for point in containing_tiles_dict[key]:
			masterXs.append(point[3]+subupcoords_dict["tile_"+str(point[0])][0])
			masterYs.append(point[4]+subupcoords_dict["tile_"+str(point[0])][1])
	proi = PolygonRoi(masterXs,masterYs,Roi.FREEROI)
	active_image.setRoi(proi)
	return active_image
コード例 #12
0
   def __init__(self):
      self.mainDir = ""
   
      self.frame = JFrame("Dots Quality Check", size=(250,300))
      self.frame.setLocation(20,120)
      self.Panel = JPanel(GridLayout(0,1))
      self.frame.add(self.Panel)

      self.openNextButton = JButton('Open Next Random',actionPerformed=openRandom)
      self.Panel.add(self.openNextButton)
      
      self.saveButton = JButton('Save',actionPerformed=save)
      self.saveButton.setEnabled(False)
      self.Panel.add(self.saveButton)

      self.cropButton = JButton('Crop values from here', actionPerformed=cropVals)
      self.Panel.add(self.cropButton)

      self.DiscardButton = JButton('Discard cell', actionPerformed=discardCell)
      self.DiscardButton.setEnabled(True)
      self.Panel.add(self.DiscardButton)

      self.quitButton = JButton('Quit script',actionPerformed=quit)
      self.Panel.add(self.quitButton)

      annoPanel = JPanel()
      #add gridlayout
      wtRButton = JRadioButton("wt", actionCommand="wt")
      defectRButton = JRadioButton("Defect", actionCommand="defect")
      annoPanel.add(wtRButton)
      annoPanel.add(defectRButton)
      self.aButtonGroup = ButtonGroup()
      self.aButtonGroup.add(wtRButton)
      self.aButtonGroup.add(defectRButton)
      
      self.Panel.add(annoPanel)

      self.ProgBar = JProgressBar()
      self.ProgBar.setStringPainted(True)
      self.ProgBar.setValue(0)
      self.Panel.add(self.ProgBar)

      self.pathLabel = JLabel("-- No main directory chosen --")
      self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
      self.Panel.add(self.pathLabel)

      
      WindowManager.addWindow(self.frame)
      self.show()
コード例 #13
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def bSaveZProject(imp, dstFolder, shortname):
	#bring to front
	impWinStr = imp.getTitle()
	IJ.selectWindow(impWinStr)
	
	bPrintLog('Making Z-Project from ' + impWinStr, 2)
	madez = 0
	z1 = 1
	z2 = imp.getNSlices()
	if z2>1:
		paramStr = 'start=%s stop=%s projection=[Max Intensity]' % (z1, z2)
		IJ.run('Z Project...', paramStr) #makes 'MAX_' window
		zWinStr = 'MAX_' + impWinStr
		zImp = WindowManager.getImage(zWinStr)
		madez = 1
	else:
		zImp = imp
			
	if dstFolder != None:
		dstFile = dstFolder + 'max_' + shortname + '.tif'
		bPrintLog('Saving Z-Project: ' + dstFile, 2)
		bSaveStack(zImp, dstFile)

	if madez:
		zImp.changes = 0
		zImp.close()
コード例 #14
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    def myrun(self):
        imp = IJ.openImage(self.path) #open imp
        if imp is None:
            print 'ERROR opening file:', self.path
            return 0
        numSlices = imp.getNSlices()
        if numSlices<2:
        	return 0
        
        middleSlice = int(math.floor(imp.getNSlices() / 2)) #int() is necc., python is f*****g picky
        
        imp.show()
        imp.setSlice(middleSlice)
        impTitle = imp.getTitle()
        impWin = WindowManager.getWindow(impTitle) #returns java.awt.Window

        transformationFile = os.path.basename(self.path)
        transformationFile = os.path.splitext(transformationFile)[0] + '.txt'
        transformationFile = '/Users/cudmore/Desktop/out/' + transformationFile
        stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' %(impWin,transformationFile)
        IJ.run('MultiStackReg', stackRegParams)
        
        imp.close()
        
        '''
        #20150723, we just aligned on a cropped copy, apply alignment to original imp
        origImpTitle = imp.getTitle()
        stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(origImpTitle,transformationFile)
        IJ.run('MultiStackReg', stackRegParams)        
        '''
        
        '''
コード例 #15
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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)
コード例 #16
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def close_non_image_window(window_name):
  # forcefully closes one specific non image window
  frames = WindowManager.getNonImageWindows()
  for i in range(len(frames)):
    #IJ.log(frames[i].getTitle())
    if (frames[i].getTitle() == window_name):
      frames[i].dispose()
コード例 #17
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    def __init__(self):
        self.mainDir = ""

        self.setTitle("Dots Quality Check")
        self.setSize(250, 300)
        self.setLocation(20,120)
        self.addWindowFocusListener(self)
        
        self.Panel = JPanel(GridLayout(0,1))
        self.add(self.Panel)
        self.openNextButton = JButton("Open Next Random", actionPerformed=self.openRandom)
        self.Panel.add(self.openNextButton)
        self.saveButton = JButton("Save", actionPerformed=self.save, enabled=False)
        self.Panel.add(self.saveButton)
        self.cropButton = JButton("Crop values from here", actionPerformed=self.cropVals)
        self.Panel.add(self.cropButton)
        self.DiscardButton = JButton("Discard cell", actionPerformed=self.discardCell)
        self.Panel.add(self.DiscardButton)
        self.quitButton = JButton("Quit script",actionPerformed=self.quit)
        self.Panel.add(self.quitButton)

        annoPanel = JPanel()
        #add gridlayout
        self.wtRButton = JRadioButton("wt", actionCommand="wt")
        self.wtRButton.addActionListener(self)
        self.defectRButton = JRadioButton("Defect", actionCommand="defect")
        self.defectRButton.addActionListener(self)
        annoPanel.add(self.wtRButton)
        annoPanel.add(self.defectRButton)
        self.aButtonGroup = ButtonGroup()
        self.aButtonGroup.add(self.wtRButton)
        self.aButtonGroup.add(self.defectRButton)
      
        self.Panel.add(annoPanel)

        self.ProgBar = JProgressBar()
        self.ProgBar.setStringPainted(True)
        self.ProgBar.setValue(0)
        self.Panel.add(self.ProgBar)

        self.pathLabel = JLabel("-- No main directory chosen --")
        self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
        self.Panel.add(self.pathLabel)
      
        WindowManager.addWindow(self)
        self.show()
コード例 #18
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def main():
    """Get options and create new image."""
    options = get_options()
    if options is not None:
        bwidth, bheight = options
        img_cur = WindowManager.getCurrentImage()
        img_new = boxed_intensities(img_cur, bwidth, bheight)
        img_new.show()
コード例 #19
0
ファイル: _1_Extract.py プロジェクト: piw/IJ_Scripts
def loadVideoSegment(fwin, start, reduction, label):
    '''
        Load a video segment, optionally trim the unused frames
        in the beginning (usually the 1st segment)
             - fwin: name of the window of the video file (already opened)
             - start: starting frame number, default = 1
             - reduction: sampling rate (i.e. frame reduction factor)
             - label: label of the loaded substack
    '''
    WM.setCurrentWindow(WM.getWindow(fwin))
    im1 = IJ.getImage()
    nSlices = im1.getStack().getSize()
    IJ.run(im1, 'Make Substack...',
           ' slices=' + str(start) + '-' + str(nSlices) + '-' + str(reduction))
    im2 = IJ.getImage()
    im2.setTitle('Substack ' + label)
    im1.close()
    return im2
コード例 #20
0
ファイル: ConvertTo8Bit_.py プロジェクト: martlj/Fiji-scripts
def Resize(imp):
	gd = GenericDialog("Image size")
	scales = ["1024","2048","4096"]
	gd.addChoice("Choose image size",scales,scales[1])
	gd.showDialog()
	scale_choice = gd.getNextChoice()
	IJ.run(imp,"Scale...", "x=- y=- z=1.0 width="+scale_choice+" height="+scale_choice+" interpolation=Bilinear average process create title=Scaled")
	scaled_imp = WindowManager.getImage("Scaled")
	return scaled_imp
コード例 #21
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def ridge_detect(imp, rd_max, rd_min, rd_width, rd_length):
    title = imp.getTitle()
    IJ.run(imp, "8-bit", "");
    IJ.run(imp, "Ridge Detection", "line_width=%s high_contrast=%s low_contrast=%s make_binary method_for_overlap_resolution=NONE minimum_line_length=%s maximum=0" % (rd_width, rd_max, rd_min, rd_length))
    IJ.run(imp, "Remove Overlay", "")
    skel = WindowManager.getImage(title + " Detected segments")
    IJ.run(skel, "Skeletonize (2D/3D)", "")
    skel.hide()
    return(skel)
コード例 #22
0
	def itemStateChanged(self,e):
		imgList = []
		imgList.append(virginImage)
		for i in range(len(checkboxObjects)):
			if checkboxObjects[i].getState() == True:
				imgList.append(self.boxImages[i])

		titles = WindowManager.getImageTitles()
		p = re.compile(r'^Result')
		for title in titles:
			m = p.search(title)
			if m is not None:
				computedImage = WindowManager.getImage(title)
				computedImage.close()

		IJ.showStatus("Computing...")
		computedImage = reduce(self.addImages,imgList)
		computedImage.show()
		IJ.showStatus("Ready")
コード例 #23
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def readResults(windowTitle):
   textPanel = WindowManager.getFrame(windowTitle).getTextPanel()
   headings = textPanel.getColumnHeadings()
   
   "get results from TextWindow with java.lang.string title"
   resolver = re.compile('\d+\t(?P<frame>\d+\.0+)\t(?P<fsDistance>\d+\.\d+)\t(?P<ffDistance>\d+\.\d+)\t(?P<ssDistance>\d+\.\d+)\t(?P<fVol>\d+\.\d+)\t(?P<sVol>\d+\.\d+)')
   frameA = []
   distA = []
   volFcA = []
   volScA = []
   #xFcA, yFcA, zFcA, xScA, yScA, zScA
   resPnl = WindowManager.getFrame(windowTitle).getTextPanel()
   for row in range(resPnl.getLineCount()):
      mo = resolver.match(resPnl.getLine(row))
      frameA.append(int(float(mo.group('frame'))))
      distA.append(mo.group("fsDistance"))
      volFcA.append(mo.group("fVol"))
      volScA.append(mo.group("sVol"))
   return frameA, distA, volFcA, volScA
コード例 #24
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def merge_images(_imp1, _imp2, force_same_bit_depth):
  imp1 = _imp1.duplicate()
  imp2 = _imp2.duplicate()
  imp1.show(); imp2.show();
  if(force_same_bit_depth):
    bd = max(imp1.getBitDepth(),imp2.getBitDepth())
    if bd==16:
      convert_to_16bit(imp1)
      convert_to_16bit(imp2)
    if bd==32:
      convert_to_32bit(imp1)
      convert_to_32bit(imp2)
  IJ.run(imp1, "Merge Channels...", "c1=[%s] c2=[%s] create" % (imp1.getTitle(), imp2.getTitle()))
  
  imp_out = WindowManager.getImage("Composite") 
  if not imp_out:
    imp_out = WindowManager.getImage("Merged")
  imp_out.hide()
  imp1.hide(); imp2.hide()
  return imp_out
コード例 #25
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def straighten(stackName):
    '''
    IJ.run("Set Measurements...", "area mean min center redirect=None decimal=3")
    IJ.open(stackName)
    imp = IJ.getImage()
    stack = imp.getImageStack()

    for i in xrange(1, imp.getNSlices()+1):
        image = ImagePlus(str(i), stack.getProcessor(i))
        xvals = []
        yvals = []
        maxvals = []
        j = 0

        for k in xrange(0, 512, 2):
            IJ.makeRectangle(k, 0, 4, 512)
            IJ.run("Measure")
            table = RT.getResultsTable()

            x = table.getValue("XM", 0)
            y = table.getValue("YM", 0)
            #maxi = IJ.getResult("Max")
            table = []

            xvals.append(k)
            yvals.append(y)
            #maxvals.append(maxi)

            #if maxvals[j] == 0 and j > 0:
                #yvals[j] = yvals[j-1]

            j += 1

        print "xvals:", xvals
        print "yvals:", yvals
        mr = MR()
        IJ.run("Make Selection...", "freeline, "+str(xvals)+" ,"+ str(yvals))

        #IJ.runMacro("makeSelection...", "freeline, "+str(xvals)+" ,"+ str(yvals));

        #IJ.run("makeSelection(\"freeline\", xvals, yvals);")
        #IJ.run("Straighten...", "line = 80")
    '''
    IJ.open(stackName)
    imp = IJ.getImage()
    stack = imp.getImageStack()
    print imp.getNSlices()
    for i in range(1, imp.getNSlices()+1):
        image = ImagePlus(str(i), stack.getProcessor(i))
        IJ.runMacroFile("/Users/juliansegert/repos/Bio119_root_tracking/straightenOneImage.ijm")
        newImp = WM.getCurrentImage()
    	fs = FileSaver(newImp)
    	fs.saveAsTiff("/Users/juliansegert/Documents/Roots/Four_root_image_stacks/Pos01/"+str(i)+".tif")
    	newImp.close()    
コード例 #26
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ファイル: MeasuresCells_.py プロジェクト: leec13/MorphoBactPy
	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
コード例 #27
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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())
コード例 #28
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    def overlayImages(self, e):
        impBase = WindowManager.getImage(self.imageIDs[self.baseImageBox.getSelectedIndex()])
        refBase = impBase.getStack().getProcessor(1)
        
        impOverlay = WindowManager.getImage(self.imageIDs[self.overlayImageBox.getSelectedIndex()])
        refOverlay = impOverlay.getStack().getProcessor(1)
        
        print "Overlaying for stack sizes " + str(impBase.getStackSize()) + "/" + str(impOverlay.getStackSize()) + "..."
        
        stack = None
        
        if self.virtualStackCheckbox.isSelected():
            stack = OverlayVirtualStack()
            stack.overlayOpacity = float(self.opacitySpinner.getValue())/100.0
            stack.overlayColor = AWTColorToArray(self.overlayColorPreviewLabel.getBackground())
            stack.base = impBase
            stack.overlay = impOverlay

            ImagePlus("Stack Overlay from " + self.imageNames[self.baseImageBox.getSelectedIndex()] + " and " + self.imageNames[self.overlayImageBox.getSelectedIndex()], stack).show()
        else:
            IJ.error("Not implemented yet", "Using normal stacks is not implemented yet. Please use the Virtual Stack option.")
コード例 #29
0
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
コード例 #30
0
ファイル: CellCropper_V4.py プロジェクト: schiklen/DotObjects
    def __init__(self):
        self.frame = JFrame("CellCropper: Experiment details", size=(400,200))
        self.frame.setLocation(20,120)
        self.Panel = JPanel(GridLayout(4,2))
        self.frame.add(self.Panel)
        self.Panel.add(JLabel("Date:"))
        self.dateField = JTextField( str(date.today()), 8 )
        self.Panel.add(self.dateField)
        self.strainField = JTextField( "2926",4 )
        self.Panel.add(self.strainField)
        self.tempField = JTextField( "34",2 )
        self.Panel.add(self.tempField)
        self.ODField = JTextField( "0.5",3 )
        self.Panel.add(self.ODField)
        self.condField = JTextField( "0.5",3 )
        self.Panel.add(self.condField)

        self.OKButton = JButton("OK",actionPerformed=closeAndMakePos)
        self.Panel.add(self.OKButton)
        self.frame.pack()
        WindowManager.addWindow(self.frame)
        self.show()
コード例 #31
0
def main():

    # Get the wanted output directory and prepare subdirectories for output.
    outdir = IJ.getDirectory("output directory")

    # Open the 'Track statistics.csv' input file and format as getresults() dictionary.
    rt = opencsv()
    rt = getresults(rt)

    # Retrieve the current image as input (source) image.
    imp = WindowManager.getCurrentImage()

    cal = imp.getCalibration()
    IJ.log("Calibration: {}".format(cal.scaled()))

    # Run the main crop function on the source image.
    croppoints(imp, spots=rt, outdir=outdir, roi_x=150, roi_y=150)

    # Combine all output stacks into one movie.
    combinestacks(outdir, height=8)
コード例 #32
0
def main():
    # Get the wanted output directory and prepare subdirectories for output.
    outdir = IJ.getDirectory("output directory")

    # Open the 'Track statistics.csv' input file and format as getresults() dictionary.
    rt = opencsv()
    rt = getresults(rt)

    # Retrieve the current image as input (source) image.
    imp = WindowManager.getCurrentImage()

    # Run the main crop function on the source image.
    # croptracks(imp, tracks, outdir, trackid="TRACK_ID",
    #            trackx="TRACK_X_LOCATION", tracky="TRACK_Y_LOCATION",
    #            trackstart="TRACK_START", trackstop="TRACK_STOP",
    #            roi_x=150, roi_y=150)
    croptracks(imp, tracks=rt, outdir=outdir, roi_x=150, roi_y=150)

    # Combine all output stacks into one movie.
    combinestacks(outdir, height=8)
コード例 #33
0
def save_current_image_as_tiff(filename, filetype, target):
    """save the currently active image as ImageJ-Tiff

    Arguments:
        filename {string} -- filename of the image
        filetype {string} -- the original filetype of the image
        target {directory} -- directory where the image will be saved

    Returns:
        nothing
    """

    imp = wm.getCurrentImage()
    savename = filename.replace(filetype, "_stitched.tif")
    savepath = target + savename
    IJ.log("now saving: " + str(savepath))
    print "now saving", savepath
    IJ.saveAs(imp, "Tiff", savepath)
    imp.close()

    return savepath
コード例 #34
0
def run():
    Ch0dir = '/Volumes/TRANSCEND/Claudia/LGR5SegmentationTraining/DeformMask/'
    Ch1dir = '/Volumes/TRANSCEND/Claudia/LGR5SegmentationTraining/DeformMask/'
    DoubleChdir = '/Volumes/TRANSCEND/Claudia/LGR5SegmentationTraining/DeformDoubleChannelMask/'
    Raw_path = os.path.join(Ch0dir, '*tif')
    X = glob.glob(Raw_path)
    axes = 'YX'
    for fname in X:
      print(fname)
      IJ.open(fname);
      imp = IJ.getImage()
      Name = os.path.basename(os.path.splitext(fname)[0])
      Ch1Name = Ch1dir + Name + '.tif'
      IJ.open(Ch1Name);
      impCh1 = IJ.getImage()
      IJ.run("Merge Channels...", "c1="+imp.getTitle()+ " c2="+impCh1.getTitle()+ " create");
      IJ.saveAs('.tif', DoubleChdir +  Name);
      imp.close();
      impCh1.close();
      composite = wm.getFrontWindow()
      if composite is not None: done = composite.close()
コード例 #35
0
def pointList3DFromRT(tableName,modifierX = 0,modifierY = 0,modifierZ = 0, XColumn='X (microns)', YColumn='Y (microns)', ZColumn='Z (microns)'):
	win = WindowManager.getWindow(tableName)
	rt = win.getResultsTable()

	X = rt.getColumn(rt.getColumnIndex(XColumn))
	Y = rt.getColumn(rt.getColumnIndex(YColumn))
	Z = rt.getColumn(rt.getColumnIndex(ZColumn))
	# X = rt.getColumn(XColumn)
	# Y = rt.getColumn(YColumn)
	# Z = rt.getColumn(ZColumn)
	
	dplist = []
	for x, y, z in zip(X, Y, Z):
		array = []
		array.append(x+modifierX)
		array.append(y+modifierY)
		array.append(z+modifierZ)
		jArray = jarray.array(array, 'd')
		dp = DoublePoint(jArray)
		dplist.append(dp)
	return dplist
コード例 #36
0
def save_current_image_as_bdv(filename, filetype, target):
    """save the currently active image as BigDataViewer hdf5/xml

    Arguments:
        filename {string} -- filename of the image
        filetype {string} -- the original filetype of the image
        target {directory} -- directory where the image will be saved

    Returns:
        nothing
    """

    imp = wm.getCurrentImage()
    savename = filename.replace(filetype, "_stitched.xml")
    savepath = target + savename
    IJ.log("now saving: " + str(savepath))
    print "now saving", savepath
    IJ.run("Export Current Image as XML/HDF5",
           "  use_deflate_compression export_path=[" + savepath + "]")
    imp.close()

    return savepath
コード例 #37
0
def main():
	#summary = False
	if (WindowManager.getImageCount() > 0):
		IJ.run("Save")
		image_dir = processImage()
#	if (WindowManager.getImageCount() > 0):
#		for image in range(WindowManager.getImageCount()):
#			processImage()
	else:
		#summary = True
		#selected_dir = IJ.getDirectory("Select Directory")
		if not selected_dir.endswith(os.path.sep):
			selected_dir = selected_dir + os.path.sep

		dir_list = list()
		file_type = [".tif", ".tiff"]
		image_list = listDir(selected_dir, file_type = file_type, recursive = False)
		for image in image_list:
			IJ.open(image)
			image_dir = processImage()

	summarize(os.path.join(image_dir, "markers" ))
	summarize(os.path.join(image_dir, "processed_markers"))
コード例 #38
0
def calculateNNDsByCluster(tableName):
	win = WindowManager.getWindow(tableName)
	rt =  win.getResultsTable()
	C = rt.getColumn(4)
	nrOfClusters = int(max(C))
	NR = rt.getColumn(0)
	C = rt.getColumn(4)
	X = rt.getColumn(1)
	Y = rt.getColumn(2)
	Z = rt.getColumn(3)
	points = list(zip(NR,X,Y,Z,C))
	points.sort(key = itemgetter(4))
	groups = groupby(points, itemgetter(4))
	clusters = [[(item[1], item[2], item[3], item[0]) for item in data] for (key, data) in groups]
	offset = 0;
	for cluster in clusters:
		dplist = []
		for x, y, z, nr in cluster:
			array = []
			array.append(x)
			array.append(y)
			array.append(z)
			array.append(nr)
			jArray = jarray.array(array, 'd')
			dp = DoublePoint(jArray)
			dplist.append(dp)
	
		nearestNeighborsDist, nearestNeighborsInd = calculateNNDs(dplist)
		index = 0
		for point in cluster:
			row = int(point[3]) - 1
			rt.setValue("nn. dist", row, nearestNeighborsDist[index])
			rt.setValue("neighbor", row, nearestNeighborsInd[index]+1+offset)
			index = index + 1
		offset = offset + len(cluster);
	win.rename("tmp")
	win.rename(tableName)
コード例 #39
0
def run():
    global numRep
    images = map(WM.getImage, WM.getIDList())
    nStacks = len(images)  #num of stacks opened
    numSlices = [images[i].getNSlices() for i in range(nStacks)]  #[12,13,12]
    maxSlice = max(
        numSlices)  #the max number of slices among all opened stacks
    #maxIndex = [i for i,j in enumerate(numSlices) if j == maxSlice] # the index of the image with maxSlice
    #move max to the head and min to the end
    imps = [
        image
        for (numSlice, image) in sorted(zip(numSlices, images), reverse=True)
    ]  #sort the images base on their nSlices

    numRep = zyGetProperty(imps[0], "nFrame")

    #add slices in imp[0], base on (nStacks-1)*numRep
    impDup(imps[0], nStacks)
    #for other imps, loop them and copy/paste every 3(numRep) into imp
    for i in range(nStacks - 1):
        n = i + 1
        binder(imps[0], imps[n], nStacks, n)

    #set the nFrame = nStacks*numRep, and save the image
    # record the numSlices, numFrame, totalSlices and numStacks in the infoStr
    zyAddProperty(imps[0])

    msgStr = "nslices=" + str(maxSlice / numRep) + " nframes=" + str(
        nStacks * numRep)
    #IJ.run(imps[0], "Properties...", msgStr)
    IJ.log("For real: " + msgStr)
    file_path = IJ.getDirectory('image')
    file_name = imps[0].getTitle()
    filename = 'C_' + file_name
    imps[0].setTitle(filename)
    destPath = os.path.join(file_path, 'combined')
    saveStack(destPath, filename, imps[0])
コード例 #40
0
def save_current_image_with_BF_as_ics1(filename, filetype, target):
    """saves a given ImagePlus as ics1 using Bio-Formats

    Parameters
    ----------
    imp : ImagePlus
        an open ImagePlus to be saved
    filename : str
        Filename of the image
    filetype : str
        The original filetype of the image
    target : string
        path to the original image on disc
    """

    imp = wm.getCurrentImage()
    savename = filename.replace(filetype, "_stitched.ids")
    savepath = os.path.join(target, savename)
    IJ.log("now saving: " + str(savepath))
    print "now saving", savepath
    IJ.run(imp, "Bio-Formats Exporter", "save=[" + savepath + "]")
    imp.close()

    return savepath
コード例 #41
0
def Compositor(timepoints, channels, dirs):
	""" Creates composite images of all channels for each timepoint. """
	 	
  	# Creates composite stack from HDD images.
 	for time in range (1, (timepoints*channels), channels):
  		
  		stack = IJ.run(
  		    "Image Sequence...", "open="
  		    + dirs["Projections"] + " number=" + str(channels)
  		    + " starting=" + str(time) + " increment=1 scale=400 file=.tif sort")
        
  		comp = IJ.run("Make Composite", "display=Composite")
  		comp = IJ.run("Stack to RGB", comp)
       
  		IJ.saveAs(comp, "Tiff", os.path.join(dirs["Composites"],
  		         "Timepoint"+str(time/channels).zfill(3)))

		# Close windows.
  		for i in range (2):
  			try:
  				imp = WindowManager.getCurrentImage()
  				imp.close()
  			except:
  				pass
コード例 #42
0
def scaleImageUI():
    gd = GenericDialog("Scale")
    gd.addSlider("Scale", 1, 200, 100)
    gd.addCheckbox("Preview", True)
    # The UI elements for the above two inputs
    slider = gd.getSliders().get(0)  # the only one
    checkbox = gd.getCheckboxes().get(0)  # the only one

    imp = WM.getCurrentImage()
    if not imp:
        print "Open an image first!"
        return

    previewer = ScalingPreviewer(imp, slider, checkbox)
    slider.addAdjustmentListener(previewer)
    checkbox.addItemListener(previewer)

    gd.showDialog()

    if gd.wasCanceled():
        previewer.reset()
        print "User canceled dialog!"
    else:
        previewer.scale()
コード例 #43
0
def generateCardiomyocyteMask(cmIp, method="Otsu", stack=True, minCmSize=500, brightfield = False):
  cmIp.setTitle("CmStain")
  if brightfield:
    IJ.run(cmIp, "Find Edges", "stack")
  if not stack:
    IJ.setAutoThreshold(cmIp, "{} dark".format(method))
    IJ.run(cmIp, "Convert to Mask", "method={} background=Dark calculate".format(method))
  else:
    IJ.setAutoThreshold(cmIp, "{} dark stack".format(method))
    IJ.run(cmIp, "Convert to Mask", "method={} background=Dark stack".format(method))
  if brightfield:
    IJ.run(cmIp, "Morphological Filters (3D)", "operation=Closing element=Ball x-radius=2 y-radius=2 z-radius=0")
    delIp = cmIp
    delIp.changes = False
    delIp.close()
    cmIp = WindowManager.getImage("CmStain-Closing")
    IJ.run(cmIp,"Fill Holes", "stack")
  cmIp.show()
  IJ.run("Set Measurements...", "stack redirect=None decimal=3")
  IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Masks] exclude in_situ stack".format(cmMinSize))
  cmMaskIp = cmIp.duplicate()
  IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Count Masks] exclude in_situ stack".format(cmMinSize))
  cmMaskIp.show(), cmIp.show()
  return cmIp, cmMaskIp
コード例 #44
0
def importMask(evt=None):
  display = Display.getFront()
  # Obtain an image stack
  #imp = IJ.getImage()
  imp = WindowManager.getImage("Labels")

  layerset = display.getLayerSet()
  p = layerset.getProject()

  ali = AreaList(p, "", 0, 0)
  layerset.add(ali)
  p.getProjectTree().insertSegmentations([ali])

  # Obtain the image stack
  stack = imp.getImageStack()
  # Iterate every slice of the stack
  for i in range(1, imp.getNSlices() + 1):
    ip = stack.getProcessor(i) # 1-based
    # Extract all areas (except background) into a map of value vs. java.awt.geom.Area
    m = AreaUtils.extractAreas(ip)
    # Report progress
    if len(m) > 0:
      IJ.log(str(i) + ":" + str(len(m)))
    # Get the Layer instance at the corresponding index
    layer = layerset.getLayers().get(i-1) # 0-based
    # Add the first Area instance to the AreaList at the proper Layer
    if ( m.values().iterator().hasNext() ):
      ali.addArea(layer.getId(), m.values().iterator().next())

  # Change the color of the AreaList
  ali.setColor(Color.red)
  ali.adjustProperties()
  # Ensure bounds are as constrained as possible
  ali.calculateBoundingBox(None)
  # Repaint
  Display.repaint()
コード例 #45
0
def duplicateMaskInRoi(imp, roi, duplicateStack=False):
    imp.setRoi(roi)
    if duplicateStack:
    	WindowManager.setCurrentWindow(imp.getWindow())
        impMT1 = IJ.run("Duplicate...", "duplicate")
        impMT1 = WindowManager.getCurrentImage()
    else:
        impMT1 = imp.crop()
    IJ.run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel")
    IJ.run(impMT1, "Create Selection", "")
    roi1 = impMT1.getRoi()
    bounds = roi1.getBounds()
    if duplicateStack:
       	WindowManager.setCurrentWindow(impMT1.getWindow())
        IJ.run("Duplicate...", "duplicate")
        impMT = WindowManager.getCurrentImage()
        impMT1.close()
    else:
        impMT = impMT1.crop()
    IJ.run(impMT, "Canvas Size...", "width="+str(bounds.width+2)+" height="+str(bounds.height+2)+" position=Center zero")  
    return impMT, bounds
コード例 #46
0
from fiji.plugin.trackmate.io import TmXmlReader, TmXmlWriter
from fiji.plugin.trackmate.util import TMUtils
from fiji.plugin.trackmate.action import ExportStatsToIJAction, ExportTracksToXML
from fiji.plugin.trackmate.detection import DetectorKeys

from fiji.plugin.trackmate.features import FeatureAnalyzer, ModelFeatureUpdater, SpotFeatureCalculator
from fiji.plugin.trackmate.features.spot import SpotContrastAndSNRAnalyzerFactory, SpotContrastAndSNRAnalyzer
from fiji.plugin.trackmate.features.track import TrackDurationAnalyzer, TrackSpeedStatisticsAnalyzer

import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer as TrackDurationAnalyzer
import fiji.plugin.trackmate.features.SpotFeatureCalculator as SpotFeatureCalculator
import fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer as SpotContrastAndSNRAnalyzer
import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory as SpotIntensityAnalyzerFactory

# Get currently selected image
imp = WindowManager.getCurrentImage()
#imp = IJ.openImage('http://fiji.sc/samples/FakeTracks.tif')
#imp.show()

#----------------------------
# Create the model object now
#----------------------------

# Some of the parameters we configure below need to have
# a reference to the model at creation. So we create an
# empty model now.

model = Model()

# Send all messages to ImageJ log window.
model.setLogger(Logger.IJ_LOGGER)
コード例 #47
0
# use the same renaming trick as for the macro recorder
imp.setTitle("current")

# IJ.run executes commands from the macro recorder
IJ.run(
    "Scale...",
    "x=.5 y=.5 z=1.0 width=128 height=128 depth=930 interpolation=Bilinear average process create"
)
imp.close()
IJ.selectWindow("current-1")
IJ.run("Z Project...", "projection=[Average Intensity]")

# Note the new imports above, WindowManager and ImageCalculator
# ic.run executes commands within image calculator; wm.getImage selects the image using WindowsManager
imp = ic.run("Subtract create 32-bit stack", wm.getImage("current-1"),
             wm.getImage("AVG_current-1"))
imp.show()
imp = ic.run("Divide create 32-bit stack", wm.getImage("Result of current-1"),
             wm.getImage("AVG_current-1"))
imp.show()
IJ.selectWindow("Result of Result of current-1")

# adjust the Brightness/Contrast
IJ.setMinAndMax(-0.0200, 0.2000)

# this is the Lookup Tables step
IJ.run("Aselfmade3")

# IJ.saveAs has 3 arguments: (image, file type, file path)
IJ.saveAs(IJ.getImage(), "Tiff", out_folder + the_file + '-processed')
コード例 #48
0
    return retSeqP


from ij.measure import ResultsTable
from ij import WindowManager
from ij.gui import NonBlockingGenericDialog
from ij import IJ
import sys
sys.path.append(
    IJ.getDirectory("imagej") + "/jars/HaralickFeaturesInteractive/")

from Haralick_Features import Haralick_Features as hf

cmChan = int(IJ.getProperty("cmChan"))

analyte = WindowManager.getCurrentImage()
analyte.setC(cmChan)
title = analyte.getTitle()
cmNumber = IJ.getProperty("cmNumber")
if cmNumber is None:
    cmNumber = 1
    IJ.setProperty("cmNumber", cmNumber)
cmNumber += 1
sarcomereLength = IJ.getProperty("sarcomereLength")
if sarcomereLength is None:
    sarcomereLength = 1.5
icalibration = analyte.getCalibration()
pixelDistance = round(icalibration.getRawX(sarcomereLength))
pixelDistance = round(icalibration.getRawX(sarcomereLength))
retval = findMaximaSeqs([
    list(hfi) for hfi in hf().calculate(analyte, "Sarcomeres", 45,
コード例 #49
0
def startTracking(filepath, fdir, ffile, filename):
    outpath = fdir
    troutpath = fdir + separator + ffile + separator + "tracked" + separator
    stackoutpath = fdir + separator + ffile + separator + "stacks" + separator

    pixwidth = 0.647
    interval_sec = 600  #pr
    if "141006" in fdir:
        interval_sec = 600
    elif "141117" in fdir:
        interval_sec = 300
    elif "141215" in fdir:
        interval_sec = 300

    if not os.path.isdir(outpath):
        os.mkdir(outpath)
    if not os.path.isdir(troutpath):
        os.mkdir(troutpath)
    if not os.path.isdir(stackoutpath):
        os.mkdir(stackoutpath)

    print 'filepath: ', filepath  #pr
    print 'fdir: ', fdir  #pr
    print 'ffile: ', ffile  #pr
    IJ.run("Image Sequence...",
           "open=" + filepath + " file=" + filename + " sort")
    #pr
    #IJ.run("Image Sequence...", "open=" + filepath + " file=molm sort"); #pr
    imp = WindowManager.getCurrentImage()
    imptitle = imp.getTitle()
    nframes = imp.getNSlices()
    IJ.run(
        imp, "Properties...", "channels=1 slices=1 frames=" + str(nframes) +
        " unit=inch pixel_width=" + str(pixwidth) + " pixel_height=" +
        str(pixwidth) + " voxel_depth=1.0000 frame=[" + str(interval_sec) +
        " sec]")

    IJ.run(imp, "Duplicate...", "title=" + imptitle + "_dup duplicate")
    imp_dup = WindowManager.getImage(imptitle + "_dup")
    IJ.run(imp_dup, "Gaussian Blur...", "sigma=50 stack")

    ic = ImageCalculator()
    imp_corr = ic.run("Divide create 32-bit stack", imp, imp_dup)
    imp_corr.setTitle(imptitle + "_corrected")
    imp_corr.show()
    imp.changes = False
    imp.close()
    imp_dup.changes = False
    imp_dup.close()

    IJ.run(imp_corr, "8-bit", "")
    IJ.run(
        imp_corr, "Normalize Local Contrast",
        "block_radius_x=100 block_radius_y=100 standard_deviations=1 stretch stack"
    )
    IJ.saveAs(imp_corr, "Tiff",
              stackoutpath + separator + imptitle + "_corrected.tif")

    IJ.run(imp_corr, "Duplicate...", "title=" + imptitle + "_bg duplicate")
    imp_bg = WindowManager.getImage(imptitle + "_bg")

    #Prefs.blackBackground = True;
    IJ.setAutoThreshold(imp_bg, "MinError dark")
    IJ.run(imp_bg, "Convert to Mask", "stack")
    IJ.run(imp_bg, "Analyze Particles...",
           "size=10000-Infinity show=Masks stack")
    imp_bg.changes = False
    imp_bg.close()

    imp_bgmask = WindowManager.getImage("Mask of " + imptitle + "_bg")

    ic = ImageCalculator()
    imp_corr_wobg = ic.run("Subtract create stack", imp_corr, imp_bgmask)
    imp_corr_wobg.setTitle(imptitle + "_corrected_womask")
    imp_corr_wobg.show()

    IJ.saveAs(imp_corr_wobg, "Tiff",
              stackoutpath + separator + imptitle + "_corrected_womask.tif")
    #pr

    # pr: substract average frames
    zp = ZProjector(imp_corr_wobg)
    zp.setMethod(ZProjector.AVG_METHOD)
    zp.doProjection()
    zpimp = zp.getProjection()
    zpimp.show()
    imp_corr_wobg_sub = ImageCalculator().run("Subtract create stack",
                                              imp_corr_wobg, zpimp)
    imp_corr_wobg_sub.show()
    #imp_corr_wobg.changes = False
    #imp_corr_wobg.close()
    # pr: subtract average frames (END)

    IJ.saveAs(
        imp_corr_wobg_sub, "Tiff", stackoutpath + separator + imptitle +
        "_corrected_womask_substracted.tif")
    #pr
    IJ.saveAs(
        zpimp, "Tiff",
        stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
    #commented out: pr
    #IJ.saveAs(imp_corr_wobg, "Tiff", stackoutpath+separator+imptitle+"_corrected_womask.tif");
    IJ.saveAs(imp_bgmask, "Tiff",
              stackoutpath + separator + imptitle + "_bgmask.tif")

    print(stackoutpath + separator + imptitle +
          "_corrected_womask_substracted.tif")
    print(stackoutpath + separator + imptitle + "_corrected_womask_avg.tif")
    print(stackoutpath + separator + imptitle + "_bgmask.tif")

    imp_corr.changes = False
    imp_corr.close()
    imp_bgmask.changes = False
    imp_bgmask.close()

    imp_corr_wobg.changes = False
    imp_corr_wobg.close()
    #imp_corr_wobg_sub.changes = False
    #imp_corr_wobg_sub.close()
    zpimp.changes = False
    zpimp.close()

    #IJ.log(System.getProperty("os.name"))
    #IJ.log(fdir)

    return imp_corr_wobg_sub
コード例 #50
0
 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
コード例 #51
0
def runOneFile(fullFilePath):

    global gNumChannels
    global gAlignBatchVersion

    if not os.path.isfile(fullFilePath):
        bPrintLog(
            '\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',
            0)
        return 0

    bPrintLog(
        time.strftime("%H:%M:%S") + ' starting runOneFile(): ' + fullFilePath,
        1)

    enclosingPath = os.path.dirname(fullFilePath)
    head, tail = os.path.split(enclosingPath)
    enclosingPath += '/'

    #make output folders
    destFolder = enclosingPath + tail + '_channels/'
    if not os.path.isdir(destFolder):
        os.makedirs(destFolder)
    destMaxFolder = destFolder + 'max/'
    if not os.path.isdir(destMaxFolder):
        os.makedirs(destMaxFolder)

    if gDoAlign:
        destAlignmentFolder = destFolder + 'alignment/'
        if not os.path.isdir(destAlignmentFolder):
            os.makedirs(destAlignmentFolder)

    if gSave8bit:
        eightBitFolder = destFolder + 'channels8/'
        if not os.path.isdir(eightBitFolder):
            os.makedirs(eightBitFolder)
        eightBitMaxFolder = eightBitFolder + 'max/'
        if not os.path.isdir(eightBitMaxFolder):
            os.makedirs(eightBitMaxFolder)

    # open image
    imp = Opener().openImage(fullFilePath)

    # get parameters of image
    (width, height, nChannels, nSlices, nFrames) = imp.getDimensions()
    bitDepth = imp.getBitDepth()
    infoStr = imp.getProperty("Info")  #get all .tif tags
    if not infoStr:
        infoStr = ''
    infoStr += 'bAlignBatch_Version=' + str(gAlignBatchVersion) + '\n'
    infoStr += 'bAlignBatch_Time=' + time.strftime(
        "%Y%m%d") + '_' + time.strftime("%H%M%S") + '\n'

    msgStr = 'w:' + str(width) + ' h:' + str(height) + ' slices:' + str(nSlices) \
       + ' channels:' + str(nChannels) + ' frames:' + str(nFrames) + ' bitDepth:' + str(bitDepth)
    bPrintLog(msgStr, 1)

    path, filename = os.path.split(fullFilePath)
    shortName, fileExtension = os.path.splitext(filename)

    #
    # look for num channels in ScanImage infoStr
    if gGetNumChanFromScanImage:
        for line in infoStr.split('\n'):
            #scanimage.SI4.channelsSave = [1;2]
            scanimage4 = find(line, 'scanimage.SI4.channelsSave =') == 0
            #state.acq.numberOfChannelsSave=2
            scanimage3 = find(line, 'state.acq.numberOfChannelsSave=') == 0
            if scanimage3:
                #print 'line:', line
                equalIdx = find(line, '=')
                line2 = line[equalIdx + 1:]
                if gGetNumChanFromScanImage:
                    gNumChannels = int(line2)
                    bPrintLog(
                        'over-riding gNumChannels with: ' + str(gNumChannels),
                        2)
            if scanimage4:
                #print '   we have a scanimage 4 file ... now i need to exptract the number of channel'
                #print 'line:', line
                equalIdx = find(line, '=')
                line2 = line[equalIdx + 1:]
                for delim in ';[]':
                    line2 = line2.replace(delim, ' ')
                if gGetNumChanFromScanImage:
                    gNumChannels = len(line2.split())
                    bPrintLog(
                        'over-riding gNumChannels with: ' + str(gNumChannels),
                        2)

    # show
    imp.show()
    # split channels if necc. and grab the original window names
    if gNumChannels == 1:
        origImpWinStr = imp.getTitle()  #use this when only one channel
        origImpWin = WindowManager.getWindow(
            origImpWinStr)  #returns java.awt.Window

    if gNumChannels == 2:
        winTitle = imp.getTitle()
        bPrintLog('Deinterleaving 2 channels...', 1)
        IJ.run('Deinterleave',
               'how=2 keep')  #makes ' #1' and ' #2', with ' #2' frontmost
        origCh1WinStr = winTitle + ' #1'
        origCh2WinStr = winTitle + ' #2'
        origCh1Imp = WindowManager.getImage(origCh1WinStr)
        origCh2Imp = WindowManager.getImage(origCh2WinStr)
        origCh1File = destFolder + shortName + '_ch1.tif'
        origCh2File = destFolder + shortName + '_ch2.tif'

    # work on a copy, mostly for alignment with cropping
    copy = Duplicator().run(imp)
    #copy.copyAttributes(imp) #don't copy attributes, it copies the name (which we do not want)
    copy.show()

    #
    # crop (on copy)
    if gDoCrop:
        bPrintLog('making cropping rectangle (left,top,width,height) ', 1)
        bPrintLog(
            str(gCropLeft) + ' ' + str(gCropTop) + ' ' + str(gCropWidth) +
            ' ' + str(gCropHeight), 2)

        roi = Roi(gCropLeft, gCropTop, gCropWidth,
                  gCropHeight)  #left,top,width,height
        copy.setRoi(roi)

        time.sleep(
            0.5
        )  # otherwise, crop SOMETIMES failes. WHAT THE F**K FIJI DEVELOPERS, REALLY, WHAT THE F**K

        #bPrintLog('cropping', 1)
        IJ.run('Crop')
        infoStr += 'bCropping=' + str(gCropLeft) + ',' + str(
            gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n'

    #
    # remove calibration ( on original)
    if gRemoveCalibration:
        cal = imp.getCalibration()
        calCoeff = cal.getCoefficients()
        if calCoeff:
            msgStr = 'Calibration is y=a+bx' + ' a=' + str(
                calCoeff[0]) + ' b=' + str(calCoeff[1])
            bPrintLog(msgStr, 1)

            #remove calibration
            bPrintLog('\tRemoving Calibration', 2)
            imp.setCalibration(None)

            #without these, 8-bit conversion goes to all 0 !!! what the f**k !!!
            #bPrintLog('calling imp.resetStack() and imp.resetDisplayRange()', 2)
            imp.resetStack()
            imp.resetDisplayRange()

            #get and print out min/max
            origMin = StackStatistics(imp).min
            origMax = StackStatistics(imp).max
            msgStr = '\torig min=' + str(origMin) + ' max=' + str(origMax)
            bPrintLog(msgStr, 2)

            # 20150723, 'shift everybody over by linear calibration intercept calCoeff[0] - (magic number)
            if 1:
                # [1] was this
                #msgStr = 'Subtracting original min '+str(origMin) + ' from stack.'
                #bPrintLog(msgStr, 2)
                #subArgVal = 'value=%s stack' % (origMin,)
                #IJ.run('Subtract...', subArgVal)
                # [2] now this
                #msgStr = 'Adding calCoeff[0] '+str(calCoeff[0]) + ' from stack.'
                #bPrintLog(msgStr, 2)
                #addArgVal = 'value=%s stack' % (int(calCoeff[0]),)
                #IJ.run('Add...', addArgVal)
                # [3] subtract a magic number 2^15-2^7 = 32768 - 128
                magicNumber = gLinearShift  #2^15 - 128
                msgStr = 'Subtracting a magic number (linear shift) ' + str(
                    magicNumber) + ' from stack.'
                bPrintLog(msgStr, 2)
                infoStr += 'bLinearShift=' + str(gLinearShift) + '\n'
                subArgVal = 'value=%s stack' % (gLinearShift, )
            IJ.run(imp, 'Subtract...', subArgVal)

            # 20150701, set any pixel <0 to 0
            if 0:
                ip = imp.getProcessor()  # returns a reference
                pixels = ip.getPixels()  # returns a reference
                msgStr = '\tSet all pixels <0 to 0. This was added 20150701 ...'
                bPrintLog(msgStr, 2)
                pixels = map(lambda x: 0 if x < 0 else x, pixels)
                bPrintLog('\t\t... done', 2)

            #get and print out min/max
            newMin = StackStatistics(imp).min
            newMax = StackStatistics(imp).max
            msgStr = '\tnew min=' + str(newMin) + ' max=' + str(newMax)
            bPrintLog(msgStr, 2)

            #append calibration to info string
            infoStr += 'bCalibCoeff_a = ' + str(calCoeff[0]) + '\n'
            infoStr += 'bCalibCoeff_b = ' + str(calCoeff[1]) + '\n'
            infoStr += 'bNewMin = ' + str(newMin) + '\n'
            infoStr += 'bNewMax = ' + str(newMax) + '\n'

    #
    # set up
    if gNumChannels == 1:
        impWinStr = copy.getTitle()  #use this when only one channel
        impWin = WindowManager.getWindow(impWinStr)  #returns java.awt.Window

    if gNumChannels == 2:
        winTitle = copy.getTitle()
        bPrintLog('Deinterleaving 2 channels...', 1)
        IJ.run('Deinterleave',
               'how=2 keep')  #makes ' #1' and ' #2', with ' #2' frontmost
        ch1WinStr = winTitle + ' #1'
        ch2WinStr = winTitle + ' #2'
        ch1Imp = WindowManager.getImage(ch1WinStr)
        ch2Imp = WindowManager.getImage(ch2WinStr)
        ch1File = destFolder + shortName + '_ch1.tif'
        ch2File = destFolder + shortName + '_ch2.tif'

    #
    # alignment
    if gDoAlign and gNumChannels == 1 and copy.getNSlices() > 1:
        infoStr += 'AlignOnChannel=1' + '\n'
        #snap to middle slice
        if gAlignOnMiddleSlice:
            middleSlice = int(
                math.floor(copy.getNSlices() /
                           2))  #int() is necc., python is f*****g picky
        else:
            middleSlice = gAlignOnThisSlice
        copy.setSlice(middleSlice)

        transformationFile = destAlignmentFolder + shortName + '.txt'

        bPrintLog('MultiStackReg aligning:' + impWinStr, 1)
        stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' % (
            impWin, transformationFile)
        IJ.run('MultiStackReg', stackRegParams)
        infoStr += 'AlignOnSlice=' + str(middleSlice) + '\n'

        #20150723, we just aligned on a cropped copy, apply alignment to original imp
        origImpTitle = imp.getTitle()
        stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
            origImpTitle, transformationFile)
        IJ.run('MultiStackReg', stackRegParams)

    if gDoAlign and gNumChannels == 2 and ch1Imp.getNSlices(
    ) > 1 and ch2Imp.getNSlices() > 1:
        #apply to gAlignThisChannel
        alignThisWindow = ''
        applyAlignmentToThisWindow = ''
        if gAlignThisChannel == 1:
            infoStr += 'AlignOnChannel=1' + '\n'
            transformationFile = destAlignmentFolder + shortName + '_ch1.txt'
            alignThisWindow = ch1WinStr
            applyAlignmentToThisWindow = ch2WinStr
        else:
            infoStr += 'AlignOnChannel=2' + '\n'
            transformationFile = destAlignmentFolder + shortName + '_ch2.txt'
            alignThisWindow = ch2WinStr
            applyAlignmentToThisWindow = ch1WinStr

        alignThisImp = WindowManager.getImage(alignThisWindow)
        #snap to middle slice
        if gAlignOnMiddleSlice:
            middleSlice = int(
                math.floor(alignThisImp.getNSlices() /
                           2))  #int() is necc., python is f*****g picky
        else:
            middleSlice = gAlignOnThisSlice
        alignThisImp.setSlice(middleSlice)

        infoStr += 'bAlignOnSlice=' + str(middleSlice) + '\n'

        bPrintLog('MultiStackReg aligning:' + alignThisWindow, 1)
        stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' % (
            alignThisWindow, transformationFile)
        IJ.run('MultiStackReg', stackRegParams)

        # 20150723, we just aligned on a copy, apply alignment to both channels of original
        # ch1
        bPrintLog('MultiStackReg applying alignment to:' + origCh1WinStr, 1)
        stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
            origCh1WinStr, transformationFile)
        IJ.run('MultiStackReg', stackRegParams)
        # ch2
        bPrintLog('MultiStackReg applying alignment to:' + origCh2WinStr, 1)
        stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
            origCh2WinStr, transformationFile)
        IJ.run('MultiStackReg', stackRegParams)

        #apply alignment to other window
        #bPrintLog('MultiStackReg applying alignment to:' + applyAlignmentToThisWindow, 1)
        #applyAlignThisImp = WindowManager.getImage(applyAlignmentToThisWindow)
        #stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(applyAlignmentToThisWindow,transformationFile)
        #IJ.run('MultiStackReg', stackRegParams)
    elif gDoAlign:
        bPrintLog('Skipping alignment, there may be only one slice?', 3)

    #
    # save
    if gNumChannels == 1:
        imp.setProperty("Info", infoStr)
        impFile = destFolder + shortName + '.tif'
        #bPrintLog('Saving:' + impFile, 1)
        bSaveStack(imp, impFile)
        #max project
        bSaveZProject(imp, destMaxFolder, shortName)

    if gNumChannels == 2:
        #ch1
        origCh1Imp.setProperty("Info", infoStr)
        #bPrintLog('Saving:' + ch1File, 1)
        bSaveStack(origCh1Imp, ch1File)
        #max project
        bSaveZProject(origCh1Imp, destMaxFolder, shortName + '_ch1')

        #ch2
        origCh2Imp.setProperty("Info", infoStr)
        #bPrintLog('Saving:' + ch2File, 1)
        bSaveStack(origCh2Imp, ch2File)
        #max project
        bSaveZProject(origCh2Imp, destMaxFolder, shortName + '_ch2')

#
    # post convert to 8-bit and save
    if gSave8bit:
        if bitDepth == 16:
            if gNumChannels == 1:
                bPrintLog('Converting to 8-bit:' + impWinStr, 1)
                IJ.selectWindow(impWinStr)
                #IJ.run('resetMinAndMax()')
                IJ.run("8-bit")
                impFile = eightBitFolder + shortName + '.tif'
                bPrintLog('Saving 8-bit:' + impFile, 2)
                bSaveStack(imp, impFile)
                #max project
                bSaveZProject(imp, eightBitMaxFolder, shortName)

            if gNumChannels == 2:
                #
                bPrintLog('Converting to 8-bit:' + origCh1WinStr, 1)
                IJ.selectWindow(origCh1WinStr)

                IJ.run("8-bit")
                impFile = eightBitFolder + shortName + '_ch1.tif'
                bPrintLog('Saving 8-bit:' + impFile, 2)
                bSaveStack(origCh1Imp, impFile)
                #max project
                bSaveZProject(origCh1Imp, eightBitMaxFolder,
                              shortName + '_ch1')

                #
                bPrintLog('Converting to 8-bit:' + origCh2WinStr, 1)
                IJ.selectWindow(origCh2WinStr)
                #IJ.run('resetMinAndMax()')
                IJ.run("8-bit")
                impFile = eightBitFolder + shortName + '_ch2.tif'
                bPrintLog('Saving 8-bit:' + impFile, 2)
                bSaveStack(origCh2Imp, impFile)
                #max project
                bSaveZProject(origCh2Imp, eightBitMaxFolder,
                              shortName + '_ch2')

    #
    # close original window
    imp.changes = 0
    imp.close()
    #copy
    copy.changes = 0
    copy.close()

    #
    # close ch1/ch2
    if gNumChannels == 2:
        #original
        origCh1Imp.changes = 0
        origCh1Imp.close()
        origCh2Imp.changes = 0
        origCh2Imp.close()
        #copy
        ch1Imp.changes = 0
        ch1Imp.close()
        ch2Imp.changes = 0
        ch2Imp.close()

    bPrintLog(
        time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath,
        1)
コード例 #52
0
from ij.text import TextPanel as TP
from ij.measure import ResultsTable as RT
# Create a non-blocking dialog to enter the metadata
psgd = NonBlockingGenericDialog(
    "Choose the frame that shows the right conformation of the heart?")
psgd.addNumericField("Which frame to choose?", 1, 0)
psgd.addCheckbox("Use table of selected frames?", False)
psgd.showDialog()
choose = psgd.getNextNumber()
choice = psgd.getCheckboxes().get(0).getState()

#open a tab separated txt file with one column Frame selected
if choice == 1:
    choose = 0
    IJ.run("Table... ", "open=")
    frametable = WM.getWindow("selected_frames.txt")
    meta = frametable.getTextPanel()
    metaRT = TP.getResultsTable(meta)

# Choose a directory
directory_load = DirectoryChooser(
    "Select the directory of your files").getDirectory()
directory_load = directory_load.replace("\\", "/")

# get a list of all files in the directory
dList = os.listdir(directory_load)
# set a counter to 1
n = 1

for i in dList:
    dL = directory_load + "/" + str(i)
コード例 #53
0
ファイル: proc_three_phase.py プロジェクト: zvtrung/tips
from ij import IJ, WindowManager
from ij.gui import Line

IJ.run("Close All")
imp = IJ.openImage("/Users/jrminter/Downloads/three_phase.jpeg")
IJ.run(imp, "RGB to CIELAB", "")
IJ.run("Stack to Images", "")
imp_L = WindowManager.getImage("L")
imp_a = WindowManager.getImage("a")
imp_b = WindowManager.getImage("b")
the_line = Line(0,178,690,178)
the_line.setWidth(20) 
imp_L.setRoi(the_line)
imp_L.show()
IJ.run(imp_L, "Plot Profile", "")
imp_a.setRoi(Line(0,231,690,220))
IJ.run(imp_a, "Plot Profile", "")
imp_a.show()

コード例 #54
0
def runOneTif(tifPath, dstTifPath):
	bPrintLog('=== runOneTif processing tif:' + tifPath, 3)

	bPrintLog('Loading file...', 3)
	imp = IJ.openImage(tifPath)  

	if imp is None:  
		bPrintLog('ERROR: could not open image from file:' + tifPath, 3)
		return 0  

	logStr = 'done loading file: ' + str(imp.width) + ' ' + str(imp.height) + ' ' + str(imp.getNSlices())
	bPrintLog(logStr, 3)

	numSlices = imp.getNSlices()
	if numSlices>1:
		pass
	else:
		bPrintLog('ERROR: number of slices must be more than one, file: ' + tifPath)
		return 0
	bPrintLog('numSlices: ' + str(numSlices), 3)
	
	infoStr = imp.getProperty("Info") #get all tags
	#print infoStr
	if infoStr is None:
		infoStr = ''
	infoStr += 'bAverageFrames=v0.1\n'
	imp.setProperty("Info", infoStr)

	imp.show()
	impWin = imp.getTitle()

	#
	# start body
	
	#infer type of file from
	# get the actual bit depth used (e.g. ScanImage is 11 bit, Prairie is 13 bit)
	header = bParseHeader(imp)
	b_sequence = ''
	if 'b_sequence' in header:
		b_sequence = str(header['b_sequence'])

	bPrintLog('b_sequence: ' + b_sequence, 3)
	
	madeAverage = 0

	
	# if numSlices is not divisable by gNumToAverage then chop a few slices off bottom/end
	if b_sequence.startswith('TSeries'):
		if globalOptions['gNumToAverage'] > 1:
			numToRemove = numSlices % globalOptions['gNumToAverage']
			if numToRemove > 0:
				bPrintLog('Removing bottom slices: ' + str(numToRemove), 3)
				# run("Slice Remover", "first=3 last=5 increment=1");
				removeArgs = 'first=' + str(numSlices-numToRemove+1) + ' last=' + str(numSlices) + ' increment=1'
				IJ.run('Slice Remover', removeArgs)
				numSlices = imp.getNSlices()
				bPrintLog('numSlices: ' + str(numSlices), 3)
				
			#fix this: if stack is really short this will not be taken
			if (numSlices > globalOptions['gNumToAverage']):
				bPrintLog('Taking average of ' + str(globalOptions['gNumToAverage']) + ' slices from ' + str(numSlices), 3)
				stackRegParams = 'projection=[Average Intensity] group=' + str(globalOptions['gNumToAverage'])
				IJ.run('Grouped Z Project...', stackRegParams) # makes window AVG_
		
				madeAverage = 1
				
				avgWindow = 'AVG_' + impWin
				avgImp = WindowManager.getImage(avgWindow)
				avgSlices = avgImp.getNSlices()
	
				# Grouped Z PRoject swaps slices for frames?
				tmpSlices = avgImp.getNSlices()
				tmpFrames = avgImp.getNFrames()
				if tmpFrames > 1:
					newSlices = tmpFrames
					newFrames = tmpSlices
					nChannels = 1
					bPrintLog('Swaping frames for slices after grouped z',3)
					bPrintLog('newSlices=' + str(newSlices) + ' newFrames='+str(newFrames), 4)
					avgImp.setDimensions(nChannels, newSlices, newFrames)
				
				infoStr += 'gNumToAverage=' + str(globalOptions['gNumToAverage']) + '\n'
				# I want to adjust the framePeriod, prairie would be 'b_framePeriod'
				avgImp.setProperty("Info", infoStr)
		else:
			avgImp = imp
			avgSlices = numSlices
		
	else:
		bPrintLog('Not taking average of sequence: ' + b_sequence,3)
		avgImp = imp
		avgSlices = numSlices

		
	if globalOptions['medianFilter']>0:
		bPrintLog('Running median filter: ' + str(globalOptions['medianFilter']), 3)
		medianArgs = 'radius=' + str(globalOptions['medianFilter']) + ' stack'
		IJ.run(avgImp, "Median...", medianArgs);
		infoStr += 'bMedianFilter=' + str(globalOptions['medianFilter']) + '\n'
		avgImp.setProperty("Info", infoStr)

	# convert to 8 bit
	# 1) read bit depth from header (e.g. 2^13)
	# 2) do math on image and convert to 8-bit
	# run("Divide...", "value=32 stack");
	if globalOptions['gConvertToEightBit']:
		bPrintLog('converting to 8-bit by dividing image down and then convert to 8-bit with ImageConverter.setDoScaling(False)', 3)
		bitDepth = 2^13
		divideBy = bitDepth / 2^8
		# divide the 13 bit image down to 8 bit
		#run("Divide...", "value=32 stack");
		bPrintLog('divideBy:' + str(divideBy), 3)
		divideArgs = 'value=' + str(divideBy) + ' stack'
		IJ.run(avgImp, "Divide...", divideArgs);
		# convert to 8-bit will automatically scale, to turn this off use
		# eval("script", "ImageConverter.setDoScaling(false)"); 
		ImageConverter.setDoScaling(False)
		# run("8-bit");
		bPrintLog('converting to 8-bit with setDoScaling False', 3)
		IJ.run(avgImp, "8-bit", '');
	
	bPrintLog('Saving stack with ' + str(avgSlices) + ' slices:' + dstTifPath, 3)
	fs = FileSaver(avgImp)
	if avgSlices>1:
		fs.saveAsTiffStack(dstTifPath)
	else:
		fs.saveAsTiff(dstTifPath)

	if madeAverage:
		avgImp.changes = 0
		avgImp.close()
	
	imp.changes = 0
	imp.close()
	
	# end body
	#
	
	# why was this here
	#imp.changes = 0
	#imp.close()

	return 1
コード例 #55
0
with open(path.getPath()) as csvfile:
    reader = csv.DictReader(csvfile)
    for row in reader:
        files.append(row)

for sets in files:
    name = ""

    for filename in sets:
        if os.path.isfile(inputDirectory + filename):
            imp = IJ.openImage(inputDirectory + filename)
        else:
            imp = IJ.openImage(empty)
        imp.show()
        name = filename

    IJ.run("Images to Stack", "name=Stack title=[] use")
    imp2 = WindowManager.getCurrentImage()  # the Stack
    #WaitForUserDialog("Title", "Try adjust balance").show()
    #try:
    IJ.run(imp2, "Make Montage...", "co	lumns=5 rows=1 scale=0.5 border = 3")
    imp3 = WindowManager.getCurrentImage()  # the Montage

    #FileSaver(imp2).saveAsTiff(outputDirectory  + time + '_' + column + '_' + condition + "superstack.tif")
    FileSaver(imp3).saveAsPng(outputDirectory + name + "_custommontage.png")
    #IJ.run(imp2, "Save", "save=" + outputDirectory  + time + '_' + column + '_' + condition + "superstack.tif")
    #IJ.run(imp3, "Save", "save=" + outputDirectory  + time + '_' + column + '_' + condition + "supermontage.tif")
    imp3.close()
    IJ.run("Close All", "")

print("Done!")
コード例 #56
0
			self.yScale=self.xScale
			self.YscaleField.setText(str(self.yScale))
			self.toXfield.setText(str(self.xScale*self.impXpixel))
			self.toYfield.setText(str(self.yScale*self.impYpixel))
		elif source==self.YscaleField:
			self.yScale=float(source.getText())
			self.toYfield.setText(str(self.yScale*self.impYpixel))
		elif source==self.toXfield:
			self.toXpixel=float(source.getText())
			self.xScale=self.toXpixel/self.impXpixel
		elif source==self.toYfield:
			self.toYpixel=float(source.getText())
			self.yScale=self.toYpixel/self.impYpixel
dg=ScaleRoiDialog()
scale=dg.inputScale()
roiMng=WindowManager.getWindow('ROI Manager')

def scaleTypeROI(roi):
	if isinstance(roi,PointRoi):
		p=roi.getFloatPolygon()
		x,y=list(p.xpoints),list(p.ypoints)
		xNew,yNew=map(lambda c:c*scale[0],x),map(lambda c:c*scale[1],y)
		roiNew=PointRoi(xNew,yNew)
	elif isinstance(roi,ShapeRoi):
		roiSels=roi.getRois()
		roiNews=map(scaleTypeROI,roiSels)
		roiNew=0
		for roi in roiNews:
			if roiNew==0:
				roiNew=ShapeRoi(roi)
			else:
コード例 #57
0
def erase():
    i = WindowManager.getImageCount()
    while i > 0:
        WindowManager.getImage(WindowManager.getNthImageID(i)).close()
        i = i - 1
コード例 #58
0
            color = 'white'
        draw(i, j, array, color)


def draw_field(field, selectedX, selectedY):
    for j in range(0, 8):
        for i in range(0, 8):
            draw_one(i, j, field, selectedX, selectedY)


IJ.setTool(Toolbar.HAND)
field = initial_field()
currentX = -1
currentY = -1
draw_field(field, currentX, currentY)
canvas = WindowManager.getCurrentImage().getCanvas()
clicked = 0

while True:
    p = canvas.getCursorLoc()
    x = int(p.x / w)
    y = int(p.y / h)
    newClicked = canvas.getModifiers() & 16
    if clicked and not newClicked:
        if currentX >= 0:
            if x != currentX or y != currentY:
                oldOffset = currentX + 8 * currentY
                field[x + 8 * y] = field[oldOffset]
                field[oldOffset] = ''
            draw_one(currentX, currentY, field, -1, -1)
            draw_one(x, y, field, -1, -1)
コード例 #59
0
        imp2 = IJ.openImage(inputDirectory + "/" +
                            image.replace("stack", "montage"))
        imp.show()
        imp2.show()

        gd = GenericDialog("?")
        gd.addChoice("Would you like to adjust this one?", ["No", "Yes"], "No")
        gd.showDialog()
        if gd.getNextChoice() == "Yes":
            imp2.close()
            IJ.run("Brightness/Contrast...")
            WaitForUserDialog("Title", "Adjust intensities").show()
            IJ.run("Stack to Images", "")
            IJ.run(imp, "Merge Channels...",
                   "c2=Green c3=Blue c6=Magenta c7=Yellow create keep")
            imp = WindowManager.getCurrentImage()
            IJ.run(imp, "RGB Color", "")
            IJ.run(imp, "Images to Stack", "name=Stack title=[] use")
            #WaitForUserDialog("Title", "Now you should have a stack check it out ").show()
            imp = WindowManager.getCurrentImage()  # the Stack

            imp.show()
            IJ.setForegroundColor(255, 255, 255)
            IJ.run(
                imp, "Make Montage...",
                "columns=5 rows=1 scale=0.5 borderWidth = 2 useForegroundColor = True"
            )
            #WaitForUserDialog("Title", "Now we should have the montage").show()
            IJ.run(
                "Save", "save=" + outputDirectory + '/' +
                image.replace("stack", "newmontage"))
コード例 #60
0
neg = IJ.openImage(folder + "\\vessels_negative.tif")
negroi = neg.getRoi()
pos.close()
IJ.run("Select None", "")

channels = ChannelSplitter.split(neg)

neg.close()
image = channels[3]
channels = channels[0:3]
proc = image.getProcessor()
directional_op = ImagePlus("directional_op", proc)

IJ.run(directional_op, "Directional Filtering",
       "type=Max operation=Opening line=30 direction=32")
directional_op = WindowManager.getImage("directional_op-directional")

tubes = range(5, 130, 12)

img_source = ImagePlus("image", proc)
src = clij2.push(img_source)
dst = clij2.create(src)
sigma = 2
clij2.gaussianBlur2D(src, dst, sigma, sigma)
img_blur2 = clij2.pull(dst)
src.close()
dst.close()

print("Tubeness mt start")
tubenesses = [None] * len(tubes)
rang = range(len(tubes))