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)
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()
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]
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
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
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()
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
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()
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
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
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
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()
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()
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)
'''
'''
def runPoreDetection():
'''roiManager=RoiManager(False)
roiManager.runCommand("open", roiname)
roiHash=roiManager.getROIs()
roi=roiHash.get("Right")
print roi'''
imageList=Utility.GetOpenImageList()
nbgd=NonBlockingGenericDialog(Messages.AddRoi)
nbgd.addMessage(Messages.ChooseImage)
if (imageList==None):
IJ.showMessage(Messages.noOpenImages)
return;
nbgd.addChoice("Image1:", imageList, imageList[0]);
nbgd.showDialog()
name = nbgd.getNextChoice()
inputImp = WindowManager.getImage(name)
inputDataset=Utility.getDatasetByName(data, name)
detectionParameters=DetectionParameters(10, 200, 0.5, 1.0, 0.3)
#inputImp.setRoi(roi)
nbgd2=NonBlockingGenericDialog(Messages.PositionRoi)
nbgd2.addMessage(Messages.PositionRoiAndPressOK)
nbgd2.showDialog()
poreDetectionUV(inputImp, inputDataset, inputImp.getRoi().clone(), ops, data, display, detectionParameters)
def 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()
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()
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()
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
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
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)
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")
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
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
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()
def __selectMeasureStack(self) :
# We allow the user to choose what to measure in the stack, and on which stack.
gd1=NonBlockingGenericDialog("Stack Choice for measures")
idimages=WindowManager.getIDList()
images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
imagesnames=[img.getTitle() for img in images]
activindex=0
for i in range(len(imagesnames)) :
if imagesnames[i] == self.__activeTitle :
activindex=i
gd1.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
gd1.showDialog()
chosenstack=gd1.getNextChoice()
self.__img=WindowManager.getImage(chosenstack)
IJ.selectWindow(self.__img.getID())
if gd1.wasOKed() : return True
else : return False
def 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())
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.")
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
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()
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)
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)
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
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()
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
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
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"))
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)
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])
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
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
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()
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
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()
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
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)
# 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')
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,
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
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
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)
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)
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()
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
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!")
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:
def erase():
i = WindowManager.getImageCount()
while i > 0:
WindowManager.getImage(WindowManager.getNthImageID(i)).close()
i = i - 1
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)
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"))
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))