def green2(): """ Displays a duplicate of the active image. """ green2 = IJ.getImage() green2 = green2.duplicate() ImageWindow.setNextLocation(int(IJ.getScreenSize().width * 1 / 3), int(IJ.getScreenSize().height * 1 / 14)) green2.show()
def subpixels(pixel): """ Math: subtraction duplicates and displayes current image. Performs puxel subtraction using Math. """ green = IJ.getImage() green = green.duplicate() IJ.run(green, "Subtract...", "value=" + pixel) ImageWindow.setNextLocation(int(IJ.getScreenSize().width * 1 / 3), int(IJ.getScreenSize().height * 1 / 14)) green.show() bgTitle()
def showTup(temp_output): if not isinstance(temp_output, tuple): print "Output is not a tuple and therefore can not be displayed correctly" return False size = 300 x = 50 y = 300 d = 50 for el in temp_output: if isinstance(el, ImagePlus): print el.title iw = ImageWindow("") iw.setNextLocation(x, y) # todo: how to also fix the size? el.show() # iw = ImageWindow(el) # iw.setLocationAndSize(x,y,size,size) x = x + size + d
def regBf(fn=None, imp=None, refId=None): """ Register a time series stack to a specified reference slice, from a file (imported by BioFormat) or a stack ImagePlus. Returns a registered ImagePlus. The stack must have only 1 z layer. refId is in the format of [int channel, int slice, int frame] If no refId is supplied, will use the first slice [1,1,1] Note: since TurboReg is used for registeration, there will be temporary opened image windows. """ ## Prepare the right ImagePlus if imp is None: if fn is None: od = OpenDialog("Choose a file", None) filename = od.getFileName() if filename is None: print "User canceled the dialog!" return else: directory = od.getDirectory() filepath = directory + filename print "Selected file path:", filepath else: if os.path.exists(fn) and os.path.isfile(fn): filepath = fn else: print "File does not exist!" return imps = BF.openImagePlus(filepath) imp = imps[0] if imp is None: print "Cannot load file!" return else: if fn is not None: print "File or ImagePlus? Cannot load both." return width = imp.getWidth() height = imp.getHeight() # C nChannels = imp.getNChannels() # Z nSlices = imp.getNSlices() # T nFrames = imp.getNFrames() # pixel size calibration = imp.getCalibration() # Only supoort one z layer if nSlices != 1: print "Only support 1 slice at Z dimension." return # set registration reference slice if refId is None: refC = 1 refZ = 1 refT = 1 else: refC = refId[0] refZ = refId[1] refT = refId[2] if (refC not in range(1, nChannels + 1) or refZ not in range(1, nSlices + 1) or refT not in range(1, nFrames + 1)): print "Invalid reference image!" return stack = imp.getImageStack() registeredStack = ImageStack(width, height, nChannels * nFrames * nSlices) # setup windows, these are needed by TurboReg tmpip = FloatProcessor(width, height) refWin = ImageWindow(ImagePlus("ref", tmpip)) bounds = refWin.getBounds() # refWin.setVisible(False) toRegWin = ImageWindow(ImagePlus("toReg", tmpip)) toRegWin.setLocation(bounds.width + bounds.x, bounds.y) # toRegWin.setVisible(False) toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip)) toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y) # toTransformWin.setVisible(False) # get reference image refImp = ImagePlus("ref", stack.getProcessor(imp.getStackIndex(refC, refZ, refT))) refWin.setImage(refImp) tr = TurboReg_() for t in xrange(1, nFrames + 1): IJ.showProgress(t - 1, nFrames) # print "t ", t # do TurboReg on reference channel toRegId = imp.getStackIndex(refC, refZ, t) toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId)) toRegWin.setImage(toRegImp) regArg = "-align " +\ "-window " + toRegImp.getTitle() + " " +\ "0 0 " + str(width - 1) + " " + str(height - 1) + " " +\ "-window " + refImp.getTitle() + " " +\ "0 0 " + str(width - 1) + " " + str(height - 1) + " " +\ "-rigidBody " +\ str(width / 2) + " " + str(height / 2) + " " +\ str(width / 2) + " " + str(height / 2) + " " +\ "0 " + str(height / 2) + " " +\ "0 " + str(height / 2) + " " +\ str(width - 1) + " " + str(height / 2) + " " +\ str(width - 1) + " " + str(height / 2) + " " +\ "-hideOutput" tr = TurboReg_() tr.run(regArg) registeredImp = tr.getTransformedImage() sourcePoints = tr.getSourcePoints() targetPoints = tr.getTargetPoints() registeredStack.setProcessor(registeredImp.getProcessor(), toRegId) # toRegImp.flush() # apply transformation on other channels for c in xrange(1, nChannels + 1): # print "c ", c if c == refC: continue toTransformId = imp.getStackIndex(c, 1, t) toTransformImp = ImagePlus("toTransform", stack.getProcessor(toTransformId)) toTransformWin.setImage(toTransformImp) transformArg = "-transform " +\ "-window " + toTransformImp.getTitle() + " " +\ str(width) + " " + str(height) + " " +\ "-rigidBody " +\ str(sourcePoints[0][0]) + " " +\ str(sourcePoints[0][1]) + " " +\ str(targetPoints[0][0]) + " " +\ str(targetPoints[0][1]) + " " +\ str(sourcePoints[1][0]) + " " +\ str(sourcePoints[1][1]) + " " +\ str(targetPoints[1][0]) + " " +\ str(targetPoints[1][1]) + " " +\ str(sourcePoints[2][0]) + " " +\ str(sourcePoints[2][1]) + " " +\ str(targetPoints[2][0]) + " " +\ str(targetPoints[2][1]) + " " +\ "-hideOutput" tr = TurboReg_() tr.run(transformArg) registeredStack.setProcessor( tr.getTransformedImage().getProcessor(), toTransformId) # toTransformImp.flush() sourcePoints = None targetPoints = None IJ.showProgress(t, nFrames) IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames)) refWin.close() toRegWin.close() toTransformWin.close() imp2 = ImagePlus("reg_" + imp.getTitle(), registeredStack) imp2.setCalibration(imp.getCalibration().copy()) imp2.setDimensions(nChannels, nSlices, nFrames) # print "type ", imp.getType() # print "type ", imp2.getType() # print nChannels, " ", nSlices, " ", nFrames # print registeredStack.getSize() for key in imp.getProperties().stringPropertyNames(): imp2.setProperty(key, imp.getProperty(key)) # comp = CompositeImage(imp2, CompositeImage.COLOR) # comp.show() # imp2 = imp.clone() # imp2.setStack(registeredStack) # imp2.setTitle("reg"+imp.getTitle()) # imp2.show() # imp.show() return imp2
def regBf(fn=None, imp=None, refId=None): """ Register a time series stack to a specified reference slice, from a file (imported by BioFormat) or a stack ImagePlus. Returns a registered ImagePlus. The stack must have only 1 z layer. refId is in the format of [int channel, int slice, int frame] If no refId is supplied, will use the first slice [1,1,1] Note: since TurboReg is used for registeration, there will be temporary opened image windows. """ ## Prepare the right ImagePlus if imp is None: if fn is None: od = OpenDialog("Choose a file", None) filename = od.getFileName() if filename is None: print "User canceled the dialog!" return else: directory = od.getDirectory() filepath = directory + filename print "Selected file path:", filepath else: if os.path.exists(fn) and os.path.isfile(fn): filepath = fn else: print "File does not exist!" return imps = BF.openImagePlus(filepath) imp = imps[0] if imp is None: print "Cannot load file!" return else: if fn is not None: print "File or ImagePlus? Cannot load both." return width = imp.getWidth() height = imp.getHeight() # C nChannels = imp.getNChannels() # Z nSlices = imp.getNSlices() # T nFrames = imp.getNFrames() # pixel size calibration = imp.getCalibration() # Only supoort one z layer if nSlices != 1: print "Only support 1 slice at Z dimension." return # set registration reference slice if refId is None: refC = 1 refZ = 1 refT = 1 else: refC = refId[0] refZ = refId[1] refT = refId[2] if (refC not in range(1, nChannels+1) or refZ not in range(1, nSlices+1) or refT not in range(1, nFrames+1) ): print "Invalid reference image!" return stack = imp.getImageStack() registeredStack = ImageStack(width, height, nChannels*nFrames*nSlices) # setup windows, these are needed by TurboReg tmpip = FloatProcessor(width, height) refWin = ImageWindow(ImagePlus("ref", tmpip)) bounds = refWin.getBounds() # refWin.setVisible(False) toRegWin = ImageWindow(ImagePlus("toReg", tmpip)) toRegWin.setLocation(bounds.width + bounds.x, bounds.y) # toRegWin.setVisible(False) toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip)) toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y) # toTransformWin.setVisible(False) # get reference image refImp = ImagePlus("ref", stack.getProcessor(imp.getStackIndex(refC, refZ, refT))) refWin.setImage(refImp) tr = TurboReg_() for t in xrange(1, nFrames+1): IJ.showProgress(t-1, nFrames) # print "t ", t # do TurboReg on reference channel toRegId = imp.getStackIndex(refC, refZ, t) toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId)) toRegWin.setImage(toRegImp) regArg = "-align " +\ "-window " + toRegImp.getTitle() + " " +\ "0 0 " + str(width - 1) + " " + str(height - 1) + " " +\ "-window " + refImp.getTitle() + " " +\ "0 0 " + str(width - 1) + " " + str(height - 1) + " " +\ "-rigidBody " +\ str(width / 2) + " " + str(height / 2) + " " +\ str(width / 2) + " " + str(height / 2) + " " +\ "0 " + str(height / 2) + " " +\ "0 " + str(height / 2) + " " +\ str(width - 1) + " " + str(height / 2) + " " +\ str(width - 1) + " " + str(height / 2) + " " +\ "-hideOutput" tr = TurboReg_() tr.run(regArg) registeredImp = tr.getTransformedImage() sourcePoints = tr.getSourcePoints() targetPoints = tr.getTargetPoints() registeredStack.setProcessor(registeredImp.getProcessor(), toRegId) # toRegImp.flush() # apply transformation on other channels for c in xrange(1, nChannels+1): # print "c ", c if c == refC: continue toTransformId = imp.getStackIndex(c, 1, t) toTransformImp = ImagePlus("toTransform", stack.getProcessor(toTransformId)) toTransformWin.setImage(toTransformImp) transformArg = "-transform " +\ "-window " + toTransformImp.getTitle() + " " +\ str(width) + " " + str(height) + " " +\ "-rigidBody " +\ str(sourcePoints[0][0]) + " " +\ str(sourcePoints[0][1]) + " " +\ str(targetPoints[0][0]) + " " +\ str(targetPoints[0][1]) + " " +\ str(sourcePoints[1][0]) + " " +\ str(sourcePoints[1][1]) + " " +\ str(targetPoints[1][0]) + " " +\ str(targetPoints[1][1]) + " " +\ str(sourcePoints[2][0]) + " " +\ str(sourcePoints[2][1]) + " " +\ str(targetPoints[2][0]) + " " +\ str(targetPoints[2][1]) + " " +\ "-hideOutput" tr = TurboReg_() tr.run(transformArg) registeredStack.setProcessor(tr.getTransformedImage().getProcessor(), toTransformId) # toTransformImp.flush() sourcePoints = None targetPoints = None IJ.showProgress(t, nFrames) IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames)) refWin.close() toRegWin.close() toTransformWin.close() imp2 = ImagePlus("reg_"+imp.getTitle(), registeredStack) imp2.setCalibration(imp.getCalibration().copy()) imp2.setDimensions(nChannels, nSlices, nFrames) # print "type ", imp.getType() # print "type ", imp2.getType() # print nChannels, " ", nSlices, " ", nFrames # print registeredStack.getSize() for key in imp.getProperties().stringPropertyNames(): imp2.setProperty(key, imp.getProperty(key)) # comp = CompositeImage(imp2, CompositeImage.COLOR) # comp.show() # imp2 = imp.clone() # imp2.setStack(registeredStack) # imp2.setTitle("reg"+imp.getTitle()) # imp2.show() # imp.show() return imp2
from org.python.core import codecs codecs.setDefaultEncoding('utf-8') import os import glob import time from ij import IJ from ij import WindowManager from ij.gui import ImageWindow inDir = "\\\\cm20st\\data\\images\\QM14-02-12A-Kosydar\\qm-04203-PMH1413\\dm3" outDir = "C:\\Users\\l837410\\Documents\\work\\proj\\QM14-02-12A-Kosydar\\Sweave\\inc\\png" for file in os.listdir(inDir): if file.endswith(".dm3"): path = inDir + "\\" + file # print(file) strLoad = "load=%s" % path IJ.run("DM3 Reader...", strLoad) IJ.run("Add Scale Bar", "width=50 height=6 font=24 color=Black location=[Lower Right] bold") IJ.run("RGB Color") l = len(file) name = file[0:l-4] print(name) path = outDir + "\\" + name + ".png" # Get the final map imp = WindowManager.getCurrentImage() iw = ImageWindow(imp) # iw.changed = False IJ.saveAs("PNG", path) iw.close()