class gui(JFrame): def __init__(self): # constructor #origing of coordinates self.coordx = 10 self.coordy = 10 #inintialize values self.Canvas = None #create panel (what is inside the GUI) self.panel = self.getContentPane() self.panel.setLayout(GridLayout(9, 2)) self.setTitle('Subdividing ROIs') #define buttons here: self.Dapi_files = DefaultListModel() mylist = JList(self.Dapi_files, valueChanged=self.open_dapi_image) #mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); mylist.setLayoutOrientation(JList.VERTICAL) mylist.setVisibleRowCount(-1) listScroller1 = JScrollPane(mylist) listScroller1.setPreferredSize(Dimension(300, 80)) self.output_files = DefaultListModel() mylist2 = JList(self.output_files) #mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); mylist2.setLayoutOrientation(JList.VERTICAL) mylist2.setVisibleRowCount(-1) listScroller2 = JScrollPane(mylist2) listScroller2.setPreferredSize(Dimension(300, 80)) quitButton = JButton("Quit", actionPerformed=self.quit) selectInputFolderButton = JButton("Select Input", actionPerformed=self.select_input) cubifyROIButton = JButton("Cubify ROI", actionPerformed=self.cubify_ROI) saveButton = JButton("Save ROIs", actionPerformed=self.save) summsaveButton = JButton("Save Summary", actionPerformed=self.save_summary) self.textfield1 = JTextField('500') #add buttons here self.panel.add(listScroller1) self.panel.add(listScroller2) self.panel.add(selectInputFolderButton) self.panel.add(Label("Adjust the size of the ROIs")) self.panel.add(self.textfield1) self.panel.add(cubifyROIButton) self.panel.add(saveButton) self.panel.add(summsaveButton) self.panel.add(quitButton) #self.panel.add(saveButton) #self.panel.add(Zslider) #other stuff to improve the look self.pack() # packs the frame self.setVisible(True) # shows the JFrame self.setLocation(self.coordx, self.coordy) #define functions for the buttons: def quit(self, event): #quit the gui self.dispose() IJ.run("Close All") def select_input(self, event): self.input_path = IJ.getDirectory( "Select Directory containing your data") # get the files in that directory self.input_files = listdir(self.input_path) self.input_dapi = [s for s in self.input_files if "DAPI.tif" in s] self.core_names = get_core_names(self.input_dapi) # create output directory self.output_path = path.join( path.dirname(path.dirname(self.input_path)), "Cubified_ROIs") if path.isdir(self.output_path): print "Output path already created" else: mkdir(self.output_path) print "Output path created" # get the processed data self.processed_files = listdir(self.output_path) self.out_core_names = get_core_names( get_core_names(self.processed_files) ) # needs the channel and roi to be removed # populate the lists for f in set(self.core_names): if f not in set(self.out_core_names): # skip if processed self.Dapi_files.addElement(f) for f in set(self.out_core_names ): # a set so that only unique ones are shown self.output_files.addElement(f) def open_dapi_image(self, e): sender = e.getSource() IJ.run("Close All") if not e.getValueIsAdjusting(): self.name = sender.getSelectedValue() print self.name dapi_filename = path.join(self.input_path, self.name + '_DAPI.tif') #print dapi_filename if not path.exists(dapi_filename): print "I don't find the DAPI file, which is weird as I just found it before" else: #open stack and make the reslice self.dapi_image = ImagePlus(dapi_filename) #read the image # duplicate image to play with that one, and do the real processing in the background self.imp_main = Duplicator().run(self.dapi_image) self.imp_main.setTitle(self.name) self.imp_main.show() #show image on the left #self.original_image.getWindow().setLocation(self.coordx-self.original_image.getWindow().getWidth()-10,self.coordy-10) #reposition image def cubify_ROI(self, e): self.L = int(self.textfield1.text) # get info tit = self.imp_main.getTitle() self.roi = self.imp_main.getRoi() # get corners corners = get_corners(self.roi, self.L) self.corners_cleaned = clean_corners(corners, self.roi, self.L) print 'found corners' # get the overlay self.ov = overlay_corners(self.corners_cleaned, self.L) self.ov = overlay_roi(self.roi, self.ov) # write roi name self.ov = write_roi_numbers(self.ov, self.corners_cleaned, self.L) # overlay self.imp_main.setOverlay(self.ov) self.imp_main.updateAndDraw() def save(self, e): # open the other channels d1_filename = path.join(self.input_path, self.name + '_D1.tif') d2_filename = path.join(self.input_path, self.name + '_D2.tif') self.d1_image = ImagePlus(d1_filename) #read the image print "d1 image opened" self.d2_image = ImagePlus(d2_filename) #read the image print "d2 image opened" for image in [self.dapi_image, self.d1_image, self.d2_image]: print "saving rois for image " + image.getTitle() save_rois(image, self.corners_cleaned, self.L, self.output_path) print "ROIs saved" def save_summary(self, e): IJ.selectWindow(self.name) IJ.run("Flatten") imp = IJ.getImage() # downsample # scale ENLARGING or SHRINKING the canvas dimensions scale_factor = .2 new_width = str(int(imp.getWidth() * scale_factor)) new_height = str(int(imp.getHeight() * scale_factor)) IJ.selectWindow(self.name + "-1") str_to_scale = "x=" + str(scale_factor) + " y=" + str( scale_factor ) + " width=" + new_width + " height=" + new_height + " interpolation=Bilinear average create" IJ.run("Scale...", str_to_scale) # save imp2 = IJ.getImage() #IJ.saveAs("Tiff", path.join(OUTDIR, self.name + "_summaryOfROIs")) IJ.saveAsTiff( imp2, path.join(self.output_path, self.name + "_summaryOfROIs.tif")) print "summary image saved"
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)
def runOneFile(fullFilePath): global gFileType 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) if gFileType=='tif': # open .tif image imp = Opener().openImage(fullFilePath) else: # open .lsm cmdStr = 'open=%s autoscale color_mode=Default view=Hyperstack stack_order=XYCZT' % (fullFilePath,) IJ.run('Bio-Formats Importer', cmdStr) lsmpath, lsmfilename = os.path.split(fullFilePath) lsWindow = lsmfilename imp = WindowManager.getImage(lsWindow) # 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)