def runOneFile(fullFilePath): global gNumChannels 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 = '' 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) #this is too much work for ScanImage4 #try and guess channels if it is a scanimage file #scanImage3 = string.find(infoStr, 'scanimage') != -1 #scanimage4 = find(infoStr, 'scanimage.SI4.channelSave = ') #print 'scanimage4:', scanimage4 # # 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() infoStr += 'bAlignBatch6=' + time.strftime("%Y%m%d") + '\n' # # crop 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 imp.setRoi(roi) #time.sleep(1) #bPrintLog('cropping', 1) IJ.run('Crop') infoStr += 'cropping=' + str(gCropLeft) + ',' + str( gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n' # # remove negative (<0) pixel values #ip = imp.getProcessor() #pixels = ip.getPixels() # this returns a reference (not a copy) #for i in xrange(len(pixels)): # if pixels[i] < 0: # pixels[i] = 0 # or this, for each pixel 'x', if x<0 then 0 else x #pixels = map(lambda x: 0 if x<0 else x, pixels) #set our new values (without pixels <0) back into original (I hope this handles stacks and channels???) #ip.setPixels(pixels) # # remove calibration 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) #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) #msgStr = 'adding calCoeff[0]='+str(calCoeff[0]) + ' to stack.' #bPrintLog(msgStr, 2) #subArgVal = 'value=%s stack' % (calCoeff[0],) #IJ.run('Add...', subArgVal) # 20150701, 'shift everybody over by linear calibration intercept calCoeff[0]' 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 = 32768 - 128 msgStr = 'Subtracting a magic number ' + str( magicNumber) + ' from stack.' bPrintLog(msgStr, 2) subArgVal = 'value=%s stack' % (origMin, ) IJ.run('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) #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() #append calibration to info string infoStr += 'calibCoeff_a = ' + str(calCoeff[0]) + '\n' infoStr += 'calibCoeff_b = ' + str(calCoeff[1]) + '\n' infoStr += 'origMin = ' + str(origMin) + '\n' infoStr += 'origMax = ' + str(origMax) + '\n' # # set up if gNumChannels == 1: impWinStr = imp.getTitle() #use this when only one channel impWin = WindowManager.getWindow(impWinStr) #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 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 imp.getNSlices() > 1: infoStr += 'AlignOnChannel=1' + '\n' #snap to middle slice if gAlignOnMiddleSlice: middleSlice = int( math.floor(imp.getNSlices() / 2)) #int() is necc., python is f*****g picky else: middleSlice = gAlignOnThisSlice imp.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' 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 += 'AlignOnSlice=' + 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) #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 ch1Imp.setProperty("Info", infoStr) #bPrintLog('Saving:' + ch1File, 1) bSaveStack(ch1Imp, ch1File) #max project bSaveZProject(ch1Imp, destMaxFolder, shortName + '_ch1') #ch2 ch2Imp.setProperty("Info", infoStr) #bPrintLog('Saving:' + ch2File, 1) bSaveStack(ch2Imp, ch2File) #max project bSaveZProject(ch2Imp, 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:' + ch1WinStr, 1) IJ.selectWindow(ch1WinStr) #IJ.run('resetMinAndMax()') #ch1Imp.resetStack() #ch1Imp.resetDisplayRange() IJ.run("8-bit") impFile = eightBitFolder + shortName + '_ch1.tif' bPrintLog('Saving 8-bit:' + impFile, 2) bSaveStack(ch1Imp, impFile) #max project bSaveZProject(ch1Imp, eightBitMaxFolder, shortName + '_ch1') # bPrintLog('Converting to 8-bit:' + ch2WinStr, 1) IJ.selectWindow(ch2WinStr) #IJ.run('resetMinAndMax()') IJ.run("8-bit") impFile = eightBitFolder + shortName + '_ch2.tif' bPrintLog('Saving 8-bit:' + impFile, 2) bSaveStack(ch2Imp, impFile) #max project bSaveZProject(ch2Imp, eightBitMaxFolder, shortName + '_ch2') # # close original window imp.changes = 0 imp.close() # # close ch1/ch2 if 1 and gNumChannels == 2: ch1Imp.changes = 0 ch1Imp.close() ch2Imp.changes = 0 ch2Imp.close() bPrintLog( time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath, 1)
def runOneFile(fullFilePath): global gNumChannels 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 = '' 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) #this is too much work for ScanImage4 #try and guess channels if it is a scanimage file #scanImage3 = string.find(infoStr, 'scanimage') != -1 #scanimage4 = find(infoStr, 'scanimage.SI4.channelSave = ') #print 'scanimage4:', scanimage4 # # 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() infoStr += 'bAlignBatch6=' + time.strftime("%Y%m%d") + '\n' # # crop 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 imp.setRoi(roi) #time.sleep(1) #bPrintLog('cropping', 1) IJ.run('Crop') infoStr += 'cropping=' + str(gCropLeft) + ',' + str(gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n' # # remove negative (<0) pixel values #ip = imp.getProcessor() #pixels = ip.getPixels() # this returns a reference (not a copy) #for i in xrange(len(pixels)): # if pixels[i] < 0: # pixels[i] = 0 # or this, for each pixel 'x', if x<0 then 0 else x #pixels = map(lambda x: 0 if x<0 else x, pixels) #set our new values (without pixels <0) back into original (I hope this handles stacks and channels???) #ip.setPixels(pixels) # # remove calibration 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) #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) #msgStr = 'adding calCoeff[0]='+str(calCoeff[0]) + ' to stack.' #bPrintLog(msgStr, 2) #subArgVal = 'value=%s stack' % (calCoeff[0],) #IJ.run('Add...', subArgVal) # 20150701, 'shift everybody over by linear calibration intercept calCoeff[0]' 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 = 32768 - 128 msgStr = 'Subtracting a magic number '+str(magicNumber) + ' from stack.' bPrintLog(msgStr, 2) subArgVal = 'value=%s stack' % (origMin,) IJ.run('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) #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() #append calibration to info string infoStr += 'calibCoeff_a = ' + str(calCoeff[0]) + '\n' infoStr += 'calibCoeff_b = ' + str(calCoeff[1]) + '\n' infoStr += 'origMin = ' + str(origMin) + '\n' infoStr += 'origMax = ' + str(origMax) + '\n' # # set up if gNumChannels == 1: impWinStr = imp.getTitle() #use this when only one channel impWin = WindowManager.getWindow(impWinStr) #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 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 imp.getNSlices()>1: infoStr += 'AlignOnChannel=1' + '\n' #snap to middle slice if gAlignOnMiddleSlice: middleSlice = int(math.floor(imp.getNSlices() / 2)) #int() is necc., python is f*****g picky else: middleSlice = gAlignOnThisSlice imp.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' 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 += 'AlignOnSlice=' + 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) #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 ch1Imp.setProperty("Info", infoStr); #bPrintLog('Saving:' + ch1File, 1) bSaveStack(ch1Imp, ch1File) #max project bSaveZProject(ch1Imp, destMaxFolder, shortName+'_ch1') #ch2 ch2Imp.setProperty("Info", infoStr); #bPrintLog('Saving:' + ch2File, 1) bSaveStack(ch2Imp, ch2File) #max project bSaveZProject(ch2Imp, 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:' + ch1WinStr, 1) IJ.selectWindow(ch1WinStr) #IJ.run('resetMinAndMax()') #ch1Imp.resetStack() #ch1Imp.resetDisplayRange() IJ.run("8-bit") impFile = eightBitFolder + shortName + '_ch1.tif' bPrintLog('Saving 8-bit:' + impFile, 2) bSaveStack(ch1Imp, impFile) #max project bSaveZProject(ch1Imp, eightBitMaxFolder, shortName+'_ch1') # bPrintLog('Converting to 8-bit:' + ch2WinStr, 1) IJ.selectWindow(ch2WinStr) #IJ.run('resetMinAndMax()') IJ.run("8-bit") impFile = eightBitFolder + shortName + '_ch2.tif' bPrintLog('Saving 8-bit:' + impFile, 2) bSaveStack(ch2Imp, impFile) #max project bSaveZProject(ch2Imp, eightBitMaxFolder, shortName+'_ch2') # # close original window imp.changes = 0 imp.close() # # close ch1/ch2 if 1 and gNumChannels == 2: ch1Imp.changes = 0 ch1Imp.close() ch2Imp.changes = 0 ch2Imp.close() bPrintLog(time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath, 1)