def getOptions(): pixels = zeros('f', 4) # 4 elements # First Dialog Box item = [ "coralline", "tunicate", "red", "macro", "background", "more than one" ] gd = GenericDialog("Options") gd.addRadioButtonGroup("options", item, 3, 2, "coralline") gd.showDialog() button = gd.getNextRadioButton() # Second Dialog Box gd2 = GenericDialog("Multiple Options") items = ["coralline", "tunicate", "red", "macro", "garbage"] defaultVal = [False] * 5 gd2.addCheckboxGroup(2, 3, items, defaultVal) gd2.addNumericField("coralline %", 0, 0) gd2.addNumericField("tunicate %", 0, 0) gd2.addNumericField("red %", 0, 0) gd2.addNumericField("macro %", 0, 0) gd2.addNumericField("background %", 0, 0) if gd.wasCanceled(): return 0 if button == "coralline": pixels[0] = 1 elif button == "tunicate": pixels[1] = 1 elif button == "red": pixels[2] = 1 elif button == "macro": pixels[3] = 1 elif button == "more than one": gd2.showDialog() checklist = gd2.getCheckboxes() pixels[0] = int( checklist[0].state) * (float(gd2.getNextNumber()) / 100) pixels[1] = int( checklist[1].state) * (float(gd2.getNextNumber()) / 100) pixels[2] = int( checklist[2].state) * (float(gd2.getNextNumber()) / 100) pixels[3] = int( checklist[3].state) * (float(gd2.getNextNumber()) / 100) return pixels
def Options(sourceFolder): #globals global gGetNumChanFromScanImage global gNumChannels global gDoAlign global gAlignThisChannel global gDoCrop global gCropLeft global gCropTop global gCropWidth global gCropHeight global gAlignOnMiddleSlice global gAlignOnThisSlice global gRemoveCalibration global gLinearShift global gSave8bit tifNames = [file.name for file in File(sourceFolder).listFiles(Filter())] numTifs = len(tifNames) gd = GenericDialog('Align Batch 6 Options') #gd.addStringField('Command: ', '') gd.addMessage('Source Folder: ' + sourceFolder) gd.addMessage('Number of .tif files: ' + str(numTifs)) #gd.setInsets(5,0,3) #0 gd.addCheckboxGroup( 1, 1, ['Get Number Of Channels From ScanImage 3.x or 4.x header'], [gGetNumChanFromScanImage], ['Channels']) gd.addNumericField( 'Otherwise, Assume All Stacks Have This Number Of Channels: ', gNumChannels, 0) print gLinearShift #1 gd.addCheckboxGroup(1, 1, ['Remove Linear Calibration From ScanImage 4.x'], [gRemoveCalibration], ['ScanImage4']) gd.addNumericField('And offset (subtract) by this amount: ', gLinearShift, 0) #2 gd.addCheckboxGroup(1, 1, ['Crop All Images (pixels)'], [gDoCrop], ['Crop']) gd.addNumericField('Left', gCropLeft, 0) gd.addNumericField('Top', gCropTop, 0) gd.addNumericField('Width', gCropWidth, 0) gd.addNumericField('Height', gCropHeight, 0) #gd.setInsets(5,0,3) #3 gd.addCheckboxGroup(1, 1, ['Run MultiStackReg'], [gDoAlign], ['MultStackReg']) gd.addNumericField('If 2 Channels Then Align On This Channel', gAlignThisChannel, 0) #4 gd.addCheckboxGroup(1, 1, ['Start Alignment On Middle Slice'], [gAlignOnMiddleSlice], ['Align On Middle Slice']) gd.addNumericField('Otherwise, Start Alignment On This Slice', gAlignOnThisSlice, 0) #5 gd.addCheckboxGroup(1, 1, ['Save 8-bit'], [gSave8bit], ['Save 8-bit (at end)']) #gd.addCheckbox('Save 8-bit', gSave8bit) gd.showDialog() if gd.wasCanceled(): print 'Options Was Cancelled by user' return 0 else: print 'Reading values' gNumChannels = int(gd.getNextNumber()) gLinearShift = int(gd.getNextNumber()) gCropLeft = int(gd.getNextNumber()) gCropTop = int(gd.getNextNumber()) gCropWidth = int(gd.getNextNumber()) gCropHeight = int(gd.getNextNumber()) gAlignThisChannel = int(gd.getNextNumber()) gAlignOnThisSlice = int(gd.getNextNumber()) checks = gd.getCheckboxes() checkIdx = 0 for check in checks: #print check.getState() if checkIdx == 0: gGetNumChanFromScanImage = check.getState() if checkIdx == 1: gRemoveCalibration = check.getState() if checkIdx == 2: gDoCrop = check.getState() if checkIdx == 3: gDoAlign = check.getState() if checkIdx == 4: gAlignOnMiddleSlice = check.getState() if checkIdx == 5: gSave8bit = check.getState() checkIdx += 1 # print to fiji console bPrintLog('These are your global options:', 0) bPrintLog('gGetNumChanFromScanImage=' + str(gGetNumChanFromScanImage), 1) bPrintLog('gNumChannels=' + str(gNumChannels), 1) bPrintLog('gRemoveCalibration=' + str(gRemoveCalibration), 1) bPrintLog('gLinearShift=' + str(gLinearShift), 1) bPrintLog('gDoCrop=' + str(gDoCrop), 1) bPrintLog('gDoAlign=' + str(gDoAlign), 1) bPrintLog('gAlignThisChannel=' + str(gAlignThisChannel), 1) bPrintLog('gSave8bit=' + str(gSave8bit), 1) return 1
"Within (subfolders of) input directory"] overwriteChoices = ["NO overwrite existing files", "Overwrite existing files"] channelSubfolderChoices = ["yes", "no"] mipChoices = ["yes: tiff", "yes: jpg"] overwriteList = [] startTime = time.time() imageCount = 0 voxel_info = str() gd = GenericDialog("Set ToTiff Options") gd.addStringField("File extension to be processed", ".nd2") gd.addRadioButtonGroup("Output", outDirChoices, 3, 1, outDirChoices[0]) gd.addRadioButtonGroup("Overwrite", overwriteChoices, 2, 1, overwriteChoices[0]) gd.addRadioButtonGroup("Save channels in different subfolders", channelSubfolderChoices, 1, 1, channelSubfolderChoices[0]) gd.addCheckboxGroup(2, 1, mipChoices, [False, False], ["Do you want maximum intensity projections of your images?"]) gd.showDialog() if gd.wasCanceled(): exit() fileExt = gd.getNextString() outDirPref = gd.getNextRadioButton() overwritePref = gd.getNextRadioButton() channelSubfolderPref = gd.getNextRadioButton() mipPrefTIFF = gd.getNextBoolean() mipPrefJPG = gd.getNextBoolean() if not fileExt.startswith('.'): fileExt = '.' + fileExt inDir = IJ.getDirectory("Choose Directory Containing Input Files")
def Options(sourceFolder): #globals global gFileType global gGetNumChanFromScanImage global gNumChannels global gDoAlign global gAlignThisChannel global gDoCrop global gCropLeft global gCropTop global gCropWidth global gCropHeight global gAlignOnMiddleSlice global gAlignOnThisSlice global gRemoveCalibration global gLinearShift global gSave8bit tifNames = [file.name for file in File(sourceFolder).listFiles(Filter())] lsmNames = [file.name for file in File(sourceFolder).listFiles(Filter_LSM())] numTifs = len(tifNames) numLSM = len(lsmNames) gd = GenericDialog('Align Batch 7 Options') #gd.addStringField('Command: ', '') gd.addMessage('Source Folder: ' + sourceFolder) gd.addMessage('Number of .tif files: ' + str(numTifs)) gd.addMessage('Number of .lsm files: ' + str(numLSM)) gd.addChoice('File Type', ['tif','lsm'], gFileType) #gd.setInsets(5,0,3) #0 gd.addCheckboxGroup(1, 1, ['Get Number Of Channels From ScanImage 3.x or 4.x header'], [gGetNumChanFromScanImage], ['Channels']) gd.addNumericField('Otherwise, Assume All Stacks Have This Number Of Channels: ', gNumChannels, 0) print gLinearShift #1 gd.addCheckboxGroup(1, 1, ['Remove Linear Calibration From ScanImage 4.x'], [gRemoveCalibration], ['ScanImage4']) gd.addNumericField('And offset (subtract) by this amount: ', gLinearShift, 0) gd.addMessage('20151110, this number = 2^15-512 = 32768-512 = 32256') #2 gd.addCheckboxGroup(1, 1, ['Crop All Images (pixels)'], [gDoCrop], ['Crop']) gd.addNumericField('Left', gCropLeft, 0) gd.addNumericField('Top', gCropTop, 0) gd.addNumericField('Width', gCropWidth, 0) gd.addNumericField('Height', gCropHeight, 0) #gd.setInsets(5,0,3) #3 gd.addCheckboxGroup(1, 1, ['Run MultiStackReg'], [gDoAlign], ['MultStackReg']) gd.addNumericField('If 2 Channels Then Align On This Channel', gAlignThisChannel, 0) #4 gd.addCheckboxGroup(1, 1, ['Start Alignment On Middle Slice'], [gAlignOnMiddleSlice], ['Align On Middle Slice']) gd.addNumericField('Otherwise, Start Alignment On This Slice', gAlignOnThisSlice, 0) #5 gd.addCheckboxGroup(1, 1, ['Save 8-bit'], [gSave8bit], ['Save 8-bit (at end)']) #gd.addCheckbox('Save 8-bit', gSave8bit) gd.showDialog() if gd.wasCanceled(): print 'Options Was Cancelled by user' return 0 else: print 'Reading values' gFileType = gd.getNextChoice() gNumChannels = int(gd.getNextNumber()) gLinearShift = int(gd.getNextNumber()) gCropLeft = int(gd.getNextNumber()) gCropTop = int(gd.getNextNumber()) gCropWidth = int(gd.getNextNumber()) gCropHeight = int(gd.getNextNumber()) gAlignThisChannel = int(gd.getNextNumber()) gAlignOnThisSlice = int(gd.getNextNumber()) checks = gd.getCheckboxes() checkIdx = 0 for check in checks: #print check.getState() if checkIdx==0: gGetNumChanFromScanImage = check.getState() if checkIdx==1: gRemoveCalibration = check.getState() if checkIdx==2: gDoCrop = check.getState() if checkIdx==3: gDoAlign = check.getState() if checkIdx==4: gAlignOnMiddleSlice = check.getState() if checkIdx==5: gSave8bit = check.getState() checkIdx += 1 # print to fiji console bPrintLog('These are your global options:', 0) bPrintLog('gFileType=' + gFileType, 1) bPrintLog('gGetNumChanFromScanImage=' + str(gGetNumChanFromScanImage), 1) bPrintLog('gNumChannels=' + str(gNumChannels), 1) bPrintLog('gRemoveCalibration=' + str(gRemoveCalibration), 1) bPrintLog('gLinearShift=' + str(gLinearShift), 1) bPrintLog('gDoCrop=' + str(gDoCrop), 1) bPrintLog('gDoAlign=' + str(gDoAlign), 1) bPrintLog('gAlignThisChannel=' + str(gAlignThisChannel), 1) bPrintLog('gSave8bit=' + str(gSave8bit), 1) return 1