Python GenericDialog.getNextChoice方法代码示例

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
def main():
    properties = ImageProperties(imp)
    # Create a GenericDialog to configure renaming:
    gd = GenericDialog('Gatan Reamer')
    gd.addMessage('Modifying: %s' % (imp.getTitle(),))
    gd.addMessage('Recorded: %s' % (properties.date.toString(),))
    gd.addNumericField('Exposure time', properties.exposure, 4, field_width, 's')
    gd.addNumericField('Magnification:', properties.magnification, 0, field_width, 'x')
    mag_units = ('kx', 'x')
    gd.addChoice('Magnification unit:', mag_units, mag_units[0])
    gd.addMessage('The actual magnification is %.2f times larger.' % (properties.mag_factor,))
    gd.addCheckbox('Use actual magnification:', False)
    gd.addMessage('')
    gd.addNumericField('Energy loss:', properties.energyloss, 1, field_width, 'eV')
    gd.addStringField('Date:', properties.date_string, field_width)
    gd.addStringField('original name:', properties.name, field_width_long)
    gd.addStringField('Filename format', default_format_str, field_width_long)
    gd.showDialog()

    if not gd.wasCanceled():
        # Edit the properties to consiter user choices:
        properties.exposure = gd.getNextNumber()
        mag = gd.getNextNumber()
        properties.mag_unit = gd.getNextChoice()
        if gd.getNextBoolean():
            properties.calc_mag(mag)
        properties.energyloss = gd.getNextNumber()
        properties.date_string = gd.getNextString()
        properties.name = gd.getNextString()
        format_str = gd.getNextString()
        # Chenge the title:
        imp.setTitle(format_str % properties.to_dict())

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
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

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
def make_directory(imgDir):
    """ Makes the necessary output directories or overwrites current ones. """
    if not path.exists(imgDir) or not path.isdir(imgDir):
        print "Not a valid directory"
        exit(0)

    if not path.exists(imgDir+"/binary"):
        mkdir(imgDir+"/binary")

    else:
    	gd = GenericDialog("Confirm Overwrite")
    	choices = ["Yes", "No"]
    	gd.addChoice("Overwrite \"binary\" folder?", choices, choices[0])
    	gd.showDialog()
    	if gd.wasCanceled():
    		exit(0)
    	choice = gd.getNextChoice()
    	if choice == "No":
    		exit(0)
    	shutil.rmtree(imgDir+"/binary")
    	mkdir(imgDir+"/binary")


    if not path.exists(imgDir+"/greyscale"):
        mkdir(imgDir+"/greyscale")

    else:
    	gd = GenericDialog("Confirm Overwrite")
    	choices = ["Yes", "No"]
    	gd.addChoice("Overwrite \"greyscale\" folder?", choices, choices[0])
    	gd.showDialog()
    	if gd.wasCanceled():
    		exit(0)
    	choice = gd.getNextChoice()
    	if choice == "No":
    		exit(0)
    	shutil.rmtree(imgDir+"/greyscale")
    	mkdir(imgDir+"/greyscale")

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
def getChannels():
	gd = GenericDialog( "Select stack's channels" )
	# print gd.getModalityType() 
	# gd.setModal( False )
	# print gd.getModalityType() 
	color = ["red", "green", "blue"]
	gd.addChoice("Channel for mask", color, color[2])
	gd.addChoice("Channel for particles", color, color[1])
	gd.showDialog()
	maskChannel = gd.getNextChoice()  
	partChannel = gd.getNextChoice()  
	if gd.wasCanceled():  
		sys.exit()
	return maskChannel, partChannel

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
	def getOptionsDialog(self, imp):
		thr_methods = ["None", "Default", "Huang", "Intermodes", "IsoData",  "Li", "MaxEntropy","Mean", "MinError(I)", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag" , "Triangle", "Yen"]
		gd = GenericDialog("Please select channels to collocalize")
		for i in range(1, imp.getNChannels() + 1):
			gd.addChoice("Threshold method for channel %i" % i, thr_methods, "None")
		gd.showDialog()
		if gd.wasCanceled():
			self.exit()
		channels = []
		for i in range(1, imp.getNChannels() + 1):
			method = gd.getNextChoice()
			self.methods.append(method)
			if method != "None":
				channels.append(i)
		for x in channels:
			for y in channels:
				if x < y:
					self.pairs.append((x, y))

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
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:
#.........这里部分代码省略.........

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
		computedImage = reduce(self.addImages,imgList)
		computedImage.show()
		IJ.showStatus("Ready")


## Main body of script
opener = OpenDialog("Select parent LSM file...")
parentLSMFilePath = opener.getPath()
if (parentLSMFilePath is not None):
	stackInfo = parse_tile_info_file(parentLSMFilePath + "_tiles/tile_info.txt")
	channelTexts = map(lambda x: str(x), filter(lambda x:os.path.isfile(parentLSMFilePath+"_tiles/objects/C"+str(x)+".objects.keep.unique.csv"),range(1,stackInfo[0]+1)))
	gd = GenericDialog("Specify parameters...")
	gd.addChoice("Which_channel",channelTexts,channelTexts[0])
	gd.showDialog()
	if gd.wasOKed():
		channel = int(gd.getNextChoice())

		## Obtains global coordinate system for tiles
		scale_info = estimate_scale_multiplier(parentLSMFilePath+"_tiles/tile_1.ome.tif",parentLSMFilePath+"_tiles/resized/tile_1.tif")

		## Parses each of the object files
		objectDB = [[] for x in range(4)]
		objectDB[0] = parse_object_file_into_db(parentLSMFilePath+"_tiles/objects/C"+str(channel)+".objects.keep.contained.csv")
		objectDB[1] = parse_object_file_into_db(parentLSMFilePath+"_tiles/objects/C"+str(channel)+".objects.keep.duplicated.csv")
		objectDB[2] = parse_object_file_into_db(parentLSMFilePath+"_tiles/objects/C"+str(channel)+".objects.keep.restitched.csv")
		objectDB[3] = parse_object_file_into_db(parentLSMFilePath+"_tiles/objects/C"+str(channel)+".objects.keep.unique.csv")

		## Converts object global coordinates to rescaled coordinates
		for i in range(len(objectDB)):
			for j in range(len(objectDB[i])):
				rescaledTup = [objectDB[i][j][27]/scale_info[0],objectDB[i][j][28]/scale_info[0],objectDB[i][j][29],objectDB[i][j][30]/scale_info[0],objectDB[i][j][31]/scale_info[0],objectDB[i][j][32]]

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
def main_interactive():
    """The main routine for running interactively."""
    log.info('Running in interactive mode.')
    (base, fname) = ui_get_input_file()
    if (base is None):
        return
    log.warn("Parsing project file: %s" % (base + fname))
    IJ.showStatus("Parsing experiment file...")
    mosaics = fv.FluoViewMosaic(join(base, fname), runparser=False)
    IJ.showStatus("Parsing mosaics...")
    progress = 0.0
    count = len(mosaics.mosaictrees)
    step = 1.0 / count
    for subtree in mosaics.mosaictrees:
        IJ.showProgress(progress)
        mosaics.add_mosaic(subtree)
        progress += step
    IJ.showProgress(progress)
    IJ.showStatus("Parsed %i mosaics." % len(mosaics))
    dialog = GenericDialog('FluoView OIF / OIB Stitcher')
    if len(mosaics) == 0:
        msg = ("Couldn't find any (valid) mosaics in the project file.\n"
               " \n"
               "Please make sure to have all files available!\n"
               " \n"
               "Will stop now.\n")
        log.warn(msg)
        dialog.addMessage(msg)
        dialog.showDialog()
        return
    msg = "------------------------ EXPORT OPTIONS ------------------------"
    dialog.addMessage(msg)
    formats = ["OME-TIFF", "ICS/IDS"]
    dialog.addChoice("Export Format", formats, formats[0])
    dialog.addCheckbox("separate files by Z slices (OME-TIFF only)?", False)
    msg = "------------------------ EXPORT OPTIONS ------------------------"
    dialog.addMessage(msg)
    dialog.addMessage("")
    dialog.addMessage("")
    msg = gen_mosaic_details(mosaics)
    log.warn(msg)
    msg += "\n \nPress [OK] to write tile configuration files\n"
    msg += "and continue with running the stitcher."
    dialog.addMessage(msg)
    dialog.showDialog()

    opts = {}
    if dialog.getNextChoice() == 'ICS/IDS':
        opts['export_format'] = '".ids"'
    else:
        opts['export_format'] = '".ome.tif"'
        if dialog.getNextBoolean() == True:
            opts['split_z_slices'] = 'true'
    code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
                                           path=base, tplpath=imcftpl, opts=opts)
    log.warn("============= generated macro code =============")
    log.warn(flatten(code))
    log.warn("============= end of generated  macro code =============")

    if dialog.wasOKed():
        log.warn('Writing stitching macro.')
        imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
        log.warn('Writing tile configuration files.')
        imagej.write_all_tile_configs(mosaics, fixsep=True)
        log.warn('Launching stitching macro.')
        IJ.runMacro(flatten(code))

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import getNextChoice [as 别名]
    def dialog(self):
        """
        Open the classifier dialog window and return the paramters
        chosen.
        """

        # determine how many images are currently open
        image_count = WindowManager.getImageCount()
        image_titles = list(WindowManager.getImageTitles())
        image_titles.append("None")

        # now open a dialog to let the user set options
        path_listener = SetPathListener(self.path)
        path_button = TrimmedButton("Output directory",0)
        path_button.addActionListener(path_listener)

        dlg = GenericDialog("Create classifier data (v"+__version__+")")
        dlg.addMessage("Session ID: "+ str(self.session_id))
        dlg.addMessage("")
        dlg.addMessage("Select the ROI you want to save")
        dlg.addNumericField("Window size (pixels): ", self.window_size, 0)
        dlg.addChoice("Class label: ", DEFAULT_CLASSES+['Other...'], DEFAULT_CLASSES[0])
        dlg.addStringField("Class label (if other): ", "")
        dlg.addChoice("Image file #1 (BF):",image_titles,"None")
        dlg.addChoice("Image file #2 (GFP):",image_titles,"None")
        dlg.addChoice("Image file #3 (RFP):",image_titles,"None")
        dlg.addChoice("Mask file:",image_titles,"None")
        dlg.addCheckbox("Rename ROIs", True)
        dlg.addCheckbox("Exclude edges", True)
        dlg.addCheckbox("Save ROI zip", True)
        dlg.addCheckbox("Save classifier details", True)
        dlg.add(path_button)
        dlg.showDialog()

        # handle the cancelled dialog box
        if dlg.wasCanceled():
            return None


        label_option = dlg.getNextChoice()
        if label_option == 'Other...':
            label = dlg.getNextString()
        else:
            label = label_option



        # get the root path from the path listener
        root_path = path_listener.path

        if not os.path.isdir(root_path):
            w_dlg = GenericDialog("Warning")
            w_dlg.addMessage("Root path does not exist!!")
            w_dlg.showDialog()
            return None

        # try to make the directory for the label if it does not exist
        label_path = os.path.join(root_path, label)
        check_and_makedir(label_path)

		# get the options
        dialog_options = {'window_size': dlg.getNextNumber(),
                            'label': label,
                            'BF': dlg.getNextChoice(),
                            'GFP': dlg.getNextChoice(),
                            'RFP': dlg.getNextChoice(),
                            'mask': dlg.getNextChoice(),
                            'rename': dlg.getNextBoolean(),
                            'edges': dlg.getNextBoolean(),
                            'zip': dlg.getNextBoolean(),
                            'save': dlg.getNextBoolean(),
                            'path': label_path}

        # check that we actually selected an image file
        if all([dialog_options[d] == "None" for d in ['BF','GFP','RFP']]):
            w_dlg = GenericDialog("Warning")
            w_dlg.addMessage("You must select an image stream.")
            w_dlg.showDialog()
            return None

        # grab the contents and return these as a dictionary
        return dialog_options