Python GenericDialog.wasOKed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 wasOKed [as 别名]
	def _dialog(self,comment):
		gd = GenericDialog(comment)
		gd.enableYesNoCancel()
		gd.showDialog()
		if gd.wasCanceled():
			print "user cancelled dialog"
			sys.exit(1)
			
		option = gd.wasOKed()
		return option

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import wasOKed [as 别名]
def get_config_file(folder):
    '''Returns the config file name.'''
    # Get list of files in the selected directory.
    files = os.listdir(folder)

    # Check if a config file is present in folder.
    if default_config in files:
        dialog = GenericDialog('Default config file found!')
        dialog.addMessage('Use this file for the analysis?\n \n%s' % os.path.join(folder, default_config))
        dialog.enableYesNoCancel()
        dialog.showDialog()
        if dialog.wasCanceled():
            return None
        elif dialog.wasOKed():
            return default_config
        else:
            open_dialog = OpenDialog('Select a config file', folder, default_config)
            return open_dialog.getFileName()
    else:
        # Ask user to select a config file.
        open_dialog = OpenDialog('Select a config file', folder, default_config)
        return open_dialog.getFileName()

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import wasOKed [as 别名]
	# Asks for parameters
	gd = GenericDialog("Set Parameters...")
	gd.addNumericField("Start tile:",1,0)
	gd.addNumericField("Finish tile:",9,0)
	gd.addNumericField("Final disk space / Initial disk space:",0.25,2)
	gd.addNumericField("Step size (higher is faster but uses more memory):",10,0)
	gd.showDialog()
	startTile = int(gd.getNextNumber())
	finishTile = int(gd.getNextNumber())
	ratioRaw = gd.getNextNumber()
	ratio = math.sqrt(ratioRaw)
	stepSize = int(gd.getNextNumber())
	
	# Performs scaling
	if (gd.wasOKed()):
		anchorTiles = range(startTile,finishTile+1,stepSize)
		print anchorTiles
		for i in anchorTiles:
			if (i+stepSize-1 > finishTile):
				lastAnchorTile = finishTile
			else:
				lastAnchorTile = i+stepSize-1
			
			iterTiles = range(i,lastAnchorTile+1)
			params = "open=[" + theFilePath + "] color_mode=Default view=Hyperstack stack_order=XYCZT series_list=" + str(i) + "-" + str(lastAnchorTile)
			print params
			IJ.run("Bio-Formats Importer", params)
			imageIDList = WindowManager.getIDList()
			if (len(imageIDList) == len(iterTiles)):
				count = 0

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import wasOKed [as 别名]
		IJ.showStatus("Computing...")
		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])):

# 需要导入模块: from ij.gui import GenericDialog [as 别名]
# 或者: from ij.gui.GenericDialog import wasOKed [as 别名]
		sizeGD.addNumericField("Tile overlap percentage",10,0)
		sizeGD.addCheckbox("Write fused image sequence to disk",False)
		sizeGD.showDialog()
		doComputeOverlap = sizeGD.getNextBoolean()
		overlapPctStr = str(sizeGD.getNextNumber())
		doWriteToDisk = sizeGD.getNextBoolean()
		if (doComputeOverlap):
			overlapText = "compute_overlap ignore_z_stage"
		else:
			overlapText = ""
		if (doWriteToDisk):
			outputPath = imgDir + "substitched"
			diskWriteText = "image_output=[Write to disk] output_directory=[" + outputPath + "]"
		else:
			diskWriteText = "image_output=[Fuse and display]"
		if (sizeGD.wasOKed()):
			for t in tiles:
				shutil.copyfile(imgDir+"tile_"+str(t)+".ome.tif",imgDir+"temp/tile_"+str(ind)+".ome.tif")
				ind = ind + 1
			IJ.showStatus("Beginning stitch...")
			params = ("type=[Grid: row-by-row] order=[Right & Down                ] grid_size_x=" + 
				str(xs[2]) + " grid_size_y=" + str(ys[2]) + " tile_overlap=" + overlapPctStr + " first_file_index_i=1 directory=[" + 
				imgDir + "temp] file_names=tile_{i}.ome.tif output_textfile_name=TileConfiguration.txt " + 
				"fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 " +
				"absolute_displacement_threshold=3.50 " + overlapText + " subpixel_accuracy " + 
				"computation_parameters=[Save memory (but be slower)] " + diskWriteText)
			IJ.run("Grid/Collection stitching", params)
	
	gd = NonBlockingGenericDialog("Explore full resolution...")
	gd.addMessage("Select ROI for visualization at full resolution")
	gd.showDialog()

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