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Jython Scripting

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{{Scripting}}[ Jython] is an implementation of the [ Python programming language] designed to run on the Java platform.== Remark ==
== Quickstart ==This page is in a rewrite process that will take some time.
* Press {{key|[}} to bring up the [[Script Editor]].* Select an example Jython script from the {{bc | Templates | [by language] | Python}} menu.* Press {{key|Ctrl|R}} to run the script! == The Jython interpreter plugin == The interpreter provides a screen and a prompt. Type any jython code on the prompt to interact with ImageJ. Launch it from {{bc | Plugins | Scripting | Jython Interpreter}}. See [[Scripting Help]] for all keybindings, and also [[Scripting comparisons]]. {{Warning | Note that ImageJ also ships a unified Script Interpreter plugin, accessible from {{bc | Plugins | Scripting | Script Interpreter}}. But it is currently beta quality, and the Python language does not work properly due to bugs. Once this issue is fixed, the unified Script Interpreter will replace the language-specific interpreters such as the Jython Interpreter.}} Within the interpreter, all ImageJ, java.lang.* and TrakEM2 classes are automatically imported. So creating new images and manipulating them is very straighforward.  === Language basics === * Any text after a # is commented out.* There are no line terminators (such as ';' in other languages), neither curly braces to define code blocks.* Indentation defines code blocks.* Functions are defined with <i>def</i>, and classes with <i>class</i>.* Functions are objects, and thus storable in variables.* Jython (and python in general) accepts a mixture of procedural and object-oriented code.* Jython currently implements the Python language at its 2.5 version. All [ documentation for python 2.5] applies to Jython bundled with Fiji (with the remarks listed later). ==== Importing classes ==== {{ImportingClasses | lang = Jython}}You can specify imports in Jython as follows:<source lang="python">from import File</source>Where <code></code> is the class to be imported. See also section [[#Importing_other_.py_scripts_.28modules.29|Importing other ''.py'' scripts (modules)]] for importing user python modules. === Workflow for creating Jython scripts ===  To create a script for the GUI, the recommended setup is the following: * Edit and save a file in your favorite text editor. If you want ImageJ1 to insert it into the Menu structure, the file must be saved somewhere under ImageJ plugins folder, have an underscore on the name, and a .py extension.* Run {{bc | Plugins | Scripting | Refresh Jython scripts}} <b>only</b> the very first time after newly creating the file under any folder or subfolder of ImageJ's plugins folder. A menu item will appear with its name, from which it can be run.* Keep editing (and saving) the file from your editor. Just select the menu item to execute it over and over. Or use the {{bc | Plugins | Utilities | Find Commands...}} window to launch it easily (keybinding 'l'). The next time Fiji is run, it will setup all your scripts in the Plugins menu. If all you need is a script to run in headless mode, simply do:  fiji --headless === Some limitations of jython ===  {{Box | float=right | title=What about NumPy and SciPy?| If you like Python, you probably want to use Python modules such as the excellent [ NumPy] and [ SciPy] libraries. Unfortunately, Jython does not support linking to Python modules backed by native code. See [ this thread on the ImageJ forum] for some options and alternatives. This area is somewhere a dedicated programmer could make a huge splash and benefit the entire scientific community.}}Though jython tries to be as close as possible as python, there are some differences you may experience during scripting. * <u>Float "special numbers" such as ''NaN'' and ''Inf'' are not handled.</u>For instance, <source lang="python"> a = float('nan') </source>will create the correct float number in python, but will throw an exception in jython. Instead, to create a NaN in jython, use:<source lang="python">>>> a = Double.NaN>>> print aNaN </source>To test if a number is NaN:<source lang="python">>>> if Double.isNaN(a): print "a is NaN!"a is NaN! </source> * <u>Some existing python modules can't be imported in jython.</u>:: This is for instance the case of the module ''numpy'', which would have been really convenient for analysing data and results.:::: But see these java numerical libraries: , of which: :* JaMa (Java Matrix Package):* Java3D (particularly its [ vecmath] package provides general matrix and vector classes ([ GMatrix], [ GVector]).:::: ... are already included in Fiji. * <u>Your Jython version may be matching a much older Python version than you expect.</u>:: The latest Jython stable release (as of May 2015) is 2.7.0. Fiji (as of December 2015) distributes Jython 2.5.3. Any recent Python syntax such as <tt>except ExceptionType as e:</tt> or <tt>with open(filepath, 'r') as f:</tt> will fail. == Jython tutorials for ImageJ == === Defining variables: obtaining the current image === <source lang="python">imp = IJ.getImage()</source> Which is the same as:<source lang="python">imp = WindowManager.getCurrentImage()</source> Since calling the above is long and tedious, one can declare a variable that points to the above static methods: <source lang="python">c = WindowManager.getCurrentImage</source> Above note the lack of parentheses. To execute the function, just use parentheses on it: <source lang="python"> imp = c()</source> The above gets the value of <i>c</i>, which is the method named getCurrentImage in class WindowManager, and executes it, storing its returned object in <i>imp</i>.  === Manipulating pixels === ==== Creating a grayscale ramp image ====First create an image and obtain its pixels: <source lang="python">imp = ImagePlus("my new image", FloatProcessor(512, 512))pix = imp.getProcessor().getPixels()</source> The length of an array: <source lang="python">n_pixels = len(pix)</source> Then loop to modify them: <source lang="python"># catch widthw = imp.getWidth() # create a ramp gradient from left to rightfor i in range(len(pix)): pix[i] = i % w # adjust min and max, since we know themimp.getProcessor().setMinAndMax(0, w-1)</source> ... and show the new image: <source lang="python"></source>  ==== Creating a random 8-bit image ==== First import necessary packages: Random, from standard java util library, and [ jarray], the Jython module for native java arrays: <source lang="python">from java.util import Randomfrom jarray import zeros</source> Then create the array and fill it with random bytes: <source lang="python">width = 512height = 512 pix = zeros(width * height, 'b')Random().nextBytes(pix)</source> ('z' = boolean, 'c' = char, 'b' = byte, 'h' = short, 'i' = int, 'l' = long, 'f' = float and 'd' = double, as explained in the [ jarray documentation].) Now make a new IndexColorModel (that's what ImageJ's ij.process.LUT class is) for 8-bit images: <source lang="python">channel = zeros(256, 'b')for i in range(256): channel[i] = (i -128) cm = LUT(channel, channel, channel)</source> ... and compose a ByteProcessor from the pixels, and assign it to an ImagePlus: <source lang="python">imp = ImagePlus("Random", ByteProcessor(width, height, pix, cm))</source> ==== Creating a random image, the easy way ==== All the above can be summarized like the following: <source lang="python">from java.util import Randomimp = IJ.createImage("A Random Image", "8-bit", 512, 512, 1)Random().nextBytes(imp.getProcessor().getPixels())</source> === Running a watershed plugin on an image === <source lang="python"># 1 - Obtain an imageblobs = IJ.openImage("")# Make a copy with the same properties as blobs image:imp = blobs.createImagePlus()ip = blobs.getProcessor().duplicate()imp.setProcessor("blobs copy", ip) # 2 - Apply a threshold: only zeros and ones# Set the desired threshold range: keep from 0 to 74ip.setThreshold(147, 147, ImageProcessor.NO_LUT_UPDATE)# Call the Thresholder to convert the image to a, "Convert to Mask", "") # 3 - Apply watershed# Create and run new EDM object, which is an Euclidean Distance Map (EDM)# and run the watershed on the ImageProcessor:EDM().toWatershed(ip) # 4 - Show the watersheded</source> The EDM plugin that contains the watershed could have been indirectly applied to the currently active image, which is <i>not</i> recommended: <source lang="python">imp = IJ.getImage() # the current imageimp.getProcessor().setThreshold(174, 174, ImageProcessor.NO_LUT_UPDATE), "Convert to Mask", ""), "Watershed", "")</source> If you had called <i>show()</i> on the image at any early stage, just update the screen with: <source lang="python">imp.updateAndDraw()</source>  ==== ... and counting particles, and measuring their areas ==== Continuing from the <i>imp</i> above, that contains the now watersheded "blobs" sample image: <source lang="python"># Create a table to store the resultstable = ResultsTable()# Create a hidden ROI manager, to store a ROI for each blob or cellroim = RoiManager(True)# Create a ParticleAnalyzer, with arguments:# 1. options (could be SHOW_ROI_MASKS, SHOW_OUTLINES, SHOW_MASKS, SHOW_NONE, ADD_TO_MANAGER, and others; combined with bitwise-or)# 2. measurement options (see [ Measurements])# 3. a ResultsTable to store the measurements# 4. The minimum size of a particle to consider for measurement# 5. The maximum size (idem)# 6. The minimum circularity of a particle# 7. The maximum circularitypa = ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER, Measurements.AREA, table, 0, Double.POSITIVE_INFINITY, 0.0, 1.0)pa.setHideOutputImage(True) if pa.analyze(imp): print "All ok"else: print "There was a problem in analyzing", blobs # The measured areas are listed in the first column of the results table, as a float array:areas = table.getColumn(0) </source> To print out the area measurement of each:  >>> for area in areas: print area 76.0 185.0 658.0 434.0 ...  Now, we want to measure the intensity of each particle. To do so, we'll retrieve the ROI from the ROIManager, set them one at a time on view the original (non-watershed, non-thresholded) image stored in the variable <i>blobs</i>, and measure: <source lang="python"># Create a new list to store the mean intensity values of each blob:means = [] for roi in RoiManager.getInstance().getRoisAsArray(): blobs.setRoi(roi) stats = blobs.getStatistics(Measurements.MEAN) means.append(stats.mean)</source> Finally read out the measured mean intensity value of each blob, along with its area: <source lang="python">for area, mean in zip(areas, means): print area, mean</source>  6.0 191.47368421052633 185.0 179.2864864864865 658.0 205.61702127659575 434.0 217.32718894009216 477.0 212.1425576519916 ... === Creating an image from a text file === A data file containing rows with 4 columns:  ... 399 23 30 10.12 400 23 30 12.34 ... ... where the columns are X, Y, Z and value, for every pixel in the image.We assume we know the width and height of the image.From this sort of data, we create an image, read out all lines and parse the numbers: <source lang="python">width = 512height = 512stack = ImageStack(width, height) file = open("/home/albert/Desktop/data.txt", "r") try: fp = FloatProcessor(width, height) pix = fp.getPixels() cz = 0 # Add as the first slice: stack.addSlice(str(cz), fp) # Iterate over all lines in the text file: for line in file.readlines(): x, y, z, value = line.split(" ") x = int(x) y = int(y) z = int(z) value = float(value) # Advance one slice if the Z changed: if z != cz: # Next slice fp = FloatProcessor(width, height) pix = fp.getPixels() stack.addSlice(str(cz), fp) cz += 1 # Assign the value: pix[y * width + x] = value # Prepare and show a new image: imp = ImagePlus("parsed", stack) Ensure closing the file handle even if an error is thrown:finally: file.close()</source>  === Obtain/View histogram and measurements from an image === The easiest way is to grab an image and call an ImageJ command to show its histogram: <source lang="python">imp = IJ.openImage(""), "Histogram", "")</source> How ImageJ does it, internally, has to do with the [ ImageStatisics] class: <source lang="python">stats = imp.getStatistics()print stats.histogram</source>  array('i',[0, 0, 0, 0, 0, 0, 0, 0, 53, 0, 0, 0, 0, 0, 0, 0, 304, 0, 0, 0, 0, 0, 0, 0, 1209, 0, 0, 0, 0, 0, 0, 0, 3511, 0, 0, 0, 0, 0, 0, 0, 7731, 0, 0, 0, 0, 0, 0, 0, 10396, 0, 0, 0, 0, 0, 0, 0, 7456, 0, 0, 0, 0, 0, 0, 0, 3829, 0, 0, 0, 0, 0, 0, 0, 1992, 0, 0, 0, 0, 0, 0, 0, 1394, 0, 0, 0, 0, 0, 0, 0, 1158, 0, 0, 0, 0, 0, 0, 0, 1022, 0, 0, 0, 0, 0, 0, 0, 984, 0, 0, 0, 0, 0, 0, 0, 902, 0, 0, 0, 0, 0, 0, 0, 840, 0, 0, 0, 0, 0, 0, 0, 830, 0, 0, 0, 0, 0, 0, 0, 926, 0, 0, 0, 0, 0, 0, 0, 835, 0, 0, 0, 0, 0, 0, 0, 901, 0, 0, 0, 0, 0, 0, 0, 1025, 0, 0, 0, 0, 0, 0, 0, 1180, 0, 0, 0, 0, 0, 0, 0, 1209, 0, 0, 0, 0, 0, 0, 0, 1614, 0, 0, 0, 0, 0, 0, 0, 1609, 0, 0, 0, 0, 0, 0, 0, 2220, 0, 0, 0, 0, 0, 0, 0, 2037, 0, 0, 0, 0, 0, 0, 0, 2373, 0, 0, 0, 0, 0, 0, 0, 1568, 0, 0, 0, 0, 0, 0, 0, 1778, 0, 0, 0, 0, 0, 0, 0, 774, 0, 0, 0, 0, 0, 0, 0, 1364, 0, 0, 0, 0, 0, 0, 0])  The histogram, area and mean are computed by default. Other values like the median need to be specified. To calculate other parameters, specify them by bitwise-or composition (see flags in [ Measurements]): <source lang="python">stats = imp.getStatistics(Measurements.MEAN | Measurements.MEDIAN | Measurements.AREA)print "mean:", stats.mean, "median:", stats.median, "area:", stats.area</source>  mean: 103.26857775590551 median: 64.0 area: 65024.  If we set a ROI to the image, then we are measuring only for the inside of the ROI. Here we set an oval ROI of radius 25 pixels, centered:<source lang="python">radius = 25roi = OvalRoi(imp.width/2 - radius, imp.height/2 -radius, radius*2, radius*2)imp.setRoi(roi)stats = imp.getStatistics(Measurements.MEAN | Measurements.MEDIAN | Measurements.AREA)print "mean:", stats.mean, "median:", stats.median, "area:", stats.area</source>  mean: 104.96356275303644 median: 64.0 area: 1976.0   To display the histogram window ourselves, we may use the [ HistogramWindow] class: <source lang="python">hwin = HistogramWindow(imp)</source> ... of which we may grab the image (the plot itself) and save it: <source lang="python">plotimage = hwin.getImagePlus(), "/path/to/our/folder/plot.tif")</source> === Removing bleeding from one channel to another === The technique to use is to divide one channel by the other: the channel to denoise divided by the channel that bled through. The relatively high-level way to do it is to split the channels and call the ImageCalculator with a "Divide" argument: <source lang="python"># 1 - Obtain an RGB image stackimp = WindowManager.getCurrentImage()if imp.getType() != ImagePlus.COLOR_RGB: IJ.showMessage("The active image is not RGB!") raise RuntimeException("The active image is not RGB!") if 1 == imp.getNSlices(): IJ.showMessage("Not a stack!") raise RuntimeException("Not a stack!") # 2 - Prepare stacks to split slicesstack = imp.getStack()red_stack = ImageStack(imp.width, imp.height)green_stack = ImageStack(imp.width, imp.height) # 3 - Iterate all slices -- notice slices are 1<=i<=sizefor i in range(1, imp.getNSlices()+1): slice = stack.getProcessor(i) red_stack.addSlice(str(i), slice.toFloat(0, None)) green_stack.addSlice(str(i), slice.toFloat(1, None)) # 4 - Apply "divide" via ImageCalculator to the red_stack, which is a new 32-bit stack# Don't use the parameters "create" or "float" or "32" in the parameters string# of the calc.calculate call--then the result of the operation would be# in a new stack that opens beyond our control. Without them, results are# applied to the red_stackcalc = ImageCalculator()calc.calculate("Divide stack", ImagePlus("red", red_stack), ImagePlus("green", green_stack)) # 5 - Compose a new color stacknew_stack = ImageStack(imp.width, imp.height)for i in range(1, imp.getNSlices()+1): cp = stack.getProcessor(i).duplicate() cp.setPixels(0, red_stack.getProcessor(i)) new_stack.addSlice(stack.getSliceLabel(i), cp) # 6 - Show the new imageImagePlus("Normalized " + imp.title, new_stack).show()</source>  Alternatively and as an example of direct pixel manipulation, we'll iterate all slices of the image stack, divide the red channel by the green channel, and compose a new stack: <source lang="python"># 1 - Obtain an RGB image stackimp = WindowManager.getCurrentImage()if imp.getType() != ImagePlus.COLOR_RGB: IJ.showMessage("The active image is not RGB!") raise RuntimeException("The active image is not RGB!") if 1 == imp.getNSlices(): IJ.showMessage("Not a stack!") raise RuntimeException("Not a stack!") stack = imp.getStack() # 2 - Create a new stack to store the resultnew_stack = ImageStack(imp.width, imp.height) # 3 - Iterate all slices -- notice slices are 1<=i<=sizefor i in range(1, imp.getNSlices()+1): # Get the slice i slice = stack.getProcessor(i) # Get two new FloatProcessor with the green and red channel data in them red = slice.toFloat(0, None) green = slice.toFloat(1, None) pix_red = red.getPixels() pix_green = green.getPixels() # Create a new FloatProcessor for the normalized result new_red = FloatProcessor(imp.width, imp.height) pix_new_red = new_red.getPixels() # Iterate and set all normalized pixels for k in range(len(pix_red)): if 0 != pix_green[k]: pix_new_red[k] = pix_red[k] / pix_green[k] # Create a ColorProcessor that has the normalized red and the same green and blue channels cp = slice.duplicate() cp.setPixels(0, new_red) # at channel 0, the red # Store the normalized slice in the new stack, copying the same slice label new_stack.addSlice(stack.getSliceLabel(i), cp) # 4 - Show the normalized stacknew_imp = ImagePlus("Normalized " + imp.title, new_stack)</source> Notice that this second approach is much slower: accessing every pixel from jython has a high cost. If you would like to do very fast pixel-level manipulations, use java or [[Clojure Scripting|Clojure]]. === Subtract the minimal value to an image === Which is to say, translate the histogram so that the lowest value is at zero. <source lang="python"># Obtain current image and its pixelsimp = IJ.getImage()pix = imp.getProcessor().convertToFloat().getPixels() # find out the minimal pixel valuemin = reduce(Math.min, pix) # create a new pixel array with the minimal value subtractedpix2 = map(lambda x: x - min, pix) ImagePlus("min subtracted", FloatProcessor(imp.width, imp.height, pix2, None)).show()</source> Notice we used:* The <i>reduce</i> function to obtain a single value from a list of values (the pixel array) by applying a function to every pair of consecutive values (in this case, the Math.min).* <i>lambda</i>, which is used to declare an anonymous function that takes one argument.* The <i>map</i> function, which runs a function given as argument to every element of a list (here, every pixel) and returns a new list with all the results. === Extract a specific color channel for a given time frame of a composite image === Suppose you have a 4D multicolor image, and want to obtain a stack of slices corresponding to a specific color channel and time frame. The [ CompositeImage] is a stack whose slices are interpreted as belonging to specific color channels, Z slices and time frames. To find out which slice corresponds to what, use the <i>getStackIndex</i> method of the [ ImagePlus], which translates between color channels, z slices and time frames to the slice index in the underlying [ ImageStack]. <source lang="python">from ij import IJ, ImagePlus, ImageStack def extractChannel(imp, nChannel, nFrame): """ Extract a stack for a specific color channel and time frame """ stack = imp.getImageStack() ch = ImageStack(imp.width, imp.height) for i in range(1, imp.getNSlices() + 1): index = imp.getStackIndex(nChannel, i, nFrame) ch.addSlice(str(i), stack.getProcessor(index)) return ImagePlus("Channel " + str(nChannel), ch) imp = IJ.getImage()extractChannel(imp, 1, 1).show()</source> Notice that color channels, stack slices and time frames are all 1-based. For example, if you have 3 color channels, then these have indices 1, 2, and 3 (not 0, 1 and 2).  === Visualize any number of TIFF stacks in a single composite multi-color image stack === Suppose you have 1000 stacks of <i>Drosophila</i> fly brains, each with different neurons labeled in a single color channel. Suppose that you have registered all these confocal stacks. Were you to overlay them, you would see whether the labeled neurons overlap in 3D space or not. Here is a script to do that. First, it asks for a directory containing any number of TIF image stacks. It assumes all stacks have the same dimensions, and that they are all single channel (i.e. just red, or just green, etc.). Then, it displays a small window with a listing of many colors: red, green, blue, orange, gray, etc. Any of the hundreds of stacks in the directory can be assigned to each color channel. The stacks are accessed in a virtual way, so even 1000 (one thousand) stacks will be managed just fine in small laptop. One could easily add more color channels. But there are already lots. The script uses [[Imglib]] scripting to normalize images and generate the color composite. See this [ imglib scripting tutorial] for in-depth explanations. [[Image:Corti-multi-channel.png]] <source lang="python"># 2010-12-03 Albert Cardona and Arnim Jenett# At HHMI Janelia Farm, Fiji tutorials class## Select a directory with multiple image stacks# all of the same dimensions, and show a channel# chooser window to visualize up to 5 of them# in red, green, blue, orange, and gray.# # The stacks are all virtual, opened via LOCI# with BFVirtualStack. The composition of the# RGB ColorProcessor is done with the # script.imglib library.# # Each color channel is shown normalized.# Currently works only with TIF stacks,# and it will interpret them as single-channel.  from loci.plugins.util import BFVirtualStackfrom loci.formats import ChannelSeparatorfrom import DirectoryChooserimport osfrom javax.swing import JScrollPane, JPanel, JComboBox, JLabel, JFramefrom java.awt import Color, GridLayoutfrom java.awt.event import ActionListenerfrom script.imglib.math import Compute, Max, Multiplyfrom script.imglib.algorithm import Normalizefrom script.imglib.color import Red, Green, Blue, RGBAfrom mpicbg.imglib.image.display.imagej import ImageJFunctions as IJF  # Choose a directory with lots of tif stacksdc = DirectoryChooser("Choose directory with stacks")srcDir = dc.getDirectory() # Open each tif stack as a virtual BFVirtualStackbfvs = []names = []for filename in os.listdir(srcDir): if filename.endswith(".tif"): print "Reading metadata from", filename cs = ChannelSeparator() names.append(filename) cs.setId(srcDir + filename) bfvs.append( BFVirtualStack(srcDir + filename, cs, False, False, False) ) names.sort()names = ["None"] + names  colorToRGB = {'Red' : [255,0,0],'Green' : [0,255,0],'Blue' : [0,0,255],'Orange' : [255,127,0],'Cyan' : [0,255,255],'Yellow' : [255,255,0],'Magenta' : [255,0,255],'Indigo' : [75,0,130],'Violet' : [238,130,238],'Greyscale' : [255,255,255],'Aquamarine' : [127,255,212],'Navy Blue' : [0,0,128],'Sky Blye' : [135,206,235],'Turquoise' : [64,224,208],'Beige' : [245,245,220],'Brown' : [165,42,42],'Chocolate' : [210,105,30],'Dark wood' : [133,94,66],'Light wood' : [133,99,99],'Olive' : [128,128,0],'Green yellow' : [173,255,47],'Sea green' : [32,178,170],'Khaki' : [240,230,140],'Salmon' : [250,128,114],'Pink' : [255,192,203],'Tomato' : [255,99,71],'Scarlet' : [140,23,23],'Purple' : [128,0,128],'Wheat' : [245,222,179],'Silver grey' : [192,192,192]} # Encode color RGB in floats:tmp = {}for c,rgb in colorToRGB.iteritems(): tmp[c] = [v/255.0 for v in rgb]colorToRGB = tmp # Colors in the desired listing order:colors = ['Red', 'Green', 'Blue', 'Orange', 'Indigo', 'Cyan', 'Yellow', 'Magenta', 'Turquoise', 'Tomato', 'Olive', 'Violet', 'Green yellow', 'Khaki', 'Scarlet', 'Beige', 'Chocolate', 'Silver grey', 'Pink', 'Wheat', 'Sea green', 'Greyscale', 'Light wood', 'Sky Blye', 'Brown', 'Salmon', 'Navy Blue', 'Aquamarine', 'Purple', 'Dark wood'] # Initalize table of colors vs stacks to use:table = {}for k,v in zip(colors, [1] + [0 for i in range(len(colors)-1)]): table[k] = v  def asImg(color, section): global bfvs, table index = table[color] if 0 == index: return 0 # is "None" color return IJF.wrap(ImagePlus("", bfvs[index-1].getProcessor(section))) def maybeNormalize(fn): """ Do not normalize if no images are present. """ if 0 == fn: return fn cursors = [] fn.findCursors(cursors) if len(cursors) > 0: return Multiply(Normalize(fn), 255) return fn def blendColors(section): global bfvs, table, colorToRGB red = 0 green = 0 blue = 0 for colorName,index in table.iteritems(): if 0 == index: continue img = IJF.wrap(ImagePlus("", bfvs[index-1].getProcessor(section))) rgb = colorToRGB[colorName] if 0 != rgb[0]: red = Max(red, Multiply(img, rgb[0])) if 0 != rgb[1]: green = Max(green, Multiply(img, rgb[1])) if 0 != rgb[2]: blue = Max(blue, Multiply(img, rgb[2])) return red, green, blue class VS(VirtualStack): def __init__(self): self.last = None def getProcessor(self, i): """ Channel color composition into a single RGB image, as ColorProcessor. 'i' is the section index, 1<=i<=size """ red, green, blue = blendColors(i) # Transform to RGB by normalizing and scaling to 255 red = maybeNormalize(red) green = maybeNormalize(green) blue = maybeNormalize(blue) # Compose rgb = RGBA(red, green, blue).asImage() self.last = IJF.displayAsVirtualStack(rgb).getProcessor() return self.last def getSize(self): return bfvs[0].getSize() def getSliceLabel(self, i): return str(i) def getWidth(self): return self.last.getWidth() def getHeight(self): return self.last.getHeight() def getPixels(self, i): return self.getProcessor(i).getPixels() def setPixels(self, pix, i): pass  # Create a new image stackprint os.path.split(srcDir)ourImp = ImagePlus(os.path.split(srcDir)[1], VS()) # Create a bunch of panels, one for each color channelall = JPanel()layout = GridLayout(len(colors), 2)all.setLayout(layout) # GUI to choose which stacks is shown in which channelclass Listener(ActionListener): def __init__(self, color, choice, imp): self.color = color self.choice = choice self.imp = imp def actionPerformed(self, event): global table table[self.color] = self.choice.getSelectedIndex() self.imp.updateAndRepaintWindow() for color in colors: all.add(JLabel(color)) choice = JComboBox(names) choice.setSelectedIndex(table[color]) choice.addActionListener(Listener(color, choice, ourImp)) all.add(choice) frame = JFrame("Channels")frame.getContentPane().add(JScrollPane(all))frame.pack() frame.setVisible(True)</source> === Sort all points of a PointRoi into a chain by distance to each other === There may be better ways, but here is one. Read the header to understand its limitations. <source lang="python"># Albert Cardona 2010-12-17 for Victoria Butler at HHMI Janelia Farm# Given a PointRoi, order the points in a chain# Assumes that the point furthest from all points# is the start or the end of the chain. from javax.vecmath import Point2f # Obtain the PointRoi of the current imageproi = IJ.getImage().getRoi() # Interrupt if the ROI is not a PointRoi instance:if proi.getClass() != PointRoi: raise Exception("Not a PointRoi!") class Point(Comparable): def __init__(self, x, y): self.p = Point2f(x, y) self.distances = {} self.distAll = None def distance(self, point): return self.p.distance(point.p) def distanceToAll(self): if self.distAll is None: self.distAll = reduce(lambda a, b: a + b, self.distances.values()) return self.distAll def compareTo(self, point): if self.distanceToAll() < point.distanceToAll(): return -1 return 1 def toString(self): return self.p.toString() def closest(self, points): """ Find the closest point that is not contained in the set of given points. """ next = None dist = Float.MAX_VALUE for p,d in self.distances.iteritems(): if d < dist and not p in points: next = p dist = d return next # Convert PointRoi points to Point instancespx = proi.getXCoordinates()py = proi.getYCoordinates()bounds = proi.getBounds()points = []for i in range(proi.getNCoordinates()): points.append(Point(bounds.x + px[i], bounds.y + py[i])) # Precompute all-to-all distancesallToAll = {}for j in range(len(points)): for k in range(j+1, len(points)): distance = points[j].distance(points[k]) points[j].distances[points[k]] = distance points[k].distances[points[j]] = distance # Choose a starting point.# In this case, we use the point most distant from all other pointspoints.sort()first = points[-1]print "First:", first # Grow the chain from the starting pointchain = [first]seen = set() # for fast look-upseen.add(chain[0])while len(chain) < len(points): next = chain[-1].closest(seen) if next is None: break chain.append(next) seen.add(next) print "Chain:", chain</source> === Correct illumination in a stack: apply the illumination of one slice to all others === The Multi-focus 3D Microscope (Sara Abrahamsson and Matz Gustafsson) takes a single image and later, computationally, 9 image planes are extracted. The middle slice usually has the desired illumination levels, while the other 8 slices (4 before and 4 after) do not. Here is a script to apply the illumination of the 5th slice to all other slices. The script takes a directory of images and processed them all, resulting in new images stored as "*-corrected.tif" in the same directory. <source lang="python"># Albert Cardona 2011-06-09 at HHMI Janelia Farm# Takes a stack of 9 slices# and then computes the mean and stdDev of slice number 5# and normalize the intensity of the other 8 slices# to that of slice 5.## Created for Jiji Chen to process image stacks from# the multifocus 3D microscope from Matz Gustafsson# and Sara Abrahamsson  from math import sqrtimport os def computeMean(pixels): return sum(pixels) / float(len(pixels)) def computeStdDev(pixels, mean): s = 0 for i in range(len(pixels)): s += pow(pixels[i] - mean, 2) return sqrt(s / float(len(pixels) -1)) def process9ImagePlanes(imp): # reference slice refSlice = 5 ref = imp.getStack().getProcessor(5) refMean = sum(ref.getPixels()) / float(len(ref.getPixels())) refStdDev = computeStdDev(ref.getPixels(), refMean)  # New stack with the corrected slices stack = ImageStack(ref.width, ref.height)  for i in range(1, 10): # skip the reference slice if 5 == i: stack.addSlice(imp.getStack().getSliceLabel(5), ref.convertToFloat()) continue ip = imp.getStack().getProcessor(i).convertToFloat() mean = computeMean(ip.getPixels()) stdDev = computeStdDev(ip.getPixels(), mean) ip.add(-mean) ip.multiply(1/stdDev) ip.multiply(refStdDev) ip.add(refMean) stack.addSlice(imp.getStack().getSliceLabel(i), ip)  return ImagePlus(imp.title, stack)  def accept(filename): """ Work only with TIFF files. """ return len(filename) - 4 == filename.rfind(".tif") def run(): dc = DirectoryChooser("pick folder with image stacks") folder = dc.getDirectory() if folder is None: return for filename in filter(accept, os.listdir(folder)): imp = IJ.openImage(os.path.join(folder, filename)) if imp is None: print "Failed to open image:", filename continue corrected = process9ImagePlanes(imp), os.path.join(folder, filename[0:-4] + "-corrected.tif")) run() </source>  === Add a mouse listener to the canvas of every open image === <source lang="python">from java.awt.event import MouseAdapter def doSomething(imp): """ A function to react to a mouse click on an image canvas. """ IJ.log("clicked on: " + str(imp)) class ML(MouseAdapter): def mousePressed(self, event): canvas = event.getSource() imp = canvas.getImage() doSomething(imp) listener = ML() for imp in map(WindowManager.getImage, WindowManager.getIDList()): win = imp.getWindow() if win is None: continue win.getCanvas().addMouseListener(listener)</source> After running the script, clicking on any image will result inprinting a line to the log window, like:  clicked on: imp[Untitled-1 400x200x1]  === Add a key listener to the canvas of every open image === <source lang="python">from java.awt.event import KeyEvent, KeyAdapter def doSomething(imp, keyEvent): """ A function to react to key being pressed on an image canvas. """ IJ.log("clicked keyCode " + str(keyEvent.getKeyCode()) + " on image " + str(imp)) # Prevent further propagation of the key event: keyEvent.consume() class ListenToKey(KeyAdapter): def keyPressed(this, event): imp = event.getSource().getImage() doSomething(imp, event) listener = ListenToKey() for imp in map(WindowManager.getImage, WindowManager.getIDList()): win = imp.getWindow() if win is None: continue canvas = win.getCanvas() # Remove existing key listeners kls = canvas.getKeyListeners() map(canvas.removeKeyListener, kls) # Add our key listener canvas.addKeyListener(listener) # Optionally re-add existing key listeners # map(canvas.addKeyListener, kls)</source> === Create a virtual stack from the TIF files present in a folder and its subfolders, recursively === <source lang="python"># Walk recursively through an user-selected directory# and add all found filenames that end with ".tif"# to a VirtualStack, which is then shown.## It is assumed that all images are of the same type# and have the same dimensions. import osfrom import DirectoryChooserfrom ij import IJ, ImagePlus, VirtualStack def run(): srcDir = DirectoryChooser("Choose!").getDirectory() if not srcDir: # user canceled dialog return # Assumes all files have the same size vs = None for root, directories, filenames in os.walk(srcDir): for filename in filenames: # Skip non-TIFF files if not filename.endswith(".tif"): continue path = os.path.join(root, filename) # Upon finding the first image, initialize the VirtualStack if vs is None: imp = IJ.openImage(path) vs = VirtualStack(imp.width, imp.height, None, srcDir) # Add a slice, relative to the srcDir vs.addSlice(path[len(srcDir):]) # ImagePlus("Stack from subdirectories", vs).show() run()</source> === Open the slices of a very large multi-image stack file one by one, and save each as a new image file ===<source lang="python"># 2011-10-18 Albert Cardona for Nuno da Costa# Choose a multi-slice image stack file in a virtual way# and save each slice as an individual image file# in a user-chosen directory. import osfrom loci.plugins.util import BFVirtualStackfrom loci.formats import ChannelSeparator def run(): # Choose a file to open od = OpenDialog("Choose multi-image file", None) srcDir = od.getDirectory() if srcDir is None: # User canceled the dialog return path = os.path.join(srcDir, od.getFileName()) # Choose a directory to store each slice as a file targetDir = DirectoryChooser("Choose target directory").getDirectory() if targetDir is None: # User canceled the dialog return # Ready: cs = ChannelSeparator() cs.setId(path) bf = BFVirtualStack(path, cs, False, False, False) for sliceIndex in xrange(1, bf.getSize() +1): print "Processing slice", sliceIndex ip = bf.getProcessor(sliceIndex) sliceFileName = os.path.join(targetDir, str(sliceIndex) + ".tif") FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName) run()</source>  === Apply a binary mask to every slice in an image stack === Will work with regular stacks and with any kind of complex stack like a composite image or a 4d volume. Keep in mind that all stack types in ImageJ consists of a sequence of 2d images, each editable with an [ ImageProcessor] obtained from the [ ImageStack] that one can get from the [ ImagePlus]. (The [ ImagePlus] being what the opener or the [ WindowManager] provides.) <source lang="python"># Albert Cardona 2012-10-05 for Sara Abrahamsson## Take a stack of images and a mask,# and clear the area outside the mask for every image.## ASSUMES that the mask:# 1. Is 8-bit;# 2. has the area to keep as 255;# 3. has the area to clear as zeros.  from ij import IJfrom ij import WindowManager as WM # If the images are open:volume = WM.getImage("stack.tif")mask = WM.getImage("mask.tif") # Or if the images have to be loaded from files:# volume = IJ.openImage("/Users/sara/images/stack.tif")# mask ="/Users/sara/images/mask.tif") # Obtain the underlying stack content of 2d imagesstack = volume.getStack() # Fill every stack slice with zeros for the area outside the maskfor i in xrange(1, stack.getSize() + 1): # ip is the ImageProcessor for one stack slice ip = stack.getProcessor(i) ip.setValue(0) ip.fill(mask) volume.updateAndDraw()</source> Note that it is counterintuitive that the area outside the mask gets filled with zeros. If you want the area inside the mask to get filled with zeros, then add this step before the loop: <source lang="python">mask = mask.duplicate()mask.invert()</source> === Open all series in a LIF file with Bio-Formats === <source lang="python"> # 2014-11-24 Harri Jäälinoja from import ImagePlusReader,ImporterOptions,ImportProcessimport sys filename = sys.argv[1]opts = ImporterOptions()opts.setId(filename)opts.setUngroupFiles(True) # set up import processprocess = ImportProcess(opts)process.execute()nseries = process.getSeriesCount() # reader belonging to the import processreader = process.getReader() # reader external to the import processimpReader = ImagePlusReader(process)for i in range(0, nseries): print "%d/%d %s" % (i+1, nseries, process.getSeriesLabel(i)) # activate series (same as checkbox in GUI) opts.setSeriesOn(i,True)  # point import process reader to this series reader.setSeries(i)  # read and process all images in series imps = impReader.openImagePlus() for imp in imps: wait = Wait(str(i) + imp.getTitle()) imp.close()  # deactivate series (otherwise next iteration will have +1 active series) opts.setSeriesOn(i, False)</source>   === Open and save movies with the FFMPEG I/O plugin === First note that the FFMPEG I/O plugin was a proof-of-concept that is completely '''unmaintained'''. Then open the [[Fiji Updater]], push the "Manage update sites" page at the bottom left of the dialog, and install the [ FFMPEG] plugin by {{Person|Schindelin}} by ticking its checkbox, as [[How_to_follow_a_3rd_party_update_site|explained in more detail here]]. See also the Java source code for the {{GitHub|repo=fiji|tag=8164ae68|path=native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/|label=IO}} class from the [ FFMPEG plugin source code site]. <source lang="python">""" Albert Cardona for Marta Zlatic, 2014-01-24. """ from fiji.ffmpeg import IOfrom java.awt import Colorimport os def load(path, first_frame=0, last_frame=-1): """ Load the whole movie by default. """ io = IO() imp = io.readMovie(path, False, first_frame, last_frame) return imp def save(path, imp, frame_rate=30, bit_rate=400000): """ frame_rate in fps (frames per second). bit_rate defines the quality of the movie: higher bit rate results in larger, higher quality movies. The movie format (e.g. AVI, MPG, etc.) is chosen by the path filename extension. """ io = IO() io.writeMovie(imp, path, frame_rate, bit_rate)  def process(imp, convert, roi, time_zero, time_range): """ Crop, convert to another format, and time-stamp. """ stack = imp.getStack() size = stack.getSize() bounds = roi.getBounds() new_stack = ImageStack(bounds.width, bounds.height) for i in xrange(1, size + 1): ip = convert(stack.getProcessor(i)) ip.setRoi(roi) c = ip.crop() c.setColor(Color.white) time = "%.2f" % (time_zero + time_range * (float(i-1) / (size -1))) c.drawString(time, 5, 15) new_stack.addSlice(str(i), c)  return ImagePlus(imp.title, new_stack)  def batch_process(extension, source_dir, output_dir, convert, roi, time_zero, time_range): for filename in os.listdir(source_dir): if filename.endswith(extension): if os.path.exists(target_dir + filename): # Skip if movie exists at destination continue imp = load(source_dir + filename) imp2 = process(imp, convert, roi, time_zero, time_range) imp.flush() save(target_dir + filename, imp2) imp2.flush()  def convert(ip): """ Convert to 8=bit and crop the range to [0, 128] pixel values. """ c = ip.convertToByte(True) c.setMinAndMax(0, 128) return c  source_dir = '/path/to/list_of_AVI_movies/'target_dir = '/path/to/new_list_of_AVI_movies/' roi = Roi(50, 50, 256, 256)time_zero = 30 # start at 30 secondstime_range = 30 # range of (also) 30 seconds # Process all AVI movie files, saving them also as AVI filesbatch_process('.avi', source_dir, target_dir, convert, roi, time_zero, time_range) </source> === Skeletonize an image and analyze the skeleton === <source lang="python">from ij import IJfrom skeleton_analysis import AnalyzeSkeleton_,Graph,Edge,Vertex # open image, blur, make b/w, skeletonizeimp = IJ.openImage("/path/to/image.tif"),"Gaussian Blur...","sigma=5"),"Make Binary",""),"Skeletonize","") # run AnalyzeSkeleton# (see # and = AnalyzeSkeleton_()skel.setup("",imp)skelResult =, False, True, None, True, True) # get the separate skeletonsgraph = skelResult.getGraph()print len(graph)print skelResult.getNumOfTrees() def getGraphLength(graph): length = 0 for g in graph.getEdges(): length = length + g.getLength() return length # find the longest graphgraph = sorted(graph, key=lambda g: getGraphLength(g), reverse=True)longestGraph = graph[0] # find the longest edgeedges = longestGraph.getEdges()edges = sorted(edges, key=lambda edge: edge.getLength(), reverse=True)longestEdge = edges[0] </source> === Find peaks in a 3D image === <source lang="python"># @ImagePlus imp from fiji.plugin.trackmate.detection import DogDetectorfrom ij.gui import PointRoifrom ij.plugin.frame import RoiManagerfrom net.imglib2.img.display.imagej import ImageJFunctions # Set the parameters for DogDetectorimg = ImageJFunctions.wrap(imp)interval = imgcal = imp.getCalibration()calibration = [cal.pixelWidth, cal.pixelHeight, cal.pixelDepth]radius = 0.2 # the radius is half the diameterthreshold = 100doSubpixel = TruedoMedian = False # Setup spot detector# (see # public DogDetector(RandomAccessible<T> img,# Interval interval,# double[] calibration,# double radius,# double threshold,# boolean doSubPixelLocalization,# boolean doMedianFilter)detector = DogDetector(img, interval, calibration, radius, threshold, doSubpixel, doMedian) # Start processing and display the resultsif detector.process(): # Get the list of peaks found peaks = detector.getResult() print str(len(peaks)), "peaks were found."  # Add points to ROI manager rm = RoiManager.getInstance() if not rm: rm = RoiManager()  # Loop through all the peak that were found for peak in peaks: # Print the current coordinates print peak.getDoublePosition(0), peak.getDoublePosition(1), peak.getDoublePosition(2) # Add the current peak to the Roi manager proi = PointRoi(peak.getDoublePosition(0) / cal.pixelWidth, peak.getDoublePosition(1) / cal.pixelHeight) proi.setPosition(int(peak.getDoublePosition(2) / cal.pixelDepth)) rm.addRoi(proi)  # Show all ROIs on the image rm.runCommand(imp, "Show All") else: print "The detector could not process the data."</source> == Tips and Tricks == === Getting a list of all members in one package === You can use the Python function ''dir(<package>)'' to see the contents of a package: <source lang="python">import ijprint dir(ij)</source> '''Note:''' As of April 26nd, 2010, you need to start Fiji with  fiji -Dpython.cachedir.skip=false -- for ''dir(<package>)'' to work. === Specifying the encoding of the source === When your source code contains non-ASCII characters (such as umlauts), Jython will complain with a ''SyntaxError: Non-ASCII character in file '<iostream>', but no encoding declared''. You can fix this issue by putting the line  # -*- coding: iso-8859-15 -*- as first line into your source code (or if it starts with ''#!/usr/bin/python'', as second line), as suggested [ here]. You might need to replace the string ''iso-8859-15'' by something like ''utf-8'' if your source code is encoded in UTF-8. === Changing the default encoding === By default, Jython encodes the standard output (and other streams) with the ASCII encoding. Often, this is not what you want. You can change the default encoding like this: <source lang="python">from org.python.core import codecscodecs.setDefaultEncoding('utf-8')</source> === Error handling with try / except / finally === See complete documentation at: [ jython book chapter 6]. <source lang="python">x = 10y = 0 try: z = x / yexcept NameError, e1: print "A variable is not defined!", e1except ZeroDivisionError, e2: print "Dividing by zero doesn't make any sense! Error:", e2finally: print "This line will always print no matter what error occurs."</source> Which prints:  Dividing by zero doesn't make any sense! Error: integer division or modulo by zero This line will always print no matter what errors occurs To catch any kind of errors, use <i>sys.exc_info</i>: <source lang="python">import sys try: z = x / zexcept: print "Error: ", sys.exc_info()</source> Which prints:  Error: (<type 'exceptions.NameError'>, NameError("name 'x' is not defined",), <traceback object at 0x2>)  To ensure that you see the stack trace, print it to the ImageJ log window instead of stdout (whathever the latter may be): <source lang="python"> IJ.log(str(sys.exc_info()))</source> === Importing other ''.py'' scripts (modules) === If you want to import other python files, you need to ''import'' them. This requires that the files are found in the so-called ''search path'', a list of directories in which Jython looks for the modules (''.py'' files) to import. You can easily extend the search path: <source lang="python">from sys import pathfrom java.lang.System import getProperty # extend the search path by $FIJI_ROOT/bin/path.append(getProperty('fiji.dir') + '/bin') # Now you can import $FIJI_ROOT/bin/compat.pyimport compat</source> A situation you are likely to encounter is when you have multiple jython scripts in a folder under the fiji plugins folder. For example, suppose you have the folder ''my scripts'' under the fiji ''plugins'' folder, in which you have the script '''' with the following filter functions in it: <source lang="python"># Script plugins/my scripts/Filters.pyfrom ij import IJfrom ij.plugin import Duplicator def median(imp, radius): """ Apply a median filter to a copy of the given ImagePlus, and return it. """ copy = Duplicator().run(imp), "Median...", "radius=" + str(radius)) return copy def removeOutliers(imp, radius, threshold, bright): """ Apply a remove outliers filter to a copy of the given ImagePlus, and return it. """ copy = Duplicator().run(imp) which = "Bright" if bright else "Dark", "Remove Outliers...", "radius=" + str(radius) \ + " threshold=" + str(threshold) + " which=" + which) return copy</source> And now you have a second script in which you want to use a function from the '''' script: <source lang="python">from ij import IJimport sysfrom java.lang.System import getPropertysys.path.append(getProperty("fiji.dir") + "/plugins/my scripts")from Filters import median imp = IJ.getImage()medianFiltered = median(imp, 5.0)</source> === Defining a class and creating instances of the new class === A simple class to store an X,Y coordinate. (In real code, just use javax.vecmath.* classes such as Point3f, Point3d, etc.) The constructor is defined with <i>__init__</i>, and takes at least one argument , named <i>self</i> by convention (you may name it something else, like <i>this</i>). <source lang="python">from math import sqrt, pow class Point: def __init__(self, x, y): self.x = x self.y = y def distance(self, other): return sqrt(pow(self.x - other.x, 2), pow(self.y - other.y, 2))</source> ... and create two instances, and measure the distance between them. To create the new instances, we use the name of the class with the arguments in brackets: <source lang="python">p1 = Point(10, 20)p2 = Point(40, 55.3) print "Distance:", p1.distance(p2)</source> === Adding a static method to a class === A static method is a method of a class that doesn't need a <i>self</i> first argument. You may call this method by using the name of the class alone--you don't need to invoke it on an instance. To declare a method as static, decorate it with <i>@staticmethod</i>, as shown below for method <i>two</i>: <source lang="python">class Numbers:  def one(self): return 1  @staticmethod def two(): return 2</source> Now, to invoke these methods, notice how <i>two</i> doesn't need to be invoked on an instance (we merely prepend the class name), but <i>one</i> does: <source lang="python">print Numbers.two() that = Numbers()print</source> Why would you want to use a static method? It is useful to keep the namespace tidy, to avoid name collisions. === Creating multi-dimensional native java arrays === Suppose you want to create a one-dimensional double array, the equivalent of '''double[]''' in java. This is what you would do: <source lang="python">from jarray import array data = [1.0, 2.0, 3.0, 4.0] arr = array(data, 'd')</source> Other accepted primitive array types are: z boolean c char b byte h short i int l long f float d double But now suppose you want a two-dimensional double array, the equivalent of '''double[][]''' in java. How to do that? Here's how: <source lang="python">from jarray import array data = [[1.0, 2.0], [3.0, 4.0]]twoDimArr = array(data, Class.forName('[D'))</source> Essentially, what we did is to give the function '''array''' the argument '''class of a one-dimensional double array''', so that it will create an array of that--hence a two-dimensional double array. For a three-dimensional array in jython, you'd just add another '''[''' (square bracket) to the class name: <source lang="python">from jarray import array data = [[[1, 2, 3], [4, 5, 6]], [[1, 2, 3], [4, 5, 6]]]threeDimArr = array(data, Class.forName('[[D'))</source> See the [ jarray documentation]. To create primitive arrays of any class, pass along the class itself. For example, a native array of '''String''': <source lang="python">from jarray import array texts = ["one", "two", "three"] strings = array(texts, String)</source> Of course arrays can also be created empty. For numbers, all values will be zero. For an arbitrary class such as '''String''', all values will be null (or None, in python parlance). In the example below, we create an empty two-dimensional array of '''double[N][]''' type, where the smaller, inner arrays are null (just like in java a '''new double[5][]''' would have the second-order also all null): <source lang="python">from jarray import zeros twoDimArr = zeros(5, Class.forName("[D")) print twoDimArr# prints: array([D, [None, None, None, None, None]) # fill each slot with a new array of length 3:for i in range(len(twoDimArr)): twoDimArr[i] = zeros(3, 'd') print twoDimArr#prints: array([D, [array('d', [0.0, 0.0, 0.0]), array('d', [0.0, 0.0, 0.0]),# array('d', [0.0, 0.0, 0.0]), array('d', [0.0, 0.0, 0.0]), array('d', [0.0, 0.0, 0.0])])</source>  === Inline java code inside jython: the Weaver === Jython is great at doing high-level operations on images. But sometimes one wants to edit pixels specifically. Such low-level loops in jython are far from the performance offered by java. But writing a special-purpose java class for a minor piece of code is painful and requires specific java skills regarding code compilation and classpath management. The weaver removes all the pain. Here is an example, where the <i>float[]</i> pixels array of the current image is iterated to compute the mean intensity: <source lang="python">from fiji.scripting import Weaverfrom ij import IJfrom java.lang import Double # The currently open imageimp = IJ.getImage() fp = imp.getProcessor().convertToFloat()pixels = fp.getPixels() # a float array, float[]w = Weaver.inline( """ double sum = 0; for (int i=0; i<pixels.length; i++) { sum += pixels[i]; } return sum / pixels.length; """, {"pixels" : pixels}, Double) mean = print mean</source> The above is trivial and it is meant only as an example (there are better ways to get the mean value, such as via <i>imp.getStatistics()</i>. Notice that the <i>Weaver.inline</i> function takes three arguments: the java code to inline, the map of bindings, and the return type. In the example, we pass only the <i>float[]</i> pixels array, and define <i>Double</i> as the return type. The return type is optional. Internally, bindings are represented as fields in a java class, set as either primitives (like double, int ...) or the least general public class or superclass of the object to bind. There is a fourth optional argument for <i>inline</i> (boolean) to show the generated java code in a tab of the Script Editor. A better example that exploits the capabilities of the Weaver is the following: compile the function once, and then call it over and over with different parameters. The bindings cannot be changed, but if they are arrays or collections, one can change the elements of these collections. For example, to obtain a new ImageStack that is the result of applying XOR to each consecutive pair of slices (which will give you the boundaries of objects): <source lang="python">from fiji.scripting import Weaver # The currently open image, an 8-bit stackimp = IJ.openImage("") slices = [None, None] w = Weaver.inline( """ byte[] pix1 = (byte[]) slices.get(0); byte[] pix2 = (byte[]) slices.get(1);  byte[] xor = new byte[pix1.length]; for (int i=0; i<pix1.length; i++) { xor[i] = (byte)(pix1[i] ^ pix2[i]); } return xor; """, {"slices" : slices}) stack = imp.getStack()stackXOR = ImageStack(stack.width, stack.height) for i in range(2, imp.getNSlices()+1): # Put the pixel arrays into the pre-made list slices[0] = stack.getPixels(i-1) slices[1] = stack.getPixels(i) # Invoke native code stackXOR.addSlice( str(i-1), ) ImagePlus("XORed stack", stackXOR).show()</source> Of course the Weaver is a java library, and may be used from any scripting language such as [[Javascript Scripting|Javascript]], [[JRuby Scripting|JRuby]], and [[:Category:Scripting|others]]. All the above is inspired by the [ Scientific Python Weaver, or scipy Weaver], which inlines C code inside a python file. === Reading command line arguments given to a script === The Fiji launcher can execute scripts. When running scripts from the command line with the launcher, it is convenient to read out the arguments given to the script. For example, suppose you create a script to open an image file and do some processing with it, and you want to read the name of the file to open from the command line argument. Here is how: <source lang="python">import os, sysfrom ij import IJ # Expecting one argument: the file pathif len(sys.argv) < 2: print "Usage: ./fiji-linux64 <script-name> <file-path>" sys.exit(1) filepath = sys.argv[1] # Check if the file existsif not os.path.exists(filepath): print "File does not exist at path:", filepath sys.exit(1) # Open the imageimp = IJ.openImage(filepath)print "Processing:", imp.title # Do some processing ... </source> IMPORTANT: notice that, when executing scripts from the command line, there is no auto-importing of common imports. So above we <b>must</b> declare "from ij import IJ" to import the namespace <i>IJ</i> with all the static utility functions such as <i>openImage</i>. === Catching errors from a running macro === ImageJ exits with zero even when it fails (see [ bug report]). A possible fix is to convert the macro into a plugin but a quicker fix, is to wrap the macro call into a script. For this purpose, it is enough to check the returned string of <code>runMacroCode</code>, which will return the string <code>[aborted]</code> in case of [,%20java.lang.String%29 failure]: <source lang="python">from ij import IJimport sys if not len (sys.argv) > 1: raise TypeError ("No macro file argument") status = IJ.runMacroFile(sys.argv[1])if status == '[aborted]': raise StandardError ("Macro execution failed") sys.exit (0)</source> Of course, if your macro happens to return <code>[aborted]</code> for success, you're out of luck ;) === Running 3rd party java libraries === It is possible to run external java programs within Jython. To make them available, just copy the corresponding jar file into Fiji's plugins folder. To import the respective java classes, just do <source lang="python">import as foo</source>  If the class names of the external package are unknown, one possibility is to inspect the jar file manually. On Linux and Mac OS systems just do on the command line <source> jar tvf <library>.jar  </source> This will print the jar contents as plain text, look for entries ending with ".class". For the implementation of json in jython, provided at, the output looks like: <source> jar tvf jyson-1.0.2.jar 0 Sat Mar 17 14:06:40 CET 2012 META-INF/ 106 Sat Mar 17 14:06:38 CET 2012 META-INF/MANIFEST.MF 0 Sat Mar 17 14:06:40 CET 2012 com/ 0 Sat Mar 17 14:06:40 CET 2012 com/xhaus/ 0 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/ 174 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JSONDecodeError.class 174 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JSONEncodeError.class 162 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JSONError.class 1650 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JysonCodec.class 6350 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JysonDecoder.class 3899 Sat Mar 17 14:06:40 CET 2012 com/xhaus/jyson/JysonEncoder.class</source> The JysonCodec.class is the toplevel class, so to import this library include the following line in your jython script: <source lang="python">import com.xhaus.jyson.JysonCodec as jyson</source> [[Category:Scripting]][[Category:Jython]] == Jython for plugins == === Using a jython script as a plugin === The simplest way is to place the jython script file into fiji/plugins/ folder or a subfolder, and it will appear in the menus after running "'{{bc | Plugins | Scripting | Refresh Jython Scripts}}'" or "'{{bc | Help | Refresh Menus}}'", or on restarting Fiji. If you want to have the Jython script show up in a place outside the Plugins menu, just put the file into an appropriate subdirectory of fiji/plugins/Scripts/; for example, if you put a Jython script called into fiji/plugins/Scripts/File/New/, it will be available as {{bc | File | New | Animation}}. === Distributing jython scripts in a .jar file === PLEASE NOTE: there is no need to do the following -- unless you want to bundle a couple of scripts in one package. See entry above. The easiest way to distribute a (single) Jython script is to start the [[Script Editor]], open the Jython script and make the bundle with {{bc | File | Export as .jar}}. Alternatively -- or if you want to bundle multiple scripts -- you can do it the manual way: The whole idea is to be able to distribute an entire collection of scripts in a single .jar file, for best convenience. In this example, we create two jython scripts that we want to distribute in a .jar file as plugins: The <i></i> script: <source lang="python">IJ.log("Print this to the log window")</source> ... and the <i></i> script: <source lang="python">ip = ByteProcessor(400, 400)imp = ImagePlus("New", ip)ip.setRoi(OvalRoi(100, 100, 200, 200))ip.setValue(255)ip.fill(ip.getMask())</source> Place both scripts under a folder named <i>scripts/</i> . You will need a tiny .java file specifying a launcher PlugIn, such as: <source lang="java">package my;import ij.plugin.PlugIn;import Jython.Refresh_Jython_Scripts; public class Jython_Launcher implements PlugIn { public void run(String arg) { new Refresh_Jython_Scripts().runScript(getClass().getResourceAsStream(arg)); }}</source> Notice we place the above file under directory <i>my/</i>, packaged. To compile it:  $ javac -classpath .:ij.jar:../jars/fiji-scripting.jar:../plugins/Jython_Interpreter.jar my/  (check that the path to the three jars that you need is correct!)  Then we define the plugins.config file:  Plugins>My Scripts, "Print to log window", my.Jython_Launcher("/scripts/") Plugins>My Scripts, "Create image with a white circle", my.Jython_Launcher("/scripts/") Finally, we put all files in a .jar file:  $ jar cf my_jython_scripts.jar plugins.config my/Jython_Launcher.class scripts/*py Then, drop the jar file into fiji/plugins/ folder and run "Help - Update Menus", or restart fiji. Your scripts will appear under Plugins - My Scripts. For clarity, this is a summary of the files in the folder: my/ my/Jython_Launcher.class scripts/ scripts/ plugins.config  Notice, though, that <b>you don't need to do the .jar packaging at all</b>. Just place the python scripts directly under fiji/plugins/My Scripts/ and they will appear in the menus as regular plugins. = Jython examples in Fiji = *{{GitHub|repo=fiji|path=plugins/Examples/|label=Find Dimension of Raw Image}}*{{GitHub|repo=fiji|path=plugins/Examples/|label=Edit LUT As Text}}*{{GitHub|repo=fiji|path=plugins/Examples/|label=Delayed Snapshot}}*{{GitHub|repo=fiji|path=plugins/Examples/Command_Launchers/|label=Command Launcher GUI}}*{{GitHub|repo=fiji|path=plugins/Examples/|label=List all threads}}*{{GitHub|repo=fiji|path=plugins/Examples/|label=Chess}} *{{GitHub|repo=fiji|path=plugins/Examples/TrakEM2_Example_Scripts/|label=Extract stack under AreaList}} in TrakEM2.*{{GitHub|repo=fiji|path=plugins/Examples/TrakEM2_Example_Scripts/|label=Set all transforms to identity}} for TrakEM2 objects.*{{GitHub|repo=fiji|path=plugins/Examples/TrakEM2_Example_Scripts/|label=Select All}} objects in TrakEM2.*{{GitHub|repo=fiji|path=plugins/Examples/TrakEM2_Example_Scripts/|label=Measure AreaList}} in TrakEM2. = See also =*Albert Cardona's crash course in [ Jython scripting with Fiji]. *Jython for [[TrakEM2 Scripting]].