Below is a way to use StreamAPI, by introducing Jython classes implementing the Consumer interface. Stream-related syntax introduced from Java8 is useful for writing clear codes, but cannot be directly used in Jython. #allimp = ccc.concatenateHyperstacks(jaimp, newname, False)ĪtDimensions(dimA, dimA, len(GRlist)) Newname = basename + '_R' + repetition + '_B' + block + '_L' + location + '.' + extension Imp = Opener.openUsingBioFormats(os.path.join(srcDir, thisfile)) Thisfile = basename + '_R' + repetition + '_GR' + timepoint + '_B' + block + '_L' + location + '.' + extension Srcpath = IJ.getFilePath('Choose the first file') This is an expaple of using regular expression to match file names, and to collect images as a ImagePlus array then convert it to a Hyperstack. # open the file first (if its not there, newly created)Īccessing multiple files to load image sequences # prepare test data to wirte to a csv file … a bit more realistic, writing numerical data. If you need to use the array for some other purpose in Java classes, python array must be converted.į = open('/Users/miura/Desktop/eggs2.csv', 'wb') This example is very simple since it does not use Java array at all. … or purely in pythonic way using csv module. Writer = CSVWriter(FileWriter("/Users/miura/Desktop/eggs1.csv"), ',') This could be rewritten in a bit more simple way using jarray module. #String entries = "first#second#third".split("#") Writer = CSVWriter(FileWriter("c:/temp/testcsv.csv"), ',')ĭata = Array.newInstance(Class.forName(""), 3) Uses opencsv library, which is preinstalled in Fiji. # Fullpath without ext: /Users/miura/tmp/data Print "Fullpath without ext: ", pathWOext PathWOext = FilenameUtils.removeExtension(srcpath) See Javadoc for many other convenient methods.įrom import FilenameUtilsīaseName = FilenameUtils.getBaseName(srcpath)Įxt = FilenameUtils.getExtension(srcpath)įilename = FilenameUtils.getName(srcpath) Imgpath = 'Z:\\20_23h_firstSample\\20h_shifted.tif'įiji comes with ApacheIO library, and can be used quite conveniently for disintegrating file paths. Print os.path.splitext(filename) #prints /Users/miura/tmp/dataĪlternatively, one could use File class in Java. # but if you specifically want to use path separator of the os #above is enough to join directory and file name, Print os.path.join(parentdirectory, filename) #prints same as srcpath Print parentdirectory #prints /Users/miura/tmp Parentdirectory = os.path.dirname(srcpath) To extract file name and file name without extension, Same processing could be also done by replacing L7 to L23 by Imp.getProcessor().setPixels(jreplaced_signedpix) Jreplaced_signedpix = jarray.array(replaced_signedpix, 'b') Replaced_signedpix = map(lambda p: (p - 256) if p > 127 else p, replaced_unsignedpix) # convert signed pixel values to unsigned. Replaced_unsignedpix = map(lambda p: p if (p 50) else 0, unsignedpix) # replace pixels with value more than 50 and less than 200 to 0. Unsignedpix = map(lambda p: p & 0xff, signedpix) # converting signed pixel values to unsigned using bitwise operation. Signedpix = imp.getProcessor().getPixels() # ImageProcessor.getPixels() returns an array of signed pixel values The scripts load “blobs.gif” example image from NIH server, then replaces pixels with values between 50 and 200 to 0. Here is another example of going back and forth between signed and unsigned values. The Jython book "The Definitive Guide to Jython": it's saying that the book is a version from 2009, but the latest commit is in Oct. Examples below show how they are actually used in Jython scripts, to save our time for reading the source code of each. This is because the style how each algorithm is implemented is not consistent (they are written by 1000 different people!) so it takes a while to figure out how to use them when we are writing a bioimage analysis workflow. This page is like a cookbook: there are no details about how to do programming, but more centered on how to use Classes built in ImageJ and its plugins. Recently, there is a very good tutorial page for real beginners: here (UVA Research Computing Learning Portal). The former is in a tutorial style so if you want to learn how to do scripting using Jython, that's the place where you go. For learning image processing using Fiji and Jython scripting, go to excellent tutorials written by Albert Cardona, such as here in his website or here in.
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