annotate imagej2_noise_jython_script.py @ 1:29a4d422f32a draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:41:15 +0000
parents f1ba33cd9edf
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 import sys
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29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 from ij import IJ
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 # Fiji Jython interpreter implements Python 2.5 which does not
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6 # provide support for argparse.
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7 error_log = sys.argv[-19]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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8 input_file = sys.argv[-18]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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9 image_datatype = sys.argv[-17]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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10 noise = sys.argv[-16]
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11 standard_deviation = sys.argv[-15]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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12 radius = sys.argv[-14]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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13 threshold = sys.argv[-13]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 which_outliers = sys.argv[-12]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 randomj = sys.argv[-11]
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16 trials = sys.argv[-10]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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17 probability = sys.argv[-9]
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18 # Note the spelling - so things don't get confused due to Python lambda function.
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19 lammbda = sys.argv[-8]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 order = sys.argv[-7]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 mean = sys.argv[-6]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 sigma = sys.argv[-5]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 min = sys.argv[-4]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 max = sys.argv[-3]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 insertion = sys.argv[-2]
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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26 tmp_output_path = sys.argv[-1]
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 # Open the input image file.
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29 image_plus = IJ.openImage(input_file)
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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30 bit_depth = image_plus.getBitDepth()
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 image_type = image_plus.getType()
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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32 # Create an ImagePlus object for the image.
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 image_plus_copy = image_plus.duplicate()
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 # Make a copy of the image.
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35 image_processor_copy = image_plus_copy.getProcessor()
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 # Perform the analysis on the ImagePlus object.
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 if noise == 'add_noise':
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29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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39 IJ.run(image_plus_copy, "Add Noise", "")
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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40 elif noise == 'add_specified_noise':
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41 IJ.run(image_plus_copy, "Add Specified Noise", "standard=&standard_deviation")
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 elif noise == 'salt_and_pepper':
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43 IJ.run(image_plus_copy, "Salt and Pepper", "")
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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44 elif noise == 'despeckle':
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45 IJ.run(image_plus_copy, "Despeckle", "")
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46 elif noise == 'remove_outliers':
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47 IJ.run(image_plus_copy, "Remove Outliers", "radius=&radius threshold=&threshold which=&which_outliers")
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48 elif noise == 'remove_nans':
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49 IJ.run(image_plus_copy, "Remove NaNs", "")
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50 elif noise == 'rof_denoise':
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51 IJ.run(image_plus_copy, "ROF Denoise", "")
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52 elif noise == 'randomj':
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53 if randomj == 'randomj_binomial':
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54 IJ.run(image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion")
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55 elif randomj == 'randomj_exponential':
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56 IJ.run(image_plus_copy, "RandomJ Exponential", "lambda=&lammbda insertion=&insertion")
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57 elif randomj == 'randomj_gamma':
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58 IJ.run(image_plus_copy, "RandomJ Gamma", "order=&order insertion=&insertion")
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59 elif randomj == 'randomj_gaussian':
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60 IJ.run(image_plus_copy, "RandomJ Gaussian", "mean=&mean sigma=&sigma insertion=&insertion")
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61 elif randomj == 'randomj_poisson':
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62 IJ.run(image_plus_copy, "RandomJ Poisson", "mean=&mean insertion=&insertion")
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63 elif randomj == 'randomj_uniform':
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64 IJ.run(image_plus_copy, "RandomJ Uniform", "min=&min max=&max insertion=&insertion")
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65
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66 # Save the ImagePlus object as a new image.
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67 IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path)