Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
comparison test-data/regenerate_outputs.sh @ 3:bdc70b34153a draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
| author | imgteam |
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| date | Wed, 25 Sep 2024 16:15:22 +0000 |
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| 2:4deffc9540a3 | 3:bdc70b34153a |
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| 1 source $(dirname $(dirname $(which conda)))/etc/profile.d/conda.sh | |
| 2 conda_env=mulled-v1-9e9e3735532d83dd44ff0f622055395263f964e81ca8113d4dfa7e133e3156bf | |
| 3 conda activate $conda_env | |
| 4 # Adjust threshold | |
| 5 # Test 1 | |
| 6 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Default' 'red' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_default.gif' 'gif' | |
| 7 # Test 2 | |
| 8 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Percentile' 'over_under' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_percentile.gif' 'gif' | |
| 9 # Test 3 | |
| 10 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Huang' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/blobs_threshold_huang_dark.gif' 'gif' | |
| 11 # Test 4 | |
| 12 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 8.0 255.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_8-255.gif' 'gif' | |
| 13 # Test 5 | |
| 14 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 8.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_0-8.gif' 'gif' | |
| 15 # Test 6 | |
| 16 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel.tif' 0.0 255.0 'Default' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'tiff' | |
| 17 | |
| 18 | |
| 19 # Analyze particles | |
| 20 # Test 1 | |
| 21 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Nothing' 'yes' 'no' 'no' '' '' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular' | |
| 22 # Test 2 | |
| 23 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_outlines.gif' 'gif' '' | |
| 24 # Test 3 | |
| 25 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Bare_Outlines' 'no' 'yes' 'yes' 'tools/image_processing/imagej2/test-data/analyze_particles_bareoutlines.gif' 'gif' '' | |
| 26 # Test 4 | |
| 27 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_overlaymasks.gif' 'gif' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular' | |
| 28 # Test 5 | |
| 29 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal_analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default_overlay_mask.tiff' 'tiff' 'tools/image_processing/imagej2/test-data/confocal_analyze_particles.tabular' | |
| 30 | |
| 31 # Skeleton | |
| 32 # Test 1 | |
| 33 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'no' 'none' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/basic.tabular' | |
| 34 # Test 2 | |
| 35 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'no' 'shortest_branch' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/shortest_branch_basic.tabular' | |
| 36 # Test 3 | |
| 37 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'no' 'none' 'no' 'yes' 'no' 'tools/image_processing/imagej2/test-data/largest_shortest_path_basic.tabular' | |
| 38 # Test 4 | |
| 39 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_skeleton_jython_script.py' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'no' 'shortest_branch' 'no' 'yes' 'no' 'tools/image_processing/imagej2/test-data/shortest_branch_all_yes.tabular' | |
| 40 | |
| 41 # binary_to_edm | |
| 42 # Test 1 | |
| 43 ImageJ --ij2 --headless --debug --jython '/home/ldelisle/Documents/mygit/galaxytools/tools/image_processing/imagej2/imagej2_binary_to_edm_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 1 1 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_edm.gif' 'gif' | |
| 44 # Test 2 | |
| 45 ImageJ --ij2 --headless --debug --jython '/home/ldelisle/Documents/mygit/galaxytools/tools/image_processing/imagej2/imagej2_binary_to_edm_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 10 3 'yes' 'yes' 'tools/image_processing/imagej2/test-data/blobs_black_edm.gif' 'gif' | |
| 46 | |
| 47 # bunwarpj_adapt_transform | |
| 48 # Test 1 | |
| 49 bunwarpj -adapt_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/adapted_transformation.txt' 2.0 | |
| 50 | |
| 51 # bunwarpj_align gets different outputs when the number of CPUS is contrainted. | |
| 52 # When galaxy uses docker, the CPUs are always constrainted. | |
| 53 # Currently the CPUS are fixed to 1 to ensure consistency. | |
| 54 # bunwarpj_align | |
| 55 # Outputs without CPU fixed: | |
| 56 # Test 1 | |
| 57 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1.png' 'tools/image_processing/imagej2/test-data/registered_target1.png' | |
| 58 # Test 2 | |
| 59 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1.png' 'tools/image_processing/imagej2/test-data/registered_target1.png' '-save_transformation' | |
| 60 mv 'tools/image_processing/imagej2/test-data/registered_source1_transf.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation_out_full.txt' | |
| 61 mv 'tools/image_processing/imagej2/test-data/registered_target1_transf.txt' 'tools/image_processing/imagej2/test-data/target_elastic_transformation_out_full.txt' | |
| 62 # Test 3 | |
| 63 bunwarpj -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/mask_white.png' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/mask_ramp.gif' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source2.png' 'tools/image_processing/imagej2/test-data/registered_target2.png' | |
| 64 | |
| 65 # Outputs with CPU fixed to 1: | |
| 66 # Test 1 | |
| 67 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu.png' | |
| 68 # Test 2 | |
| 69 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'NULL' 'tools/image_processing/imagej2/test-data/blobs.gif' 'NULL' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu.png' '-save_transformation' | |
| 70 mv 'tools/image_processing/imagej2/test-data/registered_source1_forced1cpu_transf.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation_forced1cpu_out_full.txt' | |
| 71 mv 'tools/image_processing/imagej2/test-data/registered_target1_forced1cpu_transf.txt' 'tools/image_processing/imagej2/test-data/target_elastic_transformation_forced1cpu_out_full.txt' | |
| 72 # Test 3 | |
| 73 bunwarpj -XX:ActiveProcessorCount="1" -align 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/mask_white.png' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/mask_ramp.gif' 0 2 1 0.0 0.0 1.0 10.0 'tools/image_processing/imagej2/test-data/registered_source2_forced1cpu.png' 'tools/image_processing/imagej2/test-data/registered_target2_forced1cpu.png' | |
| 74 | |
| 75 # bunwarpj_compare_elastic_raw | |
| 76 # Test 1 | |
| 77 bunwarpj -compare_elastic_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/warping_index_raw_full.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index_raw_full.txt' | |
| 78 | |
| 79 # bunwarpj_compare_elastic | |
| 80 bunwarpj -compare_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index.txt' | |
| 81 | |
| 82 # bunwarpj_compare_raw | |
| 83 # Test 1 | |
| 84 bunwarpj -compare_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index1_full.txt' | |
| 85 # Test 2 | |
| 86 bunwarpj -compare_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 2>&1 | tee 'output_log.txt' && grep -Po 'Warping index = \K[^ ]+' 'output_log.txt' > 'tools/image_processing/imagej2/test-data/warping_index2.txt' | |
| 87 | |
| 88 # bunwarpj_compose_elastic | |
| 89 bunwarpj -compose_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/raw_transformation_full.txt' | |
| 90 | |
| 91 # bunwarpj_compose_raw_elastic | |
| 92 bunwarpj -compose_raw_elastic 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/composed_raw_elastic_transformation_full.txt' | |
| 93 | |
| 94 # bunwarpj_compose_raw | |
| 95 bunwarpj -compose_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/target_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/composed_raw_transformation_full.txt' | |
| 96 | |
| 97 # bunwarpj_convert_to_raw | |
| 98 bunwarpj -convert_to_raw 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_elastic_transformation.txt' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' | |
| 99 | |
| 100 # bunwarpj_elastic_transform | |
| 101 bunwarpj -elastic_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_direct_transf.txt' 'tools/image_processing/imagej2/test-data/elastic_trans_registered_source1.png' | |
| 102 | |
| 103 # bunwarpj_raw_transform | |
| 104 bunwarpj -raw_transform 'tools/image_processing/imagej2/test-data/dotblot.jpg' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/source_raw_transformation.txt' 'tools/image_processing/imagej2/test-data/raw_trans_registered_source1.png' | |
| 105 | |
| 106 # Create image | |
| 107 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_create_image_jython_script.py' 'MyTitle' 256 256 1 '8-bit_ramp' 'tools/image_processing/imagej2/test-data/create_image1.jpg' | |
| 108 | |
| 109 # Crop | |
| 110 # Test 1 | |
| 111 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 0 0 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' | |
| 112 # Test 2 | |
| 113 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 50 0 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs_crop_width50.gif' 'gif' | |
| 114 # Test 3 | |
| 115 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0 0 50 0 1 0 1 0 1 0 'tools/image_processing/imagej2/test-data/blobs_crop_top50.gif' 'gif' | |
| 116 # Test 4 | |
| 117 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 1 1 0 1 0 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_cropped.tiff' 'tiff' | |
| 118 # Test 5 | |
| 119 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 0 1 1 1 0 'tools/image_processing/imagej2/test-data/confocal-series-both-channels_cropped_singleZ.tiff' 'tiff' | |
| 120 # Test 6 | |
| 121 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_crop_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-both-channels.tiff' 17 16 18 8 1 1 1 1 1 0 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_cropped_singleZ.tiff' 'tiff' | |
| 122 | |
| 123 # Enhance contrast | |
| 124 # Test 1 | |
| 125 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'None' 'no' 'tools/image_processing/imagej2/test-data/blobs_equalize.gif' 'gif' | |
| 126 # Test 2 | |
| 127 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 6.2 'no' 'tools/image_processing/imagej2/test-data/blobs_saturate.gif' 'gif' | |
| 128 # Test 3 | |
| 129 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_enhance_contrast_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 13.0 'yes' 'tools/image_processing/imagej2/test-data/blobs_normalize.gif' 'gif' | |
| 130 | |
| 131 # Filter | |
| 132 # Test 1 | |
| 133 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'gaussian_blur' 5.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/gaussian_blur.gif' | |
| 134 # Test 2 | |
| 135 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'median' 2.5 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/median.gif' | |
| 136 # Test 3 | |
| 137 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'unsharp_mask' 5.0 0.1 'None' 'None' 'tools/image_processing/imagej2/test-data/unsharp_mask.gif' | |
| 138 # Test 4 | |
| 139 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'top_hat' 7.0 'None' 'light' 'dont' 'tools/image_processing/imagej2/test-data/top_hat.gif' | |
| 140 # Test 5 | |
| 141 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'top_hat' 7.0 'None' '' '' 'tools/image_processing/imagej2/test-data/top_hat2.gif' | |
| 142 # Test 6 | |
| 143 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_filter_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel.tif' 'tiff' 'gaussian_blur' 2.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_gaussian_blur.tiff' | |
| 144 | |
| 145 # Find edges | |
| 146 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_edges_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_find_edges.gif' 'gif' | |
| 147 | |
| 148 # Find maxima | |
| 149 # Test 1 | |
| 150 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'Single_Points' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_single_points.gif' 'gif' | |
| 151 # Test 2 | |
| 152 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 13 'Maxima_Within_Tolerance' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_tolerance.gif' 'gif' | |
| 153 # Test 3 | |
| 154 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 16 'Segmented_Particles' 'yes' 'no' 'tools/image_processing/imagej2/test-data/blobs_segmented.gif' 'gif' | |
| 155 # Test 4 | |
| 156 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'List' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_list.tabular' 'tabular' | |
| 157 # Test 5 | |
| 158 # ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_find_maxima_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'yes' 'no' 10 'Count' 'no' 'no' 'tools/image_processing/imagej2/test-data/blobs_count.tabular' 'tabular' | |
| 159 | |
| 160 # make binary | |
| 161 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_make_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/clown.jpg' 1 1 'no' 'no' 'tools/image_processing/imagej2/test-data/clown_binary.jpg' 'jpg' | |
| 162 | |
| 163 # Math | |
| 164 # Test 1 | |
| 165 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Multiply' 'None' 'None' 1.25 'tools/image_processing/imagej2/test-data/blobs_multiply.gif' 'gif' | |
| 166 # Test 2 | |
| 167 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Min' 'None' 'None' 255.0 'tools/image_processing/imagej2/test-data/blobs_min.gif' 'gif' | |
| 168 # Test 3 | |
| 169 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Log' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_log.gif' 'gif' | |
| 170 # Test 4 | |
| 171 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Square' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_square.gif' 'gif' | |
| 172 # Test 5 | |
| 173 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Macro' 'v=v+50*sin(d/17)' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_macro.gif' 'gif' | |
| 174 | |
| 175 # Noise | |
| 176 # Test 1 | |
| 177 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'add_specified_noise' 5.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/add_specified_noise.gif' | |
| 178 # Test 2 | |
| 179 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'despeckle' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/despeckle.gif' | |
| 180 # Test 3 | |
| 181 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_outliers' 'None' '10.0' '1' 'Bright' 'tools/image_processing/imagej2/test-data/remove_outliers.gif' | |
| 182 # Test 4 fails | |
| 183 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_nans' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/remove_nans.gif' | |
| 184 | |
| 185 # Shadows | |
| 186 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_shadows_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Northwest' 'tools/image_processing/imagej2/test-data/blobs_northwest.gif' 'gif' | |
| 187 | |
| 188 # Sharpen | |
| 189 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_sharpen_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_sharpen.gif' 'gif' | |
| 190 | |
| 191 # Skeletonized 3D | |
| 192 # Test 1 | |
| 193 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'gif' | |
| 194 # Test 2 | |
| 195 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/clown.jpg' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'jpg' | |
| 196 | |
| 197 # Smooth | |
| 198 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_smooth_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_smooth.gif' 'gif' | |
| 199 | |
| 200 # Watershed | |
| 201 # Test 1 | |
| 202 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/blobs_watershed_binary.gif' 'gif' | |
| 203 # Test 2 | |
| 204 ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_default_threshold_watershed.tiff' 'tiff' |