annotate test-data/regenerate_outputs.sh @ 3:91b8f4730a93 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:07:20 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
1 source $(dirname $(dirname $(which conda)))/etc/profile.d/conda.sh
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
2 conda_env=mulled-v1-9e9e3735532d83dd44ff0f622055395263f964e81ca8113d4dfa7e133e3156bf
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
3 conda activate $conda_env
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
4 # Adjust threshold
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
5 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
7 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
9 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
11 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
13 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
15 # Test 6
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
17
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
18
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
19 # Analyze particles
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
20 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
22 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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' ''
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
24 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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' ''
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
26 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
28 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
30
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
31 # Skeleton
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
32 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
34 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
36 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
38 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
40
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
41 # binary_to_edm
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
42 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
44 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
46
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
47 # bunwarpj_adapt_transform
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
48 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
50
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
51 # bunwarpj_align gets different outputs when the number of CPUS is contrainted.
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
52 # When galaxy uses docker, the CPUs are always constrainted.
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
53 # Currently the CPUS are fixed to 1 to ensure consistency.
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
54 # bunwarpj_align
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
55 # Outputs without CPU fixed:
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
56 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
58 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
60 mv 'tools/image_processing/imagej2/test-data/registered_source1_transf.txt' 'tools/image_processing/imagej2/test-data/source_elastic_transformation_out_full.txt'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
61 mv 'tools/image_processing/imagej2/test-data/registered_target1_transf.txt' 'tools/image_processing/imagej2/test-data/target_elastic_transformation_out_full.txt'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
62 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
64
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
65 # Outputs with CPU fixed to 1:
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
66 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
68 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
72 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
74
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
75 # bunwarpj_compare_elastic_raw
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
76 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
78
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
79 # bunwarpj_compare_elastic
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
81
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
82 # bunwarpj_compare_raw
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
83 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
85 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
87
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
88 # bunwarpj_compose_elastic
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
90
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
91 # bunwarpj_compose_raw_elastic
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
93
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
94 # bunwarpj_compose_raw
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
96
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
97 # bunwarpj_convert_to_raw
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
99
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
100 # bunwarpj_elastic_transform
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
102
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
103 # bunwarpj_raw_transform
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
105
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
106 # Create image
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
108
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
109 # Crop
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
110 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
112 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
114 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
116 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
118 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
120 # Test 6
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
122
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
123 # Enhance contrast
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
124 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
126 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
128 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
130
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
131 # Filter
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
132 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
134 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
136 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
138 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
140 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
142 # Test 6
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
144
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
145 # Find edges
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
147
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
148 # Find maxima
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
149 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
151 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
153 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
155 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
157 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
159
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
160 # make binary
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
162
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
163 # Math
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
164 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
166 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
168 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
170 # Test 4
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
172 # Test 5
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
174
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
175 # Noise
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
176 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
178 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
180 # Test 3
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
182 # Test 4 fails
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
184
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
185 # Shadows
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
187
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
188 # Sharpen
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
190
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
191 # Skeletonized 3D
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
192 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
194 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
196
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
197 # Smooth
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
199
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
200 # Watershed
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
201 # Test 1
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
203 # Test 2
91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
parents:
diff changeset
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'