Mercurial > repos > gregor.m > spyboat
changeset 4:a4c6fcf2c456 draft
"planemo upload commit 0584e8878deaf91614c6bb3c0122975300132c25"
| author | gregor.m |
|---|---|
| date | Thu, 26 Nov 2020 16:40:47 +0000 |
| parents | 4d7f30a7e2f6 |
| children | d5a4180410c4 |
| files | OutputReport.html SpyBOAT.xml __pycache__/output_report.cpython-38.pyc amplitude_frame0.png amplitude_frame16.png amplitude_frame18.png amplitude_frame2.png amplitude_frame20.png amplitude_frame32.png amplitude_frame34.png amplitude_frame40.png amplitude_frame48.png amplitude_frame50.png amplitude_frame60.png amplitude_frame64.png amplitude_frame66.png amplitude_frame80.png amplitude_frame82.png amplitude_frame96.png amplitude_twosines_out.tif input_frame0.png input_frame16.png input_frame18.png input_frame2.png input_frame20.png input_frame32.png input_frame34.png input_frame40.png input_frame48.png input_frame50.png input_frame60.png input_frame64.png input_frame66.png input_frame80.png input_frame82.png input_frame96.png notes.md output_report.py period_distr.png period_frame0.png period_frame16.png period_frame18.png period_frame2.png period_frame20.png period_frame32.png period_frame34.png period_frame40.png period_frame48.png period_frame50.png period_frame60.png period_frame64.png period_frame66.png period_frame80.png period_frame82.png period_frame96.png period_twosines_out.tif phase_distr.png phase_frame0.png phase_frame16.png phase_frame18.png phase_frame2.png phase_frame20.png phase_frame32.png phase_frame34.png phase_frame40.png phase_frame48.png phase_frame50.png phase_frame60.png phase_frame64.png phase_frame66.png phase_frame80.png phase_frame82.png phase_frame96.png phase_twosines_out.tif power_distr.png power_twosines_out.tif preproc_two_sines.tif run_tests.sh spyboat_cli.py test-data/test-movie.tif |
| diffstat | 80 files changed, 130 insertions(+), 54 deletions(-) [+] |
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--- a/OutputReport.html Tue Nov 24 13:06:26 2020 +0000 +++ b/OutputReport.html Thu Nov 26 16:40:47 2020 +0000 @@ -1,5 +1,6 @@ <html> + <!-- this file got automatically created by 'output_report.py' --> <title>SpyBOAT Output Report</title> <head> <!-- that doesn't work with galaxy.. --> @@ -83,139 +84,162 @@ <!-- defines all elements of the "FrameSlides" class ---> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 2 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 20 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame2.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame20.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame2.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame20.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame2.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame20.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame2.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame20.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 18 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 29 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame18.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame29.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame18.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame29.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame18.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame29.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame18.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame29.png" alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> Frame Nr. 38 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> + <img src="input_frame38.png" alt="The Input" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> + <img src="phase_frame38.png" alt="Phase" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> + <img src="period_frame38.png" alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> + <img src="amplitude_frame38.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 34 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 47 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame34.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame47.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame34.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame47.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame34.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame47.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame34.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame47.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 50 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 56 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame50.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame56.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame50.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame56.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame50.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame56.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame50.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame56.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 66 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 65 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame66.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame65.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame66.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame65.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame66.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame65.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame66.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame65.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> <div class="FrameSlides"> - <h3 style="text-align:center; color=#363333"> Frame Nr. 82 </h3> + <h3 style="text-align:center; color=#363333"> Frame Nr. 74 </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> - <img src="input_frame82.png" alt="The Input" class="snapshot_gallery__img"> + <img src="input_frame74.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> - <img src="phase_frame82.png" alt="Phase" class="snapshot_gallery__img"> + <img src="phase_frame74.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> - <img src="period_frame82.png" alt="Period" class="snapshot_gallery__img"> + <img src="period_frame74.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> - <img src="amplitude_frame82.png" alt="Amplitude" class="snapshot_gallery__img"> + <img src="amplitude_frame74.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div>
--- a/SpyBOAT.xml Tue Nov 24 13:06:26 2020 +0000 +++ b/SpyBOAT.xml Thu Nov 26 16:40:47 2020 +0000 @@ -1,6 +1,11 @@ -<tool id="SpyBOAT" name="SpyBOAT" version="0.1.0"> +<tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@"> +<description>wavelet transforms image stacks</description> + <macros> + <token name="@TOOL_VERSION@">0.1.1</token> + </macros> + <requirements> - <requirement type="package" version="0.1.0">spyboat</requirement> + <requirement type="package" version="@TOOL_VERSION@">spyboat</requirement> </requirements> <version_command>python $__tool_directory__/spyboat_cli.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -47,10 +52,11 @@ --ncpu "\${GALAXY_SLOTS:-8}" > $log - ]]></command> + ]]></command> + <!-- "\${GALAXY_SLOTS:-8}" --> <inputs> - <param name="movie" type="data" format="tiff" label="Movie to process" - help="Select a movie to Wavelet process"/> + <param name="movie" type="data" format="tiff" label="Movie to analyze" + help="Select a movie to wavelet analyze"/> <!-- The following Wavelet parameters must have the same numerical type as defined in the @@ -74,6 +80,8 @@ <option value="create_static_mask">Create a static mask</option> <option value="create_dynamic_mask">Create a dynamic mask</option> </param> + <when value="no_masking"> + </when> <when value="create_static_mask"> <param name="mask_frame" type="integer" value="1" label="Create mask from frame" help="Creates a static mask from the chosen frame of the input movie."> @@ -95,12 +103,12 @@ <param name="dt" type="float" value="1" label="Sampling interval" help="Time span between two frames"> <validator type="in_range" min="0" max="9999999"/> </param> - <param name="tmin" type="float" value="2" label="Smallest period" help="Minimal period to scan for"> + <param name="tmin" type="float" value="20" label="Smallest period" help="Lowest period for the wavelet transform"> <validator type="in_range" min="0" max="9999999"/> </param> <param name="tmax" type="float" value="30" label="Largest period" - help="Maximal period to scan for"> + help="Largest period for the wavelet transform"> <validator type="in_range" min="0" max="9999999"/> </param> @@ -125,26 +133,31 @@ <option selected="true" value="No">No</option> <option value="Yes">Yes</option> </param> + <!-- there is an output filter picking up the choice --> + <when value="No"> + </when> + <when value="Yes"> + </when> </conditional> </inputs> <outputs> - <data name="phase_out" format="tiff" label="phase_${movie.name}"/> - <data name="period_out" format="tiff" label="period_${movie.name}"/> - <data name="power_out" format="tiff" label="power_${movie.name}"/> - <data name="amplitude_out" format="tiff" label="amplitude_${movie.name}"/> - <data name="preprocessed_out" format="tiff" label="preproc_${movie.name}"> + <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase"/> + <data name="period_out" format="tiff" label="${movie.name[:-4]}_period"/> + <data name="power_out" format="tiff" label="${movie.name[:-4]}_power"/> + <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude"/> + <data name="preprocessed_out" format="tiff" label="${movie.namee[:-4]}_preproc"> <filter>save_preprocessed['selection'] == 'Yes'</filter> </data> - <data name="log" format="txt" label="log_${movie.name}.txt"/> - <data format="html" name="html_out" label="Report_${movie.name}"/> + <data name="log" format="txt" label="log ${movie.name[:-4]}.txt"/> + <data format="html" name="html_out" label="Report ${movie.name[:-4]}"/> </outputs> <tests> <test> - <param name="movie" value="test_movie.tif" ftype="tiff"/> + <param name="movie" value="test-movie.tif" ftype="tiff"/> <output name="phase_out" file="phase_out.tif" ftype="tiff" compare="sim_size"/> <output name="period_out" file="period_out.tif" ftype="tiff" compare="sim_size"/> <output name="power_out" file="power_out.tif" ftype="tiff" compare="sim_size"/> @@ -220,5 +233,16 @@ advantage is that signal with strong amplitude trends will have more meaningful Wavelet powers after normalization. - ]]></help> + ]]></help> + <citations> + + <citation type="bibtex"> @article{monke2020optimal, + title={Optimal time frequency analysis for biological data-pyBOAT}, + author={M{\"o}nke, Gregor and Sorgenfrei, Frieda A and Schmal, Christoph and Granada, Adri{\'a}n E}, + journal={bioRxiv}, + year={2020}, + publisher={Cold Spring Harbor Laboratory} +} + </citation> + </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/notes.md Thu Nov 26 16:40:47 2020 +0000 @@ -0,0 +1,27 @@ +## Notes for setting up the SpyBOAT Galaxy tool + +### Toolshed(s) + +Register at: + +- https://testtoolshed.g2.bx.psu.edu/ +- https://toolshed.g2.bx.psu.edu/ + + +### commands + +First put toolshed account details into `.planemo.yml` + +- planemo lint [tool.xml] +- planemo shed_init --name spyboat +- planemo shed_create --shed_target testtoolshed +- planemo shed_update --shed_target toolshed + + +### Hosting repo + +- https://github.com/galaxyproject/tools-iuc + +#### Guidelines + +- https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html \ No newline at end of file
--- a/output_report.py Tue Nov 24 13:06:26 2020 +0000 +++ b/output_report.py Thu Nov 26 16:40:47 2020 +0000 @@ -48,7 +48,7 @@ ppl.close(fig) spyplot.period_snapshot(results['period'][frame], - Wkwargs, + Wkwargs['Tmin'],Wkwargs['Tmax'], time_unit = 'a.u.') fig = ppl.gcf() @@ -130,6 +130,7 @@ html_string =f''' <html> + <!-- this file got automatically created by 'output_report.py' --> <title>SpyBOAT Output Report</title> <head> <!-- that doesn't work with galaxy.. -->
--- a/run_tests.sh Tue Nov 24 13:06:26 2020 +0000 +++ b/run_tests.sh Thu Nov 26 16:40:47 2020 +0000 @@ -4,9 +4,8 @@ INPUT_PATH='./test-data/test-movie.tif' SCRIPT_PATH='.' -python3 $SCRIPT_PATH/spyboat_cli.py --input_path $INPUT_PATH --phase_out phase_twosines_out.tif --period_out period_twosines_out.tif --power_out power_twosines_out.tif --amplitude_out amplitude_twosines_out.tif --dt 1 --Tmin 2 --Tmax 30 --nT 200 --ncpu 6 --masking dynamic --preprocessed_out preproc_two_sines.tif --gauss_sigma 3 --rescale 80 --Tcutoff 40 --masking static --mask_frame 10 --mask_thresh 8 +python3 $SCRIPT_PATH/spyboat_cli.py --input_path $INPUT_PATH --phase_out phase_test-movie.tif --period_out period_test-movie.tif --power_out power_test-movie.tif --amplitude_out amplitude_test-movie.tif --dt 1 --Tmin 20 --Tmax 30 --nT 200 --ncpu 6 --masking dynamic --preprocessed_out preproc_two_sines.tif --gauss_sigma 2 --rescale 80 --Tcutoff 40 --masking static --mask_frame 10 --mask_thresh 300 printf "\n" # printf "\nError examples:\n" -# python3 $SCRIPT_PATH/cl_wrapper.py --input_path $INPUT_PATH --phase_out phase_twosines_out.tif --period_out period_twosines_out.tif --power_out power_twosines_out.tif --amplitude_out amplitude_twosines_out.tif --dt 2. --Tmin 20 --Tmax 30 --nT 200 --ncpu 6 --save_input True --masking fixed
--- a/spyboat_cli.py Tue Nov 24 13:06:26 2020 +0000 +++ b/spyboat_cli.py Thu Nov 26 16:40:47 2020 +0000 @@ -12,7 +12,7 @@ import output_report logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True) -logger = logging.getLogger('wrapper') +logger = logging.getLogger('spyboat-cli') # ----------command line parameters --------------- @@ -79,9 +79,10 @@ movie = spyboat.open_tif(arguments.input_path) except FileNotFoundError: logger.critical(f"Couldn't open {arguments.input_path}, check movie storage directory!") - sys.exit(1) - +# problems get logged in 'open_tif' +if movie is None: + sys.exit(1) # -------- Do (optional) spatial downsampling --------------------------- scale_factor = arguments.rescale @@ -162,8 +163,8 @@ logger.info(f'Creating report directory {arguments.report_img_path}') os.mkdir(arguments.report_img_path) - # make 6 times 4 snapshots each - Nsnap = 6 + # 4 snapshots each + Nsnap = 7 NFrames = movie.shape[0] # show only frames at least one Tmin # away from the edge (-effects)