# HG changeset patch # User gregor.m # Date 1606408847 0 # Node ID a4c6fcf2c456c26fc62b132aade42c73612dbef8 # Parent 4d7f30a7e2f6637596f3b24f38586e10aedfaf86 "planemo upload commit 0584e8878deaf91614c6bb3c0122975300132c25" diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 OutputReport.html --- 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 @@ + SpyBOAT Output Report @@ -83,139 +84,162 @@
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diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 SpyBOAT.xml --- 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 @@ - + +wavelet transforms image stacks + + 0.1.1 + + - spyboat + spyboat python $__tool_directory__/spyboat_cli.py --version $log - ]]> + ]]> + - + + + + + - - - - - + + + + + save_preprocessed['selection'] == 'Yes' - - + + - + @@ -220,5 +233,16 @@ advantage is that signal with strong amplitude trends will have more meaningful Wavelet powers after normalization. - ]]> + ]]> + + + @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} +} + + diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 __pycache__/output_report.cpython-38.pyc Binary file __pycache__/output_report.cpython-38.pyc has changed diff -r 4d7f30a7e2f6 -r 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https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html \ No newline at end of file diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 output_report.py --- 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''' + SpyBOAT Output Report diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 period_distr.png Binary file period_distr.png has changed diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 period_frame0.png Binary file period_frame0.png has changed diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 period_frame16.png Binary file period_frame16.png has changed diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 period_frame18.png Binary file period_frame18.png has changed diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 period_frame2.png Binary file period_frame2.png has changed diff -r 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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 diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 spyboat_cli.py --- 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) diff -r 4d7f30a7e2f6 -r a4c6fcf2c456 test-data/test-movie.tif Binary file test-data/test-movie.tif has changed