# HG changeset patch
# User gregor.m
# Date 1606138307 0
# Node ID 1d62de03829da13d8906ea3311f5513d77e37e1e
"planemo upload commit c6cd06d44dce1eef9136017289d362f144687dc1"
diff -r 000000000000 -r 1d62de03829d README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Nov 23 13:31:47 2020 +0000
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+# Galaxy Wrapper for WaveletMovies
+
+To test the wrapper use `planemo`:
+
+```bash
+# install
+conda install planemo
+
+# run the test(s)
+planemo test
+
+# run a local galaxy instance with the tool installed
+planemo serve
+
+```
diff -r 000000000000 -r 1d62de03829d SpyBOAT.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SpyBOAT.xml Mon Nov 23 13:31:47 2020 +0000
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+
+
+ spyboat
+
+ python $__tool_directory__/cl_wrapper.py --version
+ $log
+
+ ]]>
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+ save_preprocessed['selection'] == 'Yes'
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diff -r 000000000000 -r 1d62de03829d __pycache__/output_report.cpython-38.pyc
Binary file __pycache__/output_report.cpython-38.pyc has changed
diff -r 000000000000 -r 1d62de03829d cl_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cl_wrapper.py Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+
+## Gets interfaced by Galaxy or bash scripting
+import argparse
+import sys, os
+import logging
+
+from skimage import io
+from numpy import float32
+
+import spyboat
+import output_report
+
+logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
+logger = logging.getLogger('wrapper')
+
+# ----------command line parameters ---------------
+
+parser = argparse.ArgumentParser(description='Process some arguments.')
+
+# I/O
+parser.add_argument('--input_path', help="Input movie location", required=True)
+parser.add_argument('--phase_out', help='Phase output file name', required=True)
+parser.add_argument('--period_out', help='Period output file name', required=True)
+parser.add_argument('--power_out', help='Power output file name', required=True)
+parser.add_argument('--amplitude_out', help='Amplitude output file name', required=True)
+parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name, 'None'", required=False)
+
+
+# (Optional) Multiprocessing
+
+parser.add_argument('--ncpu', help='Number of processors to use',
+ required=False, type=int, default=1)
+
+# Optional spatial downsampling
+parser.add_argument('--rescale', help='Rescale the image by a factor given in %%, None means no rescaling',
+ required=False, type=int)
+# Optional Gaussian smoothing
+parser.add_argument('--gauss_sigma', help='Gaussian smoothing parameter, None means no smoothing', required=False, type=float)
+
+# Wavelet Analysis Parameters
+parser.add_argument('--dt', help='Sampling interval', required=True, type=float)
+parser.add_argument('--Tmin', help='Smallest period', required=True, type=float)
+parser.add_argument('--Tmax', help='Biggest period', required=True, type=float)
+parser.add_argument('--nT', help='Number of periods to scan for', required=True, type=int)
+
+parser.add_argument('--Tcutoff', help='Sinc cut-off period, disables detrending if not set', required=False, type=float)
+parser.add_argument('--win_size', help='Sliding window size for amplitude normalization, None means no normalization',
+ required=False, type=float)
+
+# Optional masking
+parser.add_argument('--masking', help="Set to either 'dynamic', 'fixed' or 'None' which is the default", default='None', required=False, type=str)
+
+parser.add_argument('--mask_frame',
+ help="The frame of the input movie to create a fixed mask from, needs masking set to 'fixed'",
+ required=False, type=int)
+
+
+parser.add_argument('--mask_thresh', help='The threshold of the mask, all pixels with less than this value get masked (if masking enabled).',
+ required=False, type=float,
+ default=0)
+
+# output overview/snapshots
+parser.add_argument('--html_fname', help="Name of the html report.",
+ default='OutputReport.html', required=False, type=str)
+
+parser.add_argument('--report_img_path', help="For the html report, can be set in Galaxy. Defaults to cwd.", default='.', required=False, type=str)
+
+parser.add_argument('--version', action='version', version='0.0.1')
+
+arguments = parser.parse_args()
+
+logger.info("Received following arguments:")
+for arg in vars(arguments):
+ logger.info(f'{arg} -> {getattr(arguments, arg)}')
+
+# ------------Read the input----------------------------------------
+try:
+ 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)
+
+# -------- Do (optional) spatial downsampling ---------------------------
+
+scale_factor = arguments.rescale
+
+# defaults to None
+if not scale_factor:
+ logger.info('No downsampling requested..')
+
+elif 0 < scale_factor < 100:
+ logger.info(f'Downsampling the movie to {scale_factor:d}% of its original size..')
+ movie = spyboat.down_sample(movie, scale_factor / 100)
+else:
+ raise ValueError('Scale factor must be between 0 and 100!')
+
+# -------- Do (optional) pre-smoothing -------------------------
+# note that downsampling already is a smoothing operation..
+
+# check if pre-smoothing requested
+if not arguments.gauss_sigma:
+ logger.info('No pre-smoothing requested..')
+else:
+ logger.info(f'Pre-smoothing the movie with Gaussians, sigma = {arguments.gauss_sigma:.2f}..')
+
+ movie = spyboat.gaussian_blur(movie, arguments.gauss_sigma)
+
+# ----- Set up Masking before processing ----
+
+mask = None
+if arguments.masking == 'fixed':
+ if not arguments.mask_frame:
+ logger.critical("Frame number for fixed masking is missing!")
+ sys.exit(1)
+
+ if (arguments.mask_frame > movie.shape[0]) or (arguments.mask_frame < 0):
+ logger.critical(f'Requested frame does not exist, input only has {movie.shape[0]} frames.. exiting')
+ sys.exit(1)
+
+ else:
+ logger.info(f'Creating fixed mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}')
+ mask = spyboat.create_fixed_mask(movie, arguments.mask_frame,
+ arguments.mask_thresh)
+elif arguments.masking == 'dynamic':
+ logger.info(f'Creating dynamic mask with threshold {arguments.mask_thresh}')
+ mask = spyboat.create_dynamic_mask(movie, arguments.mask_thresh)
+
+else:
+ logger.info('No masking requested..')
+
+# ------ Retrieve wavelet parameters ---------------------------
+
+Wkwargs = {'dt': arguments.dt,
+ 'Tmin': arguments.Tmin,
+ 'Tmax': arguments.Tmax,
+ 'nT': arguments.nT,
+ 'T_c' : arguments.Tcutoff, # defaults to None
+ 'win_size' : arguments.win_size # defaults to None
+}
+
+# start parallel processing
+results = spyboat.run_parallel(movie, arguments.ncpu, **Wkwargs)
+
+# --- masking? ---
+
+if mask is not None:
+ # mask all output movies (in place!)
+ for key in results:
+ logger.info(f'Masking {key}')
+ spyboat.apply_mask(results[key], mask, fill_value=-1)
+
+# --- Produce Output Report Figures/png's ---
+
+# create the directory, yes we have to do that ourselves :)
+# galaxy then magically renders the html from that
+try:
+
+ if arguments.report_img_path != '.':
+ logger.info(f'Creating report directory {arguments.report_img_path}')
+ os.mkdir(arguments.report_img_path)
+
+ # jump to the middle of the movie
+ snapshot_frame = int(movie.shape[0]/2)
+ output_report.produce_snapshots(movie, results, snapshot_frame, Wkwargs, img_path=arguments.report_img_path)
+
+ output_report.produce_distr_plots(results, Wkwargs, img_path=arguments.report_img_path)
+
+ output_report.create_html(snapshot_frame, arguments.html_fname)
+
+
+except FileExistsError as e:
+ logger.critical(f"Could not create html report directory: {repr(e)}")
+
+
+# --- save out result movies ---
+
+# save phase movie
+io.imsave(arguments.phase_out, results['phase'], plugin="tifffile")
+logger.info(f'Written {arguments.phase_out}')
+# save period movie
+io.imsave(arguments.period_out, results['period'], plugin="tifffile")
+logger.info(f'Written {arguments.period_out}')
+# save power movie
+io.imsave(arguments.power_out, results['power'], plugin="tifffile")
+logger.info(f'Written {arguments.power_out}')
+# save amplitude movie
+io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile")
+logger.info(f'Written {arguments.amplitude_out}')
+
+# save out the probably pre-processed (scaled and blurred) input movie for
+# direct comparison to results and coordinate mapping etc.
+if arguments.preprocessed_out:
+ io.imsave(arguments.preprocessed_out, movie, plugin='tifffile')
+ logger.info(f'Written {arguments.preprocessed_out}')
diff -r 000000000000 -r 1d62de03829d output_report.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output_report.py Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,199 @@
+''' Produces plots and a summary html 'headless' '''
+
+import os
+import matplotlib
+# headless plotting and disable latex
+matplotlib.use('Agg')
+matplotlib.rcParams['text.usetex'] = False
+import matplotlib.pyplot as ppl
+
+import logging
+
+import spyboat.plotting as spyplot
+
+logger = logging.getLogger(__name__)
+
+# figure resolution
+DPI=250
+
+def produce_snapshots(input_movie, results, frame, Wkwargs,
+ img_path='.'):
+
+ '''
+ Takes the *input_movie* and the
+ *results* dictionary from spyboat.processing.run_parallel
+ and produces phase, period and amplitude snapshot png's.
+
+ For the period snapshot also the period range is needed,
+ hence the analysis dictionary 'Wkwargs' also gets passed.
+
+ The output files name pattern is:
+ [input, phase, period, amplitude]_frame{frame}.png
+ and the storage location in *img_path*.
+
+ These get picked up by 'create_html'
+ '''
+
+
+ spyplot.input_snapshot(input_movie[frame])
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'input_frame{frame}.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ spyplot.phase_snapshot(results['phase'][frame])
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'phase_frame{frame}.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ spyplot.period_snapshot(results['period'][frame],
+ Wkwargs,
+ time_unit = 'a.u.')
+
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'period_frame{frame}.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ spyplot.amplitude_snapshot(results['amplitude'][frame])
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'amplitude_frame{frame}.png')
+ fig.savefig(out_path, dpi=DPI)
+
+
+ logger.info(f'Produced 4 snapshots for frame {frame}..')
+
+def produce_distr_plots(results, Wkwargs, img_path='.'):
+
+ '''
+ Output file names are:
+
+ period_distr.png, power_distr.png and phase_distr.png
+ '''
+
+ spyplot.period_distr_dynamics(results['period'], Wkwargs)
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'period_distr.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ spyplot.power_distr_dynamics(results['power'], Wkwargs)
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'power_distr.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ spyplot.phase_coherence_dynamics(results['phase'], Wkwargs)
+ fig = ppl.gcf()
+ out_path = os.path.join(img_path, f'phase_distr.png')
+ fig.savefig(out_path, dpi=DPI)
+
+ logger.info(f'Produced 3 distribution plots..')
+
+
+def create_html(frame_num, html_fname='OutputReport.html'):
+
+ '''
+ The html generated assumes the respective png's (7 in total)
+ have been created with 'produce_snapshots' and 'produce_distr_plots'
+ and can be found at the cwd (that's how Galaxy works..)
+ '''
+
+ html_string =f'''
+
+ SpyBOAT Output Report
+
+
+
+
+
+
+ SpyBOAT Results Report
+
+
+
+ 
+
+
+
+ 
+
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+ 
+
+
+
Snapshots - Frame {frame_num}
+
+
+ 
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+