Mercurial > repos > iuc > spyboat
changeset 0:76733d05d8ef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
| author | iuc |
|---|---|
| date | Sat, 28 Nov 2020 13:45:34 +0000 |
| parents | |
| children | 639d2031d998 |
| files | output_report.py run_tests.sh spyboat.xml spyboat_cli.py test-data/output1.html test-data/test-movie.tif |
| diffstat | 6 files changed, 1083 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output_report.py Sat Nov 28 13:45:34 2020 +0000 @@ -0,0 +1,253 @@ +""" Produces plots and a summary html 'headless' """ +import logging +import os + +import matplotlib +import matplotlib.pyplot as ppl +import spyboat.plotting as spyplot + +ppl.switch_backend('Agg') +matplotlib.rcParams["text.usetex"] = False +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) + ppl.close(fig) + + 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) + ppl.close(fig) + + spyplot.period_snapshot( + results["period"][frame], Wkwargs["Tmin"], + Wkwargs["Tmax"], 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) + ppl.close(fig) + + 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) + ppl.close(fig) + + 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, "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, "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, "phase_distr.png") + fig.savefig(out_path, dpi=DPI) + + logger.info("Produced 3 distribution plots..") + + +def create_html(frame_nums, html_fname="OutputReport.html"): + """ + The html generated assumes the respective png's + have been created with 'produce_snapshots' and 'produce_distr_plots' + and can be found at the cwd (that's how Galaxy works..) + """ + + # -- create a gallery for every frame in frame_nums -- + + galleries = "" + for frame_num in frame_nums: + new_gal = f""" + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. {frame_num} </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame{frame_num}.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame{frame_num}.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame{frame_num}.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame{frame_num}.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + """ + galleries += new_gal + + 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.. --> + <!--link rel="stylesheet" href="styles.css"--> + <style type="text/css"> + body{{ margin:10 100; background:whitesmoke; }} + /*body{{ margin:10 100; background:darkslategrey; }}*/ + .center{{ + text-align: center; + display: block; + margin-left: auto; + margin-right: auto; + width: 100%;}} + + /* matplotlib output at 1600x1200 */ + .distr_gallery {{ + display: grid; + margin: 0 auto; + text-align: center; + /* border: 1px dashed rgba(4, 4, 4, 0.35); */ + grid-template-columns: repeat(3,1fr); + grid-template-rows: 20vw; + grid-gap: 0px; + column-gap: 0px + }} + .distr_gallery__img {{ + width: 100%; + height: 100%; + object-fit: contain; + }} + + + /* matplotlib output at 1600x1200 */ + .snapshot_gallery {{ + display: grid; + margin: 0 auto; + border: 1px dashed rgba(4, 4, 4, 0.35); + text-align: center; + grid-template-columns: repeat(2,1fr); + grid-template-rows: repeat(2,20vw); + grid-gap: 5px; + }} + .snapshot_gallery__img {{ + width: 100%; + height: 100%; + object-fit: contain; + }} + .subheader{{ + text-align:center; + font-size: 160%; + color:#363333;}} + </style> + </head> + <body> + <h1 style="text-align:center; color:#363333">SpyBOAT Results Report</h1> + <hr style="width:50%"> + <h1 class="subheader"> Distribution Dynamics </h1> + <div class="distr_gallery"> + <figure class=”distr_gallery__item distr_gallery__item--1"> + <img src="period_distr.png" alt="Period" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--2"> + <img src="power_distr.png" alt="Power" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--3"> + <img src="phase_distr.png" alt="Phase" class="distr_gallery__img"> + </figure> + + </div> + + <h1 class="subheader"> Output Movie Snapshots </h1> + + <!-- trigger the javascript at the end---> + <div class="center"> + <button class="w3-button" onclick="plusDivs(-1)">❮ Prev</button> + <button class="w3-button" onclick="plusDivs(1)">Next ❯</button> + </div> + + <!-- defines all elements of the "FrameSlides" class ---> + {galleries} + </div> + + <!-- javascript with escaped '{{'---> + <script> + var slideIndex = 1; + showDivs(slideIndex); + + function plusDivs(n) {{ + showDivs(slideIndex += n); + }} + + function showDivs(n) {{ + var i; + var x = document.getElementsByClassName("FrameSlides"); + if (n > x.length) {{slideIndex = 1}} + if (n < 1) {{slideIndex = x.length}} ; + for (i = 0; i < x.length; i++) {{ + x[i].style.display = "none"; + }} + x[slideIndex-1].style.display = "block"; + }} + </script> + </body> + </html> + """ + + with open(html_fname, "w") as OUT: + OUT.write(html_string) + + logger.info("Created html report") + return html_string + +# for local testing +# create_html([0,20,40,60,80])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_tests.sh Sat Nov 28 13:45:34 2020 +0000 @@ -0,0 +1,15 @@ +#!/usr/bin/env bash + + +INPUT_PATH='./test-data/test-movie.tif' +SCRIPT_PATH='.' + +# set to galaxy defaults!! +python3 $SCRIPT_PATH/spyboat_cli.py --input_path $INPUT_PATH --phase_out phase_out.tif --period_out period_out.tif --dt 1 --Tmin 20 --Tmax 30 --nT 150 --ncpu 6 --Tcutoff 40 + +# additional paramters +#--masking static --mask_frame 10 --mask_thresh 300 --rescale 80 --gauss_sigma 1 + +printf "\n" +# printf "\nError examples:\n" +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spyboat.xml Sat Nov 28 13:45:34 2020 +0000 @@ -0,0 +1,264 @@ +<tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01" license="GPL-3.0-or-later"> +<description>wavelet transforms image stacks</description> + <macros> + <token name="@TOOL_VERSION@">0.1.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">spyboat</requirement> + </requirements> + <version_command>python '$__tool_directory__/spyboat_cli.py' --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ## needed for pulsar combat + cat '$__tool_directory__/output_report.py' > /dev/null && + ## run tool + python '$__tool_directory__/spyboat_cli.py' + --input_path '$movie' + #if str($PreProc.gauss_sigma): + --gauss_sigma $PreProc.gauss_sigma + #end if + #if str($PreProc.rescale_factor): + --rescale $PreProc.rescale_factor + #end if + + #if $masking.selection_mode == "create_static_mask": + --masking static + --mask_frame $masking.mask_frame + --mask_thresh $masking.mask_thresh + #else if $masking.selection_mode == "create_dynamic_mask": + --masking dynamic + --mask_thresh $masking.mask_thresh + #end if + + --dt $wavana.dt + --Tmin $wavana.tmin + --Tmax $wavana.tmax + --nT $wavana.nt + #if str($wavana.tcutoff) + --Tcutoff $wavana.tcutoff + #end if + #if str($wavana.win_size): + --win_size $wavana.win_size + #end if + + #if 'save_phase' in $outputs: + --phase_out '$phase_out' + #end if + + #if 'save_period' in $outputs: + --period_out '$period_out' + #end if + + #if 'save_power' in $outputs: + --power_out '$power_out' + #end if + + #if 'save_amplitude' in $outputs: + --amplitude_out '$amplitude_out' + #end if + + #if 'save_preprocessed' in $outputs: + --preprocessed_out '$preprocessed_out' + #end if + + --html_fname '$html_out' + --report_img_path '$html_out.extra_files_path' + + --ncpu "\${GALAXY_SLOTS:-8}" + + + ]]></command> + <inputs> + <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 + argparse parser in spyboat_cli.py + --> + <section name="PreProc" title="Preprocessing" expanded="true"> + <param argument="gauss_sigma" type="float" min="0" max="9999999" optional="true" label="Sigma" + help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" /> + <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor" + help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" /> + </section> + <section name="wavana" title="Wavelet Analysis" expanded="true"> + <param name="dt" type="float" value="1" min="0" max="9999999" label="Sampling interval" help="Time span between two frames" /> + <param name="tmin" type="float" value="20" min="0" max="9999999" label="Smallest period" help="Lowest period for the wavelet transform" /> + <param name="tmax" type="float" value="30" min="0" max="9999999" label="Largest period" + help="Largest period for the wavelet transform" /> + <param name="nt" type="integer" value="150" min="0" max="9999999" label="Number of periods to scan for" + help="Determines period resolution of the Wavelet power spectra" /> + <param name="tcutoff" type="float" value="40" min="0" max="9999999" label="T cutoff" + help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true" /> + <param name="win_size" type="float" value="" min="0" max="9999999" optional="true" label="Sliding window size" + help="Window size for amplitude envelope estimation, leave blank to disable normalization" /> + </section> + <conditional name="masking"> + <param name="selection_mode" type="select" label="Masking the output" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output"> + <option selected="true" value="no_masking">No masking</option> + <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 value="create_static_mask"> + <param name="mask_frame" type="integer" value="1" min="1" max="99999" label="Create mask from frame" + help="Creates a static mask from the chosen frame of the input movie." /> + <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold" + help="All pixels below this threshold will be masked in the output." /> + </when> + <when value="create_dynamic_mask"> + <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold" + help="For each frame of the input, all pixels below this threshold will be masked in the output." /> + </when> + </conditional> + <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help=""> + <option value="save_phase">Phase Movie</option> + <option value="save_period">Period Movie</option> + <option value="save_amplitude">Amplitude Movie</option> + <option value="save_power">Power Movie</option> + <option value="save_preprocessed">Preprocessed Movie</option> + </param> + </inputs> + + <outputs> + <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase"> + <filter>'save_phase' in ouputs</filter> + </data> + <data name="period_out" format="tiff" label="${movie.name[:-4]}_period"> + <filter>'save_period' in outputs</filter> + </data> + <data name="power_out" format="tiff" label="${movie.name[:-4]}_power"> + <filter>'save_power' in outputs</filter> + </data> + <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude"> + <filter>'save_amplitude' in outputs</filter> + </data> + <data name="preprocessed_out" format="tiff" label="${movie.name[:-4]}_preproc"> + <filter>'save_preprocessed' in outputs</filter> + </data> + <data name="html_out" format="html" label="Report ${movie.name[:-4]}" /> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="movie" value="test-movie.tif" ftype="tiff"/> + <param name="outputs" value="save_phase"/> + <conditional name="masking"> + <param name="selection_mode" value="no_masking" /> + </conditional> + <output name="phase_out" ftype="tiff"> + <assert_contents> + <has_size value="1764430" delta="100" /> + </assert_contents> + </output> + <output name="html_out" file="output1.html" ftype="html"/> + </test> + <test expect_num_outputs="4"> + <section name="wavana"> + <param name="tmin" value="20"/> + <param name="nt" value="150"/> + <param name="tcutoff" value="40"/> + </section> + <conditional name="masking"> + <param name="selection_mode" value="create_static_mask" /> + </conditional> + <param name="movie" value="test-movie.tif" ftype="tiff"/> + <param name="outputs" value="save_phase,save_preprocessed,save_power"/> + <output name="phase_out" ftype="tiff"> + <assert_contents> + <has_size value="1764430" delta="100" /> + </assert_contents> + </output> + <output name="html_out" file="output1.html" ftype="html"/> + </test> + <test expect_num_outputs="4"> + <section name="wavana"> + <param name="tmin" value="20"/> + <param name="nt" value="150"/> + <param name="tcutoff" value="40"/> + </section> + <conditional name="masking"> + <param name="selection_mode" value="create_dynamic_mask" /> + </conditional> + <param name="movie" value="test-movie.tif" ftype="tiff"/> + <param name="outputs" value="save_phase,save_preprocessed,save_power"/> + <output name="phase_out" ftype="tiff"> + <assert_contents> + <has_size value="1764430" delta="100" /> + </assert_contents> + </output> + <output name="html_out" file="output1.html" ftype="html"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +------------------- + + Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel along the time axis and extracts/evaluates the wavelet ridge. Removal of low-frequency trends is provided via sinc filtering. + There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input. + + Pre-smoothing of the data with Gaussian kernels is supported and often recommendable. + + To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended. + Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing. + + If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji). + + **Author**: Gregor Mönke (gregor.moenke@embl.de). + + **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de). + + **Know what you are doing** + + .. class:: warningmark + + You need to have a basic understanding of time-frequency analysis with Wavelets, find more information about the analysis strategy employed at https://github.com/tensionhead/pyBOAT or the publication cited below. + +------------------- + +**Parameter List** + + - Sigma: + The Kernel bandwidth (in pixels) for the Gaussian kernels to use for pre-smoothing the input data. The default value of zero means that no pre-smoothing is done. Set this number to a desired kernel width to turn on pre-smoothing. + + - Rescale factor: + Given in %, downsamples the spatial resolution of the input movie. This speeds up the whole analysis by a lot. + + - Masking: + SpyBOAT offers 'static' and 'dynamic' masking. 'static' means that a single mask is created by thresholding from a user selected frame. 'dynamic' creates a mask for each frame by thresholding, works better for moving/expanding/shrinking oscillatory fields. + + - Sampling interval: + Time passed between consecutive measurements, e.g 'an image every 10 minutes'. + + - Smallest Period: + The minimal period to scan for, this is the higher (in frequency) end of the spectrum. A warning will be given during processing if the chosen value deceeds the Nyquist limit (2 times the sampling interval). + + - Largest period: + The maximal period to scan for, this is the lower (in frequency) end of the spectrum. The inbuild Sinc filter will remove any periods larger than this form the data. Due to the 'roll off' of the filter, this value should be chosen generously. A warning will be given during processing if the chosen value exceeds the length of the time series. + + - Number of periods to scan for: + This is the the number of convolutions computed per pixel. + + Spectral resolution = ( biggest period - smallest period ) / number of periods + + - Tcutoff: + The cut-off period for the sinc filter, periods larger than this one will + be removed from the signal before the transform. If no value is given, + no detrending is performed. At least a gracious cut-off of around ~3 times + the largest period to be expected is recommended. + + - Sliding window size + Length (in time units, e.g. hours) of the sliding window to estimate + an amplitude envelope. The signal then gets normalized by this envelope, + meaning that all amplitudes will be around ~1 after the transform. The + advantage is that signal with strong amplitude trends will have more + meaningful Wavelet powers after normalization. + + + ]]></help> + <citations> + <citation type="doi">10.1101/2020.04.29.067744</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spyboat_cli.py Sat Nov 28 13:45:34 2020 +0000 @@ -0,0 +1,217 @@ +#!/usr/bin/env python + +# Gets interfaced by Galaxy or can be used for bash scripting +import argparse +import logging +import os +import sys + +import output_report +import spyboat +from numpy import float32 +from skimage import io + +logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True) +logger = logging.getLogger('spyboat-cli') + +# ----------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=False) +parser.add_argument('--period_out', help='Period output file name', required=False) +parser.add_argument('--power_out', help='Power output file name', required=False) +parser.add_argument('--amplitude_out', help='Amplitude output file name', required=False) +parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name", 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_factor', 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', 'static' 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 static mask from, needs masking set to 'static'", + 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 html report/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, to be set in Galaxy. Without galaxy leave at cwd!", + default='.', required=False, type=str) + +parser.add_argument('--version', action='version', version='0.1.0') + +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) +# problems get logged in 'open_tif' +if movie is None: + sys.exit(1) +# -------- Do (optional) spatial downsampling --------------------------- + +scale_factor = arguments.rescale_factor + +# 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 == 'static': + if not arguments.mask_frame: + logger.critical("Frame number for static 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 static mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}') + mask = spyboat.create_static_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 HTML Report Figures/png's --- + +# create the directory, yes we have to do that ourselves :) +# galaxy then magically renders the html from that directory +try: + + if arguments.report_img_path != '.': + logger.info(f'Creating report directory {arguments.report_img_path}') + os.mkdir(arguments.report_img_path) + + # 4 snapshots each + Nsnap = 7 + NFrames = movie.shape[0] + # show only frames at least one Tmin + # away from the edge (-effects) + start_frame = int(Wkwargs['Tmin'] / Wkwargs['dt']) + + if (start_frame > NFrames // 2): + logger.warning("Smallest period already is larger than half the observation time!") + # set to 0 in this case + start_frame = 0 + + frame_increment = int((NFrames - 2 * start_frame) / Nsnap) + snapshot_frames = range(start_frame, NFrames - start_frame, frame_increment) + + for snapshot_frame in snapshot_frames: + 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_frames, arguments.html_fname) + +except FileExistsError as e: + logger.critical(f"Could not create html report directory: {repr(e)}") + +# --- save out result movies --- + +# None means output is filtered from galaxy settings +if arguments.phase_out is not None: + # save phase movie + io.imsave(arguments.phase_out, results['phase'], plugin="tifffile") + logger.info(f'Written phase to {arguments.phase_out}') +if arguments.period_out is not None: + # save period movie + io.imsave(arguments.period_out, results['period'], plugin="tifffile") + logger.info(f'Written period to {arguments.period_out}') +if arguments.power_out is not None: + # save power movie + io.imsave(arguments.power_out, results['power'], plugin="tifffile") + logger.info(f'Written power to {arguments.power_out}') +if arguments.amplitude_out is not None: + # save amplitude movie + io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile") + logger.info(f'Written amplitude to {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 is not None: + io.imsave(arguments.preprocessed_out, movie.astype(float32), plugin='tifffile') + logger.info(f'Written preprocessed to {arguments.preprocessed_out}')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.html Sat Nov 28 13:45:34 2020 +0000 @@ -0,0 +1,334 @@ + + <html> + <!-- this file got automatically created by 'output_report.py' --> + <title>SpyBOAT Output Report</title> + <head> + <!-- that doesn't work with galaxy.. --> + <!--link rel="stylesheet" href="styles.css"--> + <style type="text/css"> + body{ margin:10 100; background:whitesmoke; } + /*body{ margin:10 100; background:darkslategrey; }*/ + .center{ + text-align: center; + display: block; + margin-left: auto; + margin-right: auto; + width: 100%;} + + /* matplotlib output at 1600x1200 */ + .distr_gallery { + display: grid; + margin: 0 auto; + text-align: center; + /* border: 1px dashed rgba(4, 4, 4, 0.35); */ + grid-template-columns: repeat(3,1fr); + grid-template-rows: 20vw; + grid-gap: 0px; + column-gap: 0px + } + .distr_gallery__img { + width: 100%; + height: 100%; + object-fit: contain; + } + + + /* matplotlib output at 1600x1200 */ + .snapshot_gallery { + display: grid; + margin: 0 auto; + border: 1px dashed rgba(4, 4, 4, 0.35); + text-align: center; + grid-template-columns: repeat(2,1fr); + grid-template-rows: repeat(2,20vw); + grid-gap: 5px; + } + .snapshot_gallery__img { + width: 100%; + height: 100%; + object-fit: contain; + } + .subheader{ + text-align:center; + font-size: 160%; + color:#363333;} + </style> + </head> + <body> + <h1 style="text-align:center; color:#363333">SpyBOAT Results Report</h1> + <hr style="width:50%"> + <h1 class="subheader"> Distribution Dynamics </h1> + <div class="distr_gallery"> + <figure class=”distr_gallery__item distr_gallery__item--1"> + <img src="period_distr.png" alt="Period" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--2"> + <img src="power_distr.png" alt="Power" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--3"> + <img src="phase_distr.png" alt="Phase" class="distr_gallery__img"> + </figure> + + </div> + + <h1 class="subheader"> Output Movie Snapshots </h1> + + <!-- trigger the javascript at the end---> + <div class="center"> + <button class="w3-button" onclick="plusDivs(-1)">❮ Prev</button> + <button class="w3-button" onclick="plusDivs(1)">Next ❯</button> + </div> + + <!-- defines all elements of the "FrameSlides" class ---> + + <div class="FrameSlides"> + <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_frame20.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame20.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame20.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <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. 28 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame28.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame28.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame28.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame28.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. 36 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame36.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame36.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame36.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame36.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. 44 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame44.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame44.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame44.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame44.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. 52 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame52.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame52.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame52.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame52.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. 60 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame60.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame60.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame60.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame60.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + <div class="FrameSlides"> + <h3 style="text-align:center; color=#363333"> + Frame Nr. 68 </h3> + + <div class="snapshot_gallery"> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--1"> + <img src="input_frame68.png" alt="The Input" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--2"> + <img src="phase_frame68.png" alt="Phase" + class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--3"> + <img src="period_frame68.png" + alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item + snapshot_gallery__item--4"> + <img src="amplitude_frame68.png" + alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + </div> + + </div> + + <!-- javascript with escaped '{'---> + <script> + var slideIndex = 1; + showDivs(slideIndex); + + function plusDivs(n) { + showDivs(slideIndex += n); + } + + function showDivs(n) { + var i; + var x = document.getElementsByClassName("FrameSlides"); + if (n > x.length) {slideIndex = 1} + if (n < 1) {slideIndex = x.length} ; + for (i = 0; i < x.length; i++) { + x[i].style.display = "none"; + } + x[slideIndex-1].style.display = "block"; + } + </script> + </body> + </html> + \ No newline at end of file