--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,15 @@
+# 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
+
+```

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SpyBOAT.xml	Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,222 @@
+<tool id="SpyBOAT" name="SpyBOAT" version="0.0.1">
+    <requirements>
+        <requirement type="package" version="0.0.2">spyboat</requirement>
+    </requirements>
+    <version_command>python $__tool_directory__/cl_wrapper.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/cl_wrapper.py
+          --input_path '$movie'
+          #if $gauss_sigma:
+             --gauss_sigma $gauss_sigma
+          #end if
+          #if $rescale_factor:
+              --rescale $rescale_factor
+          #end if
+
+          #if $masking.selection_mode == "create_fixed_mask":
+	  --masking fixed
+          --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 $dt
+          --Tmin $tmin
+          --Tmax $tmax
+          --nT $nt
+	  #if $tcutoff
+             --Tcutoff $tcutoff
+	  #end if
+          #if $win_size:
+             --win_size $win_size
+          #end if
+
+          --phase_out $phase_out
+          --period_out $period_out
+          --power_out $power_out
+          --amplitude_out $amplitude_out
+	  #if $preprocessed_out:
+	     --preprocessed_out $preprocessed_out
+	  #end if
+
+	  --html_fname $html_out
+	  --report_img_path '$html_out.extra_files_path'
+
+          --ncpu "\${GALAXY_SLOTS:-8}"
+          > $log
+
+    ]]></command>
+    <inputs>
+        <param name="movie" type="data" format="tiff" label="Movie to process"
+               help="Select a movie to Wavelet process"/>
+
+        <!--
+        The following Wavelet parameters must have the same numerical type as defined in the
+        argparse parser in cl_wrapper.py
+        -->
+
+        <param name="gauss_sigma" type="float" label="Sigma" 
+               help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired." optional="true">
+            <validator type="in_range" min="0" max="9999999"/>
+        </param>
+
+        <param name="rescale_factor" type="integer" value="" label="Rescale factor"
+               help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling"
+               optional="true">
+            <validator type="in_range" min="0" max="99"/>
+        </param>
+
+        <conditional name="masking">
+            <param label="Masking the output" name="selection_mode" type="select" 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_fixed_mask">Create a fixed mask</option>
+		<option value="create_dynamic_mask">Create a dynamic mask</option>
+	    </param>
+            <when value="create_fixed_mask">
+                <param name="mask_frame" type="integer" value="1" label="Create mask from frame"
+                       help="Creates a fixed mask from the chosen frame of the input movie.">
+                    <validator type="in_range" min="1" max="99999"/>
+                </param>
+                <param name="mask_thresh" type="float" value="0" label="Threshold"
+                       help="All pixels below this threshold will be masked in the output.">
+                    <validator type="in_range" min="0" max="999999"/>
+                </param>
+            </when>
+            <when value="create_dynamic_mask">
+                <param name="mask_thresh" type="float" value="0" label="Threshold"
+                       help="For each frame of the input, all pixels below this threshold will be masked in the output.">
+                    <validator type="in_range" min="0" max="999999"/>
+                </param>
+            </when>	    
+        </conditional>
+
+        <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">
+            <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">
+            <validator type="in_range" min="0" max="9999999"/>
+        </param>
+
+        <param name="nt" type="integer" value="150" label="Number of periods to scan for"
+               help="Determines period resolution of the Wavelet power spectra">
+            <validator type="in_range" min="0" max="9999999"/>
+        </param>
+
+        <param name="tcutoff" type="float" value="40" label="Tcutoff"
+               help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true">
+            <validator type="in_range" min="0" max="9999999"/>
+        </param>
+
+        <param name="win_size" type="float" value="" label="Sliding window size"
+               help="Window size for amplitude envelope estimation, leave blank to disable normalization "
+               optional="true">
+            <validator type="in_range" min="0" max="9999999"/>
+        </param>
+
+        <conditional name="save_preprocessed">
+            <param label="Save preprocessed input" name="selection" type="select" help="Save the blurred/rescaled input to history? ">
+                <option selected="true" value="No">No</option>
+                <option value="Yes">Yes</option>
+	    </param>
+	</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}">
+	  <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}"/>
+
+    </outputs>
+
+    <tests>
+        <test>
+            <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"/>
+            <output name="amplitude_out" file="amplitude_out.tif" ftype="tiff" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    **What it does**
+
+    Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel 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 will want to have understood the basics of time-frequency analysis with Wavelets, find more information about the analysis strategy employed at https://github.com/tensionhead/pyBOAT
+
+    **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.
+
+    - 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>
+</tool>

Binary file __pycache__/output_report.cpython-38.pyc has changed

--- /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}')

--- /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'''
+    <html>
+    <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{{
+            display: block;
+            margin-left: auto;
+            margin-right: auto;
+            width: 40%;}}
+
+        /* 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: 25vw;    
+            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;
+        }}
+     </style>
+    </head>
+    <body>
+    <h1 style="text-align:center">SpyBOAT Results Report</h1>
+    <hr style="width:50%"> 
+    <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>
+
+    <h2 style="text-align:center"> Snapshots - Frame {frame_num}</h2>
+    <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>
+    
+
+        <!-- *** Section 1 *** --->
+    </body>
+    </html>
+    '''
+
+    with open(html_fname, 'w') as OUT:
+
+        OUT.write(html_string)
+
+    logger.info(f'Created html report')
+    return html_string
+
+# for local testing
+# create_html(125)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_tests.sh	Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# example command, minimal options: no detrending,
+# no rescaling, no masking, no amplitude norm., no blurring
+
+INPUT_PATH='./test-data/test-movie.tif'
+# INPUT_PATH='./test-data/SCN_L20_Evans2013-half.tif'
+SCRIPT_PATH='.'
+
+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 .5 --Tmin 20 --Tmax 30 --nT 200 --ncpu 6 --masking dynamic --preprocessed_out preproc_two_sines.tif --gauss_sigma 3 --rescale 50 --Tcutoff 40 --masking fixed --mask_frame 10 --mask_thresh 8
+
+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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/styles.css	Mon Nov 23 13:31:47 2020 +0000
@@ -0,0 +1,50 @@
+
+body{ margin:10 100; background:whitesmoke; }
+/*body{ margin:10 100; background:darkslategrey; }*/
+.center{
+    display: block;
+    margin-left: auto;
+    margin-right: auto;
+    width: 40%;}
+
+/* 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;
+}
+
+#areaA {
+  background-color: lime;
+}
+
+#areaB {
+  background-color: yellow;
+}

Binary file test-data/test-movie.tif has changed