--- /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}')