Mercurial > repos > gregor.m > spyboat

comparison cl_wrapper.py @ 0:1d62de03829d draft

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"planemo upload commit c6cd06d44dce1eef9136017289d362f144687dc1"
author gregor.m
date Mon, 23 Nov 2020 13:31:47 +0000
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-1:000000000000 0:1d62de03829d
1 #!/usr/bin/env python
2
3 ## Gets interfaced by Galaxy or bash scripting
4 import argparse
5 import sys, os
6 import logging
7
8 from skimage import io
9 from numpy import float32
10
11 import spyboat
12 import output_report
13
14 logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
15 logger = logging.getLogger('wrapper')
16
17 # ----------command line parameters ---------------
18
19 parser = argparse.ArgumentParser(description='Process some arguments.')
20
21 # I/O
22 parser.add_argument('--input_path', help="Input movie location", required=True)
23 parser.add_argument('--phase_out', help='Phase output file name', required=True)
24 parser.add_argument('--period_out', help='Period output file name', required=True)
25 parser.add_argument('--power_out', help='Power output file name', required=True)
26 parser.add_argument('--amplitude_out', help='Amplitude output file name', required=True)
27 parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name, 'None'", required=False)
28
29
30 # (Optional) Multiprocessing
31
32 parser.add_argument('--ncpu', help='Number of processors to use',
33 required=False, type=int, default=1)
34
35 # Optional spatial downsampling
36 parser.add_argument('--rescale', help='Rescale the image by a factor given in %%, None means no rescaling',
37 required=False, type=int)
38 # Optional Gaussian smoothing
39 parser.add_argument('--gauss_sigma', help='Gaussian smoothing parameter, None means no smoothing', required=False, type=float)
40
41 # Wavelet Analysis Parameters
42 parser.add_argument('--dt', help='Sampling interval', required=True, type=float)
43 parser.add_argument('--Tmin', help='Smallest period', required=True, type=float)
44 parser.add_argument('--Tmax', help='Biggest period', required=True, type=float)
45 parser.add_argument('--nT', help='Number of periods to scan for', required=True, type=int)
46
47 parser.add_argument('--Tcutoff', help='Sinc cut-off period, disables detrending if not set', required=False, type=float)
48 parser.add_argument('--win_size', help='Sliding window size for amplitude normalization, None means no normalization',
49 required=False, type=float)
50
51 # Optional masking
52 parser.add_argument('--masking', help="Set to either 'dynamic', 'fixed' or 'None' which is the default", default='None', required=False, type=str)
53
54 parser.add_argument('--mask_frame',
55 help="The frame of the input movie to create a fixed mask from, needs masking set to 'fixed'",
56 required=False, type=int)
57
58
59 parser.add_argument('--mask_thresh', help='The threshold of the mask, all pixels with less than this value get masked (if masking enabled).',
60 required=False, type=float,
61 default=0)
62
63 # output overview/snapshots
64 parser.add_argument('--html_fname', help="Name of the html report.",
65 default='OutputReport.html', required=False, type=str)
66
67 parser.add_argument('--report_img_path', help="For the html report, can be set in Galaxy. Defaults to cwd.", default='.', required=False, type=str)
68
69 parser.add_argument('--version', action='version', version='0.0.1')
70
71 arguments = parser.parse_args()
72
73 logger.info("Received following arguments:")
74 for arg in vars(arguments):
75 logger.info(f'{arg} -> {getattr(arguments, arg)}')
76
77 # ------------Read the input----------------------------------------
78 try:
79 movie = spyboat.open_tif(arguments.input_path)
80 except FileNotFoundError:
81 logger.critical(f"Couldn't open {arguments.input_path}, check movie storage directory!")
82
83 sys.exit(1)
84
85 # -------- Do (optional) spatial downsampling ---------------------------
86
87 scale_factor = arguments.rescale
88
89 # defaults to None
90 if not scale_factor:
91 logger.info('No downsampling requested..')
92
93 elif 0 < scale_factor < 100:
94 logger.info(f'Downsampling the movie to {scale_factor:d}% of its original size..')
95 movie = spyboat.down_sample(movie, scale_factor / 100)
96 else:
97 raise ValueError('Scale factor must be between 0 and 100!')
98
99 # -------- Do (optional) pre-smoothing -------------------------
100 # note that downsampling already is a smoothing operation..
101
102 # check if pre-smoothing requested
103 if not arguments.gauss_sigma:
104 logger.info('No pre-smoothing requested..')
105 else:
106 logger.info(f'Pre-smoothing the movie with Gaussians, sigma = {arguments.gauss_sigma:.2f}..')
107
108 movie = spyboat.gaussian_blur(movie, arguments.gauss_sigma)
109
110 # ----- Set up Masking before processing ----
111
112 mask = None
113 if arguments.masking == 'fixed':
114 if not arguments.mask_frame:
115 logger.critical("Frame number for fixed masking is missing!")
116 sys.exit(1)
117
118 if (arguments.mask_frame > movie.shape[0]) or (arguments.mask_frame < 0):
119 logger.critical(f'Requested frame does not exist, input only has {movie.shape[0]} frames.. exiting')
120 sys.exit(1)
121
122 else:
123 logger.info(f'Creating fixed mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}')
124 mask = spyboat.create_fixed_mask(movie, arguments.mask_frame,
125 arguments.mask_thresh)
126 elif arguments.masking == 'dynamic':
127 logger.info(f'Creating dynamic mask with threshold {arguments.mask_thresh}')
128 mask = spyboat.create_dynamic_mask(movie, arguments.mask_thresh)
129
130 else:
131 logger.info('No masking requested..')
132
133 # ------ Retrieve wavelet parameters ---------------------------
134
135 Wkwargs = {'dt': arguments.dt,
136 'Tmin': arguments.Tmin,
137 'Tmax': arguments.Tmax,
138 'nT': arguments.nT,
139 'T_c' : arguments.Tcutoff, # defaults to None
140 'win_size' : arguments.win_size # defaults to None
141 }
142
143 # start parallel processing
144 results = spyboat.run_parallel(movie, arguments.ncpu, **Wkwargs)
145
146 # --- masking? ---
147
148 if mask is not None:
149 # mask all output movies (in place!)
150 for key in results:
151 logger.info(f'Masking {key}')
152 spyboat.apply_mask(results[key], mask, fill_value=-1)
153
154 # --- Produce Output Report Figures/png's ---
155
156 # create the directory, yes we have to do that ourselves :)
157 # galaxy then magically renders the html from that
158 try:
159
160 if arguments.report_img_path != '.':
161 logger.info(f'Creating report directory {arguments.report_img_path}')
162 os.mkdir(arguments.report_img_path)
163
164 # jump to the middle of the movie
165 snapshot_frame = int(movie.shape[0]/2)
166 output_report.produce_snapshots(movie, results, snapshot_frame, Wkwargs, img_path=arguments.report_img_path)
167
168 output_report.produce_distr_plots(results, Wkwargs, img_path=arguments.report_img_path)
169
170 output_report.create_html(snapshot_frame, arguments.html_fname)
171
172
173 except FileExistsError as e:
174 logger.critical(f"Could not create html report directory: {repr(e)}")
175
176
177 # --- save out result movies ---
178
179 # save phase movie
180 io.imsave(arguments.phase_out, results['phase'], plugin="tifffile")
181 logger.info(f'Written {arguments.phase_out}')
182 # save period movie
183 io.imsave(arguments.period_out, results['period'], plugin="tifffile")
184 logger.info(f'Written {arguments.period_out}')
185 # save power movie
186 io.imsave(arguments.power_out, results['power'], plugin="tifffile")
187 logger.info(f'Written {arguments.power_out}')
188 # save amplitude movie
189 io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile")
190 logger.info(f'Written {arguments.amplitude_out}')
191
192 # save out the probably pre-processed (scaled and blurred) input movie for
193 # direct comparison to results and coordinate mapping etc.
194 if arguments.preprocessed_out:
195 io.imsave(arguments.preprocessed_out, movie, plugin='tifffile')
196 logger.info(f'Written {arguments.preprocessed_out}')