Mercurial > repos > gregor.m > spyboat

annotate cl_wrapper.py @ 2:c59d1373230e draft

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"planemo upload commit eeba34c94465f41d13c2f5bcf68177d23c92d971-dirty"
author gregor.m
date Mon, 23 Nov 2020 14:38:37 +0000
parents 1d62de03829d
children
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1 #!/usr/bin/env python
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2
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3 ## Gets interfaced by Galaxy or bash scripting
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4 import argparse
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5 import sys, os
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6 import logging
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7
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8 from skimage import io
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9 from numpy import float32
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10
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11 import spyboat
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12 import output_report
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13
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14 logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
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15 logger = logging.getLogger('wrapper')
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16
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17 # ----------command line parameters ---------------
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18
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19 parser = argparse.ArgumentParser(description='Process some arguments.')
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20
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21 # I/O
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22 parser.add_argument('--input_path', help="Input movie location", required=True)
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23 parser.add_argument('--phase_out', help='Phase output file name', required=True)
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24 parser.add_argument('--period_out', help='Period output file name', required=True)
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25 parser.add_argument('--power_out', help='Power output file name', required=True)
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26 parser.add_argument('--amplitude_out', help='Amplitude output file name', required=True)
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27 parser.add_argument('--preprocessed_out', help="Preprocessed-input output file name, 'None'", required=False)
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28
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29
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30 # (Optional) Multiprocessing
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31
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32 parser.add_argument('--ncpu', help='Number of processors to use',
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33 required=False, type=int, default=1)
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34
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35 # Optional spatial downsampling
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36 parser.add_argument('--rescale', help='Rescale the image by a factor given in %%, None means no rescaling',
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37 required=False, type=int)
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38 # Optional Gaussian smoothing
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39 parser.add_argument('--gauss_sigma', help='Gaussian smoothing parameter, None means no smoothing', required=False, type=float)
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40
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41 # Wavelet Analysis Parameters
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42 parser.add_argument('--dt', help='Sampling interval', required=True, type=float)
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43 parser.add_argument('--Tmin', help='Smallest period', required=True, type=float)
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44 parser.add_argument('--Tmax', help='Biggest period', required=True, type=float)
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45 parser.add_argument('--nT', help='Number of periods to scan for', required=True, type=int)
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46
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47 parser.add_argument('--Tcutoff', help='Sinc cut-off period, disables detrending if not set', required=False, type=float)
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48 parser.add_argument('--win_size', help='Sliding window size for amplitude normalization, None means no normalization',
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49 required=False, type=float)
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50
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51 # Optional masking
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52 parser.add_argument('--masking', help="Set to either 'dynamic', 'fixed' or 'None' which is the default", default='None', required=False, type=str)
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53
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54 parser.add_argument('--mask_frame',
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55 help="The frame of the input movie to create a fixed mask from, needs masking set to 'fixed'",
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56 required=False, type=int)
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57
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58
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59 parser.add_argument('--mask_thresh', help='The threshold of the mask, all pixels with less than this value get masked (if masking enabled).',
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60 required=False, type=float,
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61 default=0)
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62
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63 # output overview/snapshots
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64 parser.add_argument('--html_fname', help="Name of the html report.",
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65 default='OutputReport.html', required=False, type=str)
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66
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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)
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68
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69 parser.add_argument('--version', action='version', version='0.0.1')
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70
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71 arguments = parser.parse_args()
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72
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73 logger.info("Received following arguments:")
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74 for arg in vars(arguments):
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75 logger.info(f'{arg} -> {getattr(arguments, arg)}')
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76
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77 # ------------Read the input----------------------------------------
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78 try:
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79 movie = spyboat.open_tif(arguments.input_path)
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80 except FileNotFoundError:
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81 logger.critical(f"Couldn't open {arguments.input_path}, check movie storage directory!")
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82
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83 sys.exit(1)
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84
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85 # -------- Do (optional) spatial downsampling ---------------------------
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86
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87 scale_factor = arguments.rescale
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88
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89 # defaults to None
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90 if not scale_factor:
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91 logger.info('No downsampling requested..')
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92
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93 elif 0 < scale_factor < 100:
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94 logger.info(f'Downsampling the movie to {scale_factor:d}% of its original size..')
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95 movie = spyboat.down_sample(movie, scale_factor / 100)
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96 else:
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97 raise ValueError('Scale factor must be between 0 and 100!')
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98
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99 # -------- Do (optional) pre-smoothing -------------------------
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100 # note that downsampling already is a smoothing operation..
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101
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102 # check if pre-smoothing requested
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103 if not arguments.gauss_sigma:
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104 logger.info('No pre-smoothing requested..')
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105 else:
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106 logger.info(f'Pre-smoothing the movie with Gaussians, sigma = {arguments.gauss_sigma:.2f}..')
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107
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108 movie = spyboat.gaussian_blur(movie, arguments.gauss_sigma)
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109
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110 # ----- Set up Masking before processing ----
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111
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112 mask = None
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113 if arguments.masking == 'fixed':
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114 if not arguments.mask_frame:
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115 logger.critical("Frame number for fixed masking is missing!")
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116 sys.exit(1)
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117
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118 if (arguments.mask_frame > movie.shape[0]) or (arguments.mask_frame < 0):
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119 logger.critical(f'Requested frame does not exist, input only has {movie.shape[0]} frames.. exiting')
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120 sys.exit(1)
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121
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122 else:
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123 logger.info(f'Creating fixed mask from frame {arguments.mask_frame} with threshold {arguments.mask_thresh}')
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124 mask = spyboat.create_fixed_mask(movie, arguments.mask_frame,
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125 arguments.mask_thresh)
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126 elif arguments.masking == 'dynamic':
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127 logger.info(f'Creating dynamic mask with threshold {arguments.mask_thresh}')
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128 mask = spyboat.create_dynamic_mask(movie, arguments.mask_thresh)
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129
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130 else:
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131 logger.info('No masking requested..')
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132
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133 # ------ Retrieve wavelet parameters ---------------------------
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134
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135 Wkwargs = {'dt': arguments.dt,
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136 'Tmin': arguments.Tmin,
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137 'Tmax': arguments.Tmax,
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138 'nT': arguments.nT,
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139 'T_c' : arguments.Tcutoff, # defaults to None
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140 'win_size' : arguments.win_size # defaults to None
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141 }
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142
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143 # start parallel processing
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144 results = spyboat.run_parallel(movie, arguments.ncpu, **Wkwargs)
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145
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146 # --- masking? ---
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147
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148 if mask is not None:
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149 # mask all output movies (in place!)
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150 for key in results:
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151 logger.info(f'Masking {key}')
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152 spyboat.apply_mask(results[key], mask, fill_value=-1)
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153
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154 # --- Produce Output Report Figures/png's ---
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155
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156 # create the directory, yes we have to do that ourselves :)
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157 # galaxy then magically renders the html from that
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158 try:
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159
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160 if arguments.report_img_path != '.':
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161 logger.info(f'Creating report directory {arguments.report_img_path}')
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162 os.mkdir(arguments.report_img_path)
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163
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164 # jump to the middle of the movie
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165 snapshot_frame = int(movie.shape[0]/2)
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166 output_report.produce_snapshots(movie, results, snapshot_frame, Wkwargs, img_path=arguments.report_img_path)
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167
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168 output_report.produce_distr_plots(results, Wkwargs, img_path=arguments.report_img_path)
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169
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170 output_report.create_html(snapshot_frame, arguments.html_fname)
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171
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172
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173 except FileExistsError as e:
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174 logger.critical(f"Could not create html report directory: {repr(e)}")
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175
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176
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177 # --- save out result movies ---
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178
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179 # save phase movie
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180 io.imsave(arguments.phase_out, results['phase'], plugin="tifffile")
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181 logger.info(f'Written {arguments.phase_out}')
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182 # save period movie
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183 io.imsave(arguments.period_out, results['period'], plugin="tifffile")
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184 logger.info(f'Written {arguments.period_out}')
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185 # save power movie
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186 io.imsave(arguments.power_out, results['power'], plugin="tifffile")
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187 logger.info(f'Written {arguments.power_out}')
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188 # save amplitude movie
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189 io.imsave(arguments.amplitude_out, results['amplitude'], plugin="tifffile")
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190 logger.info(f'Written {arguments.amplitude_out}')
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191
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192 # save out the probably pre-processed (scaled and blurred) input movie for
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193 # direct comparison to results and coordinate mapping etc.
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194 if arguments.preprocessed_out:
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195 io.imsave(arguments.preprocessed_out, movie, plugin='tifffile')
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196 logger.info(f'Written {arguments.preprocessed_out}')