Mercurial > repos > agpetit > calculate_diameter

annotate estimate_nb_sub_trajectories.py @ 10:afd0260e676f draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 3111e03da3d8644ceaf94e9796f6c4206d3fe440-dirty"
author agpetit
date Tue, 07 Jun 2022 12:04:45 +0000
parents e5cf7698a2af
children f5064c93f7ab
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1 #!/usr/bin/env python3
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2
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3 # coding: utf-8
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4 """
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5 The script allows to estimate the number of sub-trajectories to obtain.
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6 It also allows to split the trajectory into a number of sub-trajectories.
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7 # USAGE : estimate_nb_sub_trajectories.py -c : file obtaining with gmx check
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8 -log : name of log file (optional) -d : output directory (optional)
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9 -o : name of output file (optional)
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10 -f : desired number of frames per sub-trajectory (optional)
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11 -start : start time of the trajectory (optional)
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12 -end : end time of the trajectory (optional)
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13 """
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14
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15 __all__ = []
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16 __author__ = "Agnès-Elisabeth Petit"
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17 __date__ = "30/05/2022"
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18 __version__ = "0.8"
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19 __copyright__ = "(c) 2022 CC-BY-NC-SA"
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20
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21 # Library import
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22 import argparse
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23 import logging
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24 import os
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25 import sys
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26
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27 import numpy as np
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28
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29
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30 def test_setup():
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31 global args
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32 args = parse_arguments()
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33 args.verbose = True
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34
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35
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36 def parse_arguments():
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37 parser = argparse.ArgumentParser(
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38 description="The script allows to estimate the number of "
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39 "sub-trajectories to obtain. It also allows to split"
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40 " the trajectory into a number of sub-trajectories.",
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41 formatter_class=argparse.ArgumentDefaultsHelpFormatter,
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42 prefix_chars="-",
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43 add_help=True,
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44 )
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45 parser.add_argument(
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46 "-v",
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47 "--verbose",
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48 action="store_true",
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49 help="""Information messages to stderr""",
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50 )
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51 parser.add_argument(
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52 "-c",
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53 "--input_check",
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54 type=str,
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55 nargs=1,
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56 help=""".txt file obtained with gmx check -f.
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57 It contains information about the trajectory""",
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58 )
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59 parser.add_argument(
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60 "-log", "--log_output", type=str,
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61 default="log/estimate_nb_sub_trajectories.log",
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62 help="""Output for log file. Default :
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63 log/estimate_nb_sub_trajectories.log"""
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64 )
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65 parser.add_argument(
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66 "-d", "--output_directory", type=str, nargs=1,
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67 default="./",
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68 help="""It's output Directory. Default : ./"""
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69 )
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70 parser.add_argument(
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71 "-o",
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72 "--output_file",
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73 type=str,
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74 default="estimated_number_of_sub_trajectories.tsv",
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75 help="""Output file. Default :
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76 estimated_number_of_sub_trajectories.tsv""",
5
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77 )
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78 parser.add_argument(
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79 "-f",
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80 "--nb_frames",
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81 type=int,
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82 default=30,
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83 help="""Number of frames per sub-trajectory. Default : 30""",
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84 )
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85 parser.add_argument(
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86 "-start", "--start_traj", type=str,
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87 help="""Start of the trajectory to be cut"""
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88 )
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89 parser.add_argument(
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90 "-end", "--end_traj", type=str,
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91 help="""End of the trajectory to be cut"""
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92 )
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93 return parser.parse_args()
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94
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95
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96 def search_nbr_steps_time_step(txt_file):
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97 """
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98 Description : Keeping the number of frames of the complete trajectory and
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99 the time between each frame.
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100 param txt_file: file obtained with gmx check.
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101 return: list that contains the number of frames of the complete trajectory
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102 and time between each frame.
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103 """
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104 if args.verbose:
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105 logging.info("\nFunction search_nbr_steps_time_step")
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106 logging.info("The input file is " + txt_file)
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107 with open(txt_file, "r") as f:
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108 len_traj = ""
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109 time_step = ""
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110 for li in f:
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111 li = li.rstrip()
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112 if li.startswith("Step"):
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113 li2 = li.split()
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114 len_traj = int(li2[1])
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115 time_step = int(li2[2])
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116 if args.verbose:
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117 logging.info("The length of the trajectory is " + str(len_traj))
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118 logging.info(
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119 "The elapsed time between two steps is : " + str(time_step) + " ps"
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120 )
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121 logging.info("End search_nbr_steps_time_step functions")
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122 return len_traj, time_step
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123
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124
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125 def estimate_nbr_sub_trajectories(nbr_step_time_step, nbr_frames_traj,
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126 out_file):
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127 """
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128 Description: Creation of a tsv file that contains the number of frames
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129 of the complete trajectory, the number of sub-trajectories to create,
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130 the duration between each frame and the number of frames
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131 per sub-trajectory.
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132 param nbr_step_time_step: list which contains the number of frames of
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133 the complete trajectory and the time between each frame
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134 param nbr_frames_traj: number of frames per sub-trajectory
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135 param out_file: output file name
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136 return: list that contains the number of frames of the complete trajectory,
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137 the number of sub-trajectories to create, the duration between
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138 each frame and the number of frames per sub-trajectory.
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139 output: tsv file
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140 """
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141 if args.verbose:
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142 logging.info("\nFunction estimate_nbr_means")
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143 logging.info("The length of the trajectory is " +
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144 str(nbr_step_time_step[0]))
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145 logging.info(
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146 "The elapsed time between two steps is : "
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147 + str(nbr_step_time_step[1])
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148 + " ps"
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149 )
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150 logging.info("The output file is " + str(out_file))
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151 name_columns = [
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152 "Length_trajectory (frames)",
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153 "Number_sub_trajectories",
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154 "Time_steps (ps)",
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155 "Number_frames_per_sub_trajectory",
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156 "Start_trajectory (frames)",
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157 "End_trajectory (frames)",
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158 ]
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159 time_step = nbr_step_time_step[1]
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160 if nbr_step_time_step[2] is not None:
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161 start_traj = nbr_step_time_step[2]
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162 else:
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163 start_traj = 0
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164 if nbr_step_time_step[3] is not None:
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165 end_traj = nbr_step_time_step[3]
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166 else:
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167 end_traj = nbr_step_time_step[0] - 1
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168 if args.verbose:
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169 logging.info(
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170 "The first frame of the trajectory is the number "
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171 + str(start_traj)
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172 )
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173 logging.info("The first frame of the trajectory is the number "
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174 + str(end_traj))
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
175 len_traj = end_traj - start_traj + 1
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
176 n_sub_traj = len_traj // nbr_frames_traj
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
177 if args.verbose:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
178 logging.info("The estimated number of sub-trajectories is : "
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
179 + str(n_sub_traj))
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
180 list_values = [
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
181 str(len_traj),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
182 str(n_sub_traj),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
183 str(time_step),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
184 str(nbr_frames_traj),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
185 str(start_traj),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
186 str(end_traj),
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
187 ]
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
188 tab_values = np.asarray([name_columns, list_values])
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
189 np.savetxt(out_file, tab_values, delimiter="\t", fmt="%s")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
190 if args.verbose:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
191 logging.info("Save table in the file : " + str(out_file))
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
192 logging.info("End estimate_nbr_sub_trajectories function")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
193
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
194
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
195 if __name__ == "__main__":
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
196 args = parse_arguments()
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
197 if args.output_directory[0].endswith("/"):
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
198 out_directory = args.output_directory[0]
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
199 else:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
200 out_directory = args.output_directory[0] + "/"
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
201 if args.verbose:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
202 if "/" in args.log_output:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
203 log_dir = args.log_output.rsplit("/", 1)[0]
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
204 else:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
205 log_dir = "log/"
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
206 log_file = args.log_output
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
207 if not os.path.exists(log_dir):
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
208 os.makedirs(log_dir)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
209 if os.path.isfile(log_file):
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
210 os.remove(log_file)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
211 if args.log_output:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
212 logging.basicConfig(
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
213 filename=log_file,
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
214 format="%(levelname)s - %(message)s",
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
215 level=logging.INFO,
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
216 )
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
217 else:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
218 logging.basicConfig(
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
219 filename=log_file,
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
220 format="%(levelname)s - %(message)s",
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
221 level=logging.INFO,
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
222 )
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
223 logging.info("verbose mode on")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
224 nb_frames_traj = args.nb_frames
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
225 if args.start_traj and args.start_traj != "":
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
226 start_trajectory = int(args.start_traj)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
227 else:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
228 start_trajectory = None
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
229 if args.end_traj and args.end_traj != "":
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
230 end_trajectory = int(args.end_traj)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
231 else:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
232 end_trajectory = None
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
233 if args.verbose:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
234 logging.info("Start estimate number sub-trajectories")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
235 output_file = args.output_file
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
236 if not args.input_check:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
237 print("Please enter the file created with 'gmx_check -f'")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
238 if args.verbose:
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
239 logging.error("Please enter the file created with 'gmx_check -f'")
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
240 sys.exit(1)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
241 nb_steps_time_step = list(search_nbr_steps_time_step(
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
242 args.input_check[0]))
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
243 nb_steps_time_step.append(start_trajectory)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
244 nb_steps_time_step.append(end_trajectory)
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
245 output_file = out_directory + output_file
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
246 estimate_nbr_sub_trajectories(nb_steps_time_step, nb_frames_traj,
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents:
diff changeset
247 output_file)