Mercurial > repos > ximgchess > hedm_npz_to_tesr

annotate hedm_npz_to_tesr.py @ 0:bd74229f61e8 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
author ximgchess
date Thu, 01 Apr 2021 18:30:44 +0000
parents
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bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3 """
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4 Created on Mon Nov 19 08:32:06 2018
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5
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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6 @author: dcp99
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7 """
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8
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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9
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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10 #%%
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11
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12 import argparse
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13 import numpy as np
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14 import re
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16 def __main__():
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17
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18 parser = argparse.ArgumentParser(
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19 description='Convert an HEDM_map.npz file to a neper tesr file')
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20 parser.add_argument(
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21 'input',
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22 type=argparse.FileType('rb'),
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23 help='HEDM_map.npz')
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24 parser.add_argument(
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25 'output',
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26 type=argparse.FileType('w'),
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27 help='neper tesr file' )
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28 parser.add_argument('-s', '--voxel_spacing', type=float, default=0.005, help='voxel spacing')
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29 parser.add_argument('-x', '--x_name', default='^.*X.*$', help='X array name')
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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30 parser.add_argument('-y', '--y_name', default='^.*Y.*$', help='Y array name')
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31 parser.add_argument('-z', '--z_name', default='^.*Z.*$', help='Z array name')
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32 parser.add_argument('-g', '--grain_map', default='^.*grain.*$', help='grain map name')
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33 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
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34 args = parser.parse_args()
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35 data=np.load(args.input)
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36 grain_map = Xs = Ys = Zs = None
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37 for f in data.files:
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38 if re.match(args.grain_map, f):
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39 grain_map = data[f]
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40 elif re.match(args.x_name, f):
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41 Xs = data[f]
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42 elif re.match(args.y_name, f):
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43 Ys = data[f]
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44 elif re.match(args.z_name, f):
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45 Zs = data[f]
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46 voxel_spacing = args.voxel_spacing
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47
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48 #CREATE ASSEMBLED DATA -- LIST OF [VOXEL COORDINATES (X,Y,Z),GRAIN ID]
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49
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50 coordinate_list=np.vstack((Xs.ravel(),Ys.ravel(),Zs.ravel()))
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51 assembled_data=np.hstack((coordinate_list.T,np.atleast_2d(grain_map.ravel()).T))
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52
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53 #%% SORT BY ROWS Z AND THEN Y
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54
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55 assembled_data=assembled_data[assembled_data[:,2].argsort()]
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56 total_size=int(grain_map.shape[0]*grain_map.shape[1]*grain_map.shape[2])
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57
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58 stack_size=int(grain_map.shape[0]*grain_map.shape[1])
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59 for ii in np.arange(int(total_size/stack_size)):
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60 tmp_args=assembled_data[ii*stack_size:(ii+1)*stack_size,1].argsort()
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61 assembled_data[ii*stack_size:(ii+1)*stack_size,:]=assembled_data[ii*stack_size+tmp_args,:]
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62
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63 stack_size=grain_map.shape[1]
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64 for ii in np.arange(int(total_size/stack_size)):
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65 tmp_args=assembled_data[ii*stack_size:(ii+1)*stack_size,0].argsort()
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66 assembled_data[ii*stack_size:(ii+1)*stack_size,:]=assembled_data[ii*stack_size+tmp_args,:]
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67
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68 #%%
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69
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70 np.set_printoptions(threshold=np.inf)
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71 l1 = '***tesr'
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72 l2 = ' **format'
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73 l3 = ' 2.0 ascii'
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74 l4 = ' **general'
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75 l5 = ' 3'
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76 l6 = ' ' + str(grain_map.shape[1]) + ' ' + str(grain_map.shape[0]) + ' ' + str(grain_map.shape[2])
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77 l7 = ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing)
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78 l8 = ' **cell';
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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79 l9 = ' ' + str(np.max(grain_map).astype('int'))
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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80 l10 = ' *id';
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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81 l11 = ' ' + str(np.arange(1,np.max(grain_map)+1).astype('int'))[1:-1]
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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82 l12 = ' **data'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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83 #l13 = ' ' + str(assembled_data[:,3].astype('int'))[1:-1]
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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84 l14 = '***end'
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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85
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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86 #%%
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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87 output = args.output
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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88 output.write('%s\n' % l1)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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89 output.write('%s\n' % l2)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
90 output.write('%s\n' % l3)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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91 output.write('%s\n' % l4)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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92 output.write('%s\n' % l5)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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93 output.write('%s\n' % l6)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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94 output.write('%s\n' % l7)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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95 output.write('%s\n' % l8)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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96 output.write('%s\n' % l9)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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97 output.write('%s\n' % l10)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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98 output.write('%s\n' % l11)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
99 output.write('%s\n' % l12)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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100 output.write(' ')
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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101 np.savetxt(output,np.atleast_2d(assembled_data[:,3]).T,fmt='%d')
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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102 #output.write('%s\n' % l13)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
diff changeset
103 output.write('%s\n' % l14)
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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104 output.close()
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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105
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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106
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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107 if __name__ == "__main__":
bd74229f61e8 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
ximgchess
parents:
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108 __main__()