Mercurial > repos > ximgchess > hexrd

annotate hedm_npz_to_tesr.py @ 4:b49a8ef3351d draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
author ximgchess
date Thu, 01 Apr 2021 18:29:39 +0000
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4
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
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diff changeset
1 #!/usr/bin/env python3
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
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2 # -*- coding: utf-8 -*-
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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3 """
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
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4 Created on Mon Nov 19 08:32:06 2018
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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5
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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6 @author: dcp99
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7 """
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8
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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9
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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10 #%%
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11
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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12 import argparse
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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13 import numpy as np
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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14 import re
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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15
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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16 def __main__():
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17
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18 parser = argparse.ArgumentParser(
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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19 description='Convert an HEDM_map.npz file to a neper tesr file')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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20 parser.add_argument(
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21 'input',
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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22 type=argparse.FileType('rb'),
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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23 help='HEDM_map.npz')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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24 parser.add_argument(
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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25 'output',
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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26 type=argparse.FileType('w'),
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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27 help='neper tesr file' )
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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28 parser.add_argument('-s', '--voxel_spacing', type=float, default=0.005, help='voxel spacing')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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29 parser.add_argument('-x', '--x_name', default='^.*X.*$', help='X array name')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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30 parser.add_argument('-y', '--y_name', default='^.*Y.*$', help='Y array name')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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31 parser.add_argument('-z', '--z_name', default='^.*Z.*$', help='Z array name')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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32 parser.add_argument('-g', '--grain_map', default='^.*grain.*$', help='grain map name')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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33 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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34 args = parser.parse_args()
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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35 data=np.load(args.input)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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36 grain_map = Xs = Ys = Zs = None
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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37 for f in data.files:
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38 if re.match(args.grain_map, f):
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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39 grain_map = data[f]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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40 elif re.match(args.x_name, f):
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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41 Xs = data[f]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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42 elif re.match(args.y_name, f):
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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43 Ys = data[f]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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44 elif re.match(args.z_name, f):
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45 Zs = data[f]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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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()))
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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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])
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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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()
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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61 assembled_data[ii*stack_size:(ii+1)*stack_size,:]=assembled_data[ii*stack_size+tmp_args,:]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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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()
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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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
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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70 np.set_printoptions(threshold=np.inf)
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71 l1 = '***tesr'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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72 l2 = ' **format'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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73 l3 = ' 2.0 ascii'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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74 l4 = ' **general'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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75 l5 = ' 3'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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76 l6 = ' ' + str(grain_map.shape[1]) + ' ' + str(grain_map.shape[0]) + ' ' + str(grain_map.shape[2])
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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77 l7 = ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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78 l8 = ' **cell';
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
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79 l9 = ' ' + str(np.max(grain_map).astype('int'))
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
80 l10 = ' *id';
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
81 l11 = ' ' + str(np.arange(1,np.max(grain_map)+1).astype('int'))[1:-1]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
82 l12 = ' **data'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
83 #l13 = ' ' + str(assembled_data[:,3].astype('int'))[1:-1]
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
84 l14 = '***end'
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
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85
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
86 #%%
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
87 output = args.output
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
88 output.write('%s\n' % l1)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
89 output.write('%s\n' % l2)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
90 output.write('%s\n' % l3)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
91 output.write('%s\n' % l4)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
92 output.write('%s\n' % l5)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
93 output.write('%s\n' % l6)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
94 output.write('%s\n' % l7)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
95 output.write('%s\n' % l8)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
96 output.write('%s\n' % l9)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
97 output.write('%s\n' % l10)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
98 output.write('%s\n' % l11)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
99 output.write('%s\n' % l12)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
100 output.write(' ')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
101 np.savetxt(output,np.atleast_2d(assembled_data[:,3]).T,fmt='%d')
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
102 #output.write('%s\n' % l13)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
103 output.write('%s\n' % l14)
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
104 output.close()
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
105
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
106
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
107 if __name__ == "__main__":
b49a8ef3351d "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"
ximgchess
parents:
diff changeset
108 __main__()