| Next changeset 1:e90d5493a744 (2022-07-07) |
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Commit message:
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty" |
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added:
example_data.tesr hedm_npz_to_tesr.py hedm_npz_to_tesr.xml |
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| diff -r 000000000000 -r bd74229f61e8 example_data.tesr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/example_data.tesr Thu Apr 01 18:30:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,1000020 @@\n+***tesr\n+ **format\n+ 2.0 ascii\n+ **general\n+ 3\n+ 100 100 100\n+ 0.005 0.005 0.005\n+ **cell\n+ 133\n+ *id\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18\n+ 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36\n+ 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54\n+ 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72\n+ 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108\n+ 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126\n+ 127 128 129 130 131 132 133\n+ **data\n+ 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| b |
| diff -r 000000000000 -r bd74229f61e8 hedm_npz_to_tesr.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hedm_npz_to_tesr.py Thu Apr 01 18:30:44 2021 +0000 |
| [ |
| @@ -0,0 +1,108 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Mon Nov 19 08:32:06 2018 + +@author: dcp99 +""" + + +#%% + +import argparse +import numpy as np +import re + +def __main__(): + + parser = argparse.ArgumentParser( + description='Convert an HEDM_map.npz file to a neper tesr file') + parser.add_argument( + 'input', + type=argparse.FileType('rb'), + help='HEDM_map.npz') + parser.add_argument( + 'output', + type=argparse.FileType('w'), + help='neper tesr file' ) + parser.add_argument('-s', '--voxel_spacing', type=float, default=0.005, help='voxel spacing') + parser.add_argument('-x', '--x_name', default='^.*X.*$', help='X array name') + parser.add_argument('-y', '--y_name', default='^.*Y.*$', help='Y array name') + parser.add_argument('-z', '--z_name', default='^.*Z.*$', help='Z array name') + parser.add_argument('-g', '--grain_map', default='^.*grain.*$', help='grain map name') + parser.add_argument('-d', '--debug', action='store_true', help='Debug') + args = parser.parse_args() + data=np.load(args.input) + grain_map = Xs = Ys = Zs = None + for f in data.files: + if re.match(args.grain_map, f): + grain_map = data[f] + elif re.match(args.x_name, f): + Xs = data[f] + elif re.match(args.y_name, f): + Ys = data[f] + elif re.match(args.z_name, f): + Zs = data[f] + voxel_spacing = args.voxel_spacing + + #CREATE ASSEMBLED DATA -- LIST OF [VOXEL COORDINATES (X,Y,Z),GRAIN ID] + + coordinate_list=np.vstack((Xs.ravel(),Ys.ravel(),Zs.ravel())) + assembled_data=np.hstack((coordinate_list.T,np.atleast_2d(grain_map.ravel()).T)) + + #%% SORT BY ROWS Z AND THEN Y + + assembled_data=assembled_data[assembled_data[:,2].argsort()] + total_size=int(grain_map.shape[0]*grain_map.shape[1]*grain_map.shape[2]) + + stack_size=int(grain_map.shape[0]*grain_map.shape[1]) + for ii in np.arange(int(total_size/stack_size)): + tmp_args=assembled_data[ii*stack_size:(ii+1)*stack_size,1].argsort() + assembled_data[ii*stack_size:(ii+1)*stack_size,:]=assembled_data[ii*stack_size+tmp_args,:] + + stack_size=grain_map.shape[1] + for ii in np.arange(int(total_size/stack_size)): + tmp_args=assembled_data[ii*stack_size:(ii+1)*stack_size,0].argsort() + assembled_data[ii*stack_size:(ii+1)*stack_size,:]=assembled_data[ii*stack_size+tmp_args,:] + + #%% + + np.set_printoptions(threshold=np.inf) + l1 = '***tesr' + l2 = ' **format' + l3 = ' 2.0 ascii' + l4 = ' **general' + l5 = ' 3' + l6 = ' ' + str(grain_map.shape[1]) + ' ' + str(grain_map.shape[0]) + ' ' + str(grain_map.shape[2]) + l7 = ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing) + ' ' + str(voxel_spacing) + l8 = ' **cell'; + l9 = ' ' + str(np.max(grain_map).astype('int')) + l10 = ' *id'; + l11 = ' ' + str(np.arange(1,np.max(grain_map)+1).astype('int'))[1:-1] + l12 = ' **data' + #l13 = ' ' + str(assembled_data[:,3].astype('int'))[1:-1] + l14 = '***end' + + #%% + output = args.output + output.write('%s\n' % l1) + output.write('%s\n' % l2) + output.write('%s\n' % l3) + output.write('%s\n' % l4) + output.write('%s\n' % l5) + output.write('%s\n' % l6) + output.write('%s\n' % l7) + output.write('%s\n' % l8) + output.write('%s\n' % l9) + output.write('%s\n' % l10) + output.write('%s\n' % l11) + output.write('%s\n' % l12) + output.write(' ') + np.savetxt(output,np.atleast_2d(assembled_data[:,3]).T,fmt='%d') + #output.write('%s\n' % l13) + output.write('%s\n' % l14) + output.close() + + +if __name__ == "__main__": + __main__() |
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| diff -r 000000000000 -r bd74229f61e8 hedm_npz_to_tesr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hedm_npz_to_tesr.xml Thu Apr 01 18:30:44 2021 +0000 |
| [ |
| @@ -0,0 +1,51 @@ +<tool id="hedm_npz_to_tesr" name="HEDM to tesr" version="0.1.0" python_template_version="3.5"> + <description>Convert HEDM npz to a Neper tesr</description> + <requirements> + <requirement type="package" version="1.19">numpy</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + $__tool_directory__/hedm_npz_to_tesr.py + --voxel_spacing $voxel_spacing + #if $names.x_name: + -x '$names.x_name' + #end if + #if $names.y_name: + -y '$names.y_name' + #end if + #if $names.z_name: + -z '$names.z_name' + #end if + #if $names.grain_map: + --grain_map '$names.grain_map' + #end if + '$input' + '$output' + ]]></command> + <inputs> + <!-- change format to approriate npz subclass when available --> + <param name="input" type="data" format="zip" label="HEDM npz file"/> + <param name="voxel_spacing" type="float" value="0.005" min="0" label="Voxel spacing"/> + <section name="names" expanded="false" title="Specify names used in HEDM.npz input file"> + <param name="x_name" type="text" value="" label="Name of the X array in the input" optional="true" help="Deafault is a name containing 'X'"/> + <param name="y_name" type="text" value="" label="Name of the Y array in the input" optional="true" help="Deafault is a name containing 'Y'"/> + <param name="z_name" type="text" value="" label="Name of the Z array in the input" optional="true" help="Deafault is a name containing 'Z'"/> + <param name="grain_map" type="text" value="" label="Name of the grain map in the input" optional="true" help="Deafault is a name containing 'grain'"/> + </section> + </inputs> + <outputs> + <!-- output format should be changed to tesr when that is available --> + <data name="output" format="txt" label="${input.name.rsplit(sep='.',maxsplit=1)[0]}.tesr"/> + </outputs> + <tests> + <test> + <!-- change format to approriate npz subclass when available --> + <param name="input" ftype="zip" value="HEDM_map.npz"/> + <output name="output" file="HEDM_map.tesr"/> + </test> + </tests> + <help><![CDATA[ + Create a neper compatible tesr format file from a HEDM numpy compressed file. + The converter will look for columns named: Xs, Ys, Zs, and grain_map by default, + If the input file uses different names, the user should specify them. + ]]></help> +</tool> |