diff hedm_npz_to_tesr.py @ 4:b49a8ef3351d draft

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_npz_to_tesr commit 0db0d2633f65e2ceca2e34c8899a52b18965d059"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hedm_npz_to_tesr.py	Thu Apr 01 18:29:39 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__()