centralized functionality for ang import
This commit is contained in:
Martin Diehl
parent
b4ae91f817
commit
48c21045d7
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@ -1,8 +1,10 @@
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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#!/usr/bin/env python3
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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@ -19,47 +21,10 @@ Convert TSL/EDAX *.ang file to ASCIItable
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""", version = scriptID)
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(options, filenames) = parser.parse_args()
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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outname = os.path.splitext(name)[0]+'.txt' if name else name,
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buffered = False, labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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# --- interpret header -----------------------------------------------------------------------------
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table.head_read()
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# --- read comments --------------------------------------------------------------------------------
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table.info_clear()
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while table.data_read(advance = False) and table.line.startswith('#'): # cautiously (non-progressing) read header
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table.info_append(table.line) # add comment to info part
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table.data_read() # wind forward
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table.labels_clear()
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table.labels_append(['1_Euler','2_Euler','3_Euler',
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'1_pos','2_pos',
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'IQ','CI','PhaseID','Intensity','Fit',
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], # OIM Analysis 7.2 Manual, p 403 (of 517)
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reset = True)
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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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#--- write remainder of data file ------------------------------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read():
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outputAlive = table.data_write()
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# ------------------------------------------ finalize output ---------------------------------------
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table.close()
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table = damask.Table.from_ang(StringIO(''.join(sys.stdin.read())) if name is None else name)
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table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.txt')
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@ -3,6 +3,8 @@ import re
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import pandas as pd
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import numpy as np
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from . import version
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class Table():
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"""Store spreadsheet-like data."""
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@ -20,7 +22,7 @@ class Table():
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Additional, human-readable information.
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"""
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self.comments = [] if comments is None else [c for c in comments]
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self.comments = ['table.py v {}'.format(version)] if not comments else [c for c in comments]
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self.data = pd.DataFrame(data=data)
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self.shapes = shapes
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self.__label_condensed()
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@ -69,13 +71,16 @@ class Table():
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f = open(fname)
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except TypeError:
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f = fname
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f.seek(0)
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header,keyword = f.readline().split()
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if keyword == 'header':
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header = int(header)
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else:
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raise Exception
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comments = [f.readline()[:-1] for i in range(1,header)]
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comments = ['table.py:from_ASCII v {}'.format(version)]
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comments+= [f.readline()[:-1] for i in range(1,header)]
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labels = f.readline().split()
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shapes = {}
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@ -95,6 +100,47 @@ class Table():
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return Table(data,shapes,comments)
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@staticmethod
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def from_ang(fname):
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"""
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Create table from TSL ang file.
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A valid TSL ang file needs to contains the following columns:
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* Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
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* Spatial position in meters, 2 floats, label 'pos'.
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* Image quality, 1 float, label 'IQ'.
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* Confidence index, 1 float, label 'CI'.
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* Phase ID, 1 int, label 'ID'.
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* SEM signal, 1 float, label 'intensity'.
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* Fit, 1 float, label 'fit'.
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Parameters
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----------
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fname : file, str, or pathlib.Path
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Filename or file for reading.
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"""
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shapes = {'eu':(3,), 'pos':(2,),
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'IQ':(1,), 'CI':(1,), 'ID':(1,), 'intensity':(1,), 'fit':(1,)}
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try:
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f = open(fname)
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except TypeError:
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f = fname
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f.seek(0)
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content = f.readlines()
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comments = ['table.py:from_ang v {}'.format(version)]
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for line in content:
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if line.startswith('#'):
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comments.append(line.strip())
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else:
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break
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data = np.loadtxt(content)
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return Table(data,shapes,comments)
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@property
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def labels(self):
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return list(self.shapes.keys())
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@ -0,0 +1,138 @@
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# TEM_PIXperUM 1.000000
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# x-star 240.000000
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# y-star 240.000000
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# z-star 240.000000
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# WorkingDistance 20.000000
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#
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# Phase 1
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# MaterialName Iron(Alpha)
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# Formula
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# Info
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# Symmetry 43
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# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000
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# NumberFamilies 100
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# hklFamilies 9223440 0 2 32763 0.000000 32763
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# hklFamilies 0 0 0 9218712 0.000000 9218712
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# hklFamilies 0 0 3801155 0 0.000000 0
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# hklFamilies 5570652 6619251 7536754 -1203738484 0.000000 -1203738484
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# hklFamilies 7143516 5111900 7864421 32763 0.000000 32763
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# hklFamilies 6488180 7274604 6553717 9220480 0.000000 9220480
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# hklFamilies 3145820 2949169 3145777 0 0.000000 0
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# hklFamilies 3014704 7209057 103 9220488 0.000000 9220488
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9220032 0.000000 9220032
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 -1203728363 0.000000 -1203728363
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# hklFamilies 0 0 0 32763 0.000000 32763
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# hklFamilies 0 0 0 9218628 0.000000 9218628
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9218504 0.000000 9218504
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9219904 0.000000 9219904
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 0 -0.000046 0
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 256 0.000000 256
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 -1203753636 0.000000 -1203753636
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# hklFamilies 0 0 0 32763 0.000000 32763
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# hklFamilies 0 0 0 9220576 0.000000 9220576
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9218736 0.000000 9218736
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 103219574 0.000000 103219574
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9220576 0.000000 9220576
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9220692 0.000000 9220692
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# hklFamilies 1434293657 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9218584 0.000000 9218584
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 9219976 0.000000 9219976
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 0 0 256 0.000000 256
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# hklFamilies 0 0 69473872 0 0.000000 0
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# hklFamilies 0 1889785611 -1546188227 -1203753636 -0.000046 -1203753636
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# hklFamilies 9224144 0 1434294456 32763 0.000000 32763
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# hklFamilies 0 9224160 0 9220672 0.000000 9220672
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# hklFamilies -1168390977 32763 851982 0 0.000000 0
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# hklFamilies 0 304 0 9218816 0.000000 9218816
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# hklFamilies 27030208 0 1434297593 0 0.000000 0
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# hklFamilies 0 9224160 0 101654020 0.000000 101654020
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# hklFamilies 9224064 0 0 0 0.000000 0
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# hklFamilies 0 25563456 0 9220672 0.000000 9220672
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# hklFamilies 9224544 0 25559040 0 0.000000 0
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# hklFamilies 0 25559788 0 9220788 0.000000 9220788
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# hklFamilies 176 0 304 24 0.000000 24
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# hklFamilies 0 25562304 0 4 0.000000 4
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# hklFamilies 9224208 0 0 0 0.000000 0
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# hklFamilies 0 281 0 9220032 0.000000 9220032
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# hklFamilies 0 0 0 0 0.000000 0
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# hklFamilies 0 -1168390977 32763 9220660 0.000000 9220660
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# hklFamilies 21 0 -1168390977 8 0.000000 8
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# hklFamilies 32763 2490388 0 24 0.000000 24
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# hklFamilies 48 0 69650048 25 0.000000 25
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# hklFamilies 0 -1216995621 32763 65535 -0.000046 65535
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# hklFamilies 0 0 25562688 1 0.000000 1
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# hklFamilies 0 0 21776 0 -0.000058 0
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# hklFamilies 25562688 0 25559724 0 0.000000 0
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# hklFamilies 0 25559040 0 1179652 0.000000 1179652
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# hklFamilies 25559724 0 25562304 32763 0.000000 32763
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# hklFamilies 0 48 0 9219904 0.000000 9219904
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# hklFamilies 25562304 0 28 0 0.000000 0
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# hklFamilies 0 0 0 8781958 0.000000 8781958
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# hklFamilies 31 0 0 0 0.000000 0
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# hklFamilies 0 0 0 103304392 0.000000 103304392
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# hklFamilies 3 0 48 0 0.000000 0
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# hklFamilies 0 9224505 0 103219694 -0.000046 103219694
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# hklFamilies 27000832 0 -1168393705 0 0.000000 0
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# hklFamilies 32763 25559040 0 9220192 0.000000 9220192
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# hklFamilies 0 32763 31 0 0.000000 0
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# hklFamilies 0 0 0 9219872 0.000000 9219872
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# hklFamilies 69729712 0 9224640 0 0.000000 0
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# hklFamilies 0 69729904 0 1397706823 0.000000 1397706823
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# hklFamilies 69911504 0 0 59 0.000000 59
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# hklFamilies 0 27007968 0 103219200 0.000000 103219200
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# hklFamilies 0 0 -1216843775 0 0.000000 0
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# hklFamilies 32763 69911504 0 0 0.000000 0
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# hklFamilies -1168296496 32763 9225328 0 0.000000 0
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# hklFamilies 0 1434343267 0 9632160 0.000000 9632160
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# hklFamilies 69908840 0 -1216995621 0 0.000000 0
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# hklFamilies 32763 256 0 9632112 0.000000 9632112
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# hklFamilies 0 0 399376220 0 0.000000 0
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# hklFamilies 21776 1966087 4456474 262148 0.000000 262148
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# hklFamilies 9224704 0 1434198234 0 0.000000 0
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# hklFamilies 0 0 0 9704044 0.000000 9704044
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# hklFamilies -1168373699 32763 1 0 0.000000 0
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# hklFamilies 0 69911504 0 94961568 -0.000046 94961568
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# hklFamilies 1 0 69911504 0 0.000000 0
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# hklFamilies 0 10 0 9220016 0.000000 9220016
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# hklFamilies -1 0 27030208 0 0.000000 0
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# hklFamilies 0 1434488087 18 9219992 -0.000046 9219992
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# ElasticConstants 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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# Categories1 1 1 1 1
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#
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# GRID: SqrGrid
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# XSTEP: 0.050000
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# YSTEP: 0.050000
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# NCOLS_ODD: 2
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# NCOLS_EVEN: 2
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# NROWS: 2
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#
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# OPERATOR:
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#
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# SAMPLEID:
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#
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# SCANID:
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#
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0.0 0.0 0.0 0.00 0.00 60.0 20.0 1 2.0 1.5
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0.0 2.0 0.0 0.05 0.00 60.0 20.0 1 2.0 1.5
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0.0 2.0 0.0 0.00 0.05 60.0 20.0 1 2.0 1.5
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0.0 0.0 1.0 0.05 0.05 60.0 20.0 1 2.0 1.5
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@ -47,6 +47,17 @@ class TestTable:
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new = Table.from_ASCII(f)
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assert all(default.data==new.data)
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def test_read_ang_str(self,reference_dir):
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new = Table.from_ang(os.path.join(reference_dir,'simple.ang'))
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assert new.data.shape == (4,10) and \
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new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
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def test_read_ang_file(self,reference_dir):
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f = open(os.path.join(reference_dir,'simple.ang'))
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new = Table.from_ang(f)
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assert new.data.shape == (4,10) and \
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new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
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@pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
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def test_read_strange(self,reference_dir,fname):
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with open(os.path.join(reference_dir,fname)) as f:
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