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centralized functionality for ang import

This commit is contained in:
Martin Diehl 2019-12-22 09:04:50 +01:00
parent b4ae91f817
commit 48c21045d7
4 changed files with 204 additions and 44 deletions
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49
processing/misc/ang_toTable.py
View File

@ -1,8 +1,10 @@
#!/usr/bin/env python2.7 #!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os import os
import sys
from io import StringIO
from optparse import OptionParser from optparse import OptionParser
import damask import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
@ -19,47 +21,10 @@ Convert TSL/EDAX *.ang file to ASCIItable
""", version = scriptID) """, version = scriptID)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: damask.util.report(scriptName,name)
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.txt' if name else name,
buffered = False, labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------- table = damask.Table.from_ang(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.txt')
table.head_read()
# --- read comments --------------------------------------------------------------------------------
table.info_clear()
while table.data_read(advance = False) and table.line.startswith('#'): # cautiously (non-progressing) read header
table.info_append(table.line) # add comment to info part
table.data_read() # wind forward
table.labels_clear()
table.labels_append(['1_Euler','2_Euler','3_Euler',
'1_pos','2_pos',
'IQ','CI','PhaseID','Intensity','Fit',
], # OIM Analysis 7.2 Manual, p 403 (of 517)
reset = True)
# ------------------------------------------ assemble header ---------------------------------------
table.head_write()
#--- write remainder of data file ------------------------------------------------------------------
outputAlive = True
while outputAlive and table.data_read():
outputAlive = table.data_write()
# ------------------------------------------ finalize output ---------------------------------------
table.close()

50
python/damask/table.py
View File

@ -3,6 +3,8 @@ import re
import pandas as pd import pandas as pd
import numpy as np import numpy as np
from . import version
class Table(): class Table():
"""Store spreadsheet-like data.""" """Store spreadsheet-like data."""
@ -20,7 +22,7 @@ class Table():
Additional, human-readable information. Additional, human-readable information.
""" """
self.comments = [] if comments is None else [c for c in comments] self.comments = ['table.py v {}'.format(version)] if not comments else [c for c in comments]
self.data = pd.DataFrame(data=data) self.data = pd.DataFrame(data=data)
self.shapes = shapes self.shapes = shapes
self.__label_condensed() self.__label_condensed()
@ -69,13 +71,16 @@ class Table():
f = open(fname) f = open(fname)
except TypeError: except TypeError:
f = fname f = fname
f.seek(0)
header,keyword = f.readline().split() header,keyword = f.readline().split()
if keyword == 'header': if keyword == 'header':
header = int(header) header = int(header)
else: else:
raise Exception raise Exception
comments = [f.readline()[:-1] for i in range(1,header)]
comments = ['table.py:from_ASCII v {}'.format(version)]
comments+= [f.readline()[:-1] for i in range(1,header)]
labels = f.readline().split() labels = f.readline().split()
shapes = {} shapes = {}
@ -95,6 +100,47 @@ class Table():
return Table(data,shapes,comments) return Table(data,shapes,comments)
@staticmethod
def from_ang(fname):
"""
Create table from TSL ang file.
A valid TSL ang file needs to contains the following columns:
* Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
* Spatial position in meters, 2 floats, label 'pos'.
* Image quality, 1 float, label 'IQ'.
* Confidence index, 1 float, label 'CI'.
* Phase ID, 1 int, label 'ID'.
* SEM signal, 1 float, label 'intensity'.
* Fit, 1 float, label 'fit'.
Parameters
----------
fname : file, str, or pathlib.Path
Filename or file for reading.
"""
shapes = {'eu':(3,), 'pos':(2,),
'IQ':(1,), 'CI':(1,), 'ID':(1,), 'intensity':(1,), 'fit':(1,)}
try:
f = open(fname)
except TypeError:
f = fname
f.seek(0)
content = f.readlines()
comments = ['table.py:from_ang v {}'.format(version)]
for line in content:
if line.startswith('#'):
comments.append(line.strip())
else:
break
data = np.loadtxt(content)
return Table(data,shapes,comments)
@property @property
def labels(self): def labels(self):
return list(self.shapes.keys()) return list(self.shapes.keys())

138
python/tests/reference/Table/simple.ang Normal file
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@ -0,0 +1,138 @@
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11
python/tests/test_Table.py
View File

@ -47,6 +47,17 @@ class TestTable:
new = Table.from_ASCII(f) new = Table.from_ASCII(f)
assert all(default.data==new.data) assert all(default.data==new.data)
def test_read_ang_str(self,reference_dir):
new = Table.from_ang(os.path.join(reference_dir,'simple.ang'))
assert new.data.shape == (4,10) and \
new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
def test_read_ang_file(self,reference_dir):
f = open(os.path.join(reference_dir,'simple.ang'))
new = Table.from_ang(f)
assert new.data.shape == (4,10) and \
new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
@pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt']) @pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
def test_read_strange(self,reference_dir,fname): def test_read_strange(self,reference_dir,fname):
with open(os.path.join(reference_dir,fname)) as f: with open(os.path.join(reference_dir,fname)) as f: