223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

changed "labels" property to "tags". added method to inquire about (abstract) labels, i.e. interpreting the tag list to distill underlying label "meaning".

This commit is contained in:
Aritra Chakraborty 2016-05-16 19:54:00 -04:00
parent 8540748220
commit dc6260be58
1 changed files with 75 additions and 37 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

106
lib/damask/asciitable.py
View File

@ -1,6 +1,5 @@
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys import os,sys
import numpy as np import numpy as np
@ -26,7 +25,7 @@ class ASCIItable():
self.__IO__ = {'output': [], self.__IO__ = {'output': [],
'buffered': buffered, 'buffered': buffered,
'labeled': labeled, # header contains labels 'labeled': labeled, # header contains labels
'labels': [], # labels according to file info 'tags': [], # labels according to file info
'readBuffer': [], # buffer to hold non-advancing reads 'readBuffer': [], # buffer to hold non-advancing reads
'dataStart': 0, 'dataStart': 0,
} }
@ -50,7 +49,7 @@ class ASCIItable():
self.__IO__['out'] = outname self.__IO__['out'] = outname
self.info = [] self.info = []
self.labels = [] self.tags = []
self.data = [] self.data = []
self.line = '' self.line = ''
@ -160,7 +159,7 @@ class ASCIItable():
if self.__IO__['labeled']: # table features labels if self.__IO__['labeled']: # table features labels
self.info = [self.__IO__['in'].readline().strip() for i in xrange(1,int(m.group(1)))] self.info = [self.__IO__['in'].readline().strip() for i in xrange(1,int(m.group(1)))]
self.labels = shlex.split(self.__IO__['in'].readline()) # store labels found in last line self.tags = shlex.split(self.__IO__['in'].readline()) # store tags found in last line
else: else:
@ -179,11 +178,11 @@ class ASCIItable():
else: break # last line of comments else: break # last line of comments
if self.__IO__['labeled']: # table features labels if self.__IO__['labeled']: # table features labels
self.labels = self.data # get labels from last line in "header"... self.tags = self.data # get tags from last line in "header"...
self.data_read() # ...and remove from buffer self.data_read() # ...and remove from buffer
if self.__IO__['labeled']: # table features labels if self.__IO__['labeled']: # table features tags
self.__IO__['labels'] = list(self.labels) # backup labels (make COPY, not link) self.__IO__['tags'] = list(self.tags) # backup tags (make COPY, not link)
try: try:
self.__IO__['dataStart'] = self.__IO__['in'].tell() # current file position is at start of data self.__IO__['dataStart'] = self.__IO__['in'].tell() # current file position is at start of data
@ -196,7 +195,7 @@ class ASCIItable():
"""write current header information (info + labels)""" """write current header information (info + labels)"""
head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else [] head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
head.append(self.info) head.append(self.info)
if self.__IO__['labeled']: head.append('\t'.join(map(self._quote,self.labels))) if self.__IO__['labeled']: head.append('\t'.join(map(self._quote,self.tags)))
return self.output_write(head) return self.output_write(head)
@ -260,19 +259,58 @@ class ASCIItable():
try: try:
for item in what: self.labels_append(item) for item in what: self.labels_append(item)
except: except:
self.labels += [self._removeCRLF(str(what))] self.tags += [self._removeCRLF(str(what))]
else: else:
self.labels += [self._removeCRLF(what)] self.tags += [self._removeCRLF(what)]
self.__IO__['labeled'] = True # switch on processing (in particular writing) of labels self.__IO__['labeled'] = True # switch on processing (in particular writing) of tags
if reset: self.__IO__['labels'] = list(self.labels) # subsequent data_read uses current labels as data size if reset: self.__IO__['tags'] = list(self.tags) # subsequent data_read uses current tags as data size
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def labels_clear(self): def labels_clear(self):
"""delete existing labels and switch to no labeling""" """delete existing labels and switch to no labeling"""
self.labels = [] self.tags = []
self.__IO__['labeled'] = False self.__IO__['labeled'] = False
# ------------------------------------------------------------------
def labels(self,
tags = None,
raw = False,
):
"""
returns abstract labels (e.g. "x" for "1_x","2_x",...)
unless raw output is requested.
operates on object tags or given list.
"""
from collections import Iterable
if tags is None: tags = self.tags
if isinstance(tags, Iterable) and not raw: # check whether list of tags is requested
id = 0
dim = 1
labelList = []
while id < len(tags):
if not tags[id].startswith('1_'):
labelList.append(tags[id])
else:
label = tags[id][2:] # get label
while id < len(tags) and tags[id] == '{}_{}'.format(dim,label): # check successors
id += 1 # next label...
dim += 1 # ...should be one higher dimension
LabelList.append(label) # reached end --> store
id -= 1 # rewind one to consider again
id += 1
dim = 1
else:
labelList = self.tags
return labelList
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def label_index(self, def label_index(self,
labels): labels):
@ -292,10 +330,10 @@ class ASCIItable():
idx.append(int(label)-1) # column given as integer number? idx.append(int(label)-1) # column given as integer number?
except ValueError: except ValueError:
try: try:
idx.append(self.labels.index(label)) # locate string in label list idx.append(self.tags.index(label)) # locate string in label list
except ValueError: except ValueError:
try: try:
idx.append(self.labels.index('1_'+label)) # locate '1_'+string in label list idx.append(self.tags.index('1_'+label)) # locate '1_'+string in label list
except ValueError: except ValueError:
idx.append(-1) # not found... idx.append(-1) # not found...
else: else:
@ -303,10 +341,10 @@ class ASCIItable():
idx = int(labels)-1 # offset for python array indexing idx = int(labels)-1 # offset for python array indexing
except ValueError: except ValueError:
try: try:
idx = self.labels.index(labels) idx = self.tags.index(labels)
except ValueError: except ValueError:
try: try:
idx = self.labels.index('1_'+labels) # locate '1_'+string in label list idx = self.tags.index('1_'+labels) # locate '1_'+string in label list
except ValueError: except ValueError:
idx = None if labels is None else -1 idx = None if labels is None else -1
@ -331,16 +369,16 @@ class ASCIItable():
try: # column given as number? try: # column given as number?
idx = int(label)-1 idx = int(label)-1
myDim = 1 # if found has at least dimension 1 myDim = 1 # if found has at least dimension 1
if self.labels[idx].startswith('1_'): # column has multidim indicator? if self.tags[idx].startswith('1_'): # column has multidim indicator?
while idx+myDim < len(self.labels) and self.labels[idx+myDim].startswith("%i_"%(myDim+1)): while idx+myDim < len(self.tags) and self.tags[idx+myDim].startswith("%i_"%(myDim+1)):
myDim += 1 # add while found myDim += 1 # add while found
except ValueError: # column has string label except ValueError: # column has string label
if label in self.labels: # can be directly found? if label in self.tags: # can be directly found?
myDim = 1 # scalar by definition myDim = 1 # scalar by definition
elif '1_'+label in self.labels: # look for first entry of possible multidim object elif '1_'+label in self.tags: # look for first entry of possible multidim object
idx = self.labels.index('1_'+label) # get starting column idx = self.tags.index('1_'+label) # get starting column
myDim = 1 # (at least) one-dimensional myDim = 1 # (at least) one-dimensional
while idx+myDim < len(self.labels) and self.labels[idx+myDim].startswith("%i_"%(myDim+1)): while idx+myDim < len(self.tags) and self.tags[idx+myDim].startswith("%i_"%(myDim+1)):
myDim += 1 # keep adding while going through object myDim += 1 # keep adding while going through object
dim.append(myDim) dim.append(myDim)
@ -350,16 +388,16 @@ class ASCIItable():
try: # column given as number? try: # column given as number?
idx = int(labels)-1 idx = int(labels)-1
dim = 1 # if found has at least dimension 1 dim = 1 # if found has at least dimension 1
if self.labels[idx].startswith('1_'): # column has multidim indicator? if self.tags[idx].startswith('1_'): # column has multidim indicator?
while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)): while idx+dim < len(self.tags) and self.tags[idx+dim].startswith("%i_"%(dim+1)):
dim += 1 # add as long as found dim += 1 # add as long as found
except ValueError: # column has string label except ValueError: # column has string label
if labels in self.labels: # can be directly found? if labels in self.tags: # can be directly found?
dim = 1 # scalar by definition dim = 1 # scalar by definition
elif '1_'+labels in self.labels: # look for first entry of possible multidim object elif '1_'+labels in self.tags: # look for first entry of possible multidim object
idx = self.labels.index('1_'+labels) # get starting column idx = self.tags.index('1_'+labels) # get starting column
dim = 1 # is (at least) one-dimensional dim = 1 # is (at least) one-dimensional
while idx+dim < len(self.labels) and self.labels[idx+dim].startswith("%i_"%(dim+1)): while idx+dim < len(self.tags) and self.tags[idx+dim].startswith("%i_"%(dim+1)):
dim += 1 # keep adding while going through object dim += 1 # keep adding while going through object
return np.array(dim) if isinstance(dim,Iterable) else dim return np.array(dim) if isinstance(dim,Iterable) else dim
@ -403,8 +441,8 @@ class ASCIItable():
def data_rewind(self): def data_rewind(self):
self.__IO__['in'].seek(self.__IO__['dataStart']) # position file to start of data section self.__IO__['in'].seek(self.__IO__['dataStart']) # position file to start of data section
self.__IO__['readBuffer'] = [] # delete any non-advancing data reads self.__IO__['readBuffer'] = [] # delete any non-advancing data reads
self.labels = list(self.__IO__['labels']) # restore label info found in header (as COPY, not link) self.tags = list(self.__IO__['tags']) # restore label info found in header (as COPY, not link)
self.__IO__['labeled'] = len(self.labels) > 0 self.__IO__['labeled'] = len(self.tags) > 0
# ------------------------------------------------------------------ # ------------------------------------------------------------------
def data_skipLines(self, def data_skipLines(self,
@ -431,8 +469,8 @@ class ASCIItable():
self.line = self.line.rstrip('\n') self.line = self.line.rstrip('\n')
if self.__IO__['labeled'] and respectLabels: # if table has labels if self.__IO__['labeled'] and respectLabels: # if table has labels
items = shlex.split(self.line)[:len(self.__IO__['labels'])] # use up to label count (from original file info) items = shlex.split(self.line)[:len(self.__IO__['tags'])] # use up to label count (from original file info)
self.data = items if len(items) == len(self.__IO__['labels']) else [] # take entries if label count matches self.data = items if len(items) == len(self.__IO__['tags']) else [] # take entries if label count matches
else: else:
self.data = shlex.split(self.line) # otherwise take all self.data = shlex.split(self.line) # otherwise take all
@ -469,7 +507,7 @@ class ASCIItable():
1)) 1))
use = np.array(columns) use = np.array(columns)
self.labels = list(np.array(self.labels)[use]) # update labels with valid subset self.tags = list(np.array(self.tags)[use]) # update labels with valid subset
self.data = np.loadtxt(self.__IO__['in'],usecols=use,ndmin=2) self.data = np.loadtxt(self.__IO__['in'],usecols=use,ndmin=2)