1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
|
"""mrecords
Defines the equivalent of recarrays for maskedarray.
Masked arrays already support named fields, but masking works only by records.
By comparison, mrecarrays support masking individual fields.
:author: Pierre Gerard-Marchant
"""
#TODO: We should make sure that no field is called '_mask','mask','_fieldmask',
#TODO: ...or whatever restricted keywords.
#TODO: An idea would be to no bother in the first place, and then rename the
#TODO: invalid fields with a trailing underscore...
#TODO: Maybe we could just overload the parser function ?
__author__ = "Pierre GF Gerard-Marchant"
import sys
import types
import numpy as np
from numpy import bool_, complex_, float_, int_, str_, object_, dtype, \
chararray, ndarray, recarray, record, array as narray
import numpy.core.numerictypes as ntypes
from numpy.core.records import find_duplicate, format_parser
from numpy.core.records import fromarrays as recfromarrays, \
fromrecords as recfromrecords
_byteorderconv = np.core.records._byteorderconv
_typestr = ntypes._typestr
import numpy.ma as ma
from numpy.ma import MAError, MaskedArray, masked, nomask, masked_array,\
make_mask, mask_or, getdata, getmask, getmaskarray, filled, \
default_fill_value, masked_print_option
_check_fill_value = ma.core._check_fill_value
import warnings
__all__ = ['MaskedRecords','mrecarray',
'fromarrays','fromrecords','fromtextfile','addfield',
]
reserved_fields = ['_data','_mask','_fieldmask', 'dtype']
def _getformats(data):
"Returns the formats of each array of arraylist as a comma-separated string."
if hasattr(data,'dtype'):
return ",".join([desc[1] for desc in data.dtype.descr])
formats = ''
for obj in data:
obj = np.asarray(obj)
# if not isinstance(obj, ndarray):
## if not isinstance(obj, ndarray):
# raise ValueError, "item in the array list must be an ndarray."
formats += _typestr[obj.dtype.type]
if issubclass(obj.dtype.type, ntypes.flexible):
formats += `obj.itemsize`
formats += ','
return formats[:-1]
def _checknames(descr, names=None):
"""Checks that the field names of the descriptor ``descr`` are not some
reserved keywords. If this is the case, a default 'f%i' is substituted.
If the argument `names` is not None, updates the field names to valid names.
"""
ndescr = len(descr)
default_names = ['f%i' % i for i in range(ndescr)]
if names is None:
new_names = default_names
else:
if isinstance(names, (tuple, list)):
new_names = names
elif isinstance(names, str):
new_names = names.split(',')
else:
raise NameError, "illegal input names %s" % `names`
nnames = len(new_names)
if nnames < ndescr:
new_names += default_names[nnames:]
ndescr = []
for (n, d, t) in zip(new_names, default_names, descr.descr):
if n in reserved_fields:
if t[0] in reserved_fields:
ndescr.append((d,t[1]))
else:
ndescr.append(t)
else:
ndescr.append((n,t[1]))
return numeric.dtype(ndescr)
def _get_fieldmask(self):
mdescr = [(n,'|b1') for n in self.dtype.names]
fdmask = np.empty(self.shape, dtype=mdescr)
fdmask.flat = tuple([False]*len(mdescr))
return fdmask
class MaskedRecords(MaskedArray, object):
"""
*IVariables*:
_data : {recarray}
Underlying data, as a record array.
_mask : {boolean array}
Mask of the records. A record is masked when all its fields are masked.
_fieldmask : {boolean recarray}
Record array of booleans, setting the mask of each individual field of each record.
_fill_value : {record}
Filling values for each field.
"""
_defaultfieldmask = nomask
_defaulthardmask = False
#............................................
def __new__(cls, shape, dtype=None, buf=None, offset=0, strides=None,
formats=None, names=None, titles=None,
byteorder=None, aligned=False,
mask=nomask, hard_mask=False, fill_value=None, keep_mask=True,
copy=False,
**options):
#
self = recarray.__new__(cls, shape, dtype=dtype, buf=buf, offset=offset,
strides=strides, formats=formats,
byteorder=byteorder, aligned=aligned,)
# self = self.view(cls)
#
mdtype = [(k,'|b1') for (k,_) in self.dtype.descr]
if mask is nomask or not np.size(mask):
if not keep_mask:
self._fieldmask = tuple([False]*len(mdtype))
else:
mask = np.array(mask, copy=copy)
if mask.shape != self.shape:
(nd, nm) = (self.size, mask.size)
if nm == 1:
mask = np.resize(mask, self.shape)
elif nm == nd:
mask = np.reshape(mask, self.shape)
else:
msg = "Mask and data not compatible: data size is %i, "+\
"mask size is %i."
raise MAError(msg % (nd, nm))
copy = True
if not keep_mask:
self.__setmask__(mask)
self._sharedmask = True
else:
if mask.dtype == mdtype:
_fieldmask = mask
else:
_fieldmask = np.array([tuple([m]*len(mdtype)) for m in mask],
dtype=mdtype)
self._fieldmask = _fieldmask
return self
#......................................................
def __array_finalize__(self,obj):
# Make sure we have a _fieldmask by default ..
_fieldmask = getattr(obj, '_fieldmask', None)
if _fieldmask is None:
mdescr = [(n,'|b1') for (n,_) in self.dtype.descr]
_mask = getattr(obj, '_mask', nomask)
if _mask is nomask:
_fieldmask = np.empty(self.shape, dtype=mdescr).view(recarray)
_fieldmask.flat = tuple([False]*len(mdescr))
else:
_fieldmask = narray([tuple([m]*len(mdescr)) for m in _mask],
dtype=mdescr).view(recarray)
# Update some of the attributes
if obj is not None:
_baseclass = getattr(obj,'_baseclass',type(obj))
else:
_baseclass = recarray
attrdict = dict(_fieldmask=_fieldmask,
_hardmask=getattr(obj,'_hardmask',False),
_fill_value=getattr(obj,'_fill_value',None),
_sharedmask=getattr(obj,'_sharedmask',False),
_baseclass=_baseclass)
self.__dict__.update(attrdict)
# Finalize as a regular maskedarray .....
# Update special attributes ...
self._basedict = getattr(obj, '_basedict', getattr(obj,'__dict__',{}))
self.__dict__.update(self._basedict)
return
#......................................................
def _getdata(self):
"Returns the data as a recarray."
return ndarray.view(self,recarray)
_data = property(fget=_getdata)
#......................................................
def __setmask__(self, mask):
"Sets the mask and update the fieldmask."
names = self.dtype.names
fmask = self.__dict__['_fieldmask']
#
if isinstance(mask,ndarray) and mask.dtype.names == names:
for n in names:
fmask[n] = mask[n].astype(bool)
# self.__dict__['_fieldmask'] = fmask.view(recarray)
return
newmask = make_mask(mask, copy=False)
if names is not None:
if self._hardmask:
for n in names:
fmask[n].__ior__(newmask)
else:
for n in names:
fmask[n].flat = newmask
return
_setmask = __setmask__
#
def _getmask(self):
"""Return the mask of the mrecord.
A record is masked when all the fields are masked.
"""
if self.size > 1:
return self._fieldmask.view((bool_, len(self.dtype))).all(1)
else:
return self._fieldmask.view((bool_, len(self.dtype))).all()
mask = _mask = property(fget=_getmask, fset=_setmask)
#......................................................
def get_fill_value(self):
"""Return the filling value.
"""
if self._fill_value is None:
ddtype = self.dtype
fillval = _check_fill_value(None, ddtype)
self._fill_value = np.array(tuple(fillval), dtype=ddtype)
return self._fill_value
def set_fill_value(self, value=None):
"""Set the filling value to value.
If value is None, use a default based on the data type.
"""
ddtype = self.dtype
fillval = _check_fill_value(value, ddtype)
self._fill_value = np.array(tuple(fillval), dtype=ddtype)
fill_value = property(fget=get_fill_value, fset=set_fill_value,
doc="Filling value.")
#......................................................
def __len__(self):
"Returns the length"
# We have more than one record
if self.ndim:
return len(self._data)
# We have only one record: return the nb of fields
return len(self.dtype)
#......................................................
def __getattribute__(self, attr):
"Returns the given attribute."
try:
# Returns a generic attribute
return object.__getattribute__(self,attr)
except AttributeError:
# OK, so attr must be a field name
pass
# Get the list of fields ......
_names = self.dtype.names
if attr in _names:
_data = self._data
_mask = self._fieldmask
# obj = masked_array(_data.__getattribute__(attr), copy=False,
# mask=_mask.__getattribute__(attr))
# Use a view in order to avoid the copy of the mask in MaskedArray.__new__
obj = narray(_data.__getattribute__(attr), copy=False).view(MaskedArray)
obj._mask = _mask.__getattribute__(attr)
if not obj.ndim and obj._mask:
return masked
return obj
raise AttributeError,"No attribute '%s' !" % attr
def __setattr__(self, attr, val):
"Sets the attribute attr to the value val."
# newattr = attr not in self.__dict__
try:
# Is attr a generic attribute ?
ret = object.__setattr__(self, attr, val)
except:
# Not a generic attribute: exit if it's not a valid field
fielddict = self.dtype.names or {}
if attr not in fielddict:
exctype, value = sys.exc_info()[:2]
raise exctype, value
else:
if attr in ['_mask','fieldmask']:
self.__setmask__(val)
return
# Get the list of names ......
_names = self.dtype.names
if _names is None:
_names = []
else:
_names = list(_names)
# Check the attribute
self_dict = self.__dict__
if attr not in _names+list(self_dict):
return ret
if attr not in self_dict: # We just added this one
try: # or this setattr worked on an internal
# attribute.
object.__delattr__(self, attr)
except:
return ret
# Case #1.: Basic field ............
base_fmask = self._fieldmask
_names = self.dtype.names or []
if attr in _names:
if val is masked:
fval = self.fill_value[attr]
mval = True
else:
fval = filled(val)
mval = getmaskarray(val)
if self._hardmask:
mval = mask_or(mval, base_fmask.__getattr__(attr))
self._data.__setattr__(attr, fval)
base_fmask.__setattr__(attr, mval)
return
#............................................
def __getitem__(self, indx):
"""Returns all the fields sharing the same fieldname base.
The fieldname base is either `_data` or `_mask`."""
_localdict = self.__dict__
_fieldmask = _localdict['_fieldmask']
_data = self._data
# We want a field ........
if isinstance(indx, basestring):
obj = _data[indx].view(MaskedArray)
obj._set_mask(_fieldmask[indx])
# Force to nomask if the mask is empty
if not obj._mask.any():
obj._mask = nomask
# Force to masked if the mask is True
if not obj.ndim and obj._mask:
return masked
return obj
# We want some elements ..
# First, the data ........
obj = narray(_data[indx], copy=False).view(mrecarray)
obj._fieldmask = narray(_fieldmask[indx], copy=False).view(recarray)
return obj
#....
def __setitem__(self, indx, value):
"Sets the given record to value."
MaskedArray.__setitem__(self, indx, value)
if isinstance(indx, basestring):
self._fieldmask[indx] = ma.getmaskarray(value)
#............................................
def __setslice__(self, i, j, value):
"Sets the slice described by [i,j] to `value`."
_localdict = self.__dict__
d = self._data
m = _localdict['_fieldmask']
names = self.dtype.names
if value is masked:
for n in names:
m[i:j][n] = True
elif not self._hardmask:
fval = filled(value)
mval = getmaskarray(value)
for n in names:
d[n][i:j] = fval
m[n][i:j] = mval
else:
mindx = getmaskarray(self)[i:j]
dval = np.asarray(value)
valmask = getmask(value)
if valmask is nomask:
for n in names:
mval = mask_or(m[n][i:j], valmask)
d[n][i:j][~mval] = value
elif valmask.size > 1:
for n in names:
mval = mask_or(m[n][i:j], valmask)
d[n][i:j][~mval] = dval[~mval]
m[n][i:j] = mask_or(m[n][i:j], mval)
self._fieldmask = m
#......................................................
def __str__(self):
"Calculates the string representation."
if self.size > 1:
mstr = ["(%s)" % ",".join([str(i) for i in s])
for s in zip(*[getattr(self,f) for f in self.dtype.names])]
return "[%s]" % ", ".join(mstr)
else:
mstr = ["%s" % ",".join([str(i) for i in s])
for s in zip([getattr(self,f) for f in self.dtype.names])]
return "(%s)" % ", ".join(mstr)
#
def __repr__(self):
"Calculates the repr representation."
_names = self.dtype.names
fmt = "%%%is : %%s" % (max([len(n) for n in _names])+4,)
reprstr = [fmt % (f,getattr(self,f)) for f in self.dtype.names]
reprstr.insert(0,'masked_records(')
reprstr.extend([fmt % (' fill_value', self.fill_value),
' )'])
return str("\n".join(reprstr))
#......................................................
def view(self, obj):
"""Returns a view of the mrecarray."""
try:
if issubclass(obj, ndarray):
return ndarray.view(self, obj)
except TypeError:
pass
dtype = np.dtype(obj)
if dtype.fields is None:
return self.__array__().view(dtype)
return ndarray.view(self, obj)
#......................................................
def filled(self, fill_value=None):
"""Returns an array of the same class as the _data part, where masked
values are filled with fill_value.
If fill_value is None, self.fill_value is used instead.
Subclassing is preserved.
"""
_localdict = self.__dict__
d = self._data
fm = _localdict['_fieldmask']
if not np.asarray(fm, dtype=bool_).any():
return d
#
if fill_value is None:
value = _check_fill_value(_localdict['_fill_value'],self.dtype)
else:
value = fill_value
if np.size(value) == 1:
value = [value,] * len(self.dtype)
#
if self is masked:
result = np.asanyarray(value)
else:
result = d.copy()
for (n, v) in zip(d.dtype.names, value):
np.putmask(np.asarray(result[n]), np.asarray(fm[n]), v)
return result
#......................................................
def harden_mask(self):
"Forces the mask to hard"
self._hardmask = True
def soften_mask(self):
"Forces the mask to soft"
self._hardmask = False
#......................................................
def copy(self):
"""Returns a copy of the masked record."""
_localdict = self.__dict__
copied = self._data.copy().view(type(self))
copied._fieldmask = self._fieldmask.copy()
return copied
#......................................................
def tolist(self, fill_value=None):
"""Copy the data portion of the array to a hierarchical python
list and returns that list.
Data items are converted to the nearest compatible Python
type. Masked values are converted to fill_value. If
fill_value is None, the corresponding entries in the output
list will be ``None``.
"""
if fill_value is not None:
return self.filled(fill_value).tolist()
result = narray(self.filled().tolist(), dtype=object)
mask = narray(self._fieldmask.tolist())
result[mask] = None
return result.tolist()
#--------------------------------------------
# Pickling
def __getstate__(self):
"""Return the internal state of the masked array, for pickling purposes.
"""
state = (1,
self.shape,
self.dtype,
self.flags.fnc,
self._data.tostring(),
self._fieldmask.tostring(),
self._fill_value,
)
return state
#
def __setstate__(self, state):
"""Restore the internal state of the masked array, for pickling purposes.
``state`` is typically the output of the ``__getstate__`` output, and is a
5-tuple:
- class name
- a tuple giving the shape of the data
- a typecode for the data
- a binary string for the data
- a binary string for the mask.
"""
(ver, shp, typ, isf, raw, msk, flv) = state
ndarray.__setstate__(self, (shp, typ, isf, raw))
mdtype = dtype([(k,bool_) for (k,_) in self.dtype.descr])
self.__dict__['_fieldmask'].__setstate__((shp, mdtype, isf, msk))
self.fill_value = flv
#
def __reduce__(self):
"""Return a 3-tuple for pickling a MaskedArray.
"""
return (_mrreconstruct,
(self.__class__, self._baseclass, (0,), 'b', ),
self.__getstate__())
def _mrreconstruct(subtype, baseclass, baseshape, basetype,):
"""Internal function that builds a new MaskedArray from the
information stored in a pickle.
"""
_data = ndarray.__new__(baseclass, baseshape, basetype).view(subtype)
# _data._mask = ndarray.__new__(ndarray, baseshape, 'b1')
# return _data
_mask = ndarray.__new__(ndarray, baseshape, 'b1')
return subtype.__new__(subtype, _data, mask=_mask, dtype=basetype,)
mrecarray = MaskedRecords
#####---------------------------------------------------------------------------
#---- --- Constructors ---
#####---------------------------------------------------------------------------
def fromarrays(arraylist, dtype=None, shape=None, formats=None,
names=None, titles=None, aligned=False, byteorder=None,
fill_value=None):
"""Creates a mrecarray from a (flat) list of masked arrays.
Parameters
----------
arraylist : sequence
A list of (masked) arrays. Each element of the sequence is first converted
to a masked array if needed. If a 2D array is passed as argument, it is
processed line by line
dtype : numeric.dtype
Data type descriptor.
shape : integer
Number of records. If None, shape is defined from the shape of the
first array in the list.
formats : sequence
Sequence of formats for each individual field. If None, the formats will
be autodetected by inspecting the fields and selecting the highest dtype
possible.
names : sequence
Sequence of the names of each field.
titles : sequence
(Description to write)
aligned : boolean
(Description to write, not used anyway)
byteorder: boolean
(Description to write, not used anyway)
fill_value : sequence
Sequence of data to be used as filling values.
Notes
-----
Lists of tuples should be preferred over lists of lists for faster processing.
"""
datalist = [getdata(x) for x in arraylist]
masklist = [getmaskarray(x) for x in arraylist]
_array = recfromarrays(datalist,
dtype=dtype, shape=shape, formats=formats,
names=names, titles=titles, aligned=aligned,
byteorder=byteorder).view(mrecarray)
_array._fieldmask[:] = zip(*masklist)
if fill_value is not None:
_array.fill_value = fill_value
return _array
#..............................................................................
def fromrecords(reclist, dtype=None, shape=None, formats=None, names=None,
titles=None, aligned=False, byteorder=None,
fill_value=None, mask=nomask):
"""Creates a MaskedRecords from a list of records.
Parameters
----------
arraylist : sequence
A list of (masked) arrays. Each element of the sequence is first converted
to a masked array if needed. If a 2D array is passed as argument, it is
processed line by line
dtype : numeric.dtype
Data type descriptor.
shape : integer
Number of records. If None, ``shape`` is defined from the shape of the
first array in the list.
formats : sequence
Sequence of formats for each individual field. If None, the formats will
be autodetected by inspecting the fields and selecting the highest dtype
possible.
names : sequence
Sequence of the names of each field.
titles : sequence
(Description to write)
aligned : boolean
(Description to write, not used anyway)
byteorder: boolean
(Description to write, not used anyway)
fill_value : sequence
Sequence of data to be used as filling values.
mask : sequence or boolean.
External mask to apply on the data.
*Notes*:
Lists of tuples should be preferred over lists of lists for faster processing.
"""
# Grab the initial _fieldmask, if needed:
_fieldmask = getattr(reclist, '_fieldmask', None)
# Get the list of records.....
nfields = len(reclist[0])
if isinstance(reclist, ndarray):
# Make sure we don't have some hidden mask
if isinstance(reclist,MaskedArray):
reclist = reclist.filled().view(ndarray)
# Grab the initial dtype, just in case
if dtype is None:
dtype = reclist.dtype
reclist = reclist.tolist()
mrec = recfromrecords(reclist, dtype=dtype, shape=shape, formats=formats,
names=names, titles=titles,
aligned=aligned, byteorder=byteorder).view(mrecarray)
# Set the fill_value if needed
if fill_value is not None:
mrec.fill_value = fill_value
# Now, let's deal w/ the mask
if mask is not nomask:
mask = np.array(mask, copy=False)
maskrecordlength = len(mask.dtype)
if maskrecordlength:
mrec._fieldmask.flat = mask
elif len(mask.shape) == 2:
mrec._fieldmask.flat = [tuple(m) for m in mask]
else:
mrec._mask = mask
if _fieldmask is not None:
mrec._fieldmask[:] = _fieldmask
return mrec
def _guessvartypes(arr):
"""Tries to guess the dtypes of the str_ ndarray `arr`, by testing element-wise
conversion. Returns a list of dtypes.
The array is first converted to ndarray. If the array is 2D, the test is performed
on the first line. An exception is raised if the file is 3D or more.
"""
vartypes = []
arr = np.asarray(arr)
if len(arr.shape) == 2 :
arr = arr[0]
elif len(arr.shape) > 2:
raise ValueError, "The array should be 2D at most!"
# Start the conversion loop .......
for f in arr:
try:
val = int(f)
except ValueError:
try:
val = float(f)
except ValueError:
try:
val = complex(f)
except ValueError:
vartypes.append(arr.dtype)
else:
vartypes.append(complex)
else:
vartypes.append(float)
else:
vartypes.append(int)
return vartypes
def openfile(fname):
"Opens the file handle of file `fname`"
# A file handle ...................
if hasattr(fname, 'readline'):
return fname
# Try to open the file and guess its type
try:
f = open(fname)
except IOError:
raise IOError, "No such file: '%s'" % fname
if f.readline()[:2] != "\\x":
f.seek(0,0)
return f
raise NotImplementedError, "Wow, binary file"
def fromtextfile(fname, delimitor=None, commentchar='#', missingchar='',
varnames=None, vartypes=None):
"""Creates a mrecarray from data stored in the file `filename`.
*Parameters* :
filename : {file name/handle}
Handle of an opened file.
delimitor : {string}
Alphanumeric character used to separate columns in the file.
If None, any (group of) white spacestring(s) will be used.
commentchar : {string}
Alphanumeric character used to mark the start of a comment.
missingchar` : {string}
String indicating missing data, and used to create the masks.
varnames : {sequence}
Sequence of the variable names. If None, a list will be created from
the first non empty line of the file.
vartypes : {sequence}
Sequence of the variables dtypes. If None, it will be estimated from
the first non-commented line.
Ultra simple: the varnames are in the header, one line"""
# Try to open the file ......................
f = openfile(fname)
# Get the first non-empty line as the varnames
while True:
line = f.readline()
firstline = line[:line.find(commentchar)].strip()
_varnames = firstline.split(delimitor)
if len(_varnames) > 1:
break
if varnames is None:
varnames = _varnames
# Get the data ..............................
_variables = masked_array([line.strip().split(delimitor) for line in f
if line[0] != commentchar and len(line) > 1])
(_, nfields) = _variables.shape
# Try to guess the dtype ....................
if vartypes is None:
vartypes = _guessvartypes(_variables[0])
else:
vartypes = [np.dtype(v) for v in vartypes]
if len(vartypes) != nfields:
msg = "Attempting to %i dtypes for %i fields!"
msg += " Reverting to default."
warnings.warn(msg % (len(vartypes), nfields))
vartypes = _guessvartypes(_variables[0])
# Construct the descriptor ..................
mdescr = [(n,f) for (n,f) in zip(varnames, vartypes)]
# Get the data and the mask .................
# We just need a list of masked_arrays. It's easier to create it like that:
_mask = (_variables.T == missingchar)
_datalist = [masked_array(a,mask=m,dtype=t)
for (a,m,t) in zip(_variables.T, _mask, vartypes)]
return fromarrays(_datalist, dtype=mdescr)
#....................................................................
def addfield(mrecord, newfield, newfieldname=None):
"""Adds a new field to the masked record array, using `newfield` as data
and `newfieldname` as name. If `newfieldname` is None, the new field name is
set to 'fi', where `i` is the number of existing fields.
"""
_data = mrecord._data
_mask = mrecord._fieldmask
if newfieldname is None or newfieldname in reserved_fields:
newfieldname = 'f%i' % len(_data.dtype)
newfield = ma.array(newfield)
# Get the new data ............
# Create a new empty recarray
newdtype = np.dtype(_data.dtype.descr + [(newfieldname, newfield.dtype)])
newdata = recarray(_data.shape, newdtype)
# Add the exisintg field
[newdata.setfield(_data.getfield(*f),*f)
for f in _data.dtype.fields.values()]
# Add the new field
newdata.setfield(newfield._data, *newdata.dtype.fields[newfieldname])
newdata = newdata.view(MaskedRecords)
# Get the new mask .............
# Create a new empty recarray
newmdtype = np.dtype([(n,bool_) for n in newdtype.names])
newmask = recarray(_data.shape, newmdtype)
# Add the old masks
[newmask.setfield(_mask.getfield(*f),*f)
for f in _mask.dtype.fields.values()]
# Add the mask of the new field
newmask.setfield(getmaskarray(newfield),
*newmask.dtype.fields[newfieldname])
newdata._fieldmask = newmask
return newdata
###############################################################################
|