File: spyfile.py

package info (click to toggle)
python-spectral 0.22.4-1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, forky, sid, trixie
  • size: 1,064 kB
  • sloc: python: 13,161; makefile: 7
file content (862 lines) | stat: -rw-r--r-- 29,846 bytes parent folder | download
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
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
'''
:class:`~spectral.SpyFile` is the base class for creating objects to read
hyperspectral data files.  When a :class:`~spectral.SpyFile` object is created,
it provides an interface to read data from a corresponding file.  When an image
is opened, the actual object returned will be a subclass of
:class:`~spectral.SpyFile` (BipFile, BilFile, or BsqFile) corresponding to the
interleave of the data within the image file.

Let's open our sample image.

.. ipython::

    In [1]: from spectral import *

    In [2]: img = open_image('92AV3C.lan')

    In [3]: img.__class__
    Out[3]: spectral.io.bilfile.BilFile

    In [4]: print(img)
            Data Source:   '/Users/thomas/spectral_data/92AV3C.lan'
            # Rows:            145
            # Samples:         145
            # Bands:           220
            Interleave:        BIL
            Quantization:  16 bits
            Data format:     int16

The image was not located in the working directory but it was still opened
because it was in a directory specified by the *SPECTRAL_DATA* environment
variable.  Because the image pixel data are interleaved by line, the *image*
function returned a *BilFile* instance.

Since hyperspectral image files can be quite large, only
metadata are read from the file when the :class:`~spectral.SpyFile` object is
first created. Image data values are only read when specifically requested via
:class:`~spectral.SpyFile` methods.  The :class:`~spectral.SpyFile` class
provides a subscript operator that behaves much like the numpy array subscript
operator. The :class:`~spectral.SpyFile` object is subscripted as an *MxNxB*
array where *M* is the number of rows in the image, *N* is the number of
columns, and *B* is thenumber of bands.

.. ipython::

    In [5]: img.shape
    Out[5]: (145, 145, 220)

    In [6]: pixel = img[50,100]

    In [7]: pixel.shape
    Out[7]: (220,)

    In [8]: band6 = img[:,:,5]

    In [9]: band6.shape
    Out[9]: (145, 145, 1)

The image data values were not read from the file until the subscript operator
calls were performed.  Note that since Python indices start at 0,
``img[50,100]`` refers to the pixel at 51st row and 101st column of the image.
Similarly, ``img[:,:,5]`` refers to all the rows and columns for the 6th band
of the image.

:class:`~spectral.SpyFile` subclass instances returned for particular image
files will also provide the following methods:

==============   ===============================================================
   Method                               Description
==============   ===============================================================
read_band        Reads a single band into an *MxN* array
read_bands       Reads multiple bands into an *MxNxC* array
read_pixel       Reads a single pixel into a length *B* array
read_subregion   Reads multiple bands from a rectangular sub-region of the image
read_subimage    Reads specified rows, columns, and bands
==============   ===============================================================

:class:`~spectral.SpyFile` objects have a ``bands`` member, which is an
instance of a :class:`~spectral.BandInfo` object that contains optional
information about the images spectral bands.
'''

from __future__ import absolute_import, division, print_function, unicode_literals

import array
import numpy as np
import os
import warnings

import spectral as spy
from .. import SpyException
from ..image import Image, ImageArray
from ..utilities.errors import has_nan, NaNValueWarning
from ..utilities.python23 import typecode, tobytes, frombytes


class FileNotFoundError(SpyException):
    pass

class InvalidFileError(SpyException):
    '''Raised when file contents are invalid for the exepected file type.'''
    pass

def find_file_path(filename):
    '''
    Search cwd and SPECTRAL_DATA directories for the given file.
    '''
    pathname = None
    dirs = [os.curdir]
    if 'SPECTRAL_DATA' in os.environ:
        dirs += os.environ['SPECTRAL_DATA'].split(os.pathsep)
    for d in dirs:
        testpath = os.path.join(d, filename)
        if os.path.isfile(testpath):
            pathname = testpath
            break
    if not pathname:
        msg = 'Unable to locate file "%s". If the file exists, ' \
          'use its full path or place its directory in the ' \
          'SPECTRAL_DATA environment variable.'  % filename
        raise FileNotFoundError(msg)
    return pathname


class SpyFile(Image):
    '''A base class for accessing spectral image files'''

    def __init__(self, params, metadata=None):
        Image.__init__(self, params, metadata)
        # Number by which to divide values read from file.
        self.scale_factor = 1.0

    def set_params(self, params, metadata):
        Image.set_params(self, params, metadata)

        try:
            self.filename = params.filename
            self.offset = params.offset
            self.byte_order = params.byte_order
            if spy.byte_order != self.byte_order:
                self.swap = 1
            else:
                self.swap = 0
            self.sample_size = np.dtype(params.dtype).itemsize

            self.fid = open(find_file_path(self.filename), "rb")

            # So that we can use this more like a Numeric array
            self.shape = (self.nrows, self.ncols, self.nbands)

        except:
            raise

    def transform(self, xform):
        '''Returns a SpyFile image with the linear transform applied.'''
        # This allows a LinearTransform object to take the SpyFile as an arg.
        return transform_image(xform, self)

    def __str__(self):
        '''Prints basic parameters of the associated file.'''
        s = '\tData Source:   \'%s\'\n' % self.filename
        s += '\t# Rows:         %6d\n' % (self.nrows)
        s += '\t# Samples:      %6d\n' % (self.ncols)
        s += '\t# Bands:        %6d\n' % (self.shape[2])
        if self.interleave == spy.BIL:
            interleave = 'BIL'
        elif self.interleave == spy.BIP:
            interleave = 'BIP'
        else:
            interleave = 'BSQ'
        s += '\tInterleave:     %6s\n' % (interleave)
        s += '\tQuantization: %3d bits\n' % (self.sample_size * 8)

        s += '\tData format:  %8s' % np.dtype(self.dtype).name
        return s

    def load(self, **kwargs):
        '''Loads entire image into memory in a :class:`spectral.image.ImageArray`.

        Keyword Arguments:

            `dtype` (numpy.dtype):

                An optional dtype to which the loaded array should be cast.

            `scale` (bool, default True):

                Specifies whether any applicable scale factor should be applied
                to the data after loading.

        :class:`spectral.image.ImageArray` is derived from both
        :class:`spectral.image.Image` and :class:`numpy.ndarray` so it supports the
        full :class:`numpy.ndarray` interface.  The returns object will have
        shape `(M,N,B)`, where `M`, `N`, and `B` are the numbers of rows,
        columns, and bands in the image.
        '''
        for k in list(kwargs.keys()):
            if k not in ('dtype', 'scale'):
                raise ValueError('Invalid keyword %s.' % str(k))
        dtype = kwargs.get('dtype', ImageArray.format)
        data = array.array(typecode('b'))
        self.fid.seek(self.offset)
        data.fromfile(self.fid, self.nrows * self.ncols *
                      self.nbands * self.sample_size)
        npArray = np.frombuffer(tobytes(data), dtype=self.dtype)
        if self.interleave == spy.BIL:
            npArray.shape = (self.nrows, self.nbands, self.ncols)
            npArray = npArray.transpose([0, 2, 1])
        elif self.interleave == spy.BSQ:
            npArray.shape = (self.nbands, self.nrows, self.ncols)
            npArray = npArray.transpose([1, 2, 0])
        else:
            npArray.shape = (self.nrows, self.ncols, self.nbands)
        npArray = npArray.astype(dtype)
        if self.scale_factor != 1 and kwargs.get('scale', True):
            npArray = npArray / float(self.scale_factor)
        imarray = ImageArray(npArray, self)
        if has_nan(imarray):
            warnings.warn('Image data contains NaN values.', NaNValueWarning)
        return imarray        

    def __getitem__(self, args):
        '''Subscripting operator that provides a numpy-like interface.
        Usage::

            x = img[i, j]
            x = img[i, j, k]

        Arguments:

            `i`, `j`, `k` (int or :class:`slice` object)

                Integer subscript indices or slice objects.

        The subscript operator emulates the :class:`numpy.ndarray` subscript
        operator, except data are read from the corresponding image file
        instead of an array object in memory.  For frequent access or when
        accessing a large fraction of the image data, consider calling
        :meth:`spectral.SpyFile.load` to load the data into an
        :meth:`spectral.image.ImageArray` object and using its subscript operator
        instead.

        Examples:

            Read the pixel at the 30th row and 51st column of the image::

                pixel = img[29, 50]

            Read the 10th band::

                band = img[:, :, 9]

            Read the first 30 bands for a square sub-region of the image::

                region = img[50:100, 50:100, :30]
        '''

        atypes = [type(a) for a in args]

        if len(args) < 2:
            raise IndexError('Too few subscript indices.')

        fix_negative_indices = self._fix_negative_indices

        if atypes[0] == atypes[1] == int and len(args) == 2:
            row = fix_negative_indices(args[0], 0)
            col = fix_negative_indices(args[1], 1)
            return self.read_pixel(row, col)
        elif len(args) == 3 and atypes[0] == atypes[1] == atypes[2] == int:
            row = fix_negative_indices(args[0], 0)
            col = fix_negative_indices(args[1], 1)
            band = fix_negative_indices(args[2], 2)
            return self.read_datum(row, col, band)
        else:
            #  At least one arg should be a slice
            if atypes[0] == slice:
                (xstart, xstop, xstep) = (args[0].start, args[0].stop,
                                          args[0].step)
                if xstart is None:
                    xstart = 0
                if xstop is None:
                    xstop = self.nrows
                if xstep is None:
                    xstep = 1
                rows = list(range(xstart, xstop, xstep))
            else:
                rows = [args[0]]
            if atypes[1] == slice:
                (ystart, ystop, ystep) = (args[1].start, args[1].stop,
                                          args[1].step)
                if ystart is None:
                    ystart = 0
                if ystop is None:
                    ystop = self.ncols
                if ystep is None:
                    ystep = 1
                cols = list(range(ystart, ystop, ystep))
            else:
                cols = [args[1]]

        if len(args) == 2 or args[2] is None:
            bands = None
        elif atypes[2] == slice:
            (zstart, zstop, zstep) = (args[2].start, args[2].stop,
                                      args[2].step)
            if zstart == zstop == zstep == None:
                bands = None
            else:
                if zstart is None:
                    zstart = 0
                if zstop is None:
                    zstop = self.nbands
                if zstep is None:
                    zstep = 1
                bands = list(range(zstart, zstop, zstep))
        elif atypes[2] == int:
            bands = [args[2]]
        else:
            # Band indices should be in a list
            bands = args[2]

        if atypes[0] == slice and xstep == 1 \
          and atypes[1] == slice and ystep == 1 \
          and (bands is None or type(bands) == list):
            xstart = fix_negative_indices(xstart, 0)
            xstop = fix_negative_indices(xstop, 0)
            ystart = fix_negative_indices(ystart, 0)
            ystop = fix_negative_indices(ystop, 0)
            bands = fix_negative_indices(bands, 2)
            return self.read_subregion((xstart, xstop), (ystart, ystop), bands)

        rows = fix_negative_indices(rows, 0)
        cols = fix_negative_indices(cols, 1)
        bands = fix_negative_indices(bands, 2)
        return self.read_subimage(rows, cols, bands)

    def _fix_negative_indices(self, indices, dim):
        if not indices:
            return indices

        dim_len = self.shape[dim]
        try:
            return [i if i >= 0 else dim_len + i
                    for i in indices]
        except:
            return indices if indices >= 0 else dim_len + indices

    def params(self):
        '''Return an object containing the SpyFile parameters.'''
        p = Image.params(self)

        p.filename = self.filename
        p.offset = self.offset
        p.byte_order = self.byte_order
        p.sample_size = self.sample_size

        return p

    def __del__(self):
        self.fid.close()


class SubImage(SpyFile):
    '''
    Represents a rectangular sub-region of a larger SpyFile object.
    '''
    def __init__(self, image, row_range, col_range):
        '''Creates a :class:`Spectral.SubImage` for a rectangular sub-region.

        Arguments:

            `image` (SpyFile):

                The image for which to define the sub-image.

            `row_range` (2-tuple):

                Integers [i, j) defining the row limits of the sub-region.

            `col_range` (2-tuple):

                Integers [i, j) defining the col limits of the sub-region.

        Returns:

            A :class:`spectral.SubImage` object providing a
            :class:`spectral.SpyFile` interface to a sub-region of the image.

        Raises:

            :class:`IndexError`

        Row and column ranges must be 2-tuples (i,j) where i >= 0 and i < j.

        '''
        if row_range[0] < 0 or \
            row_range[1] > image.nrows or \
            col_range[0] < 0 or \
                col_range[1] > image.ncols:
            raise IndexError('SubImage index out of range.')

        p = image.params()

        SpyFile.__init__(self, p, image.metadata)
        self.parent = image
        self.row_offset = row_range[0]
        self.col_offset = col_range[0]
        self.nrows = row_range[1] - row_range[0]
        self.ncols = col_range[1] - col_range[0]
        self.shape = (self.nrows, self.ncols, self.nbands)

    def read_band(self, band):
        '''Reads a single band from the image.

        Arguments:

            `band` (int):

                Index of band to read.

        Returns:

           :class:`numpy.ndarray`

                An `MxN` array of values for the specified band.
        '''
        return self.parent.read_subregion([self.row_offset,
                                           self.row_offset + self.nrows - 1],
                                          [self.col_offset,
                                           self.col_offset + self.ncols - 1],
                                          [band])

    def read_bands(self, bands):
        '''Reads multiple bands from the image.

        Arguments:

            `bands` (list of ints):

                Indices of bands to read.

        Returns:

           :class:`numpy.ndarray`

                An `MxNxL` array of values for the specified bands. `M` and `N`
                are the number of rows & columns in the image and `L` equals
                len(`bands`).
        '''
        return self.parent.read_subregion([self.row_offset,
                                           self.row_offset + self.nrows - 1],
                                          [self.col_offset,
                                           self.col_offset + self.ncols - 1],
                                          bands)

    def read_pixel(self, row, col):
        '''Reads the pixel at position (row,col) from the file.

        Arguments:

            `row`, `col` (int):

                Indices of the row & column for the pixel

        Returns:

           :class:`numpy.ndarray`

                A length-`B` array, where `B` is the number of image bands.
        '''
        return self.parent.read_pixel(row + self.row_offset,
                                      col + self.col_offset)

    def read_subimage(self, rows, cols, bands=[]):
        '''
        Reads arbitrary rows, columns, and bands from the image.

        Arguments:

            `rows` (list of ints):

                Indices of rows to read.

            `cols` (list of ints):

                Indices of columns to read.

            `bands` (list of ints):

                Optional list of bands to read.  If not specified, all bands
                are read.

        Returns:

           :class:`numpy.ndarray`

                An `MxNxL` array, where `M` = len(`rows`), `N` = len(`cols`),
                and `L` = len(bands) (or # of image bands if `bands` == None).
        '''
        return self.parent.read_subimage(list(array.array(rows) \
                                              + self.row_offset),
                                         list(array.array(cols) \
                                              + self.col_offset),
                                         bands)

    def read_subregion(self, row_bounds, col_bounds, bands=None):
        '''
        Reads a contiguous rectangular sub-region from the image.

        Arguments:

            `row_bounds` (2-tuple of ints):

                (a, b) -> Rows a through b-1 will be read.

            `col_bounds` (2-tuple of ints):

                (a, b) -> Columnss a through b-1 will be read.

            `bands` (list of ints):

                Optional list of bands to read.  If not specified, all bands
                are read.

        Returns:

           :class:`numpy.ndarray`

                An `MxNxL` array.
        '''
        return self.parent.read_subimage(list(np.array(row_bounds) \
                                              + self.row_offset),
                                         list(np.array(col_bounds) \
                                              + self.col_offset),
                                         bands)


def tile_image(im, nrows, ncols):
    '''
    Break an image into nrows x ncols tiles.

    USAGE: tiles = tile_image(im, nrows, ncols)

    ARGUMENTS:
        im              The SpyFile to tile.
        nrows           Number of tiles in the veritical direction.
        ncols           Number of tiles in the horizontal direction.

    RETURN VALUE:
        tiles           A list of lists of SubImage objects. tiles
                        contains nrows lists, each of which contains
                        ncols SubImage objects.
    '''
    x = (np.array(list(range(nrows + 1))) * float(im.nrows) / nrows).astype(int)
    y = (np.array(list(range(ncols + 1))) * float(im.ncols) / ncols).astype(int)
    x[-1] = im.nrows
    y[-1] = im.ncols

    tiles = []
    for r in range(len(x) - 1):
        row = []
        for c in range(len(y) - 1):
            si = SubImage(im, [x[r], x[r + 1]], [y[c], y[c + 1]])
            row.append(si)
        tiles.append(row)
    return tiles

def transform_image(transform, img):
    '''Applies a linear transform to an image.

    Arguments:

        `transform` (ndarray or LinearTransform):

            The `CxB` linear transform to apply.

        `img` (ndarray or :class:`spectral.SpyFile`):

            The `MxNxB` image to be transformed.

    Returns (ndarray or :class:spectral.spyfile.TransformedImage`):

        The transformed image.

    If `img` is an ndarray, then a `MxNxC` ndarray is returned.  If `img` is
    a :class:`spectral.SpyFile`, then a
    :class:`spectral.spyfile.TransformedImage` is returned.
    '''
    from ..algorithms.transforms import LinearTransform
    if isinstance(img, np.ndarray):
        if isinstance(transform, LinearTransform):
            return transform(img)
        ret = np.empty(img.shape[:2] + (transform.shape[0],), img.dtype)
        for i in range(img.shape[0]):
            for j in range(img.shape[1]):
                ret[i, j] = np.dot(transform, img[i, j])
        return ret
    else:
        return TransformedImage(transform, img)


class TransformedImage(Image):
    '''
    An image with a linear transformation applied to each pixel spectrum.
    The transformation is not applied until data is read from the image file.
    '''
    dtype = np.dtype('f4').char

    def __init__(self, transform, img):
        from ..algorithms.transforms import LinearTransform
        if not isinstance(img, Image):
            raise Exception(
                'Invalid image argument to to TransformedImage constructor.')

        if isinstance(transform, np.ndarray):
            transform = LinearTransform(transform)
        self.transform = transform

        if self.transform.dim_in not in (None, img.shape[-1]):
            raise Exception('Number of bands in image (%d) do not match the '
                            ' input dimension of the transform (%d).'
                            % (img.shape[-1], transform.dim_in))

        params = img.params()
        self.set_params(params, params.metadata)

        # If img is also a TransformedImage, then just modify the transform
        if isinstance(img, TransformedImage):
            self.transform = self.transform.chain(img.transform)
            self.image = img.image
        else:
            self.image = img
        if self.transform.dim_out is not None:
            self.shape = self.image.shape[:2] + (self.transform.dim_out,)
            self.nbands = self.transform.dim_out
        else:
            self.shape = self.image.shape
            self.nbands = self.image.nbands

    @property
    def bands(self):
        return self.image.bands

    def __getitem__(self, args):
        '''
        Get data from the image and apply the transform.
        '''
        if len(args) < 2:
            raise Exception('Must pass at least two subscript arguments')

        # Note that band indices are wrt transformed features
        if len(args) == 2 or args[2] is None:
            bands = list(range(self.nbands))
        elif type(args[2]) == slice:
            (zstart, zstop, zstep) = (args[2].start, args[2].stop,
                                      args[2].step)
            if zstart is None:
                zstart = 0
            if zstop is None:
                zstop = self.nbands
            if zstep is None:
                zstep = 1
            bands = list(range(zstart, zstop, zstep))
        elif isinstance(args[2], int):
            bands = [args[2]]
        else:
            # Band indices should be in a list
            bands = args[2]

        orig = self.image.__getitem__(args[:2])
        if len(orig.shape) == 1:
            orig = orig[np.newaxis, np.newaxis, :]
        elif len(orig.shape) == 2:
            orig = orig[np.newaxis, :]
        transformed_xy = np.zeros(orig.shape[:2] + (self.shape[2],),
                                  self.transform.dtype)
        for i in range(transformed_xy.shape[0]):
            for j in range(transformed_xy.shape[1]):
                transformed_xy[i, j] = self.transform(orig[i, j])
        # Remove unnecessary dimensions

        transformed = np.take(transformed_xy, bands, 2)

        return transformed.squeeze()

    def __str__(self):
        s = '\tTransformedImage object with output dimensions:\n'
        s += '\t# Rows:         %6d\n' % (self.nrows)
        s += '\t# Samples:      %6d\n' % (self.ncols)
        s += '\t# Bands:        %6d\n\n' % (self.shape[2])
        s += '\tThe linear transform is applied to the following image:\n\n'
        s += str(self.image)
        return s

    def read_pixel(self, row, col):
        return self.transform(self.image.read_pixel(row, col))

    def load(self):
        '''Loads all image data, transforms it, and returns an ndarray).'''
        data = self.image.load()
        return self.transform(data)

    def read_subregion(self, row_bounds, col_bounds, bands=None):
        '''
        Reads a contiguous rectangular sub-region from the image. First
        arg is a 2-tuple specifying min and max row indices.  Second arg
        specifies column min and max.  If third argument containing list
        of band indices is not given, all bands are read.
        '''
        data = self.image.read_subregion(row_bounds, col_bounds)
        xdata = self.transform(data)
        if bands:
            return np.take(xdata, bands, 2)
        else:
            return xdata

    def read_subimage(self, rows, cols, bands=None):
        '''
        Reads a sub-image from a rectangular region within the image.
        First arg is a 2-tuple specifying min and max row indices.
        Second arg specifies column min and max. If third argument
        containing list of band indices is not given, all bands are read.
        '''
        data = self.image.read_subimage(rows, cols)
        xdata = self.transform(data)
        if bands:
            return np.take(xdata, bands, 2)
        else:
            return xdata

    def read_datum(self, i, j, k):
        return self.read_pixel(i, j)[k]

    def read_bands(self, bands):
        shape = (self.image.nrows, self.image.ncols, len(bands))
        data = np.zeros(shape, float)
        for i in range(shape[0]):
            for j in range(shape[1]):
                data[i, j] = self.read_pixel(i, j)[bands]
        return data

class MemmapFile(object):
    '''Interface class for SpyFile subclasses using `numpy.memmap` objects.'''

    def _disable_memmap(self):
        '''Disables memmap and reverts to direct file reads (slower).'''
        self._memmap = None

    @property
    def using_memmap(self):
        '''Returns True if object is using a `numpy.memmap` to read data.'''
        return self._memmap is not None

    def open_memmap(self, **kwargs):
        '''Returns a new `numpy.memmap` object for image file data access.

        Keyword Arguments:

            `interleave` (str, default 'bip'):

                Specifies the shape/interleave of the returned object. Must be
                one of ['bip', 'bil', 'bsq', 'source']. If not specified, the
                memmap will be returned as 'bip'. If the interleave is
                'source', the interleave of the memmap will be the same as the
                source data file. If the number of rows, columns, and bands in
                the file are R, C, and B, the shape of the returned memmap
                array will be as follows:

                .. table::

                    ========== ===========
                    interleave array shape
                    ========== ===========
                    'bip'      (R, C, B)
                    'bil'      (R, B, C)
                    'bsq'      (B, R, C)
                    ========== ===========

            `writable` (bool, default False):

                If `writable` is True, modifying values in the returned memmap
                will result in corresponding modification to the image data
                file.
        '''        
        src_inter = {spy.BIL: 'bil',
                     spy.BIP: 'bip',
                     spy.BSQ: 'bsq'}[self.interleave]
        dst_inter = kwargs.get('interleave', 'bip').lower()
        if dst_inter not in ['bip', 'bil', 'bsq', 'source']:
            raise ValueError('Invalid interleave specified.')
        if kwargs.get('writable', False) is True:
            mode = 'r+'
        else:
            mode = 'r'
        memmap = self._open_memmap(mode)
        if dst_inter == 'source':
            dst_inter = src_inter
        if src_inter == dst_inter:
            return memmap
        else:
            return np.transpose(memmap, interleave_transpose(src_inter,
                                                             dst_inter))

    def asarray(self, writable=False):
        '''Returns an object with a standard numpy array interface.

        The function returns a numpy memmap created with the
        `open_memmap` method.

        This function is for compatibility with ImageArray objects.

        Keyword Arguments:

            `writable` (bool, default False):

                If `writable` is True, modifying values in the returned
                memmap will result in corresponding modification to the
                image data file.
        '''
        return self.open_memmap(writable=writable)

def interleave_transpose(int1, int2):
    '''Returns the 3-tuple of indices to transpose between interleaves.

    Arguments:

        `int1`, `int2` (string):

            The input and output interleaves.  Each should be one of "bil",
            "bip", or "bsq".

    Returns:

        A 3-tuple of integers that can be passed to `numpy.transpose` to
        convert and RxCxB image between the two interleaves.
    '''
    if int1.lower() not in ('bil', 'bip', 'bsq'):
        raise ValueError('Invalid interleave: %s' % str(int1))
    if int2.lower() not in ('bil', 'bip', 'bsq'):
        raise ValueError('Invalid interleave: %s' % str(int2))
    int1 = int1.lower()
    int2 = int2.lower()
    if int1 == 'bil':
        if int2 == 'bil':
            return (1, 1, 1)
        elif int2 == 'bip':
            return (0, 2, 1)
        else:
            return (1, 0, 2)
    elif int1 == 'bip':
        if int2 == 'bil':
            return (0, 2, 1)
        elif int2 == 'bip':
            return (1, 1, 1)
        else:
            return (2, 0, 1)
    else:  # bsq
        if int2 == 'bil':
            return (1, 0, 2)
        elif int2 == 'bip':
            return (1, 2, 0)
        else:
            return (1, 1, 1)