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
|
""" Implements an array of TIFF sample images.
"""
# Author: Pearu Peterson
# Created: Nov 2010
import sys
import numpy
__all__ = ['TiffArray']
class TiffArray:
""" Holds a sequence of homogeneous TiffPlane's.
TiffPlane's are homogeneous if they contain sample images of same
shape and type. Otherwise TiffPlane's may contain images from
different TIFF files with different pixel content.
"""
def __init__(self, planes):
self.planes = []
self.shape = ()
self.dtype = None
list(map(self.append, planes))
def __len__(self):
return self.shape[0]
def __iter__(self):
for plane in self.planes:
yield plane
def __getitem__(self, index):
try:
if isinstance(index, int):
if self.sample_index is None:
print(self.shape)
return self.planes[index][()]
elif isinstance(index, slice):
indices = list(range(*index.indices(self.shape[0])))
r = numpy.empty((len(indices), ) + self.shape[1:],
dtype=self.dtype)
for i, j in enumerate(indices):
r[i] = self.planes[j][()]
return r
elif isinstance(index, tuple):
if len(index) == 0:
return self[:]
if len(index) == 1:
return self[index[0]]
index0 = index[0]
if isinstance(index0, int):
return self.planes[index0][index[1:]]
elif isinstance(index0, slice):
indices = list(range(*index0.indices(self.shape[0])))
for i, j in enumerate(indices):
s = self.planes[j][index[1:]]
if i == 0:
r = numpy.empty((len(indices), ) + s.shape,
dtype=self.dtype)
r[i] = s
return r
except IOError as msg:
sys.stderr.write('%s.__getitem__:\n%s\n' %
(self.__class__.__name__, msg))
sys.stderr.flush()
return None
raise NotImplementedError(repr(index))
def append(self, plane):
""" Append tiff plane to tiff array.
"""
if self.planes:
if not self.planes[0].check_same_shape_and_type(plane):
raise TypeError('planes are not homogeneous (same shape and'
' sample type), expected %s but got %s'
% ((self.planes[0].shape, self.dtype),
(plane.shape, plane.dtype)))
self.shape = (self.shape[0] + 1,) + self.shape[1:]
else:
self.dtype = plane.dtype
self.shape = (1, ) + plane.shape
self.sample_index = plane.sample_index
self.planes.append(plane)
def extend(self, other):
""" Extend tiff array with the content of another.
"""
list(map(self.append, other.planes))
def get_voxel_sizes(self):
""" Return ZYX voxel sizes in microns.
"""
return self.planes[0].ifd.get_voxel_sizes()
def get_pixel_sizes(self):
""" Return YX pixel sizes in microns.
"""
return self.planes[0].ifd.get_pixel_sizes()
def get_time(self, index=0):
""" Return time parameter of a plane.
"""
return self.planes[index].time
@property
def nbytes(self):
return self.shape[0] * self.shape[1] \
* self.shape[2] * self.dtype.itemsize
|
