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
|
# coding: utf-8
#
# Project: FabIO X-ray image reader
#
# Copyright (C) 2010-2016 European Synchrotron Radiation Facility
# Grenoble, France
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""MRC image for FabIO
Authors: Jerome Kieffer
email: Jerome.Kieffer@terre-adelie.org
Specifications from:
http://ami.scripps.edu/software/mrctools/mrc_specification.php
New version on:
https://www.ccpem.ac.uk/mrc_format/mrc_format.php
https://www.fei-software-center.com/tem-apps/MRC-2014-Specifications/
"""
__authors__ = ["Jérôme Kieffer"]
__contact__ = "Jerome.Kieffer@terre-adelie.org"
__license__ = "MIT"
__copyright__ = "Jérôme Kieffer"
__date__ = "23/04/2021"
import logging
import numpy
from .fabioimage import FabioImage
from .fabioutils import previous_filename, next_filename
logger = logging.getLogger(__name__)
class MrcImage(FabioImage):
"""
FabIO image class for Images from a mrc image stack
"""
DESCRIPTION = "Medical Research Council file format for 3D electron density and 2D images"
DEFAULT_EXTENSIONS = ["mrc", "map", "fei"]
KEYS = ("NX", "NY", "NZ", "MODE", "NXSTART", "NYSTART", "NZSTART",
"MX", "MY", "MZ", "CELL_A", "CELL_B", "CELL_C",
"CELL_ALPHA", "CELL_BETA", "CELL_GAMMA",
"MAPC", "MAPR", "MAPS", "DMIN", "DMAX", "DMEAN", "ISPG", "NSYMBT",
"EXTRA", "ORIGIN", "MAP", "MACHST", "RMS", "NLABL")
_MODE_TO_DTYPE = {
0: numpy.int8,
1: numpy.int16,
2: numpy.float32,
3: numpy.complex64,
4: numpy.complex64,
6: numpy.uint16
}
def _readheader(self, infile):
"""
Read and decode the header of an image:
:param infile: Opened python file (can be stringIO or bipped file)
"""
# list of header key to keep the order (when writing)
self.header = self.check_header()
# header is composed of 56-int32 plus 10x80char lines
int_block = numpy.frombuffer(infile.read(56 * 4), dtype=numpy.int32)
for key, value in zip(self.KEYS, int_block):
self.header[key] = value
# convert some headers ...
self.header["MAP"] = self.header["MAP"].tobytes().decode()
if self.header["MAP"][:3] not in ('MAP ', 'FEI'):
logger.info("Expected 'MAP ', got %s", self.header["MAP"])
for i in range(10):
label = "LABEL_%02i" % i
self.header[label] = infile.read(80).decode().strip()
# Read extended header
self.header["extended"] = infile.read(self.header["NSYMBT"])
dim1 = int(self.header["NX"])
dim2 = int(self.header["NY"])
self._shape = dim2, dim1
self._nframes = self.header["NZ"]
mode = self.header["MODE"]
if mode not in self._MODE_TO_DTYPE:
raise IOError("Mode %s unsupported" % mode)
dtype = numpy.dtype(self._MODE_TO_DTYPE[mode])
self._dtype = dtype
self.imagesize = dim1 * dim2 * dtype.itemsize
def read(self, fname, frame=None):
"""
try to read image
:param fname: name of the file
:param frame:
"""
self.resetvals()
self.sequencefilename = fname
self.currentframe = frame or 0
with self._open(fname) as infile:
self._readheader(infile)
self._readframe(infile, self.currentframe)
return self
def _calc_offset(self, frame):
"""
Calculate the frame position in the file
:param frame: frame number
"""
assert frame < self.nframes
return 1024 + self.header["NSYMBT"] + frame * self.imagesize
def _makeframename(self):
self.filename = "%s$%04d" % (self.sequencefilename,
self.currentframe)
def _readframe(self, infile, img_num):
"""
Read a frame an populate data
:param infile: opened file
:param img_num: frame number (int)
"""
if (img_num > self.nframes or img_num < 0):
raise RuntimeError("Requested frame number is out of range")
infile.seek(self._calc_offset(img_num), 0)
data_buffer = infile.read(self.imagesize)
data = numpy.frombuffer(data_buffer, self._dtype).copy()
data.shape = self._shape
self.data = data
self._shape = None
self._dtype = None
self.currentframe = int(img_num)
self._makeframename()
def getframe(self, num):
"""
Returns a frame as a new FabioImage object
:param num: frame number
"""
if num < 0 or num > self.nframes:
raise RuntimeError("Requested frame number is out of range")
# Do a deep copy of the header to make a new one
frame = MrcImage(header=self.header.copy())
for key in ("dim1", "dim2", "nframes", "bytecode", "imagesize", "sequencefilename"):
frame.__setattr__(key, self.__getattribute__(key))
with frame._open(self.sequencefilename, "rb") as infile:
frame._readframe(infile, num)
return frame
def next(self):
"""
Get the next image in a series as a fabio image
"""
if self.currentframe < (self.nframes - 1) and self.nframes > 1:
return self.getframe(self.currentframe + 1)
else:
newobj = MrcImage()
newobj.read(next_filename(self.sequencefilename))
return newobj
def previous(self):
"""
Get the previous image in a series as a fabio image
"""
if self.currentframe > 0:
return self.getframe(self.currentframe - 1)
else:
newobj = MrcImage()
newobj.read(previous_filename(
self.sequencefilename))
return newobj
mrcimage = MrcImage
|
