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
|
# 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.
#
"""FabIO reader for Fit2D binary images
TODO: handle big-endian files
"""
__authors__ = ["Jérôme Kieffer"]
__contact__ = "jerome.kiefer@esrf.fr"
__license__ = "MIT"
__copyright__ = "2016-2016 European Synchrotron Radiation Facility"
__date__ = "06/04/2020"
import logging
logger = logging.getLogger(__name__)
import numpy
from .fabioimage import FabioImage, OrderedDict
def hex_to(stg, type_="int"):
"""convert a 8-byte-long string (bytes) into an int or a float
:param stg: bytes string
:param str type_: "int" or "float"
"""
value = int(stg, 16)
if type_ == "float":
value = numpy.array([int("38d1b717", 16)], "int32").view("float32")[0]
return value
class Fit2dImage(FabioImage):
"""
FabIO image class for Images for XXX detector
"""
DESCRIPTION = "Fit2d file format"
DEFAULT_EXTENSIONS = ["f2d"]
BUFFER_SIZE = 512 # size of the buffer
PIXELS_PER_CHUNK = 128
ENC = "ascii"
def __init__(self, *arg, **kwargs):
"""
Generic constructor
"""
FabioImage.__init__(self, *arg, **kwargs)
self.num_block = None
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)
header = OrderedDict()
self.header = self.check_header()
while True:
line = infile.read(self.BUFFER_SIZE)
if len(line) < self.BUFFER_SIZE:
break
if line[0:1] != b"\\":
for block_read in range(2, 16):
line = infile.read(self.BUFFER_SIZE)
if line[0:1] == b"\\":
self.BUFFER_SIZE *= block_read
logger.warning("Increase block size to %s ", self.BUFFER_SIZE)
infile.seek(0)
break
else:
err = "issue while reading header, expected '\', got %s" % line[0]
logger.error(err)
raise RuntimeError(err)
key, line = line.split(b":", 1)
num_block = hex_to(line[:8])
metadatatype = line[8:9].decode(self.ENC)
key = key[1:].decode(self.ENC)
if metadatatype == "s":
len_value = hex_to(line[9:17])
header[key] = line[17:17 + len_value].decode(self.ENC)
elif metadatatype == "r":
header[key] = hex_to(line[9:17], "float")
elif metadatatype == "i":
header[key] = hex_to(line[9:17])
elif metadatatype == "a" and num_block != 0: # "a"
self.num_block = num_block
array_type = line[9:10].decode(self.ENC)
dim1 = hex_to(line[26:34])
dim2 = hex_to(line[34:42])
if array_type == "i":
bytecode = "int32"
bpp = 4
elif array_type == "r":
bytecode = "float32"
bpp = 4
elif array_type == "l":
bytecode = "int8"
bpp = 1
raw = infile.read(self.num_block * self.BUFFER_SIZE)
# Fit2d stores 31 pixels per int32
i32 = numpy.frombuffer(raw, numpy.int32).copy()
if numpy.little_endian:
# lets's work in big-endian for the moment
i32.byteswap(True)
r32 = numpy.unpackbits(i32.view("uint8")).reshape((-1, 32))
# Remove the sign bit which is the first in big-endian
# all pixels are in reverse order in the group of 31
r31 = r32[:, -1:0:-1]
mask = r31.ravel()[:dim1 * dim2].reshape((dim2, dim1))
header[key] = mask
continue
else:
err = "unsupported data type: %s" % array_type
logger.error(err)
raise RuntimeError(err)
raw = infile.read(self.num_block * self.BUFFER_SIZE)
decoded = numpy.frombuffer(raw, bytecode).copy().reshape((-1, self.BUFFER_SIZE // bpp))
# There is a bug in this format: throw away 3/4 of the read data:
decoded = decoded[:, :self.PIXELS_PER_CHUNK].ravel()
header[key] = decoded[:dim1 * dim2].reshape(dim2, dim1)
self.header = header
def read(self, fname, frame=None):
"""try to read image
:param fname: name of the file
"""
self.resetvals()
with self._open(fname) as infile:
self._readheader(infile)
self.data = self.header.pop("data_array")
return self
# this is not compatibility with old code:
fit2dimage = Fit2dImage
|
