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
|
# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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
"""
Authors:
........
* Henning O. Sorensen & Erik Knudsen:
Center for Fundamental Research: Metal Structures in Four Dimensions;
Risoe National Laboratory;
Frederiksborgvej 399;
DK-4000 Roskilde;
email:erik.knudsen@risoe.dk
* Jon Wright, Jérôme Kieffer & Gaël Goret:
European Synchrotron Radiation Facility;
Grenoble (France)
Supports Mar345 imaging plate and Mar555 flat panel
Documentation on the format is available from:
http://rayonix.com/site_media/downloads/mar345_formats.pdf
"""
__authors__ = ["Henning O. Sorensen", "Erik Knudsen", "Jon Wright", "Jérôme Kieffer"]
__date__ = "03/04/2020"
__status__ = "production"
__copyright__ = "2007-2009 Risoe National Laboratory; 2010-2020 ESRF"
__licence__ = "MIT"
import struct
import time
import logging
import numpy
import fabio
from .fabioimage import FabioImage
logger = logging.getLogger(__name__)
from .compression import compPCK, decPCK
class Mar345Image(FabioImage):
_need_a_real_file = True
DESCRIPTION = "File format from Mar345 imaging plate and Mar555 flat panel"
DEFAULT_EXTENSIONS = ["mar2300", "mar1200", "mar1600", "mar2000", # 150µm pixel size
"mar3450", "mar3000", "mar2400", "mar1800"] # 100µm pixel size
def __init__(self, *args, **kwargs):
FabioImage.__init__(self, *args, **kwargs)
self.numhigh = None
self.numpixels = None
self.swap_needed = None
def read(self, fname, frame=None):
""" Read a mar345 image"""
self.filename = fname
f = self._open(self.filename, "rb")
self._readheader(f)
if 'compressed' in self.header['Format']:
dim2, dim1 = self._shape
self.data = decPCK(f, dim1, dim2, self.numhigh, swap_needed=self.swap_needed)
self._shape = None
else:
logger.error("Cannot handle these formats yet due to lack of documentation")
return None
self._bytecode = numpy.uint32
f.close()
return self
def _readheader(self, infile=None):
""" Read a mar345 image header """
# clip was not used anywhere - commented out
# clip = '\x00'
# using a couple of local variables inside this function
f = infile
h = {}
# header is 4096 bytes long
data = f.read(64)
# the contents of the mar345 header is taken to be as
# described in
# http://www.mar-usa.com/support/downloads/mar345_formats.pdf
# the first 64 bytes are 4-byte integers (but in the CBFlib
# example image it seems to 128 bytes?)
# first 4-byte integer is a marker to check endianness
if struct.unpack("<i", data[0:4])[0] == 1234:
fs = '<i'
self.swap_needed = not(numpy.little_endian)
logger.debug("Going for little endian, swap_needed %s" % self.swap_needed)
else:
self.swap_needed = numpy.little_endian
fs = '>i'
logger.debug("Going for big endian, swap_needed %s" % self.swap_needed)
# image dimensions
dim1 = int(struct.unpack(fs, data[4:8])[0])
# number of high intensity pixels
self.numhigh = struct.unpack(fs, data[2 * 4: (2 + 1) * 4])[0]
h['NumHigh'] = self.numhigh
# Image format
i = struct.unpack(fs, data[3 * 4: (3 + 1) * 4])[0]
if i == 1:
h['Format'] = 'compressed'
elif i == 2:
h['Format'] = 'spiral'
else:
h['Format'] = 'compressed'
logger.warning("image format could not be determined" +
"- assuming compressed mar345")
# collection mode
h['Mode'] = {0: 'Dose', 1: 'Time'}[struct.unpack(fs, data[4 * 4:(4 + 1) * 4])[0]]
# total number of pixels
self.numpixels = struct.unpack(fs, data[5 * 4:(5 + 1) * 4])[0]
h['NumPixels'] = str(self.numpixels)
dim2 = self.numpixels // dim1
self._shape = dim2, dim1
# pixel dimensions (length,height) in mm
h['PixelLength'] = struct.unpack(fs, data[6 * 4:(6 + 1) * 4])[0] / 1000.0
h['PixelHeight'] = struct.unpack(fs, data[7 * 4:(7 + 1) * 4])[0] / 1000.0
# x-ray wavelength in AA
h['Wavelength'] = struct.unpack(fs, data[8 * 4:(8 + 1) * 4])[0] / 1000000.0
# used distance
h['Distance'] = struct.unpack(fs, data[9 * 4:(9 + 1) * 4])[0] / 1000.0
# starting and ending phi
h['StartPhi'] = struct.unpack(fs, data[10 * 4:11 * 4])[0] / 1000.0
h['EndPhi'] = struct.unpack(fs, data[11 * 4:12 * 4])[0] / 1000.0
# starting and ending omega
h['StartOmega'] = struct.unpack(fs, data[12 * 4:13 * 4])[0] / 1000.0
h['EndOmega'] = struct.unpack(fs, data[13 * 4:14 * 4])[0] / 1000.0
# Chi and Twotheta angles
h['Chi'] = struct.unpack(fs, data[14 * 4:15 * 4])[0] / 1000.0
h['TwoTheta'] = struct.unpack(fs, data[15 * 4:16 * 4])[0] / 1000.0
# the rest of the header is ascii
# TODO: validate these values against the binaries already read
data = f.read(128)
if b'mar research' not in data:
logger.warning("the string \"mar research\" should be in " +
"bytes 65-76 of the header but was not")
start = 128
else:
start = data.index(b'mar research')
f.seek(64 + start)
data = f.read(4096 - start - 64).strip()
for m in data.splitlines():
try:
m = m.decode("ASCII")
except UnicodeDecodeError:
if m.startswith(b"DATE"):
m = m[:39].decode("ASCII")
else:
logger.warning("Skip binary trash on header line %s" % m)
continue
if m == 'END OF HEADER':
break
n = m.split(' ', 1)
if n[0] == '':
continue
if n[0] in ('PROGRAM', 'DATE', 'SCANNER', 'HIGH', 'MULTIPLIER',
'GAIN', 'WAVELENGTH', 'DISTANCE', 'RESOLUTION',
'CHI', 'TWOTHETA', 'MODE', 'TIME', 'GENERATOR',
'MONOCHROMATOR', 'REMARK'):
logger.debug("reading: %s %s", n[0], n[1])
h[n[0]] = n[1].strip()
continue
if n[0] in ('FORMAT'):
(h['DIM'], h['FORMAT_TYPE'], h['NO_PIXELS']) = n[1].split()
continue
if n[0] in ('PIXEL', 'OFFSET', 'PHI', 'OMEGA', 'COUNTS',
'CENTER', 'INTENSITY', 'HISTOGRAM', 'COLLIMATOR'):
n = m.split()
h.update([(n[0] + '_' + n[j], n[j + 1]) for j in range(1, len(n), 2)])
continue
self.header = h
return h
def write(self, fname):
"""Try to write mar345 file.
It uses a MIT implementation of the CCP4 (LGPL) PCK1 algo from JPA"""
bin_headers = self.binary_header()
asc_headers = self.ascii_header("\n", 4096 - len(bin_headers)).encode("ASCII")
hotpixels = self._high_intensity_pixel_records()
compressed_stream = compPCK(self.data)
with self._open(fname, mode="wb") as outfile:
outfile.write(bin_headers)
outfile.write(asc_headers)
outfile.write(hotpixels)
outfile.write(compressed_stream)
outfile.close()
def binary_header(self):
"""
:return: Binary header of mar345 file
"""
dim2, dim1 = self.shape
self.header["HIGH"] = str(self.nb_overflow_pixels())
binheader = numpy.zeros(16, "int32")
binheader[0] = 1234
binheader[1] = dim1
binheader[2] = self.nb_overflow_pixels()
binheader[3] = 1
binheader[4] = (self.header.get("MODE", "TIME") == "TIME")
binheader[5] = dim1 * dim2
binheader[6] = int(self.header.get("PIXEL_LENGTH", 1))
binheader[7] = int(self.header.get("PIXEL_HEIGHT", 1))
binheader[8] = int(float(self.header.get("WAVELENGTH", 1)) * 1e6)
binheader[9] = int(float(self.header.get("DISTANCE", 1)) * 1e3)
binheader[10] = int(float(self.header.get("PHI_START", 1)) * 1e3)
binheader[11] = int(float(self.header.get("PHI_END", 1)) * 1e3)
binheader[12] = int(float(self.header.get("OMEGA_START", 1)) * 1e3)
binheader[13] = int(float(self.header.get("OMEGA_END", 1)) * 1e3)
binheader[14] = int(float(self.header.get("CHI", 1)) * 1e3)
binheader[15] = int(float(self.header.get("TWOTHETA", 1)) * 1e3)
self.header["HIGH"] = str(binheader[2])
if self.swap_needed:
binheader.byteswap(True)
return binheader.tobytes()
def ascii_header(self, linesep="\n", size=4096):
"""
Generate the ASCII header for writing
:param linesep: end of line separator
:param size: size of the header (without the binary header)
:return: string (unicode) containing the mar345 header
"""
version = fabio.version
lnsep = len(linesep)
dim2, dim1 = self.shape
lstout = ['mar research'.ljust(64 - lnsep)]
lstout.append("PROGRAM".ljust(15) + (str(self.header.get("PROGRAM", "FabIO Version %s" % (version))).ljust(49 - lnsep)))
lstout.append("DATE".ljust(15) + (str(self.header.get("DATE", time.ctime()))).ljust(49 - lnsep))
key = "SCANNER"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "FORMAT_TYPE"
if key in self.header:
lstout.append("FORMAT".ljust(15) + ("%s %s %s" % (dim1, self.header[key], dim1 * dim2)).ljust(49 - lnsep))
key = "HIGH"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "PIXEL_LENGTH"
key2 = "PIXEL_HEIGHT"
if (key1 in self.header) and (key2 in self.header):
lstout.append("PIXEL".ljust(15) + ("LENGTH %s HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "OFFSET_ROFF"
key2 = "OFFSET_TOFF"
if key1 in self.header and key2 in self.header:
lstout.append("OFFSET".ljust(15) + ("ROFF %s TOFF %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "MULTIPLIER"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "GAIN"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "WAVELENGTH"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "DISTANCE"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "RESOLUTION"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "PHI_START"
key2 = "PHI_END"
key3 = "PHI_OSC"
if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
lstout.append("PHI".ljust(15) + ("START %s END %s OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key1 = "OMEGA_START"
key2 = "OMEGA_END"
key3 = "OMEGA_OSC"
if (key1 in self.header) and (key2 in self.header) and (key3 in self.header):
lstout.append("OMEGA".ljust(15) + ("START %s END %s OSC %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key = "CHI"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "TWOTHETA"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "CENTER_X"
key2 = "CENTER_Y"
if (key1 in self.header) and (key2 in self.header):
lstout.append("CENTER".ljust(15) + ("X %s Y %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "MODE"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "TIME"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "COUNTS_START"
key2 = "COUNTS_END"
key3 = "COUNTS_NMEAS"
if key1 in self.header and key2 in self.header and key3 in self.header:
lstout.append("COUNTS".ljust(15) + ("START %s END %s NMEAS %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key1 = "COUNTS_MIN"
key2 = "COUNTS_MAX"
if key1 in self.header and key2 in self.header:
lstout.append("COUNTS".ljust(15) + ("MIN %s MAX %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "COUNTS_AVE"
key2 = "COUNTS_SIG"
if key1 in self.header and key2 in self.header:
lstout.append("COUNTS".ljust(15) + ("AVE %s SIG %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key1 = "INTENSITY_MIN"
key2 = "INTENSITY_MAX"
key3 = "INTENSITY_AVE"
key4 = "INTENSITY_SIG"
if key1 in self.header and key2 in self.header and key3 in self.header and key4 in self.header:
lstout.append("INTENSITY".ljust(15) + ("MIN %s MAX %s AVE %s SIG %s" % (self.header[key1], self.header[key2], self.header[key3], self.header[key4])).ljust(49 - lnsep))
key1 = "HISTOGRAM_START"
key2 = "HISTOGRAM_END"
key3 = "HISTOGRAM_MAX"
if key1 in self.header and key2 in self.header and key3 in self.header:
lstout.append("HISTOGRAM".ljust(15) + ("START %s END %s MAX %s" % (self.header[key1], self.header[key2], self.header[key3])).ljust(49 - lnsep))
key = "GENERATOR"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key = "MONOCHROMATOR"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
key1 = "COLLIMATOR_WIDTH"
key2 = "COLLIMATOR_HEIGHT"
if key1 in self.header and key2 in self.header:
lstout.append("COLLIMATOR".ljust(15) + ("WIDTH %s HEIGHT %s" % (self.header[key1], self.header[key2])).ljust(49 - lnsep))
key = "REMARK"
if key in self.header:
lstout.append(key.ljust(15) + str(self.header[key]).ljust(49 - lnsep))
else:
lstout.append(key.ljust(64 - lnsep))
key = "END OF HEADER"
lstout.append(key)
return linesep.join(lstout).ljust(size)
def _high_intensity_pixel_records(self):
flt_data = self.data.flatten()
pix_location = numpy.where(flt_data > 65535)[0]
nb_pix = pix_location.size
if nb_pix % 8 == 0:
tmp = numpy.zeros((nb_pix, 2), dtype="int32")
else:
tmp = numpy.zeros(((nb_pix // 8 + 1) * 8, 2), dtype="int32")
tmp[:nb_pix, 0] = pix_location + 1
tmp[:nb_pix, 1] = flt_data[pix_location]
if self.swap_needed:
tmp.byteswap(True)
return tmp.tobytes()
def nb_overflow_pixels(self):
return (self.data > 65535).sum()
@staticmethod
def checkData(data=None):
if data is None:
return None
else:
# enforce square image
shape = data.shape
assert len(shape) == 2, "image has 2 dimensions"
mshape = max(shape)
z = numpy.zeros((mshape, mshape), dtype=int)
z[:shape[0], :shape[1]] = data
return z
mar345image = Mar345Image
|
