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
|
# 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.
#
"""Eiger data/master file reader for FabIO
Eiger data files are HDF5 files with one group called "entry" and a dataset
called "data" in it (now in a data group).
Those dataset are usually compressed using LZ4 and/or bitshuffle compression:
* https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4
* https://github.com/kiyo-masui/bitshuffle
H5py (>2.5) and libhdf5 (>1.8.10) with the corresponding compression plugin are needed to
actually read the data.
Under windows, those plugins can easily be installed via this repository:
https://github.com/silx-kit/hdf5plugin
"""
__authors__ = ["Jérôme Kieffer"]
__contact__ = "jerome.kieffer@esrf.fr"
__license__ = "MIT"
__copyright__ = "ESRF"
__date__ = "01/06/2022"
import logging
logger = logging.getLogger(__name__)
import posixpath
import numpy
try:
import h5py
except ImportError:
h5py = None
from .fabioimage import FabioImage
from .fabioutils import NotGoodReader
from .nexus import Nexus
try:
import hdf5plugin
except ImportError:
hdf5plugin = None
class EigerImage(FabioImage):
"""
FabIO image class for Images from Eiger data files (HDF5)
"""
DESCRIPTION = "Eiger data files based on HDF5"
DEFAULT_EXTENSIONS = ["h5", "hdf5"]
def __init__(self, data=None, header=None):
"""
Set up initial values
"""
if not h5py:
raise RuntimeError("fabio.EigerImage cannot be used without h5py. Please install h5py and restart")
if data is None:
self.dataset = [None]
else:
self.dataset = [numpy.atleast_3d(data)]
self._data = None
FabioImage.__init__(self, data, header)
self.h5 = None
def __repr__(self):
if self.h5 is not None:
return "Eiger dataset with %i frames from %s" % (self.nframes, self.h5.filename)
else:
return "%s object at %s" % (self.__class__.__name__, hex(id(self)))
def _readheader(self, infile):
"""
Read and decode the header of an image:
:param infile: Opened python file (can be stringIO or bzipped file)
"""
# list of header key to keep the order (when writing)
self.header = self.check_header()
infile.seek(0)
def read(self, fname, frame=None):
"""
Try to read image
:param fname: name of the file
:param frame: number of the frame
"""
self.resetvals()
with self._open(fname) as infile:
self._readheader(infile)
# read the image data and declare it
self.dataset = None
lstds = []
# read the image data
self.h5 = h5py.File(fname, mode="r")
if "entry" in self.h5:
entry = self.h5["entry"]
if "data" in entry:
data = entry["data"]
if isinstance(data, h5py.Group):
"Newer format /entry/data/data_000001"
datasets = [i for i in data.keys() if i.startswith("data")]
datasets.sort()
try:
for i in datasets:
lstds.append(data[i])
except KeyError:
pass
else:
lstds = [data]
else:
"elder format entry/data_01"
datasets = [i for i in entry.keys() if i.startswith("data")]
datasets.sort()
try:
for i in datasets:
lstds.append(entry[i])
except KeyError:
pass
if lstds:
self.dataset = lstds
else:
raise NotGoodReader("HDF5 file does not contain an Eiger-like structure.")
if frame is not None:
return self.getframe(int(frame))
else:
self.currentframe = 0
self._data = self.dataset[0][self.currentframe,:,:]
self._shape = None
return self
def write(self, fname):
"""
try to write image
:param fname: name of the file
"""
if hdf5plugin is None:
logger.warning("hdf5plugin is needed for bitshuffle-LZ4 compression, falling back on gzip (slower)")
compression = {"compression":"gzip",
"compression_opts":1}
else:
compression = hdf5plugin.Bitshuffle()
with Nexus(fname, mode="w") as nxs:
entry = nxs.new_entry(entry="entry", program_name=None, force_name=True)
data_grp = nxs.new_class(entry, "data", "NXdata")
entry.attrs["default"] = "data"
nxs.h5.attrs["default"] = "entry"
for i, ds in enumerate(self.dataset):
if ds is None:
# we are in a trouble
data = numpy.atleast_2d(numpy.NaN)
elif isinstance(ds, h5py.Dataset):
data = numpy.atleat_2d(ds[()])
else:
data = numpy.atleast_2d(ds)
if len(data.shape) == 2:
data.shape = (1,) + data.shape
chunks = (1,) + data.shape[-2:]
if len(self.dataset) > 1:
hds = data_grp.create_dataset(f"data_{i+1:06d}", data=data, chunks=chunks, **compression)
elif len(self.dataset) == 1:
hds = data_grp.create_dataset(f"data", data=data, chunks=chunks, **compression)
hds.attrs["interpretation"] = "image"
if "signal" not in data_grp.attrs:
data_grp.attrs["signal"] = posixpath.split(hds.name)[-1]
def getframe(self, num):
""" returns the frame numbered 'num' in the stack if applicable"""
if self.nframes > 1:
new_img = None
if (num >= 0) and num < self.nframes:
if isinstance(self.dataset, list):
nfr = num
for ds in self.dataset:
if ds is None or ds.ndim == 2:
if nfr == 0:
data = None
else:
nfr -= 1
elif ds.ndim == 3:
# Stack of images
if (nfr < ds.shape[0]):
data = ds[nfr]
break
else:
nfr -= ds.shape[0]
else:
data = self.dataset[num]
new_img = self.__class__(data=None, header=self.header)
new_img._data = data
new_img.dataset = self.dataset
new_img.h5 = self.h5
new_img._nframes = self.nframes
new_img.currentframe = num
else:
raise IOError(f"getframe {num} out of range [0 {self.nframes}[")
else:
new_img = FabioImage.getframe(self, num)
return new_img
def previous(self):
""" returns the previous file in the series as a FabioImage """
new_image = None
if self.nframes == 1:
new_image = FabioImage.previous(self)
else:
new_idx = self.currentframe - 1
new_image = self.getframe(new_idx)
return new_image
def next(self):
"""Returns the next file in the series as a fabioimage
:raise IOError: When there is no next file or image in the series.
"""
new_image = None
if self.nframes == 1:
new_image = FabioImage.next(self)
else:
new_idx = self.currentframe + 1
new_image = self.getframe(new_idx)
return new_image
def close(self):
if self.h5 is not None:
self.h5.close()
self.dataset = []
@property
def nframes(self):
"""Returns the number of frames contained in this file
:rtype: int
"""
return sum(i.shape[0] if i.ndim > 2 else 1 for i in self.dataset)
def get_data(self):
if self._data is None:
data = None
index = self.currentframe
if isinstance(self.dataset, list):
frame_idx = [len(ds) if (ds is not None and ds.ndim == 3) else 1 for ds in self.dataset]
end_ds = numpy.cumsum(frame_idx)
for idx, end in enumerate(end_ds):
start = 0 if idx == 0 else end_ds[idx - 1]
if end > index >= start:
ds = self.dataset[idx]
if ds is None or ds.ndim == 2:
data = ds
else:
data = ds[index - start]
else:
data = self.dataset[index]
self._data = data
return self._data
def set_data(self, data, index=None):
"""Set the data for frame index
:param data: numpy array
:param int index: index of the frame (by default: current one)
:raises IndexError: If the frame number is out of the available range.
"""
if index is None:
index = self.currentframe
if isinstance(self.dataset, list):
frame_idx = [len(ds) if (ds is not None and ds.ndim == 3) else 1 for ds in self.dataset]
end_ds = numpy.cumsum(frame_idx)
nframes = end_ds[-1]
if index == nframes:
self.dataset.append(data)
elif index > nframes:
# pad dataset with None ?
self.dataset += [None] * (1 + index - len(self.dataset))
self.dataset[index] = data
else:
for idx, end in enumerate(end_ds):
start = 0 if idx == 0 else end_ds[idx - 1]
if end > index >= start:
ds = self.dataset[idx]
if ds is None or ds.ndim == 2:
self.dataset[idx] = data
else:
ds[index - start] = data
if index == self.currentframe:
self._data = data
data = property(get_data, set_data)
eigerimage = EigerImage
|
