XsocsH5.py 13.2 KB
Newer Older
Damien Naudet's avatar
Damien Naudet committed
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
# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2015-2016 European Synchrotron Radiation Facility
#
# 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.
#
# ###########################################################################*/

from __future__ import absolute_import

__authors__ = ["D. Naudet"]
__license__ = "MIT"
__date__ = "15/09/2016"

32
import weakref
Damien Naudet's avatar
WIP    
Damien Naudet committed
33
from collections import OrderedDict, namedtuple
34
35
36
37
38
from contextlib import contextmanager

import h5py as _h5py
import numpy as _np

Damien Naudet's avatar
Damien Naudet committed
39
from .XsocsH5Base import XsocsH5Base
40
41


Damien Naudet's avatar
Damien Naudet committed
42
43
class InvalidEntryError(Exception):
    pass
44
45


Damien Naudet's avatar
WIP    
Damien Naudet committed
46
47
48
49
ScanPositions = namedtuple('ScanPositions',
                           ['motor_0', 'pos_0', 'motor_1', 'pos_1', 'shape'])


50
51
52
53
54
55
56
57
58
59
60
61

def _process_entry(method):
    def _method(inst, entry=None, *args, **kwargs):
        if entry is None:
            entry = inst.get_entry_name()
        elif isinstance(entry, int):
            entry = inst.get_entry_name(entry)
        return method(inst, entry, *args, **kwargs)
    return _method



62
63
64
65
66
67
68
class XsocsH5(XsocsH5Base):

    TOP_ENTRY = 'global'
    positioners_tpl = '/{0}/instrument/positioners'
    img_data_tpl = '/{0}/measurement/image/data'
    measurement_tpl = '/{0}/measurement'
    detector_tpl = '/{0}/instrument/detector'
Damien Naudet's avatar
Damien Naudet committed
69
    scan_params_tpl = '/{0}/scan'
70
71
72
73
74
75

    def __init__(self, h5_f, mode='r'):
        super(XsocsH5, self).__init__(h5_f, mode=mode)

        self.__entries = None

76
    @_process_entry
77
78
79
    def title(self, entry):
        with self._get_file() as h5_file:
            path = entry + '/title'
80
            return h5_file[path][()]
81

82
    @_process_entry
83
84
85
86
87
88
    def entry_filename(self, entry):
        with self._get_file() as h5_file:
            return h5_file[entry].file.filename

    def _update_entries(self):
        with self._get_file() as h5_file:
89
90
91
92
            # TODO : this isnt pretty but for some reason the attrs.get() fails
            # when there is no attribute NX_class (should return the default
            # None)
            self.__entries = sorted([key for key in h5_file
Damien Naudet's avatar
Damien Naudet committed
93
94
95
                if ('NX_class' in h5_file[key].attrs and
                    h5_file[key].attrs[
                        'NX_class'].decode() == 'NXentry')])
96
97
98
99
100
101

    def entries(self):
        if self.__entries is None:
            self._update_entries()
        return self.__entries[:]

102
    @_process_entry
103
104
105
106
    def scan_angle(self, entry):
        # TODO : get the correct angle name
        return self.positioner(entry, 'eta')

107
    def get_entry_name(self, entry_idx=0):
108
109
110
111
112
113
114
115
116
117
118
        """
        Get the entry found at position *entry_idx* (entries names sorted
        alphabeticaly).
        Raises InvalidEntryError if the entry is not found.
        """
        try:
            return self.entries()[entry_idx]
        except IndexError:
            raise InvalidEntryError('Entry not found (entry_idx={0}).'
                                    ''.format(entry_idx))

119
    @_process_entry
120
121
122
123
124
125
126
127
    def __detector_params(self, entry, param_names):
        with self._get_file() as h5_file:
            path = self.detector_tpl.format(entry) + '/{0}'
            if isinstance(param_names, (list, set, tuple)):
                return [h5_file.get(path.format(param), _np.array(None))[()]
                        for param in param_names]
            return h5_file.get(path.format(param_names), _np.array(None))[()]

128
    @_process_entry
129
130
131
    def beam_energy(self, entry):
        return self.__detector_params(entry, 'beam_energy')

132
    @_process_entry
133
134
135
136
    def direct_beam(self, entry):
        return self.__detector_params(entry, ['center_chan_dim0',
                                              'center_chan_dim1'])

137
    @_process_entry
138
139
140
141
    def chan_per_deg(self, entry):
        return self.__detector_params(entry, ['chan_per_deg_dim0',
                                              'chan_per_deg_dim1'])

142
    @_process_entry
143
144
145
146
147
    def n_images(self, entry):
        # TODO : make sure that data.ndims = 3
        path = self.img_data_tpl.format(entry)
        return self._get_array_data(path, shape=True)[0]

148
    @_process_entry
149
150
151
152
153
    def image_size(self, entry):
        # TODO : make sure that data.ndims = 3
        path = self.img_data_tpl.format(entry)
        return self._get_array_data(path, shape=True)[1:3]

154
    @_process_entry
155
156
157
158
    def image_dtype(self, entry):
        path = self.img_data_tpl.format(entry)
        return self._get_array_data(path, dtype=True)

159
    @_process_entry
160
161
162
    def dset_shape(self, path):
        return self._get_array_data(path, shape=True)

163
    @_process_entry
Damien Naudet's avatar
Damien Naudet committed
164
    def image_cumul(self, entry, dtype=None):
165
166
        """
        Returns the summed intensity for each image.
Damien Naudet's avatar
Damien Naudet committed
167
168
169
        :param dtype: dtype passed to the numpy.sum function.
            Default is numpy.double.
        :type dtype: numpy.dtype
170
        """
Damien Naudet's avatar
Damien Naudet committed
171
172
173
174
175
        if dtype is None:
            dtype = _np.double

        with self.image_dset_ctx(entry) as ctx:
            shape = ctx.shape
Damien Naudet's avatar
WIP    
Damien Naudet committed
176
            intensity = _np.zeros(shape=(shape[0],), dtype=dtype)
Damien Naudet's avatar
Damien Naudet committed
177
            img_buffer = _np.array(ctx[0], dtype=dtype)
178
            for idx in range(0, shape[0]):
Damien Naudet's avatar
Damien Naudet committed
179
180
181
                ctx.read_direct(img_buffer, idx)
                intensity[idx] = _np.sum(img_buffer)
        return intensity
182

183
    @_process_entry
184
185
    def scan_positions(self, entry):
        path = self.measurement_tpl.format(entry)
186
        params = self.scan_params(entry)
187
188
        m0 = '/adc{0}'.format(params['motor_0'].decode()[-1].upper())
        m1 = '/adc{0}'.format(params['motor_1'].decode()[-1].upper())
Damien Naudet's avatar
WIP    
Damien Naudet committed
189
190
        n_0 = params['motor_0_steps']
        n_1 = params['motor_1_steps']
191
192
193

        x_pos = self._get_array_data(path + m0)
        y_pos = self._get_array_data(path + m1)
Damien Naudet's avatar
WIP    
Damien Naudet committed
194
195
196
197
198
        return ScanPositions(motor_0=params['motor_0'],
                             pos_0=x_pos,
                             motor_1=params['motor_1'],
                             pos_1=y_pos,
                             shape=(n_0, n_1))
199

200
    @_process_entry
201
202
203
204
205
206
207
208
209
210
211
212
    def acquisition_params(self, entry):
        beam_energy = self.beam_energy(entry)
        direct_beam = self.direct_beam(entry)
        chan_per_deg = self.chan_per_deg(entry)

        result = OrderedDict()
        result['beam_energy'] = beam_energy
        result['direct_beam'] = direct_beam
        result['chan_per_deg'] = chan_per_deg

        return result

213
    @_process_entry
Damien Naudet's avatar
Damien Naudet committed
214
215
216
217
218
219
220
221
222
    def is_regular_grid(self, entry):
        # TODO
        """
        For now grids are always regular
        :param entry:
        :return:
        """
        return True

223
    @_process_entry
224
    def scan_params(self, entry):
Damien Naudet's avatar
Damien Naudet committed
225
226
        # TODO : make this more generic to make it compatible
        #  with irregular grids
Damien Naudet's avatar
Damien Naudet committed
227
228
229
230
231
232
233
        param_names = ['motor_0', 'motor_0_start',
                       'motor_0_end', 'motor_0_steps',
                       'motor_1', 'motor_1_start',
                       'motor_1_end', 'motor_1_steps',
                       'delay']
        with self._get_file() as h5_file:
            path = self.scan_params_tpl.format(entry) + '/{0}'
Damien Naudet's avatar
Damien Naudet committed
234
235
236
            return OrderedDict([(param, h5_file.get(path.format(param),
                                                    _np.array(None))[()])
                                for param in param_names])
237

238
    @_process_entry
239
240
241
242
    def positioner(self, entry, positioner):
        path = self.positioners_tpl.format(entry) + '/' + positioner
        return self._get_scalar_data(path)

243
    @_process_entry
244
245
246
247
248
    def measurement(self, entry, measurement):
        path = self.measurement_tpl.format(entry) + '/' + measurement
        return self._get_array_data(path)

    @contextmanager
249
    @_process_entry
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
    def image_dset_ctx(self,
                       entry,
                       create=False,
                       **kwargs):
        """
        Context manager for the image dataset.
        WARNING: only to be used as a context manager!
        """
        dset_path = self.img_data_tpl.format(entry)
        with self._get_file() as h5_file:
            if create:
                try:
                    image_dset = h5_file.require_dataset(dset_path,
                                                         **kwargs)
                except TypeError:
                    image_dset = h5_file.create_dataset(dset_path,
                                                        **kwargs)
            else:
                image_dset = h5_file[dset_path]
            yield weakref.proxy(image_dset)
            del image_dset


Damien Naudet's avatar
Damien Naudet committed
273
class XsocsH5Writer(XsocsH5):
274
275

    def __init__(self, h5_f, mode='a', **kwargs):
Damien Naudet's avatar
Damien Naudet committed
276
        super(XsocsH5Writer, self).__init__(h5_f, mode=mode, **kwargs)
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

    def __set_detector_params(self, entry, params):
        with self._get_file() as h5_file:
            path = self.detector_tpl.format(entry) + '/{0}'
            for param_name, param_value in params.items():
                self._set_scalar_data(path.format(param_name), param_value)

    def set_beam_energy(self, beam_energy, entry):
        return self.__set_detector_params(entry, {'beam_energy': beam_energy})

    def set_direct_beam(self, direct_beam, entry):
        value = {'center_chan_dim0': direct_beam[0],
                 'center_chan_dim1': direct_beam[1]}
        return self.__set_detector_params(entry, value)

    def set_chan_per_deg(self, chan_per_deg, entry):
        value = {'chan_per_deg_dim0': chan_per_deg[0],
                 'chan_per_deg_dim1': chan_per_deg[1]}
        return self.__set_detector_params(entry, value)

    def set_scan_params(self,
                        entry,
                        motor_0,
                        motor_0_start,
                        motor_0_end,
                        motor_0_steps,
                        motor_1,
                        motor_1_start,
                        motor_1_end,
                        motor_1_steps,
                        delay,
                        **kwargs):
Damien Naudet's avatar
Damien Naudet committed
309
310
311
312
313
314
315
316
317
318
319
320
321
322

        params = OrderedDict([('motor_0', _np.string_(motor_0)),
                              ('motor_0_start', float(motor_0_start)),
                              ('motor_0_end', float(motor_0_end)),
                              ('motor_0_steps', int(motor_0_steps)),
                              ('motor_1', _np.string_(motor_1)),
                              ('motor_1_start', float(motor_1_start)),
                              ('motor_1_end', float(motor_1_end)),
                              ('motor_1_steps', int(motor_1_steps)),
                              ('delay', float(delay))])
        with self._get_file():
            path = self.scan_params_tpl.format(entry) + '/{0}'
            for param_name, param_value in params.items():
                self._set_scalar_data(path.format(param_name), param_value)
323
324
325
326
327
328
329
330
331
332
333

    def create_entry(self, entry):
        with self._get_file() as h5_file:
            entry_grp = h5_file.require_group(entry)
            entry_grp.attrs['NX_class'] = _np.string_('NXentry')

            # creating mandatory groups and setting their Nexus attributes
            grp = entry_grp.require_group('measurement/image')
            grp.attrs['interpretation'] = _np.string_('image')

            # setting the nexus classes
334
            #entry_grp.attrs['NX_class'] = _np.string_('NXentry')
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350

            grp = entry_grp.require_group('instrument')
            grp.attrs['NX_class'] = _np.string_('NXinstrument')

            grp = entry_grp.require_group('instrument/detector')
            grp.attrs['NX_class'] = _np.string_('NXdetector')

            grp = entry_grp.require_group('instrument/positioners')
            grp.attrs['NX_class'] = _np.string_('NXcollection')

            grp = entry_grp.require_group('measurement')
            grp.attrs['NX_class'] = _np.string_('NXcollection')

            grp = entry_grp.require_group('measurement/image')
            grp.attrs['NX_class'] = _np.string_('NXcollection')

Damien Naudet's avatar
Damien Naudet committed
351
            # creating some links
352
353
354
355
356
            grp = entry_grp.require_group('measurement/image')
            det_grp = entry_grp.require_group('instrument/detector')
            grp['info'] = det_grp
            det_grp['data'] = _h5py.SoftLink(self.img_data_tpl.format(entry))

Damien Naudet's avatar
Damien Naudet committed
357
            self._update_entries()
358
359


Damien Naudet's avatar
Damien Naudet committed
360
class XsocsH5MasterWriter(XsocsH5Writer):
361
362
363
364

    def add_entry_file(self, entry, entry_file):
        with self._get_file() as h5_file:
            h5_file[entry] = _h5py.ExternalLink(entry_file, entry)
Damien Naudet's avatar
Damien Naudet committed
365
366
367
368


if __name__ == '__main__':
    pass