edfscan.py 25 KB
Newer Older
payno's avatar
payno committed
1
2
# coding: utf-8
#/*##########################################################################
payno's avatar
payno committed
3
# Copyright (C) 2016-2020 European Synchrotron Radiation Facility
payno's avatar
payno committed
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
#
# 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.
#
#############################################################################*/

payno's avatar
payno committed
25
26
"""contains EDFTomoScan, class to be used with EDF acquisition"""

payno's avatar
payno committed
27
28
29
30
31
32
33
34
35

__authors__ = ["H.Payno"]
__license__ = "MIT"
__date__ = "10/10/2019"


import os
import re
import fabio
36
import copy
payno's avatar
payno committed
37
38
39
from lxml import etree
import json
import io
payno's avatar
payno committed
40
from typing import Union
payno's avatar
payno committed
41
42
from ..scanbase import TomoScanBase
from .utils import get_parameters_frm_par_or_info, extract_urls_from_edf
43
from ..unitsystem.metricsystem import MetricSystem
Pierre Paleo's avatar
Pierre Paleo committed
44
from ..utils import docstring
payno's avatar
payno committed
45
46
47
48
49
50
51
52
53
54
55
import logging

_logger = logging.getLogger(__name__)


class EDFTomoScan(TomoScanBase):
    """
    TomoScanBase instanciation for scan defined from .edf files

    :param scan: path to the root folder containing the scan.
    :type: Union[str,None]
56
57
    :param n_frames: Number of frames in each EDF file.
        If not provided, it will be inferred by reading the files.
58
        In this case, the frame number is guessed from the file name.
59
    :type: Union[int, None]=None
payno's avatar
payno committed
60
61
62
63
64
65
66
67
68
69
70
71
72
    """
    _TYPE = 'edf'

    INFO_EXT = '.info'

    ABORT_FILE = '.abo'

    _REFHST_PREFIX = 'refHST'

    _DARKHST_PREFIX = 'dark.edf'

    _SCHEME = 'fabio'

73
    def __init__(self, scan: Union[str, None], n_frames: Union[int, None]=None):
payno's avatar
payno committed
74
75
76
77
        TomoScanBase.__init__(self, scan=scan, type_=self._TYPE)

        # data caches
        self._darks = None
payno's avatar
payno committed
78
79
        self._flats = None
        self._projections = None
payno's avatar
payno committed
80
81
82
83
84
85
86
87
        self.__tomo_n = None
        self.__ref_n = None
        self.__dark_n = None
        self.__dim1 = None
        self.__dim2 = None
        self.__pixel_size = None
        self.__ref_on = None
        self.__scan_range = None
88
        self._edf_n_frames = n_frames
Pierre Paleo's avatar
Pierre Paleo committed
89
        self.__distance = None
90
        self.__energy = None
91
        self.update()
payno's avatar
payno committed
92

93

94
95
96
97
98
99
100
101
102
103
104
105
106
107
    @docstring(TomoScanBase.clear_caches)
    def clear_caches(self):
        self._darks = None
        self._flats = None
        self._projections = None
        self.__tomo_n = None
        self.__ref_n = None
        self.__dark_n = None
        self.__dim1 = None
        self.__dim2 = None
        self.__pixel_size = None
        self.__ref_on = None
        self.__scan_range = None

payno's avatar
payno committed
108
109
    @docstring(TomoScanBase.tomo_n)
    @property
payno's avatar
payno committed
110
    def tomo_n(self) -> Union[None, int]:
payno's avatar
payno committed
111
112
113
114
115
116
        if self.__tomo_n is None:
            self.__tomo_n = EDFTomoScan.get_tomo_n(scan=self.path)
        return self.__tomo_n

    @property
    @docstring(TomoScanBase.dark_n)
payno's avatar
payno committed
117
    def dark_n(self) -> Union[None, int]:
payno's avatar
payno committed
118
119
120
121
122
123
        if self.__dark_n is None:
            self.__dark_n = EDFTomoScan.get_dark_n(scan=self.path)
        return self.__dark_n

    @property
    @docstring(TomoScanBase.ref_n)
payno's avatar
payno committed
124
    def ref_n(self) -> Union[None, int]:
payno's avatar
payno committed
125
126
127
128
129
130
        if self.__ref_n is None:
            self.__ref_n = EDFTomoScan.get_ref_n(scan=self.path)
        return self.__ref_n

    @property
    @docstring(TomoScanBase.pixel_size)
payno's avatar
payno committed
131
    def pixel_size(self) -> Union[None, int]:
payno's avatar
payno committed
132
133
134
135
136
137
        """

        :return: pixel size
        :rtype: float
        """
        if self.__pixel_size is None:
138
            self.__pixel_size = EDFTomoScan._get_pixel_size(scan=self.path)
payno's avatar
payno committed
139
140
141
142
        return self.__pixel_size

    @property
    @docstring(TomoScanBase.dim_1)
payno's avatar
payno committed
143
    def dim_1(self) -> Union[None, int]:
payno's avatar
payno committed
144
145
146
147
148
149
150
151
152
153
154
        """

        :return: image dim1
        :rtype: int
        """
        if self.__dim1 is None:
            self.__dim1, self.__dim2 = EDFTomoScan.get_dim1_dim2(scan=self.path)
        return self.__dim1

    @property
    @docstring(TomoScanBase.dim_2)
payno's avatar
payno committed
155
    def dim_2(self) -> Union[None, int]:
payno's avatar
payno committed
156
157
158
159
160
161
162
163
164
165
        """

        :return: image dim2
        :rtype: int
        """
        if self.__dim2 is None:
            self.__dim1, self.__dim2 = EDFTomoScan.get_dim1_dim2(scan=self.path)
        return self.__dim2

    @property
payno's avatar
payno committed
166
167
    @docstring(TomoScanBase.ff_interval)
    def ff_interval(self) -> Union[None, int]:
payno's avatar
payno committed
168
169
170
171
172
173
        if self.__ref_on is None:
            self.__ref_on = EDFTomoScan.get_ff_interval(scan=self.path)
        return self.__ref_on

    @property
    @docstring(TomoScanBase.scan_range)
payno's avatar
payno committed
174
    def scan_range(self) -> Union[None, int]:
payno's avatar
payno committed
175
176
177
178
179
180
        if self.__scan_range is None:
            self.__scan_range = EDFTomoScan.get_scan_range(scan=self.path)
        return self.__scan_range

    @property
    @docstring(TomoScanBase.flats)
payno's avatar
payno committed
181
182
183
184
185
186
187
    def flats(self) -> Union[None, dict]:
        """
        flats are given as a dictionary with index as key and DataUrl as
        value"""
        if self._flats is None:
            self._flats = self.get_refs_url(scan_path=self.path)
        return self._flats
payno's avatar
payno committed
188
189
190

    @docstring(TomoScanBase.is_tomoscan_dir)
    @staticmethod
payno's avatar
payno committed
191
    def is_tomoscan_dir(directory: str, **kwargs) -> bool:
payno's avatar
payno committed
192
193
194
195
        return os.path.isfile(EDFTomoScan.get_info_file(directory=directory,
                                                        kwargs=kwargs))

    @staticmethod
payno's avatar
payno committed
196
    def get_info_file(directory: str, **kwargs) -> str:
payno's avatar
payno committed
197
198
199
200
201
202
203
        basename = os.path.basename(directory)
        assert basename != ''
        info_file = os.path.join(directory, basename + EDFTomoScan.INFO_EXT)

        if 'src_pattern' in kwargs and kwargs['srx_pattern'] is not None:
            assert 'dest_pattern' in kwargs
            info_file = info_file.replace(kwargs['src_pattern'],
payno's avatar
payno committed
204
205
                                          kwargs['dest_pattern'],
                                          1)
payno's avatar
payno committed
206
207
208
        return info_file

    @docstring(TomoScanBase.is_abort)
payno's avatar
payno committed
209
    def is_abort(self,  **kwargs) -> bool:
payno's avatar
payno committed
210
211
        abort_file = os.path.basename(self.path) + self.ABORT_FILE
        abort_file = os.path.join(self.path, abort_file)
payno's avatar
payno committed
212
        if 'src_pattern' in kwargs and kwargs['src_pattern'] is not None:
payno's avatar
payno committed
213
214
215
216
217
218
219
            assert 'dest_pattern' in kwargs
            abort_file = abort_file.replace(kwargs['src_pattern'],
                                            kwargs['dest_pattern'])
        return os.path.isfile(abort_file)

    @property
    @docstring(TomoScanBase.darks)
payno's avatar
payno committed
220
    def darks(self) -> dict:
payno's avatar
payno committed
221
222
223
224
        if self._darks is None:
            self._darks = self.get_darks_url(scan_path=self.path)
        return self._darks

payno's avatar
payno committed
225
226
    @docstring(TomoScanBase.get_proj_angle_url)
    def get_proj_angle_url(self) -> dict:
payno's avatar
payno committed
227
228
229
230
231
        # TODO: we might use fabio.open_serie instead
        if self.path is None:
            _logger.warning('no path specified for scan, unable to retrieve'
                            ' the projections')
            return {}
payno's avatar
payno committed
232
        n_projection = self.tomo_n
233
        data_urls = EDFTomoScan.get_proj_urls(self.path)
payno's avatar
payno committed
234
235
236
237
238
239
        return TomoScanBase.map_urls_on_scan_range(urls=data_urls,
                                                   n_projection=n_projection,
                                                   scan_range=self.scan_range)

    @docstring(TomoScanBase.update)
    def update(self):
240
241
242
243
        if self.path is not None:
            self.projections = EDFTomoScan.get_proj_urls(self.path, n_frames=self._edf_n_frames)
            self._darks = EDFTomoScan.get_darks_url(self.path)
            self._flats = EDFTomoScan.get_refs_url(self.path)
payno's avatar
payno committed
244
245

    @docstring(TomoScanBase.load_from_dict)
payno's avatar
payno committed
246
    def load_from_dict(self, desc: Union[dict, io.TextIOWrapper]):
payno's avatar
payno committed
247
248
249
250
        if isinstance(desc, io.TextIOWrapper):
            data = json.load(desc)
        else:
            data = desc
251
        if not (self.DICT_TYPE_KEY in data and data[self.DICT_TYPE_KEY] == self._TYPE):
payno's avatar
payno committed
252
253
            raise ValueError('Description is not an EDFScan json description')

254
255
        assert self.DICT_PATH_KEY in data
        self.path = data[self.DICT_PATH_KEY]
payno's avatar
payno committed
256
257
258
        return self

    @staticmethod
259
    def get_proj_urls(scan: str, n_frames: Union[int, None]=None) -> dict:
payno's avatar
payno committed
260
261
262
263
264
265
266
267
        """
        Return the dict of radios / projection for the given scan.
        Keys of the dictionary is the slice number
        Return all the file on the root of scan starting by the name of scan and
        ending by .edf

        :param scan: is the path to the folder of acquisition
        :type: str
Pierre Paleo's avatar
Pierre Paleo committed
268
        :param n_frames: Number of frames in each EDF file.
269
270
            If not provided, it is inferred by reading each file.
        :type: int
payno's avatar
payno committed
271
272
273
        :return: dict of radios files with radio index as key and file as value
        :rtype: dict
        """
274
        urls = dict({})
payno's avatar
payno committed
275
        if(scan is None) or not(os.path.isdir(scan)):
276
            return urls
payno's avatar
payno committed
277
278
279

        if os.path.isdir(scan):
            for f in os.listdir(scan):
280
                if EDFTomoScan.is_a_proj_path(fileName=f, scanID=scan):
payno's avatar
payno committed
281
                    gfile = os.path.join(scan, f)
282
283
                    index = EDFTomoScan.guess_index_frm_file_name(gfile,
                                                                  basename=os.path.basename(scan))
284
                    urls.update(extract_urls_from_edf(start_index=index,
285
286
                                                      file_=gfile,
                                                      n_frames=n_frames))
payno's avatar
payno committed
287

288
        return urls
payno's avatar
payno committed
289
290

    @staticmethod
payno's avatar
payno committed
291
    def is_a_proj_path(fileName: str, scanID: str) -> bool:
payno's avatar
payno committed
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
        """Return True if the given fileName can fit to a Radio name
        """
        fileBasename = os.path.basename(fileName)
        folderBasename = os.path.basename(scanID)

        if fileBasename.endswith(".edf") and fileBasename.startswith(folderBasename):
            localstring = fileName.rstrip('.edf')
            # remove the scan
            localstring = re.sub(folderBasename, '', localstring)
            if 'slice_' in localstring:
                # case of a reconstructed file
                return False
            if 'refHST' in localstring:
                return False
            s = localstring.split('_')
            if s[-1].isdigit():
                # check that the next value is a digit
                return True

        return False

    @staticmethod
314
315
316
317
318
319
320
321
322
323
324
325
    def guess_index_frm_file_name(_file: str, basename: str) -> Union[None, int]:
        """
        Guess the index of the file. Index is most of the an integer but can be
        a float for 'ref' for example if several are taken.

        :param _file:
        :param basename:
        """

        def extract_index(my_str, type_):
            res = []
            modified_str = copy.copy(my_str)
326
            while modified_str != "" and modified_str[-1].isdigit():
327
328
329
330
331
332
333
334
335
336
                res.append(modified_str[-1])
                modified_str = modified_str[:-1]
            if len(res) == 0:
                return None, modified_str
            else:
                orignalOrder = res[::-1]
                if type_ is int:
                    return int(''.join(orignalOrder)), modified_str
                else:
                    return float('.'.join(('0', ''.join(orignalOrder)))), modified_str
337
        _file = os.path.basename(_file)
338
339
340
341
342
343
344
345
346
347
348
        if _file.endswith('.edf'):
            name = _file.replace(basename, '', 1)
            name = name.rstrip('.edf')

            part_1, name = extract_index(name, type_=int)
            if name.endswith('_'):
                name = name.rstrip('_')
                part_2, name = extract_index(name, type_=float)
            else:
                part_2 = None

349
350
            if part_1 is None:
                return None
351
            if part_2 is None:
352
353
354
355
                if part_1 is None:
                    return None
                else:
                    return int(part_1)
356
357
            else:
                return float(part_1) + part_2
payno's avatar
payno committed
358
        else:
359
            raise ValueError('only edf files are managed')
payno's avatar
payno committed
360
361

    @staticmethod
payno's avatar
payno committed
362
    def get_tomo_n(scan: str) -> Union[None, int]:
payno's avatar
payno committed
363
364
365
366
367
368
369
        return EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                                ref_file=None,
                                                key='TOMO_N',
                                                type_=int,
                                                key_aliases=['tomo_N', 'Tomo_N'])

    @staticmethod
payno's avatar
payno committed
370
    def get_dark_n(scan:str) -> Union[None, int]:
payno's avatar
payno committed
371
372
373
374
375
376
377
        return EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                                ref_file=None,
                                                key='DARK_N',
                                                type_=int,
                                                key_aliases=['dark_N', ])

    @staticmethod
payno's avatar
payno committed
378
    def get_ref_n(scan :str) -> Union[None, int]:
payno's avatar
payno committed
379
380
381
382
383
384
385
        return EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                                ref_file=None,
                                                key='REF_N',
                                                type_=int,
                                                key_aliases=['ref_N', ])

    @staticmethod
payno's avatar
payno committed
386
    def get_ff_interval(scan: str) -> Union[None, int]:
payno's avatar
payno committed
387
388
389
390
391
392
393
        return EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                                ref_file=None,
                                                key='REF_ON',
                                                type_=int,
                                                key_aliases=['ref_On', ])

    @staticmethod
payno's avatar
payno committed
394
    def get_scan_range(scan: str) -> Union[None, int]:
payno's avatar
payno committed
395
396
397
398
399
400
401
        return EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                                ref_file=None,
                                                key='ScanRange',
                                                type_=int,
                                                key_aliases=['scanRange', ])

    @staticmethod
payno's avatar
payno committed
402
    def get_dim1_dim2(scan: str) -> Union[None, tuple]:
payno's avatar
payno committed
403
404
405
406
407
408
409
410
411
412
413
414
415
416
        _info_file = os.path.join(scan, os.path.basename(scan) + '.info')
        d1 = EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                              ref_file=None,
                                              key='Dim_1',
                                              key_aliases=['projectionSize/DIM_1'],
                                              type_=int)
        d2 = EDFTomoScan.retrieve_information(scan=os.path.abspath(scan),
                                              ref_file=None,
                                              key='Dim_2',
                                              key_aliases=['projectionSize/DIM_2'],
                                              type_=int)

        return d1, d2

payno's avatar
payno committed
417
418
419
420
421
422
423
424
425
426
427
428
    @property
    @docstring(TomoScanBase.distance)
    def distance(self) -> Union[None, float]:
        if self.__distance is None:
            self.__distance = EDFTomoScan.retrieve_information(self.path,
                                                               None, "Distance",
                                                               type_=float,
                                                               key_aliases=('distance', )
                                                               )
        if self.__distance is None:
            return None
        else:
429
            return self.__distance * MetricSystem.MILLIMETER.value
payno's avatar
payno committed
430

payno's avatar
payno committed
431
432
433
434
435
436
437
438
439
440
441
442
    @property
    @docstring(TomoScanBase.energy)
    def energy(self):
        if self.__energy is None:
            self.__energy = EDFTomoScan.retrieve_information(self.path,
                                                             None,
                                                             "Energy",
                                                             type_=float,
                                                             key_aliases=('energy', )
                                                             )
        return self.__energy

payno's avatar
payno committed
443
    @staticmethod
payno's avatar
payno committed
444
    def _get_pixel_size(scan: str) -> Union[None, float]:
payno's avatar
payno committed
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
        if os.path.isdir(scan) is False:
            return None
        value = EDFTomoScan.retrieve_information(scan=scan,
                                                 ref_file=None,
                                                 key='PixelSize',
                                                 type_=float,
                                                 key_aliases=['pixelSize', ])
        if value is None:
            parFile = os.path.join(scan, os.path.basename(scan) + '.par')
            if os.path.exists(parFile):
                try:
                    ddict = get_parameters_frm_par_or_info(parFile)
                except ValueError as e:
                    _logger.error(e)
                if 'IMAGE_PIXEL_SIZE_1'.lower() in ddict:
                    value = float(ddict['IMAGE_PIXEL_SIZE_1'.lower()])
        # for now pixel size are stored in microns.
        # We want to return them in meter
        if value is not None:
464
            return value * MetricSystem.MICROMETER.value
payno's avatar
payno committed
465
466
467
468
        else:
            return None

    @staticmethod
payno's avatar
payno committed
469
470
    def get_darks_url(scan_path: str, prefix: str='dark',
                      file_ext: str='.edf') -> dict:
payno's avatar
payno committed
471
472
473
474
475
476
477
478
479
480
        """

        :param scan_path:
        :type: str
        :param prefix: ref / flat field file prefix
        :type: str
        :param file_ext: ref / flat field file extension
        :type: str
        :return: list of refs as silx's `DataUrl`
        """
payno's avatar
payno committed
481
        res = {}
payno's avatar
payno committed
482
483
484
485
        if os.path.isdir(scan_path) is False:
            _logger.error(scan_path + ' is not a directory. Cannot extract '
                                     'DarkHST files')
            return res
payno's avatar
payno committed
486
        for file_ in os.listdir(scan_path):
payno's avatar
payno committed
487
488
489
            _prefix = prefix
            if prefix.endswith(file_ext):
                _prefix = prefix.rstrip(file_ext)
payno's avatar
payno committed
490
491
492
493
494
            if file_.startswith(_prefix) and file_.endswith(file_ext):
                # usuelly the dark file name should be dark.edf, but some
                # darkHSTXXXX remains...
                file_fp = file_.lstrip(_prefix).rstrip(file_ext).lstrip('HST')
                if file_fp == '' or file_fp.isnumeric() is True:
495
496
                    index = EDFTomoScan.guess_index_frm_file_name(_file=file_,
                                                                  basename=os.path.basename(scan_path))
payno's avatar
payno committed
497
498
499
                    urls = extract_urls_from_edf(os.path.join(scan_path, file_),
                                                 start_index=index)
                    res.update(urls)
payno's avatar
payno committed
500
501
502
        return res

    @staticmethod
payno's avatar
payno committed
503
    def get_refs_url(scan_path: str,  prefix: str='refHST',
504
                     file_ext: str='.edf', ignore=None) -> dict:
payno's avatar
payno committed
505
506
507
508
509
510
511
512
513
514
        """

        :param scan_path:
        :type: str
        :param prefix: ref / flat field file prefix
        :type: str
        :param file_ext: ref / flat field file extension
        :type: str
        :return: list of refs as silx's `DataUrl`
        """
payno's avatar
payno committed
515
        res = {}
payno's avatar
payno committed
516
517
518
519
        if os.path.isdir(scan_path) is False:
            _logger.error(scan_path + ' is not a directory. Cannot extract '
                                      'RefHST files')
            return res
520

521
522
523
524
525
526
527
528
529
530
        def get_next_free_index(key, keys):
            """return next free key from keys by converting it to a string
            with `key_value (n)` after it
            """
            new_key = key
            index = 2
            while new_key in keys:
                new_key = '%s (%s)' % (key, index)
                index += 1
            return new_key
payno's avatar
payno committed
531

532
533
534
535
536
537
538
539
        def ignore_file(file_name, to_ignore):
            if to_ignore is None:
                return False
            for pattern in to_ignore:
                if pattern in file_name:
                    return True
            return False

payno's avatar
payno committed
540
        for file_ in os.listdir(scan_path):
541
542
            if (file_.startswith(prefix) and file_.endswith(file_ext)
                    and not ignore_file(file_, ignore)):
543
544
                index = EDFTomoScan.guess_index_frm_file_name(_file=file_,
                                                              basename=os.path.basename(scan_path))
payno's avatar
payno committed
545
546
                file_fp = os.path.join(scan_path, file_)
                urls = extract_urls_from_edf(start_index=index, file_=file_fp)
547
548
549
550
551
552
                for key in urls:
                    if key in res:
                        key_ = get_next_free_index(key, res.keys())
                    else:
                        key_ = key
                    res[key_] = urls[key]
payno's avatar
payno committed
553
554
555
        return res

    @staticmethod
payno's avatar
payno committed
556
557
558
    def retrieve_information(scan: str, ref_file: Union[str, None], key: str,
                             type_: type,
                             key_aliases: Union[list, tuple, None] = None):
payno's avatar
payno committed
559
560
        """
        Try to retrieve information a .info file, an .xml or a flat field file.
Pierre Paleo's avatar
Pierre Paleo committed
561

payno's avatar
payno committed
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
        file.
        Look for the key 'key' or one of it aliases.

        :param scan: root folder of an acquisition. Must be an absolute path
        :param ref_file: the refXXXX_YYYY which should contain information
                         about the scan.
        :param key: the key (information) we are looking for
        :type: str
        :param type_: requestde out type if the information is found
        :type type_: return type if the information is found.
        :param key_aliases: aliases of the key in the different file
        :type: list
        :return: the requested information or None if not found
        """
        info_aliases = [key]
        if key_aliases is not None:
            assert type(key_aliases) in (tuple, list)
            [info_aliases.append(alias) for alias in key_aliases]

        if not os.path.isdir(scan):
            return None

        # 1st look for ref file if any given
        def parseRefFile(filePath):
            header = fabio.open(filePath).header
            for k in key_aliases:
                if k in header:
                    return type_(header[k])
            return None

        if ref_file is not None and os.path.isfile(ref_file):
            try:
                info = parseRefFile(ref_file)
            except IOError as e:
                _logger.warning(e)
            else:
                if info is not None:
                    return info

        # 2nd look for .info file
        def parseInfoFile(filePath):
            def extractInformation(text, alias):
                text = text.replace(alias, '')
                text = text.replace('\n', '')
                text = text.replace(' ', '')
                text = text.replace('=', '')
                return type_(text)

            info = None
            f = open(filePath, "r")
            line = f.readline()
            while line:
                for alias in info_aliases:
                    if alias in line:
                        info = extractInformation(line, alias)
                        break
                line = f.readline()
            f.close()
            return info

        baseName = os.path.basename(scan)
        infoFiles = [os.path.join(scan, baseName + '.info')]
        infoOnDataVisitor = infoFiles[0].replace('lbsram', '')
        # hack to check in lbsram, would need to be removed to add some consistency
        if os.path.isfile(infoOnDataVisitor):
            infoFiles.append(infoOnDataVisitor)
        for infoFile in infoFiles:
            if os.path.isfile(infoFile) is True:
                info = parseInfoFile(infoFile)
                if info is not None:
                    return info

        # 3td look for xml files
        def parseXMLFile(filePath):
            try:
                for alias in info_aliases:
                    tree = etree.parse(filePath)
                    elmt = tree.find("acquisition/" + alias)
                    if elmt is None:
                        continue
                    else:
                        info = type_(elmt.text)
                        if info == -1:
                            return None
                        else:
                            return info
            except etree.XMLSyntaxError as e:
                _logger.warning(e)
                return None

        xmlFiles = [os.path.join(scan, baseName + '.xml')]
        xmlOnDataVisitor = xmlFiles[0].replace('lbsram', '')
        # hack to check in lbsram, would need to be removed to add some consistency
        if os.path.isfile(xmlOnDataVisitor):
            xmlFiles.append(xmlOnDataVisitor)
        for xmlFile in xmlFiles:
            if os.path.isfile(xmlFile) is True:
                info = parseXMLFile(xmlFile)
                if info is not None:
                    return info

        return None