File: BlissSpecFile.py

package info (click to toggle)
pymca 5.8.0%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 44,392 kB
  • sloc: python: 155,456; ansic: 15,843; makefile: 116; sh: 73; xml: 55
file content (415 lines) | stat: -rw-r--r-- 14,653 bytes parent folder | download
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
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
#!/usr/bin/env python
#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2020-2021 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# 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.
#
#############################################################################*/
__author__ = "V.A. Sole"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
"""
This class exposes scan information stored by Bliss into redis as SPEC file.
"""
import os
import sys
import numpy
import time
import logging
_logger = logging.getLogger(__name__)

try:
    import RedisTools as redis
    HAS_REDIS = True
except:
    try:
        import PyMca5.PyMcaCore.RedisTools as redis
        HAS_REDIS = True
    except:
        _logger.info("Cannot import PyMca5.PyMcaCore.RedisTools")
        HAS_REDIS = False

if HAS_REDIS:
    from collections import OrderedDict

class BlissSpecFile(object):
    def __init__(self, filename, nscans=10):
        """
        filename is the name of the bliss session
        """
        if not HAS_REDIS:
            raise ImportError("Could not import RedisTools")
        if filename not in redis.get_sessions_list():
            raise IOError("Session <%s> not available" % filename)
        self._scan_nodes = []
        self._session = filename
        self._filename = redis.get_session_filename(self._session)
        self._scan_nodes = redis.get_session_scan_list(self._session,
                                                  self._filename)
        if len(self._scan_nodes) > nscans:
            self._scan_nodes = self._scan_nodes[-10:]
        self.list()
        self.__lastTime = 0
        self.__lastKey = "0.0"

    def list(self):
        """
        Return a string with all the scan keys separated by ,
        """
        _logger.debug("list method called")
        scanlist = ["%s" % scan.name.split("_")[0] for scan in self._scan_nodes]
        self._list = ["%s.1" % idx for idx in scanlist]
        return ",".join(scanlist)

    def __getitem__(self, item):
        """
        Returns the scan data
        """
        _logger.info("__getitem__ called %s" % item)
        t0 = time.time()
        key = self._list[item]
        if key == self.__lastKey and (t0 - self.__lastTime) < 1:
            # less than one second since last call, return cached value
            _logger.info("Returning cached value for key %s" % key)
        else:
            if key == self.__lastKey:
                _logger.info("Re-reading value for key %s" % key)
            self.__lastKey = key
            self.__lastItem = BlissSpecScan(self._scan_nodes[item])
            self.__lastTime = time.time()
        return self.__lastItem

    def select(self, key):
        """
        key is of the from s.o
        scan number, scan order
        """
        _logger.info("select called %s" % key)
        n = self._list.index(key)
        return self.__getitem__(n)

    def scanno(self):
        """
        Gives back the number of scans in the file
        """
        _logger.debug("scanno called")
        return len(self._scan_nodes)

    def allmotors(self):
        _logger.debug("allmotors called")
        return []

    def isUpdated(self):
        _logger.debug("BlissSpecFile is updated called")
        # get last scan
        scan_nodes = redis.get_session_scan_list(self._session,
                                                  self._filename)
        if not len(scan_nodes):
            # if we get no scans, information was emptied/lost and we'll get errors in any case
            # just say the file was updated. Perhaps the application asks for an update
            return True
        scanlist = ["%s" % scan.name.split("_")[0] for scan in scan_nodes]
        keylist = ["%s.1" % idx for idx in scanlist]
        scankey = keylist[-1]

        # if the last node is different, there are new data
        if scankey != self._list[-1]:
            return True

        # if the number of points or of mcas in the last node are different there are new data
        # the problem is how to obtain the previous number of points and mcas but in any case
        # we are going to read again the last scan
        if self.__lastKey == scankey:
            # we have old data available
            previous_npoints = self.__lastItem.lines()
            previous_nmca = self.__lastItem.nbmca()

        # read back (I do not force to read for the time being)
        scan = self.select(scankey)
        npoints = scan.lines()
        nmca = scan.nbmca()
        if self.__lastKey == scankey:
            if npoints > previous_npoints or nmca > previous_nmca:
                _logger.info("BlissSpecFile <%s> updated. New last scan data" % self._session)
                return True
        # there might be new points or mcas in the last scan, but that is easy and fast
        # to check by the main application because data are in cache
        _logger.debug("BlissSpecFile <%s> NOT updated." % self._session)
        return False

class BlissSpecScan(object):
    def __init__(self, scanNode):
        _logger.debug("__init__ called %s" % scanNode.name)
        self._node = scanNode
        self._identification = scanNode.name.split("_")[0] + ".1"
        self._scan_info = redis.scan_info(self._node)
        # check if there are 1D detectors
        top_master, channels = next(iter(scanNode.info["acquisition_chain"].items()))
        if len(channels["spectra"]):
            # for the time being only one MCA read
            self._spectra = redis.get_spectra(scanNode, unique=True)
        else:
            self._spectra = []
        self._counters = None
        self._motors = self._scan_info.get("positioners", {})

    def _read_counters(self, force=False):
        if force or not self._counters:
            _counters = redis.get_scan_data(self._node)
            try:
                _counters = self._sort_counters(_counters)
            except:
                _logger.error("Error sorting counters %s" % sys.exc_info()[1])
            self._counters = _counters

    def _sort_counters(self, counters):
        positioners = self.allmotors()
        title = self.command()
        tokens = title.split()
        scanned = [item for item in positioners if item in counters]
        if not len(scanned):
            scanned = [item for item in tokens if item in counters]

        # do nothing if there are no scanned motors assuming that the default
        # order will have the relevant items first
        if not len(scanned):
            return counters

        pure_counters = [item for item in counters if not (item in scanned)]
        # sort the pure counters
        if len(pure_counters) > 1:
            if sys.version_info > (3, 3):
                # sort irrespective of capital or lower case
                pure_counters.sort(key=str.casefold)
            else:
                # sort (capital letters first)
                pure_counters.sort()

        # sort the scanned motors
        if len(scanned) > 1:
            if sys.version_info > (3, 3):
                # sort irrespective of capital or lower case
                scanned.sort(key=str.casefold)
            else:
                # sort (capital letters first)
                scanned.sort()
            indices = []
            offset = len(tokens) + len(scanned)
            for item in scanned:
                if item in tokens:
                    indices.append((tokens.index(item), item))
                else:
                    indices.append((offset + scanned.index(item), item))
            indices.sort()
            scanned = [item for idx, item in indices]

        ordered = OrderedDict()
        for key in scanned:
            ordered[key] = counters[key]
        for key in pure_counters:
            ordered[key] = counters[key]
        return ordered

    def alllabels(self):
        """
        These are the labels associated to the counters
        """
        _logger.debug("alllabels called")
        self._read_counters()
        return [key for key in self._counters]

    def allmotors(self):
        _logger.debug("allmotors called")
        positioners = self._motors.get("positioners_start", {})
        return [key for key in positioners if not hasattr(positioners[key], "endswith")]

    def allmotorpos(self):
        _logger.debug("allmotorpos called")
        positioners = self._motors.get("positioners_start", {})
        return [positioners[key] for key in positioners if not hasattr(positioners[key], "endswith")]

    def cols(self):
        _logger.debug("cols called")
        self._read_counters()
        return len(self._counters)

    def command(self):
        _logger.debug("command called")
        return self._scan_info.get("title", "No COMMAND")

    def data(self):
        # somehow I have to manage to get the same number of points in all counters
        _logger.info("data called")
        self._read_counters(force=True)
        counters = self._counters
        keys = list(counters.keys())
        n_actual = len(counters[keys[0]])
        n_expected = self.lines()
        data = numpy.empty((len(keys), n_expected), dtype=numpy.float32)
        i = 0
        for key in keys:
            cdata = counters[key]
            n = cdata.size
            if n >= n_expected:
                data[i] = cdata[:n_expected]
            else:
                data[i, :n] = cdata
                data[i, n:n_expected] = numpy.nan
            i += 1
        return data

    def datacol(self, col):
        _logger.debug("datacol called")
        return self.data()[col, :]

    def dataline(self,line):
        _logger.debug("dataline called")
        return self.data()[:, line]

    def date(self):
        _logger.debug("date called")
        text = 'sometime'
        text = self._scan_info.get("start_time", text)
        return self._scan_info.get("start_time_str", text)

    def fileheader(self, key=''):
        _logger.debug("fileheader called")
        # this implementations returns the scan header instead of the correct
        # keys #E (file), #D (date) #O0 (motor names)
        #
        self._read_counters()
        labels = '#L '
        for label in self._counters:
            labels += '  '+label
        return ['#S %s  %s' %(self._node.name.split("_")[0], self.command()),
                '#D %s' % self.date(),
                '#N %d' % self.cols(),
                labels]

    def header(self,key):
        _logger.debug("header called")
        if key == 'S':
            return self.fileheader()[0]
        elif key == 'D':
            return self.fileheader()[1]
        elif key == 'N':
            return self.fileheader()[-2]
        elif key == 'L':
            return self.fileheader()[-1]
        elif key == '@CALIB':
            output = []
            return output
        elif key == '@CTIME':
            # expected to send Preset Time, Live Time, Real (Elapsed) Time
            output = []
            return output
        elif key == "" or key == " ":
            return self.fileheader()
        else:
            output = []
            return output

    def order(self):
        _logger.debug("order called")
        return 1

    def number(self):
        _logger.debug("number called")
        return int(self._node.name.split("_")[0])

    def lines(self):
        _logger.debug("lines called")
        self._read_counters()
        counters = self._counters
        if len(counters):
            nlines = 0
            keyList = list(counters.keys())
            for key in keyList:
                n = len(counters[key])
                if n > nlines:
                    nlines = n 
            return nlines
        else:
            return 0

    def nbmca(self):
        _logger.debug("nbmca called")
        if len(self._spectra):
            return len(self._spectra[0])
        else:
            return 0

    def mca(self,number):
        _logger.debug("mca called")
        if number <= 0:
            raise IndexError("Mca numbering starts at 1")
        elif number > self.nbmca():
            raise IndexError("Only %d MCAs in file" % self.nbmca())
        return self._spectra[0][number - 1]

def isBlissSpecFile(filename):
    if os.path.exists(filename):
        return False
    try:
        if filename in redis.get_sessions_list():
            return True
    except:
        pass
    return False

def test(filename):
    sf = BlissSpecFile(filename)
    print(sf[0].header('D'))
    print(sf[0].alllabels())
    print(sf[0].nbmca())
    if sf[0].nbmca():
        print(sf[0].mca(1))
    print(sf[0].header('S'))
    print(sf[0].allmotors())
    print(sf[0].allmotorpos())
    print(sf[0].header('@CTIME'))
    print(sf[0].header('@CALIB'))
    print(sf[0].header(''))
    print("Number of lines = ", sf[0].lines())
    if sf[0].lines():
        print("1st column = ", sf[0].datacol(0))
        print("1st line = ", sf[0].dataline(0))
    if sf.scanno() > 1:
        t0 = time.time()
        for i in range(sf.scanno()):
            #print(i)
            print(sf[i].header('S'))
            print(sf[i].header('D'))
            print(sf[i].alllabels())
            print(sf[i].nbmca())
            if sf[i].nbmca():
                print(sf[i].mca(1))
            print(sf[i].allmotors())
            print(sf[i].allmotorpos())
        print("elapsed = ", time.time() - t0)

if __name__ == "__main__":
    test(sys.argv[1])