source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py @ 18e7309

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Last change on this file since 18e7309 was d398285, checked in by krzywon, 8 years ago

#237: Modified the CanSAS HDF5 reader to read the latest version output from Mantid. Fixed the CanSAS XML reader so the axis titles and units are displayed properly.
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[68aa210]1"""
2    CanSAS 2D data reader for reading HDF5 formatted CanSAS files.
3"""
4
5import h5py
6import numpy as np
7import re
8import os
9import sys
10
[ad52d31]11from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D, Data1D, Data2D, Sample, Source
[68aa210]12from sas.sascalc.dataloader.data_info import Process, Aperture, Collimation, TransmissionSpectrum, Detector
13
14
15class Reader():
16    """
[ad52d31]17    A class for reading in CanSAS v2.0 data files. The existing iteration opens Mantid generated HDF5 formatted files
18    with file extension .h5/.H5. Any number of data sets may be present within the file and any dimensionality of data
19    may be used. Currently 1D and 2D SAS data sets are supported, but future implementations will include 1D and 2D
20    SESANS data. This class assumes a single data set for each sasentry.
[68aa210]21
22    :Dependencies:
23        The CanSAS HDF5 reader requires h5py v2.5.0 or later.
24    """
25
26    ## CanSAS version
27    cansas_version = 2.0
28    ## Logged warnings or messages
29    logging = None
30    ## List of errors for the current data set
31    errors = None
32    ## Raw file contents to be processed
33    raw_data = None
34    ## Data set being modified
35    current_dataset = None
36    ## For recursion and saving purposes, remember parent objects
37    parent_list = None
38    ## Data type name
[ad52d31]39    type_name = "CanSAS 2.0"
[68aa210]40    ## Wildcards
[ad52d31]41    type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"]
[68aa210]42    ## List of allowed extensions
43    ext = ['.h5', '.H5']
44    ## Flag to bypass extension check
45    allow_all = False
46    ## List of files to return
47    output = None
48
49    def __init__(self):
50        """
[ad52d31]51        Create the reader object and define initial states for class variables
[68aa210]52        """
53        self.current_dataset = None
[ad52d31]54        self.datasets = []
[68aa210]55        self.raw_data = None
56        self.errors = set()
57        self.logging = []
58        self.parent_list = []
59        self.output = []
60        self.detector = Detector()
61        self.collimation = Collimation()
62        self.aperture = Aperture()
63        self.process = Process()
64        self.sample = Sample()
65        self.source = Source()
66        self.trans_spectrum  = TransmissionSpectrum()
67
68    def read(self, filename):
69        """
[ad52d31]70        This is the general read method that all SasView data_loaders must have.
[68aa210]71
72        :param filename: A path for an HDF5 formatted CanSAS 2D data file.
73        :return: List of Data1D/2D objects or a list of errors.
74        """
75
[ad52d31]76        ## Reinitialize the class when loading a new data file to reset all class variables
[68aa210]77        self.__init__()
78        ## Check that the file exists
79        if os.path.isfile(filename):
80            basename = os.path.basename(filename)
81            _, extension = os.path.splitext(basename)
82            # If the file type is not allowed, return empty list
83            if extension in self.ext or self.allow_all:
84                ## Load the data file
85                self.raw_data = h5py.File(filename, 'r')
86                ## Read in all child elements of top level SASroot
87                self.read_children(self.raw_data)
[ad52d31]88                ## Add the last data set to the list of outputs
[68aa210]89                self.add_data_set()
90        ## Return data set(s)
91        return self.output
92
93    def read_children(self, data, parent=u'SASroot'):
94        """
[ad52d31]95        A recursive method for stepping through the hierarchical data file.
[68aa210]96
97        :param data: h5py Group object of any kind
98        :param parent: h5py Group parent name
99        :return: None
100        """
101
102        ## Create regex for base sasentry and for parent
103        parent_prog = re.compile(parent)
104
105        ## Loop through each element of the parent and process accordingly
106        for key in data.keys():
107            ## Get all information for the current key
108            value = data.get(key)
109            attr_keys = value.attrs.keys()
110            attr_values = value.attrs.values()
[d398285]111            if value.attrs.get(u'canSAS_class') is not None:
112                class_name = value.attrs.get(u'canSAS_class')
113            else:
114                class_name = value.attrs.get(u'NX_class')
[68aa210]115            if class_name is not None:
116                class_prog = re.compile(class_name)
117            else:
118                class_prog = re.compile(value.name)
119
120            if isinstance(value, h5py.Group):
[ad52d31]121                ##TODO: Rework this for multiple SASdata objects within a single SASentry to allow for both 1D and 2D
122                ##TODO:     data within the same SASentry - One 1D and one 2D data object for all SASdata sets?
[68aa210]123                ## If this is a new sasentry, store the current data set and create a fresh Data1D/2D object
124                if class_prog.match(u'SASentry'):
125                    self.add_data_set(key)
[ad52d31]126                ## Recursion step to access data within the group
127                self.read_children(value, class_name)
128                self.add_intermediate(class_name)
[68aa210]129
130            elif isinstance(value, h5py.Dataset):
131                ## If this is a dataset, store the data appropriately
132                data_set = data[key][:]
133
134                for data_point in data_set:
135                    ## Top Level Meta Data
[d398285]136                    unit = self._get_unit(value)
[68aa210]137                    if key == u'definition':
138                        self.current_dataset.meta_data['reader'] = data_point
139                    elif key == u'run':
140                        self.current_dataset.run.append(data_point)
141                    elif key == u'title':
142                        self.current_dataset.title = data_point
143                    elif key == u'SASnote':
144                        self.current_dataset.notes.append(data_point)
145
146                    ## I and Q Data
147                    elif key == u'I':
148                        if type(self.current_dataset) is Data2D:
149                            self.current_dataset.data = np.append(self.current_dataset.data, data_point)
[d398285]150                            self.current_dataset.zaxis("Intensity", unit)
[68aa210]151                        else:
152                            self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[d398285]153                            self.current_dataset.yaxis("Intensity", unit)
[68aa210]154                    elif key == u'Idev':
155                        if type(self.current_dataset) is Data2D:
156                            self.current_dataset.err_data = np.append(self.current_dataset.err_data, data_point)
157                        else:
158                            self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
159                    elif key == u'Q':
[d398285]160                        self.current_dataset.xaxis("Q", unit)
[68aa210]161                        if type(self.current_dataset) is Data2D:
162                            self.current_dataset.q = np.append(self.current_dataset.q, data_point)
163                        else:
164                            self.current_dataset.x = np.append(self.current_dataset.x, data_point)
165                    elif key == u'Qy':
[d398285]166                        self.current_dataset.yaxis("Q_y", unit)
[68aa210]167                        self.current_dataset.qy_data = np.append(self.current_dataset.qy_data, data_point)
168                    elif key == u'Qydev':
169                        self.current_dataset.dqy_data = np.append(self.current_dataset.dqy_data, data_point)
170                    elif key == u'Qx':
[d398285]171                        self.current_dataset.xaxis("Q_x", unit)
[68aa210]172                        self.current_dataset.qx_data = np.append(self.current_dataset.qx_data, data_point)
173                    elif key == u'Qxdev':
174                        self.current_dataset.dqx_data = np.append(self.current_dataset.dqx_data, data_point)
175                    elif key == u'Mask':
176                        self.current_dataset.mask = np.append(self.current_dataset.mask, data_point)
177
178                    ## Sample Information
179                    elif key == u'Title' and parent == u'SASsample':
180                        self.sample.name = data_point
181                    elif key == u'thickness' and parent == u'SASsample':
182                        self.sample.thickness = data_point
183                    elif key == u'temperature' and parent == u'SASsample':
184                        self.sample.temperature = data_point
185
[ad52d31]186                    ## Instrumental Information
187                    elif key == u'name' and parent == u'SASinstrument':
188                        self.current_dataset.instrument = data_point
189                    elif key == u'name' and parent == u'SASdetector':
190                        self.detector.name = data_point
191                    elif key == u'SDD' and parent == u'SASdetector':
192                        self.detector.distance = data_point
[d398285]193                        self.detector.distance_unit = unit
[ad52d31]194                    elif key == u'SSD' and parent == u'SAScollimation':
195                        self.collimation.length = data_point
[d398285]196                        self.collimation.length_unit = unit
[ad52d31]197                    elif key == u'name' and parent == u'SAScollimation':
198                        self.collimation.name = data_point
199
[68aa210]200                    ## Process Information
201                    elif key == u'name' and parent == u'SASprocess':
202                        self.process.name = data_point
203                    elif key == u'Title' and parent == u'SASprocess':
204                        self.process.name = data_point
205                    elif key == u'description' and parent == u'SASprocess':
206                        self.process.description = data_point
207                    elif key == u'date' and parent == u'SASprocess':
208                        self.process.date = data_point
[ad52d31]209                    elif parent == u'SASprocess':
210                        self.process.notes.append(data_point)
211
212                    ## Transmission Spectrum
213                    elif key == u'T' and parent == u'SAStransmission_spectrum':
214                        self.trans_spectrum.transmission.append(data_point)
215                    elif key == u'Tdev' and parent == u'SAStransmission_spectrum':
216                        self.trans_spectrum.transmission_deviation.append(data_point)
217                    elif key == u'lambda' and parent == u'SAStransmission_spectrum':
218                        self.trans_spectrum.wavelength.append(data_point)
219
220                    ## Other Information
221                    elif key == u'wavelength' and parent == u'SASdata':
222                        self.source.wavelength = data_point
[d398285]223                        self.source.wavelength.unit = unit
[ad52d31]224                    elif key == u'radiation' and parent == u'SASsource':
225                        self.source.radiation = data_point
226                    elif key == u'transmission' and parent == u'SASdata':
227                        self.sample.transmission = data_point
[68aa210]228
229                    ## Everything else goes in meta_data
230                    else:
231                        new_key = self._create_unique_key(self.current_dataset.meta_data, key)
232                        self.current_dataset.meta_data[new_key] = data_point
233
234            else:
235                ## I don't know if this reachable code
236                self.errors.add("ShouldNeverHappenException")
237
[ad52d31]238    def add_intermediate(self, parent):
239        """
240        This method stores any intermediate objects within the final data set after fully reading the set.
241
242        :param parent: The NXclass name for the h5py Group object that just finished being processed
243        :return:
244        """
245
246        if parent == u'SASprocess':
247            self.current_dataset.process.append(self.process)
248            self.process = Process()
249        elif parent == u'SASdetector':
250            self.current_dataset.detector.append(self.detector)
251            self.detector = Detector()
252        elif parent == u'SAStransmission_spectrum':
253            self.current_dataset.trans_spectrum.append(self.trans_spectrum)
254            self.trans_spectrum = TransmissionSpectrum()
255        elif parent == u'SASsource':
256            self.current_dataset.source = self.source
257            self.source = Source()
258        elif parent == u'SASsample':
259            self.current_dataset.sample = self.sample
260            self.sample = Sample()
261        elif parent == u'SAScollimation':
262            self.current_dataset.collimation.append(self.collimation)
263            self.collimation = Collimation()
264        elif parent == u'SASaperture':
265            self.collimation.aperture.append(self.aperture)
266            self.aperture = Aperture()
[68aa210]267
268    def final_data_cleanup(self):
269        """
270        Does some final cleanup and formatting on self.current_dataset
271        """
272
273        ## Type cast data arrays to float64 and find min/max as appropriate
274        if type(self.current_dataset) is Data2D:
275            self.current_dataset.data = np.delete(self.current_dataset.data, [0])
276            self.current_dataset.data = self.current_dataset.data.astype(np.float64)
277            self.current_dataset.err_data = np.delete(self.current_dataset.err_data, [0])
278            self.current_dataset.err_data = self.current_dataset.err_data.astype(np.float64)
279            self.current_dataset.mask = np.delete(self.current_dataset.mask, [0])
280            if self.current_dataset.qx_data is not None:
281                self.current_dataset.qx_data = np.delete(self.current_dataset.qx_data, [0])
282                self.current_dataset.xmin = np.min(self.current_dataset.qx_data)
283                self.current_dataset.xmax = np.max(self.current_dataset.qx_data)
284                self.current_dataset.qx_data = self.current_dataset.qx_data.astype(np.float64)
285            if self.current_dataset.dqx_data is not None:
286                self.current_dataset.dqx_data = np.delete(self.current_dataset.dqx_data, [0])
287                self.current_dataset.dqx_data = self.current_dataset.dqx_data.astype(np.float64)
288            if self.current_dataset.qy_data is not None:
289                self.current_dataset.qy_data = np.delete(self.current_dataset.qy_data, [0])
290                self.current_dataset.ymin = np.min(self.current_dataset.qy_data)
291                self.current_dataset.ymax = np.max(self.current_dataset.qy_data)
292                self.current_dataset.qy_data = self.current_dataset.qy_data.astype(np.float64)
293            if self.current_dataset.dqy_data is not None:
294                self.current_dataset.dqy_data = np.delete(self.current_dataset.dqy_data, [0])
295                self.current_dataset.dqy_data = self.current_dataset.dqy_data.astype(np.float64)
296            if self.current_dataset.q_data is not None:
297                self.current_dataset.q_data = np.delete(self.current_dataset.q_data, [0])
298                self.current_dataset.q_data = self.current_dataset.q_data.astype(np.float64)
299            zeros = np.ones(self.current_dataset.data.size, dtype=bool)
300            try:
301                for i in range (0, self.current_dataset.mask.size - 1):
302                    zeros[i] = self.current_dataset.mask[i]
303            except:
304                self.errors.add(sys.exc_value)
305            self.current_dataset.mask = zeros
306
307            ## Calculate the actual Q matrix
308            try:
309                if self.current_dataset.q_data.size <= 1:
310                    self.current_dataset.q_data = np.sqrt(self.current_dataset.qx_data * self.current_dataset.qx_data +
311                            self.current_dataset.qy_data * self.current_dataset.qy_data)
312            except:
313                self.current_dataset.q_data = None
314
315        elif type(self.current_dataset) is Data1D:
316            if self.current_dataset.x is not None:
317                self.current_dataset.x = np.delete(self.current_dataset.x, [0])
318                self.current_dataset.x = self.current_dataset.x.astype(np.float64)
319                self.current_dataset.xmin = np.min(self.current_dataset.x)
320                self.current_dataset.xmax = np.max(self.current_dataset.x)
321            if self.current_dataset.y is not None:
322                self.current_dataset.y = np.delete(self.current_dataset.y, [0])
323                self.current_dataset.y = self.current_dataset.y.astype(np.float64)
324                self.current_dataset.ymin = np.min(self.current_dataset.y)
325                self.current_dataset.ymax = np.max(self.current_dataset.y)
326            if self.current_dataset.dx is not None:
327                self.current_dataset.dx = np.delete(self.current_dataset.dx, [0])
328                self.current_dataset.dx = self.current_dataset.dx.astype(np.float64)
329            if self.current_dataset.dxl is not None:
330                self.current_dataset.dxl = np.delete(self.current_dataset.dxl, [0])
331                self.current_dataset.dxl = self.current_dataset.dxl.astype(np.float64)
332            if self.current_dataset.dxw is not None:
333                self.current_dataset.dxw = np.delete(self.current_dataset.dxw, [0])
334                self.current_dataset.dxw = self.current_dataset.dxw.astype(np.float64)
335            if self.current_dataset.dy is not None:
336                self.current_dataset.dy = np.delete(self.current_dataset.dy, [0])
337                self.current_dataset.dy =self.current_dataset.dy.astype(np.float64)
338
[ad52d31]339        if len(self.current_dataset.trans_spectrum) is not 0:
340            spectrum_list = []
341            for spectrum in self.current_dataset.trans_spectrum:
342                spectrum.transmission = np.delete(spectrum.transmission, [0])
343                spectrum.transmission = spectrum.transmission.astype(np.float64)
344                spectrum.transmission_deviation = np.delete(spectrum.transmission_deviation, [0])
345                spectrum.transmission_deviation = spectrum.transmission_deviation.astype(np.float64)
346                spectrum.wavelength = np.delete(spectrum.wavelength, [0])
347                spectrum.wavelength = spectrum.wavelength.astype(np.float64)
348                spectrum_list.append(spectrum)
349            self.current_dataset.trans_spectrum = spectrum_list
350
[68aa210]351        else:
352            self.errors.add("ShouldNeverHappenException")
353
354        ## Append intermediate objects to data
355        self.current_dataset.sample = self.sample
356        self.current_dataset.source = self.source
357        self.current_dataset.collimation.append(self.collimation)
358
359        ## Append errors to dataset and reset class errors
360        self.current_dataset.errors = self.errors
361        self.errors.clear()
362
363    def add_data_set(self, key=""):
364        """
365        Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
366        private method to generate a new data set.
367
368        :param key: NeXus group name for current tree level
369        :return: None
370        """
371        if self.current_dataset is not None:
372            self.final_data_cleanup()
373            self.output.append(self.current_dataset)
374        self._initialize_new_data_set(key)
375
376    def _initialize_new_data_set(self, key=""):
377        """
378        A private class method to generate a new 1D or 2D data object based on the type of data within the set.
379        Outside methods should call add_data_set() to be sure any existing data is stored properly.
380
381        :param key: NeXus group name for current tree level
382        :return: None
383        """
[ad52d31]384        entry = self._find_intermediate(key, "sasentry*")
[68aa210]385        data = entry.get("sasdata")
386        if data.get("Qx") is not None:
387            self.current_dataset = Data2D()
388        else:
389            x = np.array(0)
390            y = np.array(0)
391            self.current_dataset = Data1D(x, y)
392        self.current_dataset.filename = self.raw_data.filename
393
[ad52d31]394    def _find_intermediate(self, key="", basename=""):
395        """
396        A private class used to find an entry by either using a direct key or knowing the approximate basename.
397
398        :param key: Exact keyname of an entry
399        :param basename: Approximate name of an entry
400        :return:
401        """
402        entry = []
403        if key is not "":
404            entry = self.raw_data.get(key)
405        else:
406            key_prog = re.compile(basename)
407            for key in self.raw_data.keys():
408                if (key_prog.match(key)):
409                    entry = self.raw_data.get(key)
410                    break
411        return entry
412
[68aa210]413    def _create_unique_key(self, dictionary, name, numb=0):
414        """
415        Create a unique key value for any dictionary to prevent overwriting
416        Recurses until a unique key value is found.
417
418        :param dictionary: A dictionary with any number of entries
419        :param name: The index of the item to be added to dictionary
420        :param numb: The number to be appended to the name, starts at 0
421        """
422        if dictionary.get(name) is not None:
423            numb += 1
424            name = name.split("_")[0]
425            name += "_{0}".format(numb)
426            name = self._create_unique_key(dictionary, name, numb)
[d398285]427        return name
428
429    def _get_unit(self, value):
430        """
431        Find the unit for a particular value within the h5py dictionary
432
433        :param value: attribute dictionary for a particular value set
434        :return:
435        """
436        unit = value.attrs.get(u'units')
437        if unit == None:
438            unit = value.attrs.get(u'unit')
439
440        ## Convert the unit formats
441        if unit == "1/A":
442            unit = "A^{-1}"
443        elif unit == "1/cm":
444            unit = "cm^{-1}"
445
446        return unit
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