[68aa210] | 1 | """ |
---|
| 2 | CanSAS 2D data reader for reading HDF5 formatted CanSAS files. |
---|
| 3 | """ |
---|
| 4 | |
---|
| 5 | import h5py |
---|
| 6 | import numpy as np |
---|
| 7 | import re |
---|
| 8 | import os |
---|
| 9 | import sys |
---|
| 10 | |
---|
[082239e] | 11 | from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\ |
---|
| 12 | Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ |
---|
| 13 | TransmissionSpectrum, Detector |
---|
[d72567e] | 14 | from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable |
---|
| 15 | |
---|
[68aa210] | 16 | |
---|
| 17 | class Reader(): |
---|
| 18 | """ |
---|
[082239e] | 19 | A class for reading in CanSAS v2.0 data files. The existing iteration opens |
---|
| 20 | Mantid generated HDF5 formatted files with file extension .h5/.H5. Any |
---|
| 21 | number of data sets may be present within the file and any dimensionality |
---|
| 22 | of data may be used. Currently 1D and 2D SAS data sets are supported, but |
---|
| 23 | future implementations will include 1D and 2D SESANS data. |
---|
[d72567e] | 24 | |
---|
[082239e] | 25 | Any number of SASdata sets may be present in a SASentry and the data within |
---|
| 26 | can be either 1D I(Q) or 2D I(Qx, Qy). |
---|
[68aa210] | 27 | |
---|
[5e906207] | 28 | Also supports reading NXcanSAS formatted HDF5 files |
---|
| 29 | |
---|
[68aa210] | 30 | :Dependencies: |
---|
[d72567e] | 31 | The CanSAS HDF5 reader requires h5py => v2.5.0 or later. |
---|
[68aa210] | 32 | """ |
---|
| 33 | |
---|
[082239e] | 34 | # CanSAS version |
---|
[68aa210] | 35 | cansas_version = 2.0 |
---|
[082239e] | 36 | # Logged warnings or messages |
---|
[68aa210] | 37 | logging = None |
---|
[082239e] | 38 | # List of errors for the current data set |
---|
[68aa210] | 39 | errors = None |
---|
[082239e] | 40 | # Raw file contents to be processed |
---|
[68aa210] | 41 | raw_data = None |
---|
[082239e] | 42 | # Data info currently being read in |
---|
[d72567e] | 43 | current_datainfo = None |
---|
[082239e] | 44 | # SASdata set currently being read in |
---|
[68aa210] | 45 | current_dataset = None |
---|
[082239e] | 46 | # List of plottable1D objects that should be linked to the current_datainfo |
---|
[d72567e] | 47 | data1d = None |
---|
[082239e] | 48 | # List of plottable2D objects that should be linked to the current_datainfo |
---|
[d72567e] | 49 | data2d = None |
---|
[082239e] | 50 | # Data type name |
---|
[ad52d31] | 51 | type_name = "CanSAS 2.0" |
---|
[082239e] | 52 | # Wildcards |
---|
[ad52d31] | 53 | type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] |
---|
[082239e] | 54 | # List of allowed extensions |
---|
[68aa210] | 55 | ext = ['.h5', '.H5'] |
---|
[082239e] | 56 | # Flag to bypass extension check |
---|
[54544637] | 57 | allow_all = True |
---|
[082239e] | 58 | # List of files to return |
---|
[68aa210] | 59 | output = None |
---|
| 60 | |
---|
| 61 | def read(self, filename): |
---|
| 62 | """ |
---|
[ad52d31] | 63 | This is the general read method that all SasView data_loaders must have. |
---|
[68aa210] | 64 | |
---|
| 65 | :param filename: A path for an HDF5 formatted CanSAS 2D data file. |
---|
[d72567e] | 66 | :return: List of Data1D/2D objects and/or a list of errors. |
---|
[68aa210] | 67 | """ |
---|
[082239e] | 68 | # Reinitialize when loading a new data file to reset all class variables |
---|
[d72567e] | 69 | self.reset_class_variables() |
---|
[082239e] | 70 | # Check that the file exists |
---|
[68aa210] | 71 | if os.path.isfile(filename): |
---|
| 72 | basename = os.path.basename(filename) |
---|
| 73 | _, extension = os.path.splitext(basename) |
---|
| 74 | # If the file type is not allowed, return empty list |
---|
| 75 | if extension in self.ext or self.allow_all: |
---|
[082239e] | 76 | # Load the data file |
---|
[68aa210] | 77 | self.raw_data = h5py.File(filename, 'r') |
---|
[082239e] | 78 | # Read in all child elements of top level SASroot |
---|
[d72567e] | 79 | self.read_children(self.raw_data, []) |
---|
[082239e] | 80 | # Add the last data set to the list of outputs |
---|
[68aa210] | 81 | self.add_data_set() |
---|
[082239e] | 82 | # Close the data file |
---|
[995f4eb] | 83 | self.raw_data.close() |
---|
[082239e] | 84 | # Return data set(s) |
---|
[68aa210] | 85 | return self.output |
---|
| 86 | |
---|
[d72567e] | 87 | def reset_class_variables(self): |
---|
| 88 | """ |
---|
| 89 | Create the reader object and define initial states for class variables |
---|
| 90 | """ |
---|
| 91 | self.current_datainfo = None |
---|
| 92 | self.current_dataset = None |
---|
| 93 | self.data1d = [] |
---|
| 94 | self.data2d = [] |
---|
| 95 | self.raw_data = None |
---|
| 96 | self.errors = set() |
---|
| 97 | self.logging = [] |
---|
| 98 | self.output = [] |
---|
[2651724] | 99 | self.q_name = [] |
---|
| 100 | self.mask_name = u'' |
---|
| 101 | self.i_name = u'' |
---|
| 102 | self.i_node = u'' |
---|
| 103 | self.q_uncertainties = u'' |
---|
| 104 | self.q_resolutions = u'' |
---|
| 105 | self.i_uncertainties = u'' |
---|
[d72567e] | 106 | self.parent_class = u'' |
---|
| 107 | self.detector = Detector() |
---|
| 108 | self.collimation = Collimation() |
---|
| 109 | self.aperture = Aperture() |
---|
| 110 | self.process = Process() |
---|
| 111 | self.trans_spectrum = TransmissionSpectrum() |
---|
| 112 | |
---|
| 113 | def read_children(self, data, parent_list): |
---|
[68aa210] | 114 | """ |
---|
[ad52d31] | 115 | A recursive method for stepping through the hierarchical data file. |
---|
[68aa210] | 116 | |
---|
| 117 | :param data: h5py Group object of any kind |
---|
| 118 | :param parent: h5py Group parent name |
---|
| 119 | """ |
---|
| 120 | |
---|
[082239e] | 121 | # Loop through each element of the parent and process accordingly |
---|
[68aa210] | 122 | for key in data.keys(): |
---|
[082239e] | 123 | # Get all information for the current key |
---|
[68aa210] | 124 | value = data.get(key) |
---|
[d398285] | 125 | if value.attrs.get(u'canSAS_class') is not None: |
---|
| 126 | class_name = value.attrs.get(u'canSAS_class') |
---|
[0d93464] | 127 | elif value.attrs.get(u'NX_class') is not None: |
---|
[d398285] | 128 | class_name = value.attrs.get(u'NX_class') |
---|
[0d93464] | 129 | else: |
---|
| 130 | class_name = key |
---|
[68aa210] | 131 | if class_name is not None: |
---|
| 132 | class_prog = re.compile(class_name) |
---|
| 133 | else: |
---|
| 134 | class_prog = re.compile(value.name) |
---|
| 135 | |
---|
| 136 | if isinstance(value, h5py.Group): |
---|
[d72567e] | 137 | self.parent_class = class_name |
---|
| 138 | parent_list.append(key) |
---|
[082239e] | 139 | # If a new sasentry, store the current data sets and create |
---|
| 140 | # a fresh Data1D/2D object |
---|
[68aa210] | 141 | if class_prog.match(u'SASentry'): |
---|
| 142 | self.add_data_set(key) |
---|
[d72567e] | 143 | elif class_prog.match(u'SASdata'): |
---|
[9e0dd49] | 144 | self._find_data_attributes(value) |
---|
[2651724] | 145 | self._initialize_new_data_set(parent_list) |
---|
[082239e] | 146 | # Recursion step to access data within the group |
---|
[d72567e] | 147 | self.read_children(value, parent_list) |
---|
| 148 | self.add_intermediate() |
---|
| 149 | parent_list.remove(key) |
---|
[68aa210] | 150 | |
---|
| 151 | elif isinstance(value, h5py.Dataset): |
---|
[082239e] | 152 | # If this is a dataset, store the data appropriately |
---|
[68aa210] | 153 | data_set = data[key][:] |
---|
[7bd6860a] | 154 | unit = self._get_unit(value) |
---|
[ac370c5] | 155 | |
---|
[68aa210] | 156 | for data_point in data_set: |
---|
[082239e] | 157 | # Top Level Meta Data |
---|
[68aa210] | 158 | if key == u'definition': |
---|
[d72567e] | 159 | self.current_datainfo.meta_data['reader'] = data_point |
---|
[0d93464] | 160 | # Run |
---|
[68aa210] | 161 | elif key == u'run': |
---|
[d72567e] | 162 | self.current_datainfo.run.append(data_point) |
---|
[be88076] | 163 | try: |
---|
| 164 | run_name = value.attrs['name'] |
---|
| 165 | run_dict = {data_point: run_name} |
---|
| 166 | self.current_datainfo.run_name = run_dict |
---|
| 167 | except: |
---|
| 168 | pass |
---|
[0d93464] | 169 | # Title |
---|
[68aa210] | 170 | elif key == u'title': |
---|
[d72567e] | 171 | self.current_datainfo.title = data_point |
---|
[0d93464] | 172 | # Note |
---|
[68aa210] | 173 | elif key == u'SASnote': |
---|
[d72567e] | 174 | self.current_datainfo.notes.append(data_point) |
---|
[082239e] | 175 | # Sample Information |
---|
[0d93464] | 176 | elif self.parent_class == u'SASsample': |
---|
| 177 | self.process_sample(data_point, key) |
---|
[082239e] | 178 | # Instrumental Information |
---|
[c94280c] | 179 | elif (key == u'name' |
---|
| 180 | and self.parent_class == u'SASinstrument'): |
---|
[d72567e] | 181 | self.current_datainfo.instrument = data_point |
---|
[0d93464] | 182 | # Detector |
---|
| 183 | elif self.parent_class == u'SASdetector': |
---|
| 184 | self.process_detector(data_point, key, unit) |
---|
| 185 | # Collimation |
---|
| 186 | elif self.parent_class == u'SAScollimation': |
---|
| 187 | self.process_collimation(data_point, key, unit) |
---|
| 188 | # Aperture |
---|
| 189 | elif self.parent_class == u'SASaperture': |
---|
| 190 | self.process_aperture(data_point, key) |
---|
[082239e] | 191 | # Process Information |
---|
[0d93464] | 192 | elif self.parent_class == u'SASprocess': # CanSAS 2.0 |
---|
| 193 | self.process_process(data_point, key) |
---|
[082239e] | 194 | # Source |
---|
[0d93464] | 195 | elif self.parent_class == u'SASsource': |
---|
| 196 | self.process_source(data_point, key, unit) |
---|
[082239e] | 197 | # Everything else goes in meta_data |
---|
[0d93464] | 198 | elif self.parent_class == u'SASdata': |
---|
| 199 | self.process_data_object(data_set, key, unit) |
---|
| 200 | break |
---|
| 201 | elif self.parent_class == u'SAStransmission_spectrum': |
---|
| 202 | self.process_trans_spectrum(data_set, key) |
---|
| 203 | break |
---|
[68aa210] | 204 | else: |
---|
[082239e] | 205 | new_key = self._create_unique_key( |
---|
| 206 | self.current_datainfo.meta_data, key) |
---|
[d72567e] | 207 | self.current_datainfo.meta_data[new_key] = data_point |
---|
[68aa210] | 208 | |
---|
| 209 | else: |
---|
[082239e] | 210 | # I don't know if this reachable code |
---|
[68aa210] | 211 | self.errors.add("ShouldNeverHappenException") |
---|
| 212 | |
---|
[0d93464] | 213 | def process_data_object(self, data_set, key, unit): |
---|
| 214 | """ |
---|
| 215 | SASdata processor method |
---|
| 216 | :param data_set: data from HDF5 file |
---|
| 217 | :param key: canSAS_class attribute |
---|
| 218 | :param unit: unit attribute |
---|
| 219 | """ |
---|
| 220 | # FIXME: check attributes of SASdata for Q, dQ, Mask, etc. |
---|
[2651724] | 221 | if key == self.i_name: |
---|
[0d93464] | 222 | if isinstance(self.current_dataset, plottable_2D): |
---|
| 223 | self.current_dataset.data = data_set |
---|
| 224 | self.current_dataset.zaxis("Intensity", unit) |
---|
| 225 | else: |
---|
| 226 | self.current_dataset.y = data_set.flatten() |
---|
| 227 | self.current_dataset.yaxis("Intensity", unit) |
---|
[2651724] | 228 | elif key == self.i_uncertainties: |
---|
[0d93464] | 229 | if isinstance(self.current_dataset, plottable_2D): |
---|
| 230 | self.current_dataset.err_data = data_set.flatten() |
---|
| 231 | else: |
---|
| 232 | self.current_dataset.dy = data_set.flatten() |
---|
[2651724] | 233 | elif key in self.q_name: |
---|
[0d93464] | 234 | self.current_dataset.xaxis("Q", unit) |
---|
| 235 | if isinstance(self.current_dataset, plottable_2D): |
---|
| 236 | self.current_dataset.q = data_set.flatten() |
---|
| 237 | else: |
---|
| 238 | self.current_dataset.x = data_set.flatten() |
---|
[2651724] | 239 | elif key in self.q_resolutions: |
---|
| 240 | if key == u'dQw': |
---|
| 241 | self.current_dataset.dxw = data_set.flatten() |
---|
| 242 | elif key == u'dQl': |
---|
| 243 | self.current_dataset.dxl = data_set.flatten() |
---|
| 244 | else: |
---|
| 245 | self.current_dataset.dx = data_set.flatten() |
---|
[0d93464] | 246 | elif key == u'Qy': |
---|
| 247 | self.current_dataset.yaxis("Q_y", unit) |
---|
| 248 | self.current_dataset.qy_data = data_set.flatten() |
---|
| 249 | elif key == u'Qydev': |
---|
| 250 | self.current_dataset.dqy_data = data_set.flatten() |
---|
| 251 | elif key == u'Qx': |
---|
| 252 | self.current_dataset.xaxis("Q_x", unit) |
---|
| 253 | self.current_dataset.qx_data = data_set.flatten() |
---|
| 254 | elif key == u'Qxdev': |
---|
| 255 | self.current_dataset.dqx_data = data_set.flatten() |
---|
[2651724] | 256 | elif key == self.mask_name: |
---|
[0d93464] | 257 | self.current_dataset.mask = data_set.flatten() |
---|
| 258 | elif key == u'wavelength': |
---|
| 259 | self.current_datainfo.source.wavelength = data_set[0] |
---|
| 260 | self.current_datainfo.source.wavelength_unit = unit |
---|
| 261 | |
---|
| 262 | def process_trans_spectrum(self, data_set, key): |
---|
| 263 | """ |
---|
| 264 | SAStransmission_spectrum processor |
---|
| 265 | :param data_set: data from HDF5 file |
---|
| 266 | :param key: canSAS_class attribute |
---|
| 267 | """ |
---|
| 268 | if key == u'T': |
---|
| 269 | self.trans_spectrum.transmission = data_set.flatten() |
---|
| 270 | elif key == u'Tdev': |
---|
| 271 | self.trans_spectrum.transmission_deviation = data_set.flatten() |
---|
| 272 | elif key == u'lambda': |
---|
| 273 | self.trans_spectrum.wavelength = data_set.flatten() |
---|
| 274 | |
---|
| 275 | def process_sample(self, data_point, key): |
---|
| 276 | """ |
---|
| 277 | SASsample processor |
---|
| 278 | :param data_point: Single point from an HDF5 data file |
---|
| 279 | :param key: class name data_point was taken from |
---|
| 280 | """ |
---|
| 281 | if key == u'Title': |
---|
| 282 | self.current_datainfo.sample.name = data_point |
---|
| 283 | elif key == u'name': |
---|
| 284 | self.current_datainfo.sample.name = data_point |
---|
| 285 | elif key == u'ID': |
---|
| 286 | self.current_datainfo.sample.name = data_point |
---|
| 287 | elif key == u'thickness': |
---|
| 288 | self.current_datainfo.sample.thickness = data_point |
---|
| 289 | elif key == u'temperature': |
---|
| 290 | self.current_datainfo.sample.temperature = data_point |
---|
| 291 | elif key == u'transmission': |
---|
| 292 | self.current_datainfo.sample.transmission = data_point |
---|
| 293 | elif key == u'x_position': |
---|
| 294 | self.current_datainfo.sample.position.x = data_point |
---|
| 295 | elif key == u'y_position': |
---|
| 296 | self.current_datainfo.sample.position.y = data_point |
---|
| 297 | elif key == u'pitch': |
---|
| 298 | self.current_datainfo.sample.orientation.x = data_point |
---|
| 299 | elif key == u'yaw': |
---|
| 300 | self.current_datainfo.sample.orientation.y = data_point |
---|
| 301 | elif key == u'roll': |
---|
| 302 | self.current_datainfo.sample.orientation.z = data_point |
---|
| 303 | elif key == u'details': |
---|
| 304 | self.current_datainfo.sample.details.append(data_point) |
---|
| 305 | |
---|
| 306 | def process_detector(self, data_point, key, unit): |
---|
| 307 | """ |
---|
| 308 | SASdetector processor |
---|
| 309 | :param data_point: Single point from an HDF5 data file |
---|
| 310 | :param key: class name data_point was taken from |
---|
| 311 | :param unit: unit attribute from data set |
---|
| 312 | """ |
---|
| 313 | if key == u'name': |
---|
| 314 | self.detector.name = data_point |
---|
| 315 | elif key == u'SDD': |
---|
| 316 | self.detector.distance = float(data_point) |
---|
| 317 | self.detector.distance_unit = unit |
---|
| 318 | elif key == u'slit_length': |
---|
| 319 | self.detector.slit_length = float(data_point) |
---|
| 320 | self.detector.slit_length_unit = unit |
---|
| 321 | elif key == u'x_position': |
---|
| 322 | self.detector.offset.x = float(data_point) |
---|
| 323 | self.detector.offset_unit = unit |
---|
| 324 | elif key == u'y_position': |
---|
| 325 | self.detector.offset.y = float(data_point) |
---|
| 326 | self.detector.offset_unit = unit |
---|
| 327 | elif key == u'pitch': |
---|
| 328 | self.detector.orientation.x = float(data_point) |
---|
| 329 | self.detector.orientation_unit = unit |
---|
| 330 | elif key == u'roll': |
---|
| 331 | self.detector.orientation.z = float(data_point) |
---|
| 332 | self.detector.orientation_unit = unit |
---|
| 333 | elif key == u'yaw': |
---|
| 334 | self.detector.orientation.y = float(data_point) |
---|
| 335 | self.detector.orientation_unit = unit |
---|
| 336 | elif key == u'beam_center_x': |
---|
| 337 | self.detector.beam_center.x = float(data_point) |
---|
| 338 | self.detector.beam_center_unit = unit |
---|
| 339 | elif key == u'beam_center_y': |
---|
| 340 | self.detector.beam_center.y = float(data_point) |
---|
| 341 | self.detector.beam_center_unit = unit |
---|
| 342 | elif key == u'x_pixel_size': |
---|
| 343 | self.detector.pixel_size.x = float(data_point) |
---|
| 344 | self.detector.pixel_size_unit = unit |
---|
| 345 | elif key == u'y_pixel_size': |
---|
| 346 | self.detector.pixel_size.y = float(data_point) |
---|
| 347 | self.detector.pixel_size_unit = unit |
---|
| 348 | |
---|
| 349 | def process_collimation(self, data_point, key, unit): |
---|
| 350 | """ |
---|
| 351 | SAScollimation processor |
---|
| 352 | :param data_point: Single point from an HDF5 data file |
---|
| 353 | :param key: class name data_point was taken from |
---|
| 354 | :param unit: unit attribute from data set |
---|
| 355 | """ |
---|
| 356 | if key == u'distance': |
---|
| 357 | self.collimation.length = data_point |
---|
| 358 | self.collimation.length_unit = unit |
---|
| 359 | elif key == u'name': |
---|
| 360 | self.collimation.name = data_point |
---|
| 361 | |
---|
| 362 | def process_aperture(self, data_point, key): |
---|
| 363 | """ |
---|
| 364 | SASaperture processor |
---|
| 365 | :param data_point: Single point from an HDF5 data file |
---|
| 366 | :param key: class name data_point was taken from |
---|
| 367 | """ |
---|
| 368 | if key == u'shape': |
---|
| 369 | self.aperture.shape = data_point |
---|
| 370 | elif key == u'x_gap': |
---|
| 371 | self.aperture.size.x = data_point |
---|
| 372 | elif key == u'y_gap': |
---|
| 373 | self.aperture.size.y = data_point |
---|
| 374 | |
---|
| 375 | def process_source(self, data_point, key, unit): |
---|
| 376 | """ |
---|
| 377 | SASsource processor |
---|
| 378 | :param data_point: Single point from an HDF5 data file |
---|
| 379 | :param key: class name data_point was taken from |
---|
| 380 | :param unit: unit attribute from data set |
---|
| 381 | """ |
---|
| 382 | if key == u'incident_wavelength': |
---|
| 383 | self.current_datainfo.source.wavelength = data_point |
---|
| 384 | self.current_datainfo.source.wavelength_unit = unit |
---|
| 385 | elif key == u'wavelength_max': |
---|
| 386 | self.current_datainfo.source.wavelength_max = data_point |
---|
| 387 | self.current_datainfo.source.wavelength_max_unit = unit |
---|
| 388 | elif key == u'wavelength_min': |
---|
| 389 | self.current_datainfo.source.wavelength_min = data_point |
---|
| 390 | self.current_datainfo.source.wavelength_min_unit = unit |
---|
| 391 | elif key == u'incident_wavelength_spread': |
---|
| 392 | self.current_datainfo.source.wavelength_spread = data_point |
---|
| 393 | self.current_datainfo.source.wavelength_spread_unit = unit |
---|
| 394 | elif key == u'beam_size_x': |
---|
| 395 | self.current_datainfo.source.beam_size.x = data_point |
---|
| 396 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 397 | elif key == u'beam_size_y': |
---|
| 398 | self.current_datainfo.source.beam_size.y = data_point |
---|
| 399 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 400 | elif key == u'beam_shape': |
---|
| 401 | self.current_datainfo.source.beam_shape = data_point |
---|
| 402 | elif key == u'radiation': |
---|
| 403 | self.current_datainfo.source.radiation = data_point |
---|
| 404 | |
---|
| 405 | def process_process(self, data_point, key): |
---|
| 406 | """ |
---|
| 407 | SASprocess processor |
---|
| 408 | :param data_point: Single point from an HDF5 data file |
---|
| 409 | :param key: class name data_point was taken from |
---|
| 410 | """ |
---|
| 411 | if key == u'Title': # CanSAS 2.0 |
---|
| 412 | self.process.name = data_point |
---|
| 413 | elif key == u'name': # NXcanSAS |
---|
| 414 | self.process.name = data_point |
---|
| 415 | elif key == u'description': |
---|
| 416 | self.process.description = data_point |
---|
| 417 | elif key == u'date': |
---|
| 418 | self.process.date = data_point |
---|
| 419 | elif key == u'term': |
---|
| 420 | self.process.term = data_point |
---|
| 421 | else: |
---|
| 422 | self.process.notes.append(data_point) |
---|
| 423 | |
---|
[d72567e] | 424 | def add_intermediate(self): |
---|
[ad52d31] | 425 | """ |
---|
[082239e] | 426 | This method stores any intermediate objects within the final data set |
---|
| 427 | after fully reading the set. |
---|
[ad52d31] | 428 | |
---|
[082239e] | 429 | :param parent: The NXclass name for the h5py Group object that just |
---|
| 430 | finished being processed |
---|
[ad52d31] | 431 | """ |
---|
| 432 | |
---|
[d72567e] | 433 | if self.parent_class == u'SASprocess': |
---|
| 434 | self.current_datainfo.process.append(self.process) |
---|
[ad52d31] | 435 | self.process = Process() |
---|
[d72567e] | 436 | elif self.parent_class == u'SASdetector': |
---|
| 437 | self.current_datainfo.detector.append(self.detector) |
---|
[ad52d31] | 438 | self.detector = Detector() |
---|
[d72567e] | 439 | elif self.parent_class == u'SAStransmission_spectrum': |
---|
| 440 | self.current_datainfo.trans_spectrum.append(self.trans_spectrum) |
---|
[ad52d31] | 441 | self.trans_spectrum = TransmissionSpectrum() |
---|
[d72567e] | 442 | elif self.parent_class == u'SAScollimation': |
---|
| 443 | self.current_datainfo.collimation.append(self.collimation) |
---|
[ad52d31] | 444 | self.collimation = Collimation() |
---|
[d72567e] | 445 | elif self.parent_class == u'SASaperture': |
---|
[ad52d31] | 446 | self.collimation.aperture.append(self.aperture) |
---|
| 447 | self.aperture = Aperture() |
---|
[d72567e] | 448 | elif self.parent_class == u'SASdata': |
---|
[082239e] | 449 | if isinstance(self.current_dataset, plottable_2D): |
---|
[d72567e] | 450 | self.data2d.append(self.current_dataset) |
---|
[082239e] | 451 | elif isinstance(self.current_dataset, plottable_1D): |
---|
[d72567e] | 452 | self.data1d.append(self.current_dataset) |
---|
[68aa210] | 453 | |
---|
| 454 | def final_data_cleanup(self): |
---|
| 455 | """ |
---|
[082239e] | 456 | Does some final cleanup and formatting on self.current_datainfo and |
---|
| 457 | all data1D and data2D objects and then combines the data and info into |
---|
| 458 | Data1D and Data2D objects |
---|
[68aa210] | 459 | """ |
---|
| 460 | |
---|
[082239e] | 461 | # Type cast data arrays to float64 |
---|
[d72567e] | 462 | if len(self.current_datainfo.trans_spectrum) > 0: |
---|
[ad52d31] | 463 | spectrum_list = [] |
---|
[d72567e] | 464 | for spectrum in self.current_datainfo.trans_spectrum: |
---|
[ad52d31] | 465 | spectrum.transmission = np.delete(spectrum.transmission, [0]) |
---|
| 466 | spectrum.transmission = spectrum.transmission.astype(np.float64) |
---|
[082239e] | 467 | spectrum.transmission_deviation = np.delete( |
---|
| 468 | spectrum.transmission_deviation, [0]) |
---|
| 469 | spectrum.transmission_deviation = \ |
---|
| 470 | spectrum.transmission_deviation.astype(np.float64) |
---|
[ad52d31] | 471 | spectrum.wavelength = np.delete(spectrum.wavelength, [0]) |
---|
| 472 | spectrum.wavelength = spectrum.wavelength.astype(np.float64) |
---|
[d72567e] | 473 | if len(spectrum.transmission) > 0: |
---|
| 474 | spectrum_list.append(spectrum) |
---|
| 475 | self.current_datainfo.trans_spectrum = spectrum_list |
---|
[68aa210] | 476 | |
---|
[082239e] | 477 | # Append errors to dataset and reset class errors |
---|
[d72567e] | 478 | self.current_datainfo.errors = self.errors |
---|
[68aa210] | 479 | self.errors.clear() |
---|
| 480 | |
---|
[082239e] | 481 | # Combine all plottables with datainfo and append each to output |
---|
| 482 | # Type cast data arrays to float64 and find min/max as appropriate |
---|
[d72567e] | 483 | for dataset in self.data2d: |
---|
| 484 | dataset.data = dataset.data.astype(np.float64) |
---|
| 485 | dataset.err_data = dataset.err_data.astype(np.float64) |
---|
| 486 | if dataset.qx_data is not None: |
---|
| 487 | dataset.xmin = np.min(dataset.qx_data) |
---|
| 488 | dataset.xmax = np.max(dataset.qx_data) |
---|
| 489 | dataset.qx_data = dataset.qx_data.astype(np.float64) |
---|
| 490 | if dataset.dqx_data is not None: |
---|
| 491 | dataset.dqx_data = dataset.dqx_data.astype(np.float64) |
---|
| 492 | if dataset.qy_data is not None: |
---|
| 493 | dataset.ymin = np.min(dataset.qy_data) |
---|
| 494 | dataset.ymax = np.max(dataset.qy_data) |
---|
| 495 | dataset.qy_data = dataset.qy_data.astype(np.float64) |
---|
| 496 | if dataset.dqy_data is not None: |
---|
| 497 | dataset.dqy_data = dataset.dqy_data.astype(np.float64) |
---|
| 498 | if dataset.q_data is not None: |
---|
| 499 | dataset.q_data = dataset.q_data.astype(np.float64) |
---|
| 500 | zeros = np.ones(dataset.data.size, dtype=bool) |
---|
| 501 | try: |
---|
[082239e] | 502 | for i in range(0, dataset.mask.size - 1): |
---|
[d72567e] | 503 | zeros[i] = dataset.mask[i] |
---|
| 504 | except: |
---|
| 505 | self.errors.add(sys.exc_value) |
---|
| 506 | dataset.mask = zeros |
---|
[082239e] | 507 | # Calculate the actual Q matrix |
---|
[d72567e] | 508 | try: |
---|
| 509 | if dataset.q_data.size <= 1: |
---|
[54544637] | 510 | dataset.q_data = np.sqrt(dataset.qx_data |
---|
| 511 | * dataset.qx_data |
---|
| 512 | + dataset.qy_data |
---|
| 513 | * dataset.qy_data) |
---|
[d72567e] | 514 | except: |
---|
| 515 | dataset.q_data = None |
---|
[ac370c5] | 516 | |
---|
| 517 | if dataset.data.ndim == 2: |
---|
| 518 | (n_rows, n_cols) = dataset.data.shape |
---|
[479799c] | 519 | dataset.y_bins = dataset.qy_data[0::n_cols] |
---|
[ac370c5] | 520 | dataset.x_bins = dataset.qx_data[:n_cols] |
---|
| 521 | dataset.data = dataset.data.flatten() |
---|
| 522 | |
---|
[082239e] | 523 | final_dataset = combine_data_info_with_plottable( |
---|
| 524 | dataset, self.current_datainfo) |
---|
[d72567e] | 525 | self.output.append(final_dataset) |
---|
| 526 | |
---|
| 527 | for dataset in self.data1d: |
---|
| 528 | if dataset.x is not None: |
---|
| 529 | dataset.x = dataset.x.astype(np.float64) |
---|
| 530 | dataset.xmin = np.min(dataset.x) |
---|
| 531 | dataset.xmax = np.max(dataset.x) |
---|
| 532 | if dataset.y is not None: |
---|
| 533 | dataset.y = dataset.y.astype(np.float64) |
---|
| 534 | dataset.ymin = np.min(dataset.y) |
---|
| 535 | dataset.ymax = np.max(dataset.y) |
---|
| 536 | if dataset.dx is not None: |
---|
| 537 | dataset.dx = dataset.dx.astype(np.float64) |
---|
| 538 | if dataset.dxl is not None: |
---|
| 539 | dataset.dxl = dataset.dxl.astype(np.float64) |
---|
| 540 | if dataset.dxw is not None: |
---|
| 541 | dataset.dxw = dataset.dxw.astype(np.float64) |
---|
| 542 | if dataset.dy is not None: |
---|
| 543 | dataset.dy = dataset.dy.astype(np.float64) |
---|
[082239e] | 544 | final_dataset = combine_data_info_with_plottable( |
---|
| 545 | dataset, self.current_datainfo) |
---|
[d72567e] | 546 | self.output.append(final_dataset) |
---|
| 547 | |
---|
[68aa210] | 548 | def add_data_set(self, key=""): |
---|
| 549 | """ |
---|
[082239e] | 550 | Adds the current_dataset to the list of outputs after preforming final |
---|
| 551 | processing on the data and then calls a private method to generate a |
---|
| 552 | new data set. |
---|
[68aa210] | 553 | |
---|
| 554 | :param key: NeXus group name for current tree level |
---|
| 555 | """ |
---|
[d72567e] | 556 | |
---|
| 557 | if self.current_datainfo and self.current_dataset: |
---|
[68aa210] | 558 | self.final_data_cleanup() |
---|
[d72567e] | 559 | self.data1d = [] |
---|
| 560 | self.data2d = [] |
---|
| 561 | self.current_datainfo = DataInfo() |
---|
[68aa210] | 562 | |
---|
[082239e] | 563 | def _initialize_new_data_set(self, parent_list=None): |
---|
[68aa210] | 564 | """ |
---|
[082239e] | 565 | A private class method to generate a new 1D or 2D data object based on |
---|
| 566 | the type of data within the set. Outside methods should call |
---|
| 567 | add_data_set() to be sure any existing data is stored properly. |
---|
[68aa210] | 568 | |
---|
[d72567e] | 569 | :param parent_list: List of names of parent elements |
---|
[68aa210] | 570 | """ |
---|
[d72567e] | 571 | |
---|
| 572 | if parent_list is None: |
---|
| 573 | parent_list = [] |
---|
| 574 | if self._find_intermediate(parent_list, "Qx"): |
---|
| 575 | self.current_dataset = plottable_2D() |
---|
[68aa210] | 576 | else: |
---|
| 577 | x = np.array(0) |
---|
| 578 | y = np.array(0) |
---|
[d72567e] | 579 | self.current_dataset = plottable_1D(x, y) |
---|
| 580 | self.current_datainfo.filename = self.raw_data.filename |
---|
[68aa210] | 581 | |
---|
[9e0dd49] | 582 | def _find_data_attributes(self, value): |
---|
[2651724] | 583 | """ |
---|
| 584 | A class to find the indices for Q, the name of the Qdev and Idev, and |
---|
| 585 | the name of the mask. |
---|
| 586 | :param value: SASdata/NXdata HDF5 Group |
---|
| 587 | """ |
---|
[9e0dd49] | 588 | attrs = value.attrs |
---|
| 589 | signal = attrs.get("signal") |
---|
[2651724] | 590 | |
---|
| 591 | i_axes = np.array(attrs.get("I_axes").split(",")) |
---|
| 592 | q_indices = np.array(attrs.get("Q_indices")) |
---|
| 593 | self.mask_name = attrs.get("mask") |
---|
[9e0dd49] | 594 | keys = value.keys() |
---|
[2651724] | 595 | for val in q_indices: |
---|
| 596 | self.q_name.append(i_axes[val]) |
---|
[9e0dd49] | 597 | self.i_name = signal |
---|
[2651724] | 598 | self.i_node = value.get(self.i_name) |
---|
| 599 | for item in self.q_name: |
---|
| 600 | if item in keys: |
---|
| 601 | q_vals = value.get(item) |
---|
| 602 | self.q_uncertainties = q_vals.attrs.get("uncertainty") |
---|
| 603 | self.q_resolutions = q_vals.attrs.get("resolution") |
---|
[9e0dd49] | 604 | if self.i_name in keys: |
---|
| 605 | i_vals = value.get(self.i_name) |
---|
[2651724] | 606 | self.i_uncertainties = i_vals.attrs.get("uncertainty") |
---|
[9e0dd49] | 607 | |
---|
[d72567e] | 608 | def _find_intermediate(self, parent_list, basename=""): |
---|
[ad52d31] | 609 | """ |
---|
[082239e] | 610 | A private class used to find an entry by either using a direct key or |
---|
| 611 | knowing the approximate basename. |
---|
[ad52d31] | 612 | |
---|
[082239e] | 613 | :param parent_list: List of parents nodes in the HDF5 file |
---|
[d72567e] | 614 | :param basename: Approximate name of an entry to search for |
---|
[ad52d31] | 615 | :return: |
---|
| 616 | """ |
---|
[d72567e] | 617 | |
---|
| 618 | entry = False |
---|
| 619 | key_prog = re.compile(basename) |
---|
| 620 | top = self.raw_data |
---|
| 621 | for parent in parent_list: |
---|
| 622 | top = top.get(parent) |
---|
| 623 | for key in top.keys(): |
---|
[082239e] | 624 | if key_prog.match(key): |
---|
[d72567e] | 625 | entry = True |
---|
| 626 | break |
---|
[ad52d31] | 627 | return entry |
---|
| 628 | |
---|
[68aa210] | 629 | def _create_unique_key(self, dictionary, name, numb=0): |
---|
| 630 | """ |
---|
| 631 | Create a unique key value for any dictionary to prevent overwriting |
---|
| 632 | Recurses until a unique key value is found. |
---|
| 633 | |
---|
| 634 | :param dictionary: A dictionary with any number of entries |
---|
| 635 | :param name: The index of the item to be added to dictionary |
---|
| 636 | :param numb: The number to be appended to the name, starts at 0 |
---|
[d72567e] | 637 | :return: The new name for the dictionary entry |
---|
[68aa210] | 638 | """ |
---|
| 639 | if dictionary.get(name) is not None: |
---|
| 640 | numb += 1 |
---|
| 641 | name = name.split("_")[0] |
---|
| 642 | name += "_{0}".format(numb) |
---|
| 643 | name = self._create_unique_key(dictionary, name, numb) |
---|
[d398285] | 644 | return name |
---|
| 645 | |
---|
| 646 | def _get_unit(self, value): |
---|
| 647 | """ |
---|
| 648 | Find the unit for a particular value within the h5py dictionary |
---|
| 649 | |
---|
| 650 | :param value: attribute dictionary for a particular value set |
---|
[d72567e] | 651 | :return: unit for the value passed to the method |
---|
[d398285] | 652 | """ |
---|
| 653 | unit = value.attrs.get(u'units') |
---|
[54544637] | 654 | if unit is None: |
---|
[d398285] | 655 | unit = value.attrs.get(u'unit') |
---|
[082239e] | 656 | # Convert the unit formats |
---|
[d398285] | 657 | if unit == "1/A": |
---|
| 658 | unit = "A^{-1}" |
---|
| 659 | elif unit == "1/cm": |
---|
| 660 | unit = "cm^{-1}" |
---|
[54ba66e] | 661 | return unit |
---|