Changeset fcba29a in sasview for src/sas/sascalc/dataloader/readers
- Timestamp:
- Aug 8, 2016 8:17:11 AM (8 years ago)
- Branches:
- master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- 98d32be
- Parents:
- 3931ea14 (diff), ab06de7 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent. - Location:
- src/sas/sascalc/dataloader/readers
- Files:
-
- 1 added
- 2 edited
-
cansas_reader.py (modified) (6 diffs)
-
cansas_reader_HDF5.py (modified) (20 diffs)
-
schema/cansas1d_invalid.xsd (added)
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sascalc/dataloader/readers/cansas_reader.py
r8976865 rfcba29a 34 34 from xml.dom.minidom import parseString 35 35 36 ## TODO: Refactor to load multiple <SASData> as separate Data1D objects 37 ## TODO: Refactor to allow invalid XML, but give a useful warning when loaded 38 36 39 _ZERO = 1e-16 37 40 PREPROCESS = "xmlpreprocess" … … 133 136 return False 134 137 135 def load_file_and_schema(self, xml_file ):138 def load_file_and_schema(self, xml_file, schema_path=""): 136 139 """ 137 140 Loads the file and associates a schema, if a known schema exists … … 149 152 # Generic values for the cansas file based on the version 150 153 cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0") 151 schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format\ 154 if schema_path == "": 155 schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format\ 152 156 (base, cansas_defaults.get("schema")).replace("\\", "/") 153 157 … … 156 160 return cansas_defaults 157 161 158 def read(self, xml_file): 162 ## TODO: Test loading invalid CanSAS XML files and see if this works 163 ## TODO: Once works, try adding a warning that the data is invalid 164 def read(self, xml_file, schema_path=""): 159 165 """ 160 166 Validate and read in an xml_file file in the canSAS format. … … 174 180 if extension in self.ext or self.allow_all: 175 181 # Get the file location of 176 cansas_defaults = self.load_file_and_schema(xml_file )182 cansas_defaults = self.load_file_and_schema(xml_file, schema_path) 177 183 178 184 # Try to load the file, but raise an error if unable to. … … 225 231 except: 226 232 # If the file does not match the schema, raise this error 227 raise RuntimeError, "%s cannot be read" % xml_file 233 schema_path = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid.xsd" 234 invalid_xml = self.find_invalid_xml() 235 invalid_xml = "\n\nThe loaded xml file does not fully meet the CanSAS v1.x specification. SasView " + \ 236 "loaded as much of the data as possible.\n\n" + invalid_xml 237 self.errors.add(invalid_xml) 238 self.set_schema(schema_path) 239 if self.is_cansas(): 240 output = self.read(xml_file, schema_path) 241 else: 242 raise RuntimeError, "%s cannot be read" % xml_file 228 243 return output 229 244 # Return a list of parsed entries that dataloader can manage -
src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py
rd398285 rd72567e 9 9 import sys 10 10 11 from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D, Data1D, Data2D, Sample, Source 12 from sas.sascalc.dataloader.data_info import Process, Aperture, Collimation, TransmissionSpectrum, Detector 11 from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D, Data1D, Data2D, DataInfo, Process, Aperture 12 from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, Detector 13 from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable 14 13 15 14 16 … … 18 20 with file extension .h5/.H5. Any number of data sets may be present within the file and any dimensionality of data 19 21 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. 22 SESANS data. 23 24 Any number of SASdata sets may be present in a SASentry and the data within can be either 1D I(Q) or 2D I(Qx, Qy). 21 25 22 26 :Dependencies: 23 The CanSAS HDF5 reader requires h5py v2.5.0 or later.27 The CanSAS HDF5 reader requires h5py => v2.5.0 or later. 24 28 """ 25 29 … … 32 36 ## Raw file contents to be processed 33 37 raw_data = None 34 ## Data set being modified 38 ## Data info currently being read in 39 current_datainfo = None 40 ## SASdata set currently being read in 35 41 current_dataset = None 36 ## For recursion and saving purposes, remember parent objects 37 parent_list = None 42 ## List of plottable1D objects that should be linked to the current_datainfo 43 data1d = None 44 ## List of plottable2D objects that should be linked to the current_datainfo 45 data2d = None 38 46 ## Data type name 39 47 type_name = "CanSAS 2.0" … … 47 55 output = None 48 56 49 def __init__(self):50 """51 Create the reader object and define initial states for class variables52 """53 self.current_dataset = None54 self.datasets = []55 self.raw_data = None56 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 57 def read(self, filename): 69 58 """ … … 71 60 72 61 :param filename: A path for an HDF5 formatted CanSAS 2D data file. 73 :return: List of Data1D/2D objects or a list of errors.62 :return: List of Data1D/2D objects and/or a list of errors. 74 63 """ 75 64 76 65 ## Reinitialize the class when loading a new data file to reset all class variables 77 self. __init__()66 self.reset_class_variables() 78 67 ## Check that the file exists 79 68 if os.path.isfile(filename): … … 85 74 self.raw_data = h5py.File(filename, 'r') 86 75 ## Read in all child elements of top level SASroot 87 self.read_children(self.raw_data )76 self.read_children(self.raw_data, []) 88 77 ## Add the last data set to the list of outputs 89 78 self.add_data_set() … … 91 80 return self.output 92 81 93 def read_children(self, data, parent=u'SASroot'): 82 def reset_class_variables(self): 83 """ 84 Create the reader object and define initial states for class variables 85 """ 86 self.current_datainfo = None 87 self.current_dataset = None 88 self.data1d = [] 89 self.data2d = [] 90 self.raw_data = None 91 self.errors = set() 92 self.logging = [] 93 self.output = [] 94 self.parent_class = u'' 95 self.detector = Detector() 96 self.collimation = Collimation() 97 self.aperture = Aperture() 98 self.process = Process() 99 self.trans_spectrum = TransmissionSpectrum() 100 101 def read_children(self, data, parent_list): 94 102 """ 95 103 A recursive method for stepping through the hierarchical data file. … … 97 105 :param data: h5py Group object of any kind 98 106 :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) 107 """ 104 108 105 109 ## Loop through each element of the parent and process accordingly … … 107 111 ## Get all information for the current key 108 112 value = data.get(key) 109 attr_keys = value.attrs.keys()110 attr_values = value.attrs.values()111 113 if value.attrs.get(u'canSAS_class') is not None: 112 114 class_name = value.attrs.get(u'canSAS_class') … … 119 121 120 122 if isinstance(value, h5py.Group): 121 ##TODO: Rework this for multiple SASdata objects within a single SASentry to allow for both 1D and 2D122 ##TODO: data within the same SASentry - One 1D and one 2D data object for all SASdata sets?123 ## If this is a new sasentry, store the current data set and create a fresh Data1D/2D object123 self.parent_class = class_name 124 parent_list.append(key) 125 ## If this is a new sasentry, store the current data sets and create a fresh Data1D/2D object 124 126 if class_prog.match(u'SASentry'): 125 127 self.add_data_set(key) 128 elif class_prog.match(u'SASdata'): 129 self._initialize_new_data_set(parent_list) 126 130 ## Recursion step to access data within the group 127 self.read_children(value, class_name) 128 self.add_intermediate(class_name) 131 self.read_children(value, parent_list) 132 self.add_intermediate() 133 parent_list.remove(key) 129 134 130 135 elif isinstance(value, h5py.Dataset): … … 136 141 unit = self._get_unit(value) 137 142 if key == u'definition': 138 self.current_data set.meta_data['reader'] = data_point143 self.current_datainfo.meta_data['reader'] = data_point 139 144 elif key == u'run': 140 self.current_data set.run.append(data_point)145 self.current_datainfo.run.append(data_point) 141 146 elif key == u'title': 142 self.current_data set.title = data_point147 self.current_datainfo.title = data_point 143 148 elif key == u'SASnote': 144 self.current_data set.notes.append(data_point)149 self.current_datainfo.notes.append(data_point) 145 150 146 151 ## I and Q Data 147 152 elif key == u'I': 148 if type(self.current_dataset) is Data2D:153 if type(self.current_dataset) is plottable_2D: 149 154 self.current_dataset.data = np.append(self.current_dataset.data, data_point) 150 155 self.current_dataset.zaxis("Intensity", unit) … … 153 158 self.current_dataset.yaxis("Intensity", unit) 154 159 elif key == u'Idev': 155 if type(self.current_dataset) is Data2D:160 if type(self.current_dataset) is plottable_2D: 156 161 self.current_dataset.err_data = np.append(self.current_dataset.err_data, data_point) 157 162 else: … … 159 164 elif key == u'Q': 160 165 self.current_dataset.xaxis("Q", unit) 161 if type(self.current_dataset) is Data2D:166 if type(self.current_dataset) is plottable_2D: 162 167 self.current_dataset.q = np.append(self.current_dataset.q, data_point) 163 168 else: … … 177 182 178 183 ## Sample Information 179 elif key == u'Title' and parent== u'SASsample':180 self. sample.name = data_point181 elif key == u'thickness' and parent== u'SASsample':182 self. sample.thickness = data_point183 elif key == u'temperature' and parent== u'SASsample':184 self. sample.temperature = data_point184 elif key == u'Title' and self.parent_class == u'SASsample': 185 self.current_datainfo.sample.name = data_point 186 elif key == u'thickness' and self.parent_class == u'SASsample': 187 self.current_datainfo.sample.thickness = data_point 188 elif key == u'temperature' and self.parent_class == u'SASsample': 189 self.current_datainfo.sample.temperature = data_point 185 190 186 191 ## Instrumental Information 187 elif key == u'name' and parent== u'SASinstrument':188 self.current_data set.instrument = data_point189 elif key == u'name' and parent== u'SASdetector':192 elif key == u'name' and self.parent_class == u'SASinstrument': 193 self.current_datainfo.instrument = data_point 194 elif key == u'name' and self.parent_class == u'SASdetector': 190 195 self.detector.name = data_point 191 elif key == u'SDD' and parent== u'SASdetector':192 self.detector.distance = data_point196 elif key == u'SDD' and self.parent_class == u'SASdetector': 197 self.detector.distance = float(data_point) 193 198 self.detector.distance_unit = unit 194 elif key == u'SSD' and parent== u'SAScollimation':199 elif key == u'SSD' and self.parent_class == u'SAScollimation': 195 200 self.collimation.length = data_point 196 201 self.collimation.length_unit = unit 197 elif key == u'name' and parent== u'SAScollimation':202 elif key == u'name' and self.parent_class == u'SAScollimation': 198 203 self.collimation.name = data_point 199 204 200 205 ## Process Information 201 elif key == u'name' and parent== u'SASprocess':206 elif key == u'name' and self.parent_class == u'SASprocess': 202 207 self.process.name = data_point 203 elif key == u'Title' and parent== u'SASprocess':208 elif key == u'Title' and self.parent_class == u'SASprocess': 204 209 self.process.name = data_point 205 elif key == u'description' and parent== u'SASprocess':210 elif key == u'description' and self.parent_class == u'SASprocess': 206 211 self.process.description = data_point 207 elif key == u'date' and parent== u'SASprocess':212 elif key == u'date' and self.parent_class == u'SASprocess': 208 213 self.process.date = data_point 209 elif parent== u'SASprocess':214 elif self.parent_class == u'SASprocess': 210 215 self.process.notes.append(data_point) 211 216 212 217 ## Transmission Spectrum 213 elif key == u'T' and parent== u'SAStransmission_spectrum':218 elif key == u'T' and self.parent_class == u'SAStransmission_spectrum': 214 219 self.trans_spectrum.transmission.append(data_point) 215 elif key == u'Tdev' and parent== u'SAStransmission_spectrum':220 elif key == u'Tdev' and self.parent_class == u'SAStransmission_spectrum': 216 221 self.trans_spectrum.transmission_deviation.append(data_point) 217 elif key == u'lambda' and parent== u'SAStransmission_spectrum':222 elif key == u'lambda' and self.parent_class == u'SAStransmission_spectrum': 218 223 self.trans_spectrum.wavelength.append(data_point) 219 224 220 225 ## Other Information 221 elif key == u'wavelength' and parent== u'SASdata':222 self. source.wavelength = data_point223 self. source.wavelength.unit = unit224 elif key == u'radiation' and parent== u'SASsource':225 self. source.radiation = data_point226 elif key == u'transmission' and parent== u'SASdata':227 self. sample.transmission = data_point226 elif key == u'wavelength' and self.parent_class == u'SASdata': 227 self.current_datainfo.source.wavelength = data_point 228 self.current_datainfo.source.wavelength.unit = unit 229 elif key == u'radiation' and self.parent_class == u'SASsource': 230 self.current_datainfo.source.radiation = data_point 231 elif key == u'transmission' and self.parent_class == u'SASdata': 232 self.current_datainfo.sample.transmission = data_point 228 233 229 234 ## Everything else goes in meta_data 230 235 else: 231 new_key = self._create_unique_key(self.current_data set.meta_data, key)232 self.current_data set.meta_data[new_key] = data_point236 new_key = self._create_unique_key(self.current_datainfo.meta_data, key) 237 self.current_datainfo.meta_data[new_key] = data_point 233 238 234 239 else: … … 236 241 self.errors.add("ShouldNeverHappenException") 237 242 238 def add_intermediate(self , parent):243 def add_intermediate(self): 239 244 """ 240 245 This method stores any intermediate objects within the final data set after fully reading the set. 241 246 242 247 :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 """ 249 250 if self.parent_class == u'SASprocess': 251 self.current_datainfo.process.append(self.process) 248 252 self.process = Process() 249 elif parent== u'SASdetector':250 self.current_data set.detector.append(self.detector)253 elif self.parent_class == u'SASdetector': 254 self.current_datainfo.detector.append(self.detector) 251 255 self.detector = Detector() 252 elif parent== u'SAStransmission_spectrum':253 self.current_data set.trans_spectrum.append(self.trans_spectrum)256 elif self.parent_class == u'SAStransmission_spectrum': 257 self.current_datainfo.trans_spectrum.append(self.trans_spectrum) 254 258 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) 259 elif self.parent_class == u'SAScollimation': 260 self.current_datainfo.collimation.append(self.collimation) 263 261 self.collimation = Collimation() 264 elif parent== u'SASaperture':262 elif self.parent_class == u'SASaperture': 265 263 self.collimation.aperture.append(self.aperture) 266 264 self.aperture = Aperture() 265 elif self.parent_class == u'SASdata': 266 if type(self.current_dataset) is plottable_2D: 267 self.data2d.append(self.current_dataset) 268 elif type(self.current_dataset) is plottable_1D: 269 self.data1d.append(self.current_dataset) 267 270 268 271 def final_data_cleanup(self): 269 272 """ 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) 338 339 if len(self.current_dataset.trans_spectrum) is not 0: 273 Does some final cleanup and formatting on self.current_datainfo and all data1D and data2D objects and then 274 combines the data and info into Data1D and Data2D objects 275 """ 276 277 ## Type cast data arrays to float64 278 if len(self.current_datainfo.trans_spectrum) > 0: 340 279 spectrum_list = [] 341 for spectrum in self.current_data set.trans_spectrum:280 for spectrum in self.current_datainfo.trans_spectrum: 342 281 spectrum.transmission = np.delete(spectrum.transmission, [0]) 343 282 spectrum.transmission = spectrum.transmission.astype(np.float64) … … 346 285 spectrum.wavelength = np.delete(spectrum.wavelength, [0]) 347 286 spectrum.wavelength = spectrum.wavelength.astype(np.float64) 348 spectrum_list.append(spectrum) 349 self.current_dataset.trans_spectrum = spectrum_list 350 351 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) 287 if len(spectrum.transmission) > 0: 288 spectrum_list.append(spectrum) 289 self.current_datainfo.trans_spectrum = spectrum_list 358 290 359 291 ## Append errors to dataset and reset class errors 360 self.current_data set.errors = self.errors292 self.current_datainfo.errors = self.errors 361 293 self.errors.clear() 294 295 ## Combine all plottables with datainfo and append each to output 296 ## Type cast data arrays to float64 and find min/max as appropriate 297 for dataset in self.data2d: 298 dataset.data = np.delete(dataset.data, [0]) 299 dataset.data = dataset.data.astype(np.float64) 300 dataset.err_data = np.delete(dataset.err_data, [0]) 301 dataset.err_data = dataset.err_data.astype(np.float64) 302 dataset.mask = np.delete(dataset.mask, [0]) 303 if dataset.qx_data is not None: 304 dataset.qx_data = np.delete(dataset.qx_data, [0]) 305 dataset.xmin = np.min(dataset.qx_data) 306 dataset.xmax = np.max(dataset.qx_data) 307 dataset.qx_data = dataset.qx_data.astype(np.float64) 308 if dataset.dqx_data is not None: 309 dataset.dqx_data = np.delete(dataset.dqx_data, [0]) 310 dataset.dqx_data = dataset.dqx_data.astype(np.float64) 311 if dataset.qy_data is not None: 312 dataset.qy_data = np.delete(dataset.qy_data, [0]) 313 dataset.ymin = np.min(dataset.qy_data) 314 dataset.ymax = np.max(dataset.qy_data) 315 dataset.qy_data = dataset.qy_data.astype(np.float64) 316 if dataset.dqy_data is not None: 317 dataset.dqy_data = np.delete(dataset.dqy_data, [0]) 318 dataset.dqy_data = dataset.dqy_data.astype(np.float64) 319 if dataset.q_data is not None: 320 dataset.q_data = np.delete(dataset.q_data, [0]) 321 dataset.q_data = dataset.q_data.astype(np.float64) 322 zeros = np.ones(dataset.data.size, dtype=bool) 323 try: 324 for i in range (0, dataset.mask.size - 1): 325 zeros[i] = dataset.mask[i] 326 except: 327 self.errors.add(sys.exc_value) 328 dataset.mask = zeros 329 ## Calculate the actual Q matrix 330 try: 331 if dataset.q_data.size <= 1: 332 dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data + dataset.qy_data * dataset.qy_data) 333 except: 334 dataset.q_data = None 335 final_dataset = combine_data_info_with_plottable(dataset, self.current_datainfo) 336 self.output.append(final_dataset) 337 338 for dataset in self.data1d: 339 if dataset.x is not None: 340 dataset.x = np.delete(dataset.x, [0]) 341 dataset.x = dataset.x.astype(np.float64) 342 dataset.xmin = np.min(dataset.x) 343 dataset.xmax = np.max(dataset.x) 344 if dataset.y is not None: 345 dataset.y = np.delete(dataset.y, [0]) 346 dataset.y = dataset.y.astype(np.float64) 347 dataset.ymin = np.min(dataset.y) 348 dataset.ymax = np.max(dataset.y) 349 if dataset.dx is not None: 350 dataset.dx = np.delete(dataset.dx, [0]) 351 dataset.dx = dataset.dx.astype(np.float64) 352 if dataset.dxl is not None: 353 dataset.dxl = np.delete(dataset.dxl, [0]) 354 dataset.dxl = dataset.dxl.astype(np.float64) 355 if dataset.dxw is not None: 356 dataset.dxw = np.delete(dataset.dxw, [0]) 357 dataset.dxw = dataset.dxw.astype(np.float64) 358 if dataset.dy is not None: 359 dataset.dy = np.delete(dataset.dy, [0]) 360 dataset.dy = dataset.dy.astype(np.float64) 361 final_dataset = combine_data_info_with_plottable(dataset, self.current_datainfo) 362 self.output.append(final_dataset) 362 363 363 364 def add_data_set(self, key=""): … … 367 368 368 369 :param key: NeXus group name for current tree level 369 :return: None370 """ 371 if self.current_data set is not None:370 """ 371 372 if self.current_datainfo and self.current_dataset: 372 373 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=""): 374 self.data1d = [] 375 self.data2d = [] 376 self.current_datainfo = DataInfo() 377 378 def _initialize_new_data_set(self, parent_list = None): 377 379 """ 378 380 A private class method to generate a new 1D or 2D data object based on the type of data within the set. 379 381 Outside methods should call add_data_set() to be sure any existing data is stored properly. 380 382 381 :param key: NeXus group name for current tree level382 :return: None383 """ 384 entry = self._find_intermediate(key, "sasentry*")385 data = entry.get("sasdata")386 if data.get("Qx") is not None:387 self.current_dataset = Data2D()383 :param parent_list: List of names of parent elements 384 """ 385 386 if parent_list is None: 387 parent_list = [] 388 if self._find_intermediate(parent_list, "Qx"): 389 self.current_dataset = plottable_2D() 388 390 else: 389 391 x = np.array(0) 390 392 y = np.array(0) 391 self.current_dataset = Data1D(x, y)392 self.current_data set.filename = self.raw_data.filename393 394 def _find_intermediate(self, key="", basename=""):393 self.current_dataset = plottable_1D(x, y) 394 self.current_datainfo.filename = self.raw_data.filename 395 396 def _find_intermediate(self, parent_list, basename=""): 395 397 """ 396 398 A private class used to find an entry by either using a direct key or knowing the approximate basename. 397 399 398 :param key: Exact keyname of an entry399 :param basename: Approximate name of an entry 400 :param parent_list: List of parents to the current level in the HDF5 file 401 :param basename: Approximate name of an entry to search for 400 402 :return: 401 403 """ 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 404 405 entry = False 406 key_prog = re.compile(basename) 407 top = self.raw_data 408 for parent in parent_list: 409 top = top.get(parent) 410 for key in top.keys(): 411 if (key_prog.match(key)): 412 entry = True 413 break 411 414 return entry 412 415 … … 419 422 :param name: The index of the item to be added to dictionary 420 423 :param numb: The number to be appended to the name, starts at 0 424 :return: The new name for the dictionary entry 421 425 """ 422 426 if dictionary.get(name) is not None: … … 432 436 433 437 :param value: attribute dictionary for a particular value set 434 :return: 438 :return: unit for the value passed to the method 435 439 """ 436 440 unit = value.attrs.get(u'units') 437 441 if unit == None: 438 442 unit = value.attrs.get(u'unit') 439 440 443 ## Convert the unit formats 441 444 if unit == "1/A": … … 443 446 elif unit == "1/cm": 444 447 unit = "cm^{-1}" 445 446 448 return unit
Note: See TracChangeset
for help on using the changeset viewer.
