Changes in src/sas/sascalc/dataloader/file_reader_base_class.py [9b08354:fee520ec] in sasview
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src/sas/sascalc/dataloader/file_reader_base_class.py
r9b08354 rfee520ec 16 16 from .data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D,\ 17 17 combine_data_info_with_plottable 18 from sas.sascalc.data_util.nxsunit import Converter19 18 20 19 logger = logging.getLogger(__name__) … … 38 37 "SasView cannot guarantee the accuracy of the data.") 39 38 40 41 39 class FileReader(object): 42 40 # String to describe the type of data this reader can load … … 47 45 ext = ['.txt'] 48 46 # Deprecated extensions 49 deprecated_extensions = ['.asc' ]47 deprecated_extensions = ['.asc', '.nxs'] 50 48 # Bypass extension check and try to load anyway 51 49 allow_all = False … … 100 98 if len(self.output) > 0: 101 99 # Sort the data that's been loaded 102 self. convert_data_units()103 self.sort_ data()100 self.sort_one_d_data() 101 self.sort_two_d_data() 104 102 else: 105 103 msg = "Unable to find file at: {}\n".format(filepath) … … 142 140 Returns the entire file as a string. 143 141 """ 142 #return self.f_open.read() 144 143 return decode(self.f_open.read()) 145 144 … … 167 166 self.output.append(data_obj) 168 167 169 def sort_ data(self):168 def sort_one_d_data(self): 170 169 """ 171 170 Sort 1D data along the X axis for consistency … … 175 174 # Normalize the units for 176 175 data.x_unit = self.format_unit(data.x_unit) 177 data._xunit = data.x_unit178 176 data.y_unit = self.format_unit(data.y_unit) 179 data._yunit = data.y_unit180 177 # Sort data by increasing x and remove 1st point 181 178 ind = np.lexsort((data.y, data.x)) … … 206 203 data.ymin = np.min(data.y) 207 204 data.ymax = np.max(data.y) 208 elif isinstance(data, Data2D):209 # Normalize the units for210 data.Q_unit = self.format_unit(data.Q_unit)211 data.I_unit = self.format_unit(data.I_unit)212 data._xunit = data.Q_unit213 data._yunit = data.Q_unit214 data._zunit = data.I_unit215 data.data = data.data.astype(np.float64)216 data.qx_data = data.qx_data.astype(np.float64)217 data.xmin = np.min(data.qx_data)218 data.xmax = np.max(data.qx_data)219 data.qy_data = data.qy_data.astype(np.float64)220 data.ymin = np.min(data.qy_data)221 data.ymax = np.max(data.qy_data)222 data.q_data = np.sqrt(data.qx_data * data.qx_data223 + data.qy_data * data.qy_data)224 if data.err_data is not None:225 data.err_data = data.err_data.astype(np.float64)226 if data.dqx_data is not None:227 data.dqx_data = data.dqx_data.astype(np.float64)228 if data.dqy_data is not None:229 data.dqy_data = data.dqy_data.astype(np.float64)230 if data.mask is not None:231 data.mask = data.mask.astype(dtype=bool)232 233 if len(data.data.shape) == 2:234 n_rows, n_cols = data.data.shape235 data.y_bins = data.qy_data[0::int(n_cols)]236 data.x_bins = data.qx_data[:int(n_cols)]237 data.data = data.data.flatten()238 data = self._remove_nans_in_data(data)239 if len(data.data) > 0:240 data.xmin = np.min(data.qx_data)241 data.xmax = np.max(data.qx_data)242 data.ymin = np.min(data.qy_data)243 data.ymax = np.max(data.qx_data)244 205 245 206 @staticmethod … … 281 242 return data 282 243 283 @staticmethod 284 def set_default_1d_units(data): 285 """ 286 Set the x and y axes to the default 1D units 287 :param data: 1D data set 288 :return: 289 """ 290 data.xaxis(r"\rm{Q}", '1/A') 291 data.yaxis(r"\rm{Intensity}", "1/cm") 292 return data 293 294 @staticmethod 295 def set_default_2d_units(data): 296 """ 297 Set the x and y axes to the default 2D units 298 :param data: 2D data set 299 :return: 300 """ 301 data.xaxis("\\rm{Q_{x}}", '1/A') 302 data.yaxis("\\rm{Q_{y}}", '1/A') 303 data.zaxis("\\rm{Intensity}", "1/cm") 304 return data 305 306 def convert_data_units(self, default_q_unit="1/A"): 307 """ 308 Converts al; data to the sasview default of units of A^{-1} for Q and 309 cm^{-1} for I. 310 :param default_q_unit: The default Q unit used by Sasview 311 """ 312 convert_q = True 313 new_output = [] 314 for data in self.output: 315 if data.isSesans: 316 new_output.append(data) 317 continue 318 try: 319 file_x_unit = data._xunit 320 data_conv_x = Converter(file_x_unit) 321 except KeyError: 322 logger.info("Unrecognized Q units in data file. No data " 323 "conversion attempted") 324 convert_q = False 325 try: 326 327 if isinstance(data, Data1D): 328 if convert_q: 329 data.x = data_conv_x(data.x, units=default_q_unit) 330 data._xunit = default_q_unit 331 data.x_unit = default_q_unit 332 if data.dx is not None: 333 data.dx = data_conv_x(data.dx, 334 units=default_q_unit) 335 if data.dxl is not None: 336 data.dxl = data_conv_x(data.dxl, 337 units=default_q_unit) 338 if data.dxw is not None: 339 data.dxw = data_conv_x(data.dxw, 340 units=default_q_unit) 341 elif isinstance(data, Data2D): 342 if convert_q: 343 data.qx_data = data_conv_x(data.qx_data, 344 units=default_q_unit) 345 if data.dqx_data is not None: 346 data.dqx_data = data_conv_x(data.dqx_data, 347 units=default_q_unit) 348 try: 349 file_y_unit = data._yunit 350 data_conv_y = Converter(file_y_unit) 351 data.qy_data = data_conv_y(data.qy_data, 352 units=default_q_unit) 353 if data.dqy_data is not None: 354 data.dqy_data = data_conv_y(data.dqy_data, 355 units=default_q_unit) 356 except KeyError: 357 logger.info("Unrecognized Qy units in data file. No" 358 " data conversion attempted") 359 except KeyError: 360 message = "Unable to convert Q units from {0} to 1/A." 361 message.format(default_q_unit) 362 data.errors.append(message) 363 new_output.append(data) 364 self.output = new_output 244 def sort_two_d_data(self): 245 for dataset in self.output: 246 if isinstance(dataset, Data2D): 247 # Normalize the units for 248 dataset.x_unit = self.format_unit(dataset.Q_unit) 249 dataset.y_unit = self.format_unit(dataset.I_unit) 250 dataset.data = dataset.data.astype(np.float64) 251 dataset.qx_data = dataset.qx_data.astype(np.float64) 252 dataset.xmin = np.min(dataset.qx_data) 253 dataset.xmax = np.max(dataset.qx_data) 254 dataset.qy_data = dataset.qy_data.astype(np.float64) 255 dataset.ymin = np.min(dataset.qy_data) 256 dataset.ymax = np.max(dataset.qy_data) 257 dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data 258 + dataset.qy_data * dataset.qy_data) 259 if dataset.err_data is not None: 260 dataset.err_data = dataset.err_data.astype(np.float64) 261 if dataset.dqx_data is not None: 262 dataset.dqx_data = dataset.dqx_data.astype(np.float64) 263 if dataset.dqy_data is not None: 264 dataset.dqy_data = dataset.dqy_data.astype(np.float64) 265 if dataset.mask is not None: 266 dataset.mask = dataset.mask.astype(dtype=bool) 267 268 if len(dataset.data.shape) == 2: 269 n_rows, n_cols = dataset.data.shape 270 dataset.y_bins = dataset.qy_data[0::int(n_cols)] 271 dataset.x_bins = dataset.qx_data[:int(n_cols)] 272 dataset.data = dataset.data.flatten() 273 dataset = self._remove_nans_in_data(dataset) 274 if len(dataset.data) > 0: 275 dataset.xmin = np.min(dataset.qx_data) 276 dataset.xmax = np.max(dataset.qx_data) 277 dataset.ymin = np.min(dataset.qy_data) 278 dataset.ymax = np.max(dataset.qy_data) 365 279 366 280 def format_unit(self, unit=None): … … 453 367 self.current_dataset.qy_data)) 454 368 if has_error_dy: 455 self.current_dataset.err_data = self.current_dataset.err_data[ 456 x != 0] 369 self.current_dataset.err_data = self.current_dataset.err_data[x != 0] 457 370 if has_error_dqx: 458 self.current_dataset.dqx_data = self.current_dataset.dqx_data[ 459 x != 0] 371 self.current_dataset.dqx_data = self.current_dataset.dqx_data[x != 0] 460 372 if has_error_dqy: 461 self.current_dataset.dqy_data = self.current_dataset.dqy_data[ 462 x != 0] 373 self.current_dataset.dqy_data = self.current_dataset.dqy_data[x != 0] 463 374 if has_mask: 464 375 self.current_dataset.mask = self.current_dataset.mask[x != 0]
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