Changeset 76cd1ae in sasview
- Timestamp:
- Jan 14, 2014 3:53:36 PM (11 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, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- 16bd5ca
- Parents:
- 083e993
- Files:
-
- 1 added
- 6 edited
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src/sans/dataloader/data_info.py (modified) (4 diffs)
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src/sans/dataloader/readers/cansas_constants.py (modified) (3 diffs)
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src/sans/dataloader/readers/cansas_reader.py (modified) (24 diffs)
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src/sans/dataloader/readers/xml_reader.py (modified) (3 diffs)
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src/sans/guiframe/gui_manager.py (modified) (2 diffs)
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test/sansdataloader/test/ISIS_1_1_doubletrans.xml (added)
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test/sansdataloader/test/utest_cansas.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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src/sans/dataloader/data_info.py
rbe577e7 r76cd1ae 425 425 def __str__(self): 426 426 _str = "Transmission Spectrum:\n" 427 _str += " Name: {0}".format(self.name) 428 _str += " Timestamp: {1}".format(self.timestamp) 429 _str += " Wavelength [{0}] | Transmission [{1}] | Trans Dev [{2}]\n".format(self.wavelength_unit, self.transmission_unit, self.transmission_deviation_unit) 430 for i in range(len(self.wavelength)): 431 _str += " {0}, {1}".format(self.wavelength[i], self.transmission[i]) 432 if len(self.transmission_deviation > i): 433 _str += ", {0}".format(self.transmission_deviation[i]) 434 _str += "\n" 427 _str += " Name: \t{0}\n".format(self.name) 428 _str += " Timestamp: \t{0}\n".format(self.timestamp) 429 _str += " Wavelength unit: \t{0}\n".format(self.wavelength_unit) 430 _str += " Transmission unit:\t{0}\n".format(self.transmission_unit) 431 _str += " Trans. Dev. unit: \t{0}\n".format(\ 432 self.transmission_deviation_unit) 433 length_list = [len(self.wavelength), len(self.transmission), \ 434 len(self.transmission_deviation)] 435 _str += " Number of Pts: \t{0}\n".format(max(length_list)) 435 436 return _str 436 437 … … 498 499 self.collimation = [] 499 500 ## Transmission Spectrum 500 self.trans_spectrum = TransmissionSpectrum()501 self.trans_spectrum = [] 501 502 ## Additional meta-data 502 503 self.meta_data = {} … … 533 534 for item in self.notes: 534 535 _str += "%s\n" % str(item) 535 536 for item in self.trans_spectrum: 537 _str += "%s\n" % str(item) 536 538 return _str 537 539 … … 757 759 clone = Data1D(x, y, dx=dx, dy=dy) 758 760 759 clone.title = self.title 760 clone.run = self.run 761 clone.filename = self.filename 762 clone.instrument = self.instrument 763 clone.notes = deepcopy(self.notes) 764 clone.process = deepcopy(self.process) 765 clone.detector = deepcopy(self.detector) 766 clone.sample = deepcopy(self.sample) 767 clone.source = deepcopy(self.source) 768 clone.collimation = deepcopy(self.collimation) 769 clone.meta_data = deepcopy(self.meta_data) 770 clone.errors = deepcopy(self.errors) 761 clone.title = self.title 762 clone.run = self.run 763 clone.filename = self.filename 764 clone.instrument = self.instrument 765 clone.notes = deepcopy(self.notes) 766 clone.process = deepcopy(self.process) 767 clone.detector = deepcopy(self.detector) 768 clone.sample = deepcopy(self.sample) 769 clone.source = deepcopy(self.source) 770 clone.collimation = deepcopy(self.collimation) 771 clone.trans_spectrum = deepcopy(self.trans_spectrum) 772 clone.meta_data = deepcopy(self.meta_data) 773 clone.errors = deepcopy(self.errors) 771 774 772 775 return clone -
src/sans/dataloader/readers/cansas_constants.py
r75eeb425 r76cd1ae 1 ## Left off at SASInstrument, line 178 2 1 """ 2 Information relating to the CanSAS data format. These constants are used in 3 the cansas_reader.py file to read in any version of the cansas format. 4 """ 3 5 class cansasConstants: 6 7 ns = '' 8 format = '' 9 10 def __init__(self): 11 self.ns = self.CANSAS_NS 12 self.format = self.CANSAS_FORMAT 13 """ 14 CANSAS_NS holds the base namespace and the default schema file information 15 """ 4 16 CANSAS_NS = { 5 17 "1.0" : { … … 12 24 } 13 25 } 26 27 """ 28 The constants below hold information on where to store the CanSAS data when 29 loaded in using sasview 30 """ 31 META_DATA = "{0}.meta_data[\"{2}\"] = \"{1}\"" 32 ANY = { 33 "variable" : "{0}.meta_data[\"{2}\"] = \'{1}\'", 34 "storeas" : "content", 35 } 36 TITLE = {"variable" : "{0}.title = \"{1}\""} 37 SASNOTE = {"variable" : "{0}.notes.append(\'{1}\')"} 38 SASPROCESS_TERM = { 39 "variable" : None, 40 "attributes" : { 41 "unit" : {"variable" : None}, 42 "name" : {"variable" : None} 43 } 44 } 45 SASPROCESS_SASPROCESSNOTE = { 46 "variable" : None, 47 "children" : {"<any>" : ANY} 48 } 49 SASPROCESS = { 50 "variable" : None, 51 "children" : { 52 "name" : {"variable" : "{0}.name = \'{1}\'"}, 53 "date" : {"variable" : "{0}.date = \'{1}\'"}, 54 "description" : {"variable" : \ 55 "{0}.description = \'{1}\'"}, 56 "term" : SASPROCESS_TERM, 57 "SASprocessnote" : SASPROCESS_SASPROCESSNOTE, 58 "<any>" : ANY 59 }, 60 } 61 RUN = { 62 "variable" : "{0}.run.append(\"{1}\")", 63 "attributes" : {"name" : {"variable" : \ 64 "{0}.run_name[node_value] = \"{1}\""}} 65 } 66 SASDATA_IDATA_Q = { 67 "variable" : "{0}.x = numpy.append({0}.x, {1})", 68 "unit" : "x_unit", 69 "attributes" : { 70 "unit" : { 71 "variable" : \ 72 "{0}._xunit = \"{1}\"", 73 "storeas" : "content" 74 } 75 } 76 } 77 SASDATA_IDATA_I = { 78 "variable" : "{0}.y = numpy.append({0}.y, {1})", 79 "unit" : "y_unit", 80 "attributes" : { 81 "unit" : { 82 "variable" : \ 83 "{0}._yunit = \"{1}\"", 84 "storeas" : "content" 85 } 86 } 87 } 88 SASDATA_IDATA_IDEV = { 89 "variable" : \ 90 "{0}.dy = numpy.append({0}.dy, {1})", 91 "unit" : "y_unit", 92 "attributes" : { 93 "unit" : { 94 "variable" : META_DATA, 95 "storeas" : "content" 96 } 97 }, 98 } 99 SASDATA_IDATA_QDEV = { 100 "variable" : \ 101 "{0}.dx = numpy.append({0}.dx, {1})", 102 "unit" : "x_unit", 103 "attributes" : { 104 "unit" : { 105 "variable" : META_DATA, 106 "storeas" : "content" 107 } 108 }, 109 } 110 SASDATA_IDATA_DQL = { 111 "variable" : \ 112 "{0}.dxl = numpy.append({0}.dxl, {1})", 113 "unit" : "x_unit", 114 "attributes" : { 115 "unit" : { 116 "variable" : META_DATA, 117 "storeas" : "content" 118 } 119 }, 120 } 121 SASDATA_IDATA_DQW = { 122 "variable" : \ 123 "{0}.dxw = numpy.append({0}.dxw, {1})", 124 "unit" : "x_unit", 125 "attributes" : { 126 "unit" : { 127 "variable" : META_DATA, 128 "storeas" : "content" 129 } 130 }, 131 } 132 SASDATA_IDATA_QMEAN = { 133 "storeas" : "content", 134 "unit" : "x_unit", 135 "variable" : META_DATA, 136 "attributes" : {"unit" : {"variable" : META_DATA}}, 137 } 138 SASDATA_IDATA_SHADOWFACTOR = { 139 "variable" : META_DATA, 140 "storeas" : "content", 141 } 142 SASDATA_IDATA = { 143 "storeas" : "float", 144 "units_optional" : False, 145 "variable" : None, 146 "attributes" : { 147 "name" : { 148 "variable" : META_DATA, 149 "storeas" : "content", 150 }, 151 "timestamp" : { 152 "variable" : META_DATA, 153 "storeas" : "content", 154 } 155 }, 156 "children" : { 157 "Q" : SASDATA_IDATA_Q, 158 "I" : SASDATA_IDATA_I, 159 "Idev" : SASDATA_IDATA_IDEV, 160 "Qdev" : SASDATA_IDATA_QDEV, 161 "dQw" : SASDATA_IDATA_DQW, 162 "dQl" : SASDATA_IDATA_DQL, 163 "Qmean" : SASDATA_IDATA_QMEAN, 164 "Shadowfactor" : SASDATA_IDATA_SHADOWFACTOR, 165 "<any>" : ANY 166 } 167 } 168 SASDATA = { 169 "attributes" : {"name" : {"variable" : META_DATA,}}, 170 "variable" : None, 171 "children" : { 172 "Idata" : SASDATA_IDATA, 173 "<any>" : ANY 174 } 175 } 176 SASTRANSSPEC_TDATA_LAMDBA = { 177 "variable" : "{0}.wavelength.append({1})", 178 "unit" : "wavelength_unit", 179 "attributes" : { 180 "unit" : { 181 "variable" : "{0}.wavelength_unit = \"{1}\"", 182 "storeas" : "content" 183 } 184 } 185 } 186 SASTRANSSPEC_TDATA_T = { 187 "variable" : "{0}.transmission.append({1})", 188 "unit" : "transmission_unit", 189 "attributes" : { 190 "unit" : { 191 "variable" : "{0}.transmission_unit = \"{1}\"", 192 "storeas" : "content" 193 } 194 } 195 } 196 SASTRANSSPEC_TDATA_TDEV = { 197 "variable" : \ 198 "{0}.transmission_deviation.append({1})", 199 "unit" : "transmission_deviation_unit", 200 "attributes" : { 201 "unit" : { 202 "variable" : "{0}.transmission_deviation_unit = \"{1}\"", 203 "storeas" : "content" 204 } 205 } 206 } 207 SASTRANSSPEC_TDATA = { 208 "storeas" : "float", 209 "variable" : None, 210 "children" : { 211 "Lambda" : SASTRANSSPEC_TDATA_LAMDBA, 212 "T" : SASTRANSSPEC_TDATA_T, 213 "Tdev" : SASTRANSSPEC_TDATA_TDEV, 214 "<any>" : ANY, 215 } 216 } 217 SASTRANSSPEC = { 218 "variable" : None, 219 "children" : { 220 "Tdata" : SASTRANSSPEC_TDATA, 221 "<any>" : ANY, 222 }, 223 "attributes" : {"name" : {"variable" : \ 224 "{0}.name = \"{1}\""}, 225 "timestamp" : {"variable" : \ 226 "{0}.timestamp = \"{1}\""}, 227 } 228 } 229 SASSAMPLE_THICK = { 230 "variable" : "{0}.sample.thickness = {1}", 231 "unit" : "sample.thickness_unit", 232 "storeas" : "float", 233 "attributes" : { 234 "units" : { 235 "variable" : "{0}.sample.thickness_unit = \"{1}\"", 236 "storeas" : "content" 237 } 238 }, 239 } 240 SASSAMPLE_TRANS = { 241 "variable" : "{0}.sample.transmission = {1}", 242 "storeas" : "float", 243 } 244 SASSAMPLE_TEMP = { 245 "variable" : "{0}.sample.temperature = {1}", 246 "unit" : "sample.temperature_unit", 247 "storeas" : "float", 248 "attributes" : { 249 "units" : { 250 "variable" : "{0}.sample.temperature_unit = \"{1}\"", 251 "storeas" : "content" 252 } 253 }, 254 } 255 SASSAMPLE_POS_ATTR = { 256 "units" : { 257 "variable" : \ 258 "{0}.sample.position_unit = \"{1}\"", 259 "storeas" : "content" 260 } 261 } 262 SASSAMPLE_POS_X = { 263 "variable" : "{0}.sample.position.x = {1}", 264 "unit" : "sample.position_unit", 265 "storeas" : "float", 266 "attributes" : SASSAMPLE_POS_ATTR 267 } 268 SASSAMPLE_POS_Y = { 269 "variable" : "{0}.sample.position.y = {1}", 270 "unit" : "sample.position_unit", 271 "storeas" : "float", 272 "attributes" : SASSAMPLE_POS_ATTR 273 } 274 SASSAMPLE_POS_Z = { 275 "variable" : "{0}.sample.position.z = {1}", 276 "unit" : "sample.position_unit", 277 "storeas" : "float", 278 "attributes" : SASSAMPLE_POS_ATTR 279 } 280 SASSAMPLE_POS = { 281 "children" : { 282 "variable" : None, 283 "x" : SASSAMPLE_POS_X, 284 "y" : SASSAMPLE_POS_Y, 285 "z" : SASSAMPLE_POS_Z, 286 }, 287 } 288 SASSAMPLE_ORIENT_ATTR = { 289 "units" : { 290 "variable" : "{0}.sample.orientation_unit = \"{1}\"", 291 "storeas" : "content" 292 } 293 } 294 SASSAMPLE_ORIENT_ROLL = { 295 "variable" : "{0}.sample.orientation.x = {1}", 296 "unit" : "sample.orientation_unit", 297 "storeas" : "float", 298 "attributes" : SASSAMPLE_ORIENT_ATTR 299 } 300 SASSAMPLE_ORIENT_PITCH = { 301 "variable" : "{0}.sample.orientation.y = {1}", 302 "unit" : "sample.orientation_unit", 303 "storeas" : "float", 304 "attributes" : SASSAMPLE_ORIENT_ATTR 305 } 306 SASSAMPLE_ORIENT_YAW = { 307 "variable" : "{0}.sample.orientation.z = {1}", 308 "unit" : "sample.orientation_unit", 309 "storeas" : "float", 310 "attributes" : SASSAMPLE_ORIENT_ATTR 311 } 312 SASSAMPLE_ORIENT = { 313 "variable" : None, 314 "children" : { 315 "roll" : SASSAMPLE_ORIENT_ROLL, 316 "pitch" : SASSAMPLE_ORIENT_PITCH, 317 "yaw" : SASSAMPLE_ORIENT_YAW, 318 }, 319 } 320 SASSAMPLE = { 321 "attributes" : {"name" : {\ 322 "variable" : "{0}.sample.name = \"{1}\""},}, 323 "variable" : None, 324 "children" : { 325 "ID" : {"variable" : "{0}.sample.ID = \"{1}\""}, 326 "thickness" : SASSAMPLE_THICK, 327 "transmission" : SASSAMPLE_TRANS, 328 "temperature" : SASSAMPLE_TEMP, 329 "position" : SASSAMPLE_POS, 330 "orientation" : SASSAMPLE_ORIENT, 331 "details" : {"variable" : \ 332 "{0}.sample.details.append(\"{1}\")"}, 333 "<any>" : ANY 334 }, 335 } 336 SASINSTR_SRC_BEAMSIZE_ATTR = { 337 "unit" : \ 338 "{0}.source.beam_size_unit = \"{1}\"", 339 "storeas" : "content" 340 } 341 SASINSTR_SRC_BEAMSIZE_X = { 342 "variable" : "{0}.source.beam_size.x = {1}", 343 "unit" : "source.beam_size_unit", 344 "storeas" : "float", 345 "attributes" : SASINSTR_SRC_BEAMSIZE_ATTR 346 } 347 SASINSTR_SRC_BEAMSIZE_Y = { 348 "variable" : "{0}.source.beam_size.y = {1}", 349 "unit" : "source.beam_size_unit", 350 "storeas" : "float", 351 "attributes" : SASINSTR_SRC_BEAMSIZE_ATTR 352 } 353 SASINSTR_SRC_BEAMSIZE_Z = { 354 "variable" : "{0}.source.beam_size.z = {1}", 355 "unit" : "source.beam_size_unit", 356 "storeas" : "float", 357 "attributes" : SASINSTR_SRC_BEAMSIZE_ATTR 358 } 359 SASINSTR_SRC_BEAMSIZE = { 360 "attributes" : {"name" : {"variable" : \ 361 "{0}.source.beam_size_name = \"{1}\""}}, 362 "variable" : None, 363 "children" : { 364 "x" : SASINSTR_SRC_BEAMSIZE_X, 365 "y" : SASINSTR_SRC_BEAMSIZE_Y, 366 "z" : SASINSTR_SRC_BEAMSIZE_Z, 367 } 368 } 369 SASINSTR_SRC_WL = { 370 "variable" : "{0}.source.wavelength = {1}", 371 "unit" : "source.wavelength_unit", 372 "storeas" : "float", 373 "attributes" : { 374 "unit" : { 375 "variable" : "{0}.source.wavelength_unit = \"{1}\"", 376 "storeas" : "content" 377 }, 378 } 379 } 380 SASINSTR_SRC_WL_MIN = { 381 "variable" : "{0}.source.wavelength_min = {1}", 382 "unit" : "source.wavelength_min_unit", 383 "storeas" : "float", 384 "attributes" : { 385 "unit" : { 386 "variable" : "{0}.source.wavelength_min_unit = \"{1}\"", 387 "storeas" : "content" 388 }, 389 } 390 } 391 SASINSTR_SRC_WL_MAX = { 392 "variable" : "{0}.source.wavelength_max = {1}", 393 "unit" : "source.wavelength_max_unit", 394 "storeas" : "float", 395 "attributes" : { 396 "unit" : { 397 "variable" : "{0}.source.wavelength_max_unit = \"{1}\"", 398 "storeas" : "content" 399 }, 400 } 401 } 402 SASINSTR_SRC_WL_SPR = { 403 "variable" : "{0}.source.wavelength_spread = {1}", 404 "unit" : "source.wavelength_spread_unit", 405 "storeas" : "float", 406 "attributes" : { 407 "unit" : { 408 "variable" : "{0}.source.wavelength_spread_unit = \"{1}\"", 409 "storeas" : "content" 410 }, 411 } 412 } 413 SASINSTR_SRC = { 414 "attributes" : {"name" : {"variable" : "{0}.source.name = \"{1}\""}}, 415 "variable" : None, 416 "children" : { 417 "radiation" : {"variable" : "{0}.source.radiation = \"{1}\""}, 418 "beam_size" : SASINSTR_SRC_BEAMSIZE, 419 "beam_shape" : {"variable" : \ 420 "{0}.source.beam_shape = \"{1}\""}, 421 "wavelength" : SASINSTR_SRC_WL, 422 "wavelength_min" : SASINSTR_SRC_WL_MIN, 423 "wavelength_max" : SASINSTR_SRC_WL_MAX, 424 "wavelength_spread" : SASINSTR_SRC_WL_SPR, 425 }, 426 } 427 SASINSTR_COLL_APER_ATTR = { 428 "unit" : { 429 "variable" : "{0}.size_unit = \"{1}\"", 430 "storeas" : "content" 431 }, 432 } 433 SASINSTR_COLL_APER_X = { 434 "variable" : "{0}.size.x = {1}", 435 "unit" : "size_unit", 436 "storeas" : "float", 437 "attributes" : SASINSTR_COLL_APER_ATTR 438 } 439 SASINSTR_COLL_APER_Y = { 440 "variable" : "{0}.size.y = {1}", 441 "unit" : "size_unit", 442 "storeas" : "float", 443 "attributes" : SASINSTR_COLL_APER_ATTR 444 } 445 SASINSTR_COLL_APER_Z = { 446 "variable" : "{0}.size.z = {1}", 447 "unit" : "size_unit", 448 "storeas" : "float", 449 "attributes" : SASINSTR_COLL_APER_ATTR 450 } 451 SASINSTR_COLL_APER_SIZE = { 452 "attributes" : {"unit" : {"variable" : \ 453 "{0}.size_unit = \"{1}\""}}, 454 "children" : { 455 "storeas" : "float", 456 "x" : SASINSTR_COLL_APER_X, 457 "y" : SASINSTR_COLL_APER_Y, 458 "z" : SASINSTR_COLL_APER_Z, 459 } 460 } 461 SASINSTR_COLL_APER_DIST = { 462 "storeas" : "float", 463 "attributes" : { 464 "storeas" : "content", 465 "unit" : {"variable" : \ 466 "{0}.distance_unit = \"{1}\""}}, 467 "variable" : "{0}.distance = {1}", 468 "unit" : "distance_unit", 469 } 470 SASINSTR_COLL_APER = { 471 "variable" : None, 472 "attributes" : { 473 "name" : {"variable" : \ 474 "{0}.name = \"{1}\""}, 475 "type" : {"variable" : \ 476 "{0}.type = \"{1}\""}, 477 }, 478 "children" : { 479 "size" : SASINSTR_COLL_APER_SIZE, 480 "distance" : SASINSTR_COLL_APER_DIST 481 } 482 } 483 SASINSTR_COLL = { 484 "attributes" : {"name" : {"variable" : \ 485 "{0}.name = \"{1}\""}}, 486 "variable" : None, 487 "children" : { 488 "length" : { 489 "variable" : "{0}.length = {1}", 490 "unit" : "length_unit", 491 "storeas" : "float", 492 "attributes" : { 493 "storeas" : \ 494 "content", 495 "unit" : {"variable" : "{0}.length_unit = \"{1}\""} 496 }, 497 }, 498 "aperture" : SASINSTR_COLL_APER, 499 }, 500 } 501 SASINSTR_DET_SDD = { 502 "variable" : "{0}.distance = {1}", 503 "unit" : "distance_unit", 504 "attributes" : { 505 "unit" : { 506 "variable" : \ 507 "{0}.distance_unit = \"{1}\"", 508 "storeas" : "content" 509 } 510 }, 511 } 512 SASINSTR_DET_OFF_ATTR = { 513 "unit" : { 514 "variable" : "{0}.offset_unit = \"{1}\"", 515 "storeas" : "content" 516 }, 517 } 518 SASINSTR_DET_OFF_X = { 519 "variable" : "{0}.offset.x = {1}", 520 "unit" : "offset_unit", 521 "attributes" : SASINSTR_DET_OFF_ATTR 522 } 523 SASINSTR_DET_OFF_Y = { 524 "variable" : "{0}.offset.y = {1}", 525 "unit" : "offset_unit", 526 "attributes" : SASINSTR_DET_OFF_ATTR 527 } 528 SASINSTR_DET_OFF_Z = { 529 "variable" : "{0}.offset.z = {1}", 530 "unit" : "offset_unit", 531 "attributes" : SASINSTR_DET_OFF_ATTR 532 } 533 SASINSTR_DET_OFF = { 534 "variable" : None, 535 "children" : { 536 "x" : SASINSTR_DET_OFF_X, 537 "y" : SASINSTR_DET_OFF_Y, 538 "z" : SASINSTR_DET_OFF_Z, 539 } 540 } 541 SASINSTR_DET_OR_ATTR = { 542 "unit" : "{0}.orientation_unit = \"{1}\"", 543 "storeas" : "content" 544 } 545 SASINSTR_DET_OR_ROLL = { 546 "variable" : "{0}.orientation.x = {1}", 547 "unit" : "orientation_unit", 548 "attributes" : SASINSTR_DET_OR_ATTR 549 } 550 SASINSTR_DET_OR_PITCH = { 551 "variable" : "{0}.orientation.y = {1}", 552 "unit" : "orientation_unit", 553 "attributes" : SASINSTR_DET_OR_ATTR 554 } 555 SASINSTR_DET_OR_YAW = { 556 "variable" : "{0}.orientation.z = {1}", 557 "unit" : "orientation_unit", 558 "attributes" : SASINSTR_DET_OR_ATTR 559 } 560 SASINSTR_DET_OR = { 561 "variable" : None, 562 "children" : { 563 "roll" : SASINSTR_DET_OR_ROLL, 564 "pitch" : SASINSTR_DET_OR_PITCH, 565 "yaw" : SASINSTR_DET_OR_YAW, 566 } 567 } 568 SASINSTR_DET_BC_X = { 569 "variable" : "{0}.beam_center.x = {1}", 570 "unit" : "beam_center_unit", 571 "attributes" : { 572 "unit" : \ 573 "{0}.beam_center_unit = \"{1}\"", 574 "storeas" : "content" 575 } 576 } 577 SASINSTR_DET_BC_Y = { 578 "variable" : "{0}.beam_center.y = {1}", 579 "unit" : "beam_center_unit", 580 "attributes" : { 581 "unit" : \ 582 "{0}.beam_center_unit = \"{1}\"", 583 "storeas" : "content" 584 } 585 } 586 SASINSTR_DET_BC_Z = { 587 "variable" : "{0}.beam_center.z = {1}", 588 "unit" : "beam_center_unit", 589 "attributes" : { 590 "unit" : \ 591 "{0}.beam_center_unit = \"{1}\"", 592 "storeas" : "content" 593 } 594 } 595 SASINSTR_DET_BC = { 596 "variable" : None, 597 "children" : { 598 "x" : SASINSTR_DET_BC_X, 599 "y" : SASINSTR_DET_BC_Y, 600 "z" : SASINSTR_DET_BC_Z, 601 } 602 } 603 SASINSTR_DET_PIXEL_X = { 604 "variable" : "{0}.pixel_size.x = {1}", 605 "unit" : "pixel_size_unit", 606 "attributes" : { 607 "unit" : "{0}.pixel_size_unit = \"{1}\"", 608 "storeas" : "content" 609 } 610 } 611 SASINSTR_DET_PIXEL_Y = { 612 "variable" : "{0}.pixel_size.y = {1}", 613 "unit" : "pixel_size_unit", 614 "attributes" : { 615 "unit" : "{0}.pixel_size_unit = \"{1}\"", 616 "storeas" : "content" 617 } 618 } 619 SASINSTR_DET_PIXEL_Z = { 620 "variable" : "{0}.pixel_size.z = {1}", 621 "unit" : "pixel_size_unit", 622 "attributes" : { 623 "unit" : "{0}.pixel_size_unit = \"{1}\"", 624 "storeas" : "content" 625 } 626 } 627 SASINSTR_DET_PIXEL = { 628 "variable" : None, 629 "children" : { 630 "x" : SASINSTR_DET_PIXEL_X, 631 "y" : SASINSTR_DET_PIXEL_Y, 632 "z" : SASINSTR_DET_PIXEL_Z, 633 } 634 } 635 SASINSTR_DET_SLIT = { 636 "variable" : "{0}.slit_length = {1}", 637 "unit" : "slit_length_unit", 638 "attributes" : { 639 "unit" : { 640 "variable" : "{0}.slit_length_unit = \"{1}\"", 641 "storeas" : "content" 642 } 643 } 644 } 645 SASINSTR_DET = { 646 "storeas" : "float", 647 "variable" : None, 648 "attributes" : { 649 "name" : { 650 "storeas" : "content", 651 "variable" : "{0}.name = \"{1}\"", 652 } 653 }, 654 "children" : { 655 "name" : { 656 "storeas" : "content", 657 "variable" : "{0}.name = \"{1}\"", 658 }, 659 "SDD" : SASINSTR_DET_SDD, 660 "offset" : SASINSTR_DET_OFF, 661 "orientation" : SASINSTR_DET_OR, 662 "beam_center" : SASINSTR_DET_BC, 663 "pixel_size" : SASINSTR_DET_PIXEL, 664 "slit_length" : SASINSTR_DET_SLIT, 665 } 666 } 667 SASINSTR = { 668 "variable" : None, 669 "children" : { 670 "variable" : None, 671 "name" : {"variable" : \ 672 "{0}.instrument = \"{1}\""}, 673 "SASsource" : SASINSTR_SRC, 674 "SAScollimation" : SASINSTR_COLL, 675 "SASdetector" : SASINSTR_DET, 676 }, 677 } 14 678 CANSAS_FORMAT = { 15 679 "SASentry" : { … … 17 681 "variable" : None, 18 682 "storeas" : "content", 19 "attributes" : {"name" : {"variable" : "{0}.run_name[node_value] = \"{1}\""}}, 683 "attributes" : {"name" : {"variable" : \ 684 "{0}.run_name[node_value] = \"{1}\""}}, 20 685 "children" : { 21 "Title" : {"variable" : "{0}.title = \"{1}\""}, 22 "Run" : { 23 "variable" : "{0}.run.append(\"{1}\")", 24 "attributes" : {"name" : {"variable" : "{0}.run_name[node_value] = \"{1}\""}} 25 }, 26 "SASdata" : { 27 "attributes" : {"name" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"",}}, 28 "variable" : None, 29 "children" : {"Idata" : { 30 "storeas" : "float", 31 "units_optional" : False, 32 "variable" : None, 33 "attributes" : { 34 "name" : { 35 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 36 "storeas" : "content", 37 }, 38 "timestamp" : { 39 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 40 "storeas" : "content", 41 } 42 }, 43 "children" : { 44 "Q" : { 45 "variable" : "{0}.x = numpy.append({0}.x, {1})", 46 "unit" : "x_unit", 47 "attributes" : { 48 "unit" : { 49 "variable" : "{0}._xunit = \"{1}\"", 50 "storeas" : "content" 51 } 52 } 53 }, 54 "I" : { 55 "variable" : "{0}.y = numpy.append({0}.y, {1})", 56 "unit" : "y_unit", 57 "attributes" : { 58 "unit" : { 59 "variable" : "{0}._yunit = \"{1}\"", 60 "storeas" : "content" 61 } 62 } 63 }, 64 "Idev" : { 65 "variable" : "{0}.dy = numpy.append({0}.dy, {1})", 66 "unit" : "y_unit", 67 "attributes" : { 68 "unit" : { 69 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 70 "storeas" : "content" 71 } 72 }, 73 }, 74 "Qdev" : { 75 "variable" : "{0}.dx = numpy.append({0}.dx, {1})", 76 "unit" : "x_unit", 77 "attributes" : { 78 "unit" : { 79 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 80 "storeas" : "content" 81 } 82 }, 83 }, 84 "dQw" : { 85 "variable" : "{0}.dxw = numpy.append({0}.dxw, {1})", 86 "unit" : "x_unit", 87 "attributes" : { 88 "unit" : { 89 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 90 "storeas" : "content" 91 } 92 }, 93 }, 94 "dQl" : { 95 "variable" : "{0}.dxl = numpy.append({0}.dxl, {1})", 96 "unit" : "x_unit", 97 "attributes" : { 98 "unit" : { 99 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 100 "storeas" : "content" 101 } 102 }, 103 }, 104 "Qmean" : { 105 "storeas" : "content", 106 "unit" : "x_unit", 107 "variable" : "{0}.meta_data[\"{2}\"] = {1}", 108 "attributes" : {"unit" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\""}}, 109 }, 110 "Shadowfactor" : { 111 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 112 "storeas" : "content", 113 }, 114 "<any>" : { 115 "variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"", 116 "storeas" : "content", 117 } 118 } 119 }, 120 "<any>" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\"",} 121 } 122 }, 123 "SAStransmission_spectrum" : { 124 "variable" : None, 125 "children" : { 126 "Tdata" : { 127 "storeas" : "float", 128 "variable" : None, 129 "children" : { 130 "Lambda" : { 131 "variable" : "{0}.trans_spectrum.wavelength.append({1})", 132 "unit" : "trans_spectrum.wavelength_unit", 133 "attributes" : { 134 "unit" : { 135 "variable" : "{0}.trans_spectrum.wavelength_unit = \"{1}\"", 136 "storeas" : "content" 137 } 138 } 139 }, 140 "T" : { 141 "variable" : "{0}.trans_spectrum.transmission.append({1})", 142 "unit" : "trans_spectrum.transmission_unit", 143 "attributes" : { 144 "unit" : { 145 "variable" : "{0}.trans_spectrum.transmission_unit = \"{1}\"", 146 "storeas" : "content" 147 } 148 } 149 }, 150 "Tdev" : { 151 "variable" : "{0}.trans_spectrum.transmission_deviation.append({1})", 152 "unit" : "trans_spectrum.transmission_deviation_unit", 153 "attributes" : { 154 "unit" : { 155 "variable" : "{0}.trans_spectrum.transmission_deviation_unit = \"{1}\"", 156 "storeas" : "content" 157 } 158 } 159 }, 160 "<any>" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\""}, 161 } 162 }, 163 "<any>" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\""}, 164 }, 165 "attributes" : {"name" : {"variable" : "{0}.trans_spectrum.name = \"{1}\""}, 166 "timestamp" : {"variable" : "{0}.trans_spectrum.timestamp = \"{1}\""},} 167 }, 168 "SASsample" : { 169 "attributes" : {"name" : {"variable" : "{0}.sample.name = \"{1}\""},}, 170 "variable" : None, 171 "children" : { 172 "ID" : {"variable" : "{0}.sample.ID = \"{1}\""}, 173 "thickness" : { 174 "variable" : "{0}.sample.thickness = {1}", 175 "unit" : "sample.thickness_unit", 176 "storeas" : "float", 177 "attributes" : { 178 "units" : { 179 "variable" : "{0}.sample.thickness_unit = \"{1}\"", 180 "storeas" : "content" 181 } 182 }, 183 }, 184 "transmission" : { 185 "variable" : "{0}.sample.transmission = {1}", 186 "storeas" : "float", 187 }, 188 "temperature" : { 189 "variable" : "{0}.sample.temperature = {1}", 190 "unit" : "sample.temperature_unit", 191 "storeas" : "float", 192 "attributes" : { 193 "units" : { 194 "variable" : "{0}.sample.temperature_unit = \"{1}\"", 195 "storeas" : "content" 196 } 197 }, 198 }, 199 "position" : { 200 "children" : { 201 "variable" : None, 202 "x" : { 203 "variable" : "{0}.sample.position.x = {1}", 204 "unit" : "sample.position_unit", 205 "storeas" : "float", 206 "attributes" : { 207 "units" : { 208 "variable" : "{0}.sample.position_unit = \"{1}\"", 209 "storeas" : "content" 210 } 211 } 212 }, 213 "y" : { 214 "variable" : "{0}.sample.position.y = {1}", 215 "unit" : "sample.position_unit", 216 "attributes" : { 217 "units" : { 218 "variable" : "{0}.sample.position_unit = \"{1}\"", 219 "storeas" : "content" 220 } 221 } 222 }, 223 "z" : { 224 "variable" : "{0}.sample.position.z = {1}", 225 "unit" : "sample.position_unit", 226 "attributes" : { 227 "units" : { 228 "variable" : "{0}.sample.position_unit = \"{1}\"", 229 "storeas" : "content" 230 } 231 } 232 }, 233 }, 234 }, 235 "orientation" : { 236 "variable" : None, 237 "children" : { 238 "roll" : { 239 "variable" : "{0}.sample.orientation.x = {1}", 240 "unit" : "sample.orientation_unit", 241 "storeas" : "float", 242 "attributes" : { 243 "units" : { 244 "variable" : "{0}.sample.orientation_unit = \"{1}\"", 245 "storeas" : "content" 246 } 247 } 248 }, 249 "pitch" : { 250 "variable" : "{0}.sample.orientation.y = {1}", 251 "unit" : "sample.orientation_unit", 252 "storeas" : "float", 253 "attributes" : { 254 "units" : { 255 "variable" : "{0}.sample.orientation_unit = \"{1}\"", 256 "storeas" : "content" 257 } 258 } 259 }, 260 "yaw" : { 261 "variable" : "{0}.sample.orientation.z = {1}", 262 "unit" : "sample.orientation_unit", 263 "storeas" : "float", 264 "attributes" : { 265 "units" : { 266 "variable" : "{0}.sample.orientation_unit = \"{1}\"", 267 "storeas" : "content" 268 } 269 } 270 }, 271 }, 272 }, 273 "details" : {"variable" : "{0}.sample.details.append(\"{1}\")"}, 274 "<any>" : {"variable" : "{0}.meta_data[\"{2}\"] = \"{1}\""} 275 }, 276 }, 277 "SASinstrument" : { 278 "variable" : None, 279 "children" : { 280 "variable" : None, 281 "name" : {"variable" : "{0}.instrument = \"{1}\""}, 282 "SASsource" : { 283 "attributes" : {"name" : {"variable" : "{0}.source.name = \"{1}\""}}, 284 "variable" : None, 285 "children" : { 286 "radiation" : {"variable" : "{0}.source.radiation = \"{1}\""}, 287 "beam_size" : { 288 "attributes" : {"name" : {"variable" : "{0}.source.beam_size_name = \"{1}\""}}, 289 "variable" : None, 290 "children" : { 291 "x" : { 292 "variable" : "{0}.source.beam_size.x = {1}", 293 "unit" : "source.beam_size_unit", 294 "storeas" : "float", 295 "attributes" : { 296 "unit" : "{0}.source.beam_size_unit = \"{1}\"", 297 "storeas" : "content" 298 } 299 }, 300 "y" : { 301 "variable" : "{0}.source.beam_size.y = {1}", 302 "unit" : "source.beam_size_unit", 303 "storeas" : "float", 304 "attributes" : { 305 "unit" : "{0}.source.beam_size_unit = \"{1}\"", 306 "storeas" : "content" 307 } 308 }, 309 "z" : { 310 "variable" : "{0}.source.beam_size.z = {1}", 311 "unit" : "source.beam_size_unit", 312 "storeas" : "float", 313 "attributes" : { 314 "unit" : "{0}.source.beam_size_unit = \"{1}\"", 315 "storeas" : "content" 316 } 317 }, 318 } 319 }, 320 "beam_shape" : {"variable" : "{0}.source.beam_shape = \"{1}\""}, 321 "wavelength" : { 322 "variable" : "{0}.source.wavelength = {1}", 323 "unit" : "source.wavelength_unit", 324 "storeas" : "float", 325 "attributes" : { 326 "unit" : { 327 "variable" : "{0}.source.wavelength_unit = \"{1}\"", 328 "storeas" : "content" 329 }, 330 } 331 }, 332 "wavelength_min" : { 333 "variable" : "{0}.source.wavelength_min = {1}", 334 "unit" : "source.wavelength_min_unit", 335 "storeas" : "float", 336 "attributes" : { 337 "unit" : { 338 "variable" : "{0}.source.wavelength_min_unit = \"{1}\"", 339 "storeas" : "content" 340 }, 341 } 342 }, 343 "wavelength_max" : { 344 "variable" : "{0}.source.wavelength_max = {1}", 345 "unit" : "source.wavelength_max_unit", 346 "storeas" : "float", 347 "attributes" : { 348 "unit" : { 349 "variable" : "{0}.source.wavelength_max_unit = \"{1}\"", 350 "storeas" : "content" 351 }, 352 } 353 }, 354 "wavelength_spread" : { 355 "variable" : "{0}.source.wavelength_spread = {1}", 356 "unit" : "source.wavelength_spread_unit", 357 "storeas" : "float", 358 "attributes" : { 359 "unit" : {"variable" : "{0}.source.wavelength_spread_unit = \"{1}\""}, 360 "storeas" : "content" 361 } 362 }, 363 }, 364 }, 365 "SAScollimation" : { 366 "attributes" : {"name" : {"variable" : "{0}.name = \"{1}\""}}, 367 "variable" : None, 368 "children" : { 369 "length" : { 370 "variable" : "{0}.length = {1}", 371 "unit" : "length_unit", 372 "storeas" : "float", 373 "attributes" : { 374 "storeas" : "content", 375 "unit" : {"variable" : "{0}.length_unit = \"{1}\""} 376 }, 377 }, 378 "aperture" : { 379 "variable" : None, 380 "attributes" : { 381 "name" : {"variable" : "{0}.name = \"{1}\""}, 382 "type" : {"variable" : "{0}.type = \"{1}\""}, 383 }, 384 "children" : { 385 "size" : { 386 "attributes" : {"unit" : {"variable" : "{0}.size_unit = \"{1}\""}}, 387 "children" : { 388 "storeas" : "float", 389 "x" : { 390 "variable" : "{0}.size.x = {1}", 391 "unit" : "size_unit", 392 "storeas" : "float", 393 "attributes" : { 394 "unit" : { 395 "variable" : "{0}.size_unit = \"{1}\"", 396 "storeas" : "content" 397 }, } 398 }, 399 "y" : { 400 "variable" : "{0}.size.y = {1}", 401 "unit" : "size_unit", 402 "storeas" : "float", 403 "attributes" : { 404 "unit" : { 405 "variable" : "{0}.size_unit = \"{1}\"", 406 "storeas" : "content" 407 }, 408 } 409 }, 410 "z" : { 411 "variable" : "{0}.size.z = {1}", 412 "unit" : "size_unit", 413 "storeas" : "float", 414 "attributes" : { 415 "unit" : { 416 "variable" : "{0}.size_unit = \"{1}\"", 417 "storeas" : "content" 418 }, 419 } 420 }, 421 } 422 }, 423 "distance" : { 424 "storeas" : "float", 425 "attributes" : { 426 "storeas" : "content", 427 "unit" : {"variable" : "{0}.distance_unit = \"{1}\""}}, 428 "variable" : "{0}.distance = {1}", 429 "unit" : "distance_unit", 430 } 431 } 432 }, 433 }, 434 }, 435 "SASdetector" : { 436 "storeas" : "float", 437 "variable" : None, 438 "attributes" : { 439 "name" : { 440 "storeas" : "content", 441 "variable" : "{0}.name = \"{1}\"", 442 } 443 }, 444 "children" : { 445 "name" : { 446 "storeas" : "content", 447 "variable" : "{0}.name = \"{1}\"", 448 }, 449 "SDD" : { 450 "variable" : "{0}.distance = {1}", 451 "unit" : "distance_unit", 452 "attributes" : { 453 "unit" : { 454 "variable" : "{0}.distance_unit = \"{1}\"", 455 "storeas" : "content" 456 } 457 }, 458 }, 459 "offset" : { 460 "variable" : None, 461 "children" : { 462 "x" : { 463 "variable" : "{0}.offset.x = {1}", 464 "unit" : "offset_unit", 465 "attributes" : { 466 "unit" : { 467 "variable" : "{0}.offset_unit = \"{1}\"", 468 "storeas" : "content" 469 }, 470 } 471 }, 472 "y" : { 473 "variable" : "{0}.offset.y = {1}", 474 "unit" : "offset_unit", 475 "attributes" : { 476 "unit" : { 477 "variable" : "{0}.offset_unit = \"{1}\"", 478 "storeas" : "content" 479 }, 480 } 481 }, 482 "z" : { 483 "variable" : "{0}.offset.z = {1}", 484 "unit" : "offset_unit", 485 "attributes" : { 486 "unit" : { 487 "variable" : "{0}.offset_unit = \"{1}\"", 488 "storeas" : "content" 489 }, 490 } 491 }, 492 } 493 }, 494 "orientation" : { 495 "variable" : None, 496 "children" : { 497 "roll" : { 498 "variable" : "{0}.orientation.x = {1}", 499 "unit" : "orientation_unit", 500 "attributes" : { 501 "unit" : "{0}.orientation_unit = \"{1}\"", 502 "storeas" : "content" 503 } 504 }, 505 "pitch" : { 506 "variable" : "{0}.orientation.y = {1}", 507 "unit" : "orientation_unit", 508 "attributes" : { 509 "unit" : "{0}.orientation_unit = \"{1}\"", 510 "storeas" : "content" 511 } 512 }, 513 "yaw" : { 514 "variable" : "{0}.orientation.z = {1}", 515 "unit" : "orientation_unit", 516 "attributes" : { 517 "unit" : "{0}.orientation_unit = \"{1}\"", 518 "storeas" : "content" 519 } 520 }, 521 } 522 }, 523 "beam_center" : { 524 "variable" : None, 525 "children" : { 526 "x" : { 527 "variable" : "{0}.beam_center.x = {1}", 528 "unit" : "beam_center_unit", 529 "attributes" : { 530 "unit" : "{0}.beam_center_unit = \"{1}\"", 531 "storeas" : "content" 532 } 533 }, 534 "y" : { 535 "variable" : "{0}.beam_center.y = {1}", 536 "unit" : "beam_center_unit", 537 "attributes" : { 538 "unit" : "{0}.beam_center_unit = \"{1}\"", 539 "storeas" : "content" 540 } 541 }, 542 "z" : { 543 "variable" : "{0}.beam_center.z = {1}", 544 "unit" : "beam_center_unit", 545 "attributes" : { 546 "unit" : "{0}.beam_center_unit = \"{1}\"", 547 "storeas" : "content" 548 } 549 }, 550 } 551 }, 552 "pixel_size" : { 553 "variable" : None, 554 "children" : { 555 "x" : { 556 "variable" : "{0}.pixel_size.x = {1}", 557 "unit" : "pixel_size_unit", 558 "attributes" : { 559 "unit" : "{0}.pixel_size_unit = \"{1}\"", 560 "storeas" : "content" 561 } 562 }, 563 "y" : { 564 "variable" : "{0}.pixel_size.y = {1}", 565 "unit" : "pixel_size_unit", 566 "attributes" : { 567 "unit" : "{0}.pixel_size_unit = \"{1}\"", 568 "storeas" : "content" 569 } 570 }, 571 "z" : { 572 "variable" : "{0}.pixel_size.z = {1}", 573 "unit" : "pixel_size_unit", 574 "attributes" : { 575 "unit" : "{0}.pixel_size_unit = \"{1}\"", 576 "storeas" : "content" 577 } 578 }, 579 } 580 }, 581 "slit_length" : { 582 "variable" : "{0}.slit_length = {1}", 583 "unit" : "slit_length_unit", 584 "attributes" : { 585 "unit" : { 586 "variable" : "{0}.slit_length_unit = \"{1}\"", 587 "storeas" : "content" 588 } 589 } 590 } 591 }, 592 }, 593 }, 594 }, 595 "SASprocess" : { 596 "variable" : None, 597 "children" : { 598 "name" : {"variable" : "{0}.name = \'{1}\'"}, 599 "date" : {"variable" : "{0}.date = \'{1}\'"}, 600 "description" : {"variable" : "{0}.description = \'{1}\'"}, 601 "term" : { 602 "variable" : None, 603 "attributes" : { 604 "unit" : {"variable" : None}, 605 "name" : {"variable" : None} 606 } 607 }, 608 "SASprocessnote" : { 609 "variable" : None, 610 "children" : {"<any>" : {"variable" : "{0}.notes.append(\'2}: {1}\')"}}}, 611 "<any>" : {"variable" : "{0}.notes.append(\'{2}: {1}\')",} 612 }, 613 }, 614 "SASnote" : {"variable" : "{0}.notes.append(\'{1}\')"}, 615 "<any>" : {"variable" : "{0}.meta_data[\"{2}\"] = \'{1}\'"}, 686 "Title" : TITLE, 687 "Run" : RUN, 688 "SASdata" : SASDATA, 689 "SAStransmission_spectrum" : \ 690 SASTRANSSPEC, 691 "SASsample" : SASSAMPLE, 692 "SASinstrument" : SASINSTR, 693 "SASprocess" : SASPROCESS, 694 "SASnote" : SASNOTE, 695 "<any>" : ANY, 616 696 } 617 697 } 618 698 } 699 -
src/sans/dataloader/readers/cansas_reader.py
r1ce36f37 r76cd1ae 1 1 """ 2 CanSAS data reader - new recursive cansas Version.2 CanSAS data reader - new recursive cansas_version. 3 3 """ 4 4 ############################################################################ … … 19 19 from sans.dataloader.data_info import Data1D 20 20 from sans.dataloader.data_info import Collimation 21 from sans.dataloader.data_info import TransmissionSpectrum 21 22 from sans.dataloader.data_info import Detector 22 23 from sans.dataloader.data_info import Process 23 24 from sans.dataloader.data_info import Aperture 24 import xml_reader25 import sans.dataloader.readers.xml_reader as xml_reader 25 26 import xml.dom.minidom 26 from cansas_constants import cansasConstants27 from sans.dataloader.readers.cansas_constants import cansasConstants 27 28 28 29 _ZERO = 1e-16 … … 32 33 except: 33 34 HAS_CONVERTER = False 34 35 CANSAS_FORMAT = cansasConstants.CANSAS_FORMAT 36 CANSAS_NS = cansasConstants.CANSAS_NS 35 36 constants = cansasConstants() 37 CANSAS_FORMAT = constants.format 38 CANSAS_NS = constants.ns 37 39 ALLOW_ALL = True 38 40 … … 118 120 """ 119 121 ##CanSAS version - defaults to version 1.0 120 cansas Version = "1.0"122 cansas_version = "1.0" 121 123 ##Data reader 122 124 reader = xml_reader.XMLreader() … … 137 139 self.errors = [] 138 140 139 def is Cansas(self):141 def is_cansas(self): 140 142 """ 141 143 Checks to see if the xml file is a CanSAS file … … 143 145 if self.reader.validateXML(): 144 146 xmlns = self.reader.xmlroot.keys() 145 if (CANSAS_NS.get(self.cansasVersion).get("ns") == self.reader.xmlroot.get(xmlns[1]).rsplit(" ")[0]): 147 if (CANSAS_NS.get(self.cansas_version).get("ns") == \ 148 self.reader.xmlroot.get(xmlns[1]).rsplit(" ")[0]): 146 149 return True 147 150 return False … … 176 179 base = base_name.split("/sans/")[0] 177 180 178 # Load in thexml file and get the cansas version from the header181 # Load in xml file and get the cansas version from the header 179 182 self.reader.setXMLFile(xml) 180 183 root = self.reader.xmlroot 181 184 if root is None: 182 185 root = {} 183 self.cansas Version = root.get("version", "1.0")186 self.cansas_version = root.get("version", "1.0") 184 187 185 188 # Generic values for the cansas file based on the version 186 cansas_defaults = CANSAS_NS.get(self.cansasVersion, "1.0") 187 schema_path = "{0}/sans/dataloader/readers/schema/{1}".format(base, cansas_defaults.get("schema")).replace("\\", "/") 189 cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0") 190 schema_path = "{0}/sans/dataloader/readers/schema/{1}".format\ 191 (base, cansas_defaults.get("schema")).replace("\\", "/") 188 192 189 193 # Link a schema to the XML file. … … 193 197 # Check the file matches the XML schema 194 198 try: 195 if self.is Cansas():196 # Get each SASentry from theXML file and add it to a list.199 if self.is_cansas(): 200 # Get each SASentry from XML file and add it to a list. 197 201 entry_list = root.xpath('/ns:SASroot/ns:SASentry', 198 202 namespaces={'ns': cansas_defaults.get("ns")}) 199 203 ns.append("SASentry") 200 204 201 # If there aremultiple files, modify the name for each is unique202 multiple Files = len(entry_list) - 1203 n= 0205 # If multiple files, modify the name for each is unique 206 multiple_files = len(entry_list) - 1 207 increment = 0 204 208 name = basename 205 209 # Parse each SASentry item 206 210 for entry in entry_list: 211 # Define a new Data1D object with zeroes for x and y 212 data1d = Data1D(x,y,dx,dy) 213 data1d.dxl = dxl 214 data1d.dxw = dxw 207 215 208 # Define a new Data1D object with zeroes for x and y209 data1D = Data1D(x,y,dx,dy)210 data1D.dxl = dxl211 data1D.dxw = dxw216 # If more than one SASentry, increment each in order 217 if multiple_files: 218 name += "_{0}".format(increment) 219 increment += 1 212 220 213 # If more than one SASentry, number each in order 214 if multipleFiles: 215 name += "_{0}".format(n) 216 n += 1 217 218 # Set the Data1D name and then parse the entry. The entry is appended to a list of entry values 219 data1D.filename = name 220 data1D.meta_data["loader"] = "CanSAS 1D" 221 return_value, extras = self._parse_entry(entry, ns, data1D) 221 # Set the Data1D name and then parse the entry. 222 # The entry is appended to a list of entry values 223 data1d.filename = name 224 data1d.meta_data["loader"] = "CanSAS 1D" 225 return_value, extras = \ 226 self._parse_entry(entry, ns, data1d) 222 227 del extras[:] 223 228 224 #Final cleanup - Remove empty nodes, verify array sizes are correct 229 # Final cleanup 230 # Remove empty nodes, verify array sizes are correct 225 231 for error in self.errors: 226 232 return_value.errors.append(error) … … 241 247 numpy.trim_zeros(return_value.dxl) 242 248 numpy.trim_zeros(return_value.dxw) 243 244 249 output.append(return_value) 245 250 else: … … 248 253 except: 249 254 # If the file does not match the schema, raise this error 250 raise RuntimeError, "%s cannot be read \ n" % xml255 raise RuntimeError, "%s cannot be read \increment" % xml 251 256 return output 252 257 # Return a list of parsed entries that dataloader can manage … … 254 259 255 260 def _create_unique_key(self, dictionary, name, i): 261 """ 262 Create a unique key value for any dictionary to prevent overwriting 263 264 265 :param dictionary: A dictionary with any number of entries 266 :param name: The index of the item to be added to dictionary 267 :param i: The number to be appended to the name 268 """ 256 269 if dictionary.get(name) is not None: 257 270 i += 1 … … 261 274 return name 262 275 263 def _iterate_namespace(self, ns): 276 def _iterate_namespace(self, namespace): 277 """ 278 Method to iterate through a cansas constants tree based on a list of 279 names 280 281 :param namespace: A list of names that match the tree structure of 282 cansas_constants 283 """ 264 284 # The current level to look through in cansas_constants. 265 285 current_level = CANSAS_FORMAT.get("SASentry") … … 268 288 ns_datatype = "content" 269 289 ns_optional = True 270 for name in n s:290 for name in namespace: 271 291 if name != "SASentry": 272 292 current_level = current_level.get("children").get(name, "") … … 277 297 cl_units_optional = current_level.get("units_required", "") 278 298 # Where are how to store the variable for the given namespace 279 # TheCANSAS_CONSTANTS tree is hierarchical, so is no value, inherit299 # CANSAS_CONSTANTS tree is hierarchical, so is no value, inherit 280 300 ns_variable = cl_variable if cl_variable != "" else ns_variable 281 301 ns_datatype = cl_datatype if cl_datatype != "" else ns_datatype 282 ns_optional = cl_units_optional if cl_units_optional != ns_optional else ns_optional 302 ns_optional = cl_units_optional if cl_units_optional != \ 303 ns_optional else ns_optional 283 304 return current_level, ns_variable, ns_datatype, ns_optional 284 305 285 def _unit_conversion(self, new_current_level, attr, data1D, node_value, optional = True): 306 307 def _unit_conversion(self, new_current_level, attr, data1d, \ 308 node_value, optional = True): 309 """ 310 A unit converter method used to convert the data included in the file 311 to the default units listed in data_info 312 313 :param new_current_level: cansas_constants level as returned by 314 _iterate_namespace 315 :param attr: The attributes of the node 316 :param data1d: Where the values will be saved 317 :param node_value: The value of the current dom node 318 :param optional: Boolean that says if the units are required 319 """ 286 320 value_unit = '' 287 321 if 'unit' in attr and new_current_level.get('unit') is not None: … … 291 325 default_unit = None 292 326 unitname = new_current_level.get("unit") 293 exec "default_unit = data1 D.{0}".format(unitname)327 exec "default_unit = data1d.{0}".format(unitname) 294 328 local_unit = attr['unit'] 295 if local_unit.lower() != default_unit.lower() and local_unit is not None\ 296 and local_unit.lower() != "none" and default_unit is not None: 329 if local_unit.lower() != default_unit.lower() and \ 330 local_unit is not None and local_unit.lower() != "none" and\ 331 default_unit is not None: 297 332 if HAS_CONVERTER == True: 298 333 try: 299 334 data_conv_q = Converter(attr['unit']) 300 335 value_unit = default_unit 301 exec "node_value = data_conv_q(node_value, units=data1 D.{0})".format(unitname)336 exec "node_value = data_conv_q(node_value, units=data1d.{0})".format(unitname) 302 337 except: 303 338 err_msg = "CanSAS reader: could not convert " 304 339 err_msg += "Q unit {0}; ".format(local_unit) 305 intermediate = "err_msg += \"expecting [{1}] {2}\".format(data1 D.{0}, sys.exc_info()[1])".format(unitname, "{0}", "{1}")340 intermediate = "err_msg += \"expecting [{1}] {2}\".format(data1d.{0}, sys.exc_info()[1])".format(unitname, "{0}", "{1}") 306 341 exec intermediate 307 342 self.errors.append(err_msg) … … 325 360 err_msg = "CanSAS reader: could not convert " 326 361 err_msg += "Q unit [%s]; " % attr['unit'], 327 exec "err_msg += \"expecting [%s]\n %s\" % (data1 D.{0}, sys.exc_info()[1])".format(unitname)362 exec "err_msg += \"expecting [%s]\n %s\" % (data1d.{0}, sys.exc_info()[1])".format(unitname) 328 363 self.errors.append(err_msg) 329 364 if optional: … … 336 371 return node_value, value_unit 337 372 338 def _parse_entry(self, dom, ns, data1 D, extras = []):373 def _parse_entry(self, dom, ns, data1d, extras = []): 339 374 """ 340 375 Parse a SASEntry - new recursive method for parsing the dom of … … 344 379 :param dom: dom object with a namespace base of ns 345 380 :param ns: A list of element names that lead up to the dom object 346 :param data1D: The data1D object that will be modified 381 :param data1d: The data1d object that will be modified 382 :param extras: Any values that should go into meta_data when data1d 383 is not a Data1D object 347 384 """ 348 385 349 386 # A portion of every namespace entry 350 base_ns = "{0}{1}{2}".format("{", CANSAS_NS.get(self.cansasVersion).get("ns"), "}") 387 base_ns = "{0}{1}{2}".format("{", \ 388 CANSAS_NS.get(self.cansas_version).get("ns"), "}") 351 389 unit = '' 352 390 … … 361 399 362 400 # Look for special cases 363 save_data1 D = data1D401 save_data1d = data1d 364 402 if tagname == "SASdetector": 365 data1 D= Detector()403 data1d = Detector() 366 404 elif tagname == "SAScollimation": 367 data1D = Collimation() 405 data1d = Collimation() 406 elif tagname == "SAStransmission_spectrum": 407 data1d = TransmissionSpectrum() 368 408 elif tagname == "SASprocess": 369 data1 D= Process()409 data1d = Process() 370 410 for child in node: 371 411 if child.tag.replace(base_ns, "") == "term": 372 412 term_attr = {} 373 413 for attr in child.keys(): 374 term_attr[attr] = ' '.join(child.get(attr).split()) 414 term_attr[attr] = \ 415 ' '.join(child.get(attr).split()) 375 416 if child.text is not None: 376 term_attr['value'] = ' '.join(child.text.split()) 377 data1D.term.append(term_attr) 417 term_attr['value'] = \ 418 ' '.join(child.text.split()) 419 data1d.term.append(term_attr) 378 420 elif tagname == "aperture": 379 data1 D= Aperture()421 data1d = Aperture() 380 422 381 423 # Get where to store content 382 new_current_level, ns_variable, ns_datatype, optional = self._iterate_namespace(ns) 424 new_current_level, ns_var, ns_datatype, \ 425 optional = self._iterate_namespace(ns) 383 426 # If the element is a child element, recurse 384 427 if node.getchildren() is not None: 385 428 # Returned value is new Data1D object with all previous and new values in it. 386 data1 D, extras = self._parse_entry(node, ns, data1D, extras)429 data1d, extras = self._parse_entry(node, ns, data1d, extras) 387 430 388 431 #Get the information from the node … … 396 439 if ns_datatype == "float": 397 440 # If an empty value is given, store as zero. 398 if node_value is None or node_value.isspace() or node_value.lower() == "nan": 441 if node_value is None or node_value.isspace() \ 442 or node_value.lower() == "nan": 399 443 node_value = "0.0" 400 node_value, unit = self._unit_conversion(new_current_level, attr, data1D, node_value, optional) 444 node_value, unit = self._unit_conversion(new_current_level,\ 445 attr, data1d, node_value, optional) 401 446 402 447 # If appending to a dictionary (meta_data | run_name), name sure the key is unique 403 if ns_var iable== "{0}.meta_data[\"{2}\"] = \"{1}\"":404 # If we are within a Process, Detector, Collimation or Aperture instance, pull out old data1 D405 tagname = self._create_unique_key(data1 D.meta_data, tagname, 0)406 if isinstance(data1 D, Data1D) == False:407 store_me = ns_var iable.format("data1D", node_value, tagname)448 if ns_var == "{0}.meta_data[\"{2}\"] = \"{1}\"": 449 # If we are within a Process, Detector, Collimation or Aperture instance, pull out old data1d 450 tagname = self._create_unique_key(data1d.meta_data, tagname, 0) 451 if isinstance(data1d, Data1D) == False: 452 store_me = ns_var.format("data1d", node_value, tagname) 408 453 extras.append(store_me) 409 ns_var iable= None410 if ns_var iable== "{0}.run_name[\"{2}\"] = \"{1}\"":411 tagname = self._create_unique_key(data1 D.run_name, tagname, 0)454 ns_var = None 455 if ns_var == "{0}.run_name[\"{2}\"] = \"{1}\"": 456 tagname = self._create_unique_key(data1d.run_name, tagname, 0) 412 457 413 458 # Check for Data1D object and any extra commands to save 414 if isinstance(data1 D, Data1D):459 if isinstance(data1d, Data1D): 415 460 for item in extras: 416 461 exec item 417 462 # Don't bother saving empty information unless it is a float 418 if ns_variable is not None and node_value is not None and node_value.isspace() == False: 463 if ns_var is not None and node_value is not None and \ 464 node_value.isspace() == False: 419 465 # Format a string and then execute it. 420 store_me = ns_var iable.format("data1D", node_value, tagname)466 store_me = ns_var.format("data1d", node_value, tagname) 421 467 exec store_me 422 468 # Get attributes and process them … … 430 476 else: 431 477 attrib_value = node.attrib[key] 432 store_attr = attrib_variable.format("data1D", attrib_value, key) 478 store_attr = attrib_variable.format("data1d", \ 479 attrib_value, key) 433 480 exec store_attr 434 481 except AttributeError as e: … … 441 488 print(e, exc_type, fname, exc_tb.tb_lineno, tagname, exc_obj) 442 489 finally: 443 # Save special cases in original data1D object and then restore the data1D 490 # Save special cases in original data1d object 491 # then restore the data1d 444 492 if tagname_original == "SASdetector": 445 save_data1 D.detector.append(data1D)493 save_data1d.detector.append(data1d) 446 494 elif tagname_original == "SAScollimation": 447 save_data1D.collimation.append(data1D) 495 save_data1d.collimation.append(data1d) 496 elif tagname == "SAStransmission_spectrum": 497 save_data1d.trans_spectrum.append(data1d) 448 498 elif tagname_original == "SASprocess": 449 save_data1 D.process.append(data1D)499 save_data1d.process.append(data1d) 450 500 elif tagname_original == "aperture": 451 save_data1 D.aperture.append(data1D)501 save_data1d.aperture.append(data1d) 452 502 else: 453 save_data1 D = data1D454 data1 D = save_data1D503 save_data1d = data1d 504 data1d = save_data1d 455 505 # Remove tagname from ns to restore original base 456 506 ns.remove(tagname_original) 457 507 458 return data1 D, extras508 return data1d, extras 459 509 460 510 def _to_xml_doc(self, datainfo): … … 468 518 raise RuntimeError, "The cansas writer expects a Data1D instance" 469 519 470 ns = CANSAS_NS.get(self.cansas Version).get("ns")520 ns = CANSAS_NS.get(self.cansas_version).get("ns") 471 521 doc = xml.dom.minidom.Document() 472 522 main_node = doc.createElement("SASroot") 473 main_node.setAttribute("version", self.cansas Version)523 main_node.setAttribute("version", self.cansas_version) 474 524 main_node.setAttribute("xmlns", ns) 475 525 main_node.setAttribute("xmlns:xsi", … … 502 552 write_node(doc, pt, "I", datainfo.y[i], 503 553 {'unit': datainfo.y_unit}) 504 if datainfo.dy != None and len(datainfo.dy) > =i:554 if datainfo.dy != None and len(datainfo.dy) > i: 505 555 write_node(doc, pt, "Idev", datainfo.dy[i], 506 556 {'unit': datainfo.y_unit}) 507 if datainfo.dx != None and len(datainfo.dx) > =i:557 if datainfo.dx != None and len(datainfo.dx) > i: 508 558 write_node(doc, pt, "Qdev", datainfo.dx[i], 509 559 {'unit': datainfo.x_unit}) 510 if datainfo.dxw != None and len(datainfo.dxw) > =i:560 if datainfo.dxw != None and len(datainfo.dxw) > i: 511 561 write_node(doc, pt, "dQw", datainfo.dxw[i], 512 562 {'unit': datainfo.x_unit}) 513 if datainfo.dxl != None and len(datainfo.dxl) > =i:563 if datainfo.dxl != None and len(datainfo.dxl) > i: 514 564 write_node(doc, pt, "dQl", datainfo.dxl[i], 515 565 {'unit': datainfo.x_unit}) 516 566 517 567 # Transmission Spectrum Info 518 if len(datainfo.trans_spectrum.wavelength) > 0: 568 for i in range(len(datainfo.trans_spectrum)): 569 spectrum = datainfo.trans_spectrum[i] 519 570 node = doc.createElement("SAStransmission_spectrum") 520 571 entry_node.appendChild(node) 521 for i in range(len( datainfo.trans_spectrum.wavelength)):572 for i in range(len(spectrum.wavelength)): 522 573 pt = doc.createElement("Tdata") 523 574 node.appendChild(pt) 524 write_node(doc, pt, "Lambda", datainfo.trans_spectrum.wavelength[i], 525 {'unit': datainfo.trans_spectrum.wavelength_unit}) 526 write_node(doc, pt, "T", datainfo.trans_spectrum.transmission[i], 527 {'unit': datainfo.trans_spectrum.transmission_unit}) 528 if datainfo.trans_spectrum.transmission_deviation != None \ 529 and len(datainfo.trans_spectrum.transmission_deviation) >= i: 530 write_node(doc, pt, "Tdev", datainfo.trans_spectrum.transmission_deviation[i], 531 {'unit': datainfo.trans_spectrum.transmission_deviation_unit}) 575 write_node(doc, pt, "Lambda", spectrum.wavelength[i], 576 {'unit': spectrum.wavelength_unit}) 577 write_node(doc, pt, "T", spectrum.transmission[i], 578 {'unit': spectrum.transmission_unit}) 579 if spectrum.transmission_deviation != None \ 580 and len(spectrum.transmission_deviation) >= i: 581 write_node(doc, pt, "Tdev", \ 582 spectrum.transmission_deviation[i], \ 583 {'unit': spectrum.transmission_deviation_unit}) 532 584 533 585 # Sample info -
src/sans/dataloader/readers/xml_reader.py
r17a25d4 r76cd1ae 17 17 18 18 class XMLreader(): 19 20 xml = None 21 xmldoc = None 22 xmlroot = None 23 schema = None 24 schemadoc = None 19 25 20 26 def __init__(self, xml = None, schema = None, root = None): … … 47 53 self.xmlroot = self.xmldoc.getroot() 48 54 except Exception: 49 ##!TODO: raise exception if no xml is passed to this function 50 print "No xml file was found!" 55 self.xml = None 56 self.xmldoc = None 57 self.xmlroot = None 51 58 52 59 def setSchema(self, schema): … … 55 62 self.schemadoc = etree.parse(self.schema, parser = parser) 56 63 except Exception: 57 ##!TODO: raise exception if no schema is passed to this function58 print "No schema file was found!"64 self.schema = None 65 self.schemadoc = None 59 66 60 67 def validateXML(self): -
src/sans/guiframe/gui_manager.py
r1c1b037 r76cd1ae 2485 2485 info="error")) 2486 2486 raise ValueError, msg 2487 text = data.__str__() 2487 ## text = str(data) 2488 text = data.__str__() 2488 2489 text += 'Data Min Max:\n' 2489 2490 text += 'X_min = %s: X_max = %s\n'% (xmin, max(data.x)) … … 2494 2495 x_st = "X" 2495 2496 for index in range(len(data.x)): 2496 if data.dy != None :2497 if data.dy != None and len(data.dy) > index: 2497 2498 dy_val = data.dy[index] 2498 2499 else: 2499 2500 dy_val = 0.0 2500 if data.dx != None :2501 if data.dx != None and len(data.dx) > index: 2501 2502 dx_val = data.dx[index] 2502 2503 else: 2503 2504 dx_val = 0.0 2504 if data.dxl != None :2505 if data.dxl != None and len(data.dxl) > index: 2505 2506 if index == 0: 2506 2507 x_st = "Xl" 2507 2508 dx_val = data.dxl[index] 2508 elif data.dxw != None :2509 elif data.dxw != None and len(data.dxw) > index: 2509 2510 if index == 0: 2510 2511 x_st = "Xw" -
test/sansdataloader/test/utest_cansas.py
r3f484b0 r76cd1ae 38 38 self.isis_1_1 = "ISIS_1_1.xml" 39 39 self.isis_1_1_notrans = "ISIS_1_1_notrans.xml" 40 self.isis_1_1_doubletrans = "ISIS_1_1_doubletrans.xml" 40 41 self.schema_1_0 = "cansas1d_v1_0.xsd" 41 42 self.schema_1_1 = "cansas1d_v1_1.xsd" … … 77 78 self.assertFalse(valid) 78 79 80 81 def _check_data(self, data): 82 self.assertTrue(data.title == "TK49 c10_SANS") 83 self.assertTrue(data.x.size == 138) 84 self.assertTrue(len(data.meta_data) == 2) 85 self.assertTrue(data.detector[0].distance_unit == "mm") 86 self.assertTrue(data.detector[1].distance_unit == "mm") 87 self.assertTrue(data.detector[0].name == "HAB") 88 self.assertTrue(data.detector[1].name == "main-detector-bank") 89 self.assertTrue(data.detector[0].distance == 575.0) 90 self.assertTrue(data.detector[1].distance == 4145.02) 91 spectrum = data.trans_spectrum[0] 92 self.assertTrue(len(spectrum.wavelength) == 138) 93 self.assertTrue(data.process[0].name == "Mantid generated CanSAS1D XML") 94 79 95 80 96 def test_cansas_xml(self): … … 83 99 valid = xmlreader.validateXML() 84 100 self.assertTrue(valid) 85 reader = Reader()86 dataloader = reader .read(self.isis_1_1)87 for data in dataloader:88 self.assertTrue(data.title == "TK49 c10_SANS")89 self.assertTrue(data.x.size == 138)90 self. assertTrue(len(data.meta_data) == 2)91 self. assertTrue(data.detector[0].distance_unit == "mm")92 reader .write(filename, data)101 reader_generic = Loader() 102 dataloader = reader_generic.load(self.isis_1_1) 103 reader_cansas = Reader() 104 cansasreader = reader_cansas.read(self.isis_1_1) 105 for i in range(len(dataloader)): 106 self._check_data(dataloader[i]) 107 self._check_data(cansasreader[i]) 108 reader_generic.save(filename, dataloader[i], None) 93 109 reader2 = Reader() 94 110 return_data = reader2.read(filename) 95 111 data_new = return_data 96 self.data = return_data[0] 97 self.assertTrue(self.data.x.size == 138) 98 self.assertTrue(len(self.data.meta_data) == 2) 99 self.assertTrue(self.data.detector[0].distance_unit == "mm") 100 self.assertTrue(self.data.title == "TK49 c10_SANS") 112 written_data = return_data[0] 113 self._check_data(written_data) 114 115 116 def test_double_trans_spectra(self): 117 xmlreader = XMLreader(self.isis_1_1_doubletrans, self.schema_1_1) 118 self.assertTrue(xmlreader.validateXML()) 119 reader = Loader() 120 data = reader.load(self.isis_1_1_doubletrans) 121 for item in data: 122 self._check_data(item) 123 101 124 102 125 def test_entry_name_recurse(self):
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