Changeset b1f7ec6 in sasview for prview/perspectives/pr
- Timestamp:
- Sep 10, 2009 8:39:01 PM (15 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:
- 72f719b
- Parents:
- aeb3c20
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
prview/perspectives/pr/inversion_state.py
r0d88a09 rb1f7ec6 8 8 copyright 2009, University of Tennessee 9 9 """ 10 import time, os 10 import time, os, sys 11 11 import logging 12 12 import DataLoader 13 from xml.dom.minidom import parse 14 from lxml import etree 15 13 16 from DataLoader.readers.cansas_reader import Reader as CansasReader 17 from DataLoader.readers.cansas_reader import get_content 14 18 15 19 PRNODE_NAME = 'pr_inversion' 20 CANSAS_NS = "cansas1d/1.0" 16 21 17 22 ## List of P(r) inversion inputs … … 213 218 """ 214 219 if file is not None: 215 # Check whether the file is valid 216 if not os.path.isfile(file): 217 raise RuntimeError, "P(r) reader: cannot open %s" % file 218 219 from xml.dom.minidom import parse 220 doc = parse(file) 221 node = doc.documentElement 222 223 if node.tagName == PRNODE_NAME: 224 if node.hasAttribute('version')\ 225 and node.getAttribute('version') == '1.0': 220 raise RuntimeError, "InversionState no longer supports non-CanSAS format for P(r) files" 221 222 if node.get('version')\ 223 and node.get('version') == '1.0': 224 225 # Get file name 226 entry = get_content('ns:filename', node) 227 if entry is not None: 228 self.file = entry.text.strip() 229 230 # Get time stamp 231 entry = get_content('ns:timestamp', node) 232 if entry is not None and entry.get('epoch'): 233 try: 234 self.timestamp = float(entry.get('epoch')) 235 except: 236 logging.error("InversionState.fromXML: Could not read timestamp\n %s" % sys.exc_value) 237 238 # Parse inversion inputs 239 entry = get_content('ns:inputs', node) 240 if entry is not None: 241 for item in in_list: 242 input_field = get_content('ns:%s' % item[0], entry) 243 if input_field is not None: 244 try: 245 exec '%s = float(input_field.text.strip())' % item[1] 246 except: 247 exec '%s = None' % item[1] 248 input_field = get_content('ns:estimate_bck', entry) 249 if input_field is not None: 250 try: 251 self.estimate_bck = input_field.text.strip()=='True' 252 except: 253 self.estimate_bck = False 254 255 # Parse inversion outputs 256 entry = get_content('ns:outputs', node) 257 if entry is not None: 258 # Output parameters (scalars) 259 for item in out_list: 260 input_field = get_content('ns:%s' % item[0], entry) 261 if input_field is not None: 262 try: 263 exec '%s = float(input_field.text.strip())' % item[1] 264 except: 265 exec '%s = None' % item[1] 266 267 # Look for coefficients 268 # Format is [value, value, value, value] 269 coeff = get_content('ns:coefficients', entry) 270 if coeff is not None: 271 # Remove brackets 272 c_values = coeff.text.strip().replace('[','') 273 c_values = c_values.replace(']','') 274 toks = c_values.split() 275 self.coefficients = [] 276 for c in toks: 277 try: 278 self.coefficients.append(float(c)) 279 except: 280 # Bad data, skip. We will count the number of 281 # coefficients at the very end and deal with 282 # inconsistencies then. 283 pass 284 # Sanity check 285 if not len(self.coefficients) == self.nfunc: 286 # Inconsistent number of coefficients. Don't keep the data. 287 err_msg = "InversionState.fromXML: inconsistant number of coefficients: " 288 err_msg += "%d %d" % (len(self.coefficients), self.nfunc) 289 logging.error(err_msg) 290 self.coefficients = None 226 291 227 if node.hasChildNodes(): 228 for node in node.childNodes: 229 if node.nodeName == 'filename': 230 if node.hasChildNodes(): 231 self.file = node.childNodes[0].nodeValue.strip() 232 elif node.nodeName == 'timestamp': 233 if node.hasAttribute('epoch'): 234 try: 235 self.timestamp = float(node.getAttribute('epoch')) 236 except: 237 # Could not read timestamp: pass 238 pass 239 240 # Parse inversion inputs 241 elif node.nodeName == 'inputs': 242 if node.hasChildNodes(): 243 for item in node.childNodes: 244 for out in in_list: 245 if item.nodeName == out[0]: 246 try: 247 exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1] 248 except: 249 exec '%s = None' % out[1] 250 elif item.nodeName == 'estimate_bck': 251 try: 252 self.estimate_bck = item.childNodes[0].nodeValue.strip()=='True' 253 except: 254 self.estimate_bck = False 255 256 # Parse inversion outputs 257 elif node.nodeName == 'outputs': 258 if node.hasChildNodes(): 259 for item in node.childNodes: 260 # Look for standard outputs 261 for out in out_list: 262 if item.nodeName == out[0]: 263 try: 264 exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1] 265 except: 266 exec '%s = None' % out[1] 267 268 # Look for coefficients 269 # Format is [value, value, value, value] 270 if item.nodeName == 'coefficients': 271 # Remove brackets 272 c_values = item.childNodes[0].nodeValue.strip().replace('[','') 273 c_values = c_values.replace(']','') 274 toks = c_values.split() 275 self.coefficients = [] 276 for c in toks: 277 try: 278 self.coefficients.append(float(c)) 279 except: 280 # Bad data, skip. We will count the number of 281 # coefficients at the very end and deal with 282 # inconsistencies then. 283 pass 284 # Sanity check 285 if not len(self.coefficients) == self.nfunc: 286 # Inconsistent number of coefficients. Don't keep the data. 287 err_msg = "InversionState.fromXML: inconsistant number of coefficients: " 288 err_msg += "%d %d" % (len(self.coefficients), self.nfunc) 289 logging.error(err_msg) 290 self.coefficients = None 291 292 # Look for covariance matrix 293 # Format is [ [value, value], [value, value] ] 294 elif item.nodeName == "covariance": 295 # Parse rows 296 rows = item.childNodes[0].nodeValue.strip().split('[') 297 self.covariance = [] 298 for row in rows: 299 row = row.strip() 300 if len(row) == 0: continue 301 # Remove end bracket 302 row = row.replace(']','') 303 c_values = row.split() 304 cov_row = [] 305 for c in c_values: 306 try: 307 cov_row.append(float(c)) 308 except: 309 # Bad data, skip. We will count the number of 310 # coefficients at the very end and deal with 311 # inconsistencies then. 312 pass 313 # Sanity check: check the number of entries in the row 314 if len(cov_row) == self.nfunc: 315 self.covariance.append(cov_row) 316 # Sanity check: check the number of rows in the covariance 317 # matrix 318 if not len(self.covariance) == self.nfunc: 319 # Inconsistent dimensions of the covariance matrix. 320 # Don't keep the data. 321 err_msg = "InversionState.fromXML: inconsistant dimensions of the covariance matrix: " 322 err_msg += "%d %d" % (len(self.covariance), self.nfunc) 323 logging.error(err_msg) 324 self.covariance = None 325 else: 326 raise RuntimeError, "Unsupported P(r) file version" 327 328 292 # Look for covariance matrix 293 # Format is [ [value, value], [value, value] ] 294 coeff = get_content('ns:covariance', entry) 295 if coeff is not None: 296 # Parse rows 297 rows = coeff.text.strip().split('[') 298 self.covariance = [] 299 for row in rows: 300 row = row.strip() 301 if len(row) == 0: continue 302 # Remove end bracket 303 row = row.replace(']','') 304 c_values = row.split() 305 cov_row = [] 306 for c in c_values: 307 try: 308 cov_row.append(float(c)) 309 except: 310 # Bad data, skip. We will count the number of 311 # coefficients at the very end and deal with 312 # inconsistencies then. 313 pass 314 # Sanity check: check the number of entries in the row 315 if len(cov_row) == self.nfunc: 316 self.covariance.append(cov_row) 317 # Sanity check: check the number of rows in the covariance 318 # matrix 319 if not len(self.covariance) == self.nfunc: 320 # Inconsistent dimensions of the covariance matrix. 321 # Don't keep the data. 322 err_msg = "InversionState.fromXML: inconsistant dimensions of the covariance matrix: " 323 err_msg += "%d %d" % (len(self.covariance), self.nfunc) 324 logging.error(err_msg) 325 self.covariance = None 326 329 327 class Reader(CansasReader): 330 328 """ … … 387 385 @return: InversionState object 388 386 """ 389 from xml import xpath390 391 387 # Create an empty state 392 388 state = InversionState() … … 394 390 # Locate the P(r) node 395 391 try: 396 nodes = xpath.Evaluate(PRNODE_NAME, entry)392 nodes = entry.xpath('ns:%s' % PRNODE_NAME, namespaces={'ns': CANSAS_NS}) 397 393 state.fromXML(node=nodes[0]) 398 394 except: 399 #raise RuntimeError, "%s is not a file with P(r) information." % path 400 logging.info("XML document does not contain P(r) information.") 401 import sys 402 print sys.exc_value 395 logging.info("XML document does not contain P(r) information.\n %s" % sys.exc_value) 403 396 404 397 return state … … 415 408 @raise ValueError: when the length of the data vectors are inconsistent 416 409 """ 417 from xml.dom.minidom import parse418 from xml import xpath419 410 output = [] 420 411 … … 427 418 extension.lower() == '.xml': 428 419 429 dom = parse(path) 420 tree = etree.parse(path, parser=etree.ETCompatXMLParser()) 421 # Check the format version number 422 # Specifying the namespace will take care of the file format version 423 root = tree.getroot() 430 424 431 # Format 1: check whether we have a CanSAS file 432 nodes = xpath.Evaluate('SASroot', dom) 433 # Check the format version number 434 if nodes[0].hasAttributes(): 435 for i in range(nodes[0].attributes.length): 436 if nodes[0].attributes.item(i).nodeName=='version': 437 if nodes[0].attributes.item(i).nodeValue != self.version: 438 raise ValueError, "cansas_reader: unrecognized version number %s" % \ 439 nodes[0].attributes.item(i).nodeValue 440 441 entry_list = xpath.Evaluate('SASroot/SASentry', dom) 425 entry_list = root.xpath('/ns:SASroot/ns:SASentry', namespaces={'ns': CANSAS_NS}) 426 442 427 for entry in entry_list: 443 428 sas_entry = self._parse_entry(entry) … … 490 475 prstate.toXML(file=filename) 491 476 492 493 if __name__ == "__main__": 494 #TODO: turn all this into unit tests 495 496 state = InversionState() 497 #print state.fromXML('../../test/pr_state.prv') 498 print state.fromXML('../../test/test.prv') 499 print state 500 state.toXML('test_copy.prv') 501 502 from DataLoader.loader import Loader 503 l = Loader() 504 datainfo = l.load("../../test/cansas1d.xml") 505 506 def call_back(state, datainfo=None): 507 print state 508 509 reader = Reader(call_back) 510 reader.cansas = False 511 reader.write("test_copy_from_reader.prv", prstate=state) 512 reader.cansas = True 513 reader.write("testout.prv", datainfo, state) 514 reader.write("testout_wo_datainfo.prv", prstate=state) 515 516 # Now try to load things back 517 reader.cansas = False 518 #print reader.read("test_copy_from_reader.prv") 519 reader.cansas = True 520 #data = reader.read("testout.prv") 521 data = reader.read("testout_wo_datainfo.prv") 522 print data 523 print data.meta_data['prstate'] 524 525 477 478
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