[1e62361] | 1 | """ |
---|
| 2 | Handling of P(r) inversion states |
---|
| 3 | """ |
---|
[7116b6e0] | 4 | ################################################################################ |
---|
| 5 | #This software was developed by the University of Tennessee as part of the |
---|
| 6 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
---|
| 7 | #project funded by the US National Science Foundation. |
---|
| 8 | # |
---|
| 9 | #See the license text in license.txt |
---|
| 10 | # |
---|
| 11 | #copyright 2009, University of Tennessee |
---|
| 12 | ################################################################################ |
---|
| 13 | |
---|
[6f1f129] | 14 | |
---|
[3e41f43] | 15 | import time |
---|
| 16 | import os |
---|
| 17 | import sys |
---|
[91128648] | 18 | import logging |
---|
[b1f7ec6] | 19 | from lxml import etree |
---|
[a07e72f] | 20 | from sans.guiframe.dataFitting import Data1D |
---|
[d80f7e1] | 21 | from sans.dataloader.readers.cansas_reader import Reader as CansasReader |
---|
| 22 | from sans.dataloader.readers.cansas_reader import get_content |
---|
[91128648] | 23 | |
---|
| 24 | PRNODE_NAME = 'pr_inversion' |
---|
[b1f7ec6] | 25 | CANSAS_NS = "cansas1d/1.0" |
---|
[6f1f129] | 26 | |
---|
[80d2872] | 27 | # Translation of names between stored and object data |
---|
[6f1f129] | 28 | ## List of P(r) inversion inputs |
---|
[7116b6e0] | 29 | in_list = [["nterms", "nfunc"], |
---|
[80d2872] | 30 | ["d_max", "d_max"], |
---|
| 31 | ["alpha", "alpha"], |
---|
| 32 | ["slit_width", "width"], |
---|
| 33 | ["slit_height", "height"], |
---|
| 34 | ["qmin", "qmin"], |
---|
| 35 | ["qmax", "qmax"]] |
---|
[6f1f129] | 36 | |
---|
| 37 | ## List of P(r) inversion outputs |
---|
[7116b6e0] | 38 | out_list = [["elapsed", "elapsed"], |
---|
[80d2872] | 39 | ["rg", "rg"], |
---|
| 40 | ["iq0", "iq0"], |
---|
| 41 | ["bck", "bck"], |
---|
| 42 | ["chi2", "chi2"], |
---|
| 43 | ["osc", "osc"], |
---|
| 44 | ["pos", "pos"], |
---|
| 45 | ["pos_err", "pos_err"], |
---|
| 46 | ["alpha_estimate", "alpha_estimate"], |
---|
| 47 | ["nterms_estimate", "nterms_estimate"]] |
---|
[6f1f129] | 48 | |
---|
| 49 | class InversionState(object): |
---|
| 50 | """ |
---|
[7116b6e0] | 51 | Class to hold the state information of the InversionControl panel. |
---|
[6f1f129] | 52 | """ |
---|
| 53 | def __init__(self): |
---|
| 54 | """ |
---|
[7116b6e0] | 55 | Default values |
---|
[6f1f129] | 56 | """ |
---|
| 57 | # Input |
---|
| 58 | self.file = None |
---|
| 59 | self.estimate_bck = False |
---|
| 60 | self.timestamp = time.time() |
---|
| 61 | |
---|
| 62 | # Inversion parameters |
---|
| 63 | self.nfunc = None |
---|
| 64 | self.d_max = None |
---|
| 65 | self.alpha = None |
---|
| 66 | |
---|
| 67 | # Slit parameters |
---|
| 68 | self.height = None |
---|
| 69 | self.width = None |
---|
| 70 | |
---|
| 71 | # Q range |
---|
| 72 | self.qmin = None |
---|
| 73 | self.qmax = None |
---|
| 74 | |
---|
| 75 | # Outputs |
---|
| 76 | self.elapsed = None |
---|
| 77 | self.rg = None |
---|
| 78 | self.iq0 = None |
---|
| 79 | self.bck = None |
---|
| 80 | self.chi2 = None |
---|
| 81 | self.osc = None |
---|
| 82 | self.pos = None |
---|
| 83 | self.pos_err = None |
---|
| 84 | |
---|
| 85 | # Estimates |
---|
| 86 | self.alpha_estimate = None |
---|
| 87 | self.nterms_estimate = None |
---|
| 88 | |
---|
| 89 | # Data |
---|
| 90 | self.q = None |
---|
| 91 | self.iq_obs = None |
---|
| 92 | self.iq_calc = None |
---|
[410aad8] | 93 | |
---|
| 94 | # Coefficients |
---|
| 95 | self.coefficients = None |
---|
| 96 | self.covariance = None |
---|
[6f1f129] | 97 | |
---|
| 98 | def __str__(self): |
---|
| 99 | """ |
---|
[7116b6e0] | 100 | Pretty print |
---|
| 101 | |
---|
| 102 | :return: string representing the state |
---|
| 103 | |
---|
[6f1f129] | 104 | """ |
---|
| 105 | state = "File: %s\n" % self.file |
---|
| 106 | state += "Timestamp: %s\n" % self.timestamp |
---|
| 107 | state += "Estimate bck: %s\n" % str(self.estimate_bck) |
---|
| 108 | state += "No. terms: %s\n" % str(self.nfunc) |
---|
| 109 | state += "D_max: %s\n" % str(self.d_max) |
---|
| 110 | state += "Alpha: %s\n" % str(self.alpha) |
---|
| 111 | |
---|
| 112 | state += "Slit height: %s\n" % str(self.height) |
---|
| 113 | state += "Slit width: %s\n" % str(self.width) |
---|
| 114 | |
---|
| 115 | state += "Qmin: %s\n" % str(self.qmin) |
---|
| 116 | state += "Qmax: %s\n" % str(self.qmax) |
---|
| 117 | |
---|
| 118 | state += "\nEstimates:\n" |
---|
| 119 | state += " Alpha: %s\n" % str(self.alpha_estimate) |
---|
| 120 | state += " Nterms: %s\n" % str(self.nterms_estimate) |
---|
| 121 | |
---|
| 122 | state += "\nOutputs:\n" |
---|
| 123 | state += " Elapsed: %s\n" % str(self.elapsed) |
---|
| 124 | state += " Rg: %s\n" % str(self.rg) |
---|
| 125 | state += " I(q=0): %s\n" % str(self.iq0) |
---|
| 126 | state += " Bck: %s\n" % str(self.bck) |
---|
| 127 | state += " Chi^2: %s\n" % str(self.chi2) |
---|
| 128 | state += " Oscillation:%s\n" % str(self.osc) |
---|
| 129 | state += " Positive: %s\n" % str(self.pos) |
---|
| 130 | state += " 1-sigma pos:%s\n" % str(self.pos_err) |
---|
| 131 | |
---|
| 132 | return state |
---|
| 133 | |
---|
[91128648] | 134 | def toXML(self, file="pr_state.prv", doc=None, entry_node=None): |
---|
[6f1f129] | 135 | """ |
---|
[7116b6e0] | 136 | Writes the state of the InversionControl panel to file, as XML. |
---|
| 137 | |
---|
| 138 | Compatible with standalone writing, or appending to an |
---|
| 139 | already existing XML document. In that case, the XML document |
---|
[3e41f43] | 140 | is required. An optional entry node in the XML document |
---|
| 141 | may also be given. |
---|
[7116b6e0] | 142 | |
---|
| 143 | :param file: file to write to |
---|
| 144 | :param doc: XML document object [optional] |
---|
| 145 | :param entry_node: XML node within the XML document at which |
---|
| 146 | we will append the data [optional] |
---|
| 147 | |
---|
[6f1f129] | 148 | """ |
---|
| 149 | from xml.dom.minidom import getDOMImplementation |
---|
| 150 | |
---|
[91128648] | 151 | # Check whether we have to write a standalone XML file |
---|
| 152 | if doc is None: |
---|
| 153 | impl = getDOMImplementation() |
---|
[6f1f129] | 154 | |
---|
[91128648] | 155 | doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0") |
---|
[6f1f129] | 156 | |
---|
[91128648] | 157 | newdoc = impl.createDocument(None, PRNODE_NAME, doc_type) |
---|
| 158 | top_element = newdoc.documentElement |
---|
| 159 | else: |
---|
| 160 | # We are appending to an existing document |
---|
| 161 | newdoc = doc |
---|
| 162 | top_element = newdoc.createElement(PRNODE_NAME) |
---|
| 163 | if entry_node is None: |
---|
| 164 | newdoc.documentElement.appendChild(top_element) |
---|
| 165 | else: |
---|
| 166 | entry_node.appendChild(top_element) |
---|
| 167 | |
---|
[6f1f129] | 168 | attr = newdoc.createAttribute("version") |
---|
| 169 | attr.nodeValue = '1.0' |
---|
| 170 | top_element.setAttributeNode(attr) |
---|
| 171 | |
---|
| 172 | # File name |
---|
[410aad8] | 173 | element = newdoc.createElement("filename") |
---|
[91128648] | 174 | if self.file is not None: |
---|
| 175 | element.appendChild(newdoc.createTextNode(str(self.file))) |
---|
[410aad8] | 176 | else: |
---|
| 177 | element.appendChild(newdoc.createTextNode(str(file))) |
---|
| 178 | top_element.appendChild(element) |
---|
[6f1f129] | 179 | |
---|
| 180 | element = newdoc.createElement("timestamp") |
---|
| 181 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
---|
| 182 | attr = newdoc.createAttribute("epoch") |
---|
| 183 | attr.nodeValue = str(self.timestamp) |
---|
| 184 | element.setAttributeNode(attr) |
---|
| 185 | top_element.appendChild(element) |
---|
| 186 | |
---|
| 187 | # Inputs |
---|
| 188 | inputs = newdoc.createElement("inputs") |
---|
| 189 | top_element.appendChild(inputs) |
---|
| 190 | |
---|
| 191 | for item in in_list: |
---|
| 192 | element = newdoc.createElement(item[0]) |
---|
[3e41f43] | 193 | cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))" |
---|
| 194 | exec cmd % item[1] |
---|
[6f1f129] | 195 | inputs.appendChild(element) |
---|
| 196 | |
---|
| 197 | # Outputs |
---|
| 198 | outputs = newdoc.createElement("outputs") |
---|
| 199 | top_element.appendChild(outputs) |
---|
| 200 | |
---|
| 201 | for item in out_list: |
---|
| 202 | element = newdoc.createElement(item[0]) |
---|
[3e41f43] | 203 | cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))" |
---|
| 204 | exec cmd % item[1] |
---|
[6f1f129] | 205 | outputs.appendChild(element) |
---|
| 206 | |
---|
[410aad8] | 207 | # Save output coefficients and its covariance matrix |
---|
| 208 | element = newdoc.createElement("coefficients") |
---|
| 209 | element.appendChild(newdoc.createTextNode(str(self.coefficients))) |
---|
| 210 | outputs.appendChild(element) |
---|
| 211 | element = newdoc.createElement("covariance") |
---|
| 212 | element.appendChild(newdoc.createTextNode(str(self.covariance))) |
---|
| 213 | outputs.appendChild(element) |
---|
| 214 | |
---|
[6f1f129] | 215 | # Save the file |
---|
[91128648] | 216 | if doc is None: |
---|
| 217 | fd = open(file, 'w') |
---|
| 218 | fd.write(newdoc.toprettyxml()) |
---|
| 219 | fd.close() |
---|
| 220 | return None |
---|
| 221 | else: |
---|
| 222 | return newdoc.toprettyxml() |
---|
[6f1f129] | 223 | |
---|
[91128648] | 224 | def fromXML(self, file=None, node=None): |
---|
[6f1f129] | 225 | """ |
---|
[7116b6e0] | 226 | Load a P(r) inversion state from a file |
---|
| 227 | |
---|
| 228 | :param file: .prv file |
---|
| 229 | :param node: node of a XML document to read from |
---|
| 230 | |
---|
[6f1f129] | 231 | """ |
---|
[91128648] | 232 | if file is not None: |
---|
[3e41f43] | 233 | msg = "InversionState no longer supports non-CanSAS" |
---|
| 234 | msg += " format for P(r) files" |
---|
| 235 | raise RuntimeError, msg |
---|
[91128648] | 236 | |
---|
[3e41f43] | 237 | if node.get('version') and node.get('version') == '1.0': |
---|
[b1f7ec6] | 238 | |
---|
| 239 | # Get file name |
---|
| 240 | entry = get_content('ns:filename', node) |
---|
| 241 | if entry is not None: |
---|
| 242 | self.file = entry.text.strip() |
---|
| 243 | |
---|
| 244 | # Get time stamp |
---|
| 245 | entry = get_content('ns:timestamp', node) |
---|
| 246 | if entry is not None and entry.get('epoch'): |
---|
| 247 | try: |
---|
| 248 | self.timestamp = float(entry.get('epoch')) |
---|
| 249 | except: |
---|
[3e41f43] | 250 | msg = "InversionState.fromXML: Could not read " |
---|
| 251 | msg += "timestamp\n %s" % sys.exc_value |
---|
| 252 | logging.error(msg) |
---|
[b1f7ec6] | 253 | |
---|
| 254 | # Parse inversion inputs |
---|
| 255 | entry = get_content('ns:inputs', node) |
---|
| 256 | if entry is not None: |
---|
| 257 | for item in in_list: |
---|
| 258 | input_field = get_content('ns:%s' % item[0], entry) |
---|
| 259 | if input_field is not None: |
---|
| 260 | try: |
---|
[3e41f43] | 261 | cmd = 'self.%s = float(input_field.text.strip())' |
---|
| 262 | exec cmd % item[1] |
---|
[b1f7ec6] | 263 | except: |
---|
[80d2872] | 264 | exec 'self.%s = None' % item[1] |
---|
[b1f7ec6] | 265 | input_field = get_content('ns:estimate_bck', entry) |
---|
| 266 | if input_field is not None: |
---|
| 267 | try: |
---|
| 268 | self.estimate_bck = input_field.text.strip()=='True' |
---|
| 269 | except: |
---|
| 270 | self.estimate_bck = False |
---|
[6f1f129] | 271 | |
---|
[b1f7ec6] | 272 | # Parse inversion outputs |
---|
| 273 | entry = get_content('ns:outputs', node) |
---|
| 274 | if entry is not None: |
---|
| 275 | # Output parameters (scalars) |
---|
| 276 | for item in out_list: |
---|
| 277 | input_field = get_content('ns:%s' % item[0], entry) |
---|
| 278 | if input_field is not None: |
---|
| 279 | try: |
---|
[3e41f43] | 280 | cmd = 'self.%s = float(input_field.text.strip())' |
---|
| 281 | exec cmd % item[1] |
---|
[b1f7ec6] | 282 | except: |
---|
[80d2872] | 283 | exec 'self.%s = None' % item[1] |
---|
[b1f7ec6] | 284 | |
---|
| 285 | # Look for coefficients |
---|
| 286 | # Format is [value, value, value, value] |
---|
| 287 | coeff = get_content('ns:coefficients', entry) |
---|
| 288 | if coeff is not None: |
---|
| 289 | # Remove brackets |
---|
| 290 | c_values = coeff.text.strip().replace('[','') |
---|
| 291 | c_values = c_values.replace(']','') |
---|
| 292 | toks = c_values.split() |
---|
| 293 | self.coefficients = [] |
---|
| 294 | for c in toks: |
---|
| 295 | try: |
---|
| 296 | self.coefficients.append(float(c)) |
---|
| 297 | except: |
---|
| 298 | # Bad data, skip. We will count the number of |
---|
| 299 | # coefficients at the very end and deal with |
---|
| 300 | # inconsistencies then. |
---|
| 301 | pass |
---|
| 302 | # Sanity check |
---|
| 303 | if not len(self.coefficients) == self.nfunc: |
---|
[3e41f43] | 304 | # Inconsistent number of coefficients. |
---|
| 305 | # Don't keep the data. |
---|
| 306 | err_msg = "InversionState.fromXML: inconsistant " |
---|
| 307 | err_msg += "number of coefficients: " |
---|
| 308 | err_msg += "%d %d" % (len(self.coefficients), |
---|
| 309 | self.nfunc) |
---|
[b1f7ec6] | 310 | logging.error(err_msg) |
---|
| 311 | self.coefficients = None |
---|
| 312 | |
---|
| 313 | # Look for covariance matrix |
---|
| 314 | # Format is [ [value, value], [value, value] ] |
---|
| 315 | coeff = get_content('ns:covariance', entry) |
---|
| 316 | if coeff is not None: |
---|
| 317 | # Parse rows |
---|
| 318 | rows = coeff.text.strip().split('[') |
---|
| 319 | self.covariance = [] |
---|
| 320 | for row in rows: |
---|
| 321 | row = row.strip() |
---|
| 322 | if len(row) == 0: continue |
---|
| 323 | # Remove end bracket |
---|
| 324 | row = row.replace(']','') |
---|
| 325 | c_values = row.split() |
---|
| 326 | cov_row = [] |
---|
| 327 | for c in c_values: |
---|
| 328 | try: |
---|
| 329 | cov_row.append(float(c)) |
---|
| 330 | except: |
---|
| 331 | # Bad data, skip. We will count the number of |
---|
| 332 | # coefficients at the very end and deal with |
---|
| 333 | # inconsistencies then. |
---|
| 334 | pass |
---|
| 335 | # Sanity check: check the number of entries in the row |
---|
| 336 | if len(cov_row) == self.nfunc: |
---|
| 337 | self.covariance.append(cov_row) |
---|
| 338 | # Sanity check: check the number of rows in the covariance |
---|
| 339 | # matrix |
---|
| 340 | if not len(self.covariance) == self.nfunc: |
---|
| 341 | # Inconsistent dimensions of the covariance matrix. |
---|
| 342 | # Don't keep the data. |
---|
[3e41f43] | 343 | err_msg = "InversionState.fromXML: " |
---|
| 344 | err_msg += "inconsistant dimensions of the " |
---|
| 345 | err_msg += " covariance matrix: " |
---|
[b1f7ec6] | 346 | err_msg += "%d %d" % (len(self.covariance), self.nfunc) |
---|
| 347 | logging.error(err_msg) |
---|
| 348 | self.covariance = None |
---|
| 349 | |
---|
[91128648] | 350 | class Reader(CansasReader): |
---|
[6f1f129] | 351 | """ |
---|
[7116b6e0] | 352 | Class to load a .prv P(r) inversion file |
---|
[6f1f129] | 353 | """ |
---|
| 354 | ## File type |
---|
| 355 | type_name = "P(r)" |
---|
| 356 | |
---|
| 357 | ## Wildcards |
---|
[b35d3d1] | 358 | type = ["P(r) files (*.prv)|*.prv", |
---|
| 359 | "SANSView files (*.svs)|*.svs"] |
---|
[6f1f129] | 360 | ## List of allowed extensions |
---|
[3e41f43] | 361 | ext = ['.prv', '.PRV', '.svs', '.SVS'] |
---|
[6f1f129] | 362 | |
---|
[0d88a09] | 363 | def __init__(self, call_back, cansas=True): |
---|
[6f1f129] | 364 | """ |
---|
[7116b6e0] | 365 | Initialize the call-back method to be called |
---|
| 366 | after we load a file |
---|
| 367 | |
---|
| 368 | :param call_back: call-back method |
---|
| 369 | :param cansas: True = files will be written/read in CanSAS format |
---|
| 370 | False = write CanSAS format |
---|
[91128648] | 371 | |
---|
[6f1f129] | 372 | """ |
---|
[91128648] | 373 | ## Call back method to be executed after a file is read |
---|
[6f1f129] | 374 | self.call_back = call_back |
---|
[91128648] | 375 | ## CanSAS format flag |
---|
| 376 | self.cansas = cansas |
---|
[75fbd17] | 377 | self.state = None |
---|
[6f1f129] | 378 | |
---|
| 379 | def read(self, path): |
---|
| 380 | """ |
---|
[7116b6e0] | 381 | Load a new P(r) inversion state from file |
---|
| 382 | |
---|
| 383 | :param path: file path |
---|
| 384 | |
---|
| 385 | :return: None |
---|
| 386 | |
---|
[6f1f129] | 387 | """ |
---|
[91128648] | 388 | if self.cansas==True: |
---|
| 389 | return self._read_cansas(path) |
---|
| 390 | else: |
---|
| 391 | return self._read_standalone(path) |
---|
| 392 | |
---|
| 393 | def _read_standalone(self, path): |
---|
| 394 | """ |
---|
[7116b6e0] | 395 | Load a new P(r) inversion state from file. |
---|
| 396 | The P(r) node is assumed to be the top element. |
---|
| 397 | |
---|
| 398 | :param path: file path |
---|
| 399 | |
---|
| 400 | :return: None |
---|
| 401 | |
---|
[91128648] | 402 | """ |
---|
[6f1f129] | 403 | # Read the new state from file |
---|
| 404 | state = InversionState() |
---|
[91128648] | 405 | state.fromXML(file=path) |
---|
[6f1f129] | 406 | |
---|
| 407 | # Call back to post the new state |
---|
[75fbd17] | 408 | self.state = state |
---|
| 409 | #self.call_back(state) |
---|
[6f1f129] | 410 | return None |
---|
[91128648] | 411 | |
---|
| 412 | def _parse_prstate(self, entry): |
---|
| 413 | """ |
---|
[7116b6e0] | 414 | Read a p(r) inversion result from an XML node |
---|
| 415 | |
---|
| 416 | :param entry: XML node to read from |
---|
| 417 | |
---|
| 418 | :return: InversionState object |
---|
| 419 | |
---|
[91128648] | 420 | """ |
---|
[b35d3d1] | 421 | state = None |
---|
[91128648] | 422 | |
---|
| 423 | # Locate the P(r) node |
---|
| 424 | try: |
---|
[3e41f43] | 425 | nodes = entry.xpath('ns:%s' % PRNODE_NAME, |
---|
| 426 | namespaces={'ns': CANSAS_NS}) |
---|
[b35d3d1] | 427 | if nodes !=[]: |
---|
| 428 | # Create an empty state |
---|
| 429 | state = InversionState() |
---|
| 430 | state.fromXML(node=nodes[0]) |
---|
[91128648] | 431 | except: |
---|
[3e41f43] | 432 | msg = "XML document does not contain P(r) " |
---|
| 433 | msg += "information.\n %s" % sys.exc_value |
---|
| 434 | logging.info(msg) |
---|
[91128648] | 435 | |
---|
| 436 | return state |
---|
| 437 | |
---|
| 438 | def _read_cansas(self, path): |
---|
| 439 | """ |
---|
[7116b6e0] | 440 | Load data and P(r) information from a CanSAS XML file. |
---|
| 441 | |
---|
| 442 | :param path: file path |
---|
| 443 | |
---|
| 444 | :return: Data1D object if a single SASentry was found, |
---|
| 445 | or a list of Data1D objects if multiple entries were found, |
---|
| 446 | or None of nothing was found |
---|
| 447 | |
---|
| 448 | :raise RuntimeError: when the file can't be opened |
---|
| 449 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
| 450 | |
---|
[91128648] | 451 | """ |
---|
| 452 | output = [] |
---|
| 453 | |
---|
| 454 | if os.path.isfile(path): |
---|
| 455 | basename = os.path.basename(path) |
---|
| 456 | root, extension = os.path.splitext(basename) |
---|
[410aad8] | 457 | #TODO: eventually remove the check for .xml once |
---|
| 458 | # the P(r) writer/reader is truly complete. |
---|
[3e41f43] | 459 | if extension.lower() in self.ext or extension.lower() == '.xml': |
---|
[91128648] | 460 | |
---|
[b1f7ec6] | 461 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
[91128648] | 462 | # Check the format version number |
---|
[3e41f43] | 463 | # Specifying the namespace will take care of the file |
---|
| 464 | #format version |
---|
[b1f7ec6] | 465 | root = tree.getroot() |
---|
[91128648] | 466 | |
---|
[3e41f43] | 467 | entry_list = root.xpath('/ns:SASroot/ns:SASentry', |
---|
| 468 | namespaces={'ns': CANSAS_NS}) |
---|
[b1f7ec6] | 469 | |
---|
[91128648] | 470 | for entry in entry_list: |
---|
| 471 | sas_entry = self._parse_entry(entry) |
---|
| 472 | prstate = self._parse_prstate(entry) |
---|
[b35d3d1] | 473 | #prstate could be None when .svs file is loaded |
---|
| 474 | #in this case, skip appending to output |
---|
| 475 | if prstate != None: |
---|
| 476 | sas_entry.meta_data['prstate'] = prstate |
---|
| 477 | sas_entry.filename = prstate.file |
---|
| 478 | output.append(sas_entry) |
---|
[91128648] | 479 | else: |
---|
| 480 | raise RuntimeError, "%s is not a file" % path |
---|
| 481 | |
---|
| 482 | # Return output consistent with the loader's api |
---|
[3e41f43] | 483 | if len(output) == 0: |
---|
[91128648] | 484 | return None |
---|
[3e41f43] | 485 | elif len(output) == 1: |
---|
[410aad8] | 486 | # Call back to post the new state |
---|
[229da98] | 487 | self.call_back(output[0].meta_data['prstate'], datainfo = output[0]) |
---|
| 488 | #self.state = output[0].meta_data['prstate'] |
---|
[91128648] | 489 | return output[0] |
---|
| 490 | else: |
---|
| 491 | return output |
---|
| 492 | |
---|
| 493 | |
---|
| 494 | def write(self, filename, datainfo=None, prstate=None): |
---|
| 495 | """ |
---|
[7116b6e0] | 496 | Write the content of a Data1D as a CanSAS XML file |
---|
| 497 | |
---|
| 498 | :param filename: name of the file to write |
---|
| 499 | :param datainfo: Data1D object |
---|
| 500 | :param prstate: InversionState object |
---|
| 501 | |
---|
[91128648] | 502 | """ |
---|
| 503 | # Sanity check |
---|
| 504 | if self.cansas == True: |
---|
[b35d3d1] | 505 | doc =self.write_toXML(datainfo, prstate) |
---|
[91128648] | 506 | # Write the XML document |
---|
| 507 | fd = open(filename, 'w') |
---|
| 508 | fd.write(doc.toprettyxml()) |
---|
| 509 | fd.close() |
---|
| 510 | else: |
---|
| 511 | prstate.toXML(file=filename) |
---|
| 512 | |
---|
[b35d3d1] | 513 | def write_toXML(self, datainfo=None, state=None): |
---|
| 514 | """ |
---|
| 515 | Write toXML, a helper for write() |
---|
| 516 | |
---|
| 517 | : return: xml doc |
---|
| 518 | """ |
---|
| 519 | if datainfo is None: |
---|
[a07e72f] | 520 | datainfo = Data1D(x=[], y=[]) |
---|
| 521 | elif not issubclass(datainfo.__class__, Data1D): |
---|
[3e41f43] | 522 | msg = "The cansas writer expects a Data1D " |
---|
| 523 | msg += "instance: %s" % str(datainfo.__class__.__name__) |
---|
| 524 | raise RuntimeError, msg |
---|
[91128648] | 525 | |
---|
[b35d3d1] | 526 | # Create basic XML document |
---|
| 527 | doc, sasentry = self._to_xml_doc(datainfo) |
---|
| 528 | |
---|
| 529 | # Add the invariant information to the XML document |
---|
| 530 | if state is not None: |
---|
| 531 | state.toXML(doc=doc, entry_node=sasentry) |
---|
| 532 | |
---|
| 533 | return doc |
---|
[91128648] | 534 | |
---|