diffpy.srrietveld.fitrt

28 """FitRT provides the runtime control of refinements. It uses two basic ways 29 to run a refinement, either step by step or finish everything by one call. 30 31 Data member: 32 33 fit -- a diffpy.refinementdata.Refinement object that stores a fit 34 strategy -- a refine strategy to be applied 35 index -- the index to a single fit (if multiple fits are saved 36 together as an array) 37 enginefit -- the engine fit object 38 step -- record the refinement step 39 tempDir -- the working folder 40 workdingDir -- the current working directory 41 """

42 - def __init__(self, job, fit,index=None):

43 """ Initialization. 44 45 job -- the job this fitrt belonged to 46 fit -- a diffpy.refinementdata.Refinement object that stores a fit 47 index -- the index to a single fit (if multiple fits are saved 48 together as an array) 49 """ 50 self.fit = fit 51 self.job = job 52 53 self.index = index 54 55 self.enginefit = None 56 self.step = 0 57 # temp working directory 58 self.tempDir = None 59 # main working directory 60 self.workingDir = os.getcwd() 61 # the strategy may be enabled temporarily even when the global variable 62 # is false 63 self.isStrategyEnabled = GLOBALS.isStrategyEnabled 64 65 return

66

67 - def __setStrategy(self, isStrategyEnabled):

68 '''Set the strategy based on the global settings''' 69 if isStrategyEnabled: 70 self.strategy = copy.deepcopy(self.fit.getPyObj("Strategy")) 71 else: 72 self.strategy = self.fit.getOneStepStrategy() 73 74 return

75

76 - def run(self, isStrategyEnabled = False, continuous=True):

77 """Run the refinement according to its strategy. 78 79 isStrategyEnabled -- if the strategy is enabled 80 81 continuous -- run the whole refinement continuously or not 82 83 return: True if the refinement finished. False if not. 84 """ 85 86 87 self.isStrategyEnabled = isStrategyEnabled 88 89 # Prepare 90 if self.prepare(): 91 # FIXME: if fit is built from a exp/pcr file, dry run should be skipped 92 try: 93 os.chdir(self.tempDir) 94 # fix all parameters 95 self.enginefit.fixAll() 96 self.enginefit.refine(cycle=5, srtype="l", 97 mode="refine", signature=["dry", '.']) 98 99 except (FPError, GSASError), e: 100 self.fit.setStatus(Refinement.ERROR, self.index) 101 self.enginefit = None 102 self.tempDir = None 103 os.chdir(self.workingDir) 104 self.clean() 105 UTILS.printWarning(e.message) 106 # in this case, do not go on. 107 return True 108 109 GLOBALS.project.updateFit(self) 110 if not continuous: 111 return False 112 113 else: 114 self.fit.setStatus(Refinement.ERROR, self.index) 115 self.enginefit = None 116 self.tempDir = None 117 os.chdir(self.workingDir) 118 self.clean() 119 # in this case, do not go on. 120 return True 121 122 # Run the strategy 123 self.__setStrategy(isStrategyEnabled) 124 125 while self.step < len(self.strategy): 126 127 try: 128 # when refine diverges, 129 self.refineSingleStep() 130 except (FPError, GSASError), e: 131 self.fit.setStatus(Refinement.ERROR, self.index) 132 self.enginefit = None 133 self.tempDir = None 134 os.chdir(self.workingDir) 135 self.clean() 136 return True 137 138 GLOBALS.project.updateFit(self) 139 self.step += 1 140 141 if not continuous: 142 break 143 144 # Not finish yet 145 if self.step < len(self.strategy): 146 147 os.chdir(self.workingDir) 148 return False 149 150 self.fit.setStatus(self.fit.FINISHED, self.index) 151 152 os.chdir(self.workingDir) 153 self.clean() 154 155 return True

156 157 #------------------------------------------------------------------------------ 158

159 - def prepare(self):

160 """Prepare the refinement, consisting of three steps: 161 1. Check if the engine fit object is available 162 2. Create temporary folder for running 163 3. Generate the data file 164 165 return: True if it runs sucessfully, otherwise False. 166 """ 167 #NOTE: if tempDir is created, the preparation should have been done already. 168 if self.tempDir: 169 return False 170 171 # A. check if my engine fit is available 172 if self.enginefit is None: 173 self.enginefit = self.fit.owner.exportEngineFit(self.fit, self.index) 174 175 # B. Backup Directory 176 self.tempDir = tempfile.mkdtemp() 177 178 # C. Generate the datafile 179 patterns = self.fit.getObject('Pattern') 180 181 #check the engine type 182 engineName = self.fit.getEngineType() 183 184 # loop through all tbe patterns and dump the files into the temp folder 185 186 for bankid, pattern in enumerate(patterns): 187 188 ds = pattern.get('Instrumentfile') 189 if ds is not None: 190 instFilePath = self.fit.findFileFromDataset(ds, self.index) 191 else: instFilePath = None 192 193 for param in ['Datafile', 'MFIL']: 194 # convert to gsas file 195 ds = pattern.get(param) 196 197 if ds is None: 198 if param == "Datafile": 199 __msg = 'The data file path is not specified. ' 200 UTILS.printWarning(__msg) 201 return False 202 else: 203 continue 204 205 filepath = self.fit.findFileFromDataset(ds, self.index) 206 207 if filepath: 208 # get the file abs path from the rel path stored, and the base 209 # path of the fit object 210 filepath = os.path.abspath( 211 os.path.join(GLOBALS.project.basepath, 212 filepath) 213 ) 214 else: 215 if param == 'Datafile': 216 __msg = 'The data file is not found. ' 217 UTILS.printWarning(__msg) 218 return False 219 else: 220 continue 221 222 dataFile = DataFile(filepath = filepath, engine = engineName) 223 224 filepath = dataFile.prepDataFile(self.tempDir, 225 instFilePath) 226 227 # the data file name may be updated, change the file name 228 # in engine fit 229 engPattern = self.enginefit.Pattern.get(bankid) 230 if hasattr(engPattern, param): 231 engPattern.set( param, os.path.basename(filepath) ) 232 else: 233 if param == "Datafile": 234 __msg = 'The data file path is not set in the engine file. ' 235 UTILS.printWarning(__msg) 236 return False 237 238 return True

239

240 - def clean(self):

241 '''Clean up after each refinement''' 242 from diffpy.srrietveld.gui.srrguiglobals import isDebug 243 if not isDebug: # only remove the tmp directories when not debugging 244 if self.tempDir: 245 from shutil import rmtree 246 from os import path 247 if path.exists(self.tempDir): 248 rmtree(self.tempDir) 249 250 return

251

252 - def prepareFile(self, fid, engineName, bankid = None, instFilePath = None):

253 """Write or move data/instrument files in running/tmp directory 254 255 enginename -- the type of engine, can be either gsas or fullprof 256 fid -- the file id 257 bankid -- the bankid, used to convert the file format 258 instFilePath -- The instrument file path 259 260 return the file name 261 """ 262 from hashlib import sha1 263 #FIXME:The datafile converter does not take bank id other htan 1 so far 264 bankid = 1 265 266 from diffpy.srrietveld.addon.datafile import DataFileConverter as DFC 267 268 fileList = GLOBALS.project.getObject('SourceFileList') 269 270 fileObj = fileList.findFileByID(fid) 271 272 # dump the file content to the tempDir with the file name saved 273 # in fileObj.fileName 274 fileObj.dump(self.tempDir) 275 276 oldPath = os.path.join(self.tempDir, fileObj.fileName) 277 278 # convert the fullprof type file to gsas 279 root, ext = os.path.splitext(fileObj.fileName) 280 if engineName == 'gsas': 281 282 if ext.lower() in [".chi", ".dat", ".txt"]: 283 284 fileName = root + '.gsa' 285 newPath = os.path.join(self.tempDir, fileName) 286 287 #check if the file already exist 288 289 if os.path.isfile(newPath) and \ 290 fileObj.fid == sha1(open(newPath, 'rb').read()).hexdigest(): 291 __message = "A different file with same name exist. " + \ 292 "will be replaced with the new one" 293 print __message 294 295 dfc = DFC(oldPath) 296 # FIXME: only export the first bank? 297 dfc.toGSASFile(oldPath, newPath, bankid) 298 299 300 if engineName == 'fullprof': 301 fileName = root + '.dat' 302 newPath = os.path.join(self.tempDir, fileName) 303 304 if ext.lower() in [".chi", ".gsa", ".gda", "fxye"]: 305 if instFilePath is not None: 306 instFid = sha1(open(instFilePath, 'rb').read()).hexdigest() 307 308 if ext.lower() != '.chi' and fid != instFid: 309 __warningMsg = 'To convert GSAS data file, installation of ' + \ 310 'GSAS is needed and an instrument file is required. ' 311 312 printWarning(__warningMsg) 313 # FIXM: convert gsas data file name to fullprof data file name 314 # search the local directory for EXP files, may implement a 315 # better algrethm 316 dfc = DFC(oldPath, instFilePath) 317 import glob 318 desfile = os.path.join(os.getcwd(), "*.EXP") 319 for fn in glob.glob(desfile): 320 expfilename = fn 321 if expfilename: 322 dfc.toFPFile(oldPath, newPath, bankid, expfilename) 323 elif ext.lower() == '.chi': 324 dfc.toFPFile(oldPath, newPath, bankid) 325 else: 326 __warningMsg = "To convert GSAS data file, GSAS is needed " + \ 327 "to be installed and an instrument file is required." + \ 328 "The gsas data file can not be converted. The refinment may " + \ 329 "not run. " 330 printWarning(__warningMsg) 331 332 if ext.lower() not in [".chi", ".gsa", ".gda", "fxye", '.dat', '.raw']: 333 __warningMsg = 'Data file extension is not recognized. The ' + \ 334 'refinement may not run correctly. ' 335 printWarning(__warningMsg) 336 337 return fileName

338 339

340 - def refineSingleStep(self):

341 """Refine a single step in the strategy list. 342 """ 343 import re 344 345 # Set addlist + currenttuple 346 strategystep = copy.deepcopy(self.strategy[self.step]) 347 method, paramlist = strategystep.items()[0] 348 349 headparam = paramlist[0][0] 350 refmsg = "\nRefinable Parameter = %-10s Over-all Step = %-5s Refine-Type = %-10s\n"% \ 351 (headparam, self.step, method) 352 refmsg += "%-10sNew Variables: \n"% ("") 353 for param in paramlist: 354 # Set constraint 355 fullpath = param[0] 356 formula = param[2] 357 self.setConstraint(fullpath, formula) 358 refmsg += "%-20s%-20s: %-20s\n"% ("", fullpath, formula) 359 print refmsg 360 361 # Refine and Save 362 sig = str(self.step) + "_" + headparam.split(".")[-1] 363 '''Windows directory name can not include following chars: 364 < (less than)> (greater than) : (colon) " (double quote) 365 / (forward slash) \ (backslash) | (vertical bar or pipe) 366 ? (question mark) * (asterisk)''' 367 sig = sig.replace(':','.') 368 fitsummary = self.enginefit.refine(40, srtype = method.lower()[0], 369 mode = "refine", signature=[sig, '.']) 370 371 # Screen Output 372 chi2 = fitsummary.getResidueValue(-1, residname="Chi2") 373 rwp = fitsummary.getResidueValue(-1, residname="Rwp") 374 re = fitsummary.getResidueValue(-1, residname="Re") 375 376 print "%-10s: Chi2 = %-15s Rp = %-15s Rexp = %-15s"% (method, chi2, rwp, re) 377 print ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" 378 379 return

380 381

382 - def setConstraint(self, key, formula):

383 """ Turn on the refinement flag for parameters 384 """ 385 fitname = key.split(".")[0] 386 key = key.replace(fitname+".", "") 387 try: 388 # Set the int value 389 newvalue = int(formula) 390 except: 391 # Set the float value 392 try: 393 newvalue = float(formula) 394 except: 395 self.enginefit.setConstraintByPath(key, formula) 396 return 397 self.enginefit.setByPath(key, newvalue) 398 return

Source Code for Module diffpy.srrietveld.fitrt