diff options
Diffstat (limited to 'PyMca5/PyMcaPhysics/xrf/FisxHelper.py')
| -rw-r--r-- | PyMca5/PyMcaPhysics/xrf/FisxHelper.py | 208 |
1 files changed, 114 insertions, 94 deletions
diff --git a/PyMca5/PyMcaPhysics/xrf/FisxHelper.py b/PyMca5/PyMcaPhysics/xrf/FisxHelper.py index e2b1af3..7f986aa 100644 --- a/PyMca5/PyMcaPhysics/xrf/FisxHelper.py +++ b/PyMca5/PyMcaPhysics/xrf/FisxHelper.py @@ -31,15 +31,18 @@ __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import os -import sys -import time +import logging from fisx import DataDir from fisx import Elements as FisxElements from fisx import Material from fisx import Detector from fisx import XRF +import time +import sys xcom = None -DEBUG = 0 + +_logger = logging.getLogger(__name__) + def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None): if dataDir is None: @@ -48,7 +51,7 @@ def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None): from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as pymcaDataDir from PyMca5 import getDataFile except: - print("Using fisx shell constants and ratios") + _logger.info("Using fisx shell constants and ratios") pymcaDataDir = None if bindingEnergies is None: if pymcaDataDir is None: @@ -60,11 +63,9 @@ def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None): xcomFile = os.path.join(dataDir, "XCOM_CrossSections.dat") else: xcomFile = getDataFile("XCOM_CrossSections.dat") - if DEBUG: - t0 = time.time() + t0 = time.time() instance = FisxElements(dataDir, bindingEnergies, xcomFile) - if DEBUG: - print("Shell constants") + _logger.debug("Shell constants") # the files should be taken from PyMca to make sure the same data are used for key in ["K", "L", "M"]: @@ -73,18 +74,15 @@ def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None): # we have to make sure we have got a string if hasattr(fname, "decode"): fname = fname.decode("latin-1") - if DEBUG: - print("Before %s" % fname) + _logger.debug("Before %s", fname) if pymcaDataDir is not None: fname = getDataFile(key + "ShellConstants.dat") else: fname = os.path.join(os.path.dirname(fname), key + "ShellConstants.dat") instance.setShellConstantsFile(key, fname) - if DEBUG: - print("After %s" % instance.getShellConstantsFile(key)) - if DEBUG: - print("Radiative transitions") + _logger.debug("After %s", instance.getShellConstantsFile(key)) + _logger.debug("Radiative transitions") for key in ["K", "L", "M"]: fname = instance.getShellRadiativeTransitionsFile(key) @@ -92,18 +90,15 @@ def getElementsInstance(dataDir=None, bindingEnergies=None, xcomFile=None): # we have to make sure we have got a string ... if hasattr(fname, "decode"): fname = fname.decode("latin-1") - if DEBUG: - print("Before %s" % fname) + _logger.debug("Before %s", fname) if pymcaDataDir is not None: fname = getDataFile(key + "ShellRates.dat") else: fname = os.path.join(os.path.dirname(fname), key + "ShellRates.dat") instance.setShellRadiativeTransitionsFile(key, fname) - if DEBUG: - print("After %s " % instance.getShellRadiativeTransitionsFile(key)) + _logger.debug("After %s ", instance.getShellRadiativeTransitionsFile(key)) - if DEBUG: - print("Reading Elapsed = ", time.time() - t0) + _logger.debug("Reading Elapsed = %s", time.time() - t0) return instance def getMultilayerFluorescence(multilayerSample, @@ -122,42 +117,42 @@ def getMultilayerFluorescence(multilayerSample, elementsFromMatrix=False, secondary=None, materials=None, - secondaryCalculationLimit=None): + secondaryCalculationLimit=None, + cache=1): if secondary is None: secondary=0 if secondaryCalculationLimit is None: secondaryCalculationLimit=0.0 + if cache: + cache = 1 + else: + cache = 0 - if DEBUG: - print("Library actually using secondary = ", secondary) - print("Library using secondary limit = ", secondaryCalculationLimit) + _logger.info("Library requested to use secondary = %s", secondary) + _logger.info("Library requested to use secondary limit = %s", secondaryCalculationLimit) + _logger.info("Library requested to use cache = %d", cache) global xcom if xcom is None: - if DEBUG: - print("Getting fisx elements instance") + _logger.debug("Getting fisx elements instance") xcom = getElementsInstance() if materials is not None: - if DEBUG: - print("Deleting materials") + _logger.debug("Deleting materials") xcom.removeMaterials() for material in materials: - if DEBUG: - print("Adding material making sure no duplicates") + _logger.debug("Adding material making sure no duplicates") xcom.addMaterial(material, errorOnReplace=1) # the instance - if DEBUG: - print("creating XRF instance") + _logger.debug("creating XRF instance") xrf = XRF() # the beam energies if not len(energyList): raise ValueError("Empty list of beam energies!!!") - if DEBUG: - print("setting beam") + _logger.debug("setting beam") xrf.setBeam(energyList, weights=weightList, characteristic=flagList) # the beam filters (if any) @@ -172,8 +167,7 @@ def getMultilayerFluorescence(multilayerSample, Unless you know what you are doing, the funny factors must be 1.0 """ - if DEBUG: - print("setting beamFilters") + _logger.debug("setting beamFilters") xrf.setBeamFilters(beamFilters) # the sample description @@ -186,20 +180,17 @@ def getMultilayerFluorescence(multilayerSample, Unless you know what you are doing, the funny factors must be 1.0 """ - if DEBUG: - print("setting sample") + _logger.debug("setting sample") xrf.setSample(multilayerSample) # the attenuators if attenuatorList is not None: if len(attenuatorList) > 0: - if DEBUG: - print("setting attenuators") + _logger.debug("setting attenuators") xrf.setAttenuators(attenuatorList) # the geometry - if DEBUG: - print("setting Geometry") + _logger.debug("setting Geometry") if alphaIn is None: alphaIn = 45 if alphaOut is None: @@ -207,8 +198,7 @@ def getMultilayerFluorescence(multilayerSample, xrf.setGeometry(alphaIn, alphaOut) # the detector - if DEBUG: - print("setting Detector") + _logger.debug("setting Detector") if detector is not None: # Detector can be a list as [material, density, thickness] # or a Detector instance @@ -259,38 +249,61 @@ def getMultilayerFluorescence(multilayerSample, if elementsFromMatrix: elementsList = matrixElementsList - # enabling the cascade cache gets a (miserable) 15 % speed up - if DEBUG: - print("Using cascade cache") - t0 = time.time() + t0 = time.time() + if cache: + # enabling the cascade cache gets a (miserable) 15 % speed up + _logger.debug("FisxHelper Using cache") + else: + _logger.debug("FisxHelper Not using cache") treatedElements = [] emittedLines = [] + for actualElement in actualElementsList: + element = actualElement.split()[0] + if element not in treatedElements: + if cache: + lines = xcom.getEmittedXRayLines(element) + sampleEnergies = [lines[key] for key in lines] + for e in sampleEnergies: + if e not in emittedLines: + emittedLines.append(e) + treatedElements.append(element) + for layer in multilayerSample: composition = xcom.getComposition(layer[0]) for element in composition.keys(): - xcom.setElementCascadeCacheEnabled(element, 1) - if hasattr(xcom, "updateCache"): - if element not in treatedElements: + if element not in treatedElements: + if cache: lines = xcom.getEmittedXRayLines(element) sampleEnergies = [lines[key] for key in lines] for e in sampleEnergies: if e not in emittedLines: emittedLines.append(e) + treatedElements.append(element) + + if attenuatorList is not None: + for layer in attenuatorList: + composition = xcom.getComposition(layer[0]) + for element in composition.keys(): + if element not in treatedElements: + if cache: + lines = xcom.getEmittedXRayLines(element) + sampleEnergies = [lines[key] for key in lines] + for e in sampleEnergies: + if e not in emittedLines: + emittedLines.append(e) treatedElements.append(element) if hasattr(xcom, "updateCache"): - if DEBUG: - print("Filling atenuation cache") composition = detectorInstance.getComposition(xcom) for element in composition.keys(): - xcom.setElementCascadeCacheEnabled(element, 1) if element not in treatedElements: - lines = xcom.getEmittedXRayLines(element) - sampleEnergies = [lines[key] for key in lines] - for e in sampleEnergies: - if e not in emittedLines: - emittedLines.append(e) + if cache: + lines = xcom.getEmittedXRayLines(element) + sampleEnergies = [lines[key] for key in lines] + for e in sampleEnergies: + if e not in emittedLines: + emittedLines.append(e) treatedElements.append(element) for element in actualElementsList: @@ -300,28 +313,40 @@ def getMultilayerFluorescence(multilayerSample, for element in treatedElements: # this limit seems overestimated but still reasonable if xcom.getCacheSize(element) > 5000: - print("Clearing cache") + _logger.info("Clearing cache for %s" % element) xcom.clearCache(element) - xcom.updateCache(element, energyList) - xcom.updateCache(element, emittedLines) - xcom.setCacheEnabled(element, 1) - if DEBUG: - print("Element %s cache size = %d" % (element, xcom.getCacheSize(element))) - + if cache: + _logger.info("Updating cache for %s" % element) + xcom.updateCache(element, energyList) + xcom.updateCache(element, emittedLines) + else: + # should I clear the cache to be sure? + # for the time being, yes. + _logger.info("No cache. Clearing cache for %s" % element) + xcom.clearCache(element) + xcom.setCacheEnabled(element, cache) + _logger.info("Element %s cache size = %d", + element, xcom.getCacheSize(element)) for element in actualElementsList: - xcom.setElementCascadeCacheEnabled(element.split()[0], 1) + xcom.setElementCascadeCacheEnabled(element.split()[0], cache) if hasattr(xcom, "updateEscapeCache") and \ hasattr(xcom, "setEscapeCacheEnabled"): if detector is not None: for element in actualElementsList: - lines = xcom.getEmittedXRayLines(element.split()[0]) - lines_energy = [lines[key] for key in lines] - for e in lines_energy: - if e not in emittedLines: - emittedLines.append(e) - xcom.setEscapeCacheEnabled(1) - xcom.updateEscapeCache(detectorInstance.getComposition(xcom), + if cache: + lines = xcom.getEmittedXRayLines(element.split()[0]) + lines_energy = [lines[key] for key in lines] + for e in lines_energy: + if e not in emittedLines: + emittedLines.append(e) + if not cache: + if hasattr(xcom, "clearEscapeCache"): + # the method is there but nor wrapped yet + xcom.clearEscapeCache() + xcom.setEscapeCacheEnabled(cache) + if cache: + xcom.updateEscapeCache(detectorInstance.getComposition(xcom), emittedLines, energyThreshold=detectorInstance.getEscapePeakEnergyThreshold(), \ intensityThreshold=detectorInstance.getEscapePeakIntensityThreshold(), \ @@ -329,23 +354,19 @@ def getMultilayerFluorescence(multilayerSample, alphaIn=detectorInstance.getEscapePeakAlphaIn(), thickness=0) # No escape by the back considered yet else: - if DEBUG: - print("NOT CALLING UPDATE CACHE") - if DEBUG: - print("C++ elapsed filling cache = ", time.time() - t0) + _logger.debug("NOT CALLING UPDATE CACHE") + _logger.info("C++ elapsed filling cache = %s", + time.time() - t0) - if DEBUG: - print("Calling getMultilayerFluorescence") - t0 = time.time() + _logger.debug("Calling getMultilayerFluorescence") + t0 = time.time() expectedFluorescence = xrf.getMultilayerFluorescence(actualElementsList, xcom, secondary=secondary, useGeometricEfficiency=useGeometricEfficiency, useMassFractions=elementsFromMatrix, secondaryCalculationLimit=secondaryCalculationLimit) - if DEBUG: - print("C++ elapsed TWO = ", time.time() - t0) - + _logger.info("C++ elapsed TWO = %s", time.time() - t0) if not elementsFromMatrix: # If one element was present in one layer and not on others, PyMca only # calculated contributions from the layers in which the element was @@ -417,7 +438,8 @@ def _getFisxMaterials(fitConfiguration): if fractionList[n] > 0.0: composition[compoundList[n]] = fractionList[n] else: - print("ignoring ", compoundList[n], "fraction = ", fractionList[n]) + _logger.info("ignoring %s, fraction = %s", + compoundList[n], fractionList[n]) # check the composition is expressed in terms of elements # and not in terms of other undefined materials totallyDefined = True @@ -457,7 +479,7 @@ def _getFisxMaterials(fitConfiguration): txt += "contains <%s> (defined as <%s>), " % (compound, compound + " ") else: txt += "contains <%s> (undefined)," % compound - print(txt) + _logger.info(txt) raise KeyError(txt) return fisxMaterials @@ -570,7 +592,8 @@ def _getFisxDetector(fitConfiguration, attenuatorsDetector=None): else: # make sure information is consistent if attenuatorsDetector[0] not in [detectorMaterial, detectorMaterial+"1"]: - print("%s not equal to %s" % (attenuatorsDetector[0], detectorMaterial)) + _logger.warning("%s not equal to %s", + attenuatorsDetector[0], detectorMaterial) msg = "Inconsistent detector material between DETECTOR and ATTENUATORS tab" msg += "\n%s not equal to %s" % (attenuatorsDetector[0], detectorMaterial) raise ValueError(msg) @@ -595,8 +618,7 @@ def _getSecondaryCalculationLimitFromFitConfiguration(fitConfiguration): limit = float(\ fitConfiguration["concentrations"]["secondarycalculationlimit"]) except: - if DEBUG: - print("Exception. Forcing no limit") + _logger.debug("Exception. Forcing no limit") limit = 0.0 return limit @@ -651,7 +673,7 @@ def _fisxFromFitConfigurationAction(fitConfiguration, try: secondary = fitConfiguration["concentrations"]["usemultilayersecondary"] except: - print("Exception. Forcing tertiary") + _logger.warning("Exception. Forcing tertiary") secondary = 2 if action.upper() == "FLUORESCENCE": @@ -761,7 +783,7 @@ def getFisxCorrectionFactors(*var, **kw): secondOrder = ddict[element][family][layerKey]["counts"][1] if firstOrder <= 0: if secondOrder > 0.0: - print("Inconsistency? secondary with no primary?") + _logger.warning("Inconsistency? secondary with no primary?") ddict[element][family][layerKey]["correction_factor"][1] = 1 if nItems == 3: ddict[element][family][layerKey]["correction_factor"][2] = 1 @@ -787,9 +809,7 @@ def getFisxCorrectionFactorsFromFitConfigurationFile(fileName, secondaryCalculationLimit) if __name__ == "__main__": - DEBUG = 1 - import time - import sys + _logger.setLevel(logging.DEBUG) if len(sys.argv) < 2: print("Usage: python FisxHelper FitConfigurationFile [element] [matrix_flag]") sys.exit(0) |