diff options
Diffstat (limited to 'PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py')
| -rw-r--r-- | PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py | 72 |
1 files changed, 32 insertions, 40 deletions
diff --git a/PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py b/PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py index f91f083..0b88c9e 100644 --- a/PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py +++ b/PyMca5/PyMcaPhysics/xrf/FastXRFLinearFit.py @@ -35,6 +35,7 @@ Module to perform a fast linear fit on a stack of fluorescence spectra. """ import os import numpy +import logging from PyMca5.PyMcaMath.linalg import lstsq from . import ClassMcaTheory from PyMca5.PyMcaMath.fitting import Gefit @@ -43,7 +44,8 @@ from PyMca5.PyMcaMath.fitting import SpecfitFuns from PyMca5.PyMcaIO import ConfigDict import time -DEBUG = 0 +_logger = logging.getLogger(__name__) + class FastXRFLinearFit(object): def __init__(self, mcafit=None): @@ -101,15 +103,13 @@ class FastXRFLinearFit(object): if hasattr(y, "info"): if "McaLiveTime" in y.info: livetime = y.info["McaLiveTime"] - if DEBUG: - t0 = time.time() + t0 = time.time() if configuration is not None: self._mcaTheory.setConfiguration(configuration) elif self._config is None: raise ValueError("Fit configuration missing") else: - if DEBUG: - print("Setting default configuration") + _logger.debug("Setting default configuration") self._mcaTheory.setConfiguration(self._config) # read the current configuration # it is a copy, we can modify it at will @@ -164,8 +164,7 @@ class FastXRFLinearFit(object): # background if config['fit']['stripflag']: if config['fit']['stripalgorithm'] == 1: - if DEBUG: - print("SNIP") + _logger.debug("SNIP") else: raise RuntimeError("Please use the faster SNIP background") @@ -335,9 +334,8 @@ class FastXRFLinearFit(object): uncertainties = numpy.zeros((nFree, nRows, nColumns), numpy.float32) #perform the initial fit - if DEBUG: - print("Configuration elapsed = %f" % (time.time() - t0)) - t0 = time.time() + _logger.debug("Configuration elapsed = %f", time.time() - t0) + t0 = time.time() totalSpectra = data.shape[0] * data.shape[1] jStep = min(100, data.shape[1]) if weightPolicy == 2: @@ -397,11 +395,12 @@ class FastXRFLinearFit(object): results[:, i, jStart:jEnd] = parameters uncertainties[:, i, jStart:jEnd] = ddict['uncertainties'] jStart = jEnd - if DEBUG: - t = time.time() - t0 - print("First fit elapsed = %f" % t) - print("Spectra per second = %f" % (data.shape[0]*data.shape[1]/float(t))) - t0 = time.time() + t = time.time() - t0 + _logger.debug("First fit elapsed = %f", t) + if t > 0.: + _logger.debug("Spectra per second = %f", + data.shape[0]*data.shape[1]/float(t)) + t0 = time.time() # cleanup zeros # start with the parameter with the largest amount of negative values @@ -434,7 +433,8 @@ class FastXRFLinearFit(object): i = item[1] badMask = item[2] results[i][badMask] = 0.0 - print("WARNING: %d pixels of parameter %s forced to zero" % (item[0], freeNames[i])) + _logger.warning("WARNING: %d pixels of parameter %s forced to zero", + item[0], freeNames[i]) continue zeroList.sort() zeroList.reverse() @@ -458,12 +458,10 @@ class FastXRFLinearFit(object): for i in badParameters: results[i][badMask] = 0.0 uncertainties[i][badMask] = 0.0 - if DEBUG: - print("WARNING: %d pixels of parameter %s set to zero" % (badMask.sum(), - freeNames[i])) + _logger.debug("WARNING: %d pixels of parameter %s set to zero", + badMask.sum(), freeNames[i]) else: - if DEBUG: - print("Number of secondary fits = %d" % (nFits + 1)) + _logger.debug("Number of secondary fits = %d", nFits + 1) nFits += 1 A = derivatives[:, [i for i in range(nFree) if i not in badParameters]] #assume we'll not have too many spectra @@ -533,9 +531,9 @@ class FastXRFLinearFit(object): uncertainties[i][badMask] = ddict['uncertainties'][idx] idx += 1 - if DEBUG and refit: + if refit: t = time.time() - t0 - print("Fit of negative peaks elapsed = %f" % t) + _logger.debug("Fit of negative peaks elapsed = %f", t) t0 = time.time() outputDict = {'parameters':results, 'uncertainties':uncertainties, 'names':freeNames} @@ -550,8 +548,7 @@ class FastXRFLinearFit(object): fitFirstSpectrum = False if config['concentrations']['usematrix']: - if DEBUG: - print("USING MATRIX") + _logger.debug("USING MATRIX") if config['concentrations']['reference'].upper() == "AUTO": fitFirstSpectrum = True elif autotime: @@ -611,16 +608,14 @@ class FastXRFLinearFit(object): referenceElement = addInfo['ReferenceElement'] referenceTransitions = addInfo['ReferenceTransitions'] - if DEBUG: - print("Reference <%s> transition <%s>" % (referenceElement, referenceTransitions)) + _logger.debug("Reference <%s> transition <%s>", + referenceElement, referenceTransitions) if referenceElement in ["", None, "None"]: - if DEBUG: - print("No reference") + _logger.debug("No reference") counter = 0 for i, group in enumerate(fitresult['result']['groups']): if group.lower().startswith("scatter"): - if DEBUG: - print("skept %s" % group) + _logger.debug("skept %s", group) continue outputDict['names'].append("C(%s)" % group) if counter == 0: @@ -640,8 +635,7 @@ class FastXRFLinearFit(object): fitresult['result'][group]['fitarea']) counter += 1 else: - if DEBUG: - print("With reference") + _logger.debug("With reference") idx = None testGroup = referenceElement+ " " + referenceTransitions.split()[0] for i, group in enumerate(fitresult['result']['groups']): @@ -659,8 +653,7 @@ class FastXRFLinearFit(object): counter = 0 for i, group in enumerate(fitresult['result']['groups']): if group.lower().startswith("scatter"): - if DEBUG: - print("skept %s" % group) + _logger.debug("skept %s", group) continue outputDict['names'].append("C(%s)" % group) goodI = results[nFreeBackgroundParameters+i] > 0 @@ -677,10 +670,8 @@ class FastXRFLinearFit(object): (concentrationsResult[layer]['mass fraction'][group])) counter += 1 outputDict['concentrations'] = massFractions - if DEBUG: - t = time.time() - t0 - print("Calculation of concentrations elapsed = %f" % t) - t0 = time.time() + t = time.time() - t0 + _logger.debug("Calculation of concentrations elapsed = %f", t) #################################################### return outputDict @@ -718,7 +709,8 @@ def getFileListFromPattern(pattern, begin, end, increment=None): return fileList if __name__ == "__main__": - DEBUG = True + logging.basicConfig(level=logging.INFO) + _logger.setLevel(logging.DEBUG) import glob import sys from PyMca5.PyMca import EDFStack |