Source code for PyMca5.PyMcaGui.pymca.StackSimpleFitWindow

#/*##########################################################################
# Copyright (C) 2004-2014 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
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# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
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__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import sys
import os
import traceback
import time
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5 import PyMcaDirs
from PyMca5.PyMcaGui import SimpleFitGui
from PyMca5.PyMcaGui import IconDict
from PyMca5.PyMcaMath.fitting import StackSimpleFit
from PyMca5.PyMcaIO import ArraySave
from PyMca5.PyMcaGui import CalculationThread
safe_str = qt.safe_str

[docs]class OutputParameters(qt.QWidget): def __init__(self, parent=None): qt.QWidget.__init__(self, parent) self.mainLayout = qt.QGridLayout(self) self.mainLayout.setContentsMargins(2, 2, 2, 2) self.mainLayout.setSpacing(2) self.outputDirLabel = qt.QLabel(self) self.outputDirLabel.setText("Output directory") self.outputDirLine = qt.QLineEdit(self) self.outputDirLine.setReadOnly(True) self.outputDirButton = qt.QPushButton(self) self.outputDirButton.setText("Browse") self.outputFileLabel = qt.QLabel(self) self.outputFileLabel.setText("Output file root") self.outputFileLine = qt.QLineEdit(self) self.outputFileLine.setReadOnly(True) self.outputDir = PyMcaDirs.outputDir self.outputFile = "StackSimpleFitOutput" self.setOutputDirectory(self.outputDir) self.setOutputFileBaseName(self.outputFile) self.mainLayout.addWidget(self.outputDirLabel, 0, 0) self.mainLayout.addWidget(self.outputDirLine, 0, 1) self.mainLayout.addWidget(self.outputDirButton, 0, 2) self.mainLayout.addWidget(self.outputFileLabel, 1, 0) self.mainLayout.addWidget(self.outputFileLine, 1, 1) self.outputDirButton.clicked[()].connect(self.browseDirectory)
[docs] def getOutputDirectory(self): return safe_str(self.outputDirLine.text())
[docs] def getOutputFileBaseName(self): return safe_str(self.outputFileLine.text())
[docs] def setOutputDirectory(self, txt): if os.path.exists(txt): self.outputDirLine.setText(txt) self.outputDir = txt PyMcaDirs.outputDir = txt else: raise IOError("Directory does not exists")
[docs] def setOutputFileBaseName(self, txt): if len(txt): self.outputFileLine.setText(txt) self.outputFile = txt
[docs] def browseDirectory(self): wdir = self.outputDir outputDir = qt.QFileDialog.getExistingDirectory(self, "Please select output directory", wdir) if len(outputDir): self.setOutputDirectory(safe_str(outputDir))
[docs]class StackSimpleFitWindow(qt.QWidget): def __init__(self, parent=None): qt.QWidget.__init__(self, parent) self.setWindowTitle('Stack Fit Window') self.setWindowIcon(qt.QIcon(qt.QPixmap(IconDict['gioconda16']))) self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setContentsMargins(2, 2, 2, 2) self.mainLayout.setSpacing(2) self.fitSetupWindow = SimpleFitGui.SimpleFitGui(self) self.fitSetupWindow.fitActions.dismissButton.hide() self.mainLayout.addWidget(self.fitSetupWindow) self.fitInstance = self.fitSetupWindow.fitModule self.stackFitInstance = StackSimpleFit.StackSimpleFit(fit=self.fitInstance) self.__mask = None self.importFunctions = self.fitSetupWindow.importFunctions self.outputParameters = OutputParameters(self) self.mainLayout.addWidget(self.outputParameters) self.startButton = qt.QPushButton(self) self.startButton.setText("FitStack") self.mainLayout.addWidget(self.startButton) self.startButton.clicked[()].connect(self.startStackFit) #progress handling self._total = 100 self._index = 0 self.stackFitInstance.setProgressCallback(self.progressBarUpdate) self.progressBar = qt.QProgressBar(self) self.mainLayout.addWidget(self.progressBar) #def setSpectrum(self, x, y, sigma=None, xmin=None, xmax=None):
[docs] def setSpectrum(self, *var, **kw): self.fitSetupWindow.setData(*var, **kw)
[docs] def setData(self, x, stack, data_index=-1, mask=None): self.stack_x = x self.stack_y = stack self.__mask = mask if hasattr(stack, "data") and\ hasattr(stack, "info"): data = stack.data else: data = stack if data_index < 0: data_index = range(len(data.shape))[data_index] self.data_index = data_index
[docs] def setMask(self, mask): self.__mask = mask
[docs] def processStack(self): self.stackFitInstance.processStack(mask=self.__mask)
[docs] def startStackFit(self): xmin = self.fitInstance._fitConfiguration['fit']['xmin'] xmax = self.fitInstance._fitConfiguration['fit']['xmax'] self.stackFitInstance.setOutputDirectory(self.outputParameters.getOutputDirectory()) self.stackFitInstance.setOutputFileBaseName(self.outputParameters.getOutputFileBaseName()) self.stackFitInstance.setData(self.stack_x, self.stack_y, sigma=None, xmin=xmin, xmax=xmax) self.stackFitInstance.setDataIndex(self.data_index) #check filenames fileNames = self.stackFitInstance.getOutputFileNames() deleteFiles = None for key in fileNames.keys(): fileName = fileNames[key] if os.path.exists(fileName): msg = qt.QMessageBox() msg.setWindowTitle("Output file(s) exists") msg.setIcon(qt.QMessageBox.Information) msg.setText("Do you want to delete current output files?") msg.setStandardButtons(qt.QMessageBox.Yes|qt.QMessageBox.No) answer=msg.exec_() if answer == qt.QMessageBox.Yes: deleteFiles = True else: deleteFiles = False break if deleteFiles == False: #nothing to be done (yet) return if deleteFiles: try: for key in fileNames.keys(): fileName = fileNames[key] if os.path.exists(fileName): os.remove(fileName) except: qt.QMessageBox.critical(self, "Delete Error", "ERROR while deleting file:\n%s"% fileName, qt.QMessageBox.Ok, qt.QMessageBox.NoButton, qt.QMessageBox.NoButton) return try: self._startWork() except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setWindowTitle("Stack Fitting Error") msg.setText("Error has occured while processing the data") msg.setInformativeText(safe_str(sys.exc_info()[1])) msg.setDetailedText(traceback.format_exc()) msg.exec_() finally: self.progressBar.hide() self.setEnabled(True)
def _startWork(self): self.setEnabled(False) self.progressBar.show() thread = CalculationThread.CalculationThread(parent=self, calculation_method=self.processStack) thread.start() self._total = 100 self._index = 0 while thread.isRunning(): time.sleep(2) qApp = qt.QApplication.instance() qApp.processEvents() self.progressBar.setMaximum(self._total) self.progressBar.setValue(self._index) self.progressBar.hide() self.setEnabled(True) if thread.result is not None: if len(thread.result): raise Exception(*thread.result[1:])
[docs] def progressBarUpdate(self, idx, total): self._index = int(idx) self._total = int(total) if idx % 10 == 0: print("Fited %d of %d" % (idx, total))
[docs] def threadFinished(self): self.setEnabled(True)
if __name__ == "__main__": import numpy from PyMca5.PyMcaMath.fitting import SpecfitFuns from PyMca5.PyMcaMath.fitting import SimpleFitUserEstimatedFunctions as Functions x = numpy.arange(1000.) data = numpy.zeros((50, 1000), numpy.float) #the peaks to be fitted p0 = [100., 300., 50., 200., 500., 30., 300., 800., 65] #generate the data to be fitted for i in range(data.shape[0]): nPeaks = 3 - i % 3 data[i,:] = SpecfitFuns.gauss(p0[:3*nPeaks],x) #the spectrum for setup y = data.sum(axis=0) oldShape = data.shape data.shape = 1,oldShape[0], oldShape[1] app = qt.QApplication([]) w = StackSimpleFitWindow() w.setSpectrum(x, y) w.setData(x, data) #w.importFunctions(Functions.__file__) #w.fitModule.setFitFunction('Gaussians') w.show() app.exec_()