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#/*##########################################################################
# Copyright (C) 2004-2015 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:
#
# 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.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__doc__= """
This plugin perform XAS data reduction in the complete stack, using
a previously generated configuration file (XAS plugin in plot window).
It generates secondary stacks corresponding to
- The normalized spectra
- The EXAFS signal
- The Fourier transform of the signal
The user can then perform selections based on those features and
not just on the raw data.
"""
import sys
import os
import logging
import traceback
from PyMca5 import StackPluginBase
from PyMca5.PyMcaGui import CalculationThread
# only EDGE and JUMP are always small enough to be shown ...
from PyMca5.PyMcaGui import StackPluginResultsWindow
from PyMca5.PyMcaGui import StackXASBatchWindow
from PyMca5.PyMcaGui import PyMca_Icons as PyMca_Icons
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5.PyMca import XASStackBatch
_logger = logging.getLogger(__name__)
class XASStackBatchPlugin(StackPluginBase.StackPluginBase):
"""
This plugin perform XAS data reduction of the complete stack, using
a previously generated configuration file (XAS plugin in plot window).
It generates secondary stacks corresponding to
- The normalized spectra
- The EXAFS signal
- The Fourier transform of the signal
The user can then perform selections based on those features and
not just on the raw data.
"""
def __init__(self, stackWindow, **kw):
if _logger.getEffectiveLevel() == logging.DEBUG:
StackPluginBase.pluginBaseLogger.setLevel(logging.DEBUG)
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
self.methodDict = {}
function = self.calculate
info = "Perform XAS Data reduction using a configuration file"
icon = None
self.methodDict["Calculate"] =[function,
info,
icon]
self.__methodKeys = ["Calculate"]
self.configurationWidget = None
self.workerInstance = XASStackBatch.XASStackBatch()
self._widget = None
self.thread = None
def stackUpdated(self):
_logger.debug("StackXASBatchPlugin.stackUpdated() called")
if self._widget is not None:
self._widget.close()
self._widget = None
def selectionMaskUpdated(self):
if self._widget is None:
return
if self._widget.isHidden():
return
mask = self.getStackSelectionMask()
self._widget.setSelectionMask(mask)
def mySlot(self, ddict):
_logger.debug("mySlot %s %s", ddict['event'], ddict.keys())
if ddict['event'] == "selectionMaskChanged":
self.setStackSelectionMask(ddict['current'])
elif ddict['event'] == "addImageClicked":
self.addImage(ddict['image'], ddict['title'])
elif ddict['event'] == "addAllClicked":
for i in range(len(ddict["images"])):
self.addImage(ddict['images'][i], ddict['titles'][i])
elif ddict['event'] == "removeImageClicked":
self.removeImage(ddict['title'])
elif ddict['event'] == "replaceImageClicked":
self.replaceImage(ddict['image'], ddict['title'])
elif ddict['event'] == "resetSelection":
self.setStackSelectionMask(None)
#Methods implemented by the plugin
def getMethods(self):
if self._widget is None:
return [self.__methodKeys[0]]
else:
return self.__methodKeys
def getMethodToolTip(self, name):
return self.methodDict[name][1]
def getMethodPixmap(self, name):
return self.methodDict[name][2]
def applyMethod(self, name):
return self.methodDict[name][0]()
# The specific part
def calculate(self):
if self.configurationWidget is None:
self.configurationWidget = \
StackXASBatchWindow.StackXASBatchDialog()
ret = self.configurationWidget.exec()
if ret:
self._executeFunctionAndParameters()
def _executeFunctionAndParameters(self):
self._parameters = self.configurationWidget.getParameters()
self._widget = None
if _logger.getEffectiveLevel() == logging.DEBUG:
self.thread = CalculationThread.CalculationThread(\
calculation_method=self.actualCalculation)
self.thread.result = self.actualCalculation()
self.threadFinished()
else:
self.thread = CalculationThread.CalculationThread(\
calculation_method=self.actualCalculation)
self.thread.finished.connect(self.threadFinished)
self.thread.start()
message = "Please wait. Calculation going on."
CalculationThread.waitingMessageDialog(self.thread,
parent=self.configurationWidget,
message=message)
def actualCalculation(self):
activeCurve = self.getActiveCurve()
if activeCurve is not None:
x, spectrum, legend, info = activeCurve
else:
x = None
spectrum = None
stack = self.getStackDataObject()
configurationFile = self._parameters['configuration']
net = self._parameters['mask']
self.workerInstance.setConfigurationFile(configurationFile)
if net:
mask = self.getStackSelectionMask()
else:
mask = None
outputDir = self._parameters["output_dir"]
if outputDir in [None, ""]:
outputDir=None
if not (self._parameters["file_root"] in [None, ""]):
fileRoot = self._parameters["file_root"].replace(" ","")
if fileRoot in [None, ""]:
fileRoot = None
if not os.path.exists(outputDir):
os.mkdir(outputDir)
result = self.workerInstance.processMultipleSpectra(x=x,
y=stack,
weight=None,
ysum=spectrum,
mask=mask,
directory=outputDir,
name=fileRoot)
return result
def threadFinished(self):
try:
self._threadFinished()
except:
msg = qt.QMessageBox()
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
def _threadFinished(self):
result = self.thread.result
self.thread = None
if type(result) == type((1,)):
#if we receive a tuple there was an error
if len(result):
if result[0] == "Exception":
# somehow this exception is not caught
raise Exception(result[1], result[2])#, result[3])
return
imageNames = result['names']
images = result["images"]
nImages = images.shape[0]
self._widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=False)
self._widget.buildAndConnectImageButtonBox(replace=True,
multiple=True)
qt = StackPluginResultsWindow.qt
self._widget.sigMaskImageWidgetSignal.connect(self.mySlot)
self._widget.setStackPluginResults(images,
image_names=imageNames)
self._showWidget()
def _showWidget(self):
if self._widget is None:
return
#Show
self._widget.show()
self._widget.raise_()
#update
self.selectionMaskUpdated()
MENU_TEXT = "XAS Batch"
def getStackPluginInstance(stackWindow, **kw):
ob = XASStackBatchPlugin(stackWindow)
return ob
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