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#/*##########################################################################
# Copyright (C) 2004-2013 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMca is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMca; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# PyMca follows the dual licensing model of Riverbank's PyQt and cannot be
# used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
"""
A Stack plugin is a module that will be automatically added to the PyMca
stack windows in order to perform user defined operations on the data stack.
These plugins will be compatible with any stack window that provides the
functions:
#data related
getStackDataObject
getStackData
getStackInfo
setStack
isStackFinite
#images related
addImage
removeImage
replaceImage
#mask related
setSelectionMask
getSelectionMask
#displayed curves
getActiveCurve
getGraphXLimits
getGraphYLimits
#information method
stackUpdated
selectionMaskUpdated
"""
import numpy
try:
from PyMca import StackPluginBase
from PyMca import CalculationThread
except ImportError:
#python 3 might need this
from . import StackPluginBase
from . import CalculationThread
try:
from PyMca.PCAWindow import PCAParametersDialog
from PyMca import StackPluginResultsWindow
import PyMca.PyMca_Icons as PyMca_Icons
except ImportError:
print("PCAStackPlugin importing from somewhere else")
from PCAWindow import PCAParametersDialog
import StackPluginResultsWindow
import PyMca_Icons
qt = StackPluginResultsWindow.qt
DEBUG = 0
class PCAStackPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
StackPluginBase.DEBUG = DEBUG
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
self.methodDict = {'Calculate': [self.calculate, "Perform PCA", None],
'Show': [self._showWidget,
"Show last results",
PyMca_Icons.brushselect]}
self.__methodKeys = ['Calculate', 'Show']
self.configurationWidget = None
self.widget = None
self.thread = None
def stackUpdated(self):
if DEBUG:
print("PCAStackPlugin.stackUpdated() called")
self.configurationWidget = None
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):
if DEBUG:
print("mySlot ", 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'] == "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 = PCAParametersDialog(None, regions=True)
self._status = qt.QLabel(self.configurationWidget)
self._status.setAlignment(qt.Qt.AlignHCenter)
font = qt.QFont(self._status.font())
font.setBold(True)
self._status.setFont(font)
self._status.setText("Ready")
self.configurationWidget.layout().addWidget(self._status)
activeCurve = self.getActiveCurve()
if activeCurve is None:
#I could get some defaults from the stack itslef
raise ValueError("Please select an active curve")
return
x, spectrum, legend, info = activeCurve
spectrumLength = max(spectrum.shape)
oldValue = self.configurationWidget.nPC.value()
self.configurationWidget.nPC.setMaximum(spectrumLength)
self.configurationWidget.nPC.setValue(min(oldValue, spectrumLength))
binningOptions = [1]
for number in [2, 3, 4, 5, 7, 9, 10, 11, 13, 15, 17, 19]:
if (spectrumLength % number) == 0:
binningOptions.append(number)
# TODO: Should inform the configuration widget about the possibility
# to encounter non-finite data?
ddict = {'options': binningOptions,
'binning': 1,
'method': 0}
self.configurationWidget.setParameters(ddict)
y = spectrum
self.configurationWidget.setSpectrum(x, y)
ret = self.configurationWidget.exec_()
if ret:
self._executeFunctionAndParameters()
def _executeFunctionAndParameters(self):
self.widget = None
self.configurationWidget.show()
if 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)
qt.QObject.connect(self.thread,
qt.SIGNAL('finished()'),
self.threadFinished)
self.thread.start()
message = "Please wait. PCA Calculation going on."
CalculationThread.waitingMessageDialog(self.thread,
message=message,
parent=self.configurationWidget)
def actualCalculation(self):
pcaParameters = self.configurationWidget.getParameters()
self._status.setText("Calculation going on")
self.configurationWidget.setEnabled(False)
#self.configurationWidget.close()
self.__methodlabel = pcaParameters.get('methodlabel', "")
function = pcaParameters['function']
pcaParameters['ncomponents'] = pcaParameters['npc']
# At some point I should make sure I get directly the
# function and the parameters from the configuration widget
del pcaParameters['npc']
del pcaParameters['method']
del pcaParameters['function']
del pcaParameters['methodlabel']
# binning = pcaParameters['binning']
# mask = pcaParameters['mask']
if not self.isStackFinite():
# one has to check for NaNs in the used region(s)
# for the time being only in the global image
# spatial_mask = numpy.isfinite(image_data)
spatial_mask = numpy.isfinite(self.getStackOriginalImage())
pcaParameters['mask'] = spatial_mask
stack = self.getStackDataObject()
if isinstance(stack, numpy.ndarray):
if stack.data.dtype not in [numpy.float, numpy.float32]:
print("WARNING: Non floating point data")
text = "Calculation going on."
text += " WARNING: Non floating point data."
self._status.setText(text)
oldShape = stack.data.shape
result = function(stack, **pcaParameters)
if stack.data.shape != oldShape:
stack.data.shape = oldShape
return result
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":
self._status.setText("Ready after calculation error")
self.configurationWidget.setEnabled(True)
raise Exception(result[1], result[2])
return
self._status.setText("Ready")
self.configurationWidget.setEnabled(True)
self.configurationWidget.close()
images, eigenValues, eigenVectors = result
methodlabel = self.__methodlabel
imageNames = None
vectorNames = None
nimages = images.shape[0]
imageNames = []
vectorNames = []
itmp = nimages
if " ICA " in methodlabel:
itmp = nimages / 2
for i in range(itmp):
imageNames.append("ICAimage %02d" % i)
vectorNames.append("ICAvector %02d" % i)
for i in range(itmp):
imageNames.append("Eigenimage %02d" % i)
vectorNames.append("Eigenvector %02d" % i)
self.widget = StackPluginResultsWindow.StackPluginResultsWindow(\
usetab=True)
self.widget.buildAndConnectImageButtonBox()
qt = StackPluginResultsWindow.qt
qt.QObject.connect(self.widget,
qt.SIGNAL('MaskImageWidgetSignal'),
self.mySlot)
self.widget.setStackPluginResults(images,
spectra=eigenVectors,
image_names=imageNames,
spectra_names=vectorNames)
self._showWidget()
def _showWidget(self):
if self.widget is None:
return
#Show
self.widget.show()
self.widget.raise_()
#update
self.selectionMaskUpdated()
MENU_TEXT = "PyMca PCA"
def getStackPluginInstance(stackWindow, **kw):
ob = PCAStackPlugin(stackWindow)
return ob
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