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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"
"""
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
#images related
addImage
removeImage
replaceImage
#mask related
setSelectionMask
getSelectionMask
#displayed curves
getActiveCurve
getGraphXLimits
getGraphYLimits
#information method
stackUpdated
selectionMaskUpdated
"""
import sys
import os
import numpy
import time
import traceback
from PyMca5 import StackPluginBase
from PyMca5.PyMcaCore import StackROIBatch
from PyMca5.PyMcaGui import CalculationThread
from PyMca5.PyMcaGui import StackPluginResultsWindow
from PyMca5.PyMcaGui import StackROIBatchWindow
from PyMca5.PyMcaGui import PyMca_Icons as PyMca_Icons
from PyMca5.PyMcaGui import PyMcaQt as qt
from PyMca5.PyMcaIO import ArraySave
DEBUG = 0
class StackROIBatchPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
StackPluginBase.DEBUG = DEBUG
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
self.methodDict = {}
function = self.calculate
info = "Calculate ROI images from a configuration file"
icon = PyMca_Icons.roi
self.methodDict["Calculate"] =[function,
info,
icon]
function = self._showWidget
info = "Show last results"
icon = PyMca_Icons.brushselect
self.methodDict["Show"] =[function,
info,
icon]
self.__methodKeys = ["Calculate", "Show"]
self.configurationWidget = None
self.workerInstance = None
self._widget = None
self.thread = None
def stackUpdated(self):
if DEBUG:
print("StackROIBatchPlugin.stackUpdated() called")
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'] == "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 = \
StackROIBatchWindow.StackROIBatchDialog()
ret = self.configurationWidget.exec_()
if ret:
self._executeFunctionAndParameters()
def _executeFunctionAndParameters(self):
self._parameters = self.configurationWidget.getParameters()
self._widget = None
if self.workerInstance is None:
self.workerInstance = StackROIBatch.StackROIBatch()
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)
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['net']
self.workerInstance.setConfigurationFile(configurationFile)
xAtMinMax = self._parameters['xAtMinMax']
xLabel = self.getGraphXLabel()
result = self.workerInstance.batchROIMultipleSpectra(x=x,
y=stack,
net=net,
xAtMinMax=xAtMinMax,
xLabel=xLabel)
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()
# save to output directory
parameters = self.configurationWidget.getParameters()
outputDir = parameters["output_dir"]
if outputDir in [None, ""]:
if DEBUG:
print("Nothing to be saved")
return
if parameters["file_root"] is None:
fileRoot = ""
else:
fileRoot = parameters["file_root"].replace(" ","")
if fileRoot in [None, ""]:
fileRoot = "images"
if not os.path.exists(outputDir):
os.mkdir(outputDir)
imagesDir = os.path.join(outputDir, "IMAGES")
if not os.path.exists(imagesDir):
os.mkdir(imagesDir)
imageList = [None] * (nImages)
fileImageNames = [None] * (nImages)
j = 0
for i in range(nImages):
name = imageNames[i].replace(" ","-")
fileImageNames[j] = name
imageList[j] = images[i]
j += 1
fileName = os.path.join(imagesDir, fileRoot+".edf")
ArraySave.save2DArrayListAsEDF(imageList, fileName,
labels=fileImageNames)
fileName = os.path.join(imagesDir, fileRoot+".csv")
ArraySave.save2DArrayListAsASCII(imageList, fileName, csv=True,
labels=fileImageNames)
if parameters["tiff"]:
i = 0
for i in range(len(fileImageNames)):
label = fileImageNames[i]
mass_fraction = "_" + label
fileName = os.path.join(imagesDir,
fileRoot + mass_fraction + ".tif")
ArraySave.save2DArrayListAsMonochromaticTiff([imageList[i]],
fileName,
labels=[label],
dtype=numpy.float32)
def _showWidget(self):
if self._widget is None:
return
#Show
self._widget.show()
self._widget.raise_()
#update
self.selectionMaskUpdated()
MENU_TEXT = "Stack ROI Batch"
def getStackPluginInstance(stackWindow, **kw):
ob = StackROIBatchPlugin(stackWindow)
return ob
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