#!/usr/bin/env python #/*########################################################################## # Copyright (C) 2004-2012 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. #############################################################################*/ import sys import os import numpy import copy import time from PyMca import McaWindow qt = McaWindow.qt QTVERSION = qt.qVersion() MATPLOTLIB = False if QTVERSION > '4.0.0': from PyMca import RGBCorrelator from PyMca.RGBCorrelatorWidget import ImageShapeDialog try: from PyMca import QPyMcaMatplotlibSave MATPLOTLIB = True except ImportError: MATPLOTLIB = False from PyMca import RGBCorrelatorGraph from PyMca.PyMca_Icons import IconDict from PyMca import DataObject from PyMca.PyMcaIO import EDFStack from PyMca import SpecFileStack from PyMca import ColormapDialog from PyMca import spslut from PyMca import PyMcaDirs from PyMca import SpecfitFuns from PyMca.PyMcaIO import OmnicMap from PyMca.PyMcaIO import OpusDPTMap from PyMca.PyMcaIO import LuciaMap from PyMca.PyMcaIO import SupaVisioMap from PyMca.PyMcaIO import AifiraMap from PyMca.PyMcaIO import ArraySave try: from PyMca import QHDF5Stack1D HDF5 = True except ImportError: HDF5 = False pass from PyMca import MaskImageWidget from PyMca import ExternalImagesWindow from PyMca import StackROIWindow from PyMca import CloseEventNotifyingWidget from PyMca import StackSimpleFitWindow COLORMAPLIST = [spslut.GREYSCALE, spslut.REVERSEGREY, spslut.TEMP, spslut.RED, spslut.GREEN, spslut.BLUE, spslut.MANY] PCA = False if QTVERSION > '4.0.0': from PyQt4 import Qwt5 from PyMca import PCAWindow PCA = True else: import Qwt5 NNMA = False if QTVERSION > '4.0.0': from PyQt4 import Qwt5 from PyMca import NNMAWindow NNMA = True else: import Qwt5 SNIP = False if QTVERSION > '4.0.0': from PyMca import SNIPWindow from PyMca import SGWindow SNIP = True DEBUG = 0 class SimpleThread(qt.QThread): def __init__(self, function, *var, **kw): if kw is None:kw={} qt.QThread.__init__(self) self._function = function self._var = var self._kw = kw self._result = None def run(self): if DEBUG: self._result = self._function(*self._var, **self._kw ) else: try: self._result = self._function(*self._var, **self._kw ) except: self._result = ("Exception",) + sys.exc_info() class QSpecFileStack(SpecFileStack.SpecFileStack): def onBegin(self, nfiles): self.bars =qt.QWidget() if QTVERSION < '4.0.0': self.bars.setCaption("Reading progress") self.barsLayout = qt.QGridLayout(self.bars,2,3) else: self.bars.setWindowTitle("Reading progress") self.barsLayout = qt.QGridLayout(self.bars) self.barsLayout.setMargin(2) self.barsLayout.setSpacing(3) self.progressBar = qt.QProgressBar(self.bars) self.progressLabel = qt.QLabel(self.bars) self.progressLabel.setText('Mca Progress:') self.barsLayout.addWidget(self.progressLabel,0,0) self.barsLayout.addWidget(self.progressBar,0,1) if QTVERSION < '4.0.0': self.progressBar.setTotalSteps(nfiles) self.progressBar.setProgress(0) else: self.progressBar.setMaximum(nfiles) self.progressBar.setValue(0) self.bars.show() def onProgress(self,index): if QTVERSION < '4.0.0': self.progressBar.setProgress(index) else: self.progressBar.setValue(index) def onEnd(self): self.bars.hide() del self.bars class QStack(EDFStack.EDFStack): def onBegin(self, nfiles): self.bars =qt.QWidget() if QTVERSION < '4.0.0': self.bars.setCaption("Reading progress") self.barsLayout = qt.QGridLayout(self.bars,2,3) else: self.bars.setWindowTitle("Reading progress") self.barsLayout = qt.QGridLayout(self.bars) self.barsLayout.setMargin(2) self.barsLayout.setSpacing(3) self.progressBar = qt.QProgressBar(self.bars) self.progressLabel = qt.QLabel(self.bars) self.progressLabel.setText('File Progress:') self.barsLayout.addWidget(self.progressLabel,0,0) self.barsLayout.addWidget(self.progressBar,0,1) if QTVERSION < '4.0.0': self.progressBar.setTotalSteps(nfiles) self.progressBar.setProgress(0) else: self.progressBar.setMaximum(nfiles) self.progressBar.setValue(0) self.bars.show() def onProgress(self,index): if QTVERSION < '4.0.0': self.progressBar.setProgress(index) else: self.progressBar.setValue(index) def onEnd(self): self.bars.hide() del self.bars class QEDFStackWidget(CloseEventNotifyingWidget.CloseEventNotifyingWidget): def __init__(self, parent = None, mcawidget = None, rgbwidget = None, vertical = False, master = True): CloseEventNotifyingWidget.CloseEventNotifyingWidget.__init__(self, parent) if QTVERSION < '4.0.0': self.setIcon(qt.QPixmap(IconDict['gioconda16'])) self.setCaption("PyMCA - ROI Imaging Tool") else: self.setWindowIcon(qt.QIcon(qt.QPixmap(IconDict['gioconda16']))) self.setWindowTitle("PyMCA - ROI Imaging Tool") screenHeight = qt.QDesktopWidget().height() if screenHeight > 0: if QTVERSION < '4.5.0': self.setMaximumHeight(int(0.99*screenHeight)) self.setMinimumHeight(int(0.5*screenHeight)) screenWidth = qt.QDesktopWidget().width() if screenWidth > 0: if QTVERSION < '4.5.0': self.setMaximumWidth(int(screenWidth)-5) self.setMinimumWidth(min(int(0.5*screenWidth),800)) self.mainLayout = qt.QVBoxLayout(self) self.mainLayout.setMargin(6) self.mainLayout.setSpacing(0) self._y1AxisInverted = False self.__selectionMask = None self.__stackImageData = None self.__ROIImageData = None self.__ROIImageBackground = None self.__ROIConnected = True self.__stackBackgroundCounter = 0 self.__stackBackgroundAnchors = None self.__stackColormap = None self.__stackColormapDialog = None self.mcaWidget = mcawidget self.rgbWidget = rgbwidget if QTVERSION < '4.0.0': master = False self.master = master self.slave = None self.tab = None self.externalImagesWindow = None self.externalImagesDict = {} self.pcaParametersDialog = None self.pcaWindow = None self.pcaWindowInMenu = False self.nnmaParametersDialog = None self.nnmaWindow = None self.nnmaWindowInMenu = False self.simpleFitWindow = None self._build(vertical) self._buildBottom() self._buildConnections() self._matplotlibSaveImage = None def _build(self, vertical = False): box = qt.QSplitter(self) if vertical: box.setOrientation(qt.Qt.Vertical) else: box.setOrientation(qt.Qt.Horizontal) #boxLayout.setMargin(0) #boxLayout.setSpacing(6) self.stackWindow = qt.QWidget(box) self.stackWindow.mainLayout = qt.QVBoxLayout(self.stackWindow) self.stackWindow.mainLayout.setMargin(0) self.stackWindow.mainLayout.setSpacing(0) if HDF5: self.stackGraphWidget = RGBCorrelatorGraph.RGBCorrelatorGraph(self.stackWindow, colormap=True, standalonezoom=False, standalonesave=False) self.connect(self.stackGraphWidget.saveToolButton, qt.SIGNAL("clicked()"), self._stackSaveToolButtonSignal) self._stackSaveMenu = qt.QMenu() self._stackSaveMenu.addAction(qt.QString("Stack as NeXus"), self.saveStackAsNeXus) self._stackSaveMenu.addAction(qt.QString("Stack as Float32 NeXus"), self.saveStackAsFloat32NeXus) self._stackSaveMenu.addAction(qt.QString("Stack as Float64 NeXus"), self.saveStackAsFloat64NeXus) self._stackSaveMenu.addAction(qt.QString("Stack as NeXus+/data/data"), self.saveStackAsNeXusPlus) self._stackSaveMenu.addAction(qt.QString("Stack as HDF5 /data/data"), self.saveStackAsSimpleHDF5) self._stackSaveMenu.addAction(qt.QString("Stack as HDF5 /data"), self.saveStackAsSimplestHDF5) #self._stackSaveMenu.addAction(qt.QString("Stack as NeXus NXdata"), # self.saveStackAsNXdata) self._stackSaveMenu.addAction(qt.QString("Standard Graphics"), self.stackGraphWidget._saveIconSignal) else: self.stackGraphWidget = RGBCorrelatorGraph.RGBCorrelatorGraph(self.stackWindow, colormap=True, standalonezoom=False, standalonesave=True) self.connect(self.stackGraphWidget.zoomResetToolButton, qt.SIGNAL("clicked()"), self._stackZoomResetSignal) infotext = 'If checked, spectra will be added normalized to the number\n' infotext += 'of pixels. Be carefull if you are preparing a batch and you\n' infotext += 'fit the normalized spectra because the data in the batch will\n' infotext += 'have a different weight because they are not normalized.' if QTVERSION < '4.0.0': self.normalizeIcon = qt.QIconSet(qt.QPixmap(IconDict["normalize16"])) else: self.normalizeIcon = qt.QIcon(qt.QPixmap(IconDict["normalize16"])) self.normalizeButton = self.stackGraphWidget._addToolButton(\ self.normalizeIcon, self.normalizeIconChecked, infotext, toggle = True, state = False, position = 6) self.backgroundIcon = qt.QIcon(qt.QPixmap(IconDict["subtract"])) if SNIP: infotext = 'Remove background from current stack.\n' infotext += 'Not recommended unless you really need a better\n' infotext += 'contrast to place your ROIs or you know what you\n' infotext += 'are doing.' self.backgroundButton = self.stackGraphWidget._addToolButton(\ self.backgroundIcon, #self.submitThread, self.subtractSnipBackground, infotext, position = 7) else: infotext = 'Remove background from current stack using current\n' infotext += 'ROI markers as anchors.\n' infotext += 'WARNING: Very slow. 0.01 to 0.02 seconds per pixel.\n' infotext += 'Not recommended unless you really need a better\n' infotext += 'contrast to place your ROIs and you know what you\n' infotext += 'are doing.\n' infotext += 'The ROI background subtraction is more efficient.\n' self.backgroundButton = self.stackGraphWidget._addToolButton(\ self.backgroundIcon, self.submitThread, #self.subtractBackground, infotext, position = 7) filterOffset = 0 infotext = 'Additional selection methods.\n' self.selectFromStackIcon = qt.QIcon(qt.QPixmap(IconDict["brushselect"])) self.selectFromStackButton = self.stackGraphWidget._addToolButton(\ self.selectFromStackIcon, self.selectFromStackSignal, infotext, position = 8) self.__selectFromStackMenu = qt.QMenu() self.__selectFromStackMenu.addAction(qt.QString("Show Altenative ROI Window"), self.showAlternativeRoiWindow) self.__selectFromStackMenu.addAction(qt.QString("Load external image"), self.__selectFromExternalImageDialog) self.__selectFromStackMenu.addAction(qt.QString("Show external image for selection"), self.showExternalImagesWindow) self.externalImagesWindow = ExternalImagesWindow.ExternalImagesWindow(rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=True) self.externalImagesWindow.hide() #stack simple fitting self.__selectFromStackMenu.addAction(qt.QString("Stack Simple fitting"), self.__showSimpleFitWindow) if PCA: self.__selectFromStackMenu.addAction(qt.QString("Calculate Principal Components Maps"), self.__showPCADialog) filterOffset = 1 self.pcaWindow = PCAWindow.PCAWindow(parent = None, rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=True) self.pcaWindow.hide() if NNMA: self.__selectFromStackMenu.addAction(qt.QString("Calculate NNMA Components Maps"), self.__showNNMADialog) filterOffset = 1 self.nnmaWindow = NNMAWindow.NNMAWindow(parent = None, rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=True) self.nnmaWindow.hide() if self.master: self.loadIcon = qt.QIcon(qt.QPixmap(IconDict["fileopen"])) self.loadStackButton = self.stackGraphWidget._addToolButton(\ self.loadIcon, self.loadSlaveStack, 'Load another stack of same size', position = 8 + filterOffset) standaloneSaving = True self.newRoiWindow = StackROIWindow.StackROIWindow(parent=None,crop=False, rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=True) self.roiWindow = MaskImageWidget.MaskImageWidget(parent=box, rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=standaloneSaving) if QTVERSION > '4.0.0': infotext = 'Toggle background subtraction from current image\n' infotext += 'subtracting a straight line between the ROI limits.' self.roiBackgroundIcon = qt.QIcon(qt.QPixmap(IconDict["subtract"])) self.roiBackgroundButton = self.roiWindow.graphWidget._addToolButton(\ self.roiBackgroundIcon, self.roiSubtractBackground, infotext, toggle = True, state = False, position = 6) self.stackWindow.mainLayout.addWidget(self.stackGraphWidget) if QTVERSION < '4.0.0': box.moveToLast(self.stackWindow) box.moveToLast(self.roiWindow) self.mainLayout.addWidget(box) else: box.addWidget(self.stackWindow) box.addWidget(self.roiWindow) try: #give the stretch factor to the image self.mainLayout.addWidget(box, 1) except: self.mainLayout.addWidget(box) def _stackSaveToolButtonSignal(self): self._stackSaveMenu.exec_(self.cursor().pos()) def _getOutputHDF5Filename(self, nexus=False): fileTypes = "HDF5 Files (*.h5)\nHDF5 Files (*.hdf)" message = "Enter output filename" wdir = PyMcaDirs.outputDir filename = qt.QFileDialog.getSaveFileName(self, message, wdir, fileTypes) if len(filename): return qt.safe_str(filename) else: return "" def saveStackAsNeXus(self, dtype=None): filename = self._getOutputHDF5Filename() if not len(filename): return ArraySave.save3DArrayAsHDF5(self.stack.data, filename, labels = None, dtype=dtype, mode='nexus') def saveStackAsFloat32NeXus(self): self.saveStackAsNeXus(dtype=numpy.float32) def saveStackAsFloat64NeXus(self): self.saveStackAsNeXus(dtype=numpy.float64) def saveStackAsNeXusPlus(self): filename = self._getOutputHDF5Filename() if not len(filename): return ArraySave.save3DArrayAsHDF5(self.stack.data, filename, labels = None, dtype=None, mode='nexus+') def saveStackAsSimpleHDF5(self): filename = self._getOutputHDF5Filename() if not len(filename): return ArraySave.save3DArrayAsHDF5(self.stack.data, filename, labels = None, dtype=None, mode='simple') def saveStackAsSimplestHDF5(self): filename = self._getOutputHDF5Filename() if not len(filename): return ArraySave.save3DArrayAsHDF5(self.stack.data, filename, labels = None, dtype=None, mode='simplest') def _maskImageWidgetSlot(self, ddict): if ddict['event'] == "selectionMaskChanged": self.__selectionMask = ddict['current'] self.plotStackImage(update=False) if ddict['id'] != id(self.newRoiWindow): self.newRoiWindow.setSelectionMask(ddict['current'], plot=True) if ddict['id'] != id(self.roiWindow): self.roiWindow.setSelectionMask(ddict['current'], plot=True) if ddict['id'] != id(self.pcaWindow): self.pcaWindow.setSelectionMask(ddict['current'], plot=True) if ddict['id'] != id(self.externalImagesWindow): self.externalImagesWindow.setSelectionMask(ddict['current'], plot=True) if NNMA: if ddict['id'] != id(self.nnmaWindow): self.nnmaWindow.setSelectionMask(ddict['current'], plot=True) return if ddict['event'] == "resetSelection": self.__selectionMask = None self.plotStackImage(update=True) if ddict['id'] != id(self.newRoiWindow): self.newRoiWindow._resetSelection(owncall=False) if ddict['id'] != id(self.roiWindow): self.roiWindow._resetSelection(owncall=False) if ddict['id'] != id(self.pcaWindow): self.pcaWindow._resetSelection(owncall=False) if ddict['id'] != id(self.externalImagesWindow): self.externalImagesWindow._resetSelection(owncall=False) if NNMA: if ddict['id'] != id(self.nnmaWindow): self.nnmaWindow._resetSelection(owncall=False) return if ddict['event'] == "addImageClicked": self._addImageClicked(ddict['image'], ddict['title']) return if ddict['event'] == "replaceImageClicked": self._replaceImageClicked(ddict['image'], ddict['title']) return if ddict['event'] == "removeImageClicked": self._removeImageClicked(ddict['title']) return if ddict['event'] == "hFlipSignal": if ddict['id'] == id(self.roiWindow): self._y1AxisInverted = ddict['current'] self.plotStackImage(update=True) return def normalizeIconChecked(self): pass def submitThread(self): try: threadResult = self._submitBackgroundThread() if type(threadResult) == type((1,)): if len(threadResult): if threadResult[0] == "Exception": raise Exception(threadResult[1],threadResult[2]) self.originalPlot() #self.mcaWidget.graph.newcurve("background", numpy.arange(len(self.b)), self.b) #self.mcaWidget.graph.replot() except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() def _submitPCAThread(self, function, *var, **kw): message = "Please Wait: PCA Going On" sthread = SimpleThread(function, *var, **kw) return self.__startThread(sthread, message) def _submitNNMAThread(self, function, *var, **kw): message = "Please Wait: NNMA Going On" sthread = SimpleThread(function, *var, **kw) return self.__startThread(sthread, message) def _submitBackgroundThread(self, *var, **kw): message = "Please Wait: Calculating background" sthread = SimpleThread(self.subtractBackground, *var, **kw) return self.__startThread(sthread, message) def __startThread(self, sthread, message): sthread.start() if QTVERSION < '4.0.0': msg = qt.QDialog(self, "Please Wait", 1,qt.Qt.WStyle_NoBorder) else: # TODO why this strange test if 0: msg = qt.QDialog(self, qt.Qt.FramelessWindowHint) msg.setModal(0) else: msg = qt.QDialog(self, qt.Qt.FramelessWindowHint) msg.setModal(1) msg.setWindowTitle("Please Wait") layout = qt.QHBoxLayout(msg) layout.setMargin(0) layout.setSpacing(0) l1 = qt.QLabel(msg) l1.setFixedWidth(l1.fontMetrics().width('##')) l2 = qt.QLabel(msg) l2.setText("%s" % message) l3 = qt.QLabel(msg) l3.setFixedWidth(l3.fontMetrics().width('##')) layout.addWidget(l1) layout.addWidget(l2) layout.addWidget(l3) msg.show() qt.qApp.processEvents() t0 = time.time() i = 0 ticks = ['-','\\', "|", "/","-","\\",'|','/'] if QTVERSION < '4.0.0': while (sthread.running()): i = (i+1) % 8 l1.setText(ticks[i]) l3.setText(" "+ticks[i]) qt.qApp.processEvents() time.sleep(2) msg.close(True) else: while (sthread.isRunning()): i = (i+1) % 8 l1.setText(ticks[i]) l3.setText(" "+ticks[i]) qt.qApp.processEvents() time.sleep(2) msg.close() result = sthread._result del sthread if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return result def selectFromStackSignal(self): if QTVERSION < '4.0.0': self.__selectFromStackMenu.exec_loop(self.cursor().pos()) else: self.__selectFromStackMenu.exec_(self.cursor().pos()) def showAlternativeRoiWindow(self): self.newRoiWindow.show() self.newRoiWindow.raise_() def showExternalImagesWindow(self): if self.externalImagesWindow.getQImage() is None: self.__selectFromExternalImageDialog() return if self.externalImagesWindow.getQImage() is not None: self.externalImagesWindow.show() self.externalImagesWindow.raise_() def __selectFromExternalImageDialog(self): if self.__stackImageData is None: return getfilter = True fileTypeList = ["PNG Files (*png)", "JPEG Files (*jpg *jpeg)", "IMAGE Files (*)", "EDF Files (*edf)", "EDF Files (*ccd)", "EDF Files (*)"] message = "Open image file" filenamelist, filefilter = self._getFileList(fileTypeList, message=message, getfilter=getfilter) if len(filenamelist) < 1: return imagelist = [] imagenames= [] if filefilter.split()[0] in ["EDF"]: for filename in filenamelist: #read the edf file edf = EDFStack.EdfFileDataSource.EdfFileDataSource(filename) #the list of images keylist = edf.getSourceInfo()['KeyList'] if len(keylist) < 1: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("Cannot read an image from the file") msg.exec_() return for key in keylist: #get the data dataObject = edf.getDataObject(key) data = dataObject.data imagename = dataObject.info.get('Title', os.path.basename(filename)+" "+key) #generate a grey scale image of the data (pixmapData, size, minmax)= spslut.transform(\ data, (1,0), (spslut.LINEAR,3.0), "BGRX", spslut.GREYSCALE, 1, (0,1),(0, 255),1) #generate a qimage from it xmirror = 0 ymirror = 0 image = qt.QImage(pixmapData.tostring(), size[0], size[1], qt.QImage.Format_RGB32).mirrored(xmirror, ymirror) imagelist.append(image) imagenames.append(imagename) else: #Try pure Image formats for filename in filenamelist: image = qt.QImage(filename) if image.isNull(): msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("Cannot read file %s as an image" % filename) msg.exec_() return imagelist.append(image) imagenames.append(os.path.basename(filename)) if len(imagelist) == 0: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("Cannot read a valid image from the file") msg.exec_() return shape = self.__stackImageData.shape self.externalImagesWindow.setQImageList(imagelist, shape[1], shape[0], clearmask=False, data=None, imagenames=imagenames) #data=self.__stackImageData) self.externalImagesWindow.setSelectionMask(self.__selectionMask, plot=True) self.showExternalImagesWindow() def __showNNMADialog(self): if self.__stackImageData is None: return if self.nnmaParametersDialog is None: self.nnmaParametersDialog = NNMAWindow.NNMAParametersDialog(self) spectrumLength = max(self.__mcaData0.y[0].shape) self.nnmaParametersDialog.nPC.setMaximum(spectrumLength) self.nnmaParametersDialog.nPC.setValue(min(10,spectrumLength)) binningOptions=[1] for number in [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19]: if (spectrumLength % number) == 0: binningOptions.append(number) ddict = {'options':binningOptions, 'binning': 1, 'method': 0} self.nnmaParametersDialog.setParameters(ddict) ret = self.nnmaParametersDialog.exec_() if ret: nnmaParameters = self.nnmaParametersDialog.getParameters() self.nnmaParametersDialog.close() function = nnmaParameters['function'] binning = nnmaParameters['binning'] npc = nnmaParameters['npc'] kw = nnmaParameters['kw'] if self.stack.data.dtype not in [numpy.float, numpy.float32]: self.stack.data = self.stack.data.astype(numpy.float) shape = self.stack.data.shape try: if 0: images, eigenvalues, eigenvectors = function(self.stack.data, npc, binning=binning, **kw) else: if DEBUG: import time e0 = time.time() data = self.stack.data threadResult = self._submitNNMAThread(function, data, npc, binning=binning, **kw) if type(threadResult) == type((1,)): if len(threadResult): if threadResult[0] == "Exception": raise Exception(threadResult[1],threadResult[2]) images, eigenvalues, eigenvectors = threadResult if DEBUG: print("%s Elapsed = %f " %\ (nnmaParameters['methodlabel'],\ time.time() - e0)) self.nnmaWindow.setSelectionMask(self.__selectionMask, plot=False) self.nnmaWindow.setPCAData(images, eigenvalues, eigenvectors) if not self.nnmaWindowInMenu: self.__selectFromStackMenu.addAction(qt.QString("Show NNMA Maps"), self.showNNMAWindow) self.nnmaWindowInMenu = True if isinstance(self.stack.data, numpy.ndarray): self.stack.data.shape = shape self.nnmaWindow.show() except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() if isinstance(self.stack.data, numpy.ndarray): self.stack.data.shape = shape def __showPCADialog(self): if self.__stackImageData is None: return if self.pcaParametersDialog is None: self.pcaParametersDialog = PCAWindow.PCAParametersDialog(self, regions=True) spectrumLength = max(self.__mcaData0.y[0].shape) self.pcaParametersDialog.nPC.setMaximum(spectrumLength) self.pcaParametersDialog.nPC.setValue(min(10,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) ddict = {'options':binningOptions, 'binning': 1, 'method': 0} self.pcaParametersDialog.setParameters(ddict) selection = self._addMcaClicked(action="GET_CURRENT_SELECTION") if selection is None: return y = selection['dataobject'].y[0] x = selection['dataobject'].x[0] selection['dataobject'].info['legend'] = self.__getLegend() x = self.mcaWidget.getEnergyFromChannels(x, selection['dataobject'].info) self.pcaParametersDialog.setSpectrum(x, y) ret = self.pcaParametersDialog.exec_() if ret: pcaParameters = self.pcaParametersDialog.getParameters() self.pcaParametersDialog.close() method = pcaParameters['method'] function = pcaParameters['function'] binning = pcaParameters['binning'] npc = pcaParameters['npc'] mask = pcaParameters['mask'] if self.stack.data.dtype not in [numpy.float, numpy.float32]: self.stack.data = self.stack.data.astype(numpy.float) shape = self.stack.data.shape try: if 0: images, eigenvalues, eigenvectors = function(self.stack.data, npc, binning=binning, mask=mask) else: if DEBUG: import time e0 = time.time() if 'MULTIPLE' in pcaParameters['methodlabel'].upper(): if self.slave is None: data = [self.stack.data] else: data = [self.stack.data, self.slave.stack.data] else: data = self.stack.data threadResult = self._submitPCAThread(function, data, npc, binning=binning, mask=mask) if type(threadResult) == type((1,)): if len(threadResult): if threadResult[0] == "Exception": raise Exception(threadResult[1],threadResult[2]) images, eigenvalues, eigenvectors = threadResult if DEBUG: print("%s Elapsed = %f" %\ (pcaParameters['methodlabel'], \ time.time() - e0)) self.pcaWindow.setSelectionMask(self.__selectionMask, plot=False) methodlabel = pcaParameters.get('methodlabel', "") imagenames=None vectornames=None if " ICA " in methodlabel: nimages = images.shape[0] imagenames = [] vectornames = [] 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.pcaWindow.setPCAData(images, eigenvalues, eigenvectors, imagenames=imagenames, vectornames=vectornames) if not self.pcaWindowInMenu: self.__selectFromStackMenu.addAction(qt.QString("Show PCA Maps"), self.showPCAWindow) self.pcaWindowInMenu = True if isinstance(self.stack.data, numpy.ndarray): self.stack.data.shape = shape self.pcaWindow.show() except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() if isinstance(self.stack.data, numpy.ndarray): self.stack.data.shape = shape def __showSimpleFitWindow(self): if self.simpleFitWindow is None: self.simpleFitWindow = StackSimpleFitWindow.StackSimpleFitWindow() selection = self._addMcaClicked(action="GET_CURRENT_SELECTION") if selection is None: return y = selection['dataobject'].y[0] x = selection['dataobject'].x[0] selection['dataobject'].info['legend'] = self.__getLegend() x = self.mcaWidget.getEnergyFromChannels(x, selection['dataobject'].info) xmin, xmax = self.mcaWidget.graph.getX1AxisLimits() self.simpleFitWindow.setSpectrum(x, y, xmin = xmin, xmax=xmax) self.simpleFitWindow.setData(x, self.stack.data, data_index=self.mcaIndex) self.simpleFitWindow.show() def showPCAWindow(self): self.pcaWindow.show() self.pcaWindow.raise_() def showNNMAWindow(self): self.nnmaWindow.show() self.nnmaWindow.raise_() def subtractSnipBackground(self): snipMenu = qt.QMenu() snipMenu.addAction("Savitzky-Golay Filtering", self.replaceStackWithSavitzkyGolayFiltering) snipMenu.addAction("Smooth with SNIP 1D Background", self.replaceWith1DSnipBackground) snipMenu.addAction("Subtract SNIP 1D Background", self.subtract1DSnipBackground) snipMenu.addAction("Subtract SNIP 2D Background", self.subtract2DSnipBackground) snipMenu.exec_(self.cursor().pos()) def replaceStackWithSavitzkyGolayFiltering(self): selection = self._addMcaClicked(action="GET_CURRENT_SELECTION") if selection is None: return spectrum = selection['dataobject'].y[0] snipWindow = SGWindow.SGDialog(None, spectrum) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec_() if ret: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] function(self.stack, *arguments) self.setStack(self.stack) def subtract1DSnipBackground(self, smooth=False): selection = self._addMcaClicked(action="GET_CURRENT_SELECTION") if selection is None: return spectrum = selection['dataobject'].y[0] snipWindow = SNIPWindow.SNIPDialog(None, spectrum, smooth=smooth) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec_() if ret: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] function(self.stack, *arguments) self.setStack(self.stack) def replaceWith1DSnipBackground(self): return self.subtract1DSnipBackground(smooth=True) def subtract2DSnipBackground(self): if self.__ROIImageData is None: return snipWindow = SNIPWindow.SNIPDialog(None, self.__ROIImageData*1) #snipWindow.setModal(True) snipWindow.show() ret = snipWindow.exec_() if ret: snipParametersDict = snipWindow.getParameters() snipWindow.close() function = snipParametersDict['function'] arguments = snipParametersDict['arguments'] # the index! arguments.append(2) function(self.stack,*arguments) self.setStack(self.stack) def subtractBackground(self): if 0: fitconfig = self.mcaWidget.advancedfit.mcafit.config constant = fitconfig['fit'].get('stripconstant', 1.0) iterations = int(fitconfig['fit'].get('stripiterations',4000)/2) width = fitconfig['fit'].get('stripwidth', 4) filterwidth = fitconfig['fit'].get('stripfilterwidth', 10) anchorsflag = fitconfig['fit'].get('stripanchorsflag', 0) constant = 1.0 iterations = 1000 if self.__stackBackgroundCounter == 0: width = 8 elif self.__stackBackgroundCounter == 1: width = 4 else: width = 2 self.__stackBackgroundCounter += 1 if self.__stackBackgroundAnchors is not None: anchorslist = self.__stackBackgroundAnchors else: anchorslist = [] shape = self.stack.data.shape if DEBUG:t0 = time.time() if self.fileIndex == 0: if self.mcaIndex == 1: for i in range(shape[0]): for j in range(shape[2]): data = self.stack.data[i, :, j] #data = SpecfitFuns.SavitskyGolay(data, filterwidth) data = SpecfitFuns.subacfast(data, constant, iterations, width, anchorslist) data = SpecfitFuns.subacfast(data, constant, 500, 1, anchorslist) self.stack.data[i, :, j] -= data else: #self.b = 0 * self.stack.data[0, 0, :] for i in range(shape[0]): for j in range(shape[1]): data = self.stack.data[i, j, :] #data = SpecfitFuns.SavitskyGolay(data, filterwidth) data = SpecfitFuns.subacfast(data, constant, iterations, width, anchorslist) data = SpecfitFuns.subacfast(data, constant, 500, 1, anchorslist) self.stack.data[i, j, :] -= data #self.b += data else: #self.fileIndex = 2 if self.mcaIndex == 0: for i in range(shape[1]): for j in range(shape[2]): data = self.stack.data[:, i, j] #data = SpecfitFuns.SavitskyGolay(data, filterwidth) data = SpecfitFuns.subacfast(data, constant, iterations, width, anchorslist) data = SpecfitFuns.subacfast(data, constant, 500, 1, anchorslist) self.stack.data[:, i, j] -= data else: for i in range(shape[0]): for j in range(shape[2]): data = self.stack.data[i, :, j] #data = SpecfitFuns.SavitskyGolay(data, filterwidth) data = SpecfitFuns.subacfast(data, constant, iterations, width, anchorslist) data = SpecfitFuns.subacfast(data, constant, 500, 1, anchorslist) self.stack.data[i, :, j] -= data if DEBUG: print("elapsed = %f" % (time.time() - t0)) #self.originalPlot() def roiSubtractBackground(self): if self.__ROIImageData is None: return if self.__ROIImageBackground is None: return if self.roiBackgroundButton.isChecked(): self.__ROIImageData = self.__ROIImageData - self.__ROIImageBackground self.roiWindow.graphWidget.graph.setTitle(self.roiWindow.graphWidget.__title + " Net") else: self.__ROIImageData = self.__ROIImageData + self.__ROIImageBackground self.roiWindow.graphWidget.graph.setTitle(self.roiWindow.graphWidget.__title) if self.roiWindow.colormapDialog is not None: minData = self.__ROIImageData.min() maxData = self.__ROIImageData.max() self.roiWindow.colormapDialog.setDataMinMax(minData, maxData) self.roiWindow.setImageData(self.__ROIImageData) def loadSlaveStack(self): if self.slave is None: filelist, filefilter = self._getStackOfFiles(getfilter=True) if not(len(filelist)): return #filelist.sort() PyMcaDirs.inputDir = os.path.dirname(filelist[0]) if PyMcaDirs.outputDir is None: PyMcaDirs.outputDir = os.path.dirname(filelist[0]) self.slave = QEDFStackWidget(rgbwidget=self.rgbWidget, master=False) omnicfile = False luciafile = False supavisio = False hdffile = False opusfile = False if len(filelist) == 1: f = open(filelist[0], 'rb') line = f.read(10) f.close() if filefilter.upper().startswith('HDF5'): hdffile = True elif line[0]=="\n": line = line[1:] if line.startswith('Spectral'): omnicfile = True elif line.startswith('#\tDate:'): luciafile = True elif "SupaVisio" == filefilter.split()[0]: supavisio = True elif filelist[0][-4:].upper() in ["PIGE", "PIGE"]: supavisio = True elif filelist[0][-3:].upper() in ["RBS"]: supavisio = True elif filefilter.upper().startswith('OPUS-DPT'): opusfile = True try: if hdffile: self.slave.setStack(QHDF5Stack1D.QHDF5Stack1D(filelist)) elif omnicfile: self.slave.setStack(OmnicMap.OmnicMap(filelist[0])) elif luciafile: self.slave.setStack(LuciaMap.LuciaMap(filelist[0])) elif supavisio: self.slave.setStack(SupaVisioMap.SupaVisioMap(filelist[0])) elif opusfile: self.slave.setStack(OpusDPTMap.OpusDPTMap(filelist[0])) else: self.slave.setStack(QStack(filelist)) except: self.slave.setStack(QSpecFileStack(filelist)) self.connectSlave(self.slave) self._resetSelection() if self.slave is not None: self.loadStackButton.hide() self.slave.show() return def connectSlave(self, slave = None): if slave is None: slave = self.slave #roi window self.connect(slave.newRoiWindow, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.connect(self.newRoiWindow, qt.SIGNAL('MaskImageWidgetSignal'), slave._maskImageWidgetSlot) self.connect(slave.roiWindow, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.connect(self.roiWindow, qt.SIGNAL('MaskImageWidgetSignal'), slave._maskImageWidgetSlot) if self.pcaWindow is not None: self.connect(slave.pcaWindow, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.connect(self.pcaWindow, qt.SIGNAL('MaskImageWidgetSignal'), slave._maskImageWidgetSlot) if self.externalImagesWindow is not None: self.connect(slave.externalImagesWindow, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.connect(self.externalImagesWindow, qt.SIGNAL('MaskImageWidgetSignal'), slave._maskImageWidgetSlot) if self.nnmaWindow is not None: self.connect(slave.nnmaWindow, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.connect(self.nnmaWindow, qt.SIGNAL('MaskImageWidgetSignal'), slave._maskImageWidgetSlot) def _buildBottom(self): n = 0 if self.mcaWidget is None: n += 1 if (QTVERSION > '4.0.0') and (self.rgbWidget is None): n += 1 if n == 1: if self.mcaWidget is None: self.mcaWidget = McaWindow.McaWidget(self, vertical = False) if QTVERSION < '4.0.0': self.mcaWidget.setCaption("PyMCA - Mca Window") else: self.mcaWidget.setWindowTitle("PyMCA - Mca Window") self.mainLayout.addWidget(self.mcaWidget) if self.rgbWidget is None: if QTVERSION > '4.0.0': #I have not implemented it for Qt3 #self.rgbWidget = RGBCorrelator.RGBCorrelator() self.rgbWidget = RGBCorrelator.RGBCorrelator(self) self.mainLayout.addWidget(self.rgbWidget) elif n == 2: self.tab = qt.QTabWidget(self) self.mcaWidget = McaWindow.McaWidget(vertical = False) if QTVERSION > '4.0.0': self.mcaWidget.graphBox.setMinimumWidth(0.5 * qt.QWidget.sizeHint(self).width()) self.tab.setMaximumHeight(1.3 * qt.QWidget.sizeHint(self).height()) self.mcaWidget.setWindowTitle("PyMCA - Mca Window") self.tab.addTab(self.mcaWidget, "MCA") if QTVERSION > '4.0.0': #I have not implemented it for Qt3 #self.rgbWidget = RGBCorrelator.RGBCorrelator() self.rgbWidget = RGBCorrelator.RGBCorrelator() self.tab.addTab(self.rgbWidget, "RGB Correlator") self.mainLayout.addWidget(self.tab) self.mcaWidget.setMiddleROIMarkerFlag(True) def _toggleROISelectionMode(self): if self.roiGraphWidget.graph._selecting: self.setROISelectionMode(False) else: self.setROISelectionMode(True) def setROISelectionMode(self, mode = None): if mode: self.roiGraphWidget.graph.enableSelection(True) self.__ROIBrushMode = False self.roiGraphWidget.picker.setTrackerMode(Qwt5.QwtPicker.AlwaysOn) self.roiGraphWidget.graph.enableZoom(False) if QTVERSION < '4.0.0': self.roiGraphWidget.selectionToolButton.setState(qt.QButton.On) else: self.roiGraphWidget.selectionToolButton.setChecked(True) self.roiGraphWidget.selectionToolButton.setDown(True) self.roiGraphWidget.showImageIcons() else: self.roiGraphWidget.graph.enableZoom(True) if QTVERSION < '4.0.0': self.roiGraphWidget.selectionToolButton.setState(qt.QButton.Off) else: self.roiGraphWidget.selectionToolButton.setChecked(False) self.roiGraphWidget.selectionToolButton.setDown(False) self.roiGraphWidget.hideImageIcons() #self.plotStackImage(update = True) #self.plotROIImage(update = True) if self.__stackImageData is None: return #do not reset the selection #self.__selectionMask = numpy.zeros(self.__stackImageData.shape, numpy.uint8) def _buildAndConnectButtonBox(self): #the MCA selection self.mcaButtonBox = qt.QWidget(self.stackWindow) self.mcaButtonBoxLayout = qt.QHBoxLayout(self.mcaButtonBox) self.mcaButtonBoxLayout.setMargin(0) self.mcaButtonBoxLayout.setSpacing(0) self.addMcaButton = qt.QPushButton(self.mcaButtonBox) self.addMcaButton.setText("ADD MCA") self.removeMcaButton = qt.QPushButton(self.mcaButtonBox) self.removeMcaButton.setText("REMOVE MCA") self.replaceMcaButton = qt.QPushButton(self.mcaButtonBox) self.replaceMcaButton.setText("REPLACE MCA") self.mcaButtonBoxLayout.addWidget(self.addMcaButton) self.mcaButtonBoxLayout.addWidget(self.removeMcaButton) self.mcaButtonBoxLayout.addWidget(self.replaceMcaButton) self.stackWindow.mainLayout.addWidget(self.mcaButtonBox) self.connect(self.addMcaButton, qt.SIGNAL("clicked()"), self._addMcaClicked) self.connect(self.removeMcaButton, qt.SIGNAL("clicked()"), self._removeMcaClicked) self.connect(self.replaceMcaButton, qt.SIGNAL("clicked()"), self._replaceMcaClicked) if self.rgbWidget is not None: # The IMAGE selection if 1: self.roiWindow.buildAndConnectImageButtonBox() if self.pcaWindow is not None: self.pcaWindow.buildAndConnectImageButtonBox() if self.nnmaWindow is not None: self.nnmaWindow.buildAndConnectImageButtonBox() self.externalImagesWindow.buildAndConnectImageButtonBox() def _buildConnections(self): self._buildAndConnectButtonBox() self.connect(self.stackGraphWidget.colormapToolButton, qt.SIGNAL("clicked()"), self.selectStackColormap) self.connect(self.stackGraphWidget.hFlipToolButton, qt.SIGNAL("clicked()"), self._hFlipIconSignal) #ROI Image if QTVERSION < "4.0.0": self.connect(self.roiWindow, qt.PYSIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) if self.pcaWindow is not None: self.connect(self.pcaWindow, qt.PYSIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) else: widgetList = [self.newRoiWindow, self.roiWindow, self.externalImagesWindow] if self.pcaWindow is not None: widgetList.append(self.pcaWindow) if self.nnmaWindow is not None: widgetList.append(self.nnmaWindow) for widget in widgetList: self.connect(widget, qt.SIGNAL('MaskImageWidgetSignal'), self._maskImageWidgetSlot) self.stackGraphWidget.graph.canvas().setMouseTracking(1) self.stackGraphWidget.setInfoText(" X = ???? Y = ???? Z = ????") self.stackGraphWidget.showInfo() if QTVERSION < "4.0.0": self.connect(self.stackGraphWidget.graph, qt.PYSIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) self.connect(self.mcaWidget, qt.PYSIGNAL("McaWindowSignal"), self._mcaWidgetSignal) self.connect(self.roiWindow.graphWidget.graph, qt.PYSIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) else: self.connect(self.stackGraphWidget.graph, qt.SIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) self.connect(self.mcaWidget, qt.SIGNAL("McaWindowSignal"), self._mcaWidgetSignal) self.connect(self.roiWindow.graphWidget.graph, qt.SIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) def _stackGraphSignal(self, ddict): if ddict['event'] == "MouseAt": x = round(ddict['y']) if x < 0: x = 0 y = round(ddict['x']) if y < 0: y = 0 if self.__stackImageData is None: return limits = self.__stackImageData.shape x = min(int(x), limits[0]-1) y = min(int(y), limits[1]-1) z = self.__stackImageData[x, y] self.stackGraphWidget.setInfoText(" X = %d Y = %d Z = %.4g" %\ (y, x, z)) def _otherWidgetRoiGraphSignal(self, ddict): self._roiGraphSignal(ddict, ownsignal = False) def setStack(self, stack, mcaindex=1, fileindex = None): #stack.data is an XYZ array if not hasattr(stack, "sourceName"): stack.sourceName = stack.info['SourceName'] if QTVERSION < '4.0.0': title = qt.safe_str(self.caption())+\ ": from %s to %s" % (os.path.basename(stack.sourceName[0]), os.path.basename(stack.sourceName[-1])) self.setCaption(title) else: title = qt.safe_str(self.windowTitle())+\ ": from %s to %s" % (os.path.basename(stack.sourceName[0]), os.path.basename(stack.sourceName[-1])) self.setWindowTitle(title) if (1 in stack.data.shape) and (QTVERSION > '4.0.0'): oldshape = stack.data.shape dialog = ImageShapeDialog(self, shape = oldshape[0:2]) dialog.setModal(True) ret = dialog.exec_() if ret: shape = dialog.getImageShape() dialog.close() del dialog stack.data.shape = [shape[0], shape[1], oldshape[2]] self.stack = stack shape = self.stack.data.shape if 'McaIndex' in self.stack.info: self.mcaIndex = stack.info['McaIndex'] else: self.mcaIndex = mcaindex if fileindex is None: fileindex = 2 if hasattr(self.stack, "info"): if 'FileIndex' in self.stack.info: fileindex = stack.info['FileIndex'] if 'McaIndex' in self.stack.info: self.mcaIndex = stack.info['McaIndex'] else: if fileindex == 0: self.mcaIndex = 2 self.otherIndex = 1 elif fileindex == 1: self.mcaIndex = 2 self.otherIndex = 0 else: self.mcaIndex = 1 self.otherIndex = 0 self.fileIndex = fileindex for i in range(3): if i not in [self.mcaIndex, fileindex]: self.otherIndex = i break self.originalPlot() def originalPlot(self): #original image if isinstance(self.stack.data, numpy.ndarray): self.__stackImageData = numpy.sum(self.stack.data, self.mcaIndex) #original ICR mca if DEBUG: print("(self.otherIndex, self.fileIndex) = (5d, %d)" %\ (self.otherIndex, self.fileIndex)) i = max(self.otherIndex, self.fileIndex) j = min(self.otherIndex, self.fileIndex) mcaData0 = numpy.sum(numpy.sum(self.stack.data, i), j) * 1.0 else: if DEBUG: t0 = time.time() shape = self.stack.data.shape if self.mcaIndex == 2: self.__stackImageData = numpy.zeros((shape[0], shape[1]), self.stack.data.dtype) mcaData0 = numpy.zeros((shape[2],), numpy.float) step = 1 for i in range(shape[0]): tmpData = self.stack.data[i:i+step,:,:] numpy.add(self.__stackImageData[i:i+step,:], numpy.sum(tmpData, 2), self.__stackImageData[i:i+step,:]) tmpData.shape = step*shape[1], shape[2] numpy.add(mcaData0, numpy.sum(tmpData, 0), mcaData0) elif self.mcaIndex == 0: self.__stackImageData = numpy.zeros((shape[1], shape[2]), self.stack.data.dtype) mcaData0 = numpy.zeros((shape[0],), numpy.float) step = 1 for i in range(shape[0]): tmpData = self.stack.data[i:i+step,:,:] tmpData.shape = tmpData.shape[1:] numpy.add(self.__stackImageData, tmpData, self.__stackImageData) mcaData0[i] = tmpData.sum() if DEBUG: print("Print dynamic loading elapsed = %f" %\ (time.time() -t0)) if DEBUG: print("__stackImageData.shape = ", self.__stackImageData.shape) calib = self.stack.info['McaCalib'] dataObject = DataObject.DataObject() dataObject.info = {"McaCalib": calib, "selectiontype":"1D", "SourceName":"EDF Stack", "Key":"SUM"} dataObject.x = [numpy.arange(len(mcaData0)).astype(numpy.float) + self.stack.info['Channel0']] dataObject.y = [mcaData0] #store the original spectrum self.__mcaData0 = dataObject #add the original image self.__addOriginalImage() #add the ICR ROI Image #self.updateRoiImage(roidict=None) #add the mca self.sendMcaSelection(dataObject, action = "ADD") def __addOriginalImage(self): #init the original image self.stackGraphWidget.graph.setTitle("Original Stack") if self.fileIndex == 2: self.stackGraphWidget.graph.x1Label("File") if self.mcaIndex == 0: self.stackGraphWidget.graph.y1Label('Column') else: self.stackGraphWidget.graph.y1Label('Row') elif self.stack.info["SourceType"] in ["SpecFileStack", "HDF5Stack1D"]: self.stackGraphWidget.graph.y1Label('Row') self.stackGraphWidget.graph.x1Label('Column') elif self.fileIndex == 1: self.stackGraphWidget.graph.x1Label("File") if self.mcaIndex == 1: self.stackGraphWidget.graph.y1Label('Row') else: self.stackGraphWidget.graph.y1Label('Column') else: self.stackGraphWidget.graph.y1Label("File") if self.mcaIndex == 1: self.stackGraphWidget.graph.x1Label('Row') else: self.stackGraphWidget.graph.x1Label('Column') [ymax, xmax] = self.__stackImageData.shape if self._y1AxisInverted: self.stackGraphWidget.graph.zoomReset() self.stackGraphWidget.graph.setY1AxisInverted(True) if 0: #This is not needed because there are no curves in the graph self.stackGraphWidget.graph.setY1AxisLimits(0, ymax, replot=False) self.stackGraphWidget.graph.setX1AxisLimits(0, xmax, replot=False) self.stackGraphWidget.graph.replot() #I need it to update the canvas self.plotStackImage(update=True) else: self.stackGraphWidget.graph.zoomReset() self.stackGraphWidget.graph.setY1AxisInverted(False) if 0:#This is not needed because there are no curves in the graph self.stackGraphWidget.graph.setY1AxisLimits(0, ymax, replot=False) self.stackGraphWidget.graph.setX1AxisLimits(0, xmax, replot=False) self.stackGraphWidget.graph.replot() #I need it to update the canvas self.plotStackImage(update=True) self.__selectionMask = numpy.zeros(self.__stackImageData.shape, numpy.uint8) #init the ROI self.roiWindow.graphWidget.graph.setTitle("ICR ROI") self.roiWindow.graphWidget.graph.y1Label(self.stackGraphWidget.graph.y1Label()) self.roiWindow.graphWidget.graph.x1Label(self.stackGraphWidget.graph.x1Label()) self.roiWindow.graphWidget.graph.setY1AxisInverted(self.stackGraphWidget.graph.isY1AxisInverted()) if 0:#This is not needed because there are no curves in the graph self.roiGraphWidget.graph.setX1AxisLimits(0, self.__stackImageData.shape[0]) self.roiGraphWidget.graph.setY1AxisLimits(0, self.__stackImageData.shape[1]) self.roiGraphWidget.graph.replot() self.__ROIImageData = self.__stackImageData.copy() self.roiWindow.setImageData(self.__ROIImageData) def sendMcaSelection(self, mcaObject, key = None, legend = None, action = None): if action is None: action = "ADD" if key is None: key = "SUM" if legend is None: legend = "EDF Stack SUM" if self.normalizeButton.isChecked(): npixels = self.__stackImageData.shape[0] * self.__stackImageData.shape[1] legend += "/%d" % npixels sel = {} sel['SourceName'] = "EDF Stack" sel['Key'] = key sel['legend'] = legend sel['dataobject'] = mcaObject if action == "ADD": self.mcaWidget._addSelection([sel]) elif action == "REMOVE": self.mcaWidget._removeSelection([sel]) elif action == "REPLACE": self.mcaWidget._replaceSelection([sel]) elif action == "GET_CURRENT_SELECTION": return sel if self.tab is None: self.mcaWidget.show() if QTVERSION < '4.0.0': self.mcaWidget.raiseW() else: self.mcaWidget.raise_() else: if QTVERSION < '4.0.0': self.tab.setCurrentPage(self.tab.indexOf(self.mcaWidget)) else: self.tab.setCurrentWidget(self.mcaWidget) def _mcaWidgetSignal(self, ddict): if not self.__ROIConnected:return if ddict['event'] == "ROISignal": self.__stackBackgroundAnchors = None title = "%s" % ddict["name"] self.roiWindow.graphWidget.graph.setTitle(title) self.roiWindow.graphWidget.__title = title if (ddict["name"] == "ICR"): i1 = 0 i2 = self.stack.data.shape[self.mcaIndex] xw = ddict['calibration'][0] + \ ddict['calibration'][1] * self.__mcaData0.x[0] + \ ddict['calibration'][2] * self.__mcaData0.x[0] * \ self.__mcaData0.x[0] imiddle = int(0.5 * (i1+i2)) pos = 0.5 * (ddict['from'] + ddict['to']) imiddle = max(numpy.nonzero(xw <= pos)[0]) elif (ddict["type"]).upper() != "CHANNEL": #energy roi xw = ddict['calibration'][0] + \ ddict['calibration'][1] * self.__mcaData0.x[0] + \ ddict['calibration'][2] * self.__mcaData0.x[0] * \ self.__mcaData0.x[0] if xw[0] < xw[-1]: i1 = numpy.nonzero(ddict['from'] <= xw)[0] if len(i1): i1 = min(i1) else: return i2 = numpy.nonzero(xw <= ddict['to'])[0] if len(i2): i2 = max(i2) + 1 else: return pos = 0.5 * (ddict['from'] + ddict['to']) imiddle = max(numpy.nonzero(xw <= pos)[0]) else: i2 = numpy.nonzero(ddict['from']<= xw)[0] if len(i2): i2 = max(i2) else: return i1 = numpy.nonzero(xw <= ddict['to'])[0] if len(i1): i1 = min(i1) + 1 else: return pos = 0.5 * (ddict['from'] + ddict['to']) imiddle = min(numpy.nonzero(xw <= pos)[0]) else: i1 = numpy.nonzero(ddict['from'] <= self.__mcaData0.x[0])[0] if len(i1): i1 = min(i1) else: i1 = 0 i1 = max(i1, 0) i2 = numpy.nonzero(self.__mcaData0.x[0] <= ddict['to'])[0] if len(i2): i2 = max(i2) else: i2 = 0 i2 = min(i2+1, self.stack.data.shape[self.mcaIndex]) pos = 0.5 * (ddict['from'] + ddict['to']) imiddle = max(numpy.nonzero(self.__mcaData0.x[0] <= pos)[0]) xw = self.__mcaData0.x[0] if self.fileIndex == 0: if self.mcaIndex == 1: leftImage = self.stack.data[:,i1,:] middleImage = self.stack.data[:,imiddle,:] rightImage = self.stack.data[:,i2-1,:] dataImage = self.stack.data[:,i1:i2,:] maxImage = numpy.max(dataImage, 1) minImage = numpy.min(dataImage, 1) background = 0.5 * (i2-i1) * (leftImage+rightImage) self.__ROIImageData = numpy.sum(dataImage,1) else: if DEBUG: t0 = time.time() if isinstance(self.stack.data, numpy.ndarray): leftImage = self.stack.data[:,:,i1] middleImage = self.stack.data[:,:,imiddle] rightImage = self.stack.data[:,:,i2-1] dataImage = self.stack.data[:,:,i1:i2] maxImage = numpy.max(dataImage, 2) minImage = numpy.min(dataImage, 2) background = 0.5 * (i2-i1) * (leftImage+rightImage) self.__ROIImageData = numpy.sum(dataImage,2) else: shape = self.stack.data.shape self.__ROIImageData[:,:] = 0 background = self.__ROIImageData[:,:] * 1 leftImage = self.__ROIImageData[:,:] * 1 middleImage= self.__ROIImageData[:,:] * 1 rightImage = self.__ROIImageData[:,:] * 1 maxImage = self.__ROIImageData[:,:] * 1 minImage = self.__ROIImageData[:,:] * 1 step = 1 for i in range(shape[0]): tmpData = self.stack.data[i:i+step,:, i1:i2] * 1 numpy.add(self.__ROIImageData[i:i+step,:], numpy.sum(tmpData, 2), self.__ROIImageData[i:i+step,:]) numpy.add(minImage[i:i+step,:], numpy.min(tmpData, 2), minImage[i:i+step,:]) numpy.add(maxImage[i:i+step,:], numpy.max(tmpData, 2), maxImage[i:i+step,:]) leftImage[i:i+step, :] += tmpData[:, :, 0] middleImage[i:i+step, :] += tmpData[:, :, imiddle-i1] rightImage[i:i+step, :] += tmpData[:, :,-1] background = 0.5*(i2-i1)*(leftImage+rightImage) if DEBUG: print("ROI image calculation elapsed = %f" %\ (time.time() - t0)) elif self.fileIndex == 1: if self.mcaIndex == 0: if isinstance(self.stack.data, numpy.ndarray): leftImage = self.stack.data[i1,:,:] middleImage= self.stack.data[imiddle,:,:] rightImage = self.stack.data[i2-1,:,:] dataImage = self.stack.data[i1:i2,:,:] maxImage = numpy.max(dataImage, 0) minImage = numpy.min(dataImage, 0) background = 0.5 * (i2-i1) * (leftImage+rightImage) self.__ROIImageData = numpy.sum(dataImage, 0) else: shape = self.stack.data.shape self.__ROIImageData[:,:] = 0 background = self.__ROIImageData[:,:] * 1 leftImage = self.__ROIImageData[:,:] * 1 middleImage= self.__ROIImageData[:,:] * 1 rightImage = self.__ROIImageData[:,:] * 1 maxImage = self.__ROIImageData[:,:] * 1 minImage = self.__ROIImageData[:,:] * 1 if DEBUG: t0 = time.time() istep = 1 for i in range(i1, i2): tmpData = self.stack.data[i:i+istep,:,:] tmpData.shape = self.__ROIImageData.shape numpy.add(self.__ROIImageData, tmpData, self.__ROIImageData) if i == i1: minImage = tmpData maxImage = tmpData else: minMask = tmpData < minImage maxMask = tmpData > minImage minImage[minMask] = tmpData[minMask] maxImage[maxMask] = tmpData[maxMask] if (i == i1): leftImage = tmpData if (i == imiddle): middleImage = tmpData if i == (i2-1): rightImage = tmpData if DEBUG: print("Dynamic ROI elapsed = %f" %\ (time.time() - t0)) if i2 > i1: background = (leftImage + rightImage) * 0.5 * (i2-i1) else: if DEBUG: t0 = time.time() if isinstance(self.stack.data, numpy.ndarray): leftImage = self.stack.data[:,:,i1] middleImage= self.stack.data[:,:,imiddle] rightImage = self.stack.data[:,:,i2-1] dataImage = self.stack.data[:,:,i1:i2] maxImage = numpy.max(dataImage, 2) minImage = numpy.min(dataImage, 2) background = 0.5 * (i2-i1) * (leftImage+rightImage) self.__ROIImageData = numpy.sum(dataImage,2) else: shape = self.stack.data.shape self.__ROIImageData[:,:] = 0 background = self.__ROIImageData[:,:] * 1 leftImage = self.__ROIImageData[:,:] * 1 middleImage= self.__ROIImageData[:,:] * 1 rightImage = self.__ROIImageData[:,:] * 1 maxImage = self.__ROIImageData[:,:] * 1 minImage = self.__ROIImageData[:,:] * 1 step = 1 for i in range(shape[0]): tmpData = self.stack.data[i:i+step,:, i1:i2] * 1 numpy.add(self.__ROIImageData[i:i+step,:], numpy.sum(tmpData, 2), self.__ROIImageData[i:i+step,:]) numpy.add(minImage[i:i+step,:], numpy.min(tmpData, 2), minImage[i:i+step,:]) numpy.add(maxImage[i:i+step,:], numpy.max(tmpData, 2), maxImage[i:i+step,:]) leftImage[i:i+step, :] += tmpData[:, :, 0] middleImage[i:i+step, :] += tmpData[:, :, imiddle-i1] rightImage[i:i+step, :] += tmpData[:, :,-1] background = 0.5*(i2-i1)*(leftImage+rightImage) if DEBUG: print("ROI image calculation elapsed = %f" %\ (time.time() - t0)) else: #self.fileIndex = 2 if self.mcaIndex == 0: leftImage = self.stack.data[i1,:,:] middleImage= self.stack.data[imiddle,:,:] rightImage = self.stack.data[i2-1,:,:] background = 0.5 * (i2-i1) * (leftImage+rightImage) dataImage = self.stack.data[i1:i2,:,:] minImage = numpy.min(dataImage, 0) maxImage = numpy.max(dataImage, 0) self.__ROIImageData = numpy.sum(dataImage,0) else: leftImage = self.stack.data[:,i1,:] middleImage= self.stack.data[:,imidle,:] rightImage = self.stack.data[:,i2-1,:] background = 0.5 * (i2-i1) * (leftImage+rightImage) dataImage = self.stack.data[:,i1:i2,:] minImage = numpy.min(dataImage, 1) maxImage = numpy.max(dataImage, 1) self.__ROIImageData = numpy.sum(dataImage,1) self.__ROIImageBackground = background try: if ddict["name"] == "ICR": cursor = "Energy" if abs(ddict['calibration'][0]) < 1.0e-5: if abs(ddict['calibration'][1]-1) < 1.0e-5: if abs(ddict['calibration'][2]) < 1.0e-5: cursor = "Channel" elif ddict["type"].upper() == "CHANNEL": cursor = "Channel" else: cursor = ddict["type"] self.newRoiWindow.setImageList([self.__ROIImageData * 1, maxImage, minImage, leftImage, middleImage, rightImage, background], imagenames=[title, '%s Maximum' % title, '%s Minimum' % title, '%s %.6g' % (cursor,xw[i1]), '%s %.6g' % (cursor,xw[imiddle]), '%s %.6g' % (cursor,xw[(i2-1)]), '%s Background' %title]) except: print("Error on alternative ROI window:") print(sys.exc_info()) return self.__stackBackgroundAnchors = [i1, i2-1] if self.roiBackgroundButton.isChecked(): self.__ROIImageData = self.__ROIImageData - self.__ROIImageBackground self.roiWindow.graphWidget.graph.setTitle(self.roiWindow.graphWidget.__title + " Net") if self.roiWindow.colormapDialog is not None: minData = self.__ROIImageData.min() maxData = self.__ROIImageData.max() self.roiWindow.colormapDialog.setDataMinMax(minData, maxData) #self._resetSelection() #self.plotStackImage(update = True) self.roiWindow.setImageData(self.__ROIImageData) if self.isHidden(): self.show() if self.tab is not None: if QTVERSION < '4.0.0': self.tab.setCurrentPage(self.tab.indexOf(self.rgbWidget)) else: self.tab.setCurrentWidget(self.rgbWidget) def __applyMaskToStackImage(self): if self.__selectionMask is None: return #Stack Image if self.__stackColormap is None: for i in range(4): self.__stackPixmap[:,:,i] = (self.__stackPixmap0[:,:,i] *\ (1 - (0.2 * self.__selectionMask))).astype(numpy.uint8) elif int(str(self.__stackColormap[0])) > 1: #color for i in range(4): self.__stackPixmap[:,:,i] = (self.__stackPixmap0[:,:,i] *\ (1 - (0.2 * self.__selectionMask))).astype(numpy.uint8) else: self.__stackPixmap[self.__selectionMask>0,0] = 0x40 self.__stackPixmap[self.__selectionMask>0,2] = 0x70 self.__stackPixmap[self.__selectionMask>0,1] = self.__stackPixmap0[self.__selectionMask>0, 1] self.__stackPixmap[self.__selectionMask>0,3] = 0x40 return def getStackPixmapFromData(self): colormap = self.__stackColormap if colormap is None: (self.__stackPixmap,size,minmax)= spslut.transform(\ self.__stackImageData, (1,0), (spslut.LINEAR,3.0), "BGRX", spslut.TEMP, 1, (0,1),(0, 255),1) else: if len(colormap) < 7: colormap.append(spslut.LINEAR) (self.__stackPixmap,size,minmax)= spslut.transform(\ self.__stackImageData, (1,0), (colormap[6],3.0), "BGRX", COLORMAPLIST[int(str(colormap[0]))], colormap[1], (colormap[2],colormap[3]),(0,255),1) self.__stackPixmap = self.__stackPixmap.astype(numpy.ubyte) self.__stackPixmap.shape = [self.__stackImageData.shape[0], self.__stackImageData.shape[1], 4] def plotStackImage(self, update = True): if self.__stackImageData is None: self.stackGraphWidget.graph.clear() return if update: self.getStackPixmapFromData() self.__stackPixmap0 = self.__stackPixmap.copy() self.__applyMaskToStackImage() if not self.stackGraphWidget.graph.yAutoScale: ylimits = self.stackGraphWidget.graph.getY1AxisLimits() if not self.stackGraphWidget.graph.xAutoScale: xlimits = self.stackGraphWidget.graph.getX1AxisLimits() self.stackGraphWidget.graph.pixmapPlot(self.__stackPixmap.tostring(), (self.__stackImageData.shape[1], self.__stackImageData.shape[0]), xmirror = 0, ymirror = not self._y1AxisInverted) if not self.stackGraphWidget.graph.yAutoScale: self.stackGraphWidget.graph.setY1AxisLimits(ylimits[0], ylimits[1], replot=False) if not self.stackGraphWidget.graph.xAutoScale: self.stackGraphWidget.graph.setX1AxisLimits(xlimits[0], xlimits[1], replot=False) self.stackGraphWidget.graph.replot() def _stackZoomResetSignal(self): if DEBUG: print("_stackZoomResetSignal") self.stackGraphWidget._zoomReset(replot=False) self.plotStackImage(True) def _hFlipIconSignal(self): if not self.stackGraphWidget.graph.yAutoScale: qt.QMessageBox.information(self, "Flip Image", "Please set stack Y Axis to AutoScale first") return if not self.stackGraphWidget.graph.xAutoScale: qt.QMessageBox.information(self, "Flip Image", "Please set stack X Axis to AutoScale first") return if not self.roiWindow.graphWidget.graph.yAutoScale: qt.QMessageBox.information(self, "Flip Image", "Please set ROI image Y Axis to AutoScale first") return if not self.roiWindow.graphWidget.graph.xAutoScale: qt.QMessageBox.information(self, "Flip Image", "Please set ROI image X Axis to AutoScale first") return if self._y1AxisInverted: self._y1AxisInverted = False else: self._y1AxisInverted = True self.stackGraphWidget.graph.zoomReset() self.roiWindow.graphWidget.graph.zoomReset() self.stackGraphWidget.graph.setY1AxisInverted(self._y1AxisInverted) self.roiWindow._y1AxisInverted = self._y1AxisInverted self.plotStackImage(update=True) self.roiWindow.plotImage(update=True) def selectStackColormap(self): if self.__stackImageData is None:return if self.__stackColormapDialog is None: self.__initStackColormapDialog() if self.__stackColormapDialog.isHidden(): self.__stackColormapDialog.show() if QTVERSION < '4.0.0':self.__stackColormapDialog.raiseW() else: self.__stackColormapDialog.raise_() self.__stackColormapDialog.show() def __initStackColormapDialog(self): minData = self.__stackImageData.min() maxData = self.__stackImageData.max() self.__stackColormapDialog = ColormapDialog.ColormapDialog() self.__stackColormapDialog.colormapIndex = self.__stackColormapDialog.colormapList.index("Temperature") self.__stackColormapDialog.colormapString = "Temperature" if QTVERSION < '4.0.0': self.__stackColormapDialog.setCaption("Stack Colormap Dialog") self.connect(self.__stackColormapDialog, qt.PYSIGNAL("ColormapChanged"), self.updateStackColormap) else: self.__stackColormapDialog.setWindowTitle("Stack Colormap Dialog") self.connect(self.__stackColormapDialog, qt.SIGNAL("ColormapChanged"), self.updateStackColormap) self.__stackColormapDialog.setDataMinMax(minData, maxData) self.__stackColormapDialog.setAutoscale(1) self.__stackColormapDialog.setColormap(self.__stackColormapDialog.colormapIndex) self.__stackColormap = (self.__stackColormapDialog.colormapIndex, self.__stackColormapDialog.autoscale, self.__stackColormapDialog.minValue, self.__stackColormapDialog.maxValue, minData, maxData) self.__stackColormapDialog._update() def updateStackColormap(self, *var): if len(var) > 6: self.__stackColormap = [var[0], var[1], var[2], var[3], var[4], var[5], var[6]] elif len(var) > 5: self.__stackColormap = [var[0], var[1], var[2], var[3], var[4], var[5]] else: self.__stackColormap = [var[0], var[1], var[2], var[3], var[4], var[5]] self.plotStackImage(True) def _addImageClicked(self, image, title): self.rgbWidget.addImage(image, title) if self.tab is None: if self.master: self.rgbWidget.show() else: self.tab.setCurrentWidget(self.rgbWidget) def _removeImageClicked(self, title): self.rgbWidget.removeImage(title) def _replaceImageClicked(self, image, title): self.rgbWidget.reset() self.rgbWidget.addImage(image, title) if self.rgbWidget.isHidden(): self.rgbWidget.show() if self.tab is None: self.rgbWidget.show() self.rgbWidget.raise_() else: self.tab.setCurrentWidget(self.rgbWidget) def _addMcaClicked(self, action = None): if action is None: action = "ADD" #original ICR mca if self.__stackImageData is None: return mcaData = None if self.__selectionMask is None: if self.normalizeButton.isChecked(): npixels = self.__stackImageData.shape[0] *\ self.__stackImageData.shape[1] * 1.0 dataObject = DataObject.DataObject() dataObject.info.update(self.__mcaData0.info) dataObject.x = [self.__mcaData0.x[0]] dataObject.y = [self.__mcaData0.y[0] / npixels]; else: dataObject = self.__mcaData0 return self.sendMcaSelection(dataObject, action = action) npixels = len(numpy.nonzero(numpy.ravel(self.__selectionMask)>0)[0]) * 1.0 if npixels == 0: if self.normalizeButton.isChecked(): npixels = self.__stackImageData.shape[0] * self.__stackImageData.shape[1] dataObject = DataObject.DataObject() dataObject.info.update(self.__mcaData0.info) dataObject.x = [self.__mcaData0.x[0]] dataObject.y = [self.__mcaData0.y[0] / npixels]; else: dataObject = self.__mcaData0 return self.sendMcaSelection(dataObject, action = action) mcaData = numpy.zeros(self.__mcaData0.y[0].shape, numpy.float) n_nonselected = self.__stackImageData.shape[0] *\ self.__stackImageData.shape[1] - npixels if n_nonselected < npixels: arrayMask = (self.__selectionMask == 0) else: arrayMask = (self.__selectionMask > 0) cleanMask = numpy.nonzero(arrayMask) if DEBUG: print("self.fileIndex, self.mcaIndex = %d, %d" %\ (self.fileIndex, self.mcaIndex)) if DEBUG: t0 = time.time() if len(cleanMask[0]) and len(cleanMask[1]): cleanMask = numpy.array(cleanMask).transpose() if self.fileIndex == 2: if self.mcaIndex == 0: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[:,r,c] else: if DEBUG: print("Dynamic loading case 0") #no other choice than to read all images #for the time being, one by one for i in range(self.stack.data.shape[0]): tmpData = self.stack.data[i:i+1,:,:] tmpData.shape = tmpData.shape[1:] mcaData[i] = (tmpData*arrayMask).sum() elif self.mcaIndex == 1: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[r,:,c] else: raise IndexError("Dynamic loading case 1") else: raise IndexError("Wrong combination of indices. Case 0") elif self.fileIndex == 1: if self.mcaIndex == 0: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[:,r,c] else: if DEBUG: print("Dynamic loading case 2") #no other choice than to read all images #for the time being, one by one for i in range(self.stack.data.shape[0]): tmpData = self.stack.data[i:i+1,:,:] tmpData.shape = tmpData.shape[1:] #multiplication is faster than selection #tmpData[arrayMask].sum() in my machine mcaData[i] = (tmpData*arrayMask).sum() elif self.mcaIndex == 2: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[r,c,:] else: if DEBUG: print("Dynamic loading case 3") #try to minimize access to the file row_dict = {} for r, c in cleanMask: if r not in row_dict.keys(): key = '%d' % r row_dict[key] = [] row_dict[key].append(c) for key in row_dict.keys(): r = int(key) tmpMcaData = self.stack.data[r:r+1, row_dict[key],:] tmpMcaData.shape = 1, -1 mcaData += numpy.sum(tmpMcaData,0) else: raise IndexError("Wrong combination of indices. Case 1") elif self.fileIndex == 0: if self.mcaIndex == 1: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[r,:,c] else: raise IndexError("Dynamic loading case 4") elif self.mcaIndex == 2: if isinstance(self.stack.data, numpy.ndarray): for r, c in cleanMask: mcaData += self.stack.data[r,c,:] else: if DEBUG: print("Dynamic loading case 5") #try to minimize access to the file row_dict = {} for r, c in cleanMask: if r not in row_dict.keys(): key = '%d' % r row_dict[key] = [] row_dict[key].append(c) for key in row_dict.keys(): r = int(key) tmpMcaData = self.stack.data[r:r+1, row_dict[key],:] tmpMcaData.shape = 1, -1 mcaData += numpy.sum(tmpMcaData,0) else: raise IndexError("Wrong combination of indices. Case 2") else: raise IndexError("File index undefined") if DEBUG: print("Mca sum elapsed = %f" % (time.time() - t0)) if n_nonselected < npixels: mcaData = self.__mcaData0.y[0] - mcaData if self.normalizeButton.isChecked(): mcaData = mcaData/npixels calib = self.stack.info['McaCalib'] dataObject = DataObject.DataObject() dataObject.info = {"McaCalib": calib, "selectiontype":"1D", "SourceName":"EDF Stack", "Key":"Selection"} dataObject.x = [numpy.arange(len(mcaData)).astype(numpy.float) + self.stack.info['Channel0']] dataObject.y = [mcaData] legend = self.__getLegend() if self.normalizeButton.isChecked(): legend += "/%d" % npixels return self.sendMcaSelection(dataObject, key = "Selection", legend =legend, action = action) def __getLegend(self): title = qt.safe_str(self.roiWindow.graphWidget.graph.title().text()) return "Stack " + title + " selection" def _removeMcaClicked(self): #remove the mca #dataObject = self.__mcaData0 #send a dummy object dataObject = DataObject.DataObject() legend = self.__getLegend() if self.normalizeButton.isChecked(): legend += "/" curves = self.mcaWidget.graph.curves.keys() for curve in curves: if curve.startswith(legend): legend = curve break self.sendMcaSelection(dataObject, legend = legend, action = "REMOVE") def _replaceMcaClicked(self): #replace the mca self.__ROIConnected = False self._addMcaClicked(action="REPLACE") self.__ROIConnected = True def closeEvent(self, event): if self.__stackColormapDialog is not None: self.__stackColormapDialog.close() if self.newRoiWindow.colormapDialog is not None: self.newRoiWindow.colormapDialog.close() self.newRoiWindow.close() if self.roiWindow.colormapDialog is not None: self.roiWindow.colormapDialog.close() if self.roiWindow._matplotlibSaveImage is not None: self.roiWindow._matplotlibSaveImage.close() if self.pcaWindow is not None: if self.pcaWindow.colormapDialog is not None: self.pcaWindow.colormapDialog.close() self.pcaWindow.close() if self.nnmaWindow is not None: if self.nnmaWindow.colormapDialog is not None: self.nnmaWindow.colormapDialog.close() self.nnmaWindow.close() if self.externalImagesWindow is not None: if self.externalImagesWindow.colormapDialog is not None: self.externalImagesWindow.colormapDialog.close() self.externalImagesWindow.close() CloseEventNotifyingWidget.CloseEventNotifyingWidget.closeEvent(self, event) def _resetSelection(self): if DEBUG: print("_resetSelection") if self.__stackImageData is None: return self.__selectionMask = numpy.zeros(self.__stackImageData.shape, numpy.uint8) self.plotStackImage(update = True) self.roiWindow.setSelectionMask(self.__selectionMask) def _getFileList(self, fileTypeList, message=None, getfilter=None): if message is None: message = "Please select a file" if getfilter is None: getfilter = False wdir = PyMcaDirs.inputDir filterused = None if QTVERSION < '4.0.0': if sys.platform != 'darwin': filetypes = "" for filetype in fileTypeList: filetypes += filetype+"\n" filelist = qt.QFileDialog.getOpenFileNames(filetypes, wdir, self, message, message) if not len(filelist): if getfilter: return [], filterused else: return [] else: #if (QTVERSION < '4.3.0') and (sys.platform != 'darwin'): if (PyMcaDirs.nativeFileDialogs) and (not getfilter): filetypes = "" for filetype in fileTypeList: filetypes += filetype+"\n" filelist = qt.QFileDialog.getOpenFileNames(self, message, wdir, filetypes) if not len(filelist): if getfilter: return [], filterused else: return [] else: sample = qt.safe_str(filelist[0]) for filetype in fileTypeList: ftype = filetype.replace("(", "") ftype = ftype.replace(")", "") extensions = ftype.split()[2:] for extension in extensions: if sample.endswith(extension[-3:]): filterused = filetype break else: fdialog = qt.QFileDialog(self) fdialog.setModal(True) fdialog.setWindowTitle(message) strlist = qt.QStringList() for filetype in fileTypeList: strlist.append(filetype) fdialog.setFilters(strlist) fdialog.setFileMode(fdialog.ExistingFiles) fdialog.setDirectory(wdir) if QTVERSION > '4.3.0': history = fdialog.history() if len(history) > 6: fdialog.setHistory(history[-6:]) ret = fdialog.exec_() if ret == qt.QDialog.Accepted: filelist = fdialog.selectedFiles() if getfilter: filterused = qt.safe_str(fdialog.selectedFilter()) fdialog.close() del fdialog else: fdialog.close() del fdialog if getfilter: return [], filterused else: return [] filelist = map(str, filelist) if not(len(filelist)): return [] PyMcaDirs.inputDir = os.path.dirname(filelist[0]) if PyMcaDirs.outputDir is None: PyMcaDirs.outputDir = os.path.dirname(filelist[0]) #filelist.sort() if getfilter: return filelist, filterused else: return filelist def _getStackOfFiles(self, getfilter=None): if getfilter is None: getfilter = False fileTypeList = ["EDF Files (*edf)", "EDF Files (*ccd)", "Specfile Files (*mca)", "Specfile Files (*dat)", "OMNIC Files (*map)", "OPUS-DPT Files (*.DPT *.dpt)", "HDF5 Files (*.nxs *.hdf *.h5)", "AIFIRA Files (*DAT)", "SupaVisio Files (*pige *pixe *rbs)", "Image Files (*edf)", "All Files (*)"] if not HDF5: idx = fileTypeList.index("HDF5 Files (*.nxs *.hdf *.h5)") del fileTypeList[idx] message = "Open ONE indexed stack or SEVERAL files" return self._getFileList(fileTypeList, message=message, getfilter=getfilter) def getFileListFromPattern(self, pattern, begin, end, increment=None): if type(begin) == type(1): begin = [begin] if type(end) == type(1): end = [end] if len(begin) != len(end): raise ValueError("Begin list and end list do not have same length") if increment is None: increment = [1] * len(begin) elif type(increment) == type(1): increment = [increment] if len(increment) != len(begin): raise ValueError(\ "Increment list and begin list do not have same length") fileList = [] if len(begin) == 1: for j in range(begin[0], end[0]+increment[0], increment[0]): fileList.append(pattern % (j)) elif len(begin) == 2: for j in range(begin[0], end[0]+increment[0], increment[0]): for k in range(begin[1], end[1]+increment[1], increment[1]): fileList.append(pattern % (j, k)) elif len(begin) == 3: raise ValueError("Cannot handle three indices yet.") for j in range(begin[0], end[0]+increment[0], increment[0]): for k in range(begin[1], end[1]+increment[1], increment[1]): for l in range(begin[2], end[2]+increment[2], increment[2]): fileList.append(pattern % (j, k, l)) else: raise ValueError("Cannot handle more than three indices.") return fileList def runAsMain(): import getopt options = '' longoptions = ["fileindex=","old", "filepattern=", "begin=", "end=", "increment=", "nativefiledialogs=", "imagestack="] try: opts, args = getopt.getopt( sys.argv[1:], options, longoptions) except: print(sys.exc_info()[1]) sys.exit(1) #import time #t0= time.time() fileindex = 0 #it is faster with fileindex=0 filepattern=None begin = None end = None increment = None imagestack=False for opt, arg in opts: if opt in '--begin': if "," in arg: begin = map(int,arg.split(",")) else: begin = [int(arg)] elif opt in '--end': if "," in arg: end = map(int,arg.split(",")) else: end = int(arg) elif opt in '--increment': if "," in arg: increment = map(int,arg.split(",")) else: increment = int(arg) elif opt in '--filepattern': filepattern = arg.replace('"','') filepattern = filepattern.replace("'","") elif opt in '--fileindex': fileindex = int(arg) elif opt in '--imagestack': imagestack = int(arg) elif opt in '--nativefiledialogs': if int(arg): PyMcaDirs.nativeFileDialogs=True else: PyMcaDirs.nativeFileDialogs=False if filepattern is not None: if (begin is None) or (end is None): raise ValueError(\ "A file pattern needs a set of begin and end indices") app = qt.QApplication([]) w = QEDFStackWidget(master=True) if filepattern is not None: #get the first filename filename = filepattern % tuple(begin) if not os.path.exists(filename): raise IOError("Filename %s does not exist." % filename) #ignore the args even if present args = w.getFileListFromPattern(filepattern, begin, end, increment=increment) aifirafile = False specfile = False if len(args): f = open(args[0], 'rb') #read 10 characters line = f.read(10) f.close() omnicfile = False if line[0] == "\n": line = line[1:] if line[0] == "{": if imagestack: #prevent any modification fileindex = 0 if filepattern is not None: if len(begin) != 1: raise IOError(\ "EDF stack redimensioning not supported yet") stack = QStack(imagestack=imagestack) elif line.startswith('Spectral'): stack = OmnicMap.OmnicMap(args[0]) omnicfile = True elif line.startswith('#\tDate:'): stack = LuciaMap.LuciaMap(args[0]) omnicfile = True elif args[0][-4:].upper() in ["PIGE", "PIXE"]: stack = SupaVisioMap.SupaVisioMap(args[0]) omnicfile = True elif args[0][-3:].upper() in ["RBS"]: stack = SupaVisioMap.SupaVisioMap(args[0]) omnicfile = True elif args[0][-3:].lower() in [".h5", "nxs", "hdf"]: if not HDF5: raise IOError(\ "No HDF5 support while trying to read an HDF5 file") stack = QHDF5Stack1D.QHDF5Stack1D(args) omnicfile = True else: specfile = True stack = QSpecFileStack() f.close() if len(args) > 1: shape = None if specfile and (filepattern is not None): if len(begin) == 2: if increment is None: increment = [1] * len(begin) shape = (len(range(begin[0], end[0]+1, increment[0])), len(range(begin[1], end[1]+1, increment[1]))) stack.loadFileList(args, fileindex=fileindex, shape=shape) else: stack.loadFileList(args, fileindex=fileindex) if os.path.basename(args[0]) == args[0]: filename = os.path.join(os.getcwd(), args[0]) PyMcaDirs.inputDir = os.path.dirname(filename) if PyMcaDirs.outputDir is None: PyMcaDirs.outputDir = os.path.dirname(filename) elif len(args) == 1: if not omnicfile: try: stack.loadIndexedStack(args, begin, end, fileindex=fileindex) except: msg = qt.QMessageBox() msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.setWindowTitle("Error") msg.exec_() if DEBUG: raise sys.exit(1) try: PyMcaDirs.inputDir = os.path.dirname(args[0]) if PyMcaDirs.outputDir is None: PyMcaDirs.outputDir = os.path.dirname(args[0]) except ValueError: PyMcaDirs.inputDir = os.getcwd() else: if 1: filelist, filefilter = w._getStackOfFiles(getfilter=True) if len(filelist): PyMcaDirs.inputDir = os.path.dirname(filelist[0]) f = open(filelist[0], 'rb') #read 10 characters line = f.read(10) f.close() omnicfile = False if filefilter.upper().startswith('HDF5'): stack = QHDF5Stack1D.QHDF5Stack1D(filelist) omnicfile = True elif filefilter.upper().startswith('OPUS-DPT'): stack = OpusDPTMap.OpusDPTMap(filelist[0]) omnicfile = True elif filefilter[0:6].upper() == "AIFIRA": stack = AifiraMap.AifiraMap(filelist[0]) omnicfile = True aifirafile = True elif filefilter[0:9] == "SupaVisio": stack = SupaVisioMap.SupaVisioMap(filelist[0]) omnicfile = True elif filefilter.upper().startswith("IMAGE"): imagestack = True fileindex = 0 stack = QStack(imagestack=True) elif line[0] == "{": stack = QStack(imagestack=imagestack) if imagestack: fileindex = 0 elif line.startswith('Spectral'): stack = OmnicMap.OmnicMap(filelist[0]) omnicfile = True elif line.startswith('#\tDate'): stack = LuciaMap.LuciaMap(filelist[0]) omnicfile = True elif filelist[0][-4:].upper() in ["PIGE", "PIGE"]: stack = SupaVisioMap.SupaVisioMap(filelist[0]) omnicfile = True elif filelist[0][-3:].upper() in ["RBS"]: stack = SupaVisioMap.SupaVisioMap(filelist[0]) omnicfile = True else: stack = QSpecFileStack() if len(filelist) == 1: if not omnicfile: try: stack.loadIndexedStack(filelist[0], begin, end, fileindex=fileindex) except: msg = qt.QMessageBox() msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() sys.exit(1) elif len(filelist): if not omnicfile: try: stack.loadFileList(filelist, fileindex=fileindex) except: msg = qt.QMessageBox() msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() if DEBUG: raise sys.exit(1) else: print("Usage: ") print("python QEDFStackWidget.py SET_OF_EDF_FILES") print("python QEDFStackWidget.py --begin=0 --end=XX INDEXED_EDF_FILE") print("python QEDFStackWidget.py --begin=0,0 --end=x,y --filepattern='mca_%03d%03d.fio'") sys.exit(1) elif os.path.exists(".\COTTE\ch09\ch09__mca_0005_0000_0070.edf"): stack.loadIndexedStack(".\COTTE\ch09\ch09__mca_0005_0000_0070.edf") elif os.path.exists("Z:\COTTE\ch09\ch09__mca_0005_0000_0070.edf"): stack.loadIndexedStack("Z:\COTTE\ch09\ch09__mca_0005_0000_0070.edf") else: print("Usage: ") print("python QEDFStackWidget.py SET_OF_EDF_FILES") sys.exit(1) shape = stack.data.shape def quitSlot(): sys.exit() if 1: qt.QObject.connect(app, qt.SIGNAL("lastWindowClosed()"), quitSlot) else: qt.QObject.connect(app, qt.SIGNAL("lastWindowClosed()"), app, qt.SLOT("quit()")) if aifirafile: masterStack = DataObject.DataObject() masterStack.info = copy.deepcopy(stack.info) masterStack.data = stack.data[:,:,0:1024] masterStack.info['Dim_2'] = int(masterStack.info['Dim_2'] / 2) slaveStack = DataObject.DataObject() slaveStack.info = copy.deepcopy(stack.info) slaveStack.data = stack.data[:,:, 1024:] slaveStack.info['Dim_2'] = int(slaveStack.info['Dim_2'] / 2) w.setStack(masterStack) w.slave = QEDFStackWidget(rgbwidget=w.rgbWidget, master=False) w.slave.setStack(slaveStack) w.connectSlave(w.slave) w._resetSelection() w.loadStackButton.hide() w.slave.show() else: w.setStack(stack) w.show() #print "reading elapsed = ", time.time() - t0 if qt.qVersion() < '4.0.0': app.setMainWidget(w) app.exec_loop() else: app.exec_() if __name__ == "__main__": runAsMain()