#!/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 traceback import numpy import weakref from PyMca import PyMcaQt as qt if hasattr(qt, "QString"): QString = qt.QString else: QString = qt.safe_str from PyMca import DataObject from PyMca import McaWindow from PyMca import StackBase from PyMca import CloseEventNotifyingWidget from PyMca import MaskImageWidget from PyMca import StackROIWindow from PyMca import RGBCorrelator from PyMca.RGBCorrelatorWidget import ImageShapeDialog from PyMca.PyMca_Icons import IconDict from PyMca import StackSelector from PyMca import PyMcaDirs from PyMca import ArraySave HDF5 = ArraySave.HDF5 DEBUG = 0 QTVERSION = qt.qVersion() if DEBUG: StackBase.DEBUG = DEBUG class QStackWidget(StackBase.StackBase, CloseEventNotifyingWidget.CloseEventNotifyingWidget): def __init__(self, parent = None, mcawidget = None, rgbwidget = None, vertical = False, master = True): StackBase.StackBase.__init__(self) CloseEventNotifyingWidget.CloseEventNotifyingWidget.__init__(self, parent) 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.setContentsMargins(0, 0, 0, 0) self.mainLayout.setSpacing(2) self.mcaWidget = mcawidget self.rgbWidget = rgbwidget self.master = master self._slave = None self._masterStack = None self.stackSelector = None self._build(vertical=vertical) self._buildBottom() self._buildConnections() self.__ROIConnected = True def _build(self, vertical=False): box = qt.QSplitter(self) if vertical: box.setOrientation(qt.Qt.Vertical) boxmainlayout = qt.QVBoxLayout(box) else: box.setOrientation(qt.Qt.Horizontal) boxmainlayout = qt.QHBoxLayout(box) self.stackWindow = qt.QWidget(box) self.stackWindow.mainLayout = qt.QVBoxLayout(self.stackWindow) self.stackWindow.mainLayout.setContentsMargins(0, 0, 0, 0) self.stackWindow.mainLayout.setSpacing(0) #if HDF5: if 1: self.stackWidget = MaskImageWidget.MaskImageWidget(self.stackWindow, selection=False, standalonesave=False, imageicons=False) self._stackSaveMenu = qt.QMenu() if HDF5: self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Spectra"), self.saveStackAsNeXusSpectra) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Images"), self.saveStackAsNeXusImages) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Compressed Spectra"), self.saveStackAsNeXusCompressedSpectra) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Compressed Images"), self.saveStackAsNeXusCompressedImages) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Float32 Spectra"), self.saveStackAsFloat32NeXusSpectra) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Float64 Spectra"), self.saveStackAsFloat64NeXusSpectra) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Float32 Images"), self.saveStackAsFloat32NeXusImages) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Float64 Images"), self.saveStackAsFloat64NeXusImages) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as HDF5 /data"), self.saveStackAsSimplestHDF5) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Monochromatic TIFF Images"), self.saveStackAsMonochromaticTiffImages) self._stackSaveMenu.addAction(QString("Save Zoomed Stack Region as Float32 TIFF Images"), self.saveStackAsFloat32TiffImages) self._stackSaveMenu.addAction(QString("Standard Graphics"), self.stackWidget.graphWidget._saveIconSignal) self.connect(self.stackWidget.graphWidget.saveToolButton, qt.SIGNAL("clicked()"), self._stackSaveToolButtonSignal) else: self.stackWidget = MaskImageWidget.MaskImageWidget(self.stackWindow, selection=False, imageicons=False) self.stackGraphWidget = self.stackWidget.graphWidget self.roiWindow = qt.QWidget(box) self.roiWindow.mainLayout = qt.QVBoxLayout(self.roiWindow) self.roiWindow.mainLayout.setContentsMargins(0, 0, 0, 0) self.roiWindow.mainLayout.setSpacing(0) standaloneSaving = True self.roiWidget = MaskImageWidget.MaskImageWidget(parent=self.roiWindow, rgbwidget=self.rgbWidget, selection=True, colormap=True, imageicons=True, standalonesave=standaloneSaving, profileselection=True) 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.roiWidget.graphWidget._addToolButton(\ self.roiBackgroundIcon, self._roiSubtractBackgroundClicked, infotext, toggle = True, state = False, position = 6) self.roiGraphWidget = self.roiWidget.graphWidget self.stackWindow.mainLayout.addWidget(self.stackWidget) self.roiWindow.mainLayout.addWidget(self.roiWidget) box.addWidget(self.stackWindow) box.addWidget(self.roiWindow) boxmainlayout.addWidget(self.stackWindow) boxmainlayout.addWidget(self.roiWindow) self.mainLayout.addWidget(box) #add some missing icons offset = 6 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.' self.normalizeIcon = qt.QIcon(qt.QPixmap(IconDict["normalize16"])) self.normalizeButton = self.stackGraphWidget._addToolButton(\ self.normalizeIcon, self.normalizeIconChecked, infotext, toggle = True, state = False, position = 6) offset += 1 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 shape', position = offset) offset += 1 self.pluginIcon = qt.QIcon(qt.QPixmap(IconDict["plugin"])) infotext = "Call/Load Stack Plugins" self.stackGraphWidget._addToolButton(self.pluginIcon, self._pluginClicked, infotext, toggle = False, state = False, position = offset) def setStack(self, *var, **kw): self.stackWidget.setImageData(None) self.roiWidget.setImageData(None) StackBase.StackBase.setStack(self, *var, **kw) if (1 in self._stack.data.shape) and\ isinstance(self._stack.data, numpy.ndarray): oldshape = self._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 self._stack.data.shape = [shape[0], shape[1], oldshape[2]] self.stackWidget.setImageData(None) self.roiWidget.setImageData(None) StackBase.StackBase.setStack(self, self._stack, **kw) try: if 'SourceName' in self._stack.info: if type(self._stack.info['SourceName']) == type([]): if len(self._stack.info['SourceName']) == 1: title = qt.safe_str(self._stack.info['SourceName']) else: f0 = qt.safe_str(self._stack.info['SourceName'][0]) f1 = qt.safe_str(self._stack.info['SourceName'][-1]) try: f0 = os.path.basename(f0) f1 = os.path.basename(f1) except: pass title = "Stack from %s to %s" % (f0, f1) else: title = qt.safe_str(self._stack.info['SourceName']) self.setWindowTitle(title) except: # TODO: give a reasonable title pass def normalizeIconChecked(self): pass def _roiSubtractBackgroundClicked(self): if not len(self._ROIImageList): return if self.roiBackgroundButton.isChecked(): self.roiWidget.setImageData(self._ROIImageList[0]-\ self._ROIImageList[-1]) self.roiWidget.graphWidget.graph.setTitle(self._ROIImageNames[0]+\ " Net") else: self.roiWidget.setImageData(self._ROIImageList[0]) self.roiWidget.graphWidget.graph.setTitle(self._ROIImageNames[0]) 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): try: fname = qt.safe_str(filename) if fname.endswith('.h5') or\ fname.endswith('.hdf'): return fname else: return fname + ".h5" except UnicodeEncodeError: msg = qt.QMessageBox(self) msg.setWindowTitle("Encoding error") msg.setIcon(qt.QMessageBox.Critical) msg.setText("Please use ASCII characters in file name and path") msg.exec_() return "" def _getOutputTiffFilename(self): fileTypes = "TIFF Files (*.tif *.tiff *.TIF *.TIFF)" message = "Enter output filename" wdir = PyMcaDirs.outputDir filename = qt.QFileDialog.getSaveFileName(self, message, wdir, fileTypes) if len(filename): try: fname = qt.safe_str(filename) if fname.endswith('.tif') or\ fname.endswith('.tiff') or\ fname.endswith('.TIF') or\ fname.endswith('.TIFF'): return fname else: return fname + ".tif" except UnicodeEncodeError: msg = qt.QMessageBox(self) msg.setWindowTitle("Encoding error") msg.setIcon(qt.QMessageBox.Critical) msg.setText("Please use ASCII characters in file name and path") msg.exec_() return "" def saveStackAsMonochromaticTiffImages(self, dtype=None): if dtype is None: dtype = self._stack.data.dtype if dtype in [numpy.uint32, numpy.uint64]: dtype = numpy.float32 elif dtype in [numpy.int32, numpy.int64]: dtype = numpy.float32 mcaIndex = self._stack.info.get('McaIndex', -1) filename = self._getOutputTiffFilename() if not len(filename): return ArraySave.save3DArrayAsMonochromaticTiff(self._stack.data, filename, labels = None, dtype=dtype, mcaindex=mcaIndex) def saveStackAsFloat32TiffImages(self): return self.saveStackAsMonochromaticTiffImages(dtype=numpy.float32) def saveStackAsNeXus(self, dtype=None, interpretation=None, compression=False): mcaIndex = self._stack.info.get('McaIndex', -1) if interpretation is None: if mcaIndex in [0]: interpretation = "image" else: interpretation = "spectrum" if interpretation not in ["spectrum", "image"]: raise ValueError("Unknown data interpretation %s" % interpretation) filename = self._getOutputHDF5Filename() if not len(filename): return #get limits row0, row1 = self.stackWidget.graph.getY1AxisLimits() col0, col1 = self.stackWidget.graph.getX1AxisLimits() #this should go to array save ... shape = self._stack.data.shape if mcaIndex in [0]: row0 = int(max([row0+0.5, 0])) row1 = int(min([row1+0.5, self._stack.data.shape[1]])) col0 = int(max([col0+0.5, 0])) col1 = int(min([col1+0.5, self._stack.data.shape[2]])) view = self._stack.data[:, row0:row1+1, col0:col1+1] else: row0 = int(max([row0+0.5, 0])) row1 = int(min([row1+0.5, self._stack.data.shape[0]])) col0 = int(max([col0+0.5, 0])) col1 = int(min([col1+0.5, self._stack.data.shape[1]])) view = self._stack.data[row0:row1+1, col0:col1+1,:] # the current graph axis is saved axes = [None] * len(self._stack.data.shape) labels = [None] * len(self._stack.data.shape) try: xLabel = qt.safe_str(self.mcaWidget.graph.xlabel()) except: xLabel = None try: xData, y, legend, info = self.mcaWidget.getActiveCurve() except: xData = self._mcaData0.x[0] xLabel = 'Channels' if interpretation == 'image': labels[0] = xLabel axes[0] = xData else: labels[-1] = xLabel axes[-1] = xData try: ArraySave.save3DArrayAsHDF5(view, filename, axes=axes, labels=labels, dtype=dtype, mode='nexus', mcaindex=mcaIndex, interpretation=interpretation, compression=compression) except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setWindowTitle("Save error") msg.setText("An error has occured while saving the data:") msg.setInformativeText(qt.safe_str(sys.exc_info()[1])) msg.setDetailedText(traceback.format_exc()) msg.exec_() def saveStackAsNeXusSpectra(self, compression=False): self.saveStackAsNeXus(interpretation="spectrum", compression=compression) def saveStackAsNeXusImages(self): self.saveStackAsNeXus(interpretation="image", compression=False) def saveStackAsNeXusCompressedSpectra(self): self.saveStackAsNeXusSpectra(compression=True) def saveStackAsNeXusCompressedImages(self): self.saveStackAsNeXus(interpretation="image", compression=True) def saveStackAsFloat32NeXusSpectra(self): self.saveStackAsNeXus(dtype=numpy.float32, interpretation="spectrum") def saveStackAsFloat64NeXusSpectra(self): self.saveStackAsNeXus(dtype=numpy.float64, interpretation="spectrum") def saveStackAsFloat32NeXusImages(self): self.saveStackAsNeXus(dtype=numpy.float32, interpretation="image") def saveStackAsFloat64NeXusImages(self): self.saveStackAsNeXus(dtype=numpy.float64, interpretation="image") 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 loadStack(self): if self._stackImageData is not None: #clear with a small stack stack = DataObject.DataObject() stack.data = numpy.zeros((100,100,100), numpy.float32) self.setStack(stack) if self.stackSelector is None: self.stackSelector = StackSelector.StackSelector(self) stack = self.stackSelector.getStack() if type(stack) == type([]): #aifira like, two stacks self.setStack(stack[0]) self._slave = None slave = QStackWidget(master=False, rgbwidget=self.rgbWidget) slave.setStack(stack[1]) self.setSlave(slave) else: self.setStack(stack) def loadSlaveStack(self): if self._slave is not None: actionList = ['Load Slave', 'Show Slave', 'Delete Slave'] menu = qt.QMenu(self) for action in actionList: text = QString(action) menu.addAction(text) a = menu.exec_(qt.QCursor.pos()) if a is None: return None if qt.safe_str(a.text()).startswith("Load"): self._slave = None elif qt.safe_str(a.text()).startswith("Show"): self._slave.show() self._slave.raise_() return else: self._slave = None return if self.stackSelector is None: self.stackSelector = StackSelector.StackSelector(self) try: stack = self.stackSelector.getStack() except: txt = "%s" % sys.exc_info()[1] if txt.startswith("Incomplete selection"): return msg = qt.QMessageBox(self) msg.setWindowTitle("Error loading slave stack") msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s: %s" % (sys.exc_info()[0], sys.exc_info()[1])) msg.exec_() return if stack is None: return if type(stack) == type([]): stack = stack[0] slave = QStackWidget(rgbwidget=self.rgbWidget, master=False) slave.setStack(stack) self.setSlave(slave) def setSlave(self, slave): self._slave = None self._slave = slave self._slave.setSelectionMask(self.getSelectionMask()) self._slave.show() self._slave._setMaster(self) def _setMaster(self, master=None): if self.master: self._masterStack = None return if master is None: master = self self._masterStack = weakref.proxy(master) def _pluginClicked(self): actionList = [] menu = qt.QMenu(self) text = QString("Reload Plugins") menu.addAction(text) actionList.append(text) text = QString("Set User Plugin Directory") menu.addAction(text) actionList.append(text) global DEBUG if DEBUG: text = QString("Toggle DEBUG mode OFF") else: text = QString("Toggle DEBUG mode ON") menu.addAction(text) actionList.append(text) menu.addSeparator() callableKeys = ["Dummy0", "Dummy1", "Dummy2"] for m in self.pluginList: if m == "PyMcaPlugins.StackPluginBase": continue module = sys.modules[m] if hasattr(module, 'MENU_TEXT'): text = QString(module.MENU_TEXT) else: text = os.path.basename(module.__file__) if text.endswith('.pyc'): text = text[:-4] elif text.endswith('.py'): text = text[:-3] text = QString(text) methods = self.pluginInstanceDict[m].getMethods() if not len(methods): continue menu.addAction(text) actionList.append(text) callableKeys.append(m) a = menu.exec_(qt.QCursor.pos()) if a is None: return None idx = actionList.index(a.text()) if idx == 0: n = self.getPlugins() if n < 1: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Information) msg.setText("Problem loading plugins") msg.exec_() return if idx == 1: dirName = qt.safe_str(qt.QFileDialog.getExistingDirectory(self, "Enter user plugins directory", os.getcwd())) if len(dirName): pluginsDir = self.getPluginDirectoryList() pluginsDirList = [pluginsDir[0], dirName] self.setPluginDirectoryList(pluginsDirList) return if idx == 2: if DEBUG: DEBUG = 0 else: DEBUG = 1 StackBase.DEBUG = DEBUG return key = callableKeys[idx] methods = self.pluginInstanceDict[key].getMethods() if len(methods) == 1: idx = 0 else: actionList = [] methods.sort() menu = qt.QMenu(self) for method in methods: text = QString(method) pixmap = self.pluginInstanceDict[key].getMethodPixmap(method) tip = QString(self.pluginInstanceDict[key].getMethodToolTip(method)) if pixmap is not None: action = qt.QAction(qt.QIcon(qt.QPixmap(pixmap)), text, self) else: action = qt.QAction(text, self) if tip is not None: action.setToolTip(tip) menu.addAction(action) actionList.append((text, pixmap, tip, action)) qt.QObject.connect(menu, qt.SIGNAL("hovered(QAction *)"), self._actionHovered) a = menu.exec_(qt.QCursor.pos()) if a is None: return None idx = -1 for action in actionList: if a.text() == action[0]: idx = actionList.index(action) try: self.pluginInstanceDict[key].applyMethod(methods[idx]) except: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) if QTVERSION < '4.0.0': msg.setText("%s" % sys.exc_info()[1]) else: msg.setWindowTitle("Plugin error") msg.setText("An error has occured while executing the plugin:") msg.setInformativeText(qt.safe_str(sys.exc_info()[1])) msg.setDetailedText(traceback.format_exc()) msg.exec_() if DEBUG: raise def _actionHovered(self, action): tip = action.toolTip() if qt.safe_str(tip) != qt.safe_str(action.text()): qt.QToolTip.showText(qt.QCursor.pos(), tip) def _buildBottom(self): n = 0 self.tab = None if self.mcaWidget is None: n += 1 if self.rgbWidget is None: n += 1 if n == 1: if self.mcaWidget is None: self.mcaWidget = McaWindow.McaWidget(self, vertical = False) self.mcaWidget.setWindowTitle("PyMCA - Mca Window") self.mainLayout.addWidget(self.mcaWidget) if self.rgbWidget is None: self.rgbWidget = RGBCorrelator.RGBCorrelator(self) self.mainLayout.addWidget(self.rgbWidget) elif n == 2: self.tab = qt.QTabWidget(self) self.mcaWidget = McaWindow.McaWidget(vertical = False) 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") self.rgbWidget = RGBCorrelator.RGBCorrelator() self.tab.addTab(self.rgbWidget, "RGB Correlator") self.mainLayout.addWidget(self.tab) self.mcaWidget.setMiddleROIMarkerFlag(True) def _buildAndConnectButtonBox(self): #the MCA selection self.mcaButtonBox = qt.QWidget(self.stackWindow) self.mcaButtonBoxLayout = qt.QHBoxLayout(self.mcaButtonBox) self.mcaButtonBoxLayout.setContentsMargins(0, 0, 0, 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 self.roiWidget.buildAndConnectImageButtonBox() def _buildConnections(self): self._buildAndConnectButtonBox() #self.connect(self.stackGraphWidget.hFlipToolButton, # qt.SIGNAL("clicked()"), # self._hFlipIconSignal) #ROI Image widgetList = [self.stackWidget, self.roiWidget] 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() self.connect(self.stackGraphWidget.graph, qt.SIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) self.connect(self.mcaWidget, qt.SIGNAL("McaWindowSignal"), self._mcaWidgetSignal) self.connect(self.roiWidget.graphWidget.graph, qt.SIGNAL("QtBlissGraphSignal"), self._stackGraphSignal) def showOriginalImage(self): self.stackGraphWidget.graph.setTitle("Original Stack") if self._stackImageData is None: self.stackGraphWidget.graph.clear() return self.stackWidget.setImageData(self._stackImageData) def showOriginalMca(self): goodData = numpy.isfinite(self._mcaData0.y[0].sum()) if goodData: self.sendMcaSelection(self._mcaData0, action="ADD") def handleNonFiniteData(self): self._addMcaClicked(action="ADD") msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Information) msg.setWindowTitle("Non finite data") text = "Your data contain infinite values or nans.\n" text += "Pixels containing those values will be ignored." msg.setText(text) msg.exec_() return def calculateROIImages(self, index1, index2, imiddle=None, energy=None): #overwrite base method to update the default energy with the one # currently used in the graph # TODO: Handle the case of not having an active curve!!! x, y, legend, info = self.mcaWidget.getActiveCurve() return StackBase.StackBase.calculateROIImages(self, index1, index2, imiddle=imiddle, energy=x) def showROIImageList(self, imageList, image_names=None): if self.roiBackgroundButton.isChecked(): self.roiWidget.setImageData(imageList[0]-imageList[-1]) self.roiWidget.graphWidget.graph.setTitle(image_names[0]+\ " Net") else: self.roiWidget.setImageData(imageList[0]) self.roiWidget.graphWidget.graph.setTitle(image_names[0]) self._ROIImageList = imageList self._ROIImageNames = image_names self._stackROIImageListUpdated() def addImage(self, image, name, info=None, replace=False, replot=True): self.rgbWidget.addImage(image, name) if self.tab is None: if self.master: self.rgbWidget.show() else: self.tab.setCurrentWidget(self.rgbWidget) def removeImage(self, title): self.rgbWidget.removeImage(title) def replaceImage(self, image, title, info=None, replace=True, replot=True): 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 _addImageClicked(self, image, title): self.addImage(image, title) def _removeImageClicked(self, title): self.rgbWidget.removeImage(title) def _replaceImageClicked(self, image, title): self.replaceImage(image, title) def __getLegend(self): if self._selectionMask is None: legend = "Stack SUM" elif self._selectionMask.sum() == 0: legend = "Stack SUM" else: title = qt.safe_str(self.roiGraphWidget.graph.title().text()) legend = "Stack " + title + " selection" return legend def _addMcaClicked(self, action=None): if action is None: action = "ADD" if self._stackImageData is None: return if self.normalizeButton.isChecked(): dataObject = self.calculateMcaDataObject(normalize=True) else: dataObject = self.calculateMcaDataObject(normalize=False) legend = self.__getLegend() if self.normalizeButton.isChecked(): if self._selectionMask is None: npixels = self._stackImageData.shape[0] *\ self._stackImageData.shape[1] else: npixels = self._selectionMask.sum() if npixels == 0: npixels = self._stackImageData.shape[0] *\ self._stackImageData.shape[1] legend += "/%d" % npixels return self.sendMcaSelection(dataObject, key = "Selection", legend =legend, action = action) 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 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 = "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() self.mcaWidget.raise_() else: self.tab.setCurrentWidget(self.mcaWidget) def setSelectionMask(self, mask, instance_id=None): self._selectionMask = mask if instance_id == id(self): return if DEBUG: if self._slave is not None: print("MASTER setSelectionMask CALLED") elif self._masterStack is not None: print("SLAVE setSelectionMask CALLED") #inform built in widgets for widget in [self.stackWidget, self.roiWidget]: if instance_id != id(widget): if mask is None: widget._resetSelection(owncall=False) else: widget.setSelectionMask(mask, plot=True) #inform slave if self._slave is not None: #This is a master instance instanceList = [id(self._slave), id(self._slave.stackWidget), id(self._slave.roiWidget)] for key in self._slave.pluginInstanceDict.keys(): instanceList.append(id(self._slave.pluginInstanceDict[key])) if instance_id not in instanceList: #Originated by the master if DEBUG: print("INFORMING SLAVE") self._slave.setSelectionMask(mask, instance_id=id(self)) if self._masterStack is not None: #This is a slave instance instanceList = [id(self.stackWidget), id(self.roiWidget)] for key in self.pluginInstanceDict.keys(): instanceList.append(id(self.pluginInstanceDict[key])) if instance_id in instanceList: #Originated by the slave if DEBUG: print("INFORMING MASTER") self._masterStack.setSelectionMask(mask, instance_id=id(self)) #Inform plugins for key in self.pluginInstanceDict.keys(): if key == "PyMcaPlugins.StackPluginBase": continue #I remove this optimization for the case the plugin #does not update itself the mask #if id(self.pluginInstanceDict[key]) != instance_id: self.pluginInstanceDict[key].selectionMaskUpdated() def getSelectionMask(self): return self._selectionMask def _maskImageWidgetSlot(self, ddict): if ddict['event'] == "selectionMaskChanged": self.setSelectionMask(ddict['current'], instance_id=ddict['id']) return if ddict['event'] == "resetSelection": self.setSelectionMask(None, instance_id=ddict['id']) 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.stackWidget): self.stackWidget.graphWidget.graph.zoomReset() self.stackWidget.setY1AxisInverted(ddict['current']) self.stackWidget.plotImage(update=True) if ddict['id'] != id(self.roiWidget): self.roiWidget.graphWidget.graph.zoomReset() self.roiWidget.setY1AxisInverted(ddict['current']) self.roiWidget.plotImage(update=True) return 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 _mcaWidgetSignal(self, ddict): if not self.__ROIConnected: return if ddict['event'] == "ROISignal": self.updateROIImages(ddict) def getActiveCurve(self): legend = self.mcaWidget.graph.getactivecurve(justlegend=1) if legend is None: msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Critical) msg.setText("Please select an active curve") msg.exec_() return x, y, legend, info = self.mcaWidget.getActiveCurve() return x, y, legend, info def getGraphXLimits(self): return self.mcaWidget.graph.getX1AxisLimits() def getGraphYLimits(self): return self.mcaWidget.graph.getY1AxisLimits() def test(): #create a dummy stack nrows = 100 ncols = 200 nchannels = 1024 a = numpy.ones((nrows, ncols), numpy.float) stackData = numpy.zeros((nrows, ncols, nchannels), numpy.float) for i in range(nchannels): stackData[:, :, i] = a * i stackData[0:10,:,:] = 0 w = QStackWidget() w.setStack(stackData, mcaindex=2) w.show() return w if __name__ == "__main__": 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) fileindex = 0 filepattern=None begin = None end = None imagestack=None increment=None 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 elif opt in '--old': import QEDFStackWidget sys.exit(QEDFStackWidget.runAsMain()) if filepattern is not None: if (begin is None) or (end is None): raise ValueError("A file pattern needs at least a set of begin and end indices") app = qt.QApplication([]) widget = QStackWidget() w = StackSelector.StackSelector(widget) if filepattern is not None: #ignore the args even if present stack = w.getStackFromPattern(filepattern, begin, end, increment=increment, imagestack=imagestack) else: stack = w.getStack(args, imagestack=imagestack) if type(stack) == type([]): #aifira like, two stacks widget.setStack(stack[0]) slave = QStackWidget(master=False, rgbwidget=widget.rgbWidget) slave.setStack(stack[1]) widget.setSlave(slave) stack = None else: widget.setStack(stack) widget.show() app.exec_()