Exemple #1
0
    def __init__(self, file_=None, *args, **kw):
        super(AtMainWindow, self).__init__(*args, **kw)
        loadUI(splitext(__file__)[0]+'.ui', self)

        self.setWindowTitle(version.appstr)
        self.setAcceptDrops(True)

        self.featuredlg = AtFeatureSelectionDlg(self)
        self.featuredlg.hide()

        self.loaderThread = AtThread(self)
        self.loader = AtLoader()
        self._lastdir = expanduser("~")

        try:
            self.assistant = AtAssistant(MANUAL)
            self.assistant.hide()
        except IOError:
            QMessageBox.information(self, "Information",
                                    "Sorry help files are not installed")

        self.setupToolbar()
        self.tileview = AtGraphicsView(
            parent=self,
            gsize=self.navToolBar.galsize)
        self.toolBar.valueChanged.connect(self.tileview.zoom)
        self.toolBar.flagsChanged.connect(
            self.tileview.setViewFlags, Qt.QueuedConnection)

        self.setCentralWidget(self.tileview)
        self.setupDock()
        self.setupProgressBar()

        self.loader.fileOpened.connect(self.updateToolbars)
        self.loader.progressUpdate.connect(self.updateProgressBar)
        self.loader.itemCountChanged.connect(self.batchToolBar.setItemCount)
        self.loader.itemLoaded.connect(self.tileview.addItem)
        self.abort.connect(self.loader.abort)
        self.actionNewFile.triggered.connect(self.newDataFile)
        self.actionOpenHdf.triggered.connect(self.onFileOpen)
        self.actionCloseHdf.triggered.connect(self.onFileClose)
        self.actionPreferences.triggered.connect(self.onPreferences)

        # Data Export
        self.actionExportViewPanel.triggered.connect(self.saveImage)
        self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
        self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)

        # Plots
        self.actionGroupedByClass.triggered.connect(self.plotGroupedByClass)
        self.actionGroupedByTreatment.triggered.connect(
            self.plotGroupedByTreatment)
        self.actionIntensity.triggered.connect(self.plotIntesity)
        self.actionSize.triggered.connect(self.plotSize)
        self.actionStdDev.triggered.connect(self.plotStdDev)
        self.actionPlotAll.triggered.connect(self.plotAll)

        self.actionAboutQt.triggered.connect(self.onAboutQt)
        self.actionAboutAnnotationTool.triggered.connect(self.onAbout)
        self.actionFeatureSelection.triggered.connect(
            self.showFeatureDlg)
        self.actionHelpManual.triggered.connect(self.onHelpManual)
        self.actionShortcuts.triggered.connect(self.onHelpShortcuts)
        self.actionGettingStarted.triggered.connect(self.onHelpGettingStarted)

        self.actionRefresh.triggered.connect(self.refresh)
        self.actionSelectAll.triggered.connect(
            self.tileview.actionSelectAll.trigger)
        self.actionInvertSelection.triggered.connect(
            self.tileview.actionInvertSelection.trigger)
        self.actionSelectByTreatment.triggered.connect(self.selectByTreatment)

        self.tileview.zoomChanged.connect(self.updateZoomFactor)
        self.tileview.quickSort.connect(self.sortToolBar.quickSortBtn.toggle)
        self.tileview.quickSort.connect(self.onQuickSort)

        self.featuredlg.selectionChanged.connect(
            self.annotation.predictionInvalid)

        self.loader.started.connect(self.onLoadingStarted)

        self.zoom = QtWidgets.QLabel('100%')
        self.statusbar.insertPermanentWidget(0, self.zoom)
        self.statusbar.insertPermanentWidget(1,
            QtWidgets.QLabel('Number of items:'))
        self.nitems = QtWidgets.QLabel('0')
        self.statusbar.insertPermanentWidget(2, self.nitems)

        self._restoreSettings()
        self.navToolBar.hide()
        self.show()

        if file_ is not None:
            self.loader.openFile(file_)
            self.loadItems()
Exemple #2
0
class AtMainWindow(QtWidgets.QMainWindow):

    coordUpdated = QtCore.pyqtSignal("PyQt_PyObject")
    abort = QtCore.pyqtSignal()

    def __init__(self, file_=None, *args, **kw):
        super(AtMainWindow, self).__init__(*args, **kw)
        loadUI(splitext(__file__)[0]+'.ui', self)

        self.setWindowTitle(version.appstr)
        self.setAcceptDrops(True)

        self.featuredlg = AtFeatureSelectionDlg(self)
        self.featuredlg.hide()

        self.loaderThread = AtThread(self)
        self.loader = AtLoader()
        self._lastdir = expanduser("~")

        try:
            self.assistant = AtAssistant(MANUAL)
            self.assistant.hide()
        except IOError:
            QMessageBox.information(self, "Information",
                                    "Sorry help files are not installed")

        self.setupToolbar()
        self.tileview = AtGraphicsView(
            parent=self,
            gsize=self.navToolBar.galsize)
        self.toolBar.valueChanged.connect(self.tileview.zoom)
        self.toolBar.flagsChanged.connect(
            self.tileview.setViewFlags, Qt.QueuedConnection)

        self.setCentralWidget(self.tileview)
        self.setupDock()
        self.setupProgressBar()

        self.loader.fileOpened.connect(self.updateToolbars)
        self.loader.progressUpdate.connect(self.updateProgressBar)
        self.loader.itemCountChanged.connect(self.batchToolBar.setItemCount)
        self.loader.itemLoaded.connect(self.tileview.addItem)
        self.abort.connect(self.loader.abort)
        self.actionNewFile.triggered.connect(self.newDataFile)
        self.actionOpenHdf.triggered.connect(self.onFileOpen)
        self.actionCloseHdf.triggered.connect(self.onFileClose)
        self.actionPreferences.triggered.connect(self.onPreferences)

        # Data Export
        self.actionExportViewPanel.triggered.connect(self.saveImage)
        self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
        self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)

        # Plots
        self.actionGroupedByClass.triggered.connect(self.plotGroupedByClass)
        self.actionGroupedByTreatment.triggered.connect(
            self.plotGroupedByTreatment)
        self.actionIntensity.triggered.connect(self.plotIntesity)
        self.actionSize.triggered.connect(self.plotSize)
        self.actionStdDev.triggered.connect(self.plotStdDev)
        self.actionPlotAll.triggered.connect(self.plotAll)

        self.actionAboutQt.triggered.connect(self.onAboutQt)
        self.actionAboutAnnotationTool.triggered.connect(self.onAbout)
        self.actionFeatureSelection.triggered.connect(
            self.showFeatureDlg)
        self.actionHelpManual.triggered.connect(self.onHelpManual)
        self.actionShortcuts.triggered.connect(self.onHelpShortcuts)
        self.actionGettingStarted.triggered.connect(self.onHelpGettingStarted)

        self.actionRefresh.triggered.connect(self.refresh)
        self.actionSelectAll.triggered.connect(
            self.tileview.actionSelectAll.trigger)
        self.actionInvertSelection.triggered.connect(
            self.tileview.actionInvertSelection.trigger)
        self.actionSelectByTreatment.triggered.connect(self.selectByTreatment)

        self.tileview.zoomChanged.connect(self.updateZoomFactor)
        self.tileview.quickSort.connect(self.sortToolBar.quickSortBtn.toggle)
        self.tileview.quickSort.connect(self.onQuickSort)

        self.featuredlg.selectionChanged.connect(
            self.annotation.predictionInvalid)

        self.loader.started.connect(self.onLoadingStarted)

        self.zoom = QtWidgets.QLabel('100%')
        self.statusbar.insertPermanentWidget(0, self.zoom)
        self.statusbar.insertPermanentWidget(1,
            QtWidgets.QLabel('Number of items:'))
        self.nitems = QtWidgets.QLabel('0')
        self.statusbar.insertPermanentWidget(2, self.nitems)

        self._restoreSettings()
        self.navToolBar.hide()
        self.show()

        if file_ is not None:
            self.loader.openFile(file_)
            self.loadItems()

    def updateProgressBar(self, value):

        if value < 0:
            self.progressbar.setRange(0, 0)

        self.progressbar.setValue(value)

    def updateZoomFactor(self, factor):
        self.zoom.setText("%d%s" %(round(100*factor, 0), "%"))

    def dragEnterEvent(self, event):
        event.acceptProposedAction()

    def dragMoveEvent(self, event):
        event.acceptProposedAction()

    def dropEvent(self, event):
        mimeData = event.mimeData()
        if mimeData.hasUrls():
            if len(mimeData.urls()) == 1:
                self.abort.emit()
                self.loaderThread.wait()
                self.loader.close()
                self.onDropEvent(fix_path(mimeData.urls()[0].path()))
        event.acceptProposedAction()

    def dragLeaveEvent(self, event):
        event.accept()

    def onInitalStartup(self):
        self.onHelpGettingStarted()

    def onHelpManual(self):
        self.assistant.show()
        self.assistant.raise_()
        self.assistant.openKeyword('Shortcuts')

    def onHelpShortcuts(self):
        self.onHelpManual()
        self.assistant.openKeyword("Shortcuts")

    def onHelpGettingStarted(self):
        self.onHelpManual()
        self.assistant.openKeyword("Getting started")

    def refresh(self):

        if self.loader.file is None:
            return

        self.tileview.actionRefresh.trigger()
        self.contrast.enhanceContrast()

    def showFeatureDlg(self):
        self.featuredlg.show()
        self.featuredlg.raise_()

    def onPreferences(self):
        dlg = AtPreferencesDialog(self)
        dlg.exec_()

    def onAboutQt(self):
        QMessageBox.aboutQt(self, "about Qt")

    def onAbout(self):
        dlg = AtAboutDialog(self)
        dlg.exec_()

    def resetCursor(self):
        QApplication.restoreOverrideCursor()

    def setWaitingCursor(self):
        QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))

    def _saveSettings(self):
        settings = QtCore.QSettings(version.organisation, version.appname)
        settings.beginGroup('Gui')
        settings.setValue('config', version.config)
        settings.setValue('state', self.saveState())
        settings.setValue('geometry', self.saveGeometry())
        settings.setValue('classifier',
                          self.annotation.classifiers.currentText())
        settings.endGroup()

        AtConfig().saveSettings()

    def _restoreSettings(self):
        settings = QtCore.QSettings(version.organisation, version.appname)
        settings.beginGroup('Gui')

        if settings.contains('config'):
            if version.config != settings.value('config'):
                # FIXME - helpengine needs to be delayed for unknown reason
                QtCore.QTimer.singleShot(500, self.onInitalStartup)
                return
        else:
            QtCore.QTimer.singleShot(500, self.onInitalStartup)

        if settings.contains('geometry'):
            geometry = settings.value('geometry')
            self.restoreGeometry(geometry)

        if settings.contains('state'):
            state = settings.value('state')
            self.restoreState(state)

        if settings.contains('classifier'):
            clfname = settings.value("classifier")
            self.annotation.setCurrentClassifier(clfname)

        AtConfig().restoreSettings()
        settings.endGroup()

        self.batchToolBar.setBatchSize(AtConfig().batch_size)

    def closeEvent(self, event):

        if self.annotation.isModified():
            msg = "The classifier has not been saved. Close program anyway?"
            reply = QMessageBox.question(
                self, 'Warning', msg, QMessageBox.Yes, QMessageBox.No)

            if reply == QMessageBox.Yes:
                event.accept()
            else:
                event.ignore()
                return

        self._saveSettings()
        try:
            self.abort.emit()
            self.loaderThread.wait()
            self.loader.close()

            if self.assistant is not None:
                self.assistant.close()

        except AttributeError:
            pass

    def setupDock(self):
        self.contrast = AtContrastWidget(self, self.tileview)
        self.sorting = AtSortWidget(self, self.tileview, self.featuredlg)
        self.annotation = AtAnnotationWidget(
            self, self.tileview, self.featuredlg)

        self.contrastdock = QtWidgets.QDockWidget("Contrast", self)
        self.contrastdock.setWidget(self.contrast)
        self.contrastdock.setObjectName("contrast")
        self.addDockWidget(Qt.LeftDockWidgetArea, self.contrastdock)

        self.sortdock = QtWidgets.QDockWidget("Sorting", self)
        self.sortdock.setWidget(self.sorting)
        self.sortdock.setObjectName("sorting")
        self.addDockWidget(Qt.RightDockWidgetArea, self.sortdock)

        self.annodock = QtWidgets.QDockWidget("Training", self)
        self.annodock.setWidget(self.annotation)
        self.annodock.setObjectName("training")
        self.addDockWidget(Qt.RightDockWidgetArea, self.annodock)

        self.tabifyDockWidget(self.sortdock, self.annodock)

        # add action to the view menu
        sort_action = self.sortdock.toggleViewAction()
        sort_action.setShortcuts(QKeySequence(Qt.ALT +  Qt.SHIFT + Qt.Key_S))
        self.menuView.addAction(sort_action)

        anno_action = self.annodock.toggleViewAction()
        anno_action.setShortcuts(QKeySequence(Qt.ALT +  Qt.SHIFT + Qt.Key_A))
        self.menuView.addAction(anno_action)

        contrast_action = self.contrastdock.toggleViewAction()
        contrast_action.setShortcuts(
            QKeySequence(Qt.ALT +  Qt.SHIFT + Qt.Key_C))
        self.menuView.addAction(contrast_action)

        # crosslink sorter dock and sorter toolbar
        self.sortToolBar.sortAlgorithm.currentIndexChanged.connect(
            self.sorting.sortAlgorithm.setCurrentIndex)
        self.sorting.sortAlgorithm.currentIndexChanged.connect(
            self.sortToolBar.sortAlgorithm.setCurrentIndex)

        self.sortToolBar.sortAscendingBtn.clicked.connect(
            self.sorting.sortAscending)
        self.sortToolBar.sortDescendingBtn.clicked.connect(
            self.sorting.sortDescending)

        self.sortToolBar.quickSortBtn.toggled.connect(
            self.tileview.setQuickSortMode)

    def setupProgressBar(self):
        frame = QtWidgets.QFrame(self)
        self.progressbar = QtWidgets.QProgressBar(frame)
        self.progressbar.setMaximumHeight(15)
        self.abortBtn = QtWidgets.QPushButton('abort', self)
        self.abortBtn.clicked.connect(self.abort.emit)
        self.abortBtn.setMaximumHeight(20)
        hbox = QtWidgets.QHBoxLayout(frame)
        hbox.addWidget(self.progressbar)
        hbox.addWidget(self.abortBtn)
        hbox.setContentsMargins(0, 0, 0, 0)
        self.loaderThread.started.connect(frame.show)
        self.loaderThread.started.connect(self.setWaitingCursor)
        self.loaderThread.finished.connect(frame.hide)
        self.loaderThread.finished.connect(self.resetCursor)
        frame.hide()
        self.statusBar().addPermanentWidget(frame)

    def saveImage(self):
        filename = QFileDialog.getSaveFileName(
            self, "Save image as ...",
            self._lastdir.replace('.hdf', '.png'),
            "png - Image (*.png)")[0]

        if filename:
            scene = self.tileview.scene()
            size = scene.sceneRect().size().toSize()
            image = QtGui.QImage(size, QtGui.QImage.Format_RGB32)
            painter = QtGui.QPainter(image)

            image.fill(QtCore.Qt.white)
            scene.render(painter)
            painter.end()
            image.save(filename)
            self.statusBar().showMessage("Image saved to %s" %filename)

    def saveData2Csv(self):

        filename = QFileDialog.getSaveFileName(
            self, "Save csv-file as ...",
            self._lastdir.replace(".hdf", ".csv"),
            "Comma separated values (*.csv)")[0]

        if filename:
            if AtConfig().only_classifier_features:
                features = self.featuredlg.checkedItems()
            else:
                features = self.featuredlg.allItems()

            exporter = CsvExporter(filename, self.tileview.items,
                                   features)
            exporter.save()
            self.statusBar().showMessage("Image saved to %s" %filename)

    def saveCountingStats(self):

        filename = QFileDialog.getSaveFileName(
            self, "Save csv-file as ...",
            self._lastdir.replace(".hdf", "_statistics.csv"),
            "Comma separated values (*.csv)")[0]

        if filename:
            features = self.featuredlg.checkedItems()
            exporter = StatsExporter(filename, self.tileview.items,
                                     features)
            exporter.save()
            self.statusBar().showMessage("Image saved to %s" %filename)

    def _validPlotData(self):
        flag = False
        if not self.tileview.items:
            QMessageBox.information(self, "Nothing to plot!",
                                    "No data file is opened")

        elif not self.annotation.hasValidClassifier():
            QMessageBox.information(self, "Nothing to plot!",
                                    "No valid classifier trained or loaded")
        elif not self.annotation.hasValidPrediction():
            QMessageBox.information(self, "Nothing to plot!",
                                    "Press 'Predict' before plotting")

        else:
            flag = True
        return flag

    def plotGroupedByTreatment(self, pos=False):
        if self._validPlotData():
            classes = self.annotation.currentClassifier().classes
            barplot = plots.BarGraph(self.tileview.items, classes,
                                     self.actionExcludeTrainingData.isChecked(), self)
            self.actionCloseAll.triggered.connect(barplot.close)
            if pos:
                barplot.move(pos)
                barplot.show()
            else:
                barplot.exec_()


    def plotGroupedByClass(self, pos=False):
        if self._validPlotData():
            classes = self.annotation.currentClassifier().classes
            barplot = plots.BarGraph2(self.tileview.items, classes,
                                      self.actionExcludeTrainingData.isChecked(), self)
            self.actionCloseAll.triggered.connect(barplot.close)
            if pos:
                barplot.move(pos)
                barplot.show()
            else:
                barplot.exec_()

    def plotIntesity(self, pos=False):
        if self._validPlotData():
            indices = self.featuredlg.indexByName(CoreFeatures.Intensity)
            classes = self.annotation.currentClassifier().classes
            boxplot = plots.BoxPlot(
                self.tileview.items, indices, classes, "Intensity",
                self.actionExcludeTrainingData.isChecked(), self)

            self.actionCloseAll.triggered.connect(boxplot.close)
            if pos:
                boxplot.move(pos)
                boxplot.show()
            else:
                boxplot.exec_()

    def plotSize(self, pos=False):
        if self._validPlotData():
            indices = self.featuredlg.indexByName(CoreFeatures.Size)
            classes = self.annotation.currentClassifier().classes
            boxplot = plots.BoxPlot(
                self.tileview.items, indices, classes, "Size",
                self.actionExcludeTrainingData.isChecked(),
                self)
            self.actionCloseAll.triggered.connect(boxplot.close)
            if pos:
                boxplot.move(pos)
                boxplot.show()
            else:
                boxplot.exec_()

    def plotStdDev(self, pos=False):
        if self._validPlotData():
            indices = self.featuredlg.indexByName(CoreFeatures.StdDev)
            classes = self.annotation.currentClassifier().classes
            boxplot = plots.BoxPlot(
                self.tileview.items, indices, classes,
                "Standard Deviation",
                self.actionExcludeTrainingData.isChecked(),
                self)
            self.actionCloseAll.triggered.connect(boxplot.close)
            if pos:
                boxplot.move(pos)
                boxplot.show()
            else:
                boxplot.exec_()

    def plotAll(self):
        """Plot everything for people who don't know what do"""
        if self._validPlotData():

            shift = QtCore.QPoint(20, 20)
            pos = self.pos() + 4*shift
            pos = [pos + i*shift for i in xrange(5)]

            self.plotGroupedByClass(pos[0])
            self.plotGroupedByTreatment(pos[1])
            self.plotIntesity(pos[2])
            self.plotSize(pos[3])
            self.plotStdDev(pos[4])

    def updateToolbars(self, props):
        # in case of cellh5 file

        if props.gal_settings_mutable:
            self.navToolBar.show()

        self.navToolBar.updateToolbar(props)
        self.contrast.setChannelNames(props.channel_names, props.colors)
        self.nitems.setText(str(props.n_items))

    def setupToolbar(self):

        self.toolBar = ViewToolBar(self)

        self.fileToolBar = FileToolBar(self)
        self.fileToolBar.actionOpen.triggered.connect(self.onFileOpen)
        self.fileToolBar.actionNew.triggered.connect(self.newDataFile)

        self.batchToolBar = BatchToolBar(self)
        self.batchToolBar.batchChanged.connect(self.loadItems)
        self.batchToolBar.actionReload.triggered.connect(self.loadItems)
        self.actionReloadFile.triggered.connect(self.loadItems)

        self.sortToolBar = SortToolBar(self)

        self.addToolBar(QtCore.Qt.TopToolBarArea, self.fileToolBar)
        self.addToolBar(QtCore.Qt.TopToolBarArea, self.toolBar)
        self.addToolBar(QtCore.Qt.TopToolBarArea, self.sortToolBar)
        self.addToolBar(QtCore.Qt.BottomToolBarArea, self.batchToolBar)

        self.navToolBar = NavToolBar(self)
        self.addToolBar(QtCore.Qt.BottomToolBarArea, self.navToolBar)
        self.navToolBar.coordUpdated.connect(self.loader.setCoordinate)

    def newDataFile(self):
        try:
            dlg = ImportDialog(
                self, Qt.WindowMinMaxButtonsHint|Qt.WindowCloseButtonHint)
            dlg.loadData.connect(self._openAndLoad)
            dlg.exec_()
        except Exception as e:
            QMessageBox.critical(None, "Error", str(e))

    def onQuickSort(self):
        self.sorting.removeAll()
        items = self.tileview.selectedItems()
        self.sorting.addItems(items)
        self.sorting.applyDefaultSortAlgorithm()
        self.sorting.sortAscending()
        self.tileview.centerOn(items[0])

    def selectByTreatment(self):

        label, flag = QInputDialog.getItem(self, "Select a Treatment",
                "Treatment", self.tileview.treatments, editable=False)
        if flag:
            self.tileview.selectByTreatment(label)

    def addToSortPanel(self):
        self.sorting.addItems(self.tileview.selectedItems())

    def onFileClose(self):
        self.loader.close()
        self.tileview.clear()
        self.featuredlg.clear()
        self.sorting.clear()

    def onFileOpen(self):

        file_ = QFileDialog.getOpenFileName(
            self, "Open hdf5 file", self._lastdir,
            "Hdf files (*.hdf5 *.ch5 *.hdf *.h5)")[0]

        if bool(file_):
            self.tileview.zoom(1.0)
            self._fileOpen(file_)
            self.loadItems()

    def _fileOpen(self, file_):
        self._lastdir = abspath(file_)
        try:
            self.loader.openFile(file_)
        except Exception as e:
            self.statusBar().showMessage(str(e))
            msg = "Could not open file\n %s" %str(e)
            QMessageBox.critical(self, "Error", msg)
        else:
            self.statusBar().showMessage(basename(file_))

    def _openAndLoad(self, file_):
        self.onFileClose()
        self._fileOpen(file_)
        self.loadItems()

    def onLoadingStarted(self):
        self.annotation.setFeatureNames(self.loader.featureNames)
        try:
            self.featuredlg.setFeatureGroups(self.loader.featureGroups)
            self.sorting.setFeatureGroups(self.loader.featureGroups)
        except RuntimeError as e:
            pass

    def onDropEvent(self, path):
        self._fileOpen(path)
        self.loadItems()

    def loadItems(self):

        self.abort.emit()
        self.loaderThread.wait()
        self.tileview.setViewFlags(self.toolBar.viewFlags())

        self.tileview.clear()
        self.progressbar.setValue(0)
        self.tileview.updateRaster(self.navToolBar.galsize)
        self.tileview.updateNColumns(self.tileview.size().width())

        idx = self.batchToolBar.indices()
        self.nitems.setText("%d/%d" %(len(idx), self.batchToolBar.count))
        self.progressbar.setRange(0, len(idx))
        self.loader.setBatch(idx)
        self.loader.setGallerySize(self.navToolBar.galsize)
        self.loaderThread.start(self.loader)