sampleview.py 25.7 KB
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# -*- coding: utf-8 -*-
"""
GEPARD - Gepard-Enabled PARticle Detection
Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    

This program 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 3 of the License, or
(at your option) any later version.

This program 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 this program, see COPYING.  
If not, see <https://www.gnu.org/licenses/>.
"""
from PyQt5 import QtCore, QtGui, QtWidgets
import numpy as np
import os
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import cv2
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import time
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from dataset import DataSet, loadData
from ramancom.ramancontrol import RamanControl, simulatedRaman
from opticalscan import OpticalScan
from ramanscanui import RamanScanUI
from detectionview import ParticleDetectionView
from analysis.analysisview import ParticleAnalysis
from zeissimporter import ZeissImporter
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from viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContour
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from analysis.colorlegend import getColorFromNameWithSeed
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from helperfunctions import polygoncovering, cv2imread_fix
from ramancom.configRaman import RamanConfigWin
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from analysis.particleEditor import ParticleEditor
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class SampleView(QtWidgets.QGraphicsView):
    ScalingChanged = QtCore.pyqtSignal(float)
    
    def __init__(self, logpath):
        super(SampleView, self).__init__()
        
        self.logpath = logpath
        self.item = QtWidgets.QGraphicsPixmapItem()
        self.item.setPos(0, 0)
        self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)
        self.scaleFactor = 1.0
        scene = QtWidgets.QGraphicsScene(self)
        scene.setItemIndexMethod(QtWidgets.QGraphicsScene.NoIndex)
        scene.addItem(self.item)
        scene.setBackgroundBrush(QtCore.Qt.darkGray)
        self.setScene(scene)
        self.setCacheMode(QtWidgets.QGraphicsView.CacheBackground)
        self.setViewportUpdateMode(QtWidgets.QGraphicsView.BoundingRectViewportUpdate)
        self.setRenderHint(QtGui.QPainter.Antialiasing)
        self.setTransformationAnchor(QtWidgets.QGraphicsView.AnchorUnderMouse)
        self.setResizeAnchor(QtWidgets.QGraphicsView.AnchorViewCenter)
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        self.ramanctrl = RamanControl()
        self.simulatedRaman = simulatedRaman        
        #determine, if ramanSwitch is needed:
        self.ramanctrl.connect()
        if not self.ramanctrl.connected:
            QtWidgets.QMessageBox.warning(self, 'Error', 'Please enable Raman Connection')
            return
        if self.ramanctrl.getImageDimensions(mode='bf')[0] == self.ramanctrl.getImageDimensions(mode='df')[0]:
            self.ramanSwitchNeeded = False
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        else:
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            self.ramanSwitchNeeded = True
        self.ramanctrl.disconnect()
        
        self.drag = None
        self.mode = None
        self.dataset = None
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        self.particleEditor = None
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        self.fititems = []
        self.boundaryitems = [[],[]]
        self.scanitems = []
        self.ramanscanitems = []
        self.imgdata = None
        self.isblocked = False
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        self.contourItems = []
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        self.selectedParticleIndices = []
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        self.particlePainter = None
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        self.detectionwidget = None
        self.ramanwidget = RamanScanUI(self.ramanctrl, None, self.logpath, self)
        self.ramanwidget.imageUpdate.connect(self.loadPixmap)
        self.oscanwidget = OpticalScan(self.ramanctrl, None, self.logpath, self)
        self.oscanwidget.imageUpdate.connect(self.loadPixmap)
        self.oscanwidget.boundaryUpdate.connect(self.resetBoundary)
        self.analysiswidget = None
        self.setMinimumSize(600, 600)
        self.darkenPixmap = False
        self.microscopeMode = None
        
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        self.update()
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    def takeScreenshot(self):
        #TODO:
        #LIMIT SCREENSHOT TO ACTUAL VIEWSIZE OF LOADED IMAGE...
        #hide scrollbars
        self.setHorizontalScrollBarPolicy(1)
        self.setVerticalScrollBarPolicy(1)
        #capture screen
        screen = QtWidgets.QApplication.primaryScreen()
        self.repaint()
        screenshot = screen.grabWindow(self.winId())
        #unhide scrollbars
        self.setHorizontalScrollBarPolicy(0)
        self.setVerticalScrollBarPolicy(0)
        
        fname = self.dataset.path + '/screenshot.png'
        validFileName = False
        incr = 1
        while not validFileName:
            if not os.path.exists(fname):
                validFileName = True
            else:
                fname = self.dataset.path + '/screenshot ({}).png'.format(incr)
                incr += 1
        screenshot.save(fname , 'png')
        QtWidgets.QMessageBox.about(self, 'Message', 'Saved as {} to project directory.'.format(fname.split('/')[-1]))
                    
    def closeEvent(self, event):
        reply = QtWidgets.QMessageBox.question(self, 'Message',
            "Are you sure to quit?", QtWidgets.QMessageBox.Yes | 
            QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

        if reply == QtWidgets.QMessageBox.Yes:
            self.disconnectRaman()
            self.saveDataSet()
            event.accept()
            self.oscanwidget.close()
            if self.detectionwidget is not None:
                self.detectionwidget.close()
            if self.analysiswidget is not None:
                self.analysiswidget.close()
            self.ramanwidget.close()
        else:
            event.ignore()
    
    def configureRamanControl(self):
        self.configWin = RamanConfigWin(self)
        self.configWin.show()
    
    def saveDataSet(self):
        if self.dataset is not None:
            self.dataset.save()
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    @QtCore.pyqtSlot() 
    def zoomIn(self):
        self.scaleImage(1.25)

    @QtCore.pyqtSlot() 
    def zoomOut(self):
        self.scaleImage(0.8)

    @QtCore.pyqtSlot() 
    def normalSize(self):
        self.scaleFactor = 1.0
        self.setTransform(QtGui.QTransform.fromScale(1., 1.))
        self.announceScaling()

    @QtCore.pyqtSlot() 
    def fitToWindow(self):
        brect = self.item.sceneBoundingRect()
        self.fitInView(0, 0, brect.width(), brect.height(), QtCore.Qt.KeepAspectRatio)
        self.scaleFactor = self.transform().m11()
        self.announceScaling()
        
    def switchMode(self, mode, loadnew=False):
        if mode is None:
            return
        assert mode in ["OpticalScan", "ParticleDetection", "RamanScan", "ParticleAnalysis"]
        self.oscanwidget.setVisible(False)
        self.ramanwidget.setVisible(False)
        self.mode = mode
        self.loadPixmap(self.microscopeMode)
        if mode == "OpticalScan":
            self.oscanwidget.setVisible(True)
            self.oscanwidget.resetDataset(self.dataset)
            
        elif mode == "ParticleDetection":
            if self.detectionwidget is None:
                self.detectionwidget = ParticleDetectionView(self.imgdata, self.dataset, self)
                self.detectionwidget.imageUpdate.connect(self.detectionUpdate)
                self.detectionwidget.detectionFinished.connect(self.activateMaxMode)
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            self.detectionwidget.show()
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        elif mode == "RamanScan":
            self.ramanwidget.resetDataset(self.dataset)
            self.ramanwidget.setVisible(True)
            
        elif mode == "ParticleAnalysis":
            if self.ramanwidget.isVisible():
                self.ramanwidget.setVisible(False)
            if self.analysiswidget is None:
                print('creating new analysiswidget')
                self.analysiswidget = ParticleAnalysis(self.dataset, self)
                self.analysiswidget.showMaximized()
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                self.setupParticleEditor()
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            else:
                print('show maximized already exisiting analysiswidget')
                self.analysiswidget.showMaximized()
            
            if self.detectionwidget is not None:
                self.detectionwidget.setVisible(False)
            
            #show legend:
            self.imparent.legend.show()    
        
        if loadnew:
            self.fitToWindow()
        self.imparent.updateModes(mode, self.getMaxMode())
        
    def open(self, fname):       
        self.saveDataSet()
        
        #close all widgets
        for widget in [self.detectionwidget, self.ramanwidget, self.oscanwidget, self.analysiswidget]:
            if widget is not None:
                widget.close()
                widget.destroy()
                del widget
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        self.dataset = loadData(fname)
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        self.setupParticleEditor()
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        self.setMicroscopeMode()
        self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
        self.imgdata = None
        self.activateMaxMode(loadnew=True)
        self.imparent.snapshotAct.setEnabled(True)
        
    def importProject(self, fname):
        zimp = ZeissImporter(fname, self.ramanctrl, self)
        if zimp.validimport:
            zimp.exec()
            if zimp.result() == QtWidgets.QDialog.Accepted:
                self.open(zimp.gepardname)
        
    def new(self, fname):
        self.saveDataSet()
        if self.dataset is not None:
            self.dataset.save()
        self.dataset = DataSet(fname, newProject=True)
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        self.setupParticleEditor()
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        self.setMicroscopeMode()
        self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
        self.imgdata = None
        self.activateMaxMode(loadnew=True)
        self.imparent.snapshotAct.setEnabled(True)
    
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    def setupParticleEditor(self):
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        def tryDisconnectingSignal(signal):
            try: 
                signal.disconnect()
            except TypeError:
                pass
            
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        if self.particleEditor is None:
            self.particleEditor = ParticleEditor(self, self.dataset.particleContainer)
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        tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)
        if self.analysiswidget is not None:
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            self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updateHistogramsAndContours)
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    def setMicroscopeMode(self):
        if self.ramanSwitchNeeded:
            self.imparent.ramanSwitch.connectToSampleView()
            self.imparent.ramanSwitch.show()
        self.microscopeMode = ('df' if self.imparent.ramanSwitch.df_btn.isChecked() else 'bf')
    
    @QtCore.pyqtSlot()    
    def activateMaxMode(self, loadnew=False):
        mode = self.getMaxMode()
        self.imparent.updateModes(self.mode, self.getMaxMode())
        self.switchMode(mode, loadnew=loadnew)
        
    def blockUI(self):
        self.isblocked = True
        self.imparent.blockUI()
        
    def unblockUI(self):
        self.isblocked = False
        self.imparent.unblockUI(self.ramanctrl.connected)
        self.imparent.updateModes(self.mode, self.getMaxMode())
        
    def getMaxMode(self):
        if self.dataset is None:
            return None
        if not self.ramanctrl.connected:
            self.connectRaman()
        if not self.ramanctrl.connected:
            return None
        maxmode = "OpticalScan"
        if os.path.exists(self.dataset.getImageName()):
            maxmode = "ParticleDetection"
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            if self.dataset.particleDetectionDone:
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                maxmode = "RamanScan"
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            if self.dataset.ramanscandone:  
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                maxmode = "ParticleAnalysis"
        return maxmode
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    def mousePressEvent(self, event):
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        if event.button()==QtCore.Qt.MiddleButton:
            self.drag = event.pos()
        
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        if self.particlePainter is None:
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            if event.button()==QtCore.Qt.LeftButton:
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                self.checkForContourSelection(event)
                
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                if self.mode in ["OpticalScan", "RamanScan"] and event.modifiers()==QtCore.Qt.ControlModifier:
                    p0 = self.mapToScene(event.pos())
                    self.moveStageToPosition(p0)
                    
                elif self.mode=="ParticleDetection":
                    p0 = self.mapToScene(event.pos())
                    self.detectionwidget.setImageCenter([p0.x(), p0.y()])
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                else:
                    p0 = self.mapToScene(event.pos())
                    super(SampleView, self).mousePressEvent(event)
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        else:
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            self.particlePainter.mousePressEvent(event)

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    def mouseMoveEvent(self, event):
        if self.drag is not None:
            p0 = event.pos()
            move = self.drag-p0
            self.horizontalScrollBar().setValue(move.x() + self.horizontalScrollBar().value())
            self.verticalScrollBar().setValue(move.y() + self.verticalScrollBar().value())
            
            self.drag = p0
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        elif self.particlePainter is None:
            p0 = self.mapToScene(event.pos())
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            super(SampleView, self).mouseMoveEvent(event)
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        else:
            self.particlePainter.mouseMoveEvent(event)
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    def mouseReleaseEvent(self, event):
        self.drag = None
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        if self.particlePainter is None:
            super(SampleView, self).mouseReleaseEvent(event)
        else:
            self.particlePainter.mouseReleaseEvent(event)
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    def wheelEvent(self, event):
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        if self.particlePainter is None:
            factor = 1.01**(event.angleDelta().y()/8)
            self.scaleImage(factor)
        else:
            self.particlePainter.wheelEvent(event)
            
    def keyPressEvent(self, event):
        if self.particlePainter is not None:
            self.particlePainter.keyPressEvent(event)
    
    def moveStageToPosition(self, pos):
        if self.dataset is not None and self.dataset.pshift is not None:
            if self.dataset.readin:
                reply = QtWidgets.QMessageBox.critical(self, 'Dataset is newly read from disk!',
                    "Coordinate systems might have changed since. Do you want to continue with saved coordinates?", 
                    QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
        
                if reply == QtWidgets.QMessageBox.Yes:
                    self.dataset.readin = False
                else:
                    return
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            noz = (self.mode in ['OpticalScan', 'RamanScan'])
            x, y, z = self.dataset.mapToLengthRaman([pos.x(), pos.y()], microscopeMode=self.microscopeMode, noz=noz)
            if z is not None:
                assert z>-100.
            self.ramanctrl.moveToAbsolutePosition(x, y, z)
    
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    def checkForContourSelection(self, event):
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        def acceptSelection(cnt):
            self.analysiswidget.setWidgetsToNewParticleIndex(cnt.particleIndex)
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            cnt.isSelected = True
            cnt.update()
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            if cnt.particleIndex not in self.selectedParticleIndices:
                self.selectedParticleIndices.append(cnt.particleIndex)
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        def removeContourFromSelection(cnt):
            cnt.isSelected = False
            cnt.update()
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            self.selectedParticleIndices.remove(cnt.particleIndex)
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        p = self.mapToScene(event.pos())
        p = QtCore.QPointF(p.x(), p.y())
        
        for index, cnt in enumerate(self.contourItems):
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            if cnt.polygon.containsPoint(p, QtCore.Qt.OddEvenFill):   #clicked on particle
                if not event.modifiers()==QtCore.Qt.ShiftModifier:
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                    acceptSelection(cnt)
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                else:
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                    if cnt.particleIndex not in self.selectedParticleIndices:
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                        acceptSelection(cnt)
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                    elif cnt.particleIndex in self.selectedParticleIndices:
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                        removeContourFromSelection(cnt)
            
            else:    #not clicked on particle
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                if event.modifiers()!=QtCore.Qt.ShiftModifier:
                    cnt.isSelected = False
                    cnt.update()
                    if cnt.particleIndex in self.selectedParticleIndices:
                        self.selectedParticleIndices.remove(cnt.particleIndex)
                    
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        self.update()
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    def scaleImage(self, factor):
        if factor<1 and not self.imparent.zoomOutAct.isEnabled():
            return
        if factor>1 and not self.imparent.zoomInAct.isEnabled():
            return
        self.scaleFactor *= factor      
        self.scale(factor, factor)
        self.announceScaling()
        
    def announceScaling(self):
        pixelscale = self.dataset.getPixelScale(self.microscopeMode)
        if self.dataset is None or pixelscale is None:
            self.ScalingChanged.emit(-1.0)
        else:
            self.ScalingChanged.emit(pixelscale/self.scaleFactor)           ##CURRENTLY ONLY DARKFIELD!!! FIX NEEDED!!!
        
    def connectRaman(self):
        if not self.ramanctrl.connect():
            msg = QtWidgets.QMessageBox()
            msg.setText("Connection failed! Please enable remote control.")
            msg.exec()
        else:
            mode = self.getMaxMode()
            self.switchMode(mode)
        self.imparent.updateConnected(self.ramanctrl.connected)
    
    def disconnectRaman(self):
        self.ramanctrl.disconnect()
        self.imparent.updateConnected(self.ramanctrl.connected)

    @QtCore.pyqtSlot(str)
    def detectionUpdate(self):
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        self.resetParticleContours()
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        self.prepareAnalysis()
        self.update()

    @QtCore.pyqtSlot(str) 
    def loadPixmap(self, microscope_mode='df'):
        self.clearItems()
        if self.dataset is None:
            self.item.setPixmap(QtGui.QPixmap())
        else:
            data = self.imgdata
            fname = self.dataset.getImageName()
            if self.mode == "ParticleDetection" or self.mode == "ParticleAnalysis":
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                self.resetParticleContours()
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            if data is None and os.path.exists(fname):
                data = cv2.cvtColor(cv2imread_fix(fname), cv2.COLOR_BGR2RGB)
                self.imgdata = data
            if data is not None:
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                height, width, channel = data.shape
                bytesPerLine = 3 * width
                pix = QtGui.QPixmap()
                pix.convertFromImage(QtGui.QImage(data.data, 
                                width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
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                self.item.setPixmap(pix)
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                if self.darkenPixmap:
                    self.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
                    self.item.setOpacity(0.2)
                else:
                    self.scene().setBackgroundBrush(QtCore.Qt.darkGray)
                    self.item.setOpacity(1)
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            else:
                self.item.setPixmap(QtGui.QPixmap())
            if self.mode == "OpticalScan":
                for i, p in zip(self.dataset.fitindices, self.dataset.fitpoints):
                    p = self.dataset.mapToPixel(p, mode=microscope_mode, force=True)
                    fititem = FitPosIndicator(i+1, pos=p)
                    self.scene().addItem(fititem)
                    self.fititems.append(fititem)                    
            if self.mode == "ParticleDetection" or self.mode == "ParticleAnalysis":
                self.prepareAnalysis()
            else:
                self.fitToWindow()
    
    @QtCore.pyqtSlot()        
    def resetScanPositions(self):
        micMode = ('df' if self.oscanwidget.df_btn.isChecked() else 'bf')
        for item in self.scanitems:
            self.scene().removeItem(item)
        edges, nodes = self.boundaryitems
        boundary = []
        for n in nodes:
            p = n.pos().x(), n.pos().y()
            boundary.append(self.dataset.mapToLength(p, self.microscopeMode, force=True))
        boundary = np.array(boundary)
        self.dataset.boundary = boundary
        if micMode == 'df':
            width, height, angle = self.dataset.imagedim_df
        else:
            width, height, angle = self.dataset.imagedim_bf
        
        margin = min(width, height)*0.02
        wx, wy = width-margin, height-margin
        print(wx,wy)
        p1 = polygoncovering(boundary, wx, wy)
        b2 = boundary.copy()
        b2 = b2[:,[1,0]]
        p2 = polygoncovering(b2, wy, wx)
        if len(p2)<len(p1):
            p1 = [[pi[1],pi[0]] for pi in p2]
        self.dataset.grid = p1
        pixelscale = self.dataset.getPixelScale(self.microscopeMode)
        wxs, wys = width/pixelscale, height/pixelscale
        
        self.scanitems = []
        for i, p in enumerate(p1):
            p = self.dataset.mapToPixel(p, self.microscopeMode, force=True)
            s = ScanIndicator(i+1, wxs, wys, p)
            self.scene().addItem(s)
            self.scanitems.append(s)
    
    @QtCore.pyqtSlot()        
    def resetBoundary(self):
        micMode = self.microscopeMode
        edges, nodes = self.boundaryitems
        for item in edges:
            self.scene().removeItem(item)
        for item in nodes:
            self.scene().removeItem(item)
        edges, nodes = [], []
        for p in self.dataset.boundary:
            p = self.dataset.mapToPixel(p, micMode, force=True)
            n = Node(p, self)
            nodes.append(n)
            self.scene().addItem(n)
        for i in range(len(nodes)):
            e = Edge(nodes[i-1], nodes[i])
            edges.append(e)
            self.scene().addItem(e)
        self.boundaryitems = edges, nodes
        self.resetScanPositions()
    
    def prepareAnalysis(self):
        self.clearItems()
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        if self.dataset.particleDetectionDone:
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            data = []
            for i in self.dataset.ramanscansortindex:
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                data.append(list(self.dataset.ramanpoints[i]))
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            for i in range(len(data)):
                item = RamanScanIndicator(self, i+1, 20, (data[i][0],data[i][1]))
                self.scene().addItem(item)
                self.ramanscanitems.append(item)
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#            for index, meas in enumerate(self.dataset.particleContainer.measurements):
#                number = meas.ramanScanIndex+1
#                item = RamanScanIndicator(self, number, 20, (meas.pixelcoord_x, meas.pixelcoord_y))
#                self.scene().addItem(item)
#                self.ramanscanitems.append(item)
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    def resetParticleContours(self):
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        t0 = time.time()
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        for cnt in self.contourItems:
            self.scene().removeItem(cnt)
        self.contourItems = []
        if self.dataset is not None:
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            for particleIndex, contour in enumerate(self.dataset.particleContainer.getParticleContours()):
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                self.addParticleContourToIndex(contour, particleIndex)
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            self.update()
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        print('resetted contours: {} ms'.format(round((time.time()-t0)*1000)))
        
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    def addParticleContourToIndex(self, contour, index):
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        newCnt = SegmentationContour(self, contour)
        newCnt.setIndex(index)
        assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(index)
        color = getColorFromNameWithSeed(assignment, self.dataset.colorSeed)
        newCnt.setColor(QtGui.QColor(color[0], color[1], color[2], 255))
        self.contourItems.append(newCnt)
        self.scene().addItem(newCnt)
    
    def removeParticleContour(self, contourIndex):
        correspondingParticle = self.dataset.particleContainer.getParticleOfIndex(contourIndex)   #this checks validity of contourIndex
        self.scene().removeItem(self.contourItems[contourIndex])
        del self.contourItems[contourIndex]
    
    def resetContourIndices(self):
        for index, contour in enumerate(self.contourItems):
            contour.setIndex(index)    
    
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    def updateLegend(self, legendItems):
        self.imparent.legend.setTextColorItems(legendItems)
    
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    def highLightContour(self, index):
        for contour in self.contourItems:
            contour.isSelected = False
        self.contourItems[index].isSelected = True
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        self.selectedParticleIndices =[index]
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    def centerOnRamanIndex(self, index, centerOn=True, highlightIndex=True):
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        if centerOn:
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            for scanItem in self.ramanscanitems:
                if scanItem.number == index+1:
                    self.centerOn(scanItem)

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        if highlightIndex:
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            self.highLightRamanIndex(index)
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    def highLightRamanIndex(self, index):
        if index < len(self.ramanscanitems):
            for item in self.ramanscanitems:
                if item.number == index+1:
                    item.setHighLight(True)
                else:
                    item.setHighLight(False)
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    def clearItems(self):
        for item in self.fititems:
            self.scene().removeItem(item)
        self.fititems = []
        for item in self.scanitems:
            self.scene().removeItem(item)
        edges, nodes = self.boundaryitems
        for item in edges:
            self.scene().removeItem(item)
        for item in nodes:
            self.scene().removeItem(item)
        self.scanitems = []
        self.boundaryitems = [], []
        for item in self.ramanscanitems:
            self.scene().removeItem(item)
        self.ramanscanitems = []
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