sampleview.py 21.8 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
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
from viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContours
from helperfunctions import polygoncovering, cv2imread_fix
import cv2
from ramancom.configRaman import RamanConfigWin

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)
        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
        self.fititems = []
        self.boundaryitems = [[],[]]
        self.scanitems = []
        self.ramanscanitems = []
        self.imgdata = None
        self.isblocked = False
        self.contouritem = SegmentationContours(self)
        scene.addItem(self.contouritem)
        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
        self.coordTestMode = False
        
    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()
        
    @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):
#        print("fitting to Window")
        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)
        if self.detectionwidget is not None:
            self.detectionwidget.close()
            self.detectionwidget.destroy()
        self.ramanwidget.setVisible(False)
        self.contouritem.resetContours([])
        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.show()
                self.detectionwidget.imageUpdate.connect(self.detectionUpdate)
                self.detectionwidget.detectionFinished.connect(self.activateMaxMode)
            
        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()
            else:
                print('show maximized already exisiting analysiswidget')
                self.analysiswidget.showMaximized()
            
#            self.ramanwidget.setVisible(False)
            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.contouritem.resetContours()
#        if self.dataset is not None:
#            del self.dataset
#            self.scene().removeItem(self.contouritem)
#            del self.contouritem
#            self.contouritem = SegmentationContours(self)
#            self.scene().addItem(self.contouritem)
            
        self.dataset = loadData(fname)
        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)
        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 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"
            if len(self.dataset.ramanpoints)>0:
                maxmode = "RamanScan"
            if self.dataset.ramanscandone:        #uncomment!!
                maxmode = "ParticleAnalysis"
        return maxmode
        
    def mousePressEvent(self, event):
#        if event.button()==QtCore.Qt.RightButton:
        if event.button()==QtCore.Qt.MiddleButton:
            self.drag = event.pos()
        elif event.button()==QtCore.Qt.LeftButton and self.mode in ["OpticalScan", "RamanScan"] \
             and event.modifiers()==QtCore.Qt.ControlModifier:
            p0 = self.mapToScene(event.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
                x, y, z = self.dataset.mapToLengthRaman([p0.x(), p0.y()], 
                                                         microscopeMode=self.microscopeMode,
                                                         noz=(False if self.mode=="RamanScan" else True))
                if z is not None:
                    assert z>-100.
                self.ramanctrl.moveToAbsolutePosition(x, y, z)
        elif event.button()==QtCore.Qt.LeftButton and self.mode=="ParticleDetection":
            p0 = self.mapToScene(event.pos())
            self.detectionwidget.setImageCenter([p0.x(), p0.y()])
#        elif event.button()==QtCore.Qt.LeftButton and self.mode=="ParticleAnalysis":
#            p0 = self.mapToScene(event.pos())
        
        else:
            p0 = self.mapToScene(event.pos())
            super(SampleView, self).mousePressEvent(event)
            
    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
        else:
            super(SampleView, self).mouseMoveEvent(event)
                        
    def mouseReleaseEvent(self, event):
        self.drag = None
        super(SampleView, self).mouseReleaseEvent(event)
        
    def wheelEvent(self, event):
        factor = 1.01**(event.angleDelta().y()/8)
        self.scaleImage(factor)

    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):
        self.contouritem.resetContours(self.dataset.particlecontours)
        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":
                self.contouritem.resetContours(self.dataset.particlecontours)
            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)
#        print(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()
        
    @QtCore.pyqtSlot(int, bool)
    def selectContour(self, index, centerOn=True):
        if self.analysiswidget is not None:
            self.analysiswidget.selectContour(index, centerOn)
    
    def prepareAnalysis(self):
        self.clearItems()
        if self.dataset.ramanscansortindex is not None and len(self.dataset.ramanscansortindex)>0:
            data = []
            for i in self.dataset.ramanscansortindex:
#                data.append(list(self.dataset.ramanpoints[i])+list(self.dataset.particlestats[i]))
                data.append(list(self.dataset.ramanpoints[i]))  #particlestats are not needed here. Plus, they dont need to match spectra indices anymore..
            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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    def highLightRamanIndex(self, index):
        if index < len(self.ramanscanitems):
            for item in self.ramanscanitems:
                item.setHighLight(False)
            self.ramanscanitems[index].setHighLight(True)
    
    def centerOnRamanIndex(self, index, centerOn=True, highlightContour=True):
        if centerOn:
            self.centerOn(self.ramanscanitems[index])
            
#        if highlightContour:
#            self.contouritem.selectedContours = []
#        else:
#            self.ensureVisible(self.ramanscanitems[index])
        
        
    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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