Commit 86522ed2 authored by Hackmet's avatar Hackmet
Browse files

Several Bugfixes

parent 8e5899e5

analysis/analysisview.py

+35 −25
Original line number Diff line number Diff line
@@ -336,9 +336,9 @@ class ParticleAnalysis(QtWidgets.QWidget): 
        self.specCanvas.draw()

        

        ####fake data!!!

        if self.spectraResults is None:

            self.spectraResults = ['empty']*(self.spectra.shape[1]-1)

            self.hqis = [100]*(self.spectra.shape[1]-1)

#        if self.spectraResults is None:

#            self.spectraResults = ['empty']*(self.spectra.shape[1]-1)

#            self.hqis = [100]*(self.spectra.shape[1]-1)

        

        self.loadParticleData()
@@ -362,7 +362,16 @@ class ParticleAnalysis(QtWidgets.QWidget): 
        

        #check, if dataset already contains results. Otherwise load them...

        if self.spectraResults is None or (len(self.spectraResults) != len(sortindices)):

            QtWidgets.QMessageBox.about(self, 'Info', 'No (or inconsistent) spectra results found, please run import dialog.')

            self.show()

#            QtWidgets.QMessageBox.about(self, 'Info', 'No (or inconsistent) spectra results found, please run import dialog.')

            answer = QtWidgets.QMessageBox.question(self, 'Warning', 'No (or inconsistent) spectra results found, please run import dialog.\nPress OK to import or cancel to set to empty.', QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel)

            if answer == QtWidgets.QMessageBox.Ok:

                self.importResults()

            elif answer == QtWidgets.QMessageBox.Cancel:

                self.spectraResults = ['empty']*(self.spectra.shape[1]-1)

                self.hqis = [100]*(self.spectra.shape[1]-1)

                self.updateBtn.clicked.connect(self.formatResults)

                self.formatResults()

        else:

            self.updateBtn.clicked.connect(self.formatResults)

            self.formatResults()
@@ -383,6 +392,7 @@ class ParticleAnalysis(QtWidgets.QWidget): 
            self.additivePlot.show()

    

    def formatResults(self):

        if self.spectraResults is not None:

            print('formatResults')

            self.updateBtn.setDisabled(False)

            self.optionsGroup.setDisabled(False)

analysis/editParticles.py

+1 −1
Original line number Diff line number Diff line
@@ -77,7 +77,7 @@ class ParticleEditor(object): 
        cv2.drawContours(img, [cnt], 0, 1, 1)

        img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))

        

        temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)

        temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)



        newContour = contours[0]

        stats = self.characterizeParticle(newContour)

dataset.py

+4 −0
Original line number Diff line number Diff line
@@ -75,6 +75,7 @@ class DataSet(object): 
        

        # parameters specifically for raman scan

        self.pshift = None    # shift of raman scan position relative to image center

        self.coordOffset = [0, 0]   #offset of entire coordinate system

        self.seedpoints = np.array([])

        self.seeddeletepoints = np.array([])

        self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
@@ -230,6 +231,9 @@ class DataSet(object): 
        if not force:

            assert not self.readin

        p0 = copy(self.lastpos)

        p0[0] += self.coordOffset[0] 

        p0[1] += self.coordOffset[1]

        

        if mode == 'df':

            p0[0] -= self.imagedim_df[0]/2

            p0[1] += self.imagedim_df[1]/2

gepard.py

+11 −0
Original line number Diff line number Diff line
@@ -173,6 +173,14 @@ class MeasureParticleWindow(QtWidgets.QMainWindow): 
        self.snapshotAct.triggered.connect(self.view.takeScreenshot)

        self.snapshotAct.setDisabled(True)

        

        self.checkCoordsAct = QtWidgets.QAction("Check Coordinate System", self)

        self.checkCoordsAct.triggered.connect(self.view.checkCoords)

        self.checkCoordsAct.setDisabled(True)

        

        self.configCoordsAct = QtWidgets.QAction("Reconfigure Coordinate System", self)

        self.configCoordsAct.triggered.connect(self.view.configureCoords)

        self.configCoordsAct.setDisabled(True)

        

        self.configRamanCtrlAct = QtWidgets.QAction("Configure Raman Control", self)

        self.configRamanCtrlAct.triggered.connect(self.view.configureRamanControl)

        if self.view.simulatedRaman:
@@ -254,6 +262,9 @@ class MeasureParticleWindow(QtWidgets.QMainWindow): 
        self.toolsMenu = QtWidgets.QMenu("Tools")

        self.toolsMenu.addAction(self.snapshotAct)

        self.toolsMenu.addAction(self.configRamanCtrlAct)

        self.toolsMenu.addSeparator()

        self.toolsMenu.addAction(self.checkCoordsAct)

        self.toolsMenu.addAction(self.configCoordsAct)

        

        self.helpMenu = QtWidgets.QMenu("&Help", self)

        self.helpMenu.addAction(self.aboutAct)

sampleview.py

+28 −2
Original line number Diff line number Diff line
@@ -86,6 +86,7 @@ class SampleView(QtWidgets.QGraphicsView): 
        self.setMinimumSize(600,600)

        self.darkenPixmap = False

        self.microscopeMode = None

        self.coordTestMode = False

        

    def takeScreenshot(self):

        #TODO:
@@ -210,8 +211,14 @@ class SampleView(QtWidgets.QGraphicsView): 
        

    def open(self, fname):       

        self.saveDataSet()

        if self.dataset is not None:  #####TODO: properly close and delete all widget instances for avoiding that data from a currently opened dataset is saved into the new...

        if self.dataset is not None:

            self.dataset.save()

            #close all widgets

            for widget in [self.detectionwidget, self.ramanwidget, self.oscanwidget, self.analysiswidget]:

                widget.close()

                widget.destroy()

            self.contouritem.resetContours()

            

        self.dataset = loadData(fname)

        self.setMicroscopeMode()

        self.imparent.setWindowTitle(self.dataset.name + (" SIMULATION" if simulatedRaman else ""))
@@ -470,7 +477,11 @@ class SampleView(QtWidgets.QGraphicsView): 
                self.analysiswidget.currentSpectrumIndex = specIndex

                

                selectedPolymer = self.analysiswidget.currentPolymers[specIndex]

                try:

                    self.analysiswidget.polymerIndex = self.analysiswidget.uniquePolymers.index(selectedPolymer)

                except:

                    print(selectedPolymer)

                    raise

                

                #subparticleIndex

                partIndicesOfThatPolymer = self.analysiswidget.indices[self.analysiswidget.polymerIndex]
@@ -545,3 +556,18 @@ class SampleView(QtWidgets.QGraphicsView): 
            self.scene().removeItem(item)

        self.ramanscanitems = []

    

    def checkCoords(self):

        if not os.path.exists(self.dataset.getImageName):

            QtWidgets.QMessageBox.about(self, 'No Fullimage found', 'Optical scan was not complete.\nPlease acquire fullimage first with newly defined border points.')

        else:

            self.coordTestMode = True

            QtWidgets.QMessageBox.about(self, 'Check Coordinate System', 'Microscope is moving to 5 positions.\nFirst, only x and y are moved, z only if x,y positions are confirmed')

            points = (self.dataset.fitpoints if len(self.dataset.ramanpoints) == 0 else self.dataset.ramanpoints)

            for i in range(5):

                #get random scanindex:

                point = points[np.random.randint(len(points))]

            

    

    def configureCoords(self):

        pass

        
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