Preparation for reorganizing contours and scanIndices

Have it managed by the particle!

analysis/analysisplots.py

@@ -23,10 +23,6 @@ from PyQt5 import QtWidgets, QtGui, QtCore
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
-import os
-import numpy as np
-
-from analysis import importSpectra
 
 
 class ParticleIndicator(QtWidgets.QPushButton):
@@ -132,31 +128,8 @@ class SpectraPlot(QtWidgets.QGroupBox):
         self.setLayout(layout)
         
     def loadSpectraAndInitializeSpecPlot(self):  #formerly updateData(self)....
-#        def tryLoadingNumpySpecFile():
-#            specPath = self.dataset.getSpectraFileName()
-#            if os.path.exists(specPath):
-#                return np.load(specPath)
-#            else:
-#                raise ImportError
-#        try:
-#            self.spectra = tryLoadingNumpySpecFile()
-#        except ImportError:
-#            
-#            fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]
-#    
-#            try:
-#                self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
-#            except ImportError:
-#                try:
-#                    self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
-#                except ImportError:
-#                    self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
-#                
-#            if self.spectra is None:
-#                raise ImportError
-#            else:
-#                np.save(self.dataset.getSpectraFileName(), self.spectra)
- 
+        self.spectra = self.dataset.particleContainer.spectra
+        assert self.spectra is not None
         self.canvas.draw()
         
     def updateParticleSpectrum(self, specIndex, particleSize, hqi):

analysis/analysisview.py

@@ -32,7 +32,6 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio
 from .analysiswidgets import ExpExcelDialog
 from .analysisplots import TypeHistogramView, SpectraPlot
 from .loadresults import LoadTrueMatchResults
-from .particleeditor import ParticleEditor
 from .database import DataBaseWindow
 from .colorlegend import getColorFromNameWithSeed
 
@@ -56,7 +55,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.viewparent = viewparent
         self.dataset = dataset
         self.particleContainer = dataset.particleContainer
-        self.editor = ParticleEditor(self.particleContainer, self)
         
 #        self.additivePlot = None
         self.importWindow = None
@@ -221,6 +219,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.createMenus()
         self.applyHQIThresholdToResults()
         self.createHistogramData()
+        self.particleContainer.loadSpectra()
         self.initializeSpecPlot()
         self.setTypeSelector()
         self.updateHistogramsAndContours()
@@ -556,7 +555,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
         self.currentParticleIndex = particleIndex
         partIndices = self.particleContainer.getIndicesOfParticleType(assignment)
         self.particleSelector.setMaximum(len(partIndices))
-        
+        self.particleNumberLabel.setText(f'of {len(partIndices)} particles; ')
         
         self.particleSelector.setValue(partIndices.index(particleIndex)+1)
         

analysis/particleAndMeasurement.py

@@ -19,7 +19,7 @@ along with this program, see COPYING.
 If not, see <https://www.gnu.org/licenses/>.
 """
 import numpy as np
-
+from viewitems import SegmentationContour, RamanScanIndicator
 
 class Particle(object):
     def __init__(self):
@@ -35,23 +35,9 @@ class Particle(object):
         self.viewItem = None
     
     def addMeasurement(self, refToMeasurement):
+        refToMeasurement.assignedParticle = self
         self.measurements.append(refToMeasurement)
-        
-#    def addExistingMeasurement(self, meas):
-#        self.measurements.append(meas)
-#    
-#    def addEmptyMeasurement(self):
-#        self.measurements.append(Measurement())
-#        indexOfNewMeasurment = len(self.measurements)-1
-#        return indexOfNewMeasurment
-    
-#    def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
-#        self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex
-#    
-#    def setMeasurementPixelCoords(self, indexOfMeasurment, x, y):
-#        self.measurements[indexOfMeasurment].pixelcoord_x= x
-#        self.measurements[indexOfMeasurment].pixelcoord_y = y
-#
+
     def setAllSpectraToNewAssignment(self, newAssignment):
         for meas in self.measurements:
             meas.setAssignment(newAssignment)
@@ -127,8 +113,8 @@ class Particle(object):
         for measurement in self.measurements:
             measurement.applyHQIThreshold(minHQI)
     
-#    def recreateViewItem(self):
-#        pass
+    def recreateViewItem(self):
+        self.viewItem = SegmentationContour()
             
     
 class Measurement(object):
@@ -141,6 +127,8 @@ class Measurement(object):
         self.assignment_orig = 'Not Evaluated'
         self.assignment_afterHQI = None
         self.hqi = None
+        
+        self.assignedParticle = None
     
     def setAssignment(self, assignment):
         self.assignment_orig = assignment

analysis/particleInfo.py → analysis/particleContainer.py

@@ -178,9 +178,10 @@ class ParticleContainer(object):
     
     def getMeasurementPixelCoords(self):
         coords = []
-        for particle in self.particles:
-            for measurement in particle.getMeasurements():
-                coords.append([measurement.pixelcoord_x, measurement.pixelcoord_y])
+#        for particle in self.particles:
+#            for measurement in particle.getMeasurements():
+        for meas in self.measurements:
+                coords.append([meas.pixelcoord_x, meas.pixelcoord_y])
         return coords
     
     def getNumberOfParticlesOfAssignment(self, assignment):
@@ -269,7 +270,7 @@ class ParticleContainer(object):
                 if newAssignment is not None:
                     meas.setAssignment(newAssignment)
                     meas.setHQI(100)
-                newParticle.addExistingMeasurement(meas)
+                newParticle.addMeasurement(meas)
         
         #set Particle Stats
         long, short, longellipse, shortellipse, area = newStats

dataset.py

@@ -24,7 +24,7 @@ import numpy as np
 import cv2
 from helperfunctions import cv2imread_fix, cv2imwrite_fix
 from copy import copy
-from analysis.particleInfo import ParticleContainer
+from analysis.particleContainer import ParticleContainer
 
 currentversion = 3
 

detectionview.py

@@ -677,7 +677,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
                     
                     
                 
-            self.dataset.ramanpoints = measurementPoints    #consider moving that to particleContainer
+#            self.dataset.ramanpoints = measurementPoints    #consider moving that to particleContainer
 #            self.dataset.particlecontours = contours
 #            self.dataset.particlestats = particlestats
 #            self.dataset.ramanscansortindex = []

gepard.py

@@ -100,13 +100,23 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
             fileName = QtWidgets.QFileDialog.getSaveFileName(self, "Create New Project",
                                         defaultPath, "*.pkl")[0]
         if fileName:
-#            if fileName.find(' ') < 0:
-            self.fname = str(fileName)   #TODO: No spaces for Renishaw Interface!!
-            self.view.new(self.fname)  
-            self.scalingChanged(1.)
-#            else:
-#                QtWidgets.QMessageBox.critical(self, "Error", "File path must not contain spaces.")
-     
+            isValid, msg = self.testFilename(fileName)
+            if isValid:
+                self.fname = str(fileName)   #TODO: No spaces for Renishaw Interface!!
+                self.view.new(self.fname)  
+                self.scalingChanged(1.)
+            else:
+                QtWidgets.QMessageBox.critical(self, "Error", msg)
+    
+    def testFilename(self, fileName):
+        if self.view.ramanctrl.name == 'RenishawCOM':   #the renishawCom does not allow Spaces within filePath
+            if fileName.find(' ') == 0:
+                return False, "File path must not contain spaces."
+            else:
+                return True, ""
+        else:
+            return True, ""
+        
     @QtCore.pyqtSlot() 
     def about(self):
         QtWidgets.QMessageBox.about(self, 'GEPARD',

ramancom/WITecCOM.py

@@ -47,6 +47,7 @@ class WITecCOM(RamanBase):
     
     def __init__(self, hostname=None):
         super().__init__()
+        self.name = 'WITecCOM'
         if hostname is None:
             hostname = gethostname()
         self.IBUCSAccess = win32com.client.DispatchEx(self.CLSID, machine=hostname, 

ramancom/ramanbase.py

@@ -21,6 +21,7 @@ If not, see <https://www.gnu.org/licenses/>.
 
 class RamanBase(object): 
     def __init__(self):
+        self.name = None
         self.connected = False
         self.timeseries = False
        

ramancom/simulatedraman.py

@@ -32,6 +32,7 @@ class SimulatedRaman(RamanBase):
     ramanParameters = {}
     def __init__(self):
         super().__init__()
+        self.name = 'SimulatedRaman' 
         self.currentpos = None, 0., 0.
         self.currentZ = 0.
         # some plausible data to simulate consecutively changing positions

ramanscanui.py

@@ -232,16 +232,8 @@ class RamanScanUI(QtWidgets.QWidget):
 
         if reply == QtWidgets.QMessageBox.Yes:
             self.dataset.mode = "ramanscan"
-            measurements2particles = [[int(np.where(cmin == i)[0])] for i in range(len(cmin))]   #i.e., list of scanIndicesPerParticle
-            for particleIndex, listOfScanIndices in enumerate(measurements2particles):
-                
-#                curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
-                for scanIndex in listOfScanIndices:
-                    
-                    
-                    self.particleContainer.setMeasurementScanIndex(indexOfNewMeas, scanIndex)
-            
-            
+            for measIndex, ramanScanIndex in enumerate(cmin):
+                self.particleContainer.setMeasurementScaneIndex(measIndex, ramanScanIndex)
             
 #            self.dataset.ramanscansortindex = cmin
             self.dataset.saveParticleData()

sampleview.py

@@ -34,9 +34,8 @@ from zeissimporter import ZeissImporter
 from viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContour
 from analysis.colorlegend import getColorFromNameWithSeed
 from helperfunctions import polygoncovering, cv2imread_fix
-
 from ramancom.configRaman import RamanConfigWin
-from analysis.particleeditor import ParticleEditor
+from analysis.particleEditor import ParticleEditor
 
 
 class SampleView(QtWidgets.QGraphicsView):
@@ -412,6 +411,7 @@ class SampleView(QtWidgets.QGraphicsView):
         p = QtCore.QPointF(p.x(), p.y())
         
         for index, cnt in enumerate(self.contourItems):
+            
             if cnt.polygon.containsPoint(p, QtCore.Qt.OddEvenFill):   #clicked on particle
                 if not event.modifiers()==QtCore.Qt.ShiftModifier:
                     acceptSelection(cnt)

viewitems.py

@@ -20,7 +20,7 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 #import numpy as np
 from PyQt5 import QtCore, QtWidgets, QtGui
-from analysis.particleeditor import ParticleContextMenu
+from analysis.particleEditor import ParticleContextMenu
 
 class SegmentationContour(QtWidgets.QGraphicsItem):
     def __init__(self, viewparent, contourData, pos=(0,0)):
@@ -128,15 +128,15 @@ class FitPosIndicator(QtWidgets.QGraphicsItem):
 class RamanScanIndicator(QtWidgets.QGraphicsItem):
     def __init__(self, view, number, radius, pos=(0,0)):
         super().__init__()
-#        self.setFlag(QtWidgets.QGraphicsItem.ItemIsSelectable)
         self.setAcceptedMouseButtons(QtCore.Qt.NoButton)
-        self.setZValue(100)   #higher numbers will be in foreground. Shall always be in foreground!
+        self.setZValue(100)   #higher zValues will be in foreground. Shall always be in foreground!
         self.view = view
         self.number = number
         self.radius = radius
         self.highlight = False
         self.hidden = False
         self.setPos(pos[0], pos[1])
+        self.hasNoParticleAssigned = False
         
     def setHighLight(self, highlight):
         if highlight!=self.highlight:
@@ -157,6 +157,9 @@ class RamanScanIndicator(QtWidgets.QGraphicsItem):
             if self.highlight:
                 painter.setPen(QtCore.Qt.red)
                 painter.setBrush(QtGui.QColor(100,250,100,150))
+            elif self.hasNoParticleAssigned:
+                painter.setPen(QtCore.Qt.black)
+                painter.setBrush(QtCore.Qt.red)
             else:
                 painter.setPen(QtCore.Qt.green)
                 painter.setBrush(QtGui.QColor(50,50,250,150))