Basic plots working, proceeding to contours

analysis/analysisplots.py

+#!/usr/bin/env python3
+# -*- 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 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):
+    def __init__(self, number, numtotal, color, text, parent=None):
+        super().__init__(parent)
+        self.number = number
+        self.numtotal = numtotal
+        self.color = color
+        self.text = text
+        self.setFixedHeight(30)
+        
+    def paintEvent(self, event):
+        r = self.number/self.numtotal
+        width = self.width()
+        height = self.height()
+        
+        qp = QtGui.QPainter()
+        qp.begin(self)
+        #qp.fillRect(self.rect(), QtCore.Qt.white)
+        qp.setBrush(QtCore.Qt.white)
+        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
+        qp.setPen(self.color)
+        qp.setBrush(self.color)
+        qp.drawRoundedRect(0, 0, int(width*r), height, 5. ,5.)
+        qp.setPen(QtCore.Qt.black)
+        qp.setBrush(QtCore.Qt.NoBrush)
+        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
+        font = qp.font()
+        font.setPointSize(13)
+        font.setStyleStrategy(QtGui.QFont.NoAntialias)
+        font.setWeight(0)
+        qp.setFont(font)
+        qp.setCompositionMode(QtGui.QPainter.RasterOp_SourceXorDestination)
+        qp.setPen(QtCore.Qt.white)
+        qp.drawText(5, 0, width-10, height, QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter, 
+                    self.text)
+        qp.end()
+        
+        
+class TypeHistogramView(QtWidgets.QScrollArea):
+    indexClicked = QtCore.pyqtSignal(int)
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.view = QtWidgets.QWidget(self)
+        self.view.setCursor(QtGui.QCursor(QtCore.Qt.WhatsThisCursor))
+        self.view.setMinimumWidth(250)
+        
+        group = QtWidgets.QGroupBox('Polymer Type Distribution', self.view)
+        self.indicatorbox = QtWidgets.QVBoxLayout()
+        self.indicatorbox.setContentsMargins(5,5,5,5)
+        group.setLayout(self.indicatorbox)
+        
+        hbox = QtWidgets.QHBoxLayout()
+        hbox.addWidget(group)
+        self.view.setLayout(hbox)
+        self.setWidgetResizable(True)
+        self.setWidget(self.view)
+        self.setAlignment(QtCore.Qt.AlignHCenter)
+        self.widgets = []
+        
+    def updateTypeHistogram(self, types):
+#        print("Updating polymer type view", flush=True)
+        for pi in self.widgets:
+            self.indicatorbox.removeWidget(pi)
+            pi.setParent(None)
+            pi.destroy()
+        self.indicatorbox.takeAt(0)
+        self.widgets = []
+        numtotal = sum([num for num, text, color in types])
+        
+        def getIndexFunction(index):
+            return lambda : self.indexClicked.emit(index)
+        
+        for index, entry in enumerate(types):
+            num, text, color = entry
+#            print("num, text, color:", num, text, color, flush=True)
+            pi = ParticleIndicator(num, numtotal, color, text)
+            self.indicatorbox.addWidget(pi)
+            pi.clicked.connect(getIndexFunction(index))
+            self.widgets.append(pi)
+        self.indicatorbox.addStretch()
+        self.view.update()
+
+
+class SpectraPlot(QtWidgets.QGroupBox):
+    def __init__(self, dataset):
+        super(SpectraPlot, self).__init__()
+        self.dataset = dataset
+        self.spectra = None
+        
+        layout = QtWidgets.QHBoxLayout()
+        self.canvas = FigureCanvas(Figure())
+        self.spec_axis = self.canvas.figure.subplots()
+        self.spec_axis.axis("off")
+        self.reference_ax = self.spec_axis.twinx()
+        self.canvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)
+        specNavigation = NavigationToolbar(self.canvas, self)
+        specNavigation.setOrientation(QtCore.Qt.Vertical)
+        specNavigation.setFixedWidth(50)
+        
+        layout.addWidget(specNavigation)
+        layout.addWidget(self.canvas)
+        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.canvas.draw()
+        
+    def updateParticleSpectrum(self, specIndex, particleSize, hqi):
+        if self.spectra is not None:
+            #draw Sample Spectrum
+            self.spec_axis.axis("on")
+            self.spec_axis.clear()
+            self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
+            self.spec_axis.tick_params(axis='both', which='both', labelsize=15)
+            self.spec_axis.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
+            self.spec_axis.set_ylabel('Counts', fontsize = 15)
+            self.spec_axis.set_title('ScanPoint Number {}, Size = {} µm, HQI = {}'.format(specIndex+1, particleSize, hqi))
+            self.spec_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
+            wavenumber_diff = list(self.spectra[:, 0]-100)
+            y_start = wavenumber_diff.index(min(wavenumber_diff))
+            y_min = min(self.spectra[y_start:, specIndex+1])
+            y_max = max(self.spectra[y_start:, specIndex+1])
+            self.spec_axis.set_ybound(0.9*y_min, 1.1*y_max)
+            
+        self.canvas.draw()
+    
+    def updateReferenceSpectrum(self, ref_wavenumber, ref_intensity):
+        #draw Reference
+        self.reference_axis.clear()
+        self.reference_axis.tick_params(axis='both', which='both', labelsize=15)
+        self.reference_axis.plot(ref_wavenumber, ref_intensity, color = 'r')
+        self.reference_axis.set_ylabel('Ref. Intensity', fontsize = 15, color = 'r')
+        self.reference_axis.tick_params('y', colors = 'r')
+        self.reference_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
+#        wavenumber_diff = list(ref[:, 0]-100)
+#        y_start = wavenumber_diff.index(min(wavenumber_diff))
+#        y_min = min(ref[y_start:, specIndex+1])
+#        y_max = max(ref[y_start:, specIndex+1])
+        
+        self.canvas.draw()
+
+        
+        
\ No newline at end of file

analysis/analysiswidgets.py

@@ -204,86 +204,5 @@ class AdditiveViewer(QtWidgets.QWidget):
         self.ax.hist(sortedAdditives)
         self.ax.set_ylabel('Number', fontsize = 15)
         self.ax.tick_params(axis='both', which='both', labelsize=15)
-        
-        
-class ParticleIndicator(QtWidgets.QPushButton):
-    def __init__(self, number, numtotal, color, text, parent=None):
-        super().__init__(parent)
-        self.number = number
-        self.numtotal = numtotal
-        self.color = color
-        self.text = text
-        self.setFixedHeight(30)
-        
-    def paintEvent(self, event):
-        r = self.number/self.numtotal
-        width = self.width()
-        height = self.height()
-        
-        qp = QtGui.QPainter()
-        qp.begin(self)
-        #qp.fillRect(self.rect(), QtCore.Qt.white)
-        qp.setBrush(QtCore.Qt.white)
-        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
-        qp.setPen(self.color)
-        qp.setBrush(self.color)
-        qp.drawRoundedRect(0, 0, int(width*r), height, 5. ,5.)
-        qp.setPen(QtCore.Qt.black)
-        qp.setBrush(QtCore.Qt.NoBrush)
-        qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
-        font = qp.font()
-        font.setPointSize(13)
-        font.setStyleStrategy(QtGui.QFont.NoAntialias)
-        font.setWeight(0)
-        qp.setFont(font)
-        qp.setCompositionMode(QtGui.QPainter.RasterOp_SourceXorDestination)
-        qp.setPen(QtCore.Qt.white)
-        qp.drawText(5, 0, width-10, height, QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter, 
-                    self.text)
-        qp.end()
-        
-        
-class ParticleTypeView(QtWidgets.QScrollArea):
-    indexClicked = QtCore.pyqtSignal(int)
-    def __init__(self, parent=None):
-        super().__init__(parent)
-        self.view = QtWidgets.QWidget(self)
-        self.view.setCursor(QtGui.QCursor(QtCore.Qt.WhatsThisCursor))
-        self.view.setMinimumWidth(250)
-        
-        group = QtWidgets.QGroupBox('Polymer Type Distribution', self.view)
-        self.indicatorbox = QtWidgets.QVBoxLayout()
-        self.indicatorbox.setContentsMargins(5,5,5,5)
-        group.setLayout(self.indicatorbox)
-        
-        hbox = QtWidgets.QHBoxLayout()
-        hbox.addWidget(group)
-        self.view.setLayout(hbox)
-        self.setWidgetResizable(True)
-        self.setWidget(self.view)
-        self.setAlignment(QtCore.Qt.AlignHCenter)
-        self.widgets = []
-        
-    def updateTypeHistogram(self, types):
-#        print("Updating polymer type view", flush=True)
-        for pi in self.widgets:
-            self.indicatorbox.removeWidget(pi)
-            pi.setParent(None)
-            pi.destroy()
-        self.indicatorbox.takeAt(0)
-        self.widgets = []
-        numtotal = sum([num for num, text, color in types])
-        
-        def getIndexFunction(index):
-            return lambda : self.indexClicked.emit(index)
-        
-        for index, entry in enumerate(types):
-            num, text, color = entry
-#            print("num, text, color:", num, text, color, flush=True)
-            pi = ParticleIndicator(num, numtotal, color, text)
-            self.indicatorbox.addWidget(pi)
-            pi.clicked.connect(getIndexFunction(index))
-            self.widgets.append(pi)
-        self.indicatorbox.addStretch()
-        self.view.update()        
+
         
\ No newline at end of file

colorlegend.py → analysis/colorlegend.py

@@ -20,6 +20,8 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 from PyQt5 import QtCore, QtWidgets, QtGui
 import numpy as np
+import random
+import colorsys
 
 
 WX, WY = 1024, 200
@@ -111,4 +113,23 @@ class ColorLegend(QtWidgets.QMdiSubWindow):
             
             qp.end()
         
-        
\ No newline at end of file
+class ColorHandler(object):
+    def __init__(self):
+        pass
+        #We should implement another method of getting colors, rather than taking the random color generator
+        #presets and other stuff can be defined here
+        
+    def getColorFromName(self, name, seed, base255=True):
+        random.seed(seed + name)
+        hue = random.random()
+        random.seed((seed + name)*2)
+        saturation = random.random()/4 + 0.75      #i.e., between 0.75 and 1
+        random.seed((seed + name)*3)
+        value = random.random()/5 + 0.8     #i.e., between 0.8 and 1
+        color = colorsys.hsv_to_rgb(hue, saturation, value)
+        if base255:
+            color = list(color)
+            for i in range(3):
+                color[i] = np.round(color[i]*255)
+            color = tuple(color)
+        return color
\ No newline at end of file

analysis/datastats.py → analysis/particleInfo.py

@@ -18,17 +18,16 @@ 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/>.
 """
-import os
+#import os
 import numpy as np
 import operator
-from PyQt5 import QtWidgets, QtCore
+#from PyQt5 import QtWidgets, QtCore
 
-from analysis import importSpectra
-try:
-    from dataset import loadData, recursiveDictCompare
-    print('exported dataset methods from datastats')
-except:
-    print('failed exported dataset methods from datastats')
+#try:
+#    from dataset import loadData, recursiveDictCompare
+#    print('exported dataset methods from datastats')
+#except:
+#    print('failed exported dataset methods from datastats')
 
 class ParticleContainer(object):
     def __init__(self, parent):
@@ -89,7 +88,12 @@ class ParticleContainer(object):
                 meas.setAssignment(hqiList[scanIndex])
                 indicesOfTransferredAssignments.append(scanIndex)
         assert np.unique(indicesOfTransferredAssignments) == np.unique((range(len(hqiList))))
-                
+    
+    def getParticleOfIndex(self, index):
+        particle = self.particles[index]
+        assert particle.index == index, f'particle.index ({particle.index}) does match requested index in particleList ({index})' 
+        return particle
+            
     def getNumberOfParticles(self):
         return len(self.particles)
     
@@ -99,9 +103,9 @@ class ParticleContainer(object):
     
     def getParticleContoursByIndex(self, partIndices):
         contours = []
-        for part in self.particles:
-            if part.index in partIndices:
-                contours.append(part.contour)
+        for index in partIndices:
+            particle = self.getParticleOfIndex(index)
+            contours.append(particle.contour)
         return contours
     
     def getMeasurementPixelCoords(self):
@@ -118,6 +122,14 @@ class ParticleContainer(object):
                 num += 1
         return num
     
+    def getNumberOfSpectraOfParticle(self, particleIndex):
+        particle = self.getParticleOfIndex(particleIndex)
+        return particle.getNumberOfMeasurements()
+
+    def getSpectraIndicesOfParticle(self, particleIndex):
+        particle = self.getParticleOfIndex(particleIndex)
+        return particle.getMeasurementIndices()
+        
     def getListOfParticleAssignments(self):
         particleAssignments = []
         for particle in self.particles:
@@ -130,7 +142,12 @@ class ParticleContainer(object):
             hqis.append(particle.getHighestHQI())
         return hqis
     
-    def getInconsistentParticles(self): #i.e., particles that have multiple measurements with different assignments
+    def getHQIOfSpectrumIndex(self, specIndex):
+        for particle in self.particles:
+            if specIndex in particle.getMeasurementIndices():
+                return particle.getHQIOfMeasurementIndex(specIndex)
+                
+    def testForInconsistentParticles(self): #i.e., particles that have multiple measurements with different assignments
         self.inconsistentParticles = []
         for particle in self.particles:
             if not particle.measurementsHaveSameOrigAssignment():
@@ -141,32 +158,45 @@ class ParticleContainer(object):
                 print(f'Particle with index {particle.index} has the following assignments:')
                 for assignment in particle.getOrigMeasurementAssignments():
                     print(assignment)
+        else:
+            print('All particles have consistent spectra assignments')
                     
-        return self.inconsistentParticles
-    
     def getSizesOfAllParticles(self):
         particleSizes = []
         for particle in self.particles:
             particleSizes.append(particle.getParticleSize())
+        return particleSizes
         
     def getShortSizesOfAllParticles(self):
         shortSizes = []
         for particle in self.particles:
-            shortSizes.append(particle.getShortParticleSize())
+            shortSizes.append(particle.getShortParticleSize())#
+        return shortSizes
     
     def getSizesOfParticleType(self, assignment):
         particleSizes = []
         for particle in self.particles:
             if particle.getParticleAssignment() == assignment:
                 particleSizes.append(particle.getParticleSize())
+        return particleSizes
     
-    def getSizeOfParticleByIndex(self, index):
+    def getIndicesOfParticleType(self, assignment):
+        indices = []
         for particle in self.particles:
-            if particle.index == index:
-                return particle.getParticleSize()
+            if particle.getParticleAssignment() == assignment:
+                indices.append(particle.index)
+        return indices
+    
+    def getSizeOfParticleByIndex(self, index):
+        particle = self.getParticleOfIndex(index)
+        return particle.getParticleSize()
     
+    def getUniquePolymers(self):
+        typeHist = self.getTypeHistogram()
+        return typeHist.keys()
+
     def getTypeHistogram(self):
-        uniquePolymers = self.getUniquePolymers()
+        uniquePolymers = np.unique(self.getListOfParticleAssignments())
         typehistogram = {i: 0 for i in uniquePolymers}
         for assignment in self.getListOfParticleAssignments():
             typehistogram[assignment] += 1
@@ -175,18 +205,15 @@ class ParticleContainer(object):
         #convert back to dict
         final_typehistogram = {i[0]: i[1] for i in sorted_typehistogram}
         return final_typehistogram
-        
-    def getUniquePolymers(self):
-        return np.unique(self.getListOfParticleAssignments())
     
 
 class Particle(object):
     def __init__(self, index):
         self.index = index
-        self.longSize_ellipse = None
-        self.shortSize_ellipse = None
-        self.longSize_box = None
-        self.shortSize_box = None
+        self.longSize_ellipse = np.nan
+        self.shortSize_ellipse = np.nan
+        self.longSize_box = np.nan
+        self.shortSize_box = np.nan
         self.area = None
         self.contour = None
         self.measurements = []
@@ -212,6 +239,17 @@ class Particle(object):
             hqis.append(meas.getHQI())
         return max(hqis)
     
+    def getHQIOfMeasurementIndex(self, index):
+        for meas in self.measurements:
+            if meas.ramanScanIndex == index:
+                return meas.getHQI()
+    
+    def getMeasurementIndices(self):
+        indices = []
+        for meas in self.measurements:
+            indices.append(meas.ramanScanIndex)
+        return indices
+    
     def getMeasurements(self):
         return self.measurements
     
@@ -225,23 +263,27 @@ class Particle(object):
         return assignments[indexOfHighestHQI]
         
     def getParticleSize(self):
-        if self.longSize_ellipse is not None:
-            return round(self.longSize_ellipse)
-        elif self.longSize_box is not None:
-            return round(self.longSize_box)
+        if not np.isnan(self.longSize_ellipse):
+            size = self.longSize_ellipse
+        elif not np.isnan(self.longSize_box):
+            size = self.longSize_box
         else:
             print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
             raise ValueError
+        assert size is not None, f'Error, size or particle {self.index} is None'
+        return round(size)
     
     def getShortParticleSize(self):
-        if self.shortSize_ellipse is not None:
+        if not np.isnan(self.shortSize_ellipse):
             return round(self.shortSize_ellipse)
-        elif self.shortSize_box is not None:
-            return round(self.shortSize_box )
+        elif not np.isnan(self.shortSize_box):
+            return round(self.shortSize_box)
         else:
             print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
             raise ValueError
     
+    def getNumberOfMeasurements(self):
+        return len(self.measurements)
     
     def measurementsHaveSameOrigAssignment(self):
         allResults = [meas.getOrigAssignment() for meas in self.measurements]
@@ -300,58 +342,58 @@ class Measurement(object):
     
     
         
-def readDataStats(fname):
-    ds = loadData(fname)
-    datastats = DataStats(ds)
-    datastats.update()
-    datastats.loadParticleData()
-    minHQI = datastats.dataset.resultParams['minHQI']
-    compHQI = datastats.dataset.resultParams['compHQI']
-    datastats.formatResults(minHQI, compHQI)
-    datastats.createHistogramData()
-    return datastats
-
-class DataStats(object):
-    def __init__(self, dataset):
-        self.dataset = dataset
-        
-        self.spectraResults = None                  #entire List of all spectra assignments
-        self.additiveResults = None                 #entire List of all additives
-        self.particleResults = None                 #final assignment for each particle
-        
-        self.currentPolymers = None                 #list of polymers after setting entries with low hqi to unknown
-        self.currentAdditives = None                #same thing for the additives
-        self.spectra = None                         #acquired spectra
-        self.indices = None                         #assignment of what spectra-indices belong to what substance
-        
-        self.particles2spectra = None
-        self.manualPolymers = {}
-        self.manualAdditives = {}
-        
-    def resetResults(self, spectraResults, additiveResults, hqis, addhqis):
-        self.spectraResults = spectraResults
-        self.additiveResults = additiveResults
-        self.hqis = hqis
-        self.addhqis = addhqis
-        
-    def update(self):
-        print('updating data from', self.dataset.name)
-        self.spectraResults = self.dataset.results['polymers']
-        self.additiveResults = self.dataset.results['additives']
-        self.hqis = self.dataset.results['hqis']
-        self.addhqis = self.dataset.results['additive_hqis']
-                
-        self.colorSeed = self.dataset.colorSeed
-        if type(self.colorSeed) != str:
-            self.colorSeed = 'default'
-        
-        #load Spectra
-        if self.dataset.spectraPath is None:
-            fname = os.path.join(self.dataset.path, self.dataset.name + '_000_Spec.Data 1.txt')
-        else:
-            fname = self.dataset.spectraPath
-        return self.loadSpectra(fname)
-        
+#def readDataStats(fname):
+#    ds = loadData(fname)
+#    datastats = DataStats(ds)
+#    datastats.update()
+#    datastats.loadParticleData()
+#    minHQI = datastats.dataset.resultParams['minHQI']
+#    compHQI = datastats.dataset.resultParams['compHQI']
+#    datastats.formatResults(minHQI, compHQI)
+#    datastats.createHistogramData()
+#    return datastats
+#
+#class DataStats(object):
+#    def __init__(self, dataset):
+#        self.dataset = dataset
+#        
+#        self.spectraResults = None                  #entire List of all spectra assignments
+#        self.additiveResults = None                 #entire List of all additives