MergeToNewMaster

.gitignore

 
 __pycache__/
 
+gepard\.cfg
+
+analysis/database_config\.txt
+
+*.so
+
 *.c
 
-*.pyd
+external/build/
 
-gepard\.cfg
+.idea/

gepard.py → __main__.py

@@ -18,18 +18,17 @@ 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, QtWidgets, QtGui
-from sampleview import SampleView
-from scalebar import ScaleBar
-from ramancom.ramancontrol import defaultPath
-from ramancom.ramanSwitch import RamanSwitch
-from colorlegend import ColorLegend
 import os
+from PyQt5 import QtCore, QtWidgets, QtGui
+from .sampleview import SampleView
+from .scalebar import ScaleBar
+from .ramancom.ramancontrol import defaultPath
+from .ramancom.ramanSwitch import RamanSwitch
+from .analysis.colorlegend import ColorLegend
             
-class MeasureParticleWindow(QtWidgets.QMainWindow):
-    
+class GEPARDMainWindow(QtWidgets.QMainWindow):
     def __init__(self, logpath):
-        super(MeasureParticleWindow, self).__init__()
+        super(GEPARDMainWindow, self).__init__()
 
         self.setWindowTitle("GEPARD")
         self.resize(900, 700)
@@ -101,13 +100,24 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
             fileName = QtWidgets.QFileDialog.getSaveFileName(self, "Create New Project",
                                         defaultPath, "*.pkl")[0]
         if fileName:
-            if fileName.find(' ') < 0:
+            isValid, msg = self.testFilename(fileName)
+            if isValid:
                 self.fname = str(fileName)
                 self.view.new(self.fname)  
                 self.scalingChanged(1.)
             else:
-                QtWidgets.QMessageBox.critical(self, "Error", "File path must not contain spaces.")
-     
+                QtWidgets.QMessageBox.critical(self, "Error", msg)
+            
+    @QtCore.pyqtSlot()  
+    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',
@@ -116,7 +126,7 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
 
     def createActions(self):
         fname = os.path.join(os.path.split(__file__)[0],
-                             os.path.join("data","brand.png"))
+                             os.path.join('data', 'brand.png'))
         self.aboutAct = QtWidgets.QAction(QtGui.QIcon(fname),
                                           "About Particle Measurment", self)
         self.aboutAct.triggered.connect(self.about)
@@ -125,7 +135,7 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.openAct.setShortcut("Ctrl+O")
         self.openAct.triggered.connect(self.open)
         
-        self.importAct = QtWidgets.QAction("&Import Project...", self)
+        self.importAct = QtWidgets.QAction("&Import Zeiss Project...", self)
         self.importAct.setShortcut("Ctrl+I")
         self.importAct.triggered.connect(self.importProject)
         
@@ -188,12 +198,23 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.snapshotAct = QtWidgets.QAction("Save Screenshot", self)
         self.snapshotAct.triggered.connect(self.view.takeScreenshot)
         self.snapshotAct.setDisabled(True)
-        
+
         self.configRamanCtrlAct = QtWidgets.QAction("Configure Raman Control", self)
         self.configRamanCtrlAct.triggered.connect(self.view.configureRamanControl)
         if self.view.simulatedRaman:
             self.configRamanCtrlAct.setDisabled(True)
-    
+            
+        self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
+        self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
+        self.fullOverlayAct = QtWidgets.QAction("&Full Overlay", self)
+        self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
+        self.hideLabelAct = QtWidgets.QAction('&Hide Spectra Numbers', self)
+        self.darkenAct = QtWidgets.QAction("&Darken Image", self)
+        self.seedAct = QtWidgets.QAction("&Set Color Seed", self)
+        
+        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct, self.hideLabelAct, self.transpAct, self.darkenAct, self.seedAct]:
+            act.setDisabled(True)
+            
     def updateModes(self, active=None, maxenabled=None):
         ose, osc, pde, pdc, rse, rsc, pae, pac = [False]*8
         if maxenabled=="OpticalScan":
@@ -273,6 +294,17 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.toolsMenu = QtWidgets.QMenu("&Tools")
         self.toolsMenu.addAction(self.snapshotAct)
         self.toolsMenu.addAction(self.configRamanCtrlAct)
+
+        self.dispMenu = QtWidgets.QMenu("&Display", self)
+        self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
+        self.overlayActGroup.setExclusive(True)
+        
+        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct]:
+            self.dispMenu.addAction(act)
+            self.overlayActGroup.addAction(act)
+        
+        self.dispMenu.addSeparator()
+        self.dispMenu.addActions([self.transpAct, self.hideLabelAct, self.darkenAct, self.seedAct])
         
         self.helpMenu = QtWidgets.QMenu("&Help", self)
         self.helpMenu.addAction(self.aboutAct)
@@ -281,9 +313,9 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
         self.menuBar().addMenu(self.viewMenu)
         self.menuBar().addMenu(self.modeMenu)
         self.menuBar().addMenu(self.toolsMenu)
+        self.menuBar().addMenu(self.dispMenu)
         self.menuBar().addMenu(self.helpMenu)
 
-
     def createToolBar(self):
         self.toolbar = QtWidgets.QToolBar("Tools")
         self.toolbar.setIconSize(QtCore.QSize(100,50))
@@ -322,12 +354,10 @@ if __name__ == '__main__':
         fp = open(logname, "a")
         sys.stderr = fp
         sys.stdout = fp
+    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)
     
-    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), 
-          flush=True)
-    
-    meas = MeasureParticleWindow(logpath)
-    meas.showMaximized()
+    gepard = GEPARDMainWindow(logpath)
+    gepard.showMaximized()
     ret = app.exec_()
     if fp is not None:
-        fp.close()
\ No newline at end of file
+        fp.close()

analysis/DBAssignments.py

+# -*- 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/>.
+"""
+
+import pickle
+
+def loadAssigments(fname):
+    with open(fname, "rb") as fp:
+        assignment = pickle.load(fp)
+    return assignment
+
+def saveAssignments(assignment, fname):
+    with open(fname, "wb") as fp:
+        pickle.dump(assignment, fp, protocol=-1)
+
+
+class DBAssignment(object):
+    def __init__(self):
+        self.filename = None
+        self.assignments = []
+    
+    def setFileName(self, fname):
+        self.filename = fname
+    
+    def save(self):
+        saveAssignments(self, self.filename)
+        
+    def hasAssignment(self, polymerName):
+        polymIsPresent = False
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                polymIsPresent = True
+                break
+        return polymIsPresent
+    
+    def getAssignment(self, polymerName):
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                return assignment
+    
+    def createNewAssignment(self, polymerName):
+        self.assignments.append(Assignment(polymerName))
+    
+    def updateAssignment(self, polymerName, result, catRes, indic_paint):
+        for assignment in self.assignments:
+            if assignment.polymerName == polymerName:
+                assignment.update(result, catRes, indic_paint)
+                return
+
+
+class Assignment(object):
+    def __init__(self, polymerName):
+        self.polymerName = polymerName
+        self.result = None
+        self.categorizedResult = None
+        self.indication_paint = None
+    
+    def update(self, result, catRes, indic_paint):
+        self.result = result
+        self.categorizedResult = catRes
+        self.indication_paint = indic_paint
+    

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 numpy as np
+
+from .colorlegend import getColorFromNameWithSeed
+
+class SizeHistogramPlot(QtWidgets.QGroupBox):
+    def __init__(self, dataset):
+        super(SizeHistogramPlot, self).__init__()
+        self.dataset = dataset
+        
+        self.minX = 3
+        self.maxX = 1E4
+        self.fontsize = 15
+        
+        layout = QtWidgets.QHBoxLayout()
+        self.setLayout(layout)
+        self.sizeHistogramCanvas = FigureCanvas(Figure())
+        self.sizeHist_ax = self.sizeHistogramCanvas.figure.subplots()
+        self.sizeHist_ax.axis('off')
+        self.sizeHistogramCanvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.995)
+        histNavigation = NavigationToolbar(self.sizeHistogramCanvas, self)
+        histNavigation.setOrientation(QtCore.Qt.Vertical)
+        histNavigation.setFixedWidth(50)
+        layout.addWidget(histNavigation)
+        layout.addWidget(self.sizeHistogramCanvas)
+    
+    def drawHistograms(self, listOfHistograms):
+        if type(listOfHistograms) != list:
+            assert type(listOfHistograms) == SizeHistogramData
+            listOfHistograms = [listOfHistograms]
+        
+        self.resetPlotFormat()
+        self.adjustPlotLimits(listOfHistograms)
+        
+        for histData in listOfHistograms:
+            self.drawHistogram(histData)
+        
+        self.drawLegend()
+        self.sizeHistogramCanvas.draw()
+        
+    def resetPlotFormat(self):
+        self.sizeHist_ax.clear()
+        self.sizeHist_ax.axis('on')
+        self.sizeHist_ax.tick_params(axis='both', which='both', labelsize = self.fontsize)
+        self.sizeHist_ax.set_xlabel('Size (µm)', fontsize = self.fontsize)
+        self.sizeHist_ax.set_ylabel('Number', fontsize = self.fontsize)
+        self.sizeHist_ax.set_title('Size Distribution', fontsize=self.fontsize)
+        
+    def adjustPlotLimits(self, listOfHistograms):
+        xmin, xmax = None, None
+        for histData in listOfHistograms:
+            if xmin is None:
+                xmin = np.clip(10**histData.minSizeExponent, self.minX, self.maxX)
+                xmax = np.clip(10**histData.maxSizeExponent, self.minX, self.maxX)
+            else:
+                currentXMin = np.clip(10**histData.minSizeExponent, self.minX, self.maxX)
+                currentXMax = np.clip(10**histData.maxSizeExponent, self.minX, self.maxX)
+                xmin = min(xmin, currentXMin)
+                xmax = max(xmax, currentXMax)
+        
+        self.sizeHist_ax.set_xlim(xmin, xmax)
+    
+    def drawHistogram(self, histData):
+        label = histData.label
+        x_values = histData.sizeHist_binCenters
+        y_values = histData.sizeHist_abundancies
+        color = getColorFromNameWithSeed(label, self.dataset.colorSeed, base255=False)
+        self.sizeHist_ax.semilogx(x_values, y_values, label=label, color=color)    
+        
+    def drawLegend(self):
+        self.sizeHist_ax.legend(prop = {'size': self.fontsize})
+
+
+class SizeHistogramData(object):
+    def __init__(self, label, listOfSizes):
+        self.label = label
+        self.listOfSizes = listOfSizes
+        
+        self.minSizeExponent = 0.1
+        self.maxSizeExponent = 3
+        self.numBins = 20
+        
+        self.sizeHist_binCenters = None
+        self.sizeHist_abundancies = None
+        
+        self.createSizeHistogramData()
+    
+    def createSizeHistogramData(self):
+        assert self.listOfSizes is not None
+        bins = np.logspace(self.minSizeExponent, self.maxSizeExponent, self.numBins)
+        self.sizeHist_abundancies, binEdges = np.histogram(self.listOfSizes, bins)
+        self.sizeHist_binCenters = self.getBinCenters(binEdges)
+    
+    def getBinCenters(self, binEdges):
+        binCenters = []
+        for i in range(self.numBins-1):
+            currentCenter = np.mean((binEdges[i], binEdges[i+1]))
+            binCenters.append(currentCenter)
+        return binCenters
+    
+                
+class TypeHistogramPlot(QtWidgets.QScrollArea):
+    indexClicked = QtCore.pyqtSignal(int)
+    def __init__(self, dataset):
+        super(TypeHistogramPlot, self).__init__()
+        self.dataset = dataset
+        
+        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.abundancyIndicators = []
+        
+    def updateTypeHistogram(self, typeHistogram):
+        self.resetPlot()
+        
+        colorList = []
+        abundancyList = []
+        labelList = []
+        for polymType in typeHistogram:
+            text = f'{typeHistogram[polymType]} x {polymType}'
+            labelList.append(text)
+            abundancyList.append(typeHistogram[polymType])
+            curColor = getColorFromNameWithSeed(polymType, self.dataset.colorSeed)
+            colorList.append(QtGui.QColor(*curColor))
+        
+        types = list(zip(abundancyList, labelList, colorList))
+        
+        numtotal= sum(abundancyList)
+        
+        for index, entry in enumerate(types):
+            num, text, color = entry
+            indicator = AbundancyIndicator(num, numtotal, color, text)
+            self.indicatorbox.addWidget(indicator)
+            indicator.clicked.connect(self._getIndexFunction(index))
+            self.abundancyIndicators.append(indicator)
+            
+        self.indicatorbox.addStretch()
+        self.view.update()
+        
+    def resetPlot(self):
+        for indicator in self.abundancyIndicators:
+            self.indicatorbox.removeWidget(indicator)
+            indicator.setParent(None)
+            indicator.destroy()
+        self.indicatorbox.takeAt(0)
+        self.abundancyIndicators = []
+    
+    def _getIndexFunction(self, index):
+            return lambda : self.indexClicked.emit(index)
+
+class AbundancyIndicator(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.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 SpectraPlot(QtWidgets.QGroupBox):
+    def __init__(self, dataset):
+        super(SpectraPlot, self).__init__()
+        self.dataset = dataset
+        self.spectra = None
+        self.fontsize = 15
+        
+        layout = QtWidgets.QHBoxLayout()
+        self.canvas = FigureCanvas(Figure())
+        self.spec_axis = self.canvas.figure.subplots()
+        self.reference_axis = 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):
+        self.spectra = self.dataset.particleContainer.getSpectraFromDisk()
+        self.canvas.draw()
+        
+    def updateParticleSpectrum(self, specIndex, assignment, hqi):
+        #draw Sample Spectrum
+        self.spec_axis.axis("on")
+        self.spec_axis.clear()
+        self.spec_axis.tick_params(axis='both', which='both', labelsize = self.fontsize)
+        self.spec_axis.set_xlabel('Wavenumber (cm-1)', fontsize = self.fontsize)
+        self.spec_axis.set_ylabel('Counts', fontsize = self.fontsize)
+        
+        if self.spectra is not None:
+            specInfo = f'ScanPoint Number {specIndex+1}, with assignment {assignment} (hqi = {hqi})'
+            self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
+            self.spec_axis.set_title(specInfo, fontsize = self.fontsize)
+            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 = self.fontsize)
+        self.reference_axis.plot(ref_wavenumber, ref_intensity, color = 'r')
+        self.reference_axis.set_ylabel('Ref. Intensity', fontsize = self.fontsize, 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]))
+        
+        self.canvas.draw()
\ No newline at end of file

colorlegend.py → analysis/colorlegend.py

@@ -20,10 +20,25 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 from PyQt5 import QtCore, QtWidgets, QtGui
 import numpy as np
+import random
+import colorsys
 
+def getColorFromNameWithSeed(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
 
-WX, WY = 1024, 200
-        
+  
 class ColorLegend(QtWidgets.QMdiSubWindow):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -40,7 +55,6 @@ class ColorLegend(QtWidgets.QMdiSubWindow):
         
     def setTextColorItems(self, items):
         for text, color in items:
-            print(text, color)
             assert type(text)==str or type(text)==np.str_, "items must be tuples of text and QColor"
             assert type(color)==QtGui.QColor or type(color)==QtCore.Qt.GlobalColor, "items must be tuples of text and QColor"
         self.items = items
@@ -109,6 +123,4 @@ class ColorLegend(QtWidgets.QMdiSubWindow):
                 y0 = index*(fontSize+spacer) + (fontSize - tileSize)/2 +spacer/2
                 qp.drawRect(x0, y0, tileSize, tileSize)
             
-            qp.end()
-        
-        
\ No newline at end of file
+            qp.end()
\ No newline at end of file

analysis/database.py

@@ -27,24 +27,26 @@ with permission from github user CJ Carey (perimosocordiae)
 
 from PyQt5 import QtWidgets, QtCore
 import numpy as np
-import sys
-import dill
+import dill   #TODO: Make it run with pickle... Having two different methods is not so sensefull...
 import os
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 import functools
 from scipy.linalg import solveh_banded
-from pathlib import Path
 
 class DataBaseWindow(QtWidgets.QMainWindow):
     def __init__(self, parent):
         super(DataBaseWindow, self).__init__()
         self.parent = parent
-        self.path = os.path.join(Path.home(), 'gepard', 'databases')
+        
+        logpath =