Commit 7d28e523 authored by JosefBrandt's avatar JosefBrandt
Browse files

Merge branch 'RefactoringAnalysisModules'

parents 8fc15b1e 582761bd

.gitignore

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+14 −0
Original line number Diff line number Diff line 


__pycache__/



gepard\.cfg



analysis/database_config\.txt



*.so



*.c



external/build/



.idea/

external/__init__.py→__init__.py

+0 −0

File moved.

gepard.py→__main__.py

100755 → 100644
+53 −23
Original line number Diff line number Diff line
@@ -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)
@@ -101,12 +100,23 @@ 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):
@@ -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)
@@ -194,6 +204,17 @@ class MeasureParticleWindow(QtWidgets.QMainWindow): 
        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":
@@ -274,6 +295,17 @@ class MeasureParticleWindow(QtWidgets.QMainWindow): 
        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()

analysis/DBAssignments.py

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+79 −0
Original line number Diff line number Diff line 
# -*- 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

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+278 −0
Original line number Diff line number Diff line 
#!/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()
 
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