Commit 8e5899e5 authored by Hackmet's avatar Hackmet
Browse files

Several Bugfixes

parent c438bcca

analysis/analysisWidgets.py

+5 −7
Original line number Diff line number Diff line
@@ -19,7 +19,6 @@ along with this program, see COPYING. 
If not, see <https://www.gnu.org/licenses/>.

"""

from PyQt5 import QtCore, QtWidgets, QtGui

from PIL import ImageFont

import numpy as np
@@ -60,14 +59,13 @@ class Legend(QtWidgets.QMdiSubWindow): 
        if numEntries > 0:

            

            def getSize(fontsize, text, tileSize, spacer):

#                font = ImageFont.truetype('arial.ttf', fontsize)

#                size = font.getsize(text)

                size = 5*len(text), fontsize+2

                width, height = size[0]*1.5 + tileSize + spacer, numEntries * (tileSize+1*spacer) + 2*spacer

                

                font = QtGui.QFont()

                font.setPixelSize(fontSize)

                fm = QtGui.QFontMetrics(font)

                pixelwidth = fm.width(text)

                width, height = pixelwidth + tileSize + 3*spacer, numEntries * (tileSize+1*spacer) + 2*spacer

                return width, height

            

            

            fontSize, tileSize, spacer = self.fontSize, self.tileSize, self.spacer

            longestEntry = max([i[0] for i in self.items], key=len)

            width, height = getSize(fontSize, longestEntry, tileSize, spacer)

analysis/analysisview.py

+44 −8
Original line number Diff line number Diff line
@@ -40,8 +40,12 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio 


import pandas as pd

from analysis.loadresults import LoadWITecResults

from analysis.sqlexport import SQLExport

from analysis.editParticles import ParticleEditor

try:

    from analysis.sqlexport import SQLExport

    sqlEnabled = True

except:

    sqlEnabled = False





class ParticleAnalysis(QtWidgets.QWidget):
@@ -263,7 +267,6 @@ class ParticleAnalysis(QtWidgets.QWidget): 
        self.layout_SArea.addWidget(self.resultCheckBoxes)

#        self.layout_SArea.addStretch(1)

        

        

        self.exportbtn= QtWidgets.QPushButton('Export Results')

        self.exportbtn.clicked.connect(self.exportData)

        self.exportbtn.setDisabled(True)
@@ -286,7 +289,23 @@ class ParticleAnalysis(QtWidgets.QWidget): 
         

    def loadSpectra(self, fname):

        try:

            return np.loadtxt(fname)

            specs = np.loadtxt(fname)

            #if spectra are already in correct format (WITec, first column: wavenumbers, other columns, intensities), 

            #we take them, otherwise we have to convert from Renishaw export format...

            if len(np.unique(specs[:, 0])) == len(specs[:, 0]): #--> only unique numbers -> this is the wavenumber column, we have the witec format

                return specs

            else:        

                #columns 0 and 1 are x and y coordinates. We dont need them...

                startWavenumber = specs[0, 2]

                startIndices = np.where(specs[:, 2] == startWavenumber)[0]

                

                spectra = np.zeros((startIndices[1], len(startIndices)+1))   #create array with shape (numWavenumbers, numSpectra+1) (first column holds wavenumbers)

                spectra[:, 0] = specs[startIndices[0]:startIndices[1], 2]

                for i in range(len(startIndices)-1):

                    spectra[:, i+1] = specs[startIndices[i]:startIndices[i+1], 3]

                #aaand the last spectrum:

                spectra[:, -1] = specs[startIndices[-1]:, 3]

                return np.flip(spectra, 0)    #Renishaw goes from highest to lowest wavenumber, out of whatever reason...

        except:

            return None
@@ -301,14 +320,25 @@ class ParticleAnalysis(QtWidgets.QWidget): 
            self.colorSeed = 'default'

        

        #load Spectra

        self.spectra = self.loadSpectra(os.path.join(self.parent.dataset.path, self.parent.dataset.name + '_000_Spec.Data 1.txt'))

        if self.parent.dataset.spectraPath is None:

            fname = os.path.join(self.parent.dataset.path, self.parent.dataset.name + '_000_Spec.Data 1.txt')

        else:

            fname = self.parent.dataset.spectraPath

        self.spectra = self.loadSpectra(fname)

        if self.spectra is None:

            fname = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Spectra File', self.parent.dataset.path, 'text file (*.txt)')[0]

            self.spectra = self.loadSpectra(fname)

            if self.spectra is None:

                QtWidgets.QMessageBox.critical(self, 'ERROR!', 'spectra file could not be opened with np.loadtxt...')

                return

        self.parent.dataset.spectraPath = fname

        self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))

        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)

        

        self.loadParticleData()
@@ -380,7 +410,9 @@ class ParticleAnalysis(QtWidgets.QWidget): 
        self.particleResults = [None]*len(self.particlestats)

        self.typehistogram = {i: 0 for i in self.uniquePolymers}

        

        assert len(self.particles2spectra) == len(self.particlestats), 'inconsistent data!!'

        if len(self.particles2spectra) != len(self.particlestats):

            QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')

            return

        

        for particleID, specList in enumerate(self.particles2spectra):

            assignment = self.currentPolymers[specList[0]]   #we take the first result as particle result. Hence, all spectra per particle have to have the same result
@@ -498,6 +530,7 @@ class ParticleAnalysis(QtWidgets.QWidget): 
        self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)

        self.spec_ax.set_ylabel('Counts', fontsize = 15)

        self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, np.round(self.particlestats[self.currentParticleIndex][2], 1)))

        self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))

        self.spec_ax.figure.canvas.draw()

        self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour)

        self.parent.highLightRamanIndex(specIndex)
@@ -805,7 +838,10 @@ class ExportDialog(QtWidgets.QWidget): 


        self.sqlbtn = QtWidgets.QPushButton('Export to SQL Database')

        self.sqlbtn.resize(self.sqlbtn.sizeHint()) 

        if sqlEnabled:

            self.sqlbtn.clicked.connect(self.toSQL)

        else:

            self.sqlbtn.setDisabled(True)

        

        self.sqlExport = None

analysis/editParticles.py

+24 −8
Original line number Diff line number Diff line
@@ -26,16 +26,33 @@ If not, see <https://www.gnu.org/licenses/>. 
"""

import numpy as np

import cv2

from PyQt5 import QtWidgets

#import matplotlib.pyplot as plt



class ParticleEditor(object):

    def __init__(self, parent):

        self.parent = parent    #the assigned analysis widget

        self.backupFreq = 3     #save a backup every n actions

        self.neverBackedUp = True

        self.actionCounter = 0



    def createSafetyBackup(self):

        self.actionCounter += 1

        if self.actionCounter == self.backupFreq-1 or self.neverBackedUp:            

            print('backing up')

            self.parent.parent.dataset.saveBackup()

            self.neverBackedUp = False

            self.actionCounter = 0

        

    def getNewEntry(self):

        text, okClicked = QtWidgets.QInputDialog.getText(self.parent.parent, "Custom assignment", "Enter new assignment")

        if okClicked and text != '':

            return text

    

    def combineParticles(self, contourIndices, new_assignment):

        if new_assignment == 'other':

            new_assignment = self.getNewEntry()

        

        contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index

        print('selected contours:', contourIndices)

        self.createSafetyBackup()
@@ -76,7 +93,6 @@ class ParticleEditor(object): 
            sortindices = self.parent.parent.dataset.ramanscansortindex

            self.parent.parent.dataset.particles2spectra = [[int(np.where(sortindices == i)[0])] for i in range(len(sortindices))]

        

        

        #Contour indices are the same as the original particlestats, which are contained in the dataset. 

        #We have to modify that and reload in the analysisview

        #first, overwrite first index with new particlestats
@@ -89,7 +105,6 @@ class ParticleEditor(object): 
        self.parent.parent.dataset.particlecontours[contourIndices[0]] = newContour

        self.parent.parent.dataset.particlecontours = [i for ind, i in enumerate(self.parent.parent.dataset.particlecontours) if ind not in contourIndices[1:]]

        

        

        #update particle2spectra_list

        #what is the current particle index??

        specIndices = []
@@ -98,13 +113,12 @@ class ParticleEditor(object): 
            specIndices.append(self.parent.particles2spectra[index])

        

        #flatten index list (in case, that a nested list was created...)

        specIndices = list(np.unique(np.array(specIndices)))

        specIndices = list(np.concatenate(specIndices))

        for i in specIndices:

            self.parent.spectraResults[i] = new_assignment

            self.parent.hqis[i] = 100   #avoid sorting them out again by hqi-filter...

            print(f'spectrum {i} of particle{contourIndices[0]} is now {new_assignment}')

        

        

        #modify particles2spectra..         

        self.parent.parent.dataset.particles2spectra[contourIndices[0]] = specIndices

        for index in reversed(contourIndices[1:]):
@@ -116,11 +130,13 @@ class ParticleEditor(object): 
        

        #update contours in sampleview

        self.parent.parent.contouritem.resetContours(self.parent.parent.dataset.particlecontours)

        

        self.parent.loadParticleData()

       

    

    def reassignParticles(self, contourindices, new_assignment):

        if new_assignment == 'other':

            new_assignment = self.getNewEntry()

            

        self.createSafetyBackup()

        for partIndex in contourindices:

            for specIndex in self.parent.particles2spectra[partIndex]:
@@ -128,7 +144,7 @@ class ParticleEditor(object): 
                self.parent.spectraResults[specIndex] = new_assignment

                self.parent.hqis[specIndex] = 100



        self.parent.createHistogramData()

        self.parent.loadParticleData()

            

    

    def deleteParticles(self):

dataset.py

+4 −4
Original line number Diff line number Diff line
@@ -102,7 +102,7 @@ class DataSet(object): 


        self.resultParams = {'minHQI': None,

                             'compHQI': None}

        

        self.spectraPath = None

        self.particles2spectra = None    #links idParticle to corresponding idSpectra (i.e., first measured particle (ID=0) is linked to spectra indices 0 and 1)

        self.colorSeed = 'default'

        self.resultsUploadedToSQL = []
@@ -177,12 +177,12 @@ class DataSet(object): 
                print('pixelscale was', self.pixelscale)

                self.pixelscale_bf = self.pixelscale

                self.pixelscale_df = self.pixelscale

#                del self.pixelscale

                del self.pixelscale

            

            if hasattr(self, 'imagedim'):

                self.imagedim_bf = self.imagedim

                self.imagedim_df = self.imagedim

#                del self.imagedim

                del self.imagedim



            self.version = 2

gepard.py

+9 −3
Original line number Diff line number Diff line
@@ -25,6 +25,7 @@ from ramancom.ramancontrol import defaultPath 
from ramancom.ramanSwitch import RamanSwitch

from analysis.analysisWidgets import Legend

import os

from pathlib import Path

            

class MeasureParticleWindow(QtWidgets.QMainWindow):
@@ -287,12 +288,17 @@ if __name__ == '__main__': 


    import sys

    from time import localtime, strftime

    logpath = os.path.join(Path.home(),'gepard')

    if not os.path.exists(logpath):

        os.mkdir(logpath)

    logname = os.path.join(logpath, 'logfile.txt')

#    logname = os.path.join(os.path.split(__file__)[0], os.path.join("logfile.txt"))

#    fp = open(logname, "a")

#    sys.stderr = fp

#    sys.stdout = fp

    fp = open(logname, "a")

    sys.stderr = fp

    sys.stdout = fp

    

    print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()))

    sys.stdout.flush()

    app = QtWidgets.QApplication(sys.argv)

    meas = MeasureParticleWindow()

    meas.showMaximized()