further restructuring of code in respect to analysisview; pixelscale modes are... (15c7be2e) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+48 −4

Original line number	Diff line number	Diff line
		@@ -399,7 +399,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
		#generate new checkboxes
		self.polymerCheckBoxes = []
		for index, polymer in enumerate(self.datastats.uniquePolymers):
		uniquePolymers = self.datastats.getUniquePolymers()
		for index, polymer in enumerate(uniquePolymers):
		self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
		self.polymerCheckBoxes[index].setText(polymer)
		self.resultCheckBoxesLayout.addWidget(self.polymerCheckBoxes[index])
		@@ -427,7 +428,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.navigationGroup.setEnabled(True)
		self.polymerComboBox.currentIndexChanged.disconnect()
		self.polymerComboBox.clear()
		self.polymerComboBox.addItems(self.datastats.uniquePolymers)
		self.polymerComboBox.addItems(uniquePolymers)
		self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)

		self.polymerIndex = self.polymerComboBox.currentIndex()
		@@ -490,6 +491,48 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.parent.highLightRamanIndex(specIndex)
		self.lastSpectrumInFocus = specIndex

		def selectContour(self, index, centerOn=True):
		uniquePolymers = self.datastats.getUniquePolymers()
		if uniquePolymers is not None:
		#the index is the contour index, find particle index:
		specIndex = self.datastats.particles2spectra[index][0] #select first spectrum of partoicle
		self.datastats.currentParticleIndex = index
		self.datastats.currentSpectrumIndex = specIndex

		selectedPolymer = self.datastats.currentPolymers[specIndex]
		try:
		self.polymerIndex = uniquePolymers.index(selectedPolymer)
		except:
		print(selectedPolymer)
		raise

		#subparticleIndex
		partIndicesOfThatPolymer = self.datastats.indices[self.polymerIndex]
		subPartInd = partIndicesOfThatPolymer.index(index)

		#disconnect analysis widgets:
		self.particleSelector.valueChanged.disconnect()
		self.spectrumSelector.valueChanged.disconnect()
		self.polymerComboBox.currentIndexChanged.disconnect()

		#set widgets...
		self.particleSelector.setValue(subPartInd+1)
		self.particleSelector.setMaximum(len(partIndicesOfThatPolymer))

		self.spectrumSelector.setValue(1)
		self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[index]))

		selectedPolymer = self.datastats.currentPolymers[specIndex]
		self.polymerIndex = uniquePolymers.index(selectedPolymer)
		self.polymerComboBox.setCurrentIndex(self.polymerIndex)

		#reconnect all widgets:
		self.particleSelector.valueChanged.connect(self.selectParticle)
		self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
		self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)

		self.updateSpecPlot(centerOn=centerOn)

		def displayNewPolymerType(self, resetCurrentIndex=True):
		self.polymerIndex = self.polymerComboBox.currentIndex()
		self.particleSelector.setMaximum(len(self.datastats.indices[self.polymerIndex]))
		@@ -676,6 +719,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		return color

		def createPolymerOverlay(self):
		uniquePolymers = self.datastats.getUniquePolymers()
		if not self.noOverlayAct.isChecked() and self.datastats.indices is not None:
		if len(self.datastats.indices) > 0:

		@@ -686,9 +730,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		for index, indexList in enumerate(self.datastats.indices):
		if self.fullOverlayAct.isChecked() or (self.selOverlayAct.isChecked() and self.polymerCheckBoxes[index].isChecked()):
		color = self.getColorFromName(self.datastats.uniquePolymers[index], base255=True)
		color = self.getColorFromName(uniquePolymers[index], base255=True)
		color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha)
		legendItems.append((self.datastats.uniquePolymers[index], color))
		legendItems.append((uniquePolymers[index], color))
		for i in indexList:
		colorList[i] = color

analysis/datastats.py

+27 −3

Original line number	Diff line number	Diff line
		@@ -21,6 +21,19 @@ If not, see <https://www.gnu.org/licenses/>.
		import os
		import numpy as np
		import operator
		from dataset import loadData


		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):
		@@ -34,7 +47,6 @@ class DataStats(object):

		self.currentPolymers = None #list of polymers after setting entries with low hqi to unknown
		self.currentAdditives = None #same thing for the additives
		self.uniquePolymers = None #list of present polymer types
		self.spectra = None #acquired spectra
		self.indices = None #assignment of what spectra-indices belong to what substance

		@@ -103,7 +115,7 @@ class DataStats(object):

		def loadParticleData(self):
		self.particlestats = np.array(self.dataset.particlestats)
		pixelscale = (self.dataset.pixelscale_df if self.dataset.imagescanMode == 'df' else self.dataset.pixelscale_bf)
		pixelscale = self.dataset.getPixelScale()
		#convert to mikrometer scale
		for index in range(len(self.particlestats)):
		for subindex in range(5):
		@@ -145,6 +157,11 @@ class DataStats(object):
		if self.currentAdditives is not None:
		self.currentAdditives[self.addhqis < compHqi] = 'unknown'

		def getUniquePolymers(self):
		if self.currentPolymers is None:
		return None
		return self.uniquePolymers

		def createHistogramData(self):
		self.uniquePolymers = np.unique(self.currentPolymers)
		self.particleResults = [None]*len(self.particlestats)
		@@ -192,4 +209,11 @@ class DataStats(object):
		self.dataset.resultParams = {'minHQI': minHQI,
		'compHQI': compHQI}
		self.dataset.save()
		print('saved dataset')
		No newline at end of file
		print('saved dataset; Valid:', self.testRead())


		def testRead(self):
		statsread = readDataStats(self.dataset.fname)
		return statsread.__dict__ == self.__dict__


		No newline at end of file

dataset.py

+55 −5

Original line number	Diff line number	Diff line
		@@ -53,6 +53,52 @@ def saveData(dataset, fname):
		pickle.dump(dataset, fp, protocol=-1)
		dataset.zvalimg = zvalimg

		def arrayCompare(a1, a2):
		print("array compare")
		ind = np.isnan(a1)
		if not np.any(ind):
		return np.all(a1==a2)
		if a1.shape!=a2.shape:
		return False
		return np.all(a1[~ind]==a2[~ind])

		def listCompare(l1, l2):
		print("list compare")
		if len(l1)!=len(l2):
		return False
		for l1i, l2i in zip(l1, l2):
		if isinstance(l1i, np.ndarray):
		if not isinstance(l2i, np.ndarray) or not arrayCompare(l1i, l2i):
		return False
		elif isinstance(l1i, (list, tuple)):
		if not isinstance(l2i, (list, tuple)) or not listCompare(l1i, l2i):
		return False
		elif l1i!=l2i and ((~np.isnan(l1i)) or (~np.isnan(l2i))):
		return False
		return True

		def recursiveDictCompare(d1, d2):
		for key in d1:
		if not key in d2:
		return False
		a = d1[key]
		b = d2[key]
		print(key, type(a), type(b))
		if isinstance(a, np.ndarray):
		if not isinstance(b, np.ndarray) or not arrayCompare(a, b):
		return False
		elif isinstance(a, dict):
		if not isinstance(b, dict):
		return False
		if not recursiveDictCompare(a, b):
		return False
		elif isinstance(a, (list, tuple)):
		if not isinstance(b, (list, tuple)) or not listCompare(a, b):
		return False
		elif a != b:
		return False
		return True

		class DataSet(object):
		def __init__(self, fname, newProject=False):
		self.fname = fname
		@@ -115,6 +161,14 @@ class DataSet(object):
		self.fname = self.newProject(fname)
		self.updatePath()

		def __eq__(self, other):
		return recursiveDictCompare(self.__dict__, other.__dict__)

		def getPixelScale(self, mode=None):
		if mode is None:
		mode = self.imagescanMode
		return (self.pixelscale_df if mode == 'df' else self.pixelscale_bf)

		def saveZvalImg(self):
		if self.zvalimg is not None:
		cv2imwrite_fix(self.getZvalImageName(), self.zvalimg)
		@@ -243,8 +297,7 @@ class DataSet(object):
		p0[1] += self.imagedim_bf[1]/2
		return (pixelpos[0]self.pixelscale_bf + p0[0]), (p0[1] - pixelpos[1]self.pixelscale_bf)
		else:
		print('mapToRamanMode not understood')
		return
		raise ValueError(f'mapToLength mode: {mode} not understood')

		def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False):
		p0x, p0y = self.mapToLength(pixelpos, mode = microscopeMode)
		@@ -315,9 +368,7 @@ class DataSet(object):
		saveData(self, self.fname)

		def saveBackup(self):
		# backupNameNotFound = True
		inc = 0
		# while backupNameNotFound:
		while True:
		directory = os.path.dirname(self.fname)
		filename = self.name + '_backup_' + str(inc) + '.pkl'
		@@ -327,5 +378,4 @@ class DataSet(object):
		else:
		saveData(self, path)
		return filename
		# backupNameNotFound = False

sampleview.py

+527 −568

Original line number	Diff line number	Diff line
		@@ -355,7 +355,7 @@ class SampleView(QtWidgets.QGraphicsView):
		self.announceScaling()

		def announceScaling(self):
		pixelscale = (self.dataset.pixelscale_df if self.microscopeMode == 'df' else self.dataset.pixelscale_bf)
		pixelscale = self.dataset.getPixelScale(self.microscopeMode)
		if self.dataset is None or pixelscale is None:
		self.ScalingChanged.emit(-1.0)
		else:
		@@ -453,10 +453,8 @@ class SampleView(QtWidgets.QGraphicsView):
		if len(p2)<len(p1):
		p1 = [[pi[1],pi[0]] for pi in p2]
		self.dataset.grid = p1
		if self.microscopeMode == 'df':
		wxs, wys = width/self.dataset.pixelscale_df, height/self.dataset.pixelscale_df
		else:
		wxs, wys = width/self.dataset.pixelscale_bf, height/self.dataset.pixelscale_bf
		pixelscale = self.dataset.getPixelScale(self.microscopeMode)
		wxs, wys = width/pixelscale, height/pixelscale

		self.scanitems = []
		for i, p in enumerate(p1):
		@@ -489,46 +487,7 @@ class SampleView(QtWidgets.QGraphicsView):
		@QtCore.pyqtSlot(int, bool)
		def selectContour(self, index, centerOn=True):
		if self.analysiswidget is not None:
		if self.analysiswidget.uniquePolymers is not None:
		#the index is the contour index, find particle index:
		specIndex = self.analysiswidget.particles2spectra[index][0] #select first spectrum of partoicle
		self.analysiswidget.currentParticleIndex = index
		self.analysiswidget.currentSpectrumIndex = specIndex

		selectedPolymer = self.analysiswidget.currentPolymers[specIndex]
		try:
		self.analysiswidget.polymerIndex = self.analysiswidget.uniquePolymers.index(selectedPolymer)
		except:
		print(selectedPolymer)
		raise

		#subparticleIndex
		partIndicesOfThatPolymer = self.analysiswidget.indices[self.analysiswidget.polymerIndex]
		subPartInd = partIndicesOfThatPolymer.index(index)

		#disconnect analysis widgets:
		self.analysiswidget.particleSelector.valueChanged.disconnect()
		self.analysiswidget.spectrumSelector.valueChanged.disconnect()
		self.analysiswidget.polymerComboBox.currentIndexChanged.disconnect()

		#set widgets...
		self.analysiswidget.particleSelector.setValue(subPartInd+1)
		self.analysiswidget.particleSelector.setMaximum(len(partIndicesOfThatPolymer))

		self.analysiswidget.spectrumSelector.setValue(1)
		self.analysiswidget.spectrumSelector.setMaximum(len(self.analysiswidget.particles2spectra[index]))

		selectedPolymer = self.analysiswidget.currentPolymers[specIndex]
		self.analysiswidget.polymerIndex = self.analysiswidget.uniquePolymers.index(selectedPolymer)
		self.analysiswidget.polymerComboBox.setCurrentIndex(self.analysiswidget.polymerIndex)

		#reconnect all widgets:
		self.analysiswidget.particleSelector.valueChanged.connect(self.analysiswidget.selectParticle)
		self.analysiswidget.spectrumSelector.valueChanged.connect(self.analysiswidget.selectSpectrum)
		self.analysiswidget.polymerComboBox.currentIndexChanged.connect(self.analysiswidget.displayNewPolymerType)

		self.analysiswidget.updateSpecPlot(centerOn=centerOn)

		self.analysiswidget.selectContour(index, centerOn)

		def prepareAnalysis(self):
		self.clearItems()

viewitems.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ import numpy as np
		from PyQt5 import QtCore, QtWidgets, QtGui

		class SegmentationContours(QtWidgets.QGraphicsItem):
		def __init__(self, parent=None, contours=[], pos=(0,0)):
		def __init__(self, parent, contours=[], pos=(0,0)):
		super().__init__()
		self.parent = parent
		self.setPos(pos[0], pos[1])
		@@ -122,14 +122,14 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
		for index in self.selectedContours:
		# partIndex = int(np.where(self.parent.dataset.ramanscansortindex == index)[0])
		partIndex = index
		assignments.append(self.parent.analysiswidget.particleResults[partIndex])
		assignments.append(self.analysiswidget.datastats.particleResults[partIndex])
		assignments.append("other")
		for assignment in np.unique(np.array(assignments)):
		combineActs.append(combineMenu.addAction(assignment))

		reassignActs = []
		reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")
		for polymer in self.parent.analysiswidget.uniquePolymers:
		for polymer in self.analysiswidget.datastats.getUniquePolymers():
		reassignActs.append(reassignMenu.addAction(polymer))
		reassignActs.append(reassignMenu.addAction("other"))

		@@ -156,7 +156,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
		# QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
		# return

		self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
		self.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)

		elif action in reassignActs:
		newAssignment = action.text()
		@@ -164,7 +164,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
		# QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
		# return

		self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)
		self.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)


		class FitPosIndicator(QtWidgets.QGraphicsItem):