Merge branch 'Thresholding,Background' into RefactoringAnalysisModules (d6af372b) · Commits · GEPARD / GEPARD

analysis/particleContainer.py

+7 −1

Original line number	Diff line number	Diff line
		@@ -43,6 +43,12 @@ class ParticleContainer(object):
		indexOfNewMeas = len(self.measurements)-1
		return indexOfNewMeas

		def clearParticles(self):
		self.particles = []

		def clearMeasurements(self):
		self.measurements = []

		def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
		self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex

dataset.py

+19 −44

Original line number	Diff line number	Diff line
		@@ -149,6 +149,7 @@ class DataSet(object):
		# self.particlestats = []
		# self.ramanscansortindex = None
		self.particleContainer = ParticleContainer(self)
		self.particleDetectionDone = False
		self.ramanscandone = False

		# self.results = {'polymers': None,
		@@ -247,34 +248,24 @@ class DataSet(object):
		self.imagedim_df = self.imagedim
		del self.imagedim


		if not hasattr(self, 'particles2spectra'):
		self.particles2spectra = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]

		self.version = 2

		if self.version == 2:
		self.particleContainer = ParticleContainer(self)
		def recreateMeasurement2ParticleFromScanIndices():
		measurements2particles = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]
		return measurements2particles


		self.particleContainer.initializeParticles(len(self.particlestats))
		self.particleContainer.setParticleContours(self.particlecontours)
		self.particleContainer.setParticleStats(self.particlestats)
		self.particleContainer.applyPixelScaleToParticleStats(self.getPixelScale())

		if hasattr(self, 'particles2spectra'):
		if self.particles2spectra is not None:
		measurements2particles = self.particles2spectra
		else:
		measurements2particles = recreateMeasurement2ParticleFromScanIndices()
		else:
		measurements2particles = recreateMeasurement2ParticleFromScanIndices()

		for particleIndex, listOfScanIndices in enumerate(measurements2particles):
		if len(self.particlestats) > 0: #i.e., particle detection was completed and particle data is there
		for particleIndex, listOfScanIndices in enumerate(self.particles2spectra):
		curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
		for scanIndex in listOfScanIndices:
		# curParticle.addEmptyMeasurement()
		# curParticle.setMeasurementPixelCoords(measIndex, x, y)
		# curParticle.setMeasurementScanIndex(measIndex, scanIndex)
		indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
		x, y = self.ramanpoints[particleIndex][0], self.ramanpoints[particleIndex][1]
		self.particleContainer.setMeasurementPixelCoords(indexOfNewMeas, x, y)
		@@ -292,8 +283,6 @@ class DataSet(object):
		# self.version = 3
		# add later conversion for higher version numbers here



		def getSubImage(self, img, index, draw=True):
		contour = self.particlecontours[index]
		x0, x1 = contour[:,0,0].min(), contour[:,0,0].max()
		@@ -395,29 +384,15 @@ class DataSet(object):
		def getLegacyDetectImageName(self):
		return os.path.join(self.path, "detectimage.png")

		def getBackgroundImageName(self):
		return os.path.join(self.path, "background.bmp")

		def getDetectImageName(self):
		raise NotImplementedError("No longer implemented due to change in API")

		def getTmpImageName(self):
		return os.path.join(self.path, "tmp.bmp")

		def saveParticleData(self):
		print('Not saving ParticleData into text file...:\nThe current output format might be wrong, if multiple spectra per particle are present...')
		# if len(self.ramanscansortindex)>0:
		# data = []
		# pixelscale = (self.pixelscale_df if self.imagescanMode == 'df' else self.pixelscale_bf)
		# for i in self.ramanscansortindex:
		# data.append(list(self.ramanpoints[i])+list(self.particlestats[i]))
		# data = np.array(data)
		# data[:,0], data[:,1], z = self.mapToLengthRaman((data[:,0], data[:,1]), microscopeMode=self.imagescanMode, noz=True)
		# data[:,2:7] *= pixelscale
		# header = "x [µm], y [µm], length [µm], height [µm], length_ellipse [µm], height_ellipse [µm]"
		# if data.shape[1]>6:
		# header = header + ", area [µm^2]"
		# data[:,6] *= pixelscale
		# np.savetxt(os.path.join(self.path, "particledata.txt"), data,
		# header=header)

		def save(self):
		saveData(self, self.fname)

detectionview.py

+8 −7

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@ If not, see <https://www.gnu.org/licenses/>.
		"""
		import numpy as np
		from PyQt5 import QtCore, QtWidgets, QtGui
		from segmentation import Segmentation
		from segmentation import Segmentation, MeasurementPoint
		from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
		import matplotlib.pyplot as plt
		from threading import Thread
		@@ -248,7 +248,9 @@ class ImageView(QtWidgets.QLabel):
		painter.setPen(QtCore.Qt.red)
		painter.setBrush(QtCore.Qt.red)
		for p in self.measpoints:
		painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)
		for point in self.measpoints[p]:
		# painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)
		painter.drawEllipse(point.x-2, point.y-2, 5, 5)

		if self.showseedpoints:
		painter.setPen(QtCore.Qt.white)
		@@ -581,10 +583,9 @@ class ParticleDetectionView(QtWidgets.QWidget):
		@QtCore.pyqtSlot()
		def clearDetection(self):
		if self.dataset is not None:
		self.dataset.ramanpoints = []
		self.dataset.particlecontours = []
		self.dataset.particlestats = []
		self.dataset.ramanscansortindex = []
		self.dataset.particleContainer.clearParticles()
		self.dataset.particleContainer.clearMeasurements()
		self.dataset.particleDetectionDone = False
		self.dataset.ramanscandone = False
		self.dataset.mode = "opticalscan"
		self.dataset.save()
		@@ -676,7 +677,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
		curParticle.addMeasurement(particleContainer.measurements[indexOfNewMeas])



		self.dataset.particleDetectionDone = True
		# self.dataset.ramanpoints = measurementPoints #consider moving that to particleContainer
		# self.dataset.particlecontours = contours
		# self.dataset.particlestats = particlestats

gepard.py

+5 −4

Original line number	Diff line number	Diff line
		@@ -102,12 +102,13 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
		if fileName:
		isValid, msg = self.testFilename(fileName)
		if isValid:
		self.fname = str(fileName) #TODO: No spaces for Renishaw Interface!!
		self.fname = str(fileName)
		self.view.new(self.fname)
		self.scalingChanged(1.)
		else:
		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:

imagestitch.py

+9 −6

Original line number	Diff line number	Diff line
		@@ -48,15 +48,17 @@ def imageStacking(colimgs):
		return im, zval

		def combineImages(path, nx, ny, nk, width, height, angle):
		imgs = []
		full = None
		for i in range(nx):
		for j in range(ny):
		if nk > 1:
		colimgs = []
		for k in range(nk):
		colimgs.append(cv2.imread(path + f'test_{i}_{j}_{k}.bmp'))
		img = imageStacking(colimgs)
		imgs.append(img)
		else:
		img = cv2.imread(path + f'test_{i}_{j}_1.bmp')

		dx = i.9img.shape[1]
		dy = j.8img.shape[0]
		c, s = np.cos(np.radians(angle)), np.sin(np.radians(angle))
		@@ -67,6 +69,7 @@ def combineImages(path, nx, ny, nk, width, height, angle):
		full = dst
		else:
		full = cv2.max(full,dst)

		cv2.imwrite("full_dunkel.png", full)