No further ContourApproximation + Code Cleanup (a6fa4f0e) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+1 −13

Original line number	Diff line number	Diff line
		@@ -45,7 +45,6 @@ except:
		class ParticleAnalysis(QtWidgets.QMainWindow):
		def __init__(self, dataset, viewparent=None):
		super(ParticleAnalysis, self).__init__(viewparent)
		# self.resize(1680, 1050)
		self.setWindowTitle('Results of polymer analysis')
		self.layout = QtWidgets.QHBoxLayout()
		self.widget = QtWidgets.QWidget()
		@@ -600,14 +599,3 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		self.viewparent.imparent.particelAnalysisAct.setChecked(False)
		event.accept()
		No newline at end of file


		if __name__ == '__main__':
		from ..dataset import DataSet
		def run():
		app = QtWidgets.QApplication(sys.argv)
		meas = ParticleAnalysis(DataSet("dummydata"))
		meas.showMaximized()
		return app.exec_()

		run()
		No newline at end of file

analysis/database.py

+10 −46

Original line number	Diff line number	Diff line
		@@ -27,8 +27,7 @@ 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
		@@ -317,15 +316,13 @@ class DataBaseWindow(QtWidgets.QMainWindow):
		self.removeSpecBtn.setText('Remove {}'.format(self.activeSpectrumName))
		self.removeSpecBtn.setDisabled(False)

		def save(self):
		def save(self, showMessage=True):
		for index, db in enumerate(self.databases):
		# pickling_on = open(db.title+'.dbpkl', 'wb')
		# pickle.dump(db, pickling_on)
		# pickling_on.close()
		savename = os.path.join(self.path, db.title+'.db')
		with open(savename, 'wb') as f:
		dill.dump(db, f)

		if showMessage:
		QtWidgets.QMessageBox.about(self, 'Done.', 'Saved {} database(s)'.format(len(self.databases)))

		def updateDBSelectorList(self):
		@@ -339,7 +336,6 @@ class DataBaseWindow(QtWidgets.QMainWindow):
		self.db_selector.setCurrentText(self.activeDatabase.title)

		def selectDataBase(self, refreshParent=False):
		# if not self.noDBFound:
		if len(self.databases) > 0:
		self.activeDatabaseIndex = self.db_selector.currentIndex()
		self.activeDatabase = self.databases[self.activeDatabaseIndex]
		@@ -352,13 +348,7 @@ class DataBaseWindow(QtWidgets.QMainWindow):
		self.parent.populateRefSelector()

		def closeEvent(self, event):
		# response = QtWidgets.QMessageBox.question(self, 'Warning', 'Exit without saving?', QtWidgets.QMessageBox.Yes \| QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
		# if response == QtWidgets.QMessageBox.Yes:
		# if self.parent is not None:
		# self.parent.setDisabled(False)
		# event.accept()
		# else:
		# event.ignore()
		self.save(showMessage=False)
		if self.parent is not None:
		self.parent.setDisabled(False)

		@@ -426,8 +416,6 @@ class BaseLineCorrect(QtWidgets.QDialog):
		for i in range(len(spectra)):
		spectra[i][:, 1] = self.origspectra[i][:, 1].copy() - self.als_baseline(self.origspectra[i][:, 1].copy(), asymmetry_param=self.asymSpinBox.value(),
		smoothness_param=self.smoothSpinBox.value(), max_iters = self.iterSpinBox.value())
		# self.newSpectra = spectra.copy()
		# self.parent.drawSpectrum(spectra[self.parent.activeSpectrumIndex], self.parent.activeSpectrumName)
		self.saveBtn.setDisabled(False)

		def als_baseline(self, intensities, asymmetry_param=0.05, smoothness_param=1e4,
		@@ -453,26 +441,16 @@ class BaseLineCorrect(QtWidgets.QDialog):
		if conv < conv_thresh:
		break
		w = new_w
		# else:
		# print( 'ALS did not converge in %d iterations' % max_iters)
		else:
		print( 'ALS did not converge in %d iterations' % max_iters)
		return z

		def save(self):
		# self.parent.databases[self.parent.activeDatabaseIndex].spectra = self.spectra
		# self.parent.activeDatabase = self.parent.databases[self.parent.activeDatabaseIndex]
		# self.parent.activeSpectrum = self.parent.activeDatabase.spectra[self.parent.activeSpectrumIndex]
		# self.parent.drawSpectrum(self.parent.activeSpectrum, self.parent.activeSpectrumName)
		self.close()

		def cancel(self):
		self.close()

		def closeEvent(self, event):
		if self.parent is not None:
		self.parent.setDisabled(False)
		# self.parent.drawSpectrum(self.parent.activeSpectrum, self.parent.activeSpectrumName)




		class WhittakerSmoother(object):
		@@ -550,17 +528,3 @@ class CropSpectra(QtWidgets.QDialog):
		if self.parent is not None:
		self.parent.setDisabled(False)
		event.accept()
		No newline at end of file



		def main():
		global dbWin
		#start Application
		app = QtWidgets.QApplication(sys.argv)
		dbWin = DataBaseWindow(None)
		app.exec_()


		if __name__ == '__main__':
		main()

		No newline at end of file

analysis/excelexport.py

+2 −4

Original line number	Diff line number	Diff line
		@@ -30,14 +30,12 @@ class ExpExcelDialog(QtWidgets.QDialog):
		super(ExpExcelDialog, self).__init__()
		self.setWindowTitle('Export Options')
		self.setGeometry(200, 200, 300, 300)
		self.layout = QtWidgets.QHBoxLayout()
		self.setLayout(self.layout)

		self.dataset = dataset
		self.particleContainer = dataset.particleContainer


		self.layout = QtWidgets.QHBoxLayout()
		self.setLayout(self.layout)

		excelvbox = QtWidgets.QVBoxLayout()
		excelvbox.addWidget(QtWidgets.QLabel('Select Parameters for Export'))
		excelgroup = QtWidgets.QGroupBox("Export to Excel", self)

analysis/particleCharacterization.py

+8 −12

Original line number	Diff line number	Diff line
		@@ -45,8 +45,8 @@ def particleIsValid(particle):
		return False
		return True


		def getParticleStatsWithPixelScale(cnt, fullimage, dataset):
		def getParticleStatsWithPixelScale(contour, fullimage, dataset):
		cnt = deepcopy(contour)
		pixelscale = dataset.getPixelScale()

		newStats = ParticleStats()
		@@ -76,8 +76,6 @@ def getFibreDimension(contour):
		maxThickness = np.max(dist)*2
		return longSize, maxThickness



		def getParticleColor(imgRGB, colorClassifier=None):
		img = cv2.cvtColor(imgRGB, cv2.COLOR_RGB2HSV_FULL)
		meanHSV = cv2.mean(img)
		@@ -130,6 +128,7 @@ def getParticleImageFromFullimage(contour, fullimage):
		xmin, xmax, ymin, ymax = getContourExtrema(contourCopy)

		img = fullimage[ymin:ymax, xmin:xmax]
		img = img.copy()
		mask = np.zeros(img.shape[:2])

		for i in range(len(contourCopy)):
		@@ -164,11 +163,11 @@ def contoursToImg(contours, padding=0):
		return img, xmin, ymin, padding

		def imgToCnt(img, xmin, ymin, padding=0):
		def getContour(img, flag):
		def getContour(img, contourMode):
		if cv2.__version__ > '3.5':
		contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, flag)
		contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, contourMode)
		else:
		temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, flag)
		temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_EXTERNAL, contourMode)

		if len(contours) == 0: #i.e., no contour found
		raise InvalidParticleError
		@@ -188,10 +187,7 @@ def imgToCnt(img, xmin, ymin, padding=0):
		return contours[maxIndex]

		img = closeHolesOfSubImage(img)
		contour = getContour(img, flag=cv2.CHAIN_APPROX_SIMPLE)

		if len(contour) < 5:
		contour = getContour(img, flag=cv2.CHAIN_APPROX_NONE)
		contour = getContour(img, contourMode=cv2.CHAIN_APPROX_NONE)

		for i in range(len(contour)):
		contour [i][0][0] += xmin-padding

analysis/particleClassification/colorClassification.py

+21 −19

Original line number	Diff line number	Diff line
		@@ -20,6 +20,26 @@ along with this program, see COPYING.
		If not, see <https://www.gnu.org/licenses/>.
		"""

		class ColorClassifier(object):
		def __init__(self):
		hue_tolerance = 50
		self.colors = [ColorRangeHSV('yellow', 30, hue_tolerance, 40, 255),
		ColorRangeHSV('blue', 120, hue_tolerance, 40, 255),
		ColorRangeHSV('red', 180, hue_tolerance, 40, 255),
		ColorRangeHSV('red', 0, hue_tolerance, 40, 255),
		ColorRangeHSV('green', 70, hue_tolerance, 40, 255),
		ColorRangeHSV('white', 128, 256, 0, 40)]

		def classifyColor(self, meanHSV):
		result = 'non-determinable'
		for color in self.colors:
		if color.containsHSV(meanHSV):
		result = color.name
		break

		return result


		class ColorRangeHSV(object):
		def __init__(self, name, hue, hue_tolerance, min_sat, max_sat):
		self.name = name
		@@ -41,21 +61,3 @@ class ColorRangeHSV(object):
		if sat < 128 and hsv[2] > 70:
		return True

		No newline at end of file
		class ColorClassifier(object):
		def __init__(self):
		hue_tolerance = 50
		self.colors = [ColorRangeHSV('yellow', 30, hue_tolerance, 40, 255),
		ColorRangeHSV('blue', 120, hue_tolerance, 40, 255),
		ColorRangeHSV('red', 180, hue_tolerance, 40, 255),
		ColorRangeHSV('red', 0, hue_tolerance, 40, 255),
		ColorRangeHSV('green', 70, hue_tolerance, 40, 255),
		ColorRangeHSV('white', 128, 256, 0, 40)]

		def classifyColor(self, meanHSV):
		result = 'non-determinable'
		for color in self.colors:
		if color.containsHSV(meanHSV):
		result = color.name
		break

		return result
		No newline at end of file