new logpath handling; Qt AppLocalDataLocation is now used to obtain an OS... (eb5a3c56) · Commits · GEPARD / GEPARD

gepard.py

+19 −15

Original line number	Original line	Diff line number	Diff line
	@@ -25,17 +25,16 @@ from ramancom.ramancontrol import defaultPath
	from ramancom.ramanSwitch import RamanSwitch		from ramancom.ramanSwitch import RamanSwitch
	from colorlegend import ColorLegend		from colorlegend import ColorLegend
	import os		import os
	from pathlib import Path

	class MeasureParticleWindow(QtWidgets.QMainWindow):		class MeasureParticleWindow(QtWidgets.QMainWindow):

	def __init__(self):		def __init__(self, logpath):
	super(MeasureParticleWindow, self).__init__()		super(MeasureParticleWindow, self).__init__()

	self.setWindowTitle("GEPARD")		self.setWindowTitle("GEPARD")
	self.resize(900, 700)		self.resize(900, 700)

	self.view = SampleView()		self.view = SampleView(logpath)
	self.view.imparent = self		self.view.imparent = self
	self.view.ScalingChanged.connect(self.scalingChanged)		self.view.ScalingChanged.connect(self.scalingChanged)
	self.scalebar = ScaleBar(self)		self.scalebar = ScaleBar(self)
	@@ -288,10 +287,15 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
	self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)		self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)

	if __name__ == '__main__':		if __name__ == '__main__':

	import sys		import sys
	from time import localtime, strftime		from time import localtime, strftime
	logpath = os.path.join(Path.home(),'gepard')
			app = QtWidgets.QApplication(sys.argv)
			app.setApplicationName("GEPARD") # appname needed for logpath

			logpath = QtCore.QStandardPaths.writableLocation(
			QtCore.QStandardPaths.AppLocalDataLocation)
			if logpath != "":
	if not os.path.exists(logpath):		if not os.path.exists(logpath):
	os.mkdir(logpath)		os.mkdir(logpath)
	logname = os.path.join(logpath, 'logfile.txt')		logname = os.path.join(logpath, 'logfile.txt')
	@@ -300,9 +304,9 @@ if __name__ == '__main__':
	sys.stderr = fp		sys.stderr = fp
	sys.stdout = 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()),
	sys.stdout.flush()		flush=True)
	app = QtWidgets.QApplication(sys.argv)
	meas = MeasureParticleWindow()		meas = MeasureParticleWindow(logpath)
	meas.showMaximized()		meas.showMaximized()
	ret = app.exec_()		ret = app.exec_()
			No newline at end of file

opticalscan.py

+56 −47

Original line number	Original line	Diff line number	Diff line
	@@ -27,22 +27,25 @@ from imagestitch import imageStacking
	import os		import os
	import cv2		import cv2
	from helperfunctions import cv2imread_fix, cv2imwrite_fix		from helperfunctions import cv2imread_fix, cv2imwrite_fix
	from time import sleep, time		from time import time
	import datetime		import datetime
	import sys		import sys
	from pathlib import Path

	#def scan(path, sol, zpositions, grid, controlclass, connection, ishdr=False):		def scan(path, sol, zpositions, grid, controlclass, dataqueue,
	def scan(path, sol, zpositions, grid, controlclass, dataqueue, stopevent, ishdr=False):		stopevent, logpath='', ishdr=False):
	print('starting new optical scan')
	sys.stdout.flush()
	if ishdr:		if ishdr:
	merge_mertens = cv2.createMergeMertens()		merge_mertens = cv2.createMergeMertens()

	logpath = os.path.join(Path.home(),'gepard', 'scanlog.txt')		fp = None
	with open(logpath, "a") as fp:		if logpath != '':
			try:
			fp = open(os.path.join(logpath, 'scanlog.txt'), 'a')
	sys.stderr = fp		sys.stderr = fp
	sys.stdout = fp		sys.stdout = fp
			except IOError:
			print('separate loging failed', flush=True)
			pass
			print('starting new optical scan', flush=True)

	ramanctrl = controlclass()		ramanctrl = controlclass()
	ramanctrl.connect()		ramanctrl.connect()
	@@ -52,10 +55,10 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue, stopevent, ishdr=
	z = sol[0]x + sol[1]y + sol[2]		z = sol[0]x + sol[1]y + sol[2]
	for k, zk in (zlist if i%2==0 else zlist[::-1]):		for k, zk in (zlist if i%2==0 else zlist[::-1]):
	name = f"image_{i}_{k}.bmp"		name = f"image_{i}_{k}.bmp"
	print("time:", time())		print("time:", time(), flush=True)
	zik = z+zk		zik = z+zk
	assert not np.isnan(zik)		assert not np.isnan(zik)
	print("moving to:", x, y, zik)		print("moving to:", x, y, zik, flush=True)
	ramanctrl.moveToAbsolutePosition(x, y, zik)		ramanctrl.moveToAbsolutePosition(x, y, zik)
	if ishdr:		if ishdr:
	img_list = []		img_list = []
	@@ -75,6 +78,8 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue, stopevent, ishdr=
	return		return
	dataqueue.put(i)		dataqueue.put(i)
	ramanctrl.disconnect()		ramanctrl.disconnect()
			if fp is not None:
			fp.close()


	def loadAndPasteImage(srcnames, fullimage, fullzval, width, height,		def loadAndPasteImage(srcnames, fullimage, fullzval, width, height,
	@@ -212,8 +217,9 @@ class OpticalScan(QtWidgets.QWidget):
	imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate') #str = 'df' (= darkfield) or 'bf' (=bright field)		imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate') #str = 'df' (= darkfield) or 'bf' (=bright field)
	boundaryUpdate = QtCore.pyqtSignal()		boundaryUpdate = QtCore.pyqtSignal()

	def __init__(self, ramanctrl, dataset, parent=None):		def __init__(self, ramanctrl, dataset, logpath='', parent=None):
	super().__init__(parent, QtCore.Qt.Window)		super().__init__(parent, QtCore.Qt.Window)
			self.logpath = logpath
	self.view = parent		self.view = parent
	vbox = QtWidgets.QVBoxLayout()		vbox = QtWidgets.QVBoxLayout()
	pointgroup = QtWidgets.QGroupBox("Point coordinates [µm]", self)		pointgroup = QtWidgets.QGroupBox("Point coordinates [µm]", self)
	@@ -508,7 +514,7 @@ class OpticalScan(QtWidgets.QWidget):
	A = np.ones((points.shape[0],3))		A = np.ones((points.shape[0],3))
	A[:,:2] = points[:,:2]		A[:,:2] = points[:,:2]
	b = points[:,2]		b = points[:,2]
	sol = np.linalg.lstsq(A,b)[0]		sol = np.linalg.lstsq(A, b, rcond=None)[0]
	self.dataset.heightmap = sol		self.dataset.heightmap = sol
	print("Fit deviation:", sol[0]points[:,0]+sol[1]points[:,1]+sol[2] -points[:,2] )		print("Fit deviation:", sol[0]points[:,0]+sol[1]points[:,1]+sol[2] -points[:,2] )

	@@ -545,7 +551,8 @@ class OpticalScan(QtWidgets.QWidget):
	self.dataqueue = Queue()		self.dataqueue = Queue()
	self.process = Process(target=scan, args=(path, sol, self.dataset.zpositions,		self.process = Process(target=scan, args=(path, sol, self.dataset.zpositions,
	self.dataset.grid, self.ramanctrl.__class__,		self.dataset.grid, self.ramanctrl.__class__,
	self.dataqueue, self.processstopevent, self.hdrcheck.isChecked()))		self.dataqueue, self.processstopevent,
			self.logpath, self.hdrcheck.isChecked()))
	self.process.start()		self.process.start()
	self.starttime = time()		self.starttime = time()
	self.progresstime.setEnabled(True)		self.progresstime.setEnabled(True)
	@@ -619,8 +626,10 @@ class OpticalScan(QtWidgets.QWidget):

	if __name__ == "__main__":		if __name__ == "__main__":
	from ramancom.simulatedraman import SimulatedRaman		from ramancom.simulatedraman import SimulatedRaman
			from dataset import DataSet

	app = QtWidgets.QApplication(sys.argv)		app = QtWidgets.QApplication(sys.argv)
	optscan = OpticalScan(SimulatedRaman())		ds = DataSet('Test')
			optscan = OpticalScan(SimulatedRaman(), ds)
	optscan.show()		optscan.show()
	sys.exit(app.exec_())		sys.exit(app.exec_())
			No newline at end of file

ramanscanui.py

+40 −32

Original line number	Original line	Diff line number	Diff line
	@@ -23,12 +23,11 @@ from PyQt5 import QtCore, QtWidgets
	import numpy as np		import numpy as np
	from multiprocessing import Process, Queue, Event		from multiprocessing import Process, Queue, Event
	import queue		import queue
	from time import sleep, time		from time import time
	from external import tsp		from external import tsp
	import datetime		import datetime
	import sys		import sys
	import os		import os
	from pathlib import Path

	def reorder(points, N=20):		def reorder(points, N=20):
	y0, y1 = points[:,1].min(), points[:,1].max()		y0, y1 = points[:,1].min(), points[:,1].max()
	@@ -48,27 +47,30 @@ def reorder(points, N=20):
	assert np.unique(newind).shape[0]==allind.shape[0]		assert np.unique(newind).shape[0]==allind.shape[0]
	return newind		return newind

	def scan(ramanSettings, positions, controlclass, dataqueue, stopevent):		def scan(ramanSettings, positions, controlclass, dataqueue, stopevent,
	logpath = os.path.join(Path.home(),'gepard', 'ramanscanlog.txt')		logpath=''):
	with open(logpath, "a") as fp:		fp = None
			if logpath != '':
			try:
			fp = open(os.path.join(logpath, 'ramanscanlog.txt'), 'a')
	sys.stderr = fp		sys.stderr = fp
	sys.stdout = fp		sys.stdout = fp
			except IOError:
			print('separate loging failed', flush=True)
			pass

	ramanctrl = controlclass()		ramanctrl = controlclass()
	ramanctrl.connect()		ramanctrl.connect()
	print("connected:", time())		print("connected:", time(), flush=True)
	ramanctrl.initiateMeasurement(ramanSettings)		ramanctrl.initiateMeasurement(ramanSettings)
	for i, p in enumerate(positions):		for i, p in enumerate(positions):
	x, y, z = p		x, y, z = p
	print("time:", time())		print("time:", time(), flush=True)
	print("position:", x, y, z)		print("position:", x, y, z, flush=True)
	sys.stdout.flush() #remove this line after testing
	ramanctrl.moveToAbsolutePosition(x, y, z, measurementRunning=True)		ramanctrl.moveToAbsolutePosition(x, y, z, measurementRunning=True)
	print("move done")		print("move done", flush=True)
	sys.stdout.flush()
	ramanctrl.triggerMeasurement(i)		ramanctrl.triggerMeasurement(i)
	print("trigger done")		print("trigger done", flush=True)
	sys.stdout.flush()

	if stopevent.is_set():		if stopevent.is_set():
	ramanctrl.disconnect()		ramanctrl.disconnect()
	@@ -77,15 +79,17 @@ def scan(ramanSettings, positions, controlclass, dataqueue, stopevent):
	dataqueue.put(i)		dataqueue.put(i)

	ramanctrl.disconnect()		ramanctrl.disconnect()
			if fp is not None:
			fp.close()

	class RamanScanUI(QtWidgets.QWidget):		class RamanScanUI(QtWidgets.QWidget):
	imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate') #str = 'df' (= darkfield) or 'bf' (=bright field)		imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate') #str = 'df' (= darkfield) or 'bf' (=bright field)
	ramanscanUpdate = QtCore.pyqtSignal()		ramanscanUpdate = QtCore.pyqtSignal()

	def __init__(self, ramanctrl, dataset, parent=None):		def __init__(self, ramanctrl, dataset, logpath='', parent=None):
	super().__init__(parent, QtCore.Qt.Window)		super().__init__(parent, QtCore.Qt.Window)
	self.view = parent		self.view = parent
			self.logpath = logpath
	self.ramanctrl = ramanctrl		self.ramanctrl = ramanctrl
	self.dataset = dataset		self.dataset = dataset
	self.process = None		self.process = None
	@@ -242,7 +246,11 @@ class RamanScanUI(QtWidgets.QWidget):
	self.ramanctrl.disconnect()		self.ramanctrl.disconnect()
	self.processstopevent = Event()		self.processstopevent = Event()
	self.dataqueue = Queue()		self.dataqueue = Queue()
	self.process = Process(target=scan, args=(ramanSettings, scanpoints, self.ramanctrl.__class__, self.dataqueue, self.processstopevent))		self.process = Process(target=scan, args=(ramanSettings, scanpoints,
			self.ramanctrl.__class__,
			self.dataqueue,
			self.processstopevent,
			self.logpath))
	self.process.start()		self.process.start()
	self.starttime = time()		self.starttime = time()
	self.timer = QtCore.QTimer(self)		self.timer = QtCore.QTimer(self)

sampleview.py

+6 −5

Original line number	Original line	Diff line number	Diff line
	@@ -35,9 +35,10 @@ from ramancom.configRaman import RamanConfigWin
	class SampleView(QtWidgets.QGraphicsView):		class SampleView(QtWidgets.QGraphicsView):
	ScalingChanged = QtCore.pyqtSignal(float)		ScalingChanged = QtCore.pyqtSignal(float)

	def __init__(self):		def __init__(self, logpath):
	super(SampleView, self).__init__()		super(SampleView, self).__init__()

			self.logpath = logpath
	self.item = QtWidgets.QGraphicsPixmapItem()		self.item = QtWidgets.QGraphicsPixmapItem()
	self.item.setPos(0, 0)		self.item.setPos(0, 0)
	self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)		self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)
	@@ -77,9 +78,9 @@ class SampleView(QtWidgets.QGraphicsView):
	self.contouritem = SegmentationContours(self)		self.contouritem = SegmentationContours(self)
	scene.addItem(self.contouritem)		scene.addItem(self.contouritem)
	self.detectionwidget = None		self.detectionwidget = None
	self.ramanwidget = RamanScanUI(self.ramanctrl, None, self)		self.ramanwidget = RamanScanUI(self.ramanctrl, None, self.logpath, self)
	self.ramanwidget.imageUpdate.connect(self.loadPixmap)		self.ramanwidget.imageUpdate.connect(self.loadPixmap)
	self.oscanwidget = OpticalScan(self.ramanctrl, None, self)		self.oscanwidget = OpticalScan(self.ramanctrl, None, self.logpath, self)
	self.oscanwidget.imageUpdate.connect(self.loadPixmap)		self.oscanwidget.imageUpdate.connect(self.loadPixmap)
	self.oscanwidget.boundaryUpdate.connect(self.resetBoundary)		self.oscanwidget.boundaryUpdate.connect(self.resetBoundary)
	self.analysiswidget = None		self.analysiswidget = None
	@@ -194,7 +195,7 @@ class SampleView(QtWidgets.QGraphicsView):
	self.ramanwidget.setVisible(False)		self.ramanwidget.setVisible(False)
	if self.analysiswidget is None:		if self.analysiswidget is None:
	print('creating new analysiswidget')		print('creating new analysiswidget')
	self.analysiswidget = ParticleAnalysis(self)		self.analysiswidget = ParticleAnalysis(self.dataset, self)
	self.analysiswidget.showMaximized()		self.analysiswidget.showMaximized()
	else:		else:
	print('show maximized already exisiting analysiswidget')		print('show maximized already exisiting analysiswidget')
	@@ -477,7 +478,7 @@ class SampleView(QtWidgets.QGraphicsView):
	self.boundaryitems = edges, nodes		self.boundaryitems = edges, nodes
	self.resetScanPositions()		self.resetScanPositions()

	@QtCore.pyqtSlot(int, float)		@QtCore.pyqtSlot(int, bool)
	def selectContour(self, index, centerOn=True):		def selectContour(self, index, centerOn=True):
	if self.analysiswidget is not None:		if self.analysiswidget is not None:
	if self.analysiswidget.uniquePolymers is not None:		if self.analysiswidget.uniquePolymers is not None: