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

gepard.py

+19 −15

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

		class MeasureParticleWindow(QtWidgets.QMainWindow):

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

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

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

		if __name__ == '__main__':

		import sys
		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):
		os.mkdir(logpath)
		logname = os.path.join(logpath, 'logfile.txt')
		@@ -300,9 +304,9 @@ if __name__ == '__main__':
		sys.stderr = fp
		sys.stdout = fp

		print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)
		sys.stdout.flush()
		app = QtWidgets.QApplication(sys.argv)
		meas = MeasureParticleWindow()
		print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()),
		flush=True)

		meas = MeasureParticleWindow(logpath)
		meas.showMaximized()
		ret = app.exec_()
		No newline at end of file

opticalscan.py

+56 −47

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

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

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

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


		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)
		boundaryUpdate = QtCore.pyqtSignal()

		def __init__(self, ramanctrl, dataset, parent=None):
		def __init__(self, ramanctrl, dataset, logpath='', parent=None):
		super().__init__(parent, QtCore.Qt.Window)
		self.logpath = logpath
		self.view = parent
		vbox = QtWidgets.QVBoxLayout()
		pointgroup = QtWidgets.QGroupBox("Point coordinates [µm]", self)
		@@ -508,7 +514,7 @@ class OpticalScan(QtWidgets.QWidget):
		A = np.ones((points.shape[0],3))
		A[:,:2] = 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
		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.process = Process(target=scan, args=(path, sol, self.dataset.zpositions,
		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.starttime = time()
		self.progresstime.setEnabled(True)
		@@ -619,8 +626,10 @@ class OpticalScan(QtWidgets.QWidget):

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

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

ramanscanui.py

+40 −32

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

		def reorder(points, N=20):
		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]
		return newind

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

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

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

		ramanctrl.disconnect()

		if fp is not None:
		fp.close()

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

		def __init__(self, ramanctrl, dataset, parent=None):
		def __init__(self, ramanctrl, dataset, logpath='', parent=None):
		super().__init__(parent, QtCore.Qt.Window)
		self.view = parent
		self.logpath = logpath
		self.ramanctrl = ramanctrl
		self.dataset = dataset
		self.process = None
		@@ -242,7 +246,11 @@ class RamanScanUI(QtWidgets.QWidget):
		self.ramanctrl.disconnect()
		self.processstopevent = Event()
		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.starttime = time()
		self.timer = QtCore.QTimer(self)

sampleview.py

+6 −5

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

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

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

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