diff --git a/Python code/libhreels/HREELS.py b/Python code/HREELS.py
similarity index 100%
rename from Python code/libhreels/HREELS.py
rename to Python code/HREELS.py
diff --git a/Python code/libhreels/__init__.py b/Python code/__init__.py
similarity index 100%
rename from Python code/libhreels/__init__.py
rename to Python code/__init__.py
diff --git a/Python code/libhreels/calcHREELS.py b/Python code/calcHREELS.py
similarity index 100%
rename from Python code/libhreels/calcHREELS.py
rename to Python code/calcHREELS.py
diff --git a/Python code/libhreels/calcHREELS3.png b/Python code/calcHREELS3.png
similarity index 100%
rename from Python code/libhreels/calcHREELS3.png
rename to Python code/calcHREELS3.png
diff --git a/Python code/libhreels/calcHREELS4.png b/Python code/calcHREELS4.png
similarity index 100%
rename from Python code/libhreels/calcHREELS4.png
rename to Python code/calcHREELS4.png
diff --git a/Python code/libhreels/dielectrics.py b/Python code/dielectrics.py
similarity index 100%
rename from Python code/libhreels/dielectrics.py
rename to Python code/dielectrics.py
diff --git a/Python code/dist/libhreels-2.1.1-py3-none-any.whl b/Python code/dist/libhreels-2.1.1-py3-none-any.whl
deleted file mode 100644
index f2a0fbacd237ab9d758ec240d13d233245339106..0000000000000000000000000000000000000000
Binary files a/Python code/dist/libhreels-2.1.1-py3-none-any.whl and /dev/null differ
diff --git a/Python code/dist/libhreels-2.1.1.tar.gz b/Python code/dist/libhreels-2.1.1.tar.gz
deleted file mode 100644
index 57db58bf7cf5cc78dcc6d24c48a58cad65533858..0000000000000000000000000000000000000000
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diff --git a/Python code/libhreels Wolf b/Python code/libhreels Wolf
deleted file mode 100644
index f2b17a60ab7a2674f14c968cac94314b2b2a2944..0000000000000000000000000000000000000000
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diff --git a/Python code/libhreels/Auger.py b/Python code/libhreels/Auger.py
deleted file mode 100755
index 5af1393dd2a706c3511587025bfa63a09b4299b8..0000000000000000000000000000000000000000
--- a/Python code/libhreels/Auger.py
+++ /dev/null
@@ -1,184 +0,0 @@
-#!/usr/bin/python
-# Auger library Version 0.1 (December 2018 @ WFW)
-#
-import numpy as np
-import re
-import matplotlib.pyplot as plt
-from scipy import optimize, interpolate
-from datetime import datetime
-from datetime import timedelta
-from matplotlib.transforms import offset_copy
-# from pylab import figure
-from matplotlib.pyplot import figure
-import os
-
-def offset(ax, x, y):
- return offset_copy(ax.transData, x=x, y=y, units='dots')
-
-def Auger_elog_Dictionary(file, path):
- spec = Auger(file,datapath=path)
- dic = {'Category':'Auger', 'Type':'Auger', 'Substrate':'as before',
- 'Summary':'%5.0f'% spec.xmin +'-'+'%-5.0f'% spec.xmax,
- 'Temperature':'', 'File':str(file),
- 'Scan_Range':'%5.0f'% spec.xmin +','+'%5.0f'% spec.xmax,
- 'N_channels':'%4d'%spec.totalTime, 'MDate':spec.startTimeEpoch,
- 'Author':'Python Script'}
- return dic
-
-class Auger:
- """This class handles Auger data and their plotting."""
- path = "./"
- def __init__(self, _filename, datapath=path):
- self.datapath = datapath
- self.readDataFile(_filename)
- self.Auger = interpolate.interp1d(self.xdata, self.ydata, kind='linear')
- # self.Auger = interp1d(self.xdata, self.ydata, kind='nearest')
-
- def readDataFile(self, _filename):
- # if _filename.find(".") == -1:
- # _filename +=".aes"
- self.filename = _filename
- # self.fname = self.filename[0:self.filename.find(".")]
- self.fname = _filename
- xdata = []
- ydata = []
- import glob
- f = glob.glob(self.datapath+"**/"+self.filename, recursive=True)
- if len(f) == 0:
- print('Error: No files found!')
- print('Not found:',self.filename)
- return
- f = glob.glob(self.datapath+"**/"+self.filename, recursive=True)[0]
- self.datapath = os.path.dirname(f)
- self.startTime = datetime.fromtimestamp(os.path.getmtime(f)) # Only the file saving time
- self.startTimeEpoch = os.path.getmtime(f)
- with open(f, 'r') as f:
- for line in f:
- str_x, str_d, str_y = line.split()
- # print(str_x, str_y)
- try:
- xdata.append(float(str_x))
- ydata.append(float(str_y))
- except:
- xdata.append(float(str_x.replace(",",".")))
- ydata.append(float(str_y.replace(",",".")))
- self.xdata = np.array(xdata)
- self.ydata = np.array(ydata)
- self.xmin = self.xdata[0]
- self.xmax = self.xdata[-1]
- self.deltay = max(ydata)-min(ydata)
- self.ymax = max(ydata)
- self.totalTime = 1.0 * len(self.xdata)
- self.marker = []
- self.valid = True
-
-
- def __str__(self):
- return self.datapath+self.filename
-
- def info(self):
- print("filename: \t\t",self.filename)
- print("datapath: \t\t",self.datapath)
- print("startTime: \t\t",self.startTime)
- print("xmin: \t\t\t","%6.1f"%self.xmin,"eV")
- print("xmax: \t\t\t","%6.1f"%self.xmax,"eV")
- if len(self.marker)>0:
- print("marker: \t\t")
- for each in self.marker:
- print("\t\t%6.1f\t %8.1f"%each)
- print('--------')
-
- def infoText(self):
- langtext = "filename: \t\t"+self.filename+'\n'
- langtext +="datapath: \t\t"+self.datapath+'\n'
- langtext +="startTime: \t\t"+str(self.startTime)+'\n'
- langtext +="xmin: \t\t\t"+"%6.1f"%self.xmin+" eV"+'\n'
- langtext +="xmax: \t\t\t"+"%6.1f"%self.xmax+" eV"+'\n'
- if len(self.marker)>0:
- langtext +="marker: \t\t"+'\n'
- for each in self.marker:
- langtext +="\t\t%6.1f\t %8.1f"%each+'\n'
- langtext +='--------'
- return langtext
-
-
- def findIndex(self, kinEnergy):
- for i in range(len(self.xdata)):
- if self.xdata[i] > kinEnergy:
- return i
- print('Auger.findIndex: kinEnergy', kinEnergy, 'not found in xdata')
- return len(self.xdata)-1
-
- def plot(self, xmin=None, xmax=None, label='x', color="b-",marker=True, offset=0.):
- ''' plot(self, xmin=None, xmax=None, label='x', normalized=False, color="b-",marker=True,offset=0.)'''
- if xmin:
- nstart = self.findIndex(xmin)
- else:
- nstart = 0
- if xmax:
- nend = self.findIndex(xmax)
- else:
- nend = len(self.xdata)
- if label == "x":
- label = self.filename
- plt.plot(self.xdata[nstart:nend], self.ydata[nstart:nend]+offset, color, label=label)
- plt.xlabel('Kinetic Energy (eV)')
- plt.ylabel('dN/dE (arb. u.)')
- plt.legend()
- if marker:
- for (x,y) in self.marker:
- self.setMarker(x,y)
- return
-
- def pickMarker(self):
- def onclick(event):
- # print('%s click: button=%d, x=%d, y=%d, xdata=%f, ydata=%f' %
- # ('double' if event.dblclick else 'single', event.button,
- # event.x, event.y, event.xdata, event.ydata))
- if event.button ==1:
- self.marker.append((event.xdata, event.ydata))
- self.setMarker(event.xdata, event.ydata)
- self.fig.canvas.draw()
- else:
- self.marker = []
- print("All marker deleted!")
- self.fig.canvas.draw()
- self.fig.canvas.mpl_connect('button_press_event', onclick)
- self.ax.set_title('Pick marker with left mouse button ... (right:erase all)')
-
- def figure(self):
- self.fig=figure()
- self.ax=self.fig.add_subplot(111)
-
- def show(self):
- plt.show()
-
- def selectData(self,x1, x2=None):
- """Returns the data as (x,y) list between
- x1 and x2. If x2 is omitted the full range is used."""
- if not x2:
- x2 = self.xmax
- a = self.findIndex(x1)
- b = self.findIndex(x2)+1
- return self.data[a:b]
-
- def setMarker(self, x, y, ymin=0, size=None):
- trans = offset(self.ax, 0, 10)
- plt.plot([x,x],[y,self.ymax-0.2*self.deltay], lw=1, c='b', ls='dashed')
- x = round(x*10)/10.
- plt.text(x,self.ymax-0.2*self.deltay,'%5.1f' % x, rotation=90,
- verticalalignment='bottom', horizontalalignment='center', transform=trans)
- return
-
-
-if __name__ == '__main__':
- path = 'D:\Data\Python\Auger\data'
- d1 = Auger("181207_A_01",datapath=path)
- d2 = Auger("190207_A_02",datapath=path)
- dy=0.
- d2.info();d2.plot(color='m-');dy-=0.5
- d1.info();d1.plot(offset=dy);dy-=0.5
- d2.show()
-
- import code
- code.interact(local=locals())
diff --git a/Python code/libhreels/LEED.py b/Python code/libhreels/LEED.py
deleted file mode 100755
index 196238c32148e7f2a0344366acf2a772a6b97a2d..0000000000000000000000000000000000000000
--- a/Python code/libhreels/LEED.py
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/usr/bin/python
-# LEED library Version 0.1 (July 2019 @ WFW)
-#
-import numpy as np
-import re
-import matplotlib.pyplot as plt
-from scipy import optimize, interpolate
-from datetime import datetime
-from datetime import timedelta
-from matplotlib.transforms import offset_copy
-# from pylab import figure
-from matplotlib.pyplot import figure
-import cv2
-import os
-
-def offset(ax, x, y):
- return offset_copy(ax.transData, x=x, y=y, units='dots')
-
-def LEED_elog_Dictionary(file, path):
- spec = LEED(file,datapath=path)
- dic = {'Category':'LEED', 'Type':'LEED', 'Substrate':'as before',
- 'Summary':spec.energy+' eV',
- 'Temperature':'', 'File':str(file),
- 'Scan_Range':'', 'Energy':spec.energy,
- 'N_channels':'', 'MDate':spec.startTimeEpoch,
- 'Author':'Python Script'}
- return dic
-
-class LEED:
- """This class handles LEED data and their plotting."""
- path = "./"
- def __init__(self, _filename, datapath=path):
- self.datapath = datapath
- self.readDataFile(_filename)
-
- def readDataFile(self, _filename):
- # if _filename.find(".") == -1:
- # _filename +=".aes"
- self.filename = _filename
- self.fname = self.filename[0:self.filename.find(".")]
- import glob
- f = glob.glob(self.datapath+"**/"+self.filename, recursive=True)
- if len(f) == 0:
- print('Error: No files found!')
- print('Not found:',self.filename)
- return
- f = glob.glob(self.datapath+"**/"+self.filename, recursive=True)[0]
- self.datapath = os.path.dirname(f)
- self.startTime = datetime.fromtimestamp(os.path.getmtime(f)) # Only the file saving time
- self.startTimeEpoch = os.path.getmtime(f)
- match = re.search(r"\_(\d*)eV",self.fname)
- self.energy = match.group(1)
- self.picture = cv2.imread(f)
-
- def __str__(self):
- return self.datapath+self.filename
-
- def info(self):
- print("filename: \t\t",self.filename)
- print("datapath: \t\t",self.datapath)
- print("startTime: \t\t",self.startTime)
- print("energy: \t\t",self.energy)
- print('--------')
-
- def plot(self):
- new_pic = self.picture
- # Pmin = min(new_pic.all())
- # Pmax = max(new_pic.any())
- # new_pic = (new_pic-Pmin)/(Pmax-Pmin)*255
- cv2.imshow('LEED'+self.fname,new_pic)
- cv2.waitKey(0)
- cv2.destroyAllWindows()
-
-if __name__ == '__main__':
- path = 'D:\Data\Python\LEED'
- d1 = LEED("190122_L_01_42eV.tif",datapath=path)
-
- d1.info()
- d1.plot()
-
- import code
- code.interact(local=locals())
diff --git a/Python code/libhreels/NoExpLogbook.py b/Python code/libhreels/NoExpLogbook.py
deleted file mode 100755
index 5eff614bdb0e57f92c1051faed13a3b79c7565c7..0000000000000000000000000000000000000000
--- a/Python code/libhreels/NoExpLogbook.py
+++ /dev/null
@@ -1,2 +0,0 @@
-available = False
-
diff --git a/Python code/libhreels/ViewAuger.py b/Python code/libhreels/ViewAuger.py
deleted file mode 100755
index 7e02fa08d99e954d02ab31c4fa4e0addcff5ceaf..0000000000000000000000000000000000000000
--- a/Python code/libhreels/ViewAuger.py
+++ /dev/null
@@ -1,406 +0,0 @@
-#!/usr/bin/env python3
-import os
-import re
-import sys
-
-import matplotlib.pyplot as plt
-import numpy as np
-from datetime import datetime
-import argparse
-from matplotlib.backends.backend_qt5agg import \
- FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt5agg import \
- NavigationToolbar2QT as NavigationToolbar
-from PyQt5 import QtCore, QtGui, QtWidgets, uic
-import libhreels as hh
-hhPath = hh.__path__[0]
-from libhreels.Auger import Auger
-
-# fix HighRes Displays
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling, True)
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
-
-
-class Auger_Window(QtWidgets.QMainWindow):
- """ fill in some initial data """
-
- def __init__(self,datapath= None, remoteDir=None, startWithFile=None):
- super(Auger_Window, self).__init__()
- f = os.path.join(hhPath,"viewauger.ui")
- self.ui = self.ui = uic.loadUi(f, self)
- self.xmin = 10.
- self.factor = 1.
- self.offset = 0.5
- self.useOffset = False
- self.normalized = False
- if datapath and os.path.exists(datapath):
- self.datapath = datapath
- else:
- self.datapath = "\\\\141.48.167.189\\BackUp02\\0_experiments\\EELS-PC4\\AES"
- if remoteDir and os.path.exists(remoteDir):
- self.remoteDir = remoteDir
- else:
- self.remoteDir = '\\\\141.48.167.189\\BackUp02\\0_experiments\\EELS-PC4\\Auger'
- self.wideScan = True
- self.marker = []
- # self.markerSet = False
-
- # initialize the widget "drawWidget" and attach it into the ui
- self.drawing_figure = plt.figure(frameon=False,figsize=(5, 4), dpi=150, tight_layout = True)
- self.drawing_pane = FigureCanvas(self.drawing_figure)
- self.drawing_figure.canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
- self.drawing_figure.canvas.setFocus()
- # self.drawing_figure.canvas.mpl_connect('button_press_event', self.onMouse)
- self.drawing_pane.axes = self.drawing_pane.figure.add_subplot(111)
- self.ui.drawWidget.layout().addWidget(self.drawing_pane)
- # Add toolbar
- self.xToolbar = NavigationToolbar(self.drawing_pane, self)
- self.ui.drawWidget.layout().addWidget(self.xToolbar)
- self.xToolbar.setSizePolicy(QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed))
-
- self.ui.lineEdit_directory.setText(self.datapath)
- self.ui.lineEdit_factor.setText('%4.1f'%(self.factor))
- self.ui.lineEdit_offset.setText('%4.1f'%(self.offset))
-
- # Action on user events
- self.ui.checkBoxOffset.toggled.connect(self.onUseOffset)
- self.ui.checkBoxMarker.toggled.connect(self.onMarkerSet)
- self.ui.pushButton_details.pressed.connect(self.onPushButton_details3)
- self.ui.lineEdit_factor.editingFinished.connect(self.onFactor)
- self.ui.lineEdit_offset.editingFinished.connect(self.onOffset)
- self.ui.lineEdit_directory.editingFinished.connect(self.onNewDirectory)
-
- # Create list of all datafiles in the directory
- self.createFileList()
- self.ui.listWidget.itemSelectionChanged.connect(self.onFileSelection)
- self.dataDir = QtWidgets.QFileDialog(self)
- if os.name == 'nt':
- self.dataDir.setDirectory("D:\\Data\\Python\\HREELS\\expHREELS\\data")
- else:
- self.dataDir.setDirectory("/mnt/d/Data/Python/HREELS/expHREELS/data")
-
- # Action on user menu events:
- self.action_directory.triggered.connect(self.onActionDir)
- self.action_test.triggered.connect(self.onActionTest)
- self.action_help.triggered.connect(self.onActionHelp)
-
- #Add a cursor:
- self.cursor = Cursor(self.drawing_pane, self.drawing_pane.axes)
- # self.cursorId = self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
- if startWithFile:
- self.selectFile(startWithFile)
-
-
-
- def onFactor(self):
- try:
- val = float(self.ui.lineEdit_factor.text())
- self.factor = val
- except ValueError:
- self.ui.lineEdit_factor.setText('%4.1f'%(self.factor))
- self.onFileSelection()
-
- def onUseOffset(self):
- self.useOffset = self.ui.checkBoxOffset.isChecked()
- self.onOffset()
-
- def onOffset(self):
- try:
- val = float(self.ui.lineEdit_offset.text())
- self.offset = val
- except ValueError:
- self.ui.lineEdit_offset.setText('%4.1f'%(self.offset))
- self.onFileSelection()
-
- def onNormalized(self):
- self.normalized = self.ui.checkBoxNormalized.isChecked()
- self.onFileSelection()
-
- def onActionDir(self):
- # self.dataDir.setDirectory("D:\\Data\\Python\\expHREELS\\data")
- directory = self.openDirectoryDialog()
- if directory:
- self.ui.lineEdit_directory.setText(directory)
- self.directory = directory
- self.ui.listWidget.clear()
- self.datapath = directory
- self.createFileList()
-
- def onNewDirectory(self):
- dirText = self.ui.lineEdit_directory.text()
- if os.path.exists(dirText):
- self.directory = self.ui.lineEdit_directory.text()
- self.ui.listWidget.clear()
- self.datapath = self.directory
- self.createFileList()
- else:
- self.ui.lineEdit_directory.setText('')
-
-
- def onActionTest(self):
- self.dataDir.setDirectory(self.remoteDir)
- directory = self.openDirectoryDialog()
- if directory:
- self.ui.lineEdit_directory.setText(directory)
- self.directory = directory
- self.ui.listWidget.clear()
- self.datapath = directory
- self.createFileList()
-
- def onActionHelp(self):
- pass
- msg = QtWidgets.QMessageBox()
- msg.setText('''
- This is the Auger data browser of the Martin-Luther University Halle-Wittenberg
- (Version 0.5) designed for fast data screening and plotting.
- Copyright @ wolf.widdra@physik.uni-halle.de.
- ''')
- msg.setWindowTitle("Auger data browser help")
- # msg.setStandardButtons(QtWidgets.QMessageBox.Ok)
- layout = msg.layout()
- widget = QtWidgets.QWidget()
- widget.setFixedSize(650, 1)
- layout.addWidget(widget, 3, 0, 1, 3)
- msg.buttonClicked.connect(self.onOK)
- msg.exec_()
-
- def onPushButton_details(self):
- try:
- details = self.d.infoText()
- except:
- return
- msg = QtWidgets.QMessageBox()
- msg.setText(details)
- msg.setWindowTitle("Dataset details")
- msg.setStandardButtons(QtWidgets.QMessageBox.Ok)
- layout = msg.layout()
- widget = QtWidgets.QWidget()
- widget.setFixedSize(650, 1)
- layout.addWidget(widget, 3, 0, 1, 3)
- msg.buttonClicked.connect(self.onOK)
- msg.exec_()
-
- def onPushButton_details3(self):
- """Shows a dialog containing data details"""
- self.dialog = QtWidgets.QDialog(self)
- f = os.path.join(hhPath, "viewhreels_dialog.ui")
- self.dialog.ui = uic.loadUi(f, self.dialog)
- self.dialog.ui.setWindowTitle('Dataset details')
- self.dialog.ui.textArea.setPlainText(self.d.infoText())
- self.dialog.show()
-
- def onMarkerSet(self):
- b = self.ui.checkBoxMarker.isChecked()
- self.markerSet = b
- if not b:
- # Disconnect all mouse events from canvas:
- self.drawing_figure.canvas.mpl_disconnect(self.cursorId)
- self.drawing_figure.canvas.mpl_disconnect(self.canvasId)
- else:
- # Connect all mouse events from canvas to routines:
- self.cursorId = self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
- self.canvasId = self.drawing_figure.canvas.mpl_connect('button_press_event', self.onMouse)
- print('mouse enabled')
-
- def onOK(self, button):
- print("Button pressed is:",button.text())
-
-
- def selectFile(self, file):
- '''Select the file within the QListWidget by then program, e.g. as start parameter.
- Make sure before that it exists. The file extension is dropped by re.split. '''
- itm = self.ui.listWidget.findItems(re.split('\.',file)[0], QtCore.Qt.MatchExactly)
- self.ui.listWidget.setCurrentItem(itm[0])
- return
-
-
- def onFileSelection(self):
- iMax = len(self.ui.listWidget.selectedItems())
- if iMax == 0:
- return
- firstItem = self.ui.listWidget.selectedItems()[0]
- self.d = Auger(firstItem.text(),self.datapath)
- if iMax > 1: # Remember the last plot size if there are already plots
- # Read xmin, xmax for current window and set these values for added spectra:
- self.xdmin, self.xdmax = self.drawing_pane.axes.get_xlim()
- plotColor = plt.cm.gnuplot(0) # Define the color map (coolwarm; plasma; inferno; gnuplot)
- self.updatePlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, color=plotColor)
- self.ydmin, _ = self.drawing_pane.axes.get_ylim()
-
- try:
- self.dialog.ui.textArea.setPlainText(self.d.infoText())
- except:
- pass
-
- if iMax > 1:
- i = 1.
- for item in self.ui.listWidget.selectedItems()[1:]:
- plotColor = plt.cm.gnuplot(i/iMax) # Define the color map (coolwarm; plasma; inferno; gnuplot)
- self.d = Auger(item.text(),self.datapath)
- self.secondPlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, offset=i*self.offset*self.useOffset, color=plotColor)
- # print(i, item.text())
- i += 1
- # Reversing the sequence of labels in the legend:
- handles, labels = self.drawing_pane.axes.get_legend_handles_labels()
- self.drawing_pane.axes.legend(handles[::-1], labels[::-1])
- # self.drawing_pane.axes.set_ylim(bottom=0.)
- self.drawing_figure.tight_layout()
- self.cursor = Cursor(self.drawing_pane, self.drawing_pane.axes)
- self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
- self.drawing_pane.draw()
-
- def onMouse(self, event):
- if not self.markerSet:
- return
- if (event.xdata):
- if event.button==1:
- x,y = event.xdata, event.ydata
- print(x,y)
- self.marker.append((x,y))
- self.setMarker(x,y,self.ydmin)
- elif event.button==3:
- pass
- self.drawing_pane.draw()
-
- def setMarker(self, x, y, ymin=0, size=None):
- ''' Set vertical marker with text label. Note that self.figure() needs to be
- called before use.'''
- # trans = offset(self.ax, 0, 30)
- self.drawing_pane.axes.plot([x,x],[ymin,y], lw=1, c='black', ls='dashed')
- x = round(x)
- # plt.text(x,y,'%4i' % x, rotation=90, verticalalignment='bottom', horizontalalignment='center', transform=trans)
- self.drawing_pane.axes.text(x,y,'%4i' % x, rotation=90, verticalalignment='bottom', horizontalalignment='center')
- return
-
-
- def updatePlot(self,xmin=10, factor=1, normalized=False, color="red"):
- self.drawing_pane.axes.cla()
- # self.plotWidget(normalized=normalized)
- self.plotWidget(factor=factor, color=color, normalized=normalized)
-
- def secondPlot(self,xmin=70, factor=1, normalized=False, offset = 0., color="b-"):
- self.secondPlotWidget(xmin=xmin, xdmin=self.xdmin, xdmax=self.xdmax, factor=factor, color=color, label=self.d.fname, normalized=normalized, offset = offset)
-
- def plotWidget(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="black",marker=True, offset = 0.):
- ''' plot(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="b-",marker=True)'''
- self.d.pFactor = factor
- if xmin:
- nstart = self.d.findIndex(xmin)
- else:
- nstart = 0
- if xmax:
- nend = self.d.findIndex(xmax)
- else:
- nend = len(self.d.xdata)
- if label == "x":
- label = self.d.fname
- self.drawing_pane.axes.plot(self.d.xdata[nstart:nend], factor*self.d.ydata[nstart:nend] + offset, color=color, label=label)
- self.d.factor = factor
- self.drawing_pane.axes.set_xlabel('Kinetic Energy (eV)')
- self.drawing_pane.axes.set_ylabel('Intensity (arb. units)')
- if marker:
- for (x,y) in self.d.marker:
- self.d.setMarker(x,y*factor)
- return
-
- def secondPlotWidget(self, xmin=None, xmax=None, xdmin=None, xdmax=None, factor=1, label='x', normalized=False, color="black",marker=True, offset = 0.):
- ''' plot(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="b-",marker=True)'''
- self.d.pFactor = factor
- if xmin:
- nstart = self.d.findIndex(xmin)
- else:
- nstart = 0
- if xmax:
- nend = self.d.findIndex(xmax)
- else:
- nend = len(self.d.xdata)
- if label == "x":
- label = self.d.fname
- self.drawing_pane.axes.plot(self.d.xdata[nstart:nend], factor*self.d.ydata[nstart:nend] + offset, color=color, label=label)
- self.drawing_pane.axes.set_xlim(xdmin, xdmax)
- self.d.factor = factor
- return
-
- def getFileList(self, directory):
- '''Get the list of all Auger data files. The list is
- sorted by the file creation date.'''
- list = os.listdir(directory)
- files = []
- for file in list:
- location = os.path.join(directory, file)
- size = os.path.getsize(location)
- time = os.path.getmtime(location)
- files.append((file, time, size))
- files.sort(key=lambda s: -s[1]) # sort by time
- fileNames = [item[0] for item in files]
- # SElect the specific Auger data files: E.g. 181207_A_01
- # AESFiles = [fn for fn in fileNames if (fn[6:9]=='_A_')]
- AESFiles = []
- for fn in fileNames:
- if (fn[6:9]=='_A_'):
- AESFiles.append(fn)
- elif re.search('^[1-3][0-9][0-1][0-9][0-3][0-9]_', fn):
- AESFiles.append(fn)
- return AESFiles, len(AESFiles)
-
- def createFileList(self):
- for item in self.getFileList(self.datapath)[0]:
- fname = re.split('\.',item)[0]
- self.ui.listWidget.addItem(fname)
-
- def openDirectoryDialog(self):
- self.dataDir = QtWidgets.QFileDialog(self)
- options = self.dataDir.Options()
- # options = self.dataDir.ShowDirsOnly
- options |= self.dataDir.DontUseNativeDialog
- dir =self.dataDir.getExistingDirectory(self, 'Select data directory', options=options)
- if dir:
- return dir
-
-class Cursor(object):
- def __init__(self, fig, ax):
- self.figure = fig
- self.ax = ax
- self.ly = ax.axvline(color='r') # the vert line
-
- def mouse_move(self, event):
- if not event.inaxes:
- return
- self.ly.set_data([event.xdata, event.xdata], [0, 1])
- self.figure.draw()
-
-def runViewer(datapath= None, remoteDir=None, startWithFile=None):
- """ Main function for graphical application start """
- app = QtWidgets.QApplication(sys.argv)
- form = Auger_Window(datapath= datapath, remoteDir=remoteDir, startWithFile=startWithFile)
- form.show()
- sys.exit(app.exec_())
-
-################# Command line handling ######################
-def validDate(string):
- date = datetime.strptime(string, "%Y-%m-%d")
- return date
-def is_valid_file(string):
- if not os.path.exists(string):
- parser.error("The file %s does not exist!" % string)
- return False
- else:
- return string
-
-def myMain():
- parser = argparse.ArgumentParser()
- # parser.add_argument("-v", "--verbosity", type=int, choices=[0, 1, 2],help="increase output verbosity")
- parser.add_argument("-s", "--start", help="Start date (2018-01-01)", default='2019-01-01', type=validDate)
- #parser.add_argument("-e", "--end", help="End date and time (2018-01-01_08:00)", type=validDate, required=True)
- parser.add_argument("-f", "--file", help="Start viewer with this datafile", type=is_valid_file)
- args = parser.parse_args()
- if args.file:
- fPath,fName = os.path.split(args.file)
- # print(">>> ", fPath, " <<< ", fName)
- else:
- fPath = "."
- fName = None
-
- runViewer(datapath=fPath, startWithFile=fName)
-if __name__ == '__main__':
- myMain()
\ No newline at end of file
diff --git a/Python code/libhreels/ViewHREELS.py b/Python code/libhreels/ViewHREELS.py
deleted file mode 100755
index 570b18807e39bce94f8785b9200d6bb3972a46ad..0000000000000000000000000000000000000000
--- a/Python code/libhreels/ViewHREELS.py
+++ /dev/null
@@ -1,475 +0,0 @@
-#!/usr/bin/env python3
-import os
-import re
-import sys
-
-import matplotlib.pyplot as plt
-import numpy as np
-from matplotlib.backends.backend_qt5agg import \
- FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt5agg import \
- NavigationToolbar2QT as NavigationToolbar
-from PyQt5 import QtCore, QtGui, QtWidgets, uic
-import libhreels as hh
-hhPath = os.path.dirname(__file__)
-from libhreels.HREELS import HREELS, myPath
-from datetime import datetime
-import argparse
-# import libhreels.expLogbook as lgb
-import libhreels.NoExpLogbook as lgb
-
-# fix HighRes Displays
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling, True)
-# QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
-
-class HREELS_Window(QtWidgets.QMainWindow):
- """ fill in some initial data """
- def __init__(self,datapath=None, remoteDir=None, startWithFile=None, comment=None):
- super(HREELS_Window, self).__init__()
- f = os.path.join(hhPath,"viewhreels.ui") # path to the package directory. Needed to find graphical user interface files (*.ui)
- self.ui = self.ui = uic.loadUi(f, self)
- self.xmin = 50.
- self.factor = 10.
- self.offset = 0.1
- self.useOffset = False
- self.normalized = False
- self.comment = comment
- self.showComment = lgb.available
- if datapath and os.path.exists(datapath):
- self.datapath = datapath
- else:
- self.datapath = "./"
- self.directory = self.datapath
- if remoteDir and os.path.exists(remoteDir):
- self.remoteDir = remoteDir
- else:
- self.remoteDir = '//141.48.167.189/BackUp02/0_experiments/EELS-PC4/HREELS/gph_dat/'
- self.wideScan = True
- self.marker = []
- # self.markerSet = False
-
- # initialize the widget "drawWidget" and attach it into the ui
- self.drawing_figure = plt.figure(frameon=False,figsize=(5, 4), dpi=150, tight_layout = True)
- self.drawing_pane = FigureCanvas(self.drawing_figure)
- self.drawing_figure.canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
- self.drawing_figure.canvas.setFocus()
- # self.drawing_figure.canvas.mpl_connect('button_press_event', self.onMouse)
- self.drawing_pane.axes = self.drawing_pane.figure.add_subplot(111)
- self.ui.drawWidget.layout().addWidget(self.drawing_pane)
-
- #Add a cursor:
- self.cursor = Cursor(self.drawing_pane, self.drawing_pane.axes)
- # self.cursorId = self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
-
- # Add toolbar
- self.xToolbar = NavigationToolbar(self.drawing_pane, self)
- self.ui.drawWidget.layout().addWidget(self.xToolbar)
- self.xToolbar.setSizePolicy(QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed))
-
- self.ui.lineEdit_directory.setText(self.datapath)
- self.ui.lineEdit_xmin.setText('%4.1f'%self.xmin)
- self.ui.lineEdit_factor.setText('%4.1f'%(self.factor))
- self.ui.lineEdit_offset.setText('%4.1f'%(self.offset))
- self.ui.checkBoxWideScans.setChecked(True)
- self.ui.checkBoxComment.setChecked(lgb.available)
- # self.ui.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
-
-
- # Action on user events
- self.ui.checkBoxWideScans.toggled.connect(self.onWideScans)
- self.ui.checkBoxNormalized.toggled.connect(self.onNormalized)
- self.ui.checkBoxOffset.toggled.connect(self.onUseOffset)
- self.ui.checkBoxMarker.toggled.connect(self.onMarkerSet)
- self.ui.checkBoxComment.toggled.connect(self.onCommentSet)
- self.ui.pushButton_details.clicked.connect(self.onPushButton_details)
- self.ui.lineEdit_xmin.editingFinished.connect(self.onXmin)
- self.ui.lineEdit_factor.editingFinished.connect(self.onFactor)
- self.ui.lineEdit_offset.editingFinished.connect(self.onOffset)
- self.ui.lineEdit_directory.editingFinished.connect(self.onNewDirectory)
- self.ui.listWidget.itemSelectionChanged.connect(self.onFileSelection)
-
- # Action on user menu events:
- self.action_directory.triggered.connect(self.onActionDir)
- self.action_test.triggered.connect(self.onActionTest)
- self.action_help.triggered.connect(self.onActionHelp)
- self.actionFile_info.triggered.connect(self.onPushButton_details)
-
- # Create list of all datafiles in the directory
- self.createFileList()
- self.dataDir = QtWidgets.QFileDialog(self)
- if os.name == 'nt':
- self.dataDir.setDirectory("D:\\Data\\Python\\HREELS\\expHREELS\\data")
- else:
- self.dataDir.setDirectory("/mnt/d/Data/Python/HREELS/expHREELS/data")
-
- if startWithFile:
- self.selectFile(startWithFile)
-
-
- def onXmin(self):
- '''Routine called by a new value of "Xmin". It will trigger a data window update.'''
- try:
- val = float(self.ui.lineEdit_xmin.text())
- self.xmin = val
- except ValueError:
- self.ui.lineEdit_xmin.setText('%4.1f'%self.xmin)
- self.onFileSelection()
-
- def onFactor(self):
- '''Routine called by a new value of "Factor", which defines the amplification factor for the energy loss
- region (larger than Xmin). It will trigger a data window update.'''
- try:
- val = float(self.ui.lineEdit_factor.text())
- self.factor = val
- except ValueError:
- self.ui.lineEdit_factor.setText('%4.1f'%(self.factor))
- self.onFileSelection()
-
- def onUseOffset(self):
- '''Routine called by toggling "Use Offset": If set, the energy loss
- region (larger than Xmin) will be vertically offseted if multiple spectra are selected.
- It will trigger a data window update.'''
- self.useOffset = self.ui.checkBoxOffset.isChecked()
- self.onOffset()
-
- def onOffset(self):
- try:
- val = float(self.ui.lineEdit_offset.text())
- self.offset = val
- except ValueError:
- self.ui.lineEdit_offset.setText('%4.1f'%(self.offset))
- self.onFileSelection()
-
- def onNormalized(self):
- '''Routine called by toggling "Normalized": If set, all spectra will be normalized to a maximum
- count rate of unity. It will trigger a data window update.'''
- self.normalized = self.ui.checkBoxNormalized.isChecked()
- self.onFileSelection()
-
- def onActionDir(self):
- '''Routine calls Directory Selection Interface upon Menu selection. It will
- create a data list from the chosen directory.'''
- # if os.name == 'nt':
- # self.dataDir.setDirectory("D:\\Data\\Python\\HREELS\\expHREELS\\data")
- # else:
- # self.dataDir.setDirectory("/mnt/d/Data/Python/HREELS/expHREELS/data")
- directory = self.openDirectoryDialog()
- if directory:
- self.ui.lineEdit_directory.setText(directory)
- self.directory = directory
- self.ui.listWidget.clear()
- self.datapath = directory
- self.createFileList()
-
- def onNewDirectory(self):
- '''Routine called if Directory field is modified. It will
- create a data list from the chosen new directory (but only if it exists).'''
- dirText = self.ui.lineEdit_directory.text()
- tt = myPath(dirText)
- print('New directory: ',tt)
- self.directoryOld = self.directory
- if os.path.exists(tt):
- self.directory = tt
- self.ui.listWidget.clear()
- self.datapath = self.directory
- self.createFileList()
- else:
- self.ui.lineEdit_directory.setText(self.directoryOld)
-
-
- def onActionTest(self):
- '''Routine called by Menu item 'Test'. It is for playing
- with future options.'''
- self.dataDir.setDirectory(self.remoteDir)
- directory = self.openDirectoryDialog()
- if directory:
- self.ui.lineEdit_directory.setText(directory)
- self.directory = directory
- self.ui.listWidget.clear()
- self.datapath = directory
- self.createFileList()
-
- def onActionHelp(self):
- pass
- msg = QtWidgets.QMessageBox()
- msg.setText('''
- This is the HREELS data browser of the Martin-Luther University Halle-Wittenberg
- (Version 0.9) designed for fast data screening and plotting.
- Copyright @ wolf.widdra@physik.uni-halle.de.
- ''')
- msg.setWindowTitle("HREELS data browser help")
- # msg.setStandardButtons(QtWidgets.QMessageBox.Ok)
- layout = msg.layout()
- widget = QtWidgets.QWidget()
- widget.setFixedSize(650, 1)
- layout.addWidget(widget, 3, 0, 1, 3)
- msg.buttonClicked.connect(self.onOK)
- msg.exec_()
-
- def onPushButton_details(self):
- """Routine for showing a dialog window containing HREELS data details"""
- try:
- self.d.infoText()
- except:
- return
- self.dialog = QtWidgets.QDialog(self)
- f = os.path.join(hhPath,"viewhreels_dialog.ui")
- self.dialog.ui = uic.loadUi(f, self.dialog)
- self.dialog.ui.setWindowTitle('Dataset details')
- self.dialog.ui.textArea.setPlainText(self.d.infoText())
- self.dialog.show()
-
- def onMarkerSet(self):
- '''Routine called if selection "Set Marker" is toggled. It allows to draw dashed vertical lines
- with the energy loss values. The value 'self.markerSet' is used to decide later if lines have to be drawn.'''
- b = self.ui.checkBoxMarker.isChecked()
- self.markerSet = b
- if not b:
- # Disconnect all mouse events from canvas:
- self.drawing_figure.canvas.mpl_disconnect(self.cursorId)
- self.drawing_figure.canvas.mpl_disconnect(self.canvasId)
- else:
- # Connect all mouse events from canvas to routines:
- self.cursorId = self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
- self.canvasId = self.drawing_figure.canvas.mpl_connect('button_press_event', self.onMouse)
- print('mouse enabled')
-
- def onCommentSet(self):
- '''Routine called if selection "Show Comment" is toggled. It allows to draw dashed vertical lines
- with the energy loss values. The value 'self.markerSet' is used to decide later if lines have to be drawn.'''
- self.showComment = self.ui.checkBoxComment.isChecked()
- # print('onCommentSet:', lgb.available, self.showComment, self.ui.listWidget.selectedItems()[0].text())
- if self.showComment:
- if lgb.available:
- text = lgb.logbook.getShortMessage4File(self.d.fname)
- ids = lgb.logbook.search({'file':self.d.fname})
- if len(ids) > 0:
- _, attributes, _ = lgb.logbook.read(ids[0])
- print(self.d.fname, ids[0],': ', attributes['Date'],'\t',text[:-2])
- else:
- text = self.comment if self.comment else ''
- self.comment = None
- self.pCom = self.drawing_pane.axes.text(0.12, 0.98,text, ha='left', va='top', transform=self.drawing_pane.axes.transAxes)
- else:
- try:
- self.pCom.remove()
- except:
- pass
-
- def onOK(self, button):
- print("Button pressed is:",button.text())
-
- def onWideScans(self):
- '''Routine called if selection "Only wide scans" is toggled. The switch 'self.wideScan' decides
- if all spectra or only spectra with a wider energy range (data files larger than 21 kB)
- are listed on the left side.'''
- b = self.ui.checkBoxWideScans.isChecked()
- self.wideScan = b
- self.ui.listWidget.clear()
- self.createFileList()
-
- def selectFile(self, file):
- '''Select the file within the QListWidget by the program, e.g. as start parameter.
- Make sure before that it exists. The file extension is dropped by re.split. '''
- matchingItems = self.ui.listWidget.findItems(re.split('\.',file)[0], QtCore.Qt.MatchExactly)
- self.ui.listWidget.setCurrentItem(matchingItems[0])
- for it in matchingItems:
- it.setSelected(True)
- self.ui.listWidget.setFocus()
- return
-
- def onFileSelection(self):
- '''Routine called if user makes a file selection or changes the file selection within the left list.
- The selected spectra are plotted according to the given flags (Xmin, Factor, Normalized, Offset). '''
- iMax = len(self.ui.listWidget.selectedItems())
- if iMax == 0:
- return
- # print([it.text() for it in self.ui.listWidget.selectedItems()])
- firstItem = self.ui.listWidget.selectedItems()[0]
-
- self.d = HREELS(firstItem.text(),self.datapath)
- if self.d.valid:
- plotColor = plt.cm.gnuplot(0) # Define the color map (coolwarm; plasma; inferno; gnuplot)
- self.updatePlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, color=plotColor)
- try:
- self.dialog.ui.textArea.setPlainText(self.d.infoText())
- except:
- pass
- else:
- self.drawing_pane.axes.cla()
- self.drawing_pane.draw()
- return
- if iMax > 1:
- i = 1.
- myList = self.ui.listWidget.selectedItems()[1:]
- for item in myList: # Add here sorting according to ...
- plotColor = plt.cm.gnuplot(i/iMax) # Define the color map (coolwarm; plasma; inferno; gnuplot)
- self.d = HREELS(item.text(),self.datapath)
- self.secondPlot(xmin=self.xmin, factor=self.factor, normalized=self.normalized, offset=i*self.offset*self.useOffset, color=plotColor)
- # print(i, item.text())
- i += 1
- # Reversing the sequence of labels in the legend:
- handles, labels = self.drawing_pane.axes.get_legend_handles_labels()
- self.drawing_pane.axes.legend(handles[::-1], labels[::-1])
- self.drawing_pane.axes.set_ylim(bottom=0.)
- self.drawing_figure.tight_layout()
- self.cursor = Cursor(self.drawing_pane, self.drawing_pane.axes)
- self.drawing_figure.canvas.mpl_connect('motion_notify_event', self.cursor.mouse_move)
- self.drawing_pane.draw()
-
- def onMouse(self, event):
- if not self.markerSet:
- return
- if (event.xdata):
- if event.button==1:
- x,y = event.xdata, event.ydata
- print(x,y)
- self.marker.append((x,y))
- self.setMarker(x,y)
- elif event.button==3:
- pass
- self.drawing_pane.draw()
-
- def setMarker(self, x, y, ymin=0, size=None):
- ''' Set vertical marker with text label. Note that self.figure() needs to be
- called before use.'''
- # trans = offset(self.ax, 0, 30)
- self.drawing_pane.axes.plot([x,x],[ymin,y], lw=1, c='black', ls='dashed')
- x = round(x)
- # plt.text(x,y,'%4i' % x, rotation=90, verticalalignment='bottom', horizontalalignment='center', transform=trans)
- self.drawing_pane.axes.text(x,y,'%4i' % x, rotation=90, verticalalignment='bottom', horizontalalignment='center')
- return
-
-
- def updatePlot(self,xmin=70, factor=10, normalized=False, color="red"):
- '''Plotting the first of the selected spectra. '''
- self.drawing_pane.axes.cla()
- self.plotWidget(normalized=normalized,showComment=False)
- self.plotWidget(xmin=xmin, factor=factor, color=color, label='x %3i'%factor, normalized=normalized, showComment=self.showComment)
-
- def secondPlot(self,xmin=70, factor=10, normalized=False, offset = 0., color="b-"):
- '''Plotting the second and all further selected spectra. '''
- self.plotWidget(xmin=xmin, factor=factor, color=color, label=self.d.fname, normalized=normalized, offset = offset)
-
- def plotWidget(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="black",
- marker=True, offset = 0., showComment=False):
- ''' plot(self, xmin=None, xmax=None, factor=1, label='x', normalized=False, color="b-",marker=True)'''
- self.d.pFactor = factor
- if xmin:
- nstart = self.d.findIndex(xmin)
- else:
- nstart = 0
- if xmax:
- nend = self.d.findIndex(xmax)
- else:
- nend = len(self.d.xdata)
- if normalized:
- factor /= self.d.maxIntensity
- if label == "x":
- label = self.d.fname
- self.drawing_pane.axes.plot(self.d.xdata[nstart:nend], factor*self.d.ydata[nstart:nend] + offset, color=color, label=label)
- self.d.factor = factor
- if showComment: self.onCommentSet()
- self.drawing_pane.axes.set_xlabel('Energy Loss (cm$^{-1}$)')
- if normalized:
- self.drawing_pane.axes.set_ylabel('Normalized Intensity')
- else:
- self.drawing_pane.axes.set_ylabel('Intensity (s$^{-1}$)')
- if marker:
- for (x,y) in self.d.marker:
- self.d.setMarker(x,y*factor)
- return
-
- def getFileList(self, directory, sizeMin=0.):
- '''Get the list of all *.gph or *.GPH data files with a file size larger
- than sizeMin. A good value to remove the datfile with just the elastic peak is
- sizeMin=21000. The list is sorted by the file creation date.'''
- list = os.listdir(directory)
- files = []
- for file in list:
- location = os.path.join(directory, file)
- size = os.path.getsize(location)
- time = os.path.getmtime(location)
- if size>sizeMin:
- files.append((file, time, size))
- # files.sort(key=lambda s: -s[1]) # sort by time
- files.sort(key=lambda s: s[1]) # sort by reversed time
- fileNames = [item[0] for item in files]
- data_ext = ['gph', 'GPH']
- gphFiles = [fn for fn in fileNames
- if any(fn.endswith(ext) for ext in data_ext)]
- return gphFiles, len(gphFiles)
-
- def createFileList(self):
- if self.wideScan:
- sizeMin = 21000.
- else:
- sizeMin = 5.
- for item in self.getFileList(self.datapath,sizeMin=sizeMin)[0]:
- fname = re.split('\.',item)[0]
- self.ui.listWidget.addItem(fname)
-
- def openDirectoryDialog(self):
- self.dataDir = QtWidgets.QFileDialog(self)
- options = self.dataDir.Options()
- # options = self.dataDir.ShowDirsOnly
- options |= self.dataDir.DontUseNativeDialog
- dir =self.dataDir.getExistingDirectory(self, 'Select data directory', options=options)
- if dir:
- return dir
-
-class Cursor(object):
- def __init__(self, fig, ax):
- self.figure = fig
- self.ax = ax
- self.ly = ax.axvline(color='r') # the vert line
-
- def mouse_move(self, event):
- if not event.inaxes:
- return
- self.ly.set_data([event.xdata, event.xdata], [0, 1])
- self.figure.draw()
-
-def runViewer(datapath= None, remoteDir=None, startWithFile=None, comment=None):
- """ Main function for graphical application start """
- app = QtWidgets.QApplication(sys.argv)
- form = HREELS_Window(datapath=datapath, remoteDir=remoteDir, startWithFile=startWithFile, comment=comment)
- form.show()
- sys.exit(app.exec_())
-
-
-def myMain():
- parser = argparse.ArgumentParser()
- ################# Command line handling ######################
- def is_valid_file(string):
- if not os.path.exists(string):
- parser.error("The file %s does not exist!" % string)
- return False
- else:
- return string
- parser.add_argument("file", nargs='?', help="Start viewer with this datafile", type=is_valid_file)
- parser.add_argument("-f", "--file2", help="Start viewer with this datafile")
- parser.add_argument("-c", "--comment", default=None, help="Text comment")
- args = parser.parse_args()
-
- if args.file:
- fPath,fName = os.path.split(args.file)
- # print(">>> ", fPath, " <<< ", fName)
- elif args.file2:
- fPath,fName = os.path.split(args.file2)
- # print(">>> ", fPath, " <<< ", fName)
- else:
- if os.name == 'nt':
- fPath = "D:\\Data\\Python\\HREELS\\expHREELS\\data"
- else:
- fPath = "/mnt/d/Data/Python/HREELS/expHREELS/data"
- fPath = "/mnt/c/Users/user/ownCloud/Backup02-EP3/0_experiments/EELS-PC4/HREELS/gph_dat/2021"
- fName = None
-
- runViewer(datapath=fPath, startWithFile=fName, comment=args.comment)
-
-
-
-
-if __name__ == '__main__':
- myMain()
\ No newline at end of file
diff --git a/Python code/libhreels/analysizeData.py b/Python code/libhreels/analysizeData.py
deleted file mode 100755
index 5184c1ef186f696163dc21f2f6cb7b9467e04ffa..0000000000000000000000000000000000000000
--- a/Python code/libhreels/analysizeData.py
+++ /dev/null
@@ -1,45 +0,0 @@
-import numpy as np
-from matplotlib import pyplot as plt
-
-def findPeriod(list, period):
- '''For a list of times (relative to a sync pulse) calculate the average time deviation squared.
- '''
- residuum = []
- sum_residuum = 0
- for each in list:
- r = each % period
- residuum.append(r)
- sum_residuum += r
- av_res = sum_residuum / len(list)
- deviation = 0
- for res in residuum:
- deviation += (res - av_res)**2
- deviation /= (len(residuum)*period**2)
- return deviation, av_res
-
-def makeTimeRelative(times, durations):
- list = []
- synced = False
- t_zero = 0
- for each in pulses:
- if synced:
- list.append(pulses[each][0]-t_zero)
- if 9000 < pulses[each][2] < 9800:
- print("synced")
- t_zero = pulses[each][0]
- synced = True
- return list
-
-data = [] # read dat from file [[time in microsec, low duration, high duration], [...], ...]
-with open("data433_Signal2.txt", 'r') as f:
- for line in f:
- data.append([int(each) for each in line.split(',')])
-
-sumOn = 0; sumOff = 0
-for pulse in data[1:]:
- sumOn += pulse[2]
- sumOff += pulse[1]
-sumOn /= len(data)
-sumOff /= len(data)
-
-print("Average on and off times:", sumOn, sumOff)
diff --git a/Python code/libhreels/expLogbook.py b/Python code/libhreels/expLogbook.py
deleted file mode 100755
index 04ce7c4b26a446bd74c9f308ff90e3159543d125..0000000000000000000000000000000000000000
--- a/Python code/libhreels/expLogbook.py
+++ /dev/null
@@ -1,48 +0,0 @@
-# print('Executing expLogbook.py')
-# from getComment4File import *
-import requests
-import urllib.parse
-import os
-import builtins
-import re
-from elog.logbook_exceptions import *
-import elog
-from datetime import datetime
-from time import localtime
-
-# disable warnings about ssl verification
-from requests.packages.urllib3.exceptions import InsecureRequestWarning
-requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
-
-
-class myLogbook(elog.Logbook):
-
- def getMessage4File(self, filename):
- ids = super().search({'file':filename})
- if len(ids) > 0:
- message, _ , _ = super().read(ids[0])
- return message
- else:
- print("File {} in eLog not found!".format(filename))
- return None
-
- def getShortMessage4File(self,filename):
- stuff = self.getMessage4File(filename)
- import html2text
- h = html2text.HTML2Text()
- # Ignore converting links from HTML
- h.ignore_links = True
- if stuff: return h.handle(stuff)
- return
-
-
-##########################################################################################################
-# ogf settings:
-try:
- from libhreels.eLogCredentials import dummy, unsafe # Defines User credentials
- logbook = myLogbook('https://labor-ep3.physik.uni-halle.de/HREELS/', user=dummy, password=unsafe)
- print('eLog available!')
- available = True
-except:
- available = False
-
diff --git a/Python code/libhreels/viewauger.ui b/Python code/libhreels/viewauger.ui
deleted file mode 100755
index 226a8c13d88881d4cdf92d9b4e27a7cb22da2b6a..0000000000000000000000000000000000000000
--- a/Python code/libhreels/viewauger.ui
+++ /dev/null
@@ -1,280 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Auger_data_browser</class>
- <widget class="QMainWindow" name="Auger_data_browser">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1004</width>
- <height>685</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Auger data browser</string>
- </property>
- <widget class="QWidget" name="centralwidget">
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <property name="leftMargin">
- <number>5</number>
- </property>
- <property name="rightMargin">
- <number>5</number>
- </property>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <property name="leftMargin">
- <number>5</number>
- </property>
- <property name="rightMargin">
- <number>5</number>
- </property>
- <item>
- <widget class="QLineEdit" name="lineEdit_directory">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QListWidget" name="listWidget">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- <property name="alternatingRowColors">
- <bool>true</bool>
- </property>
- <property name="selectionMode">
- <enum>QAbstractItemView::ExtendedSelection</enum>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <property name="topMargin">
- <number>1</number>
- </property>
- <property name="bottomMargin">
- <number>1</number>
- </property>
- <item>
- <widget class="QPushButton" name="pushButton_details">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>14</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Show all details for the last data file</string>
- </property>
- <property name="text">
- <string>Details</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Factor:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_factor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxOffset">
- <property name="text">
- <string>Offset</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_offset">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxMarker">
- <property name="text">
- <string>set Marker</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>300</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="drawWidget">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="MinimumExpanding">
- <horstretch>1</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>50</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_2"/>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit"/>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QMenuBar" name="menubar">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1004</width>
- <height>22</height>
- </rect>
- </property>
- <widget class="QMenu" name="menuSelect_directory">
- <property name="title">
- <string>Select directory</string>
- </property>
- <addaction name="action_test"/>
- <addaction name="action_directory"/>
- </widget>
- <widget class="QMenu" name="menuHelp">
- <property name="title">
- <string>Help</string>
- </property>
- <addaction name="action_help"/>
- </widget>
- <widget class="QMenu" name="menuDetails">
- <property name="title">
- <string>Details</string>
- </property>
- </widget>
- <addaction name="menuSelect_directory"/>
- <addaction name="menuHelp"/>
- <addaction name="menuDetails"/>
- </widget>
- <widget class="QStatusBar" name="statusbar"/>
- <widget class="QToolBar" name="toolBar">
- <property name="windowTitle">
- <string>toolBar</string>
- </property>
- <attribute name="toolBarArea">
- <enum>TopToolBarArea</enum>
- </attribute>
- <attribute name="toolBarBreak">
- <bool>false</bool>
- </attribute>
- </widget>
- <action name="action_test">
- <property name="text">
- <string>Backup directory</string>
- </property>
- </action>
- <action name="action_directory">
- <property name="text">
- <string>Data directory</string>
- </property>
- </action>
- <action name="action_help">
- <property name="text">
- <string>About</string>
- </property>
- </action>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Python code/libhreels/viewhreels.ui b/Python code/libhreels/viewhreels.ui
deleted file mode 100755
index ab9f52a78bc470925448d9cbe1aa64c246cbfebb..0000000000000000000000000000000000000000
--- a/Python code/libhreels/viewhreels.ui
+++ /dev/null
@@ -1,330 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>HREELS_data_browser</class>
- <widget class="QMainWindow" name="HREELS_data_browser">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1364</width>
- <height>673</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>HREELS data browser</string>
- </property>
- <widget class="QWidget" name="centralwidget">
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <property name="leftMargin">
- <number>5</number>
- </property>
- <property name="rightMargin">
- <number>5</number>
- </property>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <property name="leftMargin">
- <number>5</number>
- </property>
- <property name="rightMargin">
- <number>5</number>
- </property>
- <item>
- <widget class="QLineEdit" name="lineEdit_directory">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QListWidget" name="listWidget">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>0</height>
- </size>
- </property>
- <property name="alternatingRowColors">
- <bool>true</bool>
- </property>
- <property name="selectionMode">
- <enum>QAbstractItemView::ExtendedSelection</enum>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <property name="topMargin">
- <number>1</number>
- </property>
- <property name="bottomMargin">
- <number>1</number>
- </property>
- <item>
- <widget class="QCheckBox" name="checkBoxWideScans">
- <property name="text">
- <string>only wide scans</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButton_details">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>14</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Show all details for the last data file</string>
- </property>
- <property name="text">
- <string>Details</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <property name="sizeConstraint">
- <enum>QLayout::SetMinimumSize</enum>
- </property>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Start:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_xmin">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Factor:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_factor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxNormalized">
- <property name="text">
- <string>Normalized</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxOffset">
- <property name="text">
- <string>Offset</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit_offset">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>10</width>
- <height>0</height>
- </size>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxMarker">
- <property name="text">
- <string>set Marker</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxComment">
- <property name="text">
- <string>comments</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>300</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="drawWidget">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="MinimumExpanding">
- <horstretch>1</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>50</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_2"/>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit"/>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QMenuBar" name="menubar">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1364</width>
- <height>22</height>
- </rect>
- </property>
- <widget class="QMenu" name="menuSelect_directory">
- <property name="title">
- <string>Select directory</string>
- </property>
- <addaction name="action_test"/>
- <addaction name="action_directory"/>
- </widget>
- <widget class="QMenu" name="menuHelp">
- <property name="title">
- <string>Help</string>
- </property>
- <addaction name="action_help"/>
- </widget>
- <widget class="QMenu" name="menuDetails">
- <property name="title">
- <string>Details</string>
- </property>
- <addaction name="actionFile_info"/>
- </widget>
- <addaction name="menuSelect_directory"/>
- <addaction name="menuHelp"/>
- <addaction name="menuDetails"/>
- </widget>
- <widget class="QStatusBar" name="statusbar"/>
- <widget class="QToolBar" name="toolBar">
- <property name="windowTitle">
- <string>toolBar</string>
- </property>
- <attribute name="toolBarArea">
- <enum>TopToolBarArea</enum>
- </attribute>
- <attribute name="toolBarBreak">
- <bool>false</bool>
- </attribute>
- </widget>
- <action name="action_test">
- <property name="text">
- <string>Backup directory</string>
- </property>
- </action>
- <action name="action_directory">
- <property name="text">
- <string>Data directory</string>
- </property>
- </action>
- <action name="action_help">
- <property name="text">
- <string>About</string>
- </property>
- </action>
- <action name="actionFile_info">
- <property name="text">
- <string>File info</string>
- </property>
- </action>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Python code/libhreels/viewhreels_dialog.ui b/Python code/libhreels/viewhreels_dialog.ui
deleted file mode 100755
index 5663a3ad626c854108e6659ef2053ecf13a93c9a..0000000000000000000000000000000000000000
--- a/Python code/libhreels/viewhreels_dialog.ui
+++ /dev/null
@@ -1,40 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Dialog</class>
- <widget class="QDialog" name="Dialog">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>645</width>
- <height>256</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <family>Courier New</family>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="windowTitle">
- <string>Dialog</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QPlainTextEdit" name="textArea"/>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Python code/libhreels/materials.json b/Python code/materials.json
similarity index 100%
rename from Python code/libhreels/materials.json
rename to Python code/materials.json
diff --git a/Python code/libhreels/myBoson.f90 b/Python code/myBoson.f90
similarity index 100%
rename from Python code/libhreels/myBoson.f90
rename to Python code/myBoson.f90
diff --git a/Python code/libhreels/myEels2.f90 b/Python code/myEels2.f90
similarity index 100%
rename from Python code/libhreels/myEels2.f90
rename to Python code/myEels2.f90
diff --git a/Python code/libhreels/myEels3.f90 b/Python code/myEels3.f90
similarity index 100%
rename from Python code/libhreels/myEels3.f90
rename to Python code/myEels3.f90
diff --git a/Python code/libhreels/myEels3cole.f90 b/Python code/myEels3cole.f90
similarity index 100%
rename from Python code/libhreels/myEels3cole.f90
rename to Python code/myEels3cole.f90
diff --git a/Python code/libhreels/myEels4.f90 b/Python code/myEels4.f90
similarity index 100%
rename from Python code/libhreels/myEels4.f90
rename to Python code/myEels4.f90