def __init__(self):
"""
Initialize the graphical user interface
"""
QMainWindow.__init__(self)
# Set up the user interface from Designer.
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# Setup the ploting widgets
self.canvas=self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.canvas.mpl_connect('pick_event', self.on_pick)
self.save=False
# Setup the plotting layout
self.initPlotLayout()
# Ask for the directory containing the matrix files
if len(sys.argv)<2:
self.path=QFileDialog.getExistingDirectory()
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path=sys.argv[1]
# Read the Matrix file
self.M=pyO.Matrix(self.path)
# Looking for a Table of Content file (called toc.txt or ToC.txt)
self.ToC=None
f=False
if os.path.exists(self.path+"/toc.txt"):
f=open(self.path+"/toc.txt","r")
elif os.path.exists(self.path+"/ToC.txt"):
f=open(self.path+"/ToC.txt","r")
if f:
self.ToC={int(z[0]):z[1] for z in [x.split() for x in f.readlines()]}
f.close()
val=200 # value used for the colors
# colors used for the plot lines
self.colors=[(0,0,val),(0,val,0),(val,0,0),(val,val,0),(val,0,val),(0,val,val)]
# Add the found data to the combo box
self.populateUI()
# QT: SIGNALS -> SLOTS
# This set which function is called when buttons, checkboxes, etc. are clicked
self.ui.comboBox.currentIndexChanged.connect(self.updateSTSid)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.ui.DV.valueChanged.connect(self.plotUpdate)
self.ui.statCB.stateChanged.connect(self.plotUpdate)
self.ui.normCB.stateChanged.connect(self.plotUpdate)
self.ui.pushButton.clicked.connect(self.InfoShowHideToggle)
self.ui.saveBT.clicked.connect(self.export)
self.InfoShowHideToggle('Hide')
self.updateSTSid()
if len(sys.argv)>2:
ID=sys.argv[2]
self.ui.comboBox.setCurrentIndex(self.ui.comboBox.findText(ID,QtCore.Qt.MatchStartsWith))
self.plotUpdate()
def __init__(self, DIext='Aux2'):
"""
Initialize the graphical user interface
"""
QMainWindow.__init__(self)
# Set up the user interface from Designer.
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# Setup the ploting widgets
self.canvas = self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.canvas.mpl_connect('pick_event', self.on_pick)
self.save = False
self.DIext = DIext
# Setup the plotting layout
self.initPlotLayout()
# Ask for the directory containing the matrix files
if len(sys.argv) < 2:
self.path = QFileDialog.getExistingDirectory()
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path = sys.argv[1]
# Read the Matrix file
self.M = pyO.Matrix(self.path)
# Looking for a Table of Content file (called toc.txt or ToC.txt)
self.ToC = None
f = False
if os.path.exists(self.path+"/toc.txt"):
f = open(self.path+"/toc.txt", "r")
elif os.path.exists(self.path+"/ToC.txt"):
f = open(self.path+"/ToC.txt", "r")
if f:
self.ToC = {int(z[0]):z[1] for z in [x.split() for x in f.readlines()]}
f.close()
val = 200 # value used for the colors
# colors used for the plot lines
self.colors = [(0, 0, val), (0, val, 0), (val, 0, 0),\
(val, val, 0), (val, 0, val), (0, val, val)]
# Add the found data to the combo box
self.populateUI()
# QT: SIGNALS -> SLOTS
# This set which function is called when buttons, checkboxes, etc. are clicked
self.ui.comboBox.currentIndexChanged.connect(self.updateSTSid)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.ui.DV.valueChanged.connect(self.plotUpdate)
self.ui.statCB.stateChanged.connect(self.plotUpdate)
self.ui.normCB.stateChanged.connect(self.plotUpdate)
self.ui.pushButton.clicked.connect(self.InfoShowHideToggle)
self.ui.saveBT.clicked.connect(self.export)
self.InfoShowHideToggle('Hide')
self.updateSTSid()
if len(sys.argv) > 2:
ID = sys.argv[2]
self.ui.comboBox.setCurrentIndex(\
self.ui.comboBox.findText(ID,QtCore.Qt.MatchStartsWith))
self.plotUpdate()
class STSviewer(QMainWindow):
def plot_err1(self, ax,X,Y,DY,col):
"""
Function to plot the mean and the statistical error (1*sigma and 2*sigma as a filled area)
ax: The axis object
X: the vector containing the X-data
Y: the vector containing the mean data
DY: the vector containing the standard-deviation data
X,Y and DY should have the same length
"""
ax.plot(X,Y,color=col)
ax.fill_between(X,Y-DY,Y+DY,facecolor=col,alpha=0.3)
ax.fill_between(X,Y-2*DY,Y+2*DY,facecolor=col,alpha=0.2)
def on_pick(self): # Do nothing important
pass
def initPlotLayout(self):
"""
Setup the plotting layout.
"""
gs=gridspec.GridSpec(2, 2)
sp1=gs.new_subplotspec((0,0))
sp2=gs.new_subplotspec((1,0))
sp3=gs.new_subplotspec((0,1),2)
self.ax1 = self.fig.add_subplot(sp1)
self.ax2 = self.fig.add_subplot(sp2)
self.ax3 = self.fig.add_subplot(sp3)
self.ax1b = self.ax1.twinx()
self.ax3b = self.ax3.twinx()
self.fig.tight_layout()
def __init__(self):
"""
Initialize the graphical user interface
"""
QMainWindow.__init__(self)
# Set up the user interface from Designer.
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# Setup the ploting widgets
self.canvas=self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.canvas.mpl_connect('pick_event', self.on_pick)
self.save=False
# Setup the plotting layout
self.initPlotLayout()
# Ask for the directory containing the matrix files
if len(sys.argv)<2:
self.path=QFileDialog.getExistingDirectory()
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path=sys.argv[1]
# Read the Matrix file
self.M=pyO.Matrix(self.path)
# Looking for a Table of Content file (called toc.txt or ToC.txt)
self.ToC=None
f=False
if os.path.exists(self.path+"/toc.txt"):
f=open(self.path+"/toc.txt","r")
elif os.path.exists(self.path+"/ToC.txt"):
f=open(self.path+"/ToC.txt","r")
if f:
self.ToC={int(z[0]):z[1] for z in [x.split() for x in f.readlines()]}
f.close()
val=200 # value used for the colors
# colors used for the plot lines
self.colors=[(0,0,val),(0,val,0),(val,0,0),(val,val,0),(val,0,val),(0,val,val)]
# Add the found data to the combo box
self.populateUI()
# QT: SIGNALS -> SLOTS
# This set which function is called when buttons, checkboxes, etc. are clicked
self.ui.comboBox.currentIndexChanged.connect(self.updateSTSid)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.ui.DV.valueChanged.connect(self.plotUpdate)
self.ui.statCB.stateChanged.connect(self.plotUpdate)
self.ui.normCB.stateChanged.connect(self.plotUpdate)
self.ui.pushButton.clicked.connect(self.InfoShowHideToggle)
self.ui.saveBT.clicked.connect(self.export)
self.InfoShowHideToggle('Hide')
self.updateSTSid()
if len(sys.argv)>2:
ID=sys.argv[2]
self.ui.comboBox.setCurrentIndex(self.ui.comboBox.findText(ID,QtCore.Qt.MatchStartsWith))
self.plotUpdate()
def InfoShowHideToggle(self,action='Toggle'):
"""
Show a TreeWidget containing the details of a STS scan.
"""
if action=='Hide' or self.ui.treeWidget.isVisible():
self.ui.treeWidget.hide()
self.ui.pushButton.setText("<<")
else:
self.ui.treeWidget.show()
self.ui.pushButton.setText(">>")
def populateUI(self):
"""
Look for I(V) measurements and add them to the combobox list
"""
self.STS={}
self.hasDIDV=[]
for i in self.M.images:
r=re.search(r"--([0-9]+)_([0-9]+).I\(V\)_mtrx",i)
if r and os.path.exists(self.path+"/"+i):
j=int(r.group(1))
if j in self.STS: self.STS[j]+=1
else: self.STS[j]=1
if i[:-9]+'Aux2(V)_mtrx' in self.M.images: self.hasDIDV.append(j)
for i in self.STS:
if self.ToC!=None and i in self.ToC:
self.ui.comboBox.addItem(str(i)+" (%s)"%(self.ToC[i]))
else:
self.ui.comboBox.addItem(str(i))
def updateSTSid(self):
"""
If and ID is chosen, the listWidget will be populated with the correct num and selected
"""
if self.ui.comboBox.currentIndex()==-1: raise ValueError("No Data found!")
self.ui.listWidget.itemChanged.disconnect()
self.ui.listWidget.clear()
ID=int(self.ui.comboBox.currentText().split(' ')[0])
for i in range(self.STS[ID]):
item = QtGui.QListWidgetItem()
item.setText(str(i+1)+" -----")
item.setTextColor(QtGui.QColor(*self.colors[i%len(self.colors)]))
item.setFlags(item.flags()|QtCore.Qt.ItemIsUserCheckable)
self.ui.listWidget.addItem( item )
item.setCheckState(QtCore.Qt.Checked)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.plotUpdate()
def updateModel(self, value, item=None):
"""
Gather information about the STS measurement and populate the treeWidget (the one hidden on the right of the screen)
"""
if item==None:
self.ui.treeWidget.clear()
item=self.ui.treeWidget.invisibleRootItem()
if type(value) is dict:
if 'value' in value and 'unit' in value:
child=QtGui.QTreeWidgetItem()
if value['unit']=='--':
child.setText(0,str(value['value']))
else:
child.setText(0,str(value['value'])+" "+str(value['unit']))
item.addChild(child)
else:
for key, val in sorted(value.items()):
child=QtGui.QTreeWidgetItem()
child.setText(0,key)
item.addChild(child)
self.updateModel(val, child)
elif type(value) is list:
for val in value:
child=QtGui.QTreeWidgetItem()
item.addChild(child)
if type(val) is dict:
child.setText(0, '[dict]')
self.updateModel(val,child)
elif type(val) is list:
child.setText(0, '[list]')
self.updateModel(val,child)
else:
child.setText(0, str(val))
child.setExpanded(True)
else:
child=QtGui.QTreeWidgetItem()
child.setText(0,str(value))
item.addChild(child)
def export(self):
"""
Toggle the flag to save the data
"""
self.save=True
self.plotUpdate()
self.save=False
def plotUpdate(self):
"""
Most important function which is retrieving and plotting the data
"""
# Clear the plot
self.ax1.clear()
self.ax1b.clear()
self.ax2.clear()
self.ax3.clear()
self.ax3b.clear()
# Setting labels and axis
self.ax1.hold(True)
self.ax1.set_xlabel("Bias [V]",fontsize=FontSize)
self.ax2.set_xlabel("Bias [V]",fontsize=FontSize)
self.ax1.set_ylabel("Current [pA]",fontsize=FontSize)
self.ax1b.set_ylabel("dI/dV [pA/V]",fontsize=FontSize)
self.ax2.set_ylabel(r'$\frac{dI/dV}{\overline{I/V}}$',fontsize=FontSize)
self.ax3.set_xlabel("Bias [V]",fontsize=FontSize)
self.ax3.set_ylabel("I/V [$\mu$A/V]",fontsize=FontSize)
self.ax3b.yaxis.label.set_color("green")
self.ax3b.tick_params(axis='y',colors="green")
# plot the selected curves
ID=int(self.ui.comboBox.currentText().split(' ')[0])
paramsShowed=False
stat=False
norm=False
# If checkbox "statistics" is checked, then variable stat=True
if self.ui.statCB.isChecked(): stat=True
if self.ui.normCB.isChecked(): norm=True
counter=0
NumShown=[]
for i in range(self.STS[ID]): # Scan over all STS having the same ID
if self.ui.listWidget.item(i).checkState()==QtCore.Qt.Checked: # Is the curve selected by the user to be plotted?
NumShown.append(i+1) # Store in a list which num will be displayed
# Retrieve the STS data for the ID and num=i+1
V,I,IM=self.M.getSTS(ID,i+1,params=True)
NPTS=int(IM['Spectroscopy']['Device_1_Points']['value']) # Number of points in the V range
DV=self.ui.DV.value()
Vstep=(IM['Spectroscopy']['Device_1_End']['value']-IM['Spectroscopy']['Device_1_Start']['value'])/float(NPTS)
skip=int(np.ceil(DV/Vstep))
if not paramsShowed:
paramsShowed=True
p=self.M.getSTSparams(ID,i+1)
self.updateModel(p)
N=(0,NPTS)
# The follwing variables store matrices of the various signals as a list. The first element of the list is for the Up scans and the second for Down scans
Im=[np.empty(N),np.empty(N)] # Current: I
dIm=[np.empty(N),np.empty(N)] # dI/dV
IVm=[np.empty((0,NPTS+2*skip)),np.empty((0,NPTS+2*skip))] # I/V
BIVm=[np.empty(N),np.empty(N)] # Broadened I/V (BIV)
dIdVIVm=[np.empty(N),np.empty(N)] # (dI/dV)/BIV
# reconstruct the voltage array
sV=np.linspace(min(V),max(V),NPTS) # Voltage values in increading order
if len(I)<NPTS: # Missing data
I=np.pad(I,NPTS,'constant',constant_values=np.nan)
elif len(I)>NPTS: # Forward & Backward scan
if V[1]<V[0]: # Start with Downward scan
IUp=I[NPTS:]
IDown=I[NPTS-1::-1] # flip first part of the data
else:
IUp=I[:NPTS]
IDown=I[-1:NPTS-1:-1] # Flip second part of the data
if len(IDown)<NPTS: # Missing data
IDown=np.pad(IDown,NPTS,'constant',constant_values=np.nan)
Im[0]=np.vstack((Im[0],IUp)) # Im[0] contains the Up scans
Im[1]=np.vstack((Im[1],IDown)) # Im[1] contains the Down scans
if not stat:
self.ax1.plot(sV,IUp*1e-6,
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),
label="I%i (->)"%(i))
if not stat:
self.ax1.plot(sV,IDown*1e-6,'--',
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),
label="I%i (<-)"%(i))
else:
if V[0]==min(V):
Im[0]=np.vstack((Im[0],I))
else:
Im[1]=np.vstack((Im[1],I))
if not stat: self.ax1.plot(V,I*1e-6,
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),
label="I%i"%(i))
if ID in self.hasDIDV:
V2,dI=self.M.getDIDV(ID,i+1)
if norm: dI-=dI.min()
if len(I)>NPTS: # Forward & Backward scan
if V[1]<V[0]: # Start with Downward scan
dIUp=dI[NPTS:]
dIDown=dI[NPTS-1::-1]
else:
dIUp=dI[:NPTS]
dIDown=dI[-1:NPTS-1:-1]
dIm[0]=np.vstack((dIm[0],dIUp))
dIm[1]=np.vstack((dIm[1],dIDown))
Is=[IUp,IDown]
dIs=[dIUp,dIDown]
else:
Is=[I]
dIs=[dI]
if V[0]==min(V):
dIm[0]=np.vstack((dIm[0],dI))
else:
dIm[1]=np.vstack((dIm[1],dI))
for ud in range(len(Is)):
if len(dIs[ud])<NPTS: dIs[ud]=np.pad(dIs[ud],NPTS,'constant',constant_values=np.nan)
if not stat: self.ax1b.plot(sV,dIs[ud]*1e-6,[':','-.'][ud],
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),
label="dI%i (%s)"%(i,['->','<-'][ud]))
delta=NPTS-len(Is[ud])
if delta>0:
if V[1]>V[0]: # problem on the downscan
sV=sV[delta:]
else:
sV=sV[:-delta]
S=STS(sV,Is[ud],DV)
IV=S.getIV()
BIV=S.getBIV()
W=S.getW()
nV=S.getnV()
IVm[ud]=np.vstack((IVm[ud],IV))
BIVm[ud]=np.vstack((BIVm[ud],BIV))
dIdVIVm[ud]=np.vstack((dIdVIVm[ud],dIs[ud]/BIV))
if not stat: self.ax3.plot(nV,1e-12*IV,['b','--b'][ud],
label="I/V (%s)"%(["->","<-"][ud]))
if not stat: self.ax3.plot(sV,1e-12*BIV,['r','--r'][ud],
label="$\overline{I/V}$ (%s)"%(["->","<-"][ud]))
if ud==0: self.ax3b.plot(nV,W,'g',label="conv. func.")
if not stat: self.ax2.plot(sV,dIs[ud]/BIV,['-','--'][ud],
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),
label="(%s)"%(['->','<-'][ud]))
# end for ud (up/down)
# end if STS is shown
# end for i in IDs
## self.ax3.legend(prop={'size':6}) quite slow. comment it for now
## self.ax1.legend(loc=2,prop={'size':6})
## self.ax1b.legend(loc=1,prop={'size':6})
if self.save:
# Saving the data
X=np.vstack((sV,Im[0],dIm[0],Im[1],dIm[1],dIdVIVm[0],dIdVIVm[1]))
header="DV=%.3fV\nV\t"%(DV)
header+="\t".join(["I{}_Up(V)".format(i) for i in NumShown])
header+="\t"+"\t".join(["dI{}/dV_Up".format(i) for i in NumShown])
header+="\t"+"\t".join(["I{}_Down(V)".format(i) for i in NumShown])
header+="\t"+"\t".join(["dI{}/dV_Down".format(i) for i in NumShown])
header+="\t"+"\t".join(["(dI{}_Up/dV)/(I/V)".format(i) for i in NumShown])
header+="\t"+"\t".join(["(dI{}_Down/dV)/(I/V)".format(i) for i in NumShown])
np.savetxt("STS_%i.dat"%(ID),X.transpose(),header=header)
if stat: # If statistic checkbox is enabled
for ud in range(2):
if Im[ud].shape[0]==0: continue
fmt=['-','--'][ud]
col1=['blue','purple'][ud]
col2=['red','orange'][ud]
col3=['green','green'][ud]
Imm=Im[ud].mean(axis=0)
Ims=Im[ud].std(axis=0)
dImm=dIm[ud].mean(axis=0)
dIms=dIm[ud].std(axis=0)
dIVm=dIdVIVm[ud].mean(axis=0)
dIVs=dIdVIVm[ud].std(axis=0)
IVmm=IVm[ud].mean(axis=0)
IVms=IVm[ud].std(axis=0)
BIVmm=BIVm[ud].mean(axis=0)
BIVms=BIVm[ud].std(axis=0)
self.plot_err1(self.ax1,sV,Imm,Ims,col1)
self.plot_err1(self.ax1b,sV,dImm,dIms,col2)
self.plot_err1(self.ax2,sV,dIVm,dIVs,col1)
self.plot_err1(self.ax3,nV,IVmm,IVms,col1)
self.ax3.plot(sV,BIVmm,color=col2)
self.ax3.fill_between(sV,BIVmm-BIVms,BIVmm+BIVms,facecolor=col2,alpha=0.3)
self.ax3.fill_between(sV,BIVmm-2*BIVms,BIVmm+2*BIVms,facecolor=col2,alpha=0.2)
for x in [self.ax1,self.ax1b,self.ax2,self.ax3,self.ax3b]:
x.tick_params(axis='both', labelsize=FontSize)
self.canvas.draw()
class STSviewer(QMainWindow):
def plot_err1(self, ax, X, Y, DY, col):
"""
Function to plot the mean and the statistical error (1*sigma and 2*sigma as a filled area)
ax: The axis object
X: the vector containing the X-data
Y: the vector containing the mean data
DY: the vector containing the standard-deviation data
X,Y and DY should have the same length
"""
ax.plot(X, Y, color=col)
ax.fill_between(X, Y-DY, Y+DY, facecolor=col, alpha=0.3)
ax.fill_between(X, Y-2*DY, Y+2*DY, facecolor=col, alpha=0.2)
def on_pick(self): # Do nothing important
pass
def initPlotLayout(self):
"""
Setup the plotting layout.
"""
gs = gridspec.GridSpec(2, 2)
sp1 = gs.new_subplotspec((0, 0))
sp2 = gs.new_subplotspec((1, 0))
sp3 = gs.new_subplotspec((0, 1), 2)
self.ax1 = self.fig.add_subplot(sp1)
self.ax2 = self.fig.add_subplot(sp2)
self.ax3 = self.fig.add_subplot(sp3)
self.ax1b = self.ax1.twinx()
self.ax3b = self.ax3.twinx()
self.fig.tight_layout()
def __init__(self, DIext='Aux2'):
"""
Initialize the graphical user interface
"""
QMainWindow.__init__(self)
# Set up the user interface from Designer.
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# Setup the ploting widgets
self.canvas = self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.canvas.mpl_connect('pick_event', self.on_pick)
self.save = False
self.DIext = DIext
# Setup the plotting layout
self.initPlotLayout()
# Ask for the directory containing the matrix files
if len(sys.argv) < 2:
self.path = QFileDialog.getExistingDirectory()
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path = sys.argv[1]
# Read the Matrix file
self.M = pyO.Matrix(self.path)
# Looking for a Table of Content file (called toc.txt or ToC.txt)
self.ToC = None
f = False
if os.path.exists(self.path+"/toc.txt"):
f = open(self.path+"/toc.txt", "r")
elif os.path.exists(self.path+"/ToC.txt"):
f = open(self.path+"/ToC.txt", "r")
if f:
self.ToC = {int(z[0]):z[1] for z in [x.split() for x in f.readlines()]}
f.close()
val = 200 # value used for the colors
# colors used for the plot lines
self.colors = [(0, 0, val), (0, val, 0), (val, 0, 0),\
(val, val, 0), (val, 0, val), (0, val, val)]
# Add the found data to the combo box
self.populateUI()
# QT: SIGNALS -> SLOTS
# This set which function is called when buttons, checkboxes, etc. are clicked
self.ui.comboBox.currentIndexChanged.connect(self.updateSTSid)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.ui.DV.valueChanged.connect(self.plotUpdate)
self.ui.statCB.stateChanged.connect(self.plotUpdate)
self.ui.normCB.stateChanged.connect(self.plotUpdate)
self.ui.pushButton.clicked.connect(self.InfoShowHideToggle)
self.ui.saveBT.clicked.connect(self.export)
self.InfoShowHideToggle('Hide')
self.updateSTSid()
if len(sys.argv) > 2:
ID = sys.argv[2]
self.ui.comboBox.setCurrentIndex(\
self.ui.comboBox.findText(ID,QtCore.Qt.MatchStartsWith))
self.plotUpdate()
def InfoShowHideToggle(self, action='Toggle'):
"""
Show a TreeWidget containing the details of a STS scan.
"""
if action == 'Hide' or self.ui.treeWidget.isVisible():
self.ui.treeWidget.hide()
self.ui.pushButton.setText("<<")
else:
self.ui.treeWidget.show()
self.ui.pushButton.setText(">>")
def populateUI(self):
"""
Look for I(V) measurements and add them to the combobox list
"""
self.STS = {}
self.hasDIDV = []
for i in self.M.images:
r = re.search(r"--([0-9]+)_([0-9]+).I\(V\)_mtrx", i)
if r and os.path.exists(self.path+"/"+i):
j = int(r.group(1))
if j in self.STS:
self.STS[j] += 1
else:
self.STS[j] = 1
if i[:-9]+self.DIext+'(V)_mtrx' in self.M.images:
self.hasDIDV.append(j)
for i in self.STS:
if self.ToC != None and i in self.ToC:
self.ui.comboBox.addItem(str(i)+" (%s)"%(self.ToC[i]))
else:
self.ui.comboBox.addItem(str(i))
def updateSTSid(self):
"""
If and ID is chosen, the listWidget will be populated with the correct num and selected
"""
if self.ui.comboBox.currentIndex() == -1:
raise ValueError("No Data found!")
self.ui.listWidget.itemChanged.disconnect()
self.ui.listWidget.clear()
ID = int(self.ui.comboBox.currentText().split(' ')[0])
for i in range(self.STS[ID]):
item = QtGui.QListWidgetItem()
item.setText(str(i+1)+" -----")
item.setTextColor(QtGui.QColor(*self.colors[i%len(self.colors)]))
item.setFlags(item.flags()|QtCore.Qt.ItemIsUserCheckable)
self.ui.listWidget.addItem( item )
item.setCheckState(QtCore.Qt.Checked)
self.ui.listWidget.itemChanged.connect(self.plotUpdate)
self.plotUpdate()
def updateModel(self, value, item=None):
"""
Gather information about the STS measurement and populate the treeWidget (the one hidden on the right of the screen)
"""
if item == None:
self.ui.treeWidget.clear()
item = self.ui.treeWidget.invisibleRootItem()
if type(value) is dict:
if 'value' in value and 'unit' in value:
child = QtGui.QTreeWidgetItem()
if value['unit'] == '--':
child.setText(0,str(value['value']))
else:
child.setText(0,str(value['value'])+" "+str(value['unit']))
item.addChild(child)
else:
for key, val in sorted(value.items()):
child = QtGui.QTreeWidgetItem()
child.setText(0, key)
item.addChild(child)
self.updateModel(val, child)
elif type(value) is list:
for val in value:
child = QtGui.QTreeWidgetItem()
item.addChild(child)
if type(val) is dict:
child.setText(0, '[dict]')
self.updateModel(val, child)
elif type(val) is list:
child.setText(0, '[list]')
self.updateModel(val, child)
else:
child.setText(0, str(val))
child.setExpanded(True)
else:
child = QtGui.QTreeWidgetItem()
child.setText(0, str(value))
item.addChild(child)
def export(self):
"""
Toggle the flag to save the data
"""
self.save = True
self.plotUpdate()
self.save = False
def plotUpdate(self):
"""
Most important function which is retrieving and plotting the data
"""
# Clear the plot
self.ax1.clear()
self.ax1b.clear()
self.ax2.clear()
self.ax3.clear()
self.ax3b.clear()
# Setting labels and axis
self.ax1.set_xlabel("Bias [V]", fontsize=FontSize)
self.ax2.set_xlabel("Bias [V]", fontsize=FontSize)
self.ax1.set_ylabel("Current [pA]", fontsize=FontSize)
self.ax1b.set_ylabel("dI/dV [pA/V]", fontsize=FontSize)
self.ax2.set_ylabel(r'$\frac{dI/dV}{\overline{I/V}}$', fontsize=FontSize)
self.ax3.set_xlabel("Bias [V]", fontsize=FontSize)
self.ax3.set_ylabel("I/V [$\mu$A/V]", fontsize=FontSize)
self.ax3b.yaxis.label.set_color("green")
self.ax3b.tick_params(axis='y', colors="green")
# plot the selected curves
ID = int(self.ui.comboBox.currentText().split(' ')[0])
paramsShowed = False
stat = False
norm = False
# If checkbox "statistics" is checked, then variable stat=True
if self.ui.statCB.isChecked():
stat = True
if self.ui.normCB.isChecked():
norm = True
counter = 0
NumShown = []
for i in range(self.STS[ID]): # Scan over all STS having the same ID
if self.ui.listWidget.item(i).checkState() == QtCore.Qt.Checked: # Is the curve selected by the user to be plotted?
NumShown.append(i+1) # Store in a list which num will be displayed
# Retrieve the STS data for the ID and num=i+1
V, I, IM = self.M.getSTS(ID, i+1, params=True)
NPTS = int(IM['Spectroscopy']['Device_1_Points']['value']) # Number of points in the V range
DV = self.ui.DV.value()
Vstep = (IM['Spectroscopy']['Device_1_End']['value']-IM['Spectroscopy']['Device_1_Start']['value'])/float(NPTS)
skip = int(np.ceil(DV/Vstep))
if not paramsShowed:
paramsShowed = True
p = self.M.getSTSparams(ID, i+1)
self.updateModel(p)
N = (0, NPTS)
# The follwing variables store matrices of the various signals as a list. The first element of the list is for the Up scans and the second for Down scans
Im = [np.empty(N), np.empty(N)] # Current: I
dIm = [np.empty(N), np.empty(N)] # dI/dV
IVm = [np.empty((0, NPTS+2*skip)), np.empty((0, NPTS+2*skip))] # I/V
BIVm = [np.empty(N), np.empty(N)] # Broadened I/V (BIV)
dIdVIVm = [np.empty(N), np.empty(N)] # (dI/dV)/BIV
# reconstruct the voltage array
sV = np.linspace(min(V), max(V), NPTS) # Voltage values in increading order
if len(I) < NPTS: # Missing data
I = np.pad(I, NPTS, 'constant', constant_values=np.nan)
elif len(I) > NPTS: # Forward & Backward scan
if V[1] < V[0]: # Start with Downward scan
IUp = I[NPTS:]
IDown = I[NPTS-1::-1] # flip first part of the data
else:
IUp = I[:NPTS]
IDown = I[-1:NPTS-1:-1] # Flip second part of the data
if len(IDown) < NPTS: # Missing data
IDown = np.pad(IDown, NPTS, 'constant', constant_values=np.nan)
Im[0] = np.vstack((Im[0], IUp)) # Im[0] contains the Up scans
Im[1] = np.vstack((Im[1], IDown)) # Im[1] contains the Down scans
if not stat:
self.ax1.plot(sV, IUp*1e-6,\
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),\
label="I%i (->)"%(i))
if not stat:
self.ax1.plot(sV, IDown*1e-6, '--',\
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),\
label="I%i (<-)"%(i))
else:
if V[0] == min(V):
Im[0] = np.vstack((Im[0], I))
else:
Im[1] = np.vstack((Im[1], I))
if not stat:
self.ax1.plot(V, I*1e-6,\
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),\
label="I%i"%(i))
if ID in self.hasDIDV:
V2, dI = self.M.getSTS(ID, i+1, self.DIext)
if norm:
dI -= dI.min()
if len(I) > NPTS: # Forward & Backward scan
if V[1] < V[0]: # Start with Downward scan
dIUp = dI[NPTS:]
dIDown = dI[NPTS-1::-1]
else:
dIUp = dI[:NPTS]
dIDown = dI[-1:NPTS-1:-1]
dIm[0] = np.vstack((dIm[0], dIUp))
dIm[1] = np.vstack((dIm[1], dIDown))
Is = [IUp, IDown]
dIs = [dIUp, dIDown]
else:
Is = [I]
dIs = [dI]
if V[0] == min(V):
dIm[0] = np.vstack((dIm[0], dI))
else:
dIm[1] = np.vstack((dIm[1], dI))
for ud in range(len(Is)):
if len(dIs[ud]) < NPTS:
dIs[ud] = np.pad(dIs[ud], NPTS, 'constant', constant_values=np.nan)
if not stat:
self.ax1b.plot(sV, dIs[ud]*1e-6, [':','-.'][ud],\
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),\
label="dI%i (%s)"%(i,['->', '<-'][ud]))
delta = NPTS-len(Is[ud])
if delta > 0:
if V[1] > V[0]: # problem on the downscan
sV = sV[delta:]
else:
sV = sV[:-delta]
S = STS(sV, Is[ud], DV)
IV = S.getIV()
BIV = S.getBIV()
W = S.getW()
nV = S.getnV()
IVm[ud] = np.vstack((IVm[ud], IV))
BIVm[ud] = np.vstack((BIVm[ud], BIV))
dIdVIVm[ud] = np.vstack((dIdVIVm[ud], dIs[ud]/BIV))
if not stat:
self.ax3.plot(nV, 1e-12*IV, ['b', '--b'][ud],\
label="I/V (%s)"%(["->", "<-"][ud]))
if not stat:
self.ax3.plot(sV, 1e-12*BIV, ['r','--r'][ud],\
label="$\overline{I/V}$ (%s)"%(["->", "<-"][ud]))
if ud==0:
self.ax3b.plot(nV, W, 'g', label="conv. func.")
if not stat:
self.ax2.plot(sV, dIs[ud]/BIV, ['-', '--'][ud],\
color="#{0:02x}{1:02x}{2:02x}".format(*self.colors[i%len(self.colors)]),\
label="(%s)"%(['->', '<-'][ud]))
if self.save:
# Saving the data
X = np.vstack((sV, Im[0], dIm[0], Im[1], dIm[1], dIdVIVm[0], dIdVIVm[1]))
header = "DV=%.3fV\nV\t"%(DV)
header += "\t".join(["I{}_Up(V)".format(i) for i in NumShown])
header += "\t"+"\t".join(["dI{}/dV_Up".format(i) for i in NumShown])
header += "\t"+"\t".join(["I{}_Down(V)".format(i) for i in NumShown])
header += "\t"+"\t".join(["dI{}/dV_Down".format(i) for i in NumShown])
header += "\t"+"\t".join(["(dI{}_Up/dV)/(I/V)".format(i) for i in NumShown])
header += "\t"+"\t".join(["(dI{}_Down/dV)/(I/V)".format(i) for i in NumShown])
np.savetxt("STS_%i.dat"%(ID), X.transpose(), header=header)
if stat: # If statistic checkbox is enabled
for ud in range(2):
if Im[ud].shape[0] == 0:
continue
fmt = ['-', '--'][ud]
col1 = ['blue', 'purple'][ud]
col2 = ['red', 'orange'][ud]
col3 = ['green', 'green'][ud]
Imm = Im[ud].mean(axis=0)
Ims = Im[ud].std(axis=0)
dImm = dIm[ud].mean(axis=0)
dIms = dIm[ud].std(axis=0)
dIVm = dIdVIVm[ud].mean(axis=0)
dIVs = dIdVIVm[ud].std(axis=0)
IVmm = IVm[ud].mean(axis=0)
IVms = IVm[ud].std(axis=0)
BIVmm = BIVm[ud].mean(axis=0)
BIVms = BIVm[ud].std(axis=0)
self.plot_err1(self.ax1, sV, Imm, Ims, col1)
try:
self.plot_err1(self.ax1b, sV, dImm, dIms, col2)
self.plot_err1(self.ax2, sV, dIVm, dIVs, col1)
self.plot_err1(self.ax3, nV, IVmm, IVms, col1)
except:
pass # No DI signal
self.ax3.plot(sV, BIVmm, color=col2)
self.ax3.fill_between(sV, BIVmm-BIVms, BIVmm+BIVms, facecolor=col2, alpha=0.3)
self.ax3.fill_between(sV, BIVmm-2*BIVms, BIVmm+2*BIVms, facecolor=col2, alpha=0.2)
for x in [self.ax1,self.ax1b,self.ax2,self.ax3,self.ax3b]:
x.tick_params(axis='both', labelsize=FontSize)
self.canvas.draw()
