def get_spectrogram(wav: WavFile, graphics_layout: pyqtgraph.GraphicsLayoutWidget):
f, t, Sxx = signal.spectrogram(wav.data, wav.rate)
# Interpret image data as row-major instead of col-major
pyqtgraph.setConfigOptions(imageAxisOrder='row-major')
pyqtgraph.mkQApp()
graphics_layout.clear()
plot_widget = graphics_layout.addPlot()
# A plot area (ViewBox + axes) for displaying the image
# Item for displaying image data
img = pyqtgraph.ImageItem()
plot_widget.addItem(img)
# Add a histogram with which to control the gradient of the image
hist = pyqtgraph.HistogramLUTItem()
# Link the histogram to the image
hist.setImageItem(img)
# If you don't add the histogram to the window, it stays invisible, but I find it useful.
graphics_layout.addItem(hist)
# Show the window
graphics_layout.show()
# Fit the min and max levels of the histogram to the data available
#print("min: "+ str(np.min(Sxx)) + "max:" + str(np.max(Sxx)))
hist.setLevels(0, 40000)
# This gradient is roughly comparable to the gradient used by Matplotlib
# You can adjust it and then save it using hist.gradient.saveState()
hist.gradient.restoreState(
{'mode': 'rgb',
'ticks': [(0.5, (0, 182, 188, 255)),
(1.0, (246, 111, 0, 255)),
(0.0, (75, 0, 113, 255))]})
# Sxx contains the amplitude for each pixel
img.setImage(Sxx)
# Scale the X and Y Axis to time and frequency (standard is pixels)
img.scale(t[-1] / np.size(Sxx, axis=1),
f[-1] / np.size(Sxx, axis=0))
# Limit panning/zooming to the spectrogram
plot_widget.setLimits(xMin=0, xMax=t[-1], yMin=0, yMax=f[-1])
# Add labels to the axis
plot_widget.setLabel('bottom', "Time", units='s')
# If you include the units, Pyqtgraph automatically scales the axis and adjusts the SI prefix (in this case kHz)
plot_widget.setLabel('left', "Frequency", units='Hz')
class MainWidget(QWidget):
def __init__(self):
QWidget.__init__(self)
# define periodic table widget for element selection
self.periodicTableWidget = widgets.PeriodicTableDialog()
# initial molecule Zmatrix (can be empty)
# self.inp = []
self.inp = [['H'],
['O', 1, 0.9],
['O', 2, 1.4, 1, 105.],
['H', 3, 0.9, 2, 105., 1, 120.]]
self.atomList = []
self.highList = []
self.labelList = []
self.fast = False
# define & initialize ZMatModel that will contain Zmatrix data
self.ZMatModel = QStandardItemModel(len(self.inp), 7, self)
self.ZMatTable = QTableView(self)
self.ZMatTable.setModel(self.ZMatModel)
self.ZMatTable.setFixedWidth(325)
#self.ZMatTable.installEventFilter(self)
#self.ZMatModel.installEventFilter(self)
self.ZMatModel.setHorizontalHeaderLabels(['atom','','bond','','angle','','dihedral'])
for j, width in enumerate([40, 22, 65, 22, 65, 22, 65]):
self.ZMatTable.setColumnWidth(j, width)
# populate the ZMatModel
self.populateZMatModel()
#define Menu bar menus and their actions
self.menuBar = QMenuBar(self)
fileMenu = self.menuBar.addMenu('&File')
editMenu = self.menuBar.addMenu('&Edit')
viewMenu = self.menuBar.addMenu('&View')
measureMenu = self.menuBar.addMenu('&Measure')
helpMenu = self.menuBar.addMenu('&Help')
readZmatAction = QAction('&Read &ZMat', self)
readZmatAction.setShortcut('Ctrl+O')
readZmatAction.setStatusTip('Read Zmat from file')
readZmatAction.triggered.connect(self.readZmat)
fileMenu.addAction(readZmatAction)
readXYZAction = QAction('&Read &XYZ', self)
readXYZAction.setShortcut('Ctrl+Shift+O')
readXYZAction.setStatusTip('Read XYZ from file')
readXYZAction.triggered.connect(self.readXYZ)
fileMenu.addAction(readXYZAction)
readGaussianAction = QAction('&Read &Gaussian log', self)
readGaussianAction.setShortcut('Ctrl+G')
readGaussianAction.setStatusTip('Read Gaussian log file')
readGaussianAction.triggered.connect(self.readGaussian)
fileMenu.addAction(readGaussianAction)
writeZmatAction = QAction('&Write &ZMat', self)
writeZmatAction.setShortcut('Ctrl+S')
writeZmatAction.setStatusTip('Write Zmat to file')
writeZmatAction.triggered.connect(self.writeZmat)
fileMenu.addAction(writeZmatAction)
writeXYZAction = QAction('&Write &XYZ', self)
writeXYZAction.setShortcut('Ctrl+Shift+S')
writeXYZAction.setStatusTip('Write XYZ from file')
writeXYZAction.triggered.connect(self.writeXYZ)
fileMenu.addAction(writeXYZAction)
exitAction = QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(qApp.quit)
fileMenu.addAction(exitAction)
addRowAction = QAction('&Add &row', self)
addRowAction.setShortcut('Ctrl+R')
addRowAction.setStatusTip('Add row to ZMatrix')
addRowAction.triggered.connect(self.addRow)
editMenu.addAction(addRowAction)
deleteRowAction = QAction('&Delete &row', self)
deleteRowAction.setShortcut('Ctrl+Shift+R')
deleteRowAction.setStatusTip('Delete row from ZMatrix')
deleteRowAction.triggered.connect(self.deleteRow)
editMenu.addAction(deleteRowAction)
addAtomAction = QAction('&Add &atom', self)
addAtomAction.setShortcut('Ctrl+A')
addAtomAction.setStatusTip('Add atom to ZMatrix')
addAtomAction.triggered.connect(self.buildB)
editMenu.addAction(addAtomAction)
drawModeMenu = QMenu('Draw mode', self)
viewMenu.addMenu(drawModeMenu)
fastDrawAction = QAction('&Fast draw', self)
fastDrawAction.triggered.connect(self.fastDraw)
normalDrawAction = QAction('&Normal draw', self)
normalDrawAction.triggered.connect(self.normalDraw)
drawModeMenu.addAction(normalDrawAction)
drawModeMenu.addAction(fastDrawAction)
clearHighlightsAction = QAction('&Clear selection', self)
clearHighlightsAction.setShortcut('Ctrl+C')
clearHighlightsAction.setStatusTip('Clear highlighted atoms')
clearHighlightsAction.triggered.connect(self.clearHighlights)
viewMenu.addAction(clearHighlightsAction)
clearLabelsAction = QAction('&Clear labels', self)
clearLabelsAction.setShortcut('Ctrl+Alt+C')
clearLabelsAction.setStatusTip('Clear labels')
clearLabelsAction.triggered.connect(self.clearLabels)
viewMenu.addAction(clearLabelsAction)
clearUpdateViewAction = QAction('&Clear selection and labels', self)
clearUpdateViewAction.setShortcut('Ctrl+Shift+C')
clearUpdateViewAction.setStatusTip('Clear highlighted atoms and labels')
clearUpdateViewAction.triggered.connect(self.clearUpdateView)
viewMenu.addAction(clearUpdateViewAction)
self.showGaussAction = QAction('Show &Gaussian geometry optimization', self)
self.showGaussAction.setShortcut('Ctrl+G')
self.showGaussAction.setStatusTip('Show Gaussian geometry optimization plots for energy, force and displacement.')
self.showGaussAction.setEnabled(False)
self.showGaussAction.triggered.connect(self.showGauss)
viewMenu.addAction(self.showGaussAction)
self.showFreqAction = QAction('Show &IR frequency plot', self)
self.showFreqAction.setShortcut('Ctrl+I')
self.showFreqAction.setStatusTip('Show Gaussian calculated IR frequency plot.')
self.showFreqAction.setEnabled(False)
self.showFreqAction.triggered.connect(self.showFreq)
viewMenu.addAction(self.showFreqAction)
measureDistanceAction = QAction('&Measure &distance', self)
measureDistanceAction.setShortcut('Ctrl+D')
measureDistanceAction.setStatusTip('Measure distance between two atoms')
measureDistanceAction.triggered.connect(self.measureDistanceB)
measureMenu.addAction(measureDistanceAction)
measureAngleAction = QAction('&Measure &angle', self)
measureAngleAction.setShortcut('Ctrl+Shift+D')
measureAngleAction.setStatusTip('Measure angle between three atoms')
measureAngleAction.triggered.connect(self.measureAngleB)
measureMenu.addAction(measureAngleAction)
aboutAction = QAction('&About', self)
aboutAction.setStatusTip('About this program...')
aboutAction.triggered.connect(self.about)
helpMenu.addAction(aboutAction)
aboutQtAction = QAction('&About Qt', self)
aboutQtAction.setStatusTip('About Qt...')
aboutQtAction.triggered.connect(self.aboutQt)
helpMenu.addAction(aboutQtAction)
# define GL widget that displays the 3D molecule model
self.window = widgets.MyGLView()
self.window.installEventFilter(self)
self.window.setMinimumSize(500, 500)
#self.window.setBackgroundColor((50, 0, 10))
self.updateView()
self.gaussianPlot = GraphicsLayoutWidget()
self.gaussianPlot.resize(750, 250)
self.gaussianPlot.setWindowTitle('Gaussian geometry optimization')
#self.gaussianPlot.setAspectLocked(True)
#self.gaussianPlot.addLayout(rowspan=3, colspan=1)
self.FreqModel = QStandardItemModel(1, 3, self)
self.freqTable = QTableView(self)
self.freqTable.setModel(self.FreqModel)
self.freqTable.setMinimumWidth(240)
self.freqTable.installEventFilter(self)
self.FreqModel.installEventFilter(self)
self.FreqModel.setHorizontalHeaderLabels(['Frequency','IR Intensity','Raman Intensity'])
for j, width in enumerate([80, 80, 80]):
self.freqTable.setColumnWidth(j, width)
self.freqWidget = QWidget()
self.freqWidget.setWindowTitle('IR frequency plot & table')
self.freqWidget.resize(800, 400)
self.freqWidget.layout = QHBoxLayout(self.freqWidget)
self.freqWidget.layout.setSpacing(1)
self.freqWidget.layout.setContentsMargins(1, 1, 1, 1)
self.freqPlot = GraphicsLayoutWidget()
self.freqWidget.layout.addWidget(self.freqPlot)
self.freqWidget.layout.addWidget(self.freqTable)
self.freqTable.clicked.connect(self.freqCellClicked)
# define other application parts
self.statusBar = QStatusBar(self)
self.fileDialog = QFileDialog(self)
# define application layout
self.layout = QVBoxLayout(self)
self.layout.setSpacing(1)
self.layout.setContentsMargins(1, 1, 1, 1)
self.layout1 = QHBoxLayout()
self.layout1.setSpacing(1)
self.layout1.addWidget(self.ZMatTable)
self.layout1.addWidget(self.window)
self.layout.addWidget(self.menuBar)
self.layout.addLayout(self.layout1)
self.layout.addWidget(self.statusBar)
self.adjustSize()
self.setWindowTitle('Moldy')
iconPath = 'icon.png'
icon = QIcon(iconPath)
icon.addFile(iconPath, QSize(16, 16))
icon.addFile(iconPath, QSize(24, 24))
icon.addFile(iconPath, QSize(32, 32))
icon.addFile(iconPath, QSize(48, 48))
icon.addFile(iconPath, QSize(256, 256))
self.setWindowIcon(icon)
# start monitoring changes in the ZMatModel
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
# run and show the application
def run(self):
self.show()
self.ZMatTable.clicked.connect(self.ZMatCellClicked)
qt_app.instance().aboutToQuit.connect(self.deleteGLwidget)
qt_app.exec_()
# fill the ZMatModel with initial data from 'self.inp'
def populateZMatModel(self):
self.ZMatModel.removeRows(0, self.ZMatModel.rowCount())
for i, row in enumerate(self.inp):
for j, cell in enumerate(row):
item = QStandardItem(str(cell))
self.ZMatModel.setItem(i, j, item)
# some cells should not be editable, they are disabled
for i in range(min(len(self.inp), 3)):
for j in range(2*i+1, 7):
self.ZMatModel.setItem(i, j, QStandardItem())
self.ZMatModel.item(i, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(i, j).setFlags(Qt.ItemIsEnabled)
def populateFreqModel(self):
self.FreqModel.removeRows(0, self.FreqModel.rowCount())
for i, row in enumerate(zip(self.vibfreqs, self.vibirs, self.vibramans)):
for j, cell in enumerate(row):
item = QStandardItem(str(cell))
self.FreqModel.setItem(i, j, item)
# add a row to the bottom of the ZMatModel
def addRow(self):
# temporarily stop updating the GL window
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
row = self.ZMatModel.rowCount()
self.ZMatModel.insertRow(row)
# some cells should not be editable
if row < 3:
for j in range(2*row+1, 7):
self.ZMatModel.setItem(row, j, QStandardItem())
self.ZMatModel.item(row, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(row, j).setFlags(Qt.ItemIsEnabled)
# restart GL window updating
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.statusBar.clearMessage()
self.statusBar.showMessage('Added 1 row.', 3000)
# delete the last row of the ZMatModel
def deleteRow(self):
xyz = [list(vi) for vi in list(v)]
atoms = [str(elements[e]) for e in elems]
oldLen = self.ZMatModel.rowCount()
idxs = sorted(set(idx.row() for idx in self.ZMatTable.selectedIndexes()), reverse=True)
newLen = oldLen - len(idxs)
if newLen == oldLen:
self.ZMatModel.removeRow(self.ZMatModel.rowCount()-1)
else:
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
for idx in idxs:
self.ZMatModel.removeRow(idx)
if idx < 3:
for i in range(idx, min(3, newLen)):
for j in range(2*i+1, 7):
self.ZMatModel.setItem(i, j, QStandardItem())
self.ZMatModel.item(i, j).setBackground(QColor(150,150,150))
self.ZMatModel.item(i, j).setFlags(Qt.ItemIsEnabled)
if len(xyz) > idx:
xyz.pop(idx)
atoms.pop(idx)
self.inp = xyz2zmat(xyz, atoms)
self.populateZMatModel()
for i in reversed(self.highList):
self.window.removeItem(i[1])
self.highList = []
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
if idxs:
self.statusBar.showMessage('Deleted row(s): '+str([i+1 for i in idxs]), 3000)
else:
self.statusBar.showMessage('Deleted last row.', 3000)
# show the periodic table widget
def periodicTable(self):
self.statusBar.clearMessage()
self.statusBar.showMessage('Select element from periodic table.')
self.periodicTableWidget.exec_()
selection = self.periodicTableWidget.selection()
return selection
# import molecule with zmatrix coordinates
def readZmat(self):
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.zmat;;*.*')
self.inp = []
self.populateZMatModel()
if filename:
with open(filename, 'r') as f:
next(f)
next(f)
for row in f:
self.inp.append(row.split())
f.close()
self.populateZMatModel()
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.showGaussAction.setEnabled(False)
self.showFreqAction.setEnabled(False)
# import molecule with xyz coordinates
def readXYZ(self):
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.xyz;;*.*')
xyz = []
elems = []
self.inp = []
self.populateZMatModel()
if filename:
with open(filename, 'r') as f:
next(f)
next(f)
for row in f:
rs = row.split()
if len(rs) == 4:
elems.append(rs[0])
xyz.append([float(f) for f in rs[1:]])
f.close()
self.inp = xyz2zmat(xyz, elems)
self.populateZMatModel()
#print(elems)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.showGaussAction.setEnabled(False)
self.showFreqAction.setEnabled(False)
# import Gaussian log file
def readGaussian(self):
global vsShifted
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
filename = self.fileDialog.getOpenFileName(self, 'Open file', expanduser('~'), '*.log;;*.*')
if filename:
self.gaussianPlot.clear()
self.inp = []
self.populateZMatModel()
file = ccopen(filename)
data = file.parse().getattributes()
self.natom = data['natom']
self.atomnos = data['atomnos'].tolist()
self.atomsymbols = [ str(elements[e]) for e in self.atomnos ]
self.atomcoords = data['atomcoords'].tolist()
self.scfenergies = data['scfenergies'].tolist()
self.geovalues = data['geovalues'].T.tolist()
self.geotargets = data['geotargets'].tolist()
if 'vibfreqs' in data.keys():
self.vibfreqs = data['vibfreqs']
#print(self.vibfreqs)
self.vibirs = data['vibirs']
#print(self.vibirs)
#print(data.keys())
if 'vibramans' in data.keys():
self.vibramans = data['vibramans']
else:
self.vibramans = [''] * len(self.vibirs)
self.vibdisps = data['vibdisps']
#print(self.vibdisps)
self.inp = xyz2zmat(self.atomcoords[0], self.atomsymbols)
self.populateZMatModel()
titles = ['SCF Energies', 'RMS & Max Forces', 'RMS & Max Displacements']
for i in range(3):
self.gaussianPlot.addPlot(row=1, col=i+1)
plot = self.gaussianPlot.getItem(1, i+1)
plot.setTitle(title=titles[i])
if i == 0:
c = ['c']
x = [0]
y = [self.scfenergies]
else:
c = ['r', 'y']
x = [0, 0]
y = [self.geovalues[2*i-2], self.geovalues[2*i-1]]
targety = [self.geotargets[2*i-2], self.geotargets[2*i-1]]
plot.clear()
plot.maxData = plot.plot(y[0], symbol='o', symbolPen=c[0], symbolBrush=c[0], pen=c[0], symbolSize=5, pxMode=True, antialias=True, autoDownsample=False)
plot.highlight=plot.plot(x, [ yy[0] for yy in y ], symbol='o', symbolPen='w', symbolBrush=None, pen=None, symbolSize=15, pxMode=True, antialias=True, autoDownsample=False)
plot.maxData.sigPointsClicked.connect(self.gausclicked)
if i > 0:
for j in range(2):
plot.addLine(y=np.log10(targety[j]), pen=mkPen((255, 255*j, 0, int(255/2)), width=1))
plot.RMSData=plot.plot(y[1], symbol='o', symbolPen=c[1], symbolBrush=c[1], pen=c[1], symbolSize=5, pxMode=True, antialias=True, autoDownsample=False)
plot.RMSData.sigPointsClicked.connect(self.gausclicked)
plot.setLogMode(y=True)
self.showGauss()
self.updateView()
self.statusBar.clearMessage()
self.statusBar.showMessage('Read molecule from '+filename+'.', 5000)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
if self.natom:
self.showGaussAction.setEnabled(True)
if 'vibfreqs' in data.keys():
self.showFreqAction.setEnabled(True)
# populate the FreqModel
self.populateFreqModel()
self.freqPlot.clear()
irPlot = self.freqPlot.addPlot(row=1, col=1)
irPlot.clear()
minFreq = np.min(self.vibfreqs)
maxFreq = np.max(self.vibfreqs)
maxInt = np.max(self.vibirs)
x = np.sort(np.concatenate([np.linspace(minFreq-100, maxFreq+100, num=1000), self.vibfreqs]))
y = x*0
for f,i in zip(self.vibfreqs, self.vibirs):
y += lorentzv(x, f, 2*np.pi, i)
#xy = np.array([np.concatenate([x, np.array(self.vibfreqs)]), np.concatenate([y, np.array(self.vibirs)])]).T
#xysort = xy[xy[:,0].argsort()]
irPlot.maxData = irPlot.plot(x, y, antialias=True)
markers = ErrorBarItem(x=self.vibfreqs, y=self.vibirs, top=maxInt/30, bottom=None, pen='r')
irPlot.addItem(markers)
self.showFreq()
#self.vibdisps = np.append(self.vibdisps, [np.mean(self.vibdisps, axis=0)], axis=0)
maxt = 100
vsShifted = np.array([ [ vs + self.vibdisps[i]*np.sin(t*2*np.pi/maxt)/3 for t in range(maxt) ] for i in range(len(self.vibfreqs)) ])
else:
self.showFreqAction.setEnabled(False)
self.freqWidget.hide()
def showGauss(self):
self.gaussianPlot.show()
def showFreq(self):
self.freqWidget.show()
# export Zmatrix to csv
def writeZmat(self):
zm = model2list(self.ZMatModel)
filename = self.fileDialog.getSaveFileName(self, 'Save file', expanduser('~')+'/'+getFormula(list(list(zip(*zm))[0]))+'.zmat', '*.zmat;;*.*')
try:
filename
except NameError:
pass
else:
if filename:
writeOutput(zm, filename)
self.statusBar.clearMessage()
self.statusBar.showMessage('Wrote molecule to '+filename+'.', 5000)
# export XYZ coordinates to csv
def writeXYZ(self):
xyz = []
zm = model2list(self.ZMatModel)
for i in range(len(v)):
xyz.append(np.round(v[i], 7).tolist())
xyz[i][:0] = zm[i][0]
if len(v) > 0:
formula = getFormula(list(list(zip(*xyz))[0]))
else:
formula = 'moldy_output'
filename = self.fileDialog.getSaveFileName(self, 'Save file', expanduser('~')+'/'+formula+'.xyz', '*.xyz;;*.*')
try:
filename
except NameError:
pass
else:
if filename:
writeOutput(xyz, filename)
self.statusBar.clearMessage()
self.statusBar.showMessage('Wrote molecule to '+filename+'.', 5000)
# redraw the 3D molecule in GL widget
def updateView(self):
global r
global c
global v
global vs
global elems
global nelems
data = model2list(self.ZMatModel)
try:
# create a list with element coordinates
v = zmat2xyz(data)
except (AssertionError, IndexError, ZMError):
pass
else:
# clear the screen before redraw
for item in reversed(self.window.items):
self.window.removeItem(item)
# create a second coordinate list 'vs' that is centered in the GL view
self.atomList = []
if len(v) > 0:
shift = np.mean(v, axis=0)
vs = np.add(v, -shift)
elems = [ 1 + next((i for i, sublist in enumerate(colors) if row[0] in sublist), -1) for row in data ]
nelems = len(elems)
# define molecule radii and colors
r = []
c = []
for i in elems:
r.append(elements[i].covalent_radius)
c.append(colors[i-1][-1])
# draw atoms
for i in range(nelems):
addAtom(self.window, i, r, vs, c, fast=self.fast)
self.atomList.append([i, self.window.items[-1]])
#print(self.atomList)
# draw bonds where appropriate
combs = list(itertools.combinations(range(nelems), 2))
bonds = []
for i in combs:
bonds.append(addBond(self.window, i[0], i[1], r, vs, c, fast=self.fast))
if self.fast:
bondedAtoms = set(filter((None).__ne__, flatten(bonds)))
for i in set(range(nelems)) - bondedAtoms:
addUnbonded(self.window, i, vs, c)
self.atomList[i][1]=self.window.items[-1]
#print(self.atomList)
for i in self.highList:
self.window.addItem(i[1])
for i in self.labelList:
self.window.addItem(i)
if len(v) > 1:
maxDim = float('-inf')
for dim in v.T:
span = max(dim)-min(dim)
if span > maxDim:
maxDim = span
else: maxDim = 2
self.window.setCameraPosition(distance=maxDim*1.5+1)
global index
index = 0
def updateFreq(self):
global vsShifted, index, r, c
index += 1
index = index % len(vsShifted[0])
#print(index)
#print(vsShifted[index])
for item in reversed(self.window.items):
self.window.removeItem(item)
for i in range(nelems):
addAtom(self.window, i, r, vsShifted[self.freqIndex, index], c, fast=self.fast)
self.atomList.append([i, self.window.items[-1]])
combs = itertools.combinations(range(nelems), 2)
bonds = []
for i in combs:
bonds.append(addBond(self.window, i[0], i[1], r, vsShifted[self.freqIndex, index], c, fast=self.fast))
if self.fast:
bondedAtoms = set(filter((None).__ne__, flatten(bonds)))
for i in set(range(nelems)) - bondedAtoms:
addUnbonded(self.window, i, vsShifted[self.freqIndex, index], c)
self.atomList[i][1]=self.window.items[-1]
# detect mouse clicks in GL window and process them
def eventFilter(self, obj, event):
if obj == self.window:
if event.type() == event.MouseButtonPress:
itms = obj.itemsAt((event.pos().x()-2, event.pos().y()-2, 4, 4))
if len(itms):
self.highlight(obj, [itms[0]])
elif len(self.atomList) == 0:
self.build()
# also do the default click action
return super(MainWidget, self).eventFilter(obj, event)
def ZMatCellClicked(self):
idxs = sorted(set(idx.row() for idx in self.ZMatTable.selectedIndexes()), reverse=True)
itms = []
if self.highList:
highIdx = list(np.array(self.highList).T[0])
for idx in idxs:
if self.highList and idx in highIdx:
itms.append(self.highList[highIdx.index(idx)][1])
elif len(self.atomList) > idx:
itms.append(self.atomList[idx][1])
self.highlight(self.window, itms)
def freqCellClicked(self):
global vsShifted
self.timer = QTimer()
self.timer.setInterval(30)
self.timer.timeout.connect(self.updateFreq)
idxs = [ idx.row() for idx in self.freqTable.selectedIndexes() ]
if len(idxs) == 1:
self.freqIndex = idxs[0]
self.timer.stop()
self.timer.timeout.connect(self.updateFreq)
try:
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
except TypeError:
pass
self.timer.start()
if len(idxs) != 1:
self.timer.stop()
self.freqTable.clearSelection()
self.timer.timeout.disconnect(self.updateFreq)
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.clearUpdateView()
def gausclicked(self, item, point):
itemdata = item.scatter.data
points = [ row[7] for row in itemdata ]
idx = points.index(point[0])
for i in range(3):
if i == 0:
x = [idx]
y = [self.scfenergies[idx]]
else:
x = [idx, idx]
y = [self.geovalues[2*i-2][idx], self.geovalues[2*i-1][idx]]
plot = self.gaussianPlot.getItem(1, i+1)
plot.removeItem(plot.highlight)
plot.highlight=plot.plot(x, y, symbol='o', symbolPen='w', symbolBrush=None, pen=None, symbolSize=15, pxMode=True, antialias=True, autoDownsample=False)
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
self.inp = []
self.populateZMatModel()
self.inp = xyz2zmat(self.atomcoords[min(idx, len(self.atomcoords)-1)], self.atomsymbols)
self.populateZMatModel()
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
def highlight(self, obj, itms):
for itm in itms:
idx = next((i for i, sublist in enumerate(self.atomList) if itm in sublist), -1)
#print(idx)
if idx != -1:
addAtom(obj, idx, r, vs, c, opt='highlight', fast=self.fast)
self.highList.append([idx, obj.items[-1]])
self.ZMatTable.selectRow(idx)
idx = next((i for i, sublist in enumerate(self.highList) if itm in sublist), -1)
if idx != -1:
obj.removeItem(self.highList[idx][1])
self.highList.pop(idx)
self.ZMatTable.clearSelection()
self.statusBar.clearMessage()
if len(self.highList) > 0:
idxs = np.asarray(self.highList).T[0]
selected = []
for i in idxs:
selected.append(str(i+1)+str(elements[elems[i]]))
self.statusBar.showMessage('Selected atoms: '+str(selected), 5000)
def buildB(self):
try:
nelems
except NameError:
self.build()
else:
if len(self.highList) <= min(nelems, 3):
diff = min(nelems, 3) - len(self.highList)
if diff != 0:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(diff)+' more atom(s).')
else:
self.build()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def build(self):
selection = self.periodicTable()
row = self.ZMatModel.rowCount()
self.addRow()
self.ZMatModel.dataChanged.disconnect(self.clearUpdateView)
newSymbol = selection[1]
newData = [newSymbol]
if len(self.highList) >= 1:
newBond = round(2.1*gmean([ elements[e].covalent_radius for e in [selection[0], elems[self.highList[0][0]]] ]), 4)
newData.append(self.highList[0][0]+1)
newData.append(newBond)
if len(self.highList) >= 2:
newAngle = 109.4712
newData.append(self.highList[1][0]+1)
newData.append(newAngle)
if len(self.highList) == 3:
newDihedral = 120.
newData.append(self.highList[2][0]+1)
newData.append(newDihedral)
for j, cell in enumerate(newData):
item = QStandardItem(str(cell))
self.ZMatModel.setItem(row, j, item)
self.highList = []
self.ZMatModel.dataChanged.connect(self.clearUpdateView)
self.updateView()
def measureDistanceB(self):
sel = len(self.highList)
if sel <= 2:
if sel < 2:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(2-sel)+' more atom(s).')
else:
self.measureDistance()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def measureDistance(self):
pts = []
for pt in self.highList:
pts.append(vs[pt[0]])
pts = np.array(pts)
self.clearHighlights()
line = gl.GLLinePlotItem(pos=pts, color=(0., 1., 0., 1.), width=3)
self.window.addItem(line)
self.labelList.append(line)
q = pts[1]-pts[0]
dist = round(np.sqrt(np.dot(q, q)), 4)
self.window.labelPos.append(np.mean(pts[0:2], axis=0))
self.window.labelText.append(str(dist))
self.statusBar.clearMessage()
self.statusBar.showMessage('Measured distance: '+str(dist)+' A.', 3000)
def measureAngleB(self):
sel = len(self.highList)
if sel <= 3:
if sel < 3:
self.statusBar.clearMessage()
self.statusBar.showMessage('Please select '+str(3-sel)+' more atom(s).')
else:
self.measureAngle()
else:
self.statusBar.clearMessage()
self.statusBar.showMessage('Too many atoms selected.')
def measureAngle(self):
pts = []
for pt in self.highList:
pts.append(vs[pt[0]])
pts = np.array(pts)
q = pts[1]-pts[0]
r = pts[2]-pts[0]
q_u = q / np.sqrt(np.dot(q, q))
r_u = r / np.sqrt(np.dot(r, r))
angle = round(degrees(acos(np.dot(q_u, r_u))), 1)
srange = np.array([slerp(q, r, t) for t in np.arange(0.0, 13/12, 1/12)])
self.clearHighlights()
for i in range(12):
mesh = gl.MeshData(np.array([[0,0,0],srange[i],srange[i+1]]))
tri = gl.GLMeshItem(meshdata=mesh, smooth=False, computeNormals=False, color=(0.3, 1., 0.3, 0.5), glOptions=('translucent'))
tri.translate(pts[0][0], pts[0][1], pts[0][2])
self.window.addItem(tri)
self.labelList.append(tri)
self.window.labelPos.append(slerp(q, r, 0.5)+pts[0])
self.window.labelText.append(str(angle))
self.statusBar.clearMessage()
self.statusBar.showMessage('Measured angle: '+str(angle)+'°', 3000)
def clearLabels(self):
self.window.labelPos = []
self.window.labelText = []
self.labelList = []
self.updateView()
def clearHighlights(self):
for item in reversed(self.highList):
self.window.removeItem(item[1])
self.highList = []
self.updateView()
def clearUpdateView(self):
self.window.labelPos = []
self.window.labelText = []
self.labelList = []
for item in reversed(self.highList):
self.window.removeItem(item[1])
self.highList = []
self.updateView()
#print(self.highList)
def fastDraw(self):
if not self.fast:
self.fast = True
self.updateView()
def normalDraw(self):
if self.fast:
self.fast = False
self.updateView()
def about(self):
QMessageBox.about(self, 'About moldy', 'moldy beta 15. 9. 2015')
def aboutQt(self):
QMessageBox.aboutQt(self, 'About Qt')
def deleteGLwidget(self):
self.window.setParent(None)
del self.window
class MainUi(QMainWindow):
def __init__(self):
super().__init__()
pg.setConfigOption('background', '#19232D')
pg.setConfigOption('foreground', 'd')
pg.setConfigOptions(antialias=True)
# 窗口居中显示
self.center()
self.init_ui()
# 设置城市的编号
self.code = ""
# 多次查询时，查询近5天， 受限于 API 接口提供的数量
self.num = 5
# return request json file
self.rep = ""
# 创建绘图面板
self.plt = []
# 控制绘图的文件名称
self.filename = 1
# 默认的状态栏
# 可以设置其他按钮点击 参考多行文本显示 然而不行
self.status = self.statusBar()
self.status.showMessage("我在主页面～")
# 标题栏
self.setWindowTitle("天气查询软件")
self.setStyleSheet(qdarkstyle.load_stylesheet_pyqt5())
def init_ui(self):
# self.setFixedSize(960,700)
# 创建窗口主部件
self.main_widget = QWidget()
# 创建主部件的网格布局
self.main_layout = QGridLayout()
# 设置窗口主部件布局为网格布局
self.main_widget.setLayout(self.main_layout)
# 创建左侧部件
self.left_widget = QWidget()
self.left_widget.setObjectName('left_widget')
# 创建左侧部件的网格布局层
self.left_layout = QGridLayout()
# 设置左侧部件布局为网格
self.left_widget.setLayout(self.left_layout)
# 创建右侧部件
self.right_widget = QWidget()
self.right_widget.setObjectName('right_widget')
self.right_layout = QGridLayout()
self.right_widget.setLayout(self.right_layout)
# 左侧部件在第0行第0列，占8行3列
self.main_layout.addWidget(self.left_widget, 0, 0, 12, 5)
# 右侧部件在第0行第3列，占8行9列
self.main_layout.addWidget(self.right_widget, 0, 5, 12, 7)
# 设置窗口主部件
self.setCentralWidget(self.main_widget)
# function button
self.single_query = QPushButton("查询今日")
self.single_query.clicked.connect(self.request_weather)
self.single_query.setEnabled(False)
# self.single_query.setFixedSize(400, 30)
self.btn_tempa = QPushButton("温度预测(可绘图)")
self.btn_tempa.clicked.connect(self.request_weather)
self.btn_tempa.setEnabled(False)
self.btn_wind = QPushButton("风力预测(可绘图)")
self.btn_wind.clicked.connect(self.request_weather)
self.btn_wind.setEnabled(False)
self.btn_stawea = QPushButton("综合天气预测")
self.btn_stawea.clicked.connect(self.request_weather)
self.btn_stawea.setEnabled(False)
self.left_layout.addWidget(self.single_query, 2, 0, 1, 5)
self.left_layout.addWidget(self.btn_tempa, 3, 0, 1, 5)
self.left_layout.addWidget(self.btn_wind, 4, 0, 1, 5)
self.left_layout.addWidget(self.btn_stawea, 5, 0, 1, 5)
# lineEdit to input a city
self.city_line = QLineEdit()
self.city_line.setPlaceholderText("输入城市回车确认")
self.city_line.returnPressed.connect(self.match_city)
self.left_layout.addWidget(self.city_line, 1, 0, 1, 5)
# save figure and quit window
self.save_fig = QPushButton("保存绘图")
self.save_fig.setEnabled(False)
self.save_fig.clicked.connect(self.fig_save)
self.left_layout.addWidget(self.save_fig, 6, 0, 1, 5)
self.load = QPushButton("写日记")
self.left_layout.addWidget(self.load, 7, 0, 1, 5)
self.quit_btn = QPushButton("退出")
self.quit_btn.clicked.connect(self.quit_act)
self.left_layout.addWidget(self.quit_btn, 8, 0, 1, 5)
# tablewidgt to view data
self.query_result = QTableWidget()
self.left_layout.addWidget(self.query_result, 9, 0, 2, 5)
self.query_result.verticalHeader().setVisible(False)
self.label = QLabel("预测天气情况绘图展示区")
self.right_layout.addWidget(self.label, 0, 6, 1, 7)
self.plot_weather_wind = GraphicsLayoutWidget()
self.plot_weather_temp = GraphicsLayoutWidget()
self.right_layout.addWidget(self.plot_weather_temp, 1, 6, 4, 7)
self.right_layout.addWidget(self.plot_weather_wind, 6, 6, 4, 7)
self.setWindowOpacity(0.9) # 设置窗口透明度
# self.setWindowFlag(QtCore.Qt.FramelessWindowHint) # 隐藏边框
self.main_layout.setSpacing(0)
# 按照城市的code, 请求一个城市的天气 返回 json 形式
def request_weather(self):
root_url = "http://t.weather.sojson.com/api/weather/city/"
url = root_url + str(self.code)
self.rep = get_weather.run(url)
sender = self.sender()
if sender.text() == "查询今日":
self.query(1, 5, '温度', '风向', '风力', 'PM2.5', '天气描述')
if sender.text() == "温度预测(可绘图)":
self.btn_tempa.setEnabled(False)
self.query(self.num, 2, '日期', '温度')
if sender.text() == "风力预测(可绘图)":
self.btn_wind.setEnabled(False)
self.query(self.num, 2, '日期', '风力')
if sender.text() == "综合天气预测":
self.query(self.num, 4, '温度', '风向', '风力', '天气描述')
# 读取 json 文件, 获得城市的code
def match_city(self):
# 输入城市后才能点击绘图
self.btn_tempa.setEnabled(True)
self.btn_wind.setEnabled(True)
self.single_query.setEnabled(True)
self.btn_stawea.setEnabled(True)
# 在外部json文件中 读取所有城市的 code
city = read_citycode.read_code("最新_city.json")
line_city = self.city_line.text()
# code与输入的城市对比, 如果有, 返回code, 如果没有则默认为北京
if line_city in city.keys():
self.code = city[line_city]
else:
self.code = "101010100"
self.city_line.setText("北京")
Qreply = QMessageBox.about(self, "你犯了一个粗误", "输入城市无效,请示新输入,否则默认为北京")
# 保存图片成功时的提醒
def pic_messagebox(self):
string = '第' + str(self.filename) + '张图片.png'
Qreply = QMessageBox.information(self, string,
"已经成功保存图片到当前目录, 关闭软件后请及时拷贝走")
# 保存图片的设置 pyqtgraph 保存无法设置图片路径
def fig_save(self):
ex = pe.ImageExporter(self.plt.scene())
filename = '第' + str(self.filename) + '张图片.png'
self.filename += 1
ex.export(fileName=filename)
self.pic_messagebox()
def get_date(self, dateFormat="%Y-%m-%d", addDays=0):
ls = []
timeNow = datetime.datetime.now()
key = 0
if (addDays != 0) and key < addDays - 1:
for i in range(addDays):
anotherTime = timeNow + datetime.timedelta(days=key)
anotherTime.strftime(dateFormat)
ls.append(str(anotherTime)[0:10])
key += 1
else:
anotherTime = timeNow
return ls
# 查询, 可以接受多个参数, 更加灵活的查询
def query(self, row_num, col_num, *args):
# true value
tempature = self.rep.json()['data']['wendu']
wind_power = self.rep.json()['data']['forecast'][0]['fl']
wind_direction = self.rep.json()['data']['forecast'][0]['fx']
pm = self.rep.json()['data']['pm25']
type_ = self.rep.json()['data']['forecast'][0]['type']
# forecast value
pre_tempature = []
pre_wind_power = []
pre_wind_direction = []
pre_pm = []
pre_type_ = []
for i in range(self.num):
pre_tempature.append(
str(self.rep.json()['data']['forecast'][i]['low']))
pre_wind_power.append(
str(self.rep.json()['data']['forecast'][i]['fl']))
pre_wind_direction.append(
str(self.rep.json()['data']['forecast'][i]['fx']))
pre_type_.append(
str(self.rep.json()['data']['forecast'][i]['type']))
# 设置当前查询结果的行列
self.query_result.setRowCount(row_num)
# 否则不会显示
self.query_result.setColumnCount(col_num)
# 表头自适应伸缩
self.query_result.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
# 按照 传入的参数设置表头, 因为每次查询的表头都不一样
ls = [i for i in args]
self.query_result.setHorizontalHeaderLabels(ls)
if col_num > 2 and row_num == 1:
item = QTableWidgetItem(str(tempature) + "℃")
# 设置单元格文本颜色
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(0, 0, item)
item = QTableWidgetItem(str(wind_direction))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(0, 1, item)
item = QTableWidgetItem(str(wind_power))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(0, 2, item)
item = QTableWidgetItem(str(pm))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(0, 3, item)
item = QTableWidgetItem(str(type_))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(0, 4, item)
if col_num > 2 and row_num > 1:
for i in range(0, self.num):
item = QTableWidgetItem("最" + str(pre_tempature[i]))
# 设置单元格文本颜色
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(i, 0, item)
item = QTableWidgetItem(str(pre_wind_direction[i]))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(i, 1, item)
item = QTableWidgetItem(str(pre_wind_power[i]))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(i, 2, item)
item = QTableWidgetItem(str(pre_type_[i]))
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(i, 3, item)
if col_num == 2 and row_num > 1:
date = self.get_date(addDays=self.num)
key = 0
for i in date:
item = QTableWidgetItem(i)
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(key, 0, item)
key += 1
if self.query_result.horizontalHeaderItem(1).text() == '温度':
key = 0
for i in pre_tempature:
item = QTableWidgetItem("最" + i)
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(key, 1, item)
key += 1
if self.query_result.horizontalHeaderItem(1).text() == '风力':
key = 0
for i in pre_wind_power:
item = QTableWidgetItem(i)
item.setForeground(QBrush(QColor(144, 182, 240)))
self.query_result.setItem(key, 1, item)
key += 1
# 只有两列的时候才可以绘制图像,
if col_num < 4:
ls, y = [], []
x = np.linspace(1, self.num, self.num)
# 将 treeview 里面的结果以数字的形式返回到列表中, 用于绘图
for row in range(self.num):
str1 = str(self.query_result.item(row, 1).text())
ls.extend(re.findall(r'\d+(?:\.\d+)?', str1))
if len(ls) == 5:
y = [float(i) for i in ls]
if len(ls) == 10:
lt = [float(i) for i in ls]
for i in range(0, len(lt), 2):
y.append((lt[i] + lt[i + 1]) / 2)
if len(ls) == 5:
y = [float(i) for i in ls]
else:
y = [float(i) for i in ls[0:5]]
# 获取 treeview 的标题, 以得到绘图时的标得
if self.query_result.horizontalHeaderItem(1).text() == '温度':
title_ = "近期一个月温度变化（预测）"
if self.query_result.horizontalHeaderItem(1).text() == '风力':
title_ = "近期一个月风力变化（预测）"
# 绘图时先清空面板 否则会新加一列,效果不好
# 且 pyqtgraph 的新加一列有bug, 效果不是很好 下次使用 matplotlib
if title_ == "近期一个月风力变化（预测）":
self.plot_weather_wind.clear()
bg1 = pg.BarGraphItem(x=x,
height=y,
width=0.3,
brush=QColor(137, 232, 165))
self.plt1 = self.plot_weather_wind.addPlot(title=title_)
self.plt1.addItem(bg1)
if title_ == "近期一个月温度变化（预测）":
self.plot_weather_temp.clear()
self.plt = self.plot_weather_temp.addPlot(title=title_)
bg2 = pg.BarGraphItem(x=x,
height=y,
width=0.3,
brush=QColor(32, 235, 233))
self.plt.addItem(bg2)
# 绘图后才可以保存图片
self.save_fig.setEnabled(True)
# 退出按钮
def quit_act(self):
# sender 是发送信号的对象
sender = self.sender()
print(sender.text() + '键被按下')
qApp = QApplication.instance()
qApp.quit()
def center(self):
'''
获取桌面长宽
获取窗口长宽
移动
'''
screen = QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width() - size.width()) / 2,
(screen.height() - size.height()) / 2)
class centralWidget(QtWidgets.QWidget):
def __init__(self, timeData, voltsData):
super(centralWidget, self).__init__()
# first generating the widgets of the tab
self.generateUiWidgets()
# initializing important variables for plotting
self.timeData = timeData
self.originalVoltsData = voltsData
self.editedVoltsData = voltsData
self.plot = None # original Plot
self.plot1 = None # plot After Editing
self.xRangeStack = []
self.yRangeStack = []
self.sampleTime = timeData[1] - timeData[0]
yrange = voltsData[len(voltsData) - 1] - voltsData[0]
self.scrollStep_x = 100 * self.sampleTime
self.scrollStep_y = yrange / 10
# sliders values
for i in range(1, 11):
setattr(self, "_value" + str(i), 1) # self._value[1-10] = 1
#Pallete of spectrogram *viridis as deafult
self.RGB_Pallete_1 = (0, 182, 188, 255)
self.RGB_Pallete_2 = (246, 111, 0, 255)
self.RGB_Pallete_3 = (75, 0, 113, 255)
#set labels text
ft = fourierTransform(self.originalVoltsData, int(1 / self.sampleTime))
ranges = ft.rangesOfFrequancy
for i in range(10):
getattr(getattr(self, "label" + str(i + 1)),
"setText")(str(ranges[i][0] / 1000) + " Khz : \n" +
str(ranges[i][1] / 1000) + " Khz")
self.HorizontalLabel1.setText("Set Minimun Frequancy")
self.HorizontalLabel2.setText("Set Maximum Frequancy")
# values of range of spectrogram
self.minFreqOfSpectrogram = 0
self.maxFreqOfSpectrogram = ranges[-1][1]
self.horizontalSlider1.setMinimum(self.minFreqOfSpectrogram)
self.horizontalSlider1.setMaximum(self.maxFreqOfSpectrogram)
self.horizontalSlider1.setTickInterval(self.maxFreqOfSpectrogram / 10)
self.horizontalSlider2.setMinimum(self.minFreqOfSpectrogram)
self.horizontalSlider2.setMaximum(self.maxFreqOfSpectrogram)
self.horizontalSlider2.setSliderPosition(self.maxFreqOfSpectrogram)
self.horizontalSlider2.setTickInterval(self.maxFreqOfSpectrogram / 10)
self.SpectrogramViewer.clear()
self.drawSpectrogram()
self.xRangeOfSignal = None # [from , to]
self.yRangeOfSignal = None
#start plotting the data
self.startPlotting()
# get range of view of the plots
self.xRangeOfSignal = [0.0, list(self.timeData)[-1]] # [from , to]
self.yRangeOfSignal = self.plot.viewRange()[1]
def startPlotting(self):
# plot original signal
self.plot = self.OriginalSignalViewer.addPlot()
self.plot.plot(self.timeData, self.originalVoltsData)
# plot data After Editing
self.plot1 = self.EditedSignalViewer.addPlot()
self.plot1.plot(self.timeData, self.editedVoltsData)
# range edit
self.plot.setXRange(0.0, list(self.timeData)[-1], 0)
self.plot1.setXRange(0.0, list(self.timeData)[-1], 0)
def minSliderOfSpectrogram(self, value):
self.minFreqOfSpectrogram = value
self.SpectrogramViewer.clear()
self.drawSpectrogram()
def maxSliderOfSpectrogram(self, value):
self.maxFreqOfSpectrogram = value
self.SpectrogramViewer.clear()
self.drawSpectrogram()
def drawSpectrogram(self, minFreq=1, maxFreq=1):
minFreq_Slider = self.minFreqOfSpectrogram
maxFreq_Slider = self.maxFreqOfSpectrogram
freq = 1 / self.sampleTime
ft = fourierTransform(self.editedVoltsData, int(freq))
ft.deleteRangeOfFrequancy(0, minFreq_Slider)
ft.deleteRangeOfFrequancy(maxFreq_Slider, int(freq / 2))
realsAfterEdit = ft.fn_InverceFourier(ft.data_fft)
frequancyArr, timeArr, Sxx = signal.spectrogram(
np.array(realsAfterEdit), freq)
pyqtgraph.setConfigOptions(imageAxisOrder='row-major')
win = self.SpectrogramViewer
p1 = win.addPlot()
img = pyqtgraph.ImageItem()
p1.addItem(img)
hist = pyqtgraph.HistogramLUTItem()
hist.setImageItem(img)
win.addItem(hist)
hist.setLevels(np.min(Sxx), np.max(Sxx))
hist.gradient.restoreState({
'mode':
'rgb',
'ticks': [(0.5, self.RGB_Pallete_1), (1.0, self.RGB_Pallete_2),
(0.0, self.RGB_Pallete_3)]
})
img.setImage(Sxx)
img.scale(timeArr[-1] / np.size(Sxx, axis=1),
frequancyArr[-1] / np.size(Sxx, axis=0))
p1.setLimits(xMin=0, xMax=timeArr[-1], yMin=0, yMax=frequancyArr[-1])
p1.setLabel('bottom', "Time", units='s')
p1.setLabel('left', "Frequency", units='Hz')
def generateUiWidgets(self):
font = QtGui.QFont()
font.setFamily("Arial Unicode MS")
font.setPointSize(10)
font.setBold(False)
font.setItalic(False)
font.setUnderline(False)
font.setWeight(50)
font.setStrikeOut(False)
font.setKerning(True)
self.setFont(font)
self.setTabletTracking(False)
self.gridLayout_6 = QtWidgets.QGridLayout(self)
self.gridLayout_6.setObjectName("gridLayout_6")
self.gridLayout_4 = QtWidgets.QGridLayout()
self.gridLayout_4.setObjectName("gridLayout_4")
self.SpectrogramGroupBox = QtWidgets.QGroupBox(self)
font = QtGui.QFont()
font.setFamily("Arial Unicode MS")
font.setPointSize(10)
font.setBold(True)
font.setWeight(75)
self.SpectrogramGroupBox.setFont(font)
self.SpectrogramGroupBox.setStyleSheet(
"border-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(0, 0, 0, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.SpectrogramGroupBox.setObjectName("SpectrogramGroupBox")
self.gridLayout_2 = QtWidgets.QGridLayout(self.SpectrogramGroupBox)
self.gridLayout_2.setObjectName("gridLayout_2")
self.horizontalSlider2 = QtWidgets.QSlider(self.SpectrogramGroupBox)
font = QtGui.QFont()
font.setPointSize(7)
self.horizontalSlider2.setFont(font)
self.horizontalSlider2.setCursor(
QtGui.QCursor(QtCore.Qt.ClosedHandCursor))
self.horizontalSlider2.setOrientation(QtCore.Qt.Horizontal)
self.horizontalSlider2.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.horizontalSlider2.setTickInterval(1)
self.horizontalSlider2.setObjectName("horizontalSlider2")
self.gridLayout_2.addWidget(self.horizontalSlider2, 3, 0, 1, 1)
self.SpectrogramViewer = GraphicsLayoutWidget(self.SpectrogramGroupBox)
self.SpectrogramViewer.viewport().setProperty(
"cursor", QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.SpectrogramViewer.setStyleSheet("background-color:rgb(0,0,0)")
self.SpectrogramViewer.setObjectName("SpectrogramViewer")
self.gridLayout_2.addWidget(self.SpectrogramViewer, 0, 0, 1, 1)
self.horizontalSlider1 = QtWidgets.QSlider(self.SpectrogramGroupBox)
self.horizontalSlider1.setCursor(
QtGui.QCursor(QtCore.Qt.ClosedHandCursor))
self.horizontalSlider1.setOrientation(QtCore.Qt.Horizontal)
self.horizontalSlider1.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.horizontalSlider1.setTickInterval(1)
self.horizontalSlider1.setObjectName("horizontalSlider1")
self.gridLayout_2.addWidget(self.horizontalSlider1, 1, 0, 1, 1)
self.HorizontalLabel1 = QtWidgets.QLabel(self.SpectrogramGroupBox)
font = QtGui.QFont()
font.setPointSize(7)
self.HorizontalLabel1.setFont(font)
self.HorizontalLabel1.setAlignment(QtCore.Qt.AlignCenter)
self.HorizontalLabel1.setObjectName("HorizontalLabel1")
self.gridLayout_2.addWidget(self.HorizontalLabel1, 2, 0, 1, 1)
self.HorizontalLabel2 = QtWidgets.QLabel(self.SpectrogramGroupBox)
self.HorizontalLabel2.setAlignment(QtCore.Qt.AlignCenter)
self.HorizontalLabel2.setObjectName("HorizontalLabel2")
self.gridLayout_2.addWidget(self.HorizontalLabel2, 4, 0, 1, 1)
self.gridLayout_4.addWidget(self.SpectrogramGroupBox, 0, 1, 3, 1)
self.OriginalSignalGroupbox = QtWidgets.QGroupBox(self)
font = QtGui.QFont()
font.setFamily("Arial Unicode MS")
font.setPointSize(10)
font.setBold(True)
font.setWeight(75)
self.OriginalSignalGroupbox.setFont(font)
self.OriginalSignalGroupbox.setObjectName("OriginalSignalGroupbox")
self.gridLayout_5 = QtWidgets.QGridLayout(self.OriginalSignalGroupbox)
self.gridLayout_5.setObjectName("gridLayout_5")
self.OriginalSignalViewer = GraphicsLayoutWidget(
self.OriginalSignalGroupbox)
self.OriginalSignalViewer.viewport().setProperty(
"cursor", QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.OriginalSignalViewer.setStyleSheet(
"background-color: rgb(0, 0, 0);")
self.OriginalSignalViewer.setObjectName("OriginalSignalViewer")
self.gridLayout_5.addWidget(self.OriginalSignalViewer, 0, 0, 1, 1)
self.gridLayout_4.addWidget(self.OriginalSignalGroupbox, 0, 0, 1, 1)
self.EditedSignalGroupBox = QtWidgets.QGroupBox(self)
font = QtGui.QFont()
font.setFamily("Arial Unicode MS")
font.setPointSize(10)
font.setBold(True)
font.setWeight(75)
self.EditedSignalGroupBox.setFont(font)
self.EditedSignalGroupBox.setObjectName("EditedSignalGroupBox")
self.gridLayout_3 = QtWidgets.QGridLayout(self.EditedSignalGroupBox)
self.gridLayout_3.setObjectName("gridLayout_3")
self.EditedSignalViewer = GraphicsLayoutWidget(
self.EditedSignalGroupBox)
self.EditedSignalViewer.viewport().setProperty(
"cursor", QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.EditedSignalViewer.setStyleSheet("background-color:rgb(0,0,0)")
self.EditedSignalViewer.setObjectName("EditedSignalViewer")
self.gridLayout_3.addWidget(self.EditedSignalViewer, 0, 0, 1, 1)
self.gridLayout_4.addWidget(self.EditedSignalGroupBox, 2, 0, 1, 1)
self.SignalEditorGroupBox = QtWidgets.QGroupBox(self)
font = QtGui.QFont()
font.setFamily("Arial Unicode MS")
font.setPointSize(10)
font.setBold(True)
font.setWeight(75)
self.SignalEditorGroupBox.setFont(font)
self.SignalEditorGroupBox.setObjectName("SignalEditorGroupBox")
self.gridLayout = QtWidgets.QGridLayout(self.SignalEditorGroupBox)
self.gridLayout.setObjectName("gridLayout")
self.gridLayout_7 = QtWidgets.QGridLayout()
self.gridLayout_7.setObjectName("gridLayout_7")
# add 10 labels for 10 sliders
for i in range(10):
setattr(
self, "label" + str(i + 1),
QtWidgets.QLabel(self.SignalEditorGroupBox)
) # self.label[1-10] = QtWidgets.QLabel(self.SignalEditorGroupBox)
font = QtGui.QFont()
font.setPointSize(5)
font.setBold(False)
font.setWeight(50)
getattr(getattr(self, "label" + str(i + 1)),
"setFont")(font) #self.label1.setFont(font)
getattr(getattr(self, "label" + str(i + 1)), "setObjectName")(
"label" +
str(i + 1)) #self.label[1-10].setObjectName("label[1-10]")
getattr(getattr(self, "gridLayout_7"), "addWidget")(
getattr(self, "label" + str(i + 1)), 0, i, 1,
1) #self.gridLayout_7.addWidget(self.label1, 0, 0, 1, 1)
self.gridLayout.addLayout(self.gridLayout_7, 1, 0, 1, 10)
# add 10 sliders to gui
for i in range(10):
setattr(
self, "slider" + str(i + 1),
Slider(parent=self.SignalEditorGroupBox,
objectName="Slider" + str(i + 1)))
Slid = getattr(self, "slider" + str(i + 1))
getattr(getattr(self, "gridLayout"), "addWidget")(Slid, 0, i, 1, 1)
# link slider to the trigger function
Slid.valueChanged.connect(lambda v: self.fn_sliderValue(v))
self.gridLayout_4.addWidget(self.SignalEditorGroupBox, 1, 0, 1, 1)
self.gridLayout_6.addLayout(self.gridLayout_4, 0, 0, 1, 1)
self.horizontalSlider1.valueChanged[int].connect(
self.minSliderOfSpectrogram)
self.horizontalSlider2.valueChanged[int].connect(
self.maxSliderOfSpectrogram)
QtCore.QMetaObject.connectSlotsByName(self)
def fn_sliderValue(self, value):
objectName = str(self.sender().objectName())
sliderNumber = re.search("[0-9]+", objectName).group()
setattr(self, "_value" + sliderNumber, value)
self.process()
def process(self): #(freq,complex_data,reals,time,np.abs(complex_data))
ft = fourierTransform(
list(self.originalVoltsData).copy(), 1 / self.sampleTime)
complex_data = ft.gain(self._value1, self._value2, self._value3,
self._value4, self._value5, self._value6,
self._value7, self._value8, self._value9,
self._value10)
reals = ft.fn_InverceFourier(complex_data)
#update Plot
self.EditedSignalViewer.clear()
self.plot1 = self.EditedSignalViewer.addPlot()
self.plot1.plot(self.timeData, reals)
self.plot1.setXRange(self.xRangeOfSignal[0], self.xRangeOfSignal[1], 0)
self.plot1.setYRange(self.yRangeOfSignal[0], self.yRangeOfSignal[1], 0)
self.editedVoltsData = np.array(reals)
# update spectrogram
self.SpectrogramViewer.clear()
self.drawSpectrogram()
def playSound(self):
ft = fourierTransform(
list(self.editedVoltsData).copy(), 1 / self.sampleTime)
complex_data = ft.gain(self._value1, self._value2, self._value3,
self._value4, self._value5, self._value6,
self._value7, self._value8, self._value9,
self._value10)
reals = ft.fn_InverceFourier(complex_data)
sound = soundfileUtility()
sound.fn_CreateSoundFile(list(reals), int(1 / self.sampleTime))
sound.fn_PlaySoundFile()
class Viewer:
"""
abstraction layer on viewer that dispatches visualisation to specific components
and implements widgets for DataSet functionality
"""
def __init__(self, dataset):
self.dataset = dataset
self.napari_viewer = None
self.plots = None
self.blik_widget = None
def show(self, napari_viewer=None, **kwargs):
self.ensure_ready(napari_viewer=napari_viewer)
for db in self.dataset:
db.init_depictor(**kwargs)
if self.dataset.volumes:
self.show_volume(list(self.dataset.volumes.keys())[0])
if self.dataset.plots:
self.plots.show()
@property
def shown(self):
if self.napari_viewer and self.volume_selector:
return self.dataset.volumes[self.volume_selector.currentText()]
return None
def ensure_ready(self, napari_viewer=None):
if napari_viewer is not None:
self._init_viewer(napari_viewer)
self._init_plots()
self._init_blik_widget()
self._hook_keybindings()
# check if viewer exists and is still open
try:
self.napari_viewer.window.qt_viewer.actions()
except (AttributeError, RuntimeError):
self._init_viewer()
self._init_plots()
self._init_blik_widget()
self._hook_keybindings()
def _init_viewer(self, napari_viewer=None):
if napari_viewer is not None:
self.napari_viewer = napari_viewer
else:
self.napari_viewer = napari.Viewer(title='napari - Blik')
self.napari_viewer.scale_bar.unit = '0.1nm'
self.napari_viewer.scale_bar.visible = True
# TODO: workaround until layer issues are fixed (napari #2110)
self.napari_viewer.window.qt_viewer.destroyed.connect(self.dataset.purge_gui)
def _init_plots(self):
self.plots = GraphicsLayoutWidget()
self._plots_napari_widget = self.napari_viewer.window.add_dock_widget(self.plots,
name='Blik - Plots',
area='bottom')
# use napari hide and show methods
self.plots.show = self._plots_napari_widget.show
self.plots.hide = self._plots_napari_widget.hide
self.plots.hide()
def _init_blik_widget(self):
self.blik_widget = QWidget()
layout = QVBoxLayout()
self.blik_widget.setLayout(layout)
self.volume_selector = QComboBox(self.blik_widget)
self.volume_selector.addItems(self.dataset.volumes.keys())
self.volume_selector.currentTextChanged.connect(self.show_volume)
layout.addWidget(self.volume_selector)
self.plots_toggler = QPushButton('Show / Hide Plots')
self.plots_toggler.clicked.connect(self.toggle_plots)
layout.addWidget(self.plots_toggler)
self._blik_napari_widget = self.napari_viewer.window.add_dock_widget(self.blik_widget,
name='Blik',
area='left')
# use napari hide and show methods
self.blik_widget.show = self._blik_napari_widget.show
self.blik_widget.hide = self._blik_napari_widget.hide
def _hook_keybindings(self):
self.napari_viewer.bind_key('PageUp', self.previous_volume)
self.napari_viewer.bind_key('PageDown', self.next_volume)
def update_blik_widget(self):
if self.blik_widget is not None:
current_text = self.volume_selector.currentText()
with block_signals(self.volume_selector):
self.volume_selector.clear()
self.volume_selector.addItems(self.dataset.volumes.keys())
self.volume_selector.setCurrentText(current_text)
self.show()
def clear_shown(self):
for layer in self.napari_viewer.layers.copy():
if layer in self.dataset.napari_layers:
self.napari_viewer.layers.remove(layer)
self.plots.clear()
def show_volume(self, volume):
if volume is None:
return
self.volume_selector.setCurrentText(volume)
datablocks = self.dataset.omni + self.dataset.volumes[volume]
layers = []
plots = []
for db in datablocks:
for dep in db.depictors:
if hasattr(dep, 'layers'):
if not dep.layers:
dep.depict()
layers.extend(dep.layers)
elif hasattr(dep, 'plot'):
if not dep.plot.curves:
dep.depict()
plots.append(dep.plot)
layers = sorted(layers, key=lambda l: isinstance(l, napari.layers.Image), reverse=True)
self.clear_shown()
self.napari_viewer.layers.extend(layers)
for plt in plots:
self.plots.addItem(plt)
def previous_volume(self, viewer=None):
idx = self.volume_selector.currentIndex()
previous_idx = (idx - 1) % self.volume_selector.count()
self.volume_selector.setCurrentIndex(previous_idx)
def next_volume(self, viewer=None):
idx = self.volume_selector.currentIndex()
next_idx = (idx + 1) % self.volume_selector.count()
self.volume_selector.setCurrentIndex(next_idx)
def toggle_plots(self):
if self.plots.isVisible():
self.plots.hide()
else:
self.plots.show()
class EEGViewer(QThread):
"""docstring for EEGViewer"""
StoppedState = 0
PausedState = 1
RunningState = 2
def __init__(self, mode='single', rows=4):
super(EEGViewer, self).__init__()
self.mode = mode
self.rows = rows
self.view = GraphicsLayoutWidget()
self.view.setAntialiasing(True)
self.view.setWindowTitle('EEG Viewer')
self.state = self.StoppedState
self.position = 0
self.maxPosition = 0
self.plotItem = list()
self.plotTrace = dict()
# Holders
self.wait = 0
self.wsize = 0
self.hsize = 0
self.color = dict()
self.window = list([0, 0])
self.channel = list()
def widget(self):
return self.view
def show(self):
self.view.show()
def hide(self):
self.view.hide()
def getState(self):
return self.state
def isVisible(self):
return self.view.isVisible()
def setSize(self, width, height):
self.view.resize(width, height)
def configure(self, channel, color, wsize, fs=0):
# Link params
nCh = len(channel)
self.wait = 1 / (fs * nCh) if fs > 0 else 0
self.wsize = wsize
self.hsize = wsize / 2
self.color = color
self.channel = channel
self.window = np.array([0, wsize])
# Remove previous items and traces
self.view.clear()
self.plotItem.clear()
self.plotTrace.clear()
# Create new canvas
if self.mode == 'single':
self.singleLayout()
else:
self.multipleLayout()
def singleLayout(self):
canvas = self.view.addPlot(0, 0)
canvas.disableAutoRange()
canvas.setClipToView(True)
canvas.setLimits(yMin=0, yMax=1)
canvas.setDownsampling(mode='subsample')
canvas.showGrid(x=True, y=True, alpha=0.25)
for ch in self.channel:
pen = mkPen(color=self.color[ch], width=2)
self.plotTrace[ch] = canvas.plot(pen=pen)
self.plotItem.append(canvas)
def multipleLayout(self):
col = 0
rowLimit = self.rows
for i, ch in enumerate(self.channel):
pen = mkPen(color=self.color[ch], width=2)
canvas = self.view.addPlot(i % rowLimit, col)
canvas.disableAutoRange()
canvas.setClipToView(True)
canvas.setLimits(yMin=0, yMax=1)
canvas.setDownsampling(mode='subsample')
canvas.showGrid(x=True, y=True, alpha=0.25)
self.plotItem.append(canvas)
self.plotTrace[ch] = canvas.plot(pen=pen)
if (i + 1) % rowLimit == 0:
col += 1
def plotData(self, D):
for ch in self.channel:
self.plotTrace[ch].setData(D[ch].values)
self.position = 0
self.maxPosition = D.index.size
def addMark(self, position, label=None):
for canvas in self.plotItem:
pen = mkPen(color='g', width=2.5, style=Qt.DashLine)
hpen = mkPen(color='r', width=2.5, style=Qt.DashLine)
mark = canvas.addLine(x=position,
pen=pen,
label=label,
labelOpts={'position': 0.9},
movable=True,
hoverPen=hpen)
return mark
def setPosition(self, position):
self.window[0] = position - self.hsize
self.window[1] = position + self.hsize
self.position = position
self.update()
def update(self):
for plot in self.plotItem:
plot.setRange(xRange=self.window)
self.position += 1 if self.position < self.maxPosition else 0
def play(self):
self.state = self.RunningState
self.start()
def pause(self):
self.state = self.PausedState
def toggle(self):
self.state = self.PausedState if self.state == self.RunningState else self.RunningState
def stop(self):
self.state = self.StoppedState
self.quit()
self.setPosition(0)
def run(self):
while True:
if self.state == self.RunningState:
self.setPosition(self.position)
elif self.state == self.PausedState:
pass
else:
break
sleep(self.wait)
