class BaseCurveWidget(QSplitter):
"""
Construct a BaseCurveWidget object, which includes:
* A plot (:py:class:`guiqwt.curve.CurvePlot`)
* An `item list` panel (:py:class:`guiqwt.curve.PlotItemList`)
This object does nothing in itself because plot and panels are not
connected to each other.
See children class :py:class:`guiqwt.plot.CurveWidget`
"""
def __init__(self, parent=None, title=None,
xlabel=None, ylabel=None, xunit=None, yunit=None,
section="plot", show_itemlist=False, gridparam=None,
curve_antialiasing=None, **kwargs):
if PYQT5:
super(BaseCurveWidget, self).__init__(parent, **kwargs)
self.setOrientation(Qt.Horizontal)
else:
QSplitter.__init__(self, Qt.Horizontal, parent)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.plot = CurvePlot(parent=self, title=title, xlabel=xlabel,
ylabel=ylabel, xunit=xunit, yunit=yunit,
section=section, gridparam=gridparam)
if curve_antialiasing is not None:
self.plot.set_antialiasing(curve_antialiasing)
self.addWidget(self.plot)
self.itemlist = PlotItemList(self)
self.itemlist.setVisible(show_itemlist)
self.addWidget(self.itemlist)
configure_plot_splitter(self)
class BaseCurveWidget(QSplitter):
"""
Construct a BaseCurveWidget object, which includes:
* A plot (:py:class:`guiqwt.curve.CurvePlot`)
* An `item list` panel (:py:class:`guiqwt.curve.PlotItemList`)
This object does nothing in itself because plot and panels are not
connected to each other.
See children class :py:class:`guiqwt.plot.CurveWidget`
"""
def __init__(self, parent=None, title=None,
xlabel=None, ylabel=None, xunit=None, yunit=None,
section="plot", show_itemlist=False, gridparam=None,
curve_antialiasing=None, **kwargs):
if PYQT5:
super(BaseCurveWidget, self).__init__(parent, **kwargs)
self.setOrientation(Qt.Horizontal)
else:
QSplitter.__init__(self, Qt.Horizontal, parent)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.plot = CurvePlot(parent=self, title=title, xlabel=xlabel,
ylabel=ylabel, xunit=xunit, yunit=yunit,
section=section, gridparam=gridparam)
if curve_antialiasing is not None:
self.plot.set_antialiasing(curve_antialiasing)
self.addWidget(self.plot)
self.itemlist = PlotItemList(self)
self.itemlist.setVisible(show_itemlist)
self.addWidget(self.itemlist)
configure_plot_splitter(self)
class FilterTestWidget(QWidget):
"""
Filter testing widget
parent: parent widget (QWidget)
x, y: NumPy arrays
func: function object (the signal filter to be tested)
"""
def __init__(self, parent, x, y, func):
QWidget.__init__(self, parent)
self.setMinimumSize(320, 200)
self.x = x
self.y = y
self.func = func
# ---guiqwt related attributes:
self.plot = None
self.curve_item = None
# ---
def setup_widget(self, title):
# ---Create the plot widget:
self.plot = CurvePlot(self)
self.curve_item = make.curve([], [], color="b")
self.plot.add_item(self.curve_item)
self.plot.set_antialiasing(True)
# ---
button = QPushButton("Test filter: %s" % title)
button.clicked.connect(self.process_data)
vlayout = QVBoxLayout()
vlayout.addWidget(self.plot)
vlayout.addWidget(button)
self.setLayout(vlayout)
self.update_curve()
def process_data(self):
self.y = self.func(self.y)
self.update_curve()
def update_curve(self):
# ---Update curve
self.curve_item.set_data(self.x, self.y)
self.plot.replot()
class FilterTestWidget(QWidget):
"""
Filter testing widget
parent: parent widget (QWidget)
x, y: NumPy arrays
func: function object (the signal filter to be tested)
"""
def __init__(self, parent, x, y, func):
QWidget.__init__(self, parent)
self.setMinimumSize(320, 200)
self.x = x
self.y = y
self.func = func
#---guiqwt related attributes:
self.plot = None
self.curve_item = None
#---
def setup_widget(self, title):
#---Create the plot widget:
self.plot = CurvePlot(self)
self.curve_item = make.curve([], [], color='b')
self.plot.add_item(self.curve_item)
self.plot.set_antialiasing(True)
#---
button = QPushButton("Test filter: %s" % title)
button.clicked.connect(self.process_data)
vlayout = QVBoxLayout()
vlayout.addWidget(self.plot)
vlayout.addWidget(button)
self.setLayout(vlayout)
self.update_curve()
def process_data(self):
self.y = self.func(self.y)
self.update_curve()
def update_curve(self):
#---Update curve
self.curve_item.set_data(self.x, self.y)
self.plot.replot()
class PlotWidget(qg.QWidget):
"""
"""
def __init__(self, parent):
qg.QWidget.__init__(self, parent)
self.data = Dbase(DBaseName = None)
self.y1Data = np.arange(0,100) #self.data.Query()
self.y2Data = np.arange(0,100)
self.xData = np.arange(0,100) #np.arange(0, len(self.yData))
self.setMinimumSize(700, 600)
#---guiqwt related attributes:
self.plot = None
self.curve_item = None
#---
def setup_widget(self, title):
"""Create the plot widget:
"""
self.plot = CurvePlot(self)
self.curve_item = (make.curve([], [], color='b'))
self.second_curve_item = (make.curve([], [], color='g'))
self.plot.add_item(self.curve_item)
self.plot.add_item(self.second_curve_item)
self.plot.set_antialiasing(True)
self.databaseScroll = treeList(DBaseName = None)
self.databaseScroll.setSortingEnabled(True)
spacer = qg.QSpacerItem(30,40)
preprocessData = qg.QGroupBox(u"preprocess data")
# create buttons
listButton = qg.QPushButton(u"Refresh list")
processButton = qg.QPushButton(u" run preprocessing ")
addwaveletButton = qg.QPushButton(u" add wavelet spikes to DB ")
self.checkAddData = qg.QMessageBox()
self.wavelet = qg.QCheckBox(u"wavelet filter ")
label1 = qg.QLabel("enter threshold value: ")
self.waveletThreshold = qg.QLineEdit(u"10")
# connect user actions with methods:
self.connect(listButton, qc.SIGNAL('clicked()'), self.but_clicked)
self.connect(processButton, qc.SIGNAL('clicked()'),
self.run_preprocess)
self.connect(self.databaseScroll,
qc.SIGNAL("doubleClicked(QModelIndex)"),
self.double_clicked)
self.connect(addwaveletButton, qc.SIGNAL('clicked()'),
self.add_data_to_DBase)
vlayout = qg.QVBoxLayout()
hlayout = qg.QHBoxLayout()
vlayout.addWidget(self.databaseScroll)
vlayout.addWidget(listButton)
vlayout.addWidget(self.plot)
vlayout.addSpacerItem(spacer)
hlayout.addWidget(self.wavelet)
hlayout.addWidget(label1)
hlayout.addWidget(self.waveletThreshold)
hlayout.addWidget(processButton)
hlayout.addWidget(addwaveletButton)
preprocessData.setLayout(hlayout)
vlayout.addWidget(preprocessData)
self.setLayout(vlayout)
self.update_curve()
def run_preprocess(self):
"""
"""
if self.wavelet.isChecked():
try:
yData = self.y1Data
waveletFilt = pp.wavefilter(yData)
self.y1Data = waveletFilt
thresh = float(self.waveletThreshold.displayText())
foo = self.y1Data > thresh
self.y2Data = self.spikes = pp.spikeThreshold(foo)
self.y2Data = self.y2Data * max(self.y1Data)
index = self.databaseScroll
root = index.parent().parent().row()
neuron = index.parent().row()
epoch = index.row()
r = self.databaseScroll
self.data = Dbase(r, PRINT = 1)
n = self.databaseScroll
epochs = self.data.GetTree(n)
e = epochs[epoch]
self.spikeOverwriteLoc = [r, n + '.' + e + '.spikes', n + '.' + e,
n, n + '_' + e + '_spikes']
self.data.Data.CloseDatabase(PRINT=1)
print 'spike handle: ', self.spikeOverwriteLoc[0:2]
self.update_curve()
except ValueError:
print 'ValueError. Could not compute wave filter'
pass
def add_data_to_DBase(self):
"""
"""
self.checkAddData.setText("Are you sure you want to add filtered \
spikes (green trace) to the DB?")
self.checkAddData.setInformativeText("This will overwrite the existing\
spike data.")
self.checkAddData.setStandardButtons(qg.QMessageBox.Yes | qg.QMessageBox.No )
self.checkAddData.setDefaultButton(qg.QMessageBox.Yes)
choice = self.checkAddData.exec_() == qg.QMessageBox.Yes
if choice:
tim = dt.datetime.utcnow().ctime()
self.data = Dbase(self.spikeOverwriteLoc[0], PRINT = 1)
self.data.Data.RemoveChild(self.spikeOverwriteLoc[1], option=1)
self.data.Data.AddData2Database('spikes', self.spikes,
self.spikeOverwriteLoc[2])
self.data.Data.AddGitVersion(self.spikeOverwriteLoc[3],
Action = 'updated_{0}'.format(
self.spikeOverwriteLoc[4] +
str(tim.day) + '_' +
str(tim.month) + '_' +
str(tim.year) ))
self.data.Data.CloseDatabase(PRINT=1)
""" add git version here """
print 'spike data successfully overwritten.'
def update_curve(self):
"""Update curve
"""
self.curve_item.set_data(self.xData, self.y1Data)
self.second_curve_item.set_data(self.xData, self.y2Data)
self.plot.replot()
self.plot.do_autoscale()
def but_clicked(self):
"""
when refresh button is clicked, the tree is refreshed
"""
self.databaseScroll.refreshTree()
def double_clicked(self):
"""
when a name button is clicked, iterate over the model,
find the neuron with this name, and set the treeviews current item
"""
index = self.databaseScroll.currentIndex()
item = self.databaseScroll.currentItem()
clickedCol = index.column()
hasChild = True
ind = index.parent()
colCount = 1
parents = []
while hasChild:
#find root index and parents
root = ind.row()
if root != -1:
parent = str(self.databaseScroll.itemFromIndex(
ind).text(clickedCol - colCount))
parents.insert(0, parent)
if root == -1:
hasChild = False
if parents == []:
parent = str(self.databaseScroll.itemFromIndex(
index).text(0))
parents.insert(0, parent)
ind = ind.parent()
colCount += 1
name = str(item.text(clickedCol))
print 'name: ', name
print 'parents: ', parents
if len(parents) == 1:
parents.append('')
if name[:-3] == '.h5':
name = '/'
kind = self.databaseScroll.GetDtype(parents[0], name, parents[1:])
print kind
#if dtype_ == 'np.array':
# clickedData = self.databaseScroll.GetData(parents[0], name,
# parents[1:])
# print clickedData
'''
class iScopeWidget(QWidget):
"""
Filter testing widget
parent: parent widget (QWidget)
x, y: NumPy arrays
func: function object (the signal filter to be tested)
"""
def __init__(self, parent, x, y):
QWidget.__init__(self, parent)
self.setMinimumSize(320, 200)
self.x = x
self.y = y
# ---guiqwt related attributes:
self.plot = None
self.curve_item = None
# ---
def setup_widget(self):
# ---Create the plot widget:
x = self.x
y = self.y
self.plot = CurvePlot(self)
self.curve_item = make.curve([], [], color="b")
self.plot.add_item(self.curve_item)
self.plot.set_antialiasing(True)
width = x[-1] - x[0]
self.intrange = make.range(x[0] + 0.4 * width, x[-1] - 0.4 * width)
self.plot.add_item(self.intrange)
self.lbgrange = make.range(x[0] + 0.3 * width, x[-1] - 0.65 * width)
self.plot.add_item(self.lbgrange)
self.lbgrange.pen = Qt.QPen(Qt.QColor("blue"))
self.lbgrange.brush = Qt.QBrush(Qt.QColor(0, 0, 120, 100))
self.rbgrange = make.range(x[0] + 0.7 * width, x[-1] - 0.1 * width)
self.rbgrange.pen = Qt.QPen(Qt.QColor("blue"))
self.rbgrange.brush = Qt.QBrush(Qt.QColor(0, 0, 120, 100))
self.label1 = make.label(r"", "TR", (0, 0), "TR")
self.plot.add_item(self.rbgrange)
self.bg_item = make.curve([], [], color="r")
self.plot.add_item(self.bg_item)
self.fit_bg()
self.plot.add_item(self.label1)
self.connect(self.plot, SIG_RANGE_CHANGED, self.fit_bg)
# ---
vlayout = QVBoxLayout()
vlayout.addWidget(self.plot)
self.setLayout(vlayout)
self.update_curve()
def fit_bg(self):
degree = 3
table = array([self.x, self.y])
low, high = self.lbgrange.get_range()
idxlower = set(where(table[0] <= high)[0])
idxhigher = set(where(table[0] >= low)[0])
idx1 = list(idxhigher.intersection(idxlower))
low, high = self.rbgrange.get_range()
idxlower = set(where(table[0] <= high)[0])
idxhigher = set(where(table[0] >= low)[0])
idx2 = list(idxhigher.intersection(idxlower))
idx = idx1 + idx2
x, y = table[:, idx]
self.coeff = polyfit(x, y, degree)
left, right = self.intrange.get_range()
# bg = abs(quad(lambda x: polyval(self.coeff, x), left, right)[0])
idxlower = set(where(table[0] <= right)[0])
idxhigher = set(where(table[0] >= left)[0])
idx = list(idxhigher.intersection(idxlower))
x, y = table[:, idx]
self.int = abs(trapz(y - polyval(self.coeff, x), x=x))
self.update_label()
self.update_curve()
def update_label(self):
self.label1.set_text(u"""trapz(red) - int(blue) = %e""" % self.int)
def update_curve(self):
# ---Update curve
self.curve_item.set_data(self.x, self.y)
self.plot.replot()
y = polyval(self.coeff, self.x)
self.bg_item.set_data(self.x, y)
