We Keep Coding

New signal connects to old slot instead of separate slot

I am trying to tag x-spans of a data trace and populate a table with tagNames, starting x value, and the ending x value. I am using a dictionary of 'highlight' objects to keep track of the x-spans in case they need to be edited (increased or decreased) later. The dictionary maps the x Start value to the highlight object, as the x start values are expected to be unique (there is no overlap of x-spans for the tagging).
In order to do this, I am emitting a signal when the user beings to edit a cell on the table. The function that the first signal connects to emits another signal (ideally for whether the xStart is changed vs. the xEnd, but I have only implemented the xStart thus far), which actually changes the appearance of the span to match the edit.
I asked a similar question a few weeks ago but wasn't able to get an answer. The old question is here: PyQT5 slot parameters not updating after first call. In response to the tips given there, I wrote the following example:
import sys
from PyQt5.QtWidgets import *
from PyQt5 import QtCore
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import matplotlib.widgets as mwidgets
from functools import partial
class Window(QMainWindow):
def __init__(self, parent = None):
super(Window, self).__init__(parent)
self.resize(1600, 800)
self.MyUI()
def MyUI(self):
canvas = Canvas(self, width=14, height=12, dpi=100)
canvas.move(0,0)
#use this object in the dictionary to hold onto all the spans.
class highlight:
def __init__(self, tag, xStart, xEnd, highlightObj):
self.tag = tag
self.xStart = xStart
self.xEnd = xEnd
self.highlightObj = highlightObj
class Canvas(FigureCanvas):
def __init__(self, parent, width = 14, height = 12, dpi = 100):
Plot = Figure(figsize=(width, height), dpi=dpi)
self.Axes = Plot.add_subplot(111)
self.Axes.set_position([0.05, 0.58, 0.66, 0.55])
self.rowCount = 0
super().__init__(Plot)
self.setParent(parent)
##add all relevant lines to plot
self.Axes.plot([0,1,2,3,4], [3, 4, 5, 6, 7])
self.Axes.set_xlabel('Frame', fontsize = 10)
self.Axes.grid()
self.Axes.set_aspect(1)
Plot.canvas.draw()
self.highlights = {} #empty dictionary to store all the tags.
##define a table to hold the values postselection
self.taggingTable = QTableWidget(self)
self.taggingTable.setColumnCount(3)
self.taggingTable.setRowCount(100)
self.taggingTable.setGeometry(QRect(1005,85, 330, 310))
self.taggingTable.setHorizontalHeaderLabels(['Behavior','Start Frame', 'End Frame'])
Canvas.span = mwidgets.SpanSelector(self.Axes, self.onHighlight, "horizontal",
interactive = True, useblit=True, props=dict(alpha=0.5, facecolor="blue"),)
self.draw_idle()
self.taggingTable.selectionModel().selectionChanged.connect(self.onCellSelect)
self.draw_idle()
##highlighting adds a highlight item to the directory.
def onHighlight(self, xStart, xEnd):
tagName = "No Tag"
self.taggingTable.setItem(self.rowCount, 0, QTableWidgetItem(tagName))
self.taggingTable.setItem(self.rowCount, 1, QTableWidgetItem(str(int(xStart))))
self.taggingTable.setItem(self.rowCount, 2, QTableWidgetItem(str(int(xEnd))))
self.rowCount = self.rowCount + 1
highlightObj = self.Axes.axvspan(xStart, xEnd, color = 'blue', alpha = 0.5)
self.highlights[int(xStart)] = highlight(tagName, xStart, xEnd, highlightObj)
self.draw_idle()
def xStartChanged(self, xStart, rowVal):
if self.inCounter == 0:
print("xStart in slot: ", xStart)
xEnd = self.highlights[xStart].xEnd
xStartNew = int(self.taggingTable.item(rowVal, 1).text())
self.highlights[xStart].highlightObj.remove() #remove old from the plot
del self.highlights[xStart] #remove old from directory
highlightObj = self.Axes.axvspan(xStartNew, xEnd, color = 'blue', alpha = 0.5) #add new to plot
self.highlights[xStartNew] = highlight("No tagName", xStartNew, xEnd, highlightObj) #add new to directory
self.taggingTable.clearSelection() #deselect value from table
self.draw_idle()
self.inCounter = self.inCounter + 1
def onCellSelect(self):
index = self.taggingTable.selectedIndexes()
if len(index) != 0:
rowVal = index[0].row()
if not (self.taggingTable.item(rowVal, 1) is None):
xStart = int(self.taggingTable.item(rowVal, 1).text())
print("--------------")
print("xStart in signal: ", xStart)
self.inCounter = 0
self.taggingTable.itemChanged.connect(lambda: self.xStartChanged(xStart, rowVal))
app = QApplication(sys.argv)
window = Window()
window.show()
app.exec()
A test I run is when I highlight two traces:
and then I successfully change a first trace:
However, when I attempt to edit the second trace, the program crashes:
To debug, I tried to check what the signals were emitting and receiving. it produces the following output:
--------------
xStart in signal: 0
xStart in slot: 0 ##First slot call gets correct signal
--------------
xStart in signal: 3
xStart in slot: 0 ## Second slot gets the first signal instead of the second
Traceback (most recent call last):
File "//Volumes/path/file.py", line 105, in <lambda>
self.taggingTable.itemChanged.connect(lambda: self.xStartChanged(xStart, rowVal))
File "//Volumes/path/file.py", line 86, in xStartChanged
xEnd = self.highlights[xStart].xEnd
KeyError: 0
zsh: abort python Volumes/path file.py
I tried to use information online on unique connections but I am not sure how to implement them. Thank you in advance for any help.

It seems that what you need is table-widget signal that emits an item and its old text value whenever a change is made to a specific column. Unfortunately, the itemChanged signal isn't really suitable, because it doesn't indicate what changed, and it doesn't supply the previous value. So, to work around this limitation, one solution would be to subclass QTableWidget / QTableWidgetItem and emit a custom signal with the required parameters. This will completely side-step the issue with multiple signal-slot connections.
The implementation of the subclasses is quite simple:
class TableWidgetItem(QTableWidgetItem):
def setData(self, role, value):
oldval = self.text()
super().setData(role, value)
if role == Qt.EditRole and self.text() != oldval:
table = self.tableWidget()
if table is not None:
table.itemTextChanged.emit(self, oldval)
class TableWidget(QTableWidget):
itemTextChanged = pyqtSignal(TableWidgetItem, str)
Below is basic a demo based on your example that shows how to use them. (Note that I have made no attempt to handle xEnd as well, as that would go beyond the scope of the immediate issue).
import sys
from PyQt5.QtWidgets import *
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import matplotlib.widgets as mwidgets
class Window(QMainWindow):
def __init__(self, parent = None):
super(Window, self).__init__(parent)
self.resize(1600, 800)
self.MyUI()
def MyUI(self):
canvas = Canvas(self, width=14, height=12, dpi=100)
canvas.move(0,0)
# CUSTOM SUBCLASSES
class TableWidgetItem(QTableWidgetItem):
def setData(self, role, value):
oldval = self.text()
super().setData(role, value)
if role == Qt.EditRole and self.text() != oldval:
table = self.tableWidget()
if table is not None:
table.itemTextChanged.emit(self, oldval)
class TableWidget(QTableWidget):
itemTextChanged = pyqtSignal(TableWidgetItem, str)
#use this object in the dictionary to hold onto all the spans.
class highlight:
def __init__(self, tag, xStart, xEnd, highlightObj):
self.tag = tag
self.xStart = xStart
self.xEnd = xEnd
self.highlightObj = highlightObj
class Canvas(FigureCanvas):
def __init__(self, parent, width = 14, height = 12, dpi = 100):
Plot = Figure(figsize=(width, height), dpi=dpi)
self.Axes = Plot.add_subplot(111)
self.Axes.set_position([0.05, 0.58, 0.66, 0.55])
self.rowCount = 0
super().__init__(Plot)
self.setParent(parent)
##add all relevant lines to plot
self.Axes.plot([0,1,2,3,4], [3, 4, 5, 6, 7])
self.Axes.set_xlabel('Frame', fontsize = 10)
self.Axes.grid()
self.Axes.set_aspect(1)
Plot.canvas.draw()
self.highlights = {} #empty dictionary to store all the tags.
##define a table to hold the values postselection
# USE CUSTOM TABLE SUBCLASS
self.taggingTable = TableWidget(self)
self.taggingTable.setColumnCount(3)
self.taggingTable.setRowCount(100)
self.taggingTable.setGeometry(QRect(1005,85, 330, 310))
self.taggingTable.setHorizontalHeaderLabels(['Behavior','Start Frame', 'End Frame'])
# CONNECT TO CUSTOM SIGNAL
self.taggingTable.itemTextChanged.connect(self.xStartChanged)
Canvas.span = mwidgets.SpanSelector(self.Axes, self.onHighlight, "horizontal",
interactive = True, useblit=True, props=dict(alpha=0.5, facecolor="blue"),)
self.draw_idle()
##highlighting adds a highlight item to the directory.
def onHighlight(self, xStart, xEnd):
tagName = "No Tag"
self.taggingTable.setItem(self.rowCount, 0, QTableWidgetItem(tagName))
# USE CUSTOM ITEM SUBCLASS
self.taggingTable.setItem(self.rowCount, 1, TableWidgetItem(str(int(xStart))))
self.taggingTable.setItem(self.rowCount, 2, QTableWidgetItem(str(int(xEnd))))
self.rowCount = self.rowCount + 1
highlightObj = self.Axes.axvspan(xStart, xEnd, color = 'blue', alpha = 0.5)
self.highlights[int(xStart)] = highlight(tagName, xStart, xEnd, highlightObj)
self.draw_idle()
def xStartChanged(self, item, oldVal):
try:
# VALIDATE NEW VALUES
xStart = int(oldVal)
xStartNew = int(item.text())
except ValueError:
pass
else:
print("xStart in slot: ", xStart)
xEnd = self.highlights[xStart].xEnd
self.highlights[xStart].highlightObj.remove() #remove old from the plot
del self.highlights[xStart] #remove old from directory
highlightObj = self.Axes.axvspan(xStartNew, xEnd, color = 'blue', alpha = 0.5) #add new to plot
self.highlights[xStartNew] = highlight("No tagName", xStartNew, xEnd, highlightObj) #add new to directory
self.taggingTable.clearSelection() #deselect value from table
self.draw_idle()
app = QApplication(sys.argv)
window = Window()
window.show()
app.exec()

How do you increase the pickradius of a matplotlib Line2D artist?

I would like to create plot where each point is an individual artist that can be picked. This is my current solution:
import sys
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_qt5agg import \
FigureCanvasQTAgg as FigureCanvas
import matplotlib.patheffects as PathEffects
from PyQt5.QtWidgets import QDialog, QApplication, QVBoxLayout
class MainWindow(QDialog):
def __init__(self):
super().__init__()
self.fig, self.ax = plt.subplots()
self.canvas = FigureCanvas(self.fig)
a = [np.random.randint(100) for _ in range(100)]
b = [np.random.randint(100) for _ in range(100)]
self.artists = []
self.last_artist = None
for x, y in zip(a, b):
artist = self.ax.plot(
x, y, 'o', picker=True, pickradius=6, color='#ff4500'
)
self.artists += artist
self.canvas.draw()
self.cid_motion = self.fig.canvas.mpl_connect(
'motion_notify_event', self.hover
)
layout = QVBoxLayout()
layout.addWidget(self.canvas)
self.setLayout(layout)
def hover(self, event):
if event.inaxes == self.ax:
ind = 0
cont = None
while (
ind in range(len(self.artists))
and not cont
):
artist = self.artists[ind]
cont, _ = artist.contains(event)
if cont:
if artist is not self.last_artist:
if self.last_artist is not None:
self.last_artist.set_path_effects(
[PathEffects.Normal()]
)
self.last_artist.set_zorder(2)
artist.set_path_effects(
[PathEffects.withStroke(
linewidth=7, foreground="c", alpha=0.4
)]
)
artist.set_zorder(3)
self.last_artist = artist
ind += 1
if not cont and self.last_artist is not None:
self.last_artist.set_path_effects([PathEffects.Normal()])
self.last_artist.set_zorder(2)
self.last_artist = None
self.canvas.draw()
if __name__ == '__main__':
app = QApplication(sys.argv)
GUI = MainWindow()
GUI.show()
sys.exit(app.exec_())
However, the highlighting only works if you hover exactly over the center of a data point, it doesn't matter if you increase the pickradius. So I thought maybe I could change the contains method, but I don't know how. I found that matplotlib Artists come with a set_contains method which you can use to come up with your own contains method. But I don't know how to do that. I was hoping I could learn from how the default contains method is implemented and looked at the source code, but unfortunately this doesn't expain anything.

pickradius combined with picker as bool should achieve what you intend to. However, it is not doing so. On the other hand, picker if defined a float, is used as the pick radius in points. Therefore, specifying the tolerance directly to picker makes thing work. Change the following line:
artist = self.ax.plot(
x, y, 'o', picker=True, pickradius=6, color='#ff4500'
)
to
artist = self.ax.plot(
x, y, 'o', picker=6, color='#ff4500'
)

Matplotlib Animation does not update within class

I'm writing a simple class to plot a sensor value in real-time; however, the animation does not run within the class.
I've tried to return the animation object to have an instance outside of the class but this does not work.
To my understanding, this is the same issue as raised in GitHub #1656
import datetime as dt
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from random import random
class Animate:
def __init__(self, sensor):
# Create figure for plotting
self.fig = plt.figure()
self.ax = self.fig.add_subplot(1, 1, 1)
self.xs = []
self.ys = []
self.ylabel = sensor
self.readings = 20
# This function is called periodically from FuncAnimation
def _update(self, i, xs, ys):
# Get sensor value
value = random()
# Add x and y to lists
self.xs.append(dt.datetime.now().strftime('%H:%M:%S.%f'))
self.ys.append(value)
# Limit x and y lists to 20 items
self.xs = self.xs[-self.readings:]
self.ys = self.ys[-self.readings:]
# Draw x and y lists
self.ax.clear()
self.ax.plot(xs, ys)
# Format plot
plt.xticks(rotation=45, ha='right')
plt.subplots_adjust(bottom=0.30)
plt.title(self.ylabel + ' over Time')
plt.ylabel(self.ylabel)
def start(self):
print('Starting')
# Set up plot to call animate() function periodically
self.anim = animation.FuncAnimation(self.fig, self._update, fargs=(self.xs, self.ys), interval=200)
plt.show();
rand = Animate('Torque')
rand.start();

your variables xs and ys are already named self.xs and self.ys, which are accessible in the class namespace; you do not need to pass them to self.update
import datetime as dt
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from random import random
class Animate:
def __init__(self, sensor):
# Create figure for plotting
self.fig = plt.figure()
self.ax = self.fig.add_subplot(1, 1, 1)
self.xs = []
self.ys = []
self.ylabel = sensor
self.readings = 20
# This function is called periodically from FuncAnimation
def _update(self, i):
# Read temperature (Celsius) from TMP102
temp_c = random()
# Add x and y to lists
self.xs.append(dt.datetime.now().strftime('%H:%M:%S.%f'))
self.ys.append(temp_c)
# Limit x and y lists to 20 items
self.xs = self.xs[-self.readings:]
self.ys = self.ys[-self.readings:]
# Draw x and y lists
self.ax.clear()
self.ax.plot(self.xs, self.ys)
# Format plot
plt.xticks(rotation=45, ha='right')
plt.subplots_adjust(bottom=0.30)
plt.title(self.ylabel + ' over Time')
plt.ylabel(self.ylabel)
def start(self):
print('Starting')
# Set up plot to call animate() function periodically
self.anim = animation.FuncAnimation(self.fig, self._update, interval=200)
plt.show()
rand = Animate('Torque')
rand.start()

Making a plot in a second window using data from main window

I'm trying to make a program in which I have a main window and a second window. The second window should be opened by checking a Check-Box in the main window and closed by unchecking it.
The following minimal example works already fine (thanks to ImportanceOfBeingErnest !), but I want to spin the arrow (the one, which is already bent when you run the example) by changing the SpinBox in the main window.
Solution: See 5th comment in the first answer!
import sys
from PyQt4 import QtGui, QtCore
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib import animation
import numpy as np
class Newsphere(QtGui.QMainWindow):
def __init__(self):
super(Newsphere, self).__init__()
self.mainbox = QtGui.QWidget()
self.mainbox.setLayout(QtGui.QHBoxLayout())
self.setCentralWidget(self.mainbox)
self.spin = QtGui.QSpinBox()
self.spin.setValue(20)
self.spin.setMaximum(100)
self.spin.setMinimum(-100)
self.checkPlot = QtGui.QCheckBox("Check")
self.mainbox.layout().addWidget(self.spin)
self.mainbox.layout().addWidget(self.checkPlot)
self.Plot = None
self.checkPlot.clicked.connect(self.showPlot)
def showPlot(self):
if self.Plot == None:
self.Plot = Plot(self.kinematic())
self.Plot.show()
# register signal for closure
self.Plot.signalClose.connect(self.uncheck)
# register signal for spin value changed
self.spin.valueChanged.connect(self.kinematic)
else:
self.Plot.close()
self.Plot = None
def kinematic(self):
x = self.spin.value() / 100
v = np.matrix([[1.,x,0.],[0.,1.,0.],[0.,0.,1.]])
zero = np.matrix([[0.,0.,0.],[0.,0.,0.],[0.,0.,0.]])
pos = np.hstack([v, zero])
return pos
def uncheck(self):
self.checkPlot.setChecked(False)
self.Plot = None
class Plot(QtGui.QWidget):
signalClose = QtCore.pyqtSignal()
def __init__(self, pos=None):
super(Plot, self).__init__()
self.setLayout(QtGui.QHBoxLayout())
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111,projection = '3d')
self.fig.tight_layout()
self.ax.view_init(40, 225)
''' dashed coordinate system '''
self.ax.plot([0,1], [0,0], [0,0], label='$X_0$', linestyle="dashed", color="red")
self.ax.plot([0,0], [0,-10], [0,0], label='$Y_0$', linestyle="dashed", color="green")
self.ax.plot([0,0], [0,0], [0,1], label='$Z_0$', linestyle="dashed", color="blue")
self.ax.set_xlim3d(-3,3)
self.ax.set_ylim3d(-3,3)
self.ax.set_zlim3d(-3,3)
self.canvas = FigureCanvas(self.fig)
self.layout().addWidget(self.canvas)
self.pos = pos
self.setup_plot()
self.ani = animation.FuncAnimation(self.fig, self.update_plot, init_func=self.setup_plot, blit=True)
def setup_plot(self):
self.ax.legend(loc='best')
self.position = self.ax.quiver(0, 0, 0, 0, 0, 0, pivot="tail", color="black")
return self.position,
def update_plot(self, i):
x_zero = self.pos[:,3]
y_zero = self.pos[:,4]
z_zero = self.pos[:,5]
v_x = self.pos[0,0:3]
v_y = self.pos[1,0:3]
v_z = self.pos[2,0:3]
self.position = self.ax.quiver(-x_zero, -y_zero, z_zero, -v_x[0,:], v_y[0,:], v_z[0,:], pivot="tail", color="black")
self.canvas.draw()
return self.position,
# We need to make sure the animation stops, when the window is closed
def closeEvent(self, event):
self.signalClose.emit()
self.close()
super(Plot, self).closeEvent(event)
def close(self):
self.ani.event_source.stop()
super(Plot, self).close()
if __name__ == '__main__':
app = QtGui.QApplication(sys.argv)
main = Newsphere()
main.show()
sys.exit(app.exec_())

Here is an working example of what I think you are trying to achieve.
The Main Window has a spin box and a check box. Once the checkbox is clicked, a new window with a plot will show up and an animation will start. The current value and some array will be given to the plot window. If you change the spin box value while the animation is running, it will be updated. When the plot window is closed or when the checkbox is unchecked, the animation will stop (and be deleted).
import sys
from PyQt4 import QtGui, QtCore
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib import animation
import numpy as np
class Newsphere(QtGui.QMainWindow):
def __init__(self):
super(Newsphere, self).__init__()
self.mainbox = QtGui.QWidget()
self.mainbox.setLayout(QtGui.QHBoxLayout())
self.setCentralWidget(self.mainbox)
self.spin = QtGui.QSpinBox()
self.spin.setValue(5)
self.spin.setMaximum(10)
self.spin.setMinimum(1)
self.checkPlot = QtGui.QCheckBox("Check")
self.mainbox.layout().addWidget(self.spin)
self.mainbox.layout().addWidget(self.checkPlot)
self.Plot = None
self.checkPlot.clicked.connect(self.showPlot)
def showPlot(self):
if self.Plot == None:
self.Plot = Plot(self.kinematic(), self.spin.value())
self.Plot.show()
# register signal for closure
self.Plot.signalClose.connect(self.uncheck)
# register signal for spin value changed
self.spin.valueChanged.connect(self.Plot.update_factor)
else:
self.Plot.close()
self.Plot = None
def kinematic(self):
v = np.array([[1.,2.,3.],[2.,1.,3.],[3.,2.,1.]])
return v
def uncheck(self):
self.checkPlot.setChecked(False)
self.Plot = None
class Plot(QtGui.QWidget):
signalClose = QtCore.pyqtSignal()
def __init__(self, v=None, factor=1):
super(Plot, self).__init__()
self.setLayout(QtGui.QHBoxLayout())
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111,projection = '3d')
self.ax.set_aspect('equal')
self.fig.tight_layout()
self.ax.view_init(40, 225)
self.ax.set_xlim3d(0,3)
self.ax.set_ylim3d(0,3)
self.ax.set_zlim3d(0,4)
self.canvas = FigureCanvas(self.fig)
self.layout().addWidget(self.canvas)
self.pos = v
self.setup_plot()
self.update_factor(factor)
self.ani = animation.FuncAnimation(self.fig, self.update_plot, blit=False)
def setup_plot(self):
xpos, ypos = np.meshgrid(np.arange(self.pos.shape[0]),np.arange(self.pos.shape[1]) )
self.xpos = xpos.flatten('F')
self.ypos = ypos.flatten('F')
self.zpos = np.zeros_like(self.xpos)
self.bar = None
def update_factor(self, factor):
self.factor = factor
self.dx = np.ones_like(self.xpos)*np.min(np.abs(self.factor/10.), 0.1)
self.dy = self.dx.copy()
def update_plot(self, i):
if self.bar != None:
self.bar.remove()
del self.bar
pos = self.pos+np.sin(i/8.)
dz = pos.flatten()
self.bar = self.ax.bar3d(self.xpos, self.ypos, self.zpos, self.dx, self.dy, dz,
color=(1.-self.factor/10.,0,self.factor/10.), zsort='average', linewidth=0)
self.canvas.draw()
# We need to make sure the animation stops, when the window is closed
def closeEvent(self, event):
self.signalClose.emit()
self.close()
super(Plot, self).closeEvent(event)
def close(self):
self.ani.event_source.stop()
super(Plot, self).close()
if __name__ == '__main__':
app = QtGui.QApplication(sys.argv)
main = Newsphere()
main.show()
sys.exit(app.exec_())
Since I wasn't sure about what you want to animate, I changed the plot to a barplot, but you can change it back to whatever you need. Hope that helps.

Embedding a Matplotlib plot into PyQt

I have been trying unsuccessfully to embed a matplotlib into PyQt for the past few days and before you say anything, I have been to every site possible to help me.
When I run the code it produces a 1 by 1 graph but doesn't actually graph anything
from __future__ import unicode_literals
import sys
import os
import random
from matplotlib.backends import qt4_compat
use_pyside = qt4_compat.QT_API == qt4_compat.QT_API_PYSIDE
if use_pyside:
from PySide import QtGui, QtCore
else:
from PyQt4 import QtGui, QtCore
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import matplotlib.pyplot as plt
import numpy as np
import scipy.io
import os
import pandas as pd
progname = os.path.basename(sys.argv[0])
progversion = "0.1"
class MyMplCanvas(FigureCanvas):
"""Ultimately, this is a QWidget (as well as a FigureCanvasAgg, etc.)."""
def __init__(self, parent=None, width=5, height=4, dpi=100):
fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
#
FigureCanvas.__init__(self, fig)
self.setParent(parent)
FigureCanvas.setSizePolicy(self,
QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def compute_initial_figure(self):
pass
class MyStaticMplCanvas(MyMplCanvas):
def extract_data(self, name):
#setting up lists
Stim_trig = []
Stim_order = []
Sch_wav = []
data = scipy.io.loadmat(name)
for k,v in data.items():
#Sends Sch_wav data to a list
if "Sch_wav" in k:
for d in (((v[0])[0])[4]):
Sch_wav.append(d[0])
#Sends StimTrig to a list
if k=="StimTrig":
for g in (((v[0])[0])[4]):
Stim_trig.append(g[0])
Stim_trig.append(Stim_trig[-1]+1)
#Sends Stim order to a list
for w in (((v[0])[0])[5]):
Stim_order.append(w[0])
superdata = []
#Prepares grouping stimuli and trigger
for i in range(len(Stim_trig)-1):
fire = []
for p in Sch_wav:
if p > Stim_trig[i] and p < Stim_trig[i+1]:
fire.append(p - Stim_trig[i])
superdata.append([Stim_order[i],fire])
#sorts all the data
superdata.sort()
alladdedup = [[1],[2],[3],[4],[5],[6],[7],[8],[9],[10],[62]]
count = 0
for d in superdata:
if d[0] == (alladdedup[count])[0]:
for j in d[1]:
((alladdedup)[count]).append(j)
else:
count += 1
#places time stamps of triggers in lists for each trigger
for l in alladdedup:
l.pop(0)
l.sort()
#removes title and sorts data
ffmsb = []
#finds number of firings for each milisecond bin
for v in alladdedup:
fmsb = []
for b in range(100):
msbc = b/100
msb = []
for t in v:
if t > msbc and t < msbc + 0.01:
msb.append(t)
fmsb.append(len(msb))
ffmsb.append(fmsb)
#returns list of stimuli firings per milisecond bin
return ffmsb
#End of Sorting Code
#Start of Graphing Code
def stimuli_graph(self):
#Set file to use and the stimuli wanted. In this case stimuli 1 is being used
filename = ("654508_rec02_all.mat"[1])
self.extract_data(filename)
#Creates parameters for index
numberlist = []
for i in range(100):
numberlist.append(i/100)
#Adjusts the y-axis max according to the y-axis of a graphed stimuli e.g. If plotted graph has y-axis of 10
# then it'll be adjusted by 1.3. So it'll change to 13
x = 0
for i in filename:
if i > x:
x = i*1.3
#Dataframes the data from extract_data
c = pd.Series(filename, index = numberlist)
neurons = pd.DataFrame((c))
#This is where the data gets graphed. I know this is where the problem occurs, I just don't know where
#This code is a mess and for that I am sorry
times = [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]
ax = neurons.plot(
kind = 'bar',
title = 'Number of neurons firing for stimuli '+str(1),
legend = False,
xlim = (0, 100),
ylim = (0, x),
width = 1,
position = 0,
edgecolor = 'white',
xticks = (np.arange(min(times), max(times), 10)) #Makes the x-axis label in increments of 0.1 instead of 0.01
)
ax.set_xlabel('Time (s)')
ax.set_ylabel('Neurons Firing')
t = arange(0, 100, 1)
self.axes.plot(t, neurons)
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle("application main window")
self.file_menu = QtGui.QMenu('&File', self)
self.file_menu.addAction('&Quit', self.fileQuit,
QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
self.menuBar().addMenu(self.file_menu)
self.help_menu = QtGui.QMenu('&Help', self)
self.menuBar().addSeparator()
self.menuBar().addMenu(self.help_menu)
self.main_widget = QtGui.QWidget(self)
l = QtGui.QVBoxLayout(self.main_widget)
sc = MyStaticMplCanvas(self.main_widget, width=5, height=4, dpi=100)
l.addWidget(sc)
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.statusBar().showMessage("All hail matplotlib!", 2000)
def fileQuit(self):
self.close()
def closeEvent(self, ce):
self.fileQuit()
qApp = QtGui.QApplication(sys.argv)
aw = ApplicationWindow()
aw.setWindowTitle("%s" % progname)
aw.show()
sys.exit(qApp.exec_())
#qApp.exec_()
The data used in the graph is extracted from an external file