def updateSB(self):
try:
self.scale.scene().removeItem(self.scale)
except:
pass
try:
self.vscale.scene().removeItem(self.vscale)
except:
pass
if self.scalebar:
vb = self.p8.getViewBox()
xsize = vb.viewRange()[0][1] - vb.viewRange()[0][0]
ysize = vb.viewRange()[1][1] - vb.viewRange()[1][0]
if self.scalebartype == 0:
self.scale = pg.ScaleBar(size=round_to_1(xsize / 10.0),
suffix=self.xlabel)
self.scale.setParentItem(vb)
self.scale.anchor((0, 1), (1, 1), offset=(-20, -10))
self.scale.text.setText(pg.functions.siFormat(
round_to_1(xsize / 10.0), suffix=self.xlabel),
color=(0, 0, 0))
if self.scalebartype == 0 or self.scalebartype == 1:
self.vscale = verticalScaleBar(size=round_to_1(ysize / 5.0),
suffix=self.ylabel)
self.vscale.setParentItem(vb)
self.vscale.anchor((0, 1), (1, 1), offset=(-20, -5))
def plot_intensity_sums(self):
try:
self.hist_data = np.reshape(
self.hist_data,
newshape=(self.hist_data.shape[0],
self.numb_x_pixels * self.numb_y_pixels))
self.intensity_sums = np.sum(
self.hist_data, axis=0) #sum intensities for each pixel
self.intensity_sums = np.reshape(self.intensity_sums,
newshape=(self.numb_x_pixels,
self.numb_y_pixels))
self.ui.intensity_sums_viewBox.view.invertY(
False) # stop y axis invert
self.ui.intensity_sums_viewBox.setImage(self.intensity_sums,
scale=(self.x_step_size,
self.y_step_size))
self.ui.intensity_sums_viewBox.roi.setSize(
[self.x_scan_size, self.y_step_size]) #line roi
scale = pg.ScaleBar(size=1, suffix='um')
scale.setParentItem(self.ui.intensity_sums_viewBox.view)
scale.anchor((1, 1), (1, 1), offset=(-30, -30))
self.ui.intensity_sums_viewBox.view.sigRangeChanged.connect(
lambda: updateDelay(scale, 10))
except Exception as err:
print(format(err))
def plot_raw_scan(self):
try:
self.hist_image = np.reshape(self.hist_data,
newshape=(self.hist_data.shape[0],
self.numb_x_pixels,
self.numb_y_pixels))
self.times = self.time_data[:, 0, 0] * 1e-3
self.ui.raw_hist_data_viewBox.view.invertY(
False) # stops y-axis invert
self.ui.raw_hist_data_viewBox.setImage(self.hist_image,
scale=(self.x_step_size,
self.y_step_size),
xvals=self.times)
self.ui.raw_hist_data_viewBox.roi.setSize(
[self.x_scan_size, self.y_scan_size])
# if self.ui.compare_checkBox.isChecked():
# self.ui.imv2.setImage(self.hist_image, scale= (data['Scan Parameters']['X step size (um)'],
# data['Scan Parameters']['Y step size (um)']), xvals=self.times)
self.switch_compare()
self.ui.raw_hist_data_viewBox.ui.roiBtn.clicked.connect(
self.switch_compare)
scale = pg.ScaleBar(size=1, suffix='um')
scale.setParentItem(self.ui.raw_hist_data_viewBox.view)
scale.anchor((1, 1), (1, 1), offset=(-30, -30))
self.ui.raw_hist_data_viewBox.view.sigRangeChanged.connect(
lambda: updateDelay(scale, 10))
except Exception as err:
print(format(err))
def scalebar(self):
''' Not working '''
self.scale_bar = pg.ScaleBar(
10,
width=5,
suffix='m')
self.scale_bar.setParentItem(self.plotItem)
self.scale_bar.anchor((1, 1), (1, 1), offset=(-20, -20))
def plot_fit_scan(self):
try:
if self.ui.use_raw_scan_settings.isChecked():
num_x = self.numb_x_pixels
num_y = self.numb_y_pixels
else:
num_x = self.ui.num_x_spinBox.value()
num_y = self.ui.num_y_spinBox.value()
numb_of_points = num_x * num_y #75*75
fwhm = np.zeros(shape=(numb_of_points, 1))
pk_pos = np.zeros(shape=(numb_of_points, 1))
# pk_pos_plus = np.zeros(shape=(numb_of_points,1))
# pk_pos_minus = np.zeros(shape=(numb_of_points,1))
sigma = np.zeros(shape=(numb_of_points, 1))
height = np.zeros(shape=(numb_of_points, 1))
for i in range(numb_of_points):
fwhm[i, 0] = self.fit_scan_file['result_' +
str(i)].values['g1_fwhm']
pk_pos[i, 0] = self.fit_scan_file['result_' +
str(i)].values['g1_center']
sigma[i, 0] = self.fit_scan_file['result_' +
str(i)].values['g1_sigma']
height[i, 0] = self.fit_scan_file['result_' +
str(i)].values['g1_height']
newshape = (num_x, num_y)
param_selection = str(self.ui.comboBox.currentText())
self.img = np.reshape(eval(param_selection), newshape)
if self.ui.use_raw_scan_settings.isChecked():
self.ui.fit_scan_viewbox.setImage(self.img,
scale=(self.x_step_size,
self.y_step_size))
scale = pg.ScaleBar(size=2, suffix='um')
scale.setParentItem(self.ui.fit_scan_viewbox.view)
scale.anchor((1, 1), (1, 1), offset=(-30, -30))
self.ui.fit_scan_viewbox.view.sigRangeChanged.connect(
lambda: updateDelay(scale, 10))
else:
self.ui.fit_scan_viewbox.setImage(self.img)
self.ui.fit_scan_viewbox.view.invertY(False)
except Exception as e:
self.ui.result_textBrowser2.append(str(e))
pass
def __init__(self, parent=None, scalebar=True, useViewBox=False):
pg.setConfigOptions(antialias=True)
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
pg.GraphicsWindow.__init__(self)
self.useViewBox = useViewBox
#win = pg.GraphicsWindow(title="Basic plotting examples")
# self.view = pg.PlotWidget(self)
# self.view = pg.widgets.RemoteGraphicsView.RemoteGraphicsView()
#self.view.pg.setConfigOptions(antialias=True) ## prettier plots at no cost to the main process!
# self.view.setWindowTitle('pyqtgraph example: RemoteSpeedTest')
self.resize(800, 350)
#win.setWindowTitle('pyqtgraph example: Plotting')
# Enable antialiasing for prettier plots
self.scalebar = scalebar
self.scalebartype = 0
# self.setCentralWidget(self.view)
# self.curve = self.view.plot()
self.curve = []
self.p8 = self.addPlot(title="Region Selection")
pl8 = self.p8.plot() #data2, pen=(255,255,255,200))
if self.useViewBox:
self.nextRow()
self.p9 = self.addPlot(title="Zoom on selected region")
pl9 = self.p9.plot()
vb = self.p8.getViewBox()
xsize = vb.viewRange()[0][1] - vb.viewRange()[0][0]
ysize = vb.viewRange()[1][1] - vb.viewRange()[1][0]
self.scale = pg.ScaleBar(size=round_to_1(xsize / 10.0), suffix='s')
self.scale.setParentItem(vb)
self.scale.anchor((0, 1), (1, 1), offset=(-20, -10))
self.vscale = verticalScaleBar(size=round_to_1(ysize / 5.0),
suffix='s')
self.vscale.setParentItem(vb)
self.vscale.anchor((0, 1), (1, 1), offset=(-20, -10))
self.xlabel = ''
self.ylabel = ''
self.marker = pg.InfiniteLine(pos=0, pen=(0, 0, 0), movable=True)
self.markerpos = 0
self.p8.addItem(self.marker)
self.p8.sigXRangeChanged.connect(self.updateSB)
self.updateSB()
self.show()
def plot_intensity_sums(self):
try:
# TODO test line scan plots
#intensities = np.reshape(intensities, newshape=(2048, numb_pixels_X*numb_pixels_Y))
sums = np.sum(self.intensities, axis=-1)
sums = np.reshape(sums,
newshape=(self.numb_x_pixels,
self.numb_y_pixels))
self.ui.intensity_sums_viewBox.setImage(sums,
scale=(self.x_step_size,
self.y_step_size))
self.ui.intensity_sums_viewBox.view.invertY(False)
scale = pg.ScaleBar(size=2, suffix='um')
scale.setParentItem(self.ui.intensity_sums_viewBox.view)
scale.anchor((1, 1), (1, 1), offset=(-30, -30))
self.ui.intensity_sums_viewbox.view.sigRangeChanged.connect(
lambda: updateDelay(scale, 10))
except Exception as e:
self.ui.result_textBrowser2.append(str(e))
def plot_raw_scan(self):
try:
# TODO test line scan plots
intensities = self.intensities.T #this is only there because of how we are saving the data in the app
intensities = np.reshape(intensities,
newshape=(2048, self.numb_x_pixels,
self.numb_y_pixels))
self.ui.raw_scan_viewbox.setImage(intensities,
scale=(self.x_step_size,
self.y_step_size),
xvals=self.wavelengths)
#roi_plot = self.ui.raw_scan_viewBox.getRoiPlot()
#roi_plot.plot(data['Wavelengths'], intensities)
self.ui.raw_scan_viewbox.view.invertY(False)
scale = pg.ScaleBar(size=2, suffix='um')
scale.setParentItem(self.ui.raw_scan_viewbox.view)
scale.anchor((1, 1), (1, 1), offset=(-30, -30))
self.ui.raw_scan_viewbox.view.sigRangeChanged.connect(
lambda: updateDelay(scale, 10))
except Exception as e:
self.ui.result_textBrowser2.append(str(e))
# symbolSize=8, symbolBrush=color, symbolPeb='w')
# feature2_plot[3, 0].setLabels(left=['amplitude', 'V'], bottom=['rise time', 's'])
feature3_plot[0, 0].plot(grand_response[type[0]]['latency'], grand_response[type[0]]['amp'], pen=None, symbol='o',
symbolSize=8, symbolBrush=color, symbolPen='w')
feature3_plot[0, 0].setLabels(left=['Amp', 'V'], bottom=['Latency', 's'])
feature3_plot[0, 1].plot(grand_response[type[0]]['CV'], grand_response[type[0]]['amp'], pen=None, symbol='o',
symbolSize=8, symbolBrush=color, symbolPen='w')
feature3_plot[0, 1].setLabels(left=['Amp', 'V'], bottom=['CV', ''])
feature3_plot[0, 2].plot(grand_response[type[0]]['CV'], grand_response[type[0]]['latency'], pen=None, symbol='o',
symbolSize=8, symbolBrush=color, symbolPen='w')
feature3_plot[0, 2].setLabels(left=['Latency', 's'], bottom=['CV', ''])
amp_plot.plot(grand_response[type[0]]['amp'], grand_response[type[0]]['amp_measured'], pen=None, symbol='o',
symbolSize=10, symbolBrush=color, symbolPen='w')
amp_plot.setLabels(left=['Measured Amp', 'V'], bottom=['Fit Amp','V'])
if c == len(connection_types) - 1:
x_scale = pg.ScaleBar(size=10e-3, suffix='s')
x_scale.setParentItem(synapse_plot[c, 0].vb)
x_scale.anchor(scale_anchor, scale_anchor, offset=scale_offset)
amp_list = feature_anova('amp', grand_response)
feature_kw('amp', grand_response)
feature_kw('latency', grand_response)
feature_kw('rise', grand_response)
feature_kw('CV', grand_response)
latency_list = feature_anova('latency', grand_response)
rise_list = feature_anova('rise', grand_response)
decay_list = feature_anova('decay', grand_response)
# if args['organism'] == 'human':
# t, p = stats.ks_2samp(grand_response[('3', 'unknown')]['amp'], grand_response[('5', 'unknown')]['amp'])
# print ('KS: Amp = %f' % p)
# t, p = stats.ks_2samp(grand_response[('3', 'unknown')]['latency'],
"""
Demonstrates ScaleBar
"""
import initExample ## Add path to library (just for examples; you do not need this)
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
import numpy as np
pg.mkQApp()
win = pg.GraphicsWindow()
win.setWindowTitle('pyqtgraph example: ScaleBar')
vb = win.addViewBox()
vb.setAspectLocked()
img = pg.ImageItem()
img.setImage(np.random.normal(size=(100, 100)))
img.setScale(0.01)
vb.addItem(img)
scale = pg.ScaleBar(size=0.1)
scale.setParentItem(vb)
scale.anchor((1, 1), (1, 1), offset=(-20, -20))
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtWidgets.QApplication.instance().exec_()
