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added the PyQt ploting classes
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@RabiyaF
RabiyaF committed Apr 6, 2024
1 parent 53aad13 commit ea8cca8
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309 changes: 203 additions & 106 deletions RAT/plotting.py
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Original file line number Diff line number Diff line change
@@ -1,125 +1,215 @@
from RAT.rat_core import PlotEventData, makeSLDProfileXY

import pyqtgraph as pg
from PyQt6 import QtWidgets, QtGui, QtCore
from PyQt6.QtCore import pyqtSignal, QObject
from PyQt6.QtWidgets import QApplication, QWidget, QMainWindow, QVBoxLayout
from itertools import cycle

import matplotlib.pyplot as plt
import numpy as np
import sys


def plot_ref_SLD_helper_matplotlib(data: PlotEventData):
"""
Helper function to make it easier to plot from event.
Uses the matplotlib library to plot the reflectivity and the
SLD profiles.
Parameters
----------
data : PlotEventData
The plot event data that contains all the information
to generate the ref and sld plots
"""

# Create the figure with 2 sub plots
plt.close('all')
fig, (ref_plot, sld_plot) = plt.subplots(1, 2)

for i, (r, sd, sld, layer) in enumerate(zip(data.reflectivity,
data.shiftedData,
data.sldProfiles,
data.allLayers)):

r, sd, sld, layer = map(lambda x: x[0], (r, sd, sld, layer))

# Calculate the divisor
div = 1 if i == 0 else 2**(4*(i+1))

# Plot the reflectivity on plot (1,1)
ref_plot.plot(r[:, 0],
r[:, 1]/div,
label=f'ref {i+1}',
linewidth=2)

# Plot the errors on plot (1,1)
if data.dataPresent[i]:

sd_x = sd[:, 0]
sd_y, sd_e = map(lambda x: x/div, (sd[:, 1], sd[:, 2]))

# Remove values where data - error will be negative
indices_to_remove = np.flip(np.nonzero(0 > sd_y - sd_e)[0])
sd_x, sd_y, sd_e = map(lambda x: np.delete(x, indices_to_remove),
(sd_x, sd_y, sd_e))

ref_plot.errorbar(x=sd_x,
y=sd_y,
yerr=sd_e,
fmt='none',
color='red',
ecolor='red',
elinewidth=1,
capsize=2)

# Plot the scattering lenght densities (slds) on plot (1,2)
for j in range(1, sld.shape[1]):
sld_plot.plot(sld[:, 0],
sld[:, j],
label=f'sld {i+1}')

if data.resample[i] == 1 or data.modelType == 'custom xy':

new = makeSLDProfileXY(layer[0, 1],
layer[-1, 1],
data.ssubs[i],
layer,
len(layer),
1.0)

sld_plot.plot([row[0]-49 for row in new],
[row[1] for row in new])

# Convert the axis to log
ref_plot.set_yscale('log')
ref_plot.set_xscale('log')
ref_plot.set_xlabel('Qz')
ref_plot.set_ylabel('Ref')
ref_plot.legend()
ref_plot.grid()

# Label the axis and disable legend
sld_plot.set_xlabel('Z')
sld_plot.set_ylabel('SLD')
sld_plot.legend()
sld_plot.grid()

# Show plot
fig.show()


class RATPlot:
class PyQtPlots(QMainWindow):

def __init__(self):
"""
Initializes the windows
"""
super().__init__()
self.initialize_ui()
self.show()

def initialize_ui(self):
self.setWindowTitle('Reflectivity Algorithms Toolbox')
self.setWindowIcon(QtGui.QIcon("RAT/RAT-logo.png"))
self.resize(800,800)
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
self.setStyleSheet("background: white")

self.ref_plot = pg.PlotWidget(name="Reflectivity")
self.layout.addWidget(self.ref_plot)
self.ref_plot.setBackground("w")
self.ref_plot.setLabel('left', "ref")
self.ref_plot.setLabel('bottom', "Qz")
self.ref_plot.addLegend()
self.ref_plot.setLogMode(x=True, y=True)
self.ref_plot.showGrid(x=True, y=True)

self.sld_plot = pg.PlotWidget(name="Scattering Lenght Density")
self.layout.addWidget(self.sld_plot)
self.sld_plot.setBackground("w")
self.sld_plot.setLabel('left', "sld")
self.sld_plot.setLabel('bottom', "z")
self.sld_plot.addLegend()
self.sld_plot.showGrid(x=True, y=True)

def update_data(self, data: PlotEventData):
self.data = data
self.plot()

def plot(self):
"""
Helper function to make it easier to plot from event.
Uses the pyqt library to plot the reflectivity and the
SLD profiles.
Parameters
----------
data : PlotEventData
The plot event data that contains all the information
to generate the ref and sld plots
"""
self.ref_plot.clear()
self.sld_plot.clear()

self.colours = cycle(['r', 'g', 'b', 'c', 'm', 'y'])

for i, (r, sd, sld, layer) in enumerate(zip(self.data.reflectivity,
self.data.shiftedData,
self.data.sldProfiles,
self.data.allLayers)):

r, sd, sld, layer = map(lambda x: x[0], (r, sd, sld, layer))

self.colour = next(self.colours)

# Calculate the divisor
div = 1 if i == 0 else 2**(4*(i+1))

# Plot the reflectivity on plot (1,1)
self.ref_plot.plot(y=r[:, 1]/div,
x=r[:, 0],
pen=pg.mkPen(self.colour,
width=4),
name=f'ref {i+1}')

# Plot the errors on plot (1,1)
if self.data.dataPresent[i]:
self.plot_shifted_data(sd, div)

# Plot the scattering lenght densities (slds) on plot (1,2)
for j in range(1, sld.shape[1]):
self.sld_plot.plot(y=sld[:, j],
x=sld[:, 0],
pen=pg.mkPen(self.colour,
width=4),
name=f'sld {i+1}')

if self.data.resample[i] == 1 or self.data.modelType == 'custom xy':
new = makeSLDProfileXY(layer[0, 1],
layer[-1, 1],
self.data.ssubs[i],
layer,
len(layer),
1.0)

self.sld_plot.plot(y=[row[1] for row in new],
x=[row[0]-49 for row in new],
pen=pg.mkPen(self.colour),
name=f'resampled sld {i+1}')



def plot_shifted_data(self, sd, div):
"""
Plots the shifted data.
Parameters
----------
sd : nparray
The shifted data containing the x, y, e data
div : int
The divisor for the data
"""
sd_x = sd[:, 0]
sd_y, sd_e = map(lambda x: x/div, (sd[:, 1], sd[:, 2]))

# Remove values where data - error will be negative
indices_to_remove = np.flip(np.nonzero(0 > sd_y - sd_e)[0])
sd_x_r, sd_y_r, sd_e_r = map(lambda x: np.delete(x, indices_to_remove),
(sd_x, sd_y, sd_e))
sd_x_s, sd_y_s, sd_e_s = map(lambda x: [x[i] for i in indices_to_remove],
(sd_x, sd_y, sd_e))

self.plot_error_bar(sd_x_r, sd_y_r, sd_e_r)
self.plot_error_bar(sd_x_s, sd_y_s, sd_e_s, onesided=True)

def plot_error_bar(self, sd_x, sd_y, sd_e, onesided = False):
"""
Plots the error bars.
Parameters
----------
sd_x : nparray
The shifted data x axis data
sd_y : nparray
The shifted data y axis data
sd_e : nparray
The shifted data e data
onesided : bool
The bool to indicate drawing one sided errorbars
"""
for x, y, e in zip(sd_x, sd_y, sd_e):
y_error = [y+e, y] if onesided else [y+e, y-e]
self.ref_plot.plot(y=y_error,
x=[x] * 2,
pen=pg.mkPen(self.colour))
self.ref_plot.plot(y=sd_y,
x=sd_x,
pen=None,
symbolBrush=self.colour,
symbolPen='w',
symbol ='o',
symbolSize = 5)



class RATPlot(QObject):

data_updated = pyqtSignal()

def __init__(self):
"""
A method that sets up the window and the subplots
"""
self.win = pg.GraphicsLayoutWidget(show=True)
self.win.setWindowTitle('Reflectivity Algorithms Toolbox (RAT) plots')
self.win.setBackground("w")
super().__init__()

self.win = QMainWindow()
self.win.setWindowTitle('Reflectivity Algorithms Toolbox')
self.win.resize(800,800)

self.ref_plot = self.win.addPlot(title="Reflectivity")
self.widget = QWidget()
self.win.setCentralWidget(self.widget)

self.layout = QVBoxLayout()
self.widget.setLayout(self.layout)
self.widget.setStyleSheet("background: white")

self.ref_plot = pg.PlotWidget(name="Reflectivity")
self.layout.addWidget(self.ref_plot)
self.ref_plot.setBackground("w")
self.ref_plot.setLabel('left', "ref")
self.ref_plot.setLabel('bottom', "Qz")
self.ref_plot.addLegend()
self.ref_plot.setLogMode(x=True, y=True)
self.ref_plot.showGrid(x=True, y=True)

self.sld_plot = self.win.addPlot(title="Scattering Lenght Density")
self.sld_plot = pg.PlotWidget(name="Scattering Lenght Density")
self.layout.addWidget(self.sld_plot)
self.sld_plot.setBackground("w")
self.sld_plot.setLabel('left', "sld")
self.sld_plot.setLabel('bottom', "z")
self.sld_plot.addLegend()
self.sld_plot.showGrid(x=True, y=True)
self.colours = cycle(['r', 'g', 'b', 'c', 'm', 'y'])

def plot(self, data: PlotEventData):
self.data_updated.connect(self.plot)

def update_data(self, data: PlotEventData):
self.data = data
self.data_updated.emit()

def plot(self):
"""
Helper function to make it easier to plot from event.
Uses the pyqt library to plot the reflectivity and the
Expand All @@ -131,11 +221,15 @@ def plot(self, data: PlotEventData):
The plot event data that contains all the information
to generate the ref and sld plots
"""
self.ref_plot.clear()
self.sld_plot.clear()

for i, (r, sd, sld, layer) in enumerate(zip(data.reflectivity,
data.shiftedData,
data.sldProfiles,
data.allLayers)):
self.colours = cycle(['r', 'g', 'b', 'c', 'm', 'y'])

for i, (r, sd, sld, layer) in enumerate(zip(self.data.reflectivity,
self.data.shiftedData,
self.data.sldProfiles,
self.data.allLayers)):

r, sd, sld, layer = map(lambda x: x[0], (r, sd, sld, layer))

Expand All @@ -152,7 +246,7 @@ def plot(self, data: PlotEventData):
name=f'ref {i+1}')

# Plot the errors on plot (1,1)
if data.dataPresent[i]:
if self.data.dataPresent[i]:
self.plot_shifted_data(sd, div)

# Plot the scattering lenght densities (slds) on plot (1,2)
Expand All @@ -163,10 +257,10 @@ def plot(self, data: PlotEventData):
width=4),
name=f'sld {i+1}')

if data.resample[i] == 1 or data.modelType == 'custom xy':
if self.data.resample[i] == 1 or self.data.modelType == 'custom xy':
new = makeSLDProfileXY(layer[0, 1],
layer[-1, 1],
data.ssubs[i],
self.data.ssubs[i],
layer,
len(layer),
1.0)
Expand All @@ -176,6 +270,9 @@ def plot(self, data: PlotEventData):
pen=pg.mkPen(self.colour),
name=f'resampled sld {i+1}')

self.win.show()


def plot_shifted_data(self, sd, div):
"""
Plots the shifted data.
Expand Down
18 changes: 15 additions & 3 deletions RAT/test_plotting.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
import csv
import numpy as np
import pyqtgraph as pg
from PyQt6 import QtWidgets
import sys


def import_data(filename):
Expand Down Expand Up @@ -31,6 +33,16 @@ def import_data(filename):
data.shiftedData = import_data('shifted_data')
data.sldProfiles = import_data('sld_profiles')

rat = RATPlot()
rat.plot(data)
pg.exec()

app = QApplication(sys.argv)
app.setWindowIcon(QtGui.QIcon("RAT/RAT-logo.png"))
window = RATPlot()
window.update_data(data)
sys.exit(app.exec())

# app = QtWidgets.QApplication(sys.argv)
# app.setWindowIcon(QtGui.QIcon("RAT/RAT-logo.png"))
# rat = PyQtPlots()
# rat.update_data(data)
# sys.exit(app.exec())

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