diff --git a/.gitmodules b/.gitmodules
index 1bd1816..3fecbbb 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "libs/pyqtgraph"]
- path = libs/pyqtgraph
+[submodule "ui/libs/pyqtgraph"]
+ path = ui/libs/pyqtgraph
url = https://github.com/pyqtgraph/pyqtgraph-core.git
diff --git a/pydsf.py b/pydsf.py
index 23fc10e..5921841 100644
--- a/pydsf.py
+++ b/pydsf.py
@@ -6,15 +6,11 @@ import csv
# Import 3rd party packages. Check if installed and die with error message
# if not.
-try:
- import matplotlib as mpl
- import mpl_toolkits.axes_grid1
- mpl.use('Qt5Agg')
- mpl.interactive(True)
- import matplotlib.ticker as ticker
+try:
+ import ui.libs.pyqtgraph as pg
except ImportError:
- raise ImportError('----- Matplotlib must be installed. -----')
+ raise ImportError('----- pyqtgraph must be installed. -----')
try:
import peakutils
@@ -532,177 +528,194 @@ def update_progress_bar(bar, value):
class PlotResults():
- def plot_tm_heatmap_single(self, plate, widget):
- """
- Plot Tm heatmap (Fig. 1)
- """
- x = 1 # Position in columns
- y = 1 # Position in rows
- x_values = [] # Array holding the columns
- y_values = [] # Array holding the rows
- c_values = [] # Array holding the color values aka Tm
- dx_values = []
- dy_values = []
- canvas = widget.canvas
- canvas.clear()
- for well in plate.wells: # Iterate over all wells
- if well not in plate.denatured_wells:
- # Check if well is denatured (no Tm found)
- c = well.tm # If not, set color to Tm
- if c < plate.tm_cutoff_low:
- # Check if Tm is lower that the cutoff
- c = plate.tm_cutoff_low
- # If it is, set color to cutoff
- elif c > plate.tm_cutoff_high:
- # Check if Tm is higher that the cutoff
- c = plate.tm_cutoff_high
- # If it is, set color to cutoff
- else: # If the plate is denatured
- c = plate.tm_cutoff_low
- # Set its color to the low cutoff
- dx_values.append(x)
- dy_values.append(y)
- x_values.append(x) # Add values to the respective arrays
- y_values.append(y)
- c_values.append(c)
- x += 1 # Increase column by one
- if x > plate.cols: # If maximum column per row is reached
- x = 1 # reset column to one
- y += 1 # and increase row by one
-
- fig1 = canvas.fig # new figure
- ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
- ax1.autoscale(tight=True) # Scale plate size
- ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1))
- # n columns
- ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1))
- # n rows
- if plate.color_range:
- # plot wells and color using the colormap
- cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
- marker='s', vmin=plate.color_range[0],
- vmax=plate.color_range[1])
- else:
- # plot wells and color using the colormap
- cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
- marker='s')
-
- ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x',
- linewidths=(1.5,))
- ax1.invert_yaxis() # invert y axis to math plate layout
- cbar = fig1.colorbar(cax) # show colorbar
- ax1.set_xlabel('Columns') # set axis and colorbar label
- ax1.set_ylabel('Rows')
-
- if str(plate.id) == 'average':
- title = '$T_m$ heatmap (average)'
- else:
- title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
- ax1.set_title(title)
- cbar.set_label(u"Temperature [°C]")
-
- canvas.draw()
-
- def plot_derivative(self, plate, widget):
- """
- Plot derivatives (Fig. 2)
- """
- canvas = widget.canvas
- canvas.clear()
- fig2 = canvas.fig # new figure
- # set title
- fig2.suptitle(
- 'Individual Derivatives (plate #{})'.format(str(plate.id)))
-
- for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
- well = plate.wells[plot_num - 1]
- # get single well based on current plot number
- ax = fig2.add_subplot(plate.rows, plate.cols, plot_num)
- # add new subplot
- ax.autoscale(tight=True) # scale to data
- ax.set_title(well.name, size='xx-small')
- # set title of current subplot to well identifier
-
- if well in plate.denatured_wells:
- ax.patch.set_facecolor('#FFD6D6')
- # add axis label to the subplot in the bottom left corner of the
- # figure
- if plot_num == plate.wellnum - plate.cols + 1:
- ax.set_xlabel(u'T [°C]', size='xx-small')
- ax.set_ylabel('dI/dT', size='xx-small')
-
- # set values for the x axis to the given temperature range
- x = plate.temprange
- if well.baseline_correction:
- print(well.baseline)
- y = well.derivatives[1] - well.baseline
- else:
- # grab y values from the first derivative of the well
- y = well.derivatives[1]
-
- # only show three tickmarks on both axes
- ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
- ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
- # check if well is denatured (without determined Tm)
- if well not in plate.denatured_wells:
- tm = well.tm # if not, grab its Tm
- else:
- tm = np.NaN # else set Tm to np.NaN
- if tm:
- ax.axvline(x=tm) # plot vertical line at the Tm
- ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
- alpha=0.5) # shade lower cutoff area
- ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
- alpha=0.5) # shade higher cutoff area
- # set fontsize for all tick labels to xx-small
- for label in ax.get_xticklabels() + ax.get_yticklabels():
- label.set_fontsize('xx-small')
-
- ax.plot(x, y) # plot data to the current subplot
- canvas.draw()
-
def plot_raw(self, plate, widget):
- """
- Plot raw data (Fig. 3)
- """
- canvas = widget.canvas
- canvas.clear()
-
- im = np.arange(100)
- im.shape = 10, 10
-
- fig = canvas.fig
- fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
-
- grid = mpl_toolkits.axes_grid1.Grid(fig, 111,
- nrows_ncols=(plate.rows,
- plate.cols),
- axes_pad=(0.1, 0.25),
- add_all=True,
- share_x=True,
- share_y=True,
- share_all=True)
+ n = 0
for i in range(plate.wellnum):
well = plate.wells[i]
# set values for the x axis to the given temperature range
x = plate.temprange
# grab y values from the raw data of the well
y = well.raw
- ax = grid[i]
- # set title of current subplot to well identifier
- ax.set_title(well.name, size=6)
- if well in plate.denatured_wells:
- ax.patch.set_facecolor('#FFD6D6')
- # only show three tickmarks on both axes
- ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
- ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
- ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
- alpha=0.5) # shade lower cutoff area
- ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
- alpha=0.5) # shade higher cutoff area
- # set fontsize for all tick labels to xx-small
- for label in ax.get_xticklabels() + ax.get_yticklabels():
- label.set_fontsize(6)
- ax.plot(x, y)
- fig.tight_layout()
- canvas.draw()
+ print(well.name)
+ if n == plate.cols:
+ print("next row")
+ widget.nextRow()
+ n = 0
+ n += 1
+ p1 = widget.addPlot(title=well.name, x=x, y=well.raw)
+
+
+# def plot_tm_heatmap_single(self, plate, widget):
+# """
+# Plot Tm heatmap (Fig. 1)
+# """
+# x = 1 # Position in columns
+# y = 1 # Position in rows
+# x_values = [] # Array holding the columns
+# y_values = [] # Array holding the rows
+# c_values = [] # Array holding the color values aka Tm
+# dx_values = []
+# dy_values = []
+# canvas = widget.canvas
+# canvas.clear()
+# for well in plate.wells: # Iterate over all wells
+# if well not in plate.denatured_wells:
+# # Check if well is denatured (no Tm found)
+# c = well.tm # If not, set color to Tm
+# if c < plate.tm_cutoff_low:
+# # Check if Tm is lower that the cutoff
+# c = plate.tm_cutoff_low
+# # If it is, set color to cutoff
+# elif c > plate.tm_cutoff_high:
+# # Check if Tm is higher that the cutoff
+# c = plate.tm_cutoff_high
+# # If it is, set color to cutoff
+# else: # If the plate is denatured
+# c = plate.tm_cutoff_low
+# # Set its color to the low cutoff
+# dx_values.append(x)
+# dy_values.append(y)
+# x_values.append(x) # Add values to the respective arrays
+# y_values.append(y)
+# c_values.append(c)
+# x += 1 # Increase column by one
+# if x > plate.cols: # If maximum column per row is reached
+# x = 1 # reset column to one
+# y += 1 # and increase row by one
+#
+# fig1 = canvas.fig # new figure
+# ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
+# ax1.autoscale(tight=True) # Scale plate size
+# ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1))
+# # n columns
+# ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1))
+# # n rows
+# if plate.color_range:
+# # plot wells and color using the colormap
+# cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
+# marker='s', vmin=plate.color_range[0],
+# vmax=plate.color_range[1])
+# else:
+# # plot wells and color using the colormap
+# cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
+# marker='s')
+#
+# ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x',
+# linewidths=(1.5,))
+# ax1.invert_yaxis() # invert y axis to math plate layout
+# cbar = fig1.colorbar(cax) # show colorbar
+# ax1.set_xlabel('Columns') # set axis and colorbar label
+# ax1.set_ylabel('Rows')
+#
+# if str(plate.id) == 'average':
+# title = '$T_m$ heatmap (average)'
+# else:
+# title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
+# ax1.set_title(title)
+# cbar.set_label(u"Temperature [°C]")
+#
+# canvas.draw()
+#
+# def plot_derivative(self, plate, widget):
+# """
+# Plot derivatives (Fig. 2)
+# """
+# canvas = widget.canvas
+# canvas.clear()
+# fig2 = canvas.fig # new figure
+# # set title
+# fig2.suptitle(
+# 'Individual Derivatives (plate #{})'.format(str(plate.id)))
+#
+# for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
+# well = plate.wells[plot_num - 1]
+# # get single well based on current plot number
+# ax = fig2.add_subplot(plate.rows, plate.cols, plot_num)
+# # add new subplot
+# ax.autoscale(tight=True) # scale to data
+# ax.set_title(well.name, size='xx-small')
+# # set title of current subplot to well identifier
+#
+# if well in plate.denatured_wells:
+# ax.patch.set_facecolor('#FFD6D6')
+# # add axis label to the subplot in the bottom left corner of the
+# # figure
+# if plot_num == plate.wellnum - plate.cols + 1:
+# ax.set_xlabel(u'T [°C]', size='xx-small')
+# ax.set_ylabel('dI/dT', size='xx-small')
+#
+# # set values for the x axis to the given temperature range
+# x = plate.temprange
+# if well.baseline_correction:
+# print(well.baseline)
+# y = well.derivatives[1] - well.baseline
+# else:
+# # grab y values from the first derivative of the well
+# y = well.derivatives[1]
+#
+# # only show three tickmarks on both axes
+# ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
+# ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
+# # check if well is denatured (without determined Tm)
+# if well not in plate.denatured_wells:
+# tm = well.tm # if not, grab its Tm
+# else:
+# tm = np.NaN # else set Tm to np.NaN
+# if tm:
+# ax.axvline(x=tm) # plot vertical line at the Tm
+# ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
+# alpha=0.5) # shade lower cutoff area
+# ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
+# alpha=0.5) # shade higher cutoff area
+# # set fontsize for all tick labels to xx-small
+# for label in ax.get_xticklabels() + ax.get_yticklabels():
+# label.set_fontsize('xx-small')
+#
+# ax.plot(x, y) # plot data to the current subplot
+# canvas.draw()
+#
+# def plot_raw(self, plate, widget):
+# """
+# Plot raw data (Fig. 3)
+# """
+# canvas = widget.canvas
+# canvas.clear()
+#
+# im = np.arange(100)
+# im.shape = 10, 10
+#
+# fig = canvas.fig
+# fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
+#
+# grid = mpl_toolkits.axes_grid1.Grid(fig, 111,
+# nrows_ncols=(plate.rows,
+# plate.cols),
+# axes_pad=(0.1, 0.25),
+# add_all=True,
+# share_x=True,
+# share_y=True,
+# share_all=True)
+# for i in range(plate.wellnum):
+# well = plate.wells[i]
+# # set values for the x axis to the given temperature range
+# x = plate.temprange
+# # grab y values from the raw data of the well
+# y = well.raw
+# ax = grid[i]
+# # set title of current subplot to well identifier
+# ax.set_title(well.name, size=6)
+# if well in plate.denatured_wells:
+# ax.patch.set_facecolor('#FFD6D6')
+# # only show three tickmarks on both axes
+# ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
+# ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
+# ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
+# alpha=0.5) # shade lower cutoff area
+# ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
+# alpha=0.5) # shade higher cutoff area
+# # set fontsize for all tick labels to xx-small
+# for label in ax.get_xticklabels() + ax.get_yticklabels():
+# label.set_fontsize(6)
+# ax.plot(x, y)
+# fig.tight_layout()
+# canvas.draw()
diff --git a/ui/Ui_mainwindow.py b/ui/Ui_mainwindow.py
index 679dd05..6d4abc4 100644
--- a/ui/Ui_mainwindow.py
+++ b/ui/Ui_mainwindow.py
@@ -300,5 +300,3 @@ class Ui_MainWindow(object):
self.actionQuit.setText(_translate("MainWindow", "&Quit"))
self.actionAbout.setText(_translate("MainWindow", "&About"))
self.actionAbout_Qt.setText(_translate("MainWindow", "About &Qt"))
-
-from .mplwidget import MplWidget
diff --git a/ui/libs/__init__.py b/ui/libs/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/libs/pyqtgraph b/ui/libs/pyqtgraph
similarity index 100%
rename from libs/pyqtgraph
rename to ui/libs/pyqtgraph
diff --git a/ui/mainwindow.py b/ui/mainwindow.py
index 2f0a167..40c8cf7 100644
--- a/ui/mainwindow.py
+++ b/ui/mainwindow.py
@@ -13,12 +13,15 @@ from PyQt5.QtWidgets import (QMainWindow,
QDialogButtonBox,
QFileDialog,
QMessageBox,
- QApplication)
+ QApplication,
+ QScrollArea)
from .Ui_mainwindow import Ui_MainWindow
-from .mplwidget import MplWidget
+import ui.libs.pyqtgraph as pg
from pydsf import Experiment, PlotResults
+pg.setConfigOptions(antialias=True)
+
VERSION = "1.0"
@@ -152,29 +155,34 @@ class MainWindow(QMainWindow, Ui_MainWindow):
# self.groupBox_signal_threshold.setEnabled(True)
def generate_plot_tab(self, name):
- tab = MplWidget()
+ tab = QScrollArea()
tab.setObjectName(name)
+ tab.setWidgetResizable(True)
return tab
def generate_plate_tabs(self, plate):
+ # TODO: not implemented yet
+ # raise NotImplementedError
plotter = PlotResults()
if id != 'average':
- tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
- self.tabWidget.addTab(tab, "Heatmap #{}".format(plate.id))
- plotter.plot_tm_heatmap_single(plate, tab)
+ # tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
+ # self.tabWidget.addTab(tab, "Heatmap #{}".format(plate.id))
+ # plotter.plot_tm_heatmap_single(plate, tab)
tab = self.generate_plot_tab("tab_raw_{}".format(id))
+ plt = pg.GraphicsLayoutWidget()
+ tab.setWidget(plt)
self.tabWidget.addTab(tab, "Raw Data #{}".format(plate.id))
- plotter.plot_raw(plate, tab)
+ plotter.plot_raw(plate, plt)
- tab = self.generate_plot_tab("tab_derivative_{}".format(id))
- self.tabWidget.addTab(tab, "Derivatives #{}".format(plate.id))
- plotter.plot_derivative(plate, tab)
- else:
- tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
- self.tabWidget.addTab(tab, "Heatmap ({})".format(plate.id))
- plotter.plot_tm_heatmap_single(plate, tab)
+ # tab = self.generate_plot_tab("tab_derivative_{}".format(id))
+ # self.tabWidget.addTab(tab, "Derivatives #{}".format(plate.id))
+ # plotter.plot_derivative(plate, tab)
+ #else:
+ # tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
+ # self.tabWidget.addTab(tab, "Heatmap ({})".format(plate.id))
+ # plotter.plot_tm_heatmap_single(plate, tab)
@pyqtSlot()
def on_buttonBox_process_accepted(self):
diff --git a/ui/mainwindow.ui b/ui/mainwindow.ui
index 834b463..8c4bd52 100644
--- a/ui/mainwindow.ui
+++ b/ui/mainwindow.ui
@@ -478,22 +478,22 @@
0
-
+
Raw Data
-
+
&2nd derivative
-
+
Heatmap
-
+
false
@@ -563,9 +563,9 @@
- MplWidget
+ GraphicsLayoutWidget
QWidget
-
+
1
diff --git a/ui/mplwidget.py b/ui/mplwidget.py
deleted file mode 100644
index d2a37ae..0000000
--- a/ui/mplwidget.py
+++ /dev/null
@@ -1,27 +0,0 @@
-from PyQt5 import QtWidgets, QtGui, QtCore
-from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
-from matplotlib.figure import Figure
-
-class MplCanvas(FigureCanvas):
- def __init__(self):
- self.fig = Figure()
- self.ax = self.fig.add_subplot(111)
- FigureCanvas.__init__(self, self.fig)
- FigureCanvas.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
- FigureCanvas.updateGeometry(self)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
-
- def clear(self):
- self.ax.clear()
- self.fig.clear()
-
-class MplWidget(QtWidgets.QWidget):
- def __init__(self, parent = None):
- QtWidgets.QWidget.__init__(self, parent)
- self.canvas = MplCanvas()
- self.ntb = NavigationToolbar(self.canvas, self)
- self.vbl = QtWidgets.QVBoxLayout()
- self.vbl.addWidget(self.canvas)
- self.vbl.addWidget(self.ntb)
- self.setLayout(self.vbl)
\ No newline at end of file