mirror of
https://github.com/Athemis/PyDSF.git
synced 2025-04-05 06:36:04 +00:00
Switching to pyqtgraph (WIP)
This commit is contained in:
parent
a0613fb8cc
commit
86b5090b49
8 changed files with 217 additions and 225 deletions
4
.gitmodules
vendored
4
.gitmodules
vendored
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@ -1,3 +1,3 @@
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[submodule "libs/pyqtgraph"]
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path = libs/pyqtgraph
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[submodule "ui/libs/pyqtgraph"]
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path = ui/libs/pyqtgraph
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url = https://github.com/pyqtgraph/pyqtgraph-core.git
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361
pydsf.py
361
pydsf.py
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@ -6,15 +6,11 @@ import csv
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# Import 3rd party packages. Check if installed and die with error message
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# if not.
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try:
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import matplotlib as mpl
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import mpl_toolkits.axes_grid1
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mpl.use('Qt5Agg')
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mpl.interactive(True)
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import matplotlib.ticker as ticker
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try:
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import ui.libs.pyqtgraph as pg
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except ImportError:
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raise ImportError('----- Matplotlib must be installed. -----')
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raise ImportError('----- pyqtgraph must be installed. -----')
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try:
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import peakutils
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@ -532,177 +528,194 @@ def update_progress_bar(bar, value):
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class PlotResults():
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def plot_tm_heatmap_single(self, plate, widget):
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"""
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Plot Tm heatmap (Fig. 1)
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"""
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x = 1 # Position in columns
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y = 1 # Position in rows
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x_values = [] # Array holding the columns
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y_values = [] # Array holding the rows
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c_values = [] # Array holding the color values aka Tm
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dx_values = []
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dy_values = []
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canvas = widget.canvas
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canvas.clear()
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for well in plate.wells: # Iterate over all wells
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if well not in plate.denatured_wells:
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# Check if well is denatured (no Tm found)
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c = well.tm # If not, set color to Tm
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if c < plate.tm_cutoff_low:
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# Check if Tm is lower that the cutoff
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c = plate.tm_cutoff_low
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# If it is, set color to cutoff
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elif c > plate.tm_cutoff_high:
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# Check if Tm is higher that the cutoff
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c = plate.tm_cutoff_high
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# If it is, set color to cutoff
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else: # If the plate is denatured
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c = plate.tm_cutoff_low
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# Set its color to the low cutoff
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dx_values.append(x)
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dy_values.append(y)
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x_values.append(x) # Add values to the respective arrays
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y_values.append(y)
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c_values.append(c)
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x += 1 # Increase column by one
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if x > plate.cols: # If maximum column per row is reached
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x = 1 # reset column to one
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y += 1 # and increase row by one
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fig1 = canvas.fig # new figure
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ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
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ax1.autoscale(tight=True) # Scale plate size
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ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1))
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# n columns
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ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1))
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# n rows
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if plate.color_range:
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# plot wells and color using the colormap
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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marker='s', vmin=plate.color_range[0],
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vmax=plate.color_range[1])
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else:
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# plot wells and color using the colormap
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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marker='s')
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ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x',
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linewidths=(1.5,))
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ax1.invert_yaxis() # invert y axis to math plate layout
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cbar = fig1.colorbar(cax) # show colorbar
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ax1.set_xlabel('Columns') # set axis and colorbar label
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ax1.set_ylabel('Rows')
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if str(plate.id) == 'average':
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title = '$T_m$ heatmap (average)'
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else:
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title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
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ax1.set_title(title)
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cbar.set_label(u"Temperature [°C]")
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canvas.draw()
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def plot_derivative(self, plate, widget):
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"""
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Plot derivatives (Fig. 2)
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"""
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canvas = widget.canvas
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canvas.clear()
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fig2 = canvas.fig # new figure
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# set title
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fig2.suptitle(
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'Individual Derivatives (plate #{})'.format(str(plate.id)))
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for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
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well = plate.wells[plot_num - 1]
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# get single well based on current plot number
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ax = fig2.add_subplot(plate.rows, plate.cols, plot_num)
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# add new subplot
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ax.autoscale(tight=True) # scale to data
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ax.set_title(well.name, size='xx-small')
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# set title of current subplot to well identifier
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if well in plate.denatured_wells:
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ax.patch.set_facecolor('#FFD6D6')
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# add axis label to the subplot in the bottom left corner of the
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# figure
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if plot_num == plate.wellnum - plate.cols + 1:
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ax.set_xlabel(u'T [°C]', size='xx-small')
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ax.set_ylabel('dI/dT', size='xx-small')
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# set values for the x axis to the given temperature range
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x = plate.temprange
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if well.baseline_correction:
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print(well.baseline)
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y = well.derivatives[1] - well.baseline
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else:
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# grab y values from the first derivative of the well
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y = well.derivatives[1]
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# only show three tickmarks on both axes
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ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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# check if well is denatured (without determined Tm)
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if well not in plate.denatured_wells:
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tm = well.tm # if not, grab its Tm
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else:
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tm = np.NaN # else set Tm to np.NaN
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if tm:
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ax.axvline(x=tm) # plot vertical line at the Tm
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ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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alpha=0.5) # shade lower cutoff area
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ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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alpha=0.5) # shade higher cutoff area
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# set fontsize for all tick labels to xx-small
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for label in ax.get_xticklabels() + ax.get_yticklabels():
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label.set_fontsize('xx-small')
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ax.plot(x, y) # plot data to the current subplot
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canvas.draw()
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def plot_raw(self, plate, widget):
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"""
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Plot raw data (Fig. 3)
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"""
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canvas = widget.canvas
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canvas.clear()
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im = np.arange(100)
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im.shape = 10, 10
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fig = canvas.fig
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fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
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grid = mpl_toolkits.axes_grid1.Grid(fig, 111,
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nrows_ncols=(plate.rows,
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plate.cols),
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axes_pad=(0.1, 0.25),
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add_all=True,
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share_x=True,
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share_y=True,
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share_all=True)
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n = 0
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for i in range(plate.wellnum):
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well = plate.wells[i]
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# set values for the x axis to the given temperature range
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x = plate.temprange
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# grab y values from the raw data of the well
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y = well.raw
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ax = grid[i]
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# set title of current subplot to well identifier
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ax.set_title(well.name, size=6)
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if well in plate.denatured_wells:
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ax.patch.set_facecolor('#FFD6D6')
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# only show three tickmarks on both axes
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ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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alpha=0.5) # shade lower cutoff area
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ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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alpha=0.5) # shade higher cutoff area
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# set fontsize for all tick labels to xx-small
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for label in ax.get_xticklabels() + ax.get_yticklabels():
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label.set_fontsize(6)
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ax.plot(x, y)
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fig.tight_layout()
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canvas.draw()
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print(well.name)
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if n == plate.cols:
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print("next row")
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widget.nextRow()
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n = 0
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n += 1
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p1 = widget.addPlot(title=well.name, x=x, y=well.raw)
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# def plot_tm_heatmap_single(self, plate, widget):
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# """
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# Plot Tm heatmap (Fig. 1)
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# """
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# x = 1 # Position in columns
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# y = 1 # Position in rows
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# x_values = [] # Array holding the columns
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# y_values = [] # Array holding the rows
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# c_values = [] # Array holding the color values aka Tm
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# dx_values = []
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# dy_values = []
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# canvas = widget.canvas
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# canvas.clear()
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# for well in plate.wells: # Iterate over all wells
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# if well not in plate.denatured_wells:
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# # Check if well is denatured (no Tm found)
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# c = well.tm # If not, set color to Tm
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# if c < plate.tm_cutoff_low:
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# # Check if Tm is lower that the cutoff
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# c = plate.tm_cutoff_low
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# # If it is, set color to cutoff
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# elif c > plate.tm_cutoff_high:
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# # Check if Tm is higher that the cutoff
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# c = plate.tm_cutoff_high
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# # If it is, set color to cutoff
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# else: # If the plate is denatured
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# c = plate.tm_cutoff_low
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# # Set its color to the low cutoff
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# dx_values.append(x)
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# dy_values.append(y)
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# x_values.append(x) # Add values to the respective arrays
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# y_values.append(y)
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# c_values.append(c)
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# x += 1 # Increase column by one
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# if x > plate.cols: # If maximum column per row is reached
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# x = 1 # reset column to one
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# y += 1 # and increase row by one
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#
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# fig1 = canvas.fig # new figure
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# ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
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# ax1.autoscale(tight=True) # Scale plate size
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# ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1))
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# # n columns
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# ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1))
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# # n rows
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# if plate.color_range:
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# # plot wells and color using the colormap
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# cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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# marker='s', vmin=plate.color_range[0],
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# vmax=plate.color_range[1])
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# else:
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# # plot wells and color using the colormap
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# cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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# marker='s')
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#
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# ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x',
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# linewidths=(1.5,))
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# ax1.invert_yaxis() # invert y axis to math plate layout
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# cbar = fig1.colorbar(cax) # show colorbar
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# ax1.set_xlabel('Columns') # set axis and colorbar label
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# ax1.set_ylabel('Rows')
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#
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# if str(plate.id) == 'average':
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# title = '$T_m$ heatmap (average)'
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# else:
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# title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
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# ax1.set_title(title)
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# cbar.set_label(u"Temperature [°C]")
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#
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# canvas.draw()
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#
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# def plot_derivative(self, plate, widget):
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# """
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# Plot derivatives (Fig. 2)
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# """
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# canvas = widget.canvas
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# canvas.clear()
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# fig2 = canvas.fig # new figure
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# # set title
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# fig2.suptitle(
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# 'Individual Derivatives (plate #{})'.format(str(plate.id)))
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#
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# for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
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# well = plate.wells[plot_num - 1]
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# # get single well based on current plot number
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# ax = fig2.add_subplot(plate.rows, plate.cols, plot_num)
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# # add new subplot
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# ax.autoscale(tight=True) # scale to data
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# ax.set_title(well.name, size='xx-small')
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# # set title of current subplot to well identifier
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#
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# if well in plate.denatured_wells:
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# ax.patch.set_facecolor('#FFD6D6')
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# # add axis label to the subplot in the bottom left corner of the
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# # figure
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# if plot_num == plate.wellnum - plate.cols + 1:
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# ax.set_xlabel(u'T [°C]', size='xx-small')
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# ax.set_ylabel('dI/dT', size='xx-small')
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#
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# # set values for the x axis to the given temperature range
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# x = plate.temprange
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# if well.baseline_correction:
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# print(well.baseline)
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# y = well.derivatives[1] - well.baseline
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# else:
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# # grab y values from the first derivative of the well
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# y = well.derivatives[1]
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#
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# # only show three tickmarks on both axes
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# ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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# ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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# # check if well is denatured (without determined Tm)
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# if well not in plate.denatured_wells:
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# tm = well.tm # if not, grab its Tm
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# else:
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# tm = np.NaN # else set Tm to np.NaN
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# if tm:
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# ax.axvline(x=tm) # plot vertical line at the Tm
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# ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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# alpha=0.5) # shade lower cutoff area
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# ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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# alpha=0.5) # shade higher cutoff area
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# # set fontsize for all tick labels to xx-small
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# for label in ax.get_xticklabels() + ax.get_yticklabels():
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# label.set_fontsize('xx-small')
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#
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# ax.plot(x, y) # plot data to the current subplot
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# canvas.draw()
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#
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# def plot_raw(self, plate, widget):
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# """
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# Plot raw data (Fig. 3)
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# """
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# canvas = widget.canvas
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# canvas.clear()
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#
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# im = np.arange(100)
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# im.shape = 10, 10
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#
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# fig = canvas.fig
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# fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
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#
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# grid = mpl_toolkits.axes_grid1.Grid(fig, 111,
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# nrows_ncols=(plate.rows,
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# plate.cols),
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# axes_pad=(0.1, 0.25),
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# add_all=True,
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# share_x=True,
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# share_y=True,
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# share_all=True)
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# for i in range(plate.wellnum):
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# well = plate.wells[i]
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# # set values for the x axis to the given temperature range
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# x = plate.temprange
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# # grab y values from the raw data of the well
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# y = well.raw
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# ax = grid[i]
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# # set title of current subplot to well identifier
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# ax.set_title(well.name, size=6)
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# if well in plate.denatured_wells:
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# ax.patch.set_facecolor('#FFD6D6')
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# # only show three tickmarks on both axes
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# ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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# ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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# ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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# alpha=0.5) # shade lower cutoff area
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# ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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# alpha=0.5) # shade higher cutoff area
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# # set fontsize for all tick labels to xx-small
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# for label in ax.get_xticklabels() + ax.get_yticklabels():
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# label.set_fontsize(6)
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# ax.plot(x, y)
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# fig.tight_layout()
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# canvas.draw()
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@ -300,5 +300,3 @@ class Ui_MainWindow(object):
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self.actionQuit.setText(_translate("MainWindow", "&Quit"))
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self.actionAbout.setText(_translate("MainWindow", "&About"))
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self.actionAbout_Qt.setText(_translate("MainWindow", "About &Qt"))
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from .mplwidget import MplWidget
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0
ui/libs/__init__.py
Normal file
0
ui/libs/__init__.py
Normal file
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@ -13,12 +13,15 @@ from PyQt5.QtWidgets import (QMainWindow,
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QDialogButtonBox,
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QFileDialog,
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QMessageBox,
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QApplication)
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QApplication,
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QScrollArea)
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from .Ui_mainwindow import Ui_MainWindow
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from .mplwidget import MplWidget
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import ui.libs.pyqtgraph as pg
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from pydsf import Experiment, PlotResults
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pg.setConfigOptions(antialias=True)
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VERSION = "1.0"
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@ -152,29 +155,34 @@ class MainWindow(QMainWindow, Ui_MainWindow):
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# self.groupBox_signal_threshold.setEnabled(True)
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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):
|
||||
|
|
|
|||
|
|
@ -478,22 +478,22 @@
|
|||
<property name="currentIndex">
|
||||
<number>0</number>
|
||||
</property>
|
||||
<widget class="MplWidget" name="tab_raw">
|
||||
<widget class="GraphicsLayoutWidget" name="tab_raw">
|
||||
<attribute name="title">
|
||||
<string>Raw Data</string>
|
||||
</attribute>
|
||||
</widget>
|
||||
<widget class="MplWidget" name="tab_derivative">
|
||||
<widget class="GraphicsLayoutWidget" name="tab_derivative">
|
||||
<attribute name="title">
|
||||
<string>&2nd derivative</string>
|
||||
</attribute>
|
||||
</widget>
|
||||
<widget class="MplWidget" name="tab_heatmap">
|
||||
<widget class="GraphicsLayoutWidget" name="tab_heatmap">
|
||||
<attribute name="title">
|
||||
<string>Heatmap</string>
|
||||
</attribute>
|
||||
</widget>
|
||||
<widget class="MplWidget" name="tab_heatmap_avg">
|
||||
<widget class="GraphicsLayoutWidget" name="tab_heatmap_avg">
|
||||
<property name="enabled">
|
||||
<bool>false</bool>
|
||||
</property>
|
||||
|
|
@ -563,9 +563,9 @@
|
|||
</widget>
|
||||
<customwidgets>
|
||||
<customwidget>
|
||||
<class>MplWidget</class>
|
||||
<class>GraphicsLayoutWidget</class>
|
||||
<extends>QWidget</extends>
|
||||
<header>mplwidget</header>
|
||||
<header>GraphicsLayoutWidget</header>
|
||||
<container>1</container>
|
||||
</customwidget>
|
||||
</customwidgets>
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
Loading…
Add table
Reference in a new issue