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Start reimplementing plotting code
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commit
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5 changed files with 152 additions and 54 deletions
92
pydsf.py
92
pydsf.py
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@ -1,14 +1,18 @@
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#! /usr/bin/env python2
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# -*- coding: utf-8 -*-
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import csv
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import random
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try:
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import matplotlib as mpl
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#import mpl_toolkits.axes_grid
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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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import matplotlib.pyplot as plt
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import matplotlib.patches as mpatches
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import matplotlib.gridspec as gridspec
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except ImportError:
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raise ImportError('----- Matplotlib must be installed. -----')
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@ -436,9 +440,6 @@ def update_progress_bar(bar, value):
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class PlotResults():
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def __init__(self, experiment):
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self.experiment = experiment
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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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@ -550,35 +551,86 @@ class PlotResults():
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"""
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canvas = widget.canvas
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canvas.clear()
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fig3 = canvas.fig # new figure
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fig3.suptitle('Raw Data (plate #{})'.format(str(plate.id))) # set title
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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] # get single well based on current plot number
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ax = fig3.add_subplot(plate.rows, plate.cols, plot_num) # 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') # set title of current subplot to well identifier
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im = np.arange(100)
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im.shape = 10, 10
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if well in plate.denatured_wells:
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ax.patch.set_facecolor('#FFD6D6')
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if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
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ax.set_xlabel(u'T [°C]', size='xx-small')
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ax.set_ylabel('I', size='xx-small')
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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, nrows_ncols=(plate.rows, plate.cols), axes_pad=(0.1, 0.25), add_all=True, share_x=True, share_y=True, 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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x = plate.temprange # set values for the x axis to the given temperature range
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y = well.raw # grab y values from the raw data of the well
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ax = grid[i]
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#ax = fig.add_subplot(plate.rows, plate.cols, i+1)
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ax.set_title(well.name, size=6) # 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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ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes
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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', alpha=0.5) # shade lower cutoff area
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ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
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for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
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label.set_fontsize('xx-small')
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cax = ax.plot(x, y) # plot data to the current subplot
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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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#ax = grid[i]
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#ax.axhline(color='r')
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#ax.autoscale(enable=True, axis='y', tight=True)
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#ax.set_title(well.name, size='xx-small')
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#ax.plot(x, 1000*np.random.random(76))
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#ax.set_yscale('log')
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#for plot_num in range(1, plate.wellnum + 1):
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# well = plate.wells[plot_num - 1]
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# #ax = fig.add_subplot(plate.rows, plate.cols, plot_num)
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# ax.autoscale(tight=True)
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# ax.plot(plate.temprange, well.raw)
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# ax.set_title(well.name, size='xx-small')
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# if well in plate.denatured_wells:
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# ax.patch.set_facecolor('#FFD6D6')
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#for plot_num in range(1, plate.wellnum + 1):
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# ax = fig.add_subplot(plate.rows, plate.cols, plot_num)
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# ax.autoscale(tight=True)
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# fig3 = canvas.fig # new figure
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# fig3.suptitle('Raw Data (plate #{})'.format(str(plate.id))) # set title
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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] # get single well based on current plot number
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# ax = fig3.add_subplot(plate.rows, plate.cols, plot_num) # add new subplot
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# ax = fig3.add_axes(plate.rows, plate.cols, plot_num)
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# ax.autoscale(tight=True) # scale to data
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# ax.set_title(well.name, size='xx-small') # 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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#
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# if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
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# ax.set_xlabel(u'T [°C]', size='xx-small')
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# ax.set_ylabel('I', size='xx-small')
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#
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# x = plate.temprange # set values for the x axis to the given temperature range
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# y = well.raw # grab y values from the raw data of the well
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#
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# ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes
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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', alpha=0.5) # shade lower cutoff area
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# ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
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# for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
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# label.set_fontsize('xx-small')
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#
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# cax = ax.plot(x, y) # plot data to the current subplot
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# def _plot_wrapper(self, plot, plate):
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#
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@ -202,19 +202,19 @@ class Ui_MainWindow(object):
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self.tabWidget.setSizePolicy(sizePolicy)
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self.tabWidget.setMinimumSize(QtCore.QSize(300, 300))
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self.tabWidget.setObjectName("tabWidget")
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self.tab_raw = MplWidget()
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self.tab_raw.setObjectName("tab_raw")
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self.tabWidget.addTab(self.tab_raw, "")
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self.tab_derivative = MplWidget()
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self.tab_derivative.setObjectName("tab_derivative")
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self.tabWidget.addTab(self.tab_derivative, "")
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self.tab_heatmap = MplWidget()
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self.tab_heatmap.setObjectName("tab_heatmap")
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self.tabWidget.addTab(self.tab_heatmap, "")
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self.tab_heatmap_avg = MplWidget()
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self.tab_heatmap_avg.setEnabled(False)
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self.tab_heatmap_avg.setObjectName("tab_heatmap_avg")
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self.tabWidget.addTab(self.tab_heatmap_avg, "")
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#self.tab_raw = MplWidget()
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#self.tab_raw.setObjectName("tab_raw")
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#self.tabWidget.addTab(self.tab_raw, "")
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#self.tab_derivative = MplWidget()
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#self.tab_derivative.setObjectName("tab_derivative")
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#self.tabWidget.addTab(self.tab_derivative, "")
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#self.tab_heatmap = MplWidget()
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#self.tab_heatmap.setObjectName("tab_heatmap")
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#self.tabWidget.addTab(self.tab_heatmap, "")
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#self.tab_heatmap_avg = MplWidget()
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#self.tab_heatmap_avg.setEnabled(False)
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#self.tab_heatmap_avg.setObjectName("tab_heatmap_avg")
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#self.tabWidget.addTab(self.tab_heatmap_avg, "")
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self.horizontalLayout.addWidget(self.splitter)
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MainWindow.setCentralWidget(self.centralWidget)
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self.menuBar = QtWidgets.QMenuBar(MainWindow)
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@ -291,10 +291,10 @@ class Ui_MainWindow(object):
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self.doubleSpinBox_cbar_start.setSuffix(_translate("MainWindow", " °C"))
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self.label_cbar_end.setText(_translate("MainWindow", "En&d"))
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self.doubleSpinBox_cbar_end.setSuffix(_translate("MainWindow", " °C"))
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self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_raw), _translate("MainWindow", "Raw Data"))
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self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_derivative), _translate("MainWindow", "&1st derivative"))
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self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap), _translate("MainWindow", "Heatmap"))
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self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap_avg), _translate("MainWindow", "Heatmap average"))
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#self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_raw), _translate("MainWindow", "Raw Data"))
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#self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_derivative), _translate("MainWindow", "&2nd derivative"))
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#self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap), _translate("MainWindow", "Heatmap"))
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#self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap_avg), _translate("MainWindow", "Heatmap average"))
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self.menuFile.setTitle(_translate("MainWindow", "Fi&le"))
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self.menuHelp.setTitle(_translate("MainWindow", "Hel&p"))
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self.actionQuit.setText(_translate("MainWindow", "&Quit"))
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@ -6,12 +6,20 @@ Module implementing MainWindow.
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VERSION = "1.0"
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from PyQt5.QtCore import pyqtSlot
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from PyQt5.QtCore import pyqtSlot, QObject, pyqtSignal
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from PyQt5.QtWidgets import *
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from .Ui_mainwindow import Ui_MainWindow
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from .mplwidget import MplWidget
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from pydsf import *
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class ProcessData(QObject):
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finished = pyqtSignal()
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def process(self):
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raise NotImplementedError
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class MainWindow(QMainWindow, Ui_MainWindow):
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"""
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@ -70,6 +78,27 @@ class MainWindow(QMainWindow, Ui_MainWindow):
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# self.groupBox_cbar.setEnabled(True)
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# self.groupBox_signal_threshold.setEnabled(True)
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def generate_plot_tab(self, name):
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tab = MplWidget()
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tab.setObjectName(name)
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return tab
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def generate_plate_tabs(self, plate):
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plotter = PlotResults()
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if id != 'average':
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tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
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self.tabWidget.addTab(tab, "Heatmap #{}".format(plate.id))
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plotter.plot_tm_heatmap_single(plate, tab)
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tab = self.generate_plot_tab("tab_raw_{}".format(id))
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self.tabWidget.addTab(tab, "Raw Data #{}".format(plate.id))
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plotter.plot_raw(plate, tab)
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else:
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tab = self.generate_plot_tab("tab_heatmap_{}".format(id))
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self.tabWidget.addTab(tab, "Heatmap ({})".format(plate.id))
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plotter.plot_tm_heatmap_single(plate, tab)
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@pyqtSlot()
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def on_buttonBox_process_accepted(self):
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"""
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@ -128,20 +157,36 @@ class MainWindow(QMainWindow, Ui_MainWindow):
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exp.avg_plate.write_avg_tm_table('{}/plate_{}_05_tm_avg.csv'.format(folder, str(exp.avg_plate.id)))
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#plot(plate, self)
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plotter = PlotResults(exp)
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for i in range(self.tabWidget.count()):
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for plate in exp.plates:
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if i == 0:
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plotter.plot_raw(plate, self.tabWidget.widget(i))
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elif i == 1:
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plotter.plot_derivative(plate, self.tabWidget.widget(i))
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elif i == 2:
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plotter.plot_tm_heatmap_single(plate, self.tabWidget.widget(i))
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elif exp.avg_plate and i == 3:
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plotter.plot_tm_heatmap_single(exp.avg_plate, self.tabWidget.widget(i))
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self.tabWidget.setTabEnabled(i, True)
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else:
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self.tabWidget.setTabEnabled(i, False)
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for i in range(len(exp.plates)):
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plate = exp.plates[i]
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self.generate_plate_tabs(plate)
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if exp.avg_plate:
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plate = exp.avg_plate
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self.generate_plate_tabs(plate)
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#for i in range(self.tabWidget.count()):
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# for plate in exp.plates:
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# if i == 0:
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# plotter.plot_raw(plate, self.tabWidget.widget(i))
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# self.tabWidget.setTabText(i, "Raw Data #{}".format(plate.id))
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#elif i == 1:
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# plotter.plot_derivative(plate, self.tabWidget.widget(i))
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#elif i == 2:
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# plotter.plot_tm_heatmap_single(plate, self.tabWidget.widget(i))
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#elif exp.avg_plate and i == 3:
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# plotter.plot_tm_heatmap_single(exp.avg_plate, self.tabWidget.widget(i))
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# self.tabWidget.setTabEnabled(i, True)
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#else:
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# self.tabWidget.setTabEnabled(i, False)
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#fig, ax = figures[0]
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#self.tabWidget.widget(0).canvas.fig = fig
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@ -190,3 +235,4 @@ class MainWindow(QMainWindow, Ui_MainWindow):
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Slot documentation goes here.
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"""
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QApplication.aboutQt()
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@ -485,7 +485,7 @@
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</widget>
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<widget class="MplWidget" name="tab_derivative">
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<attribute name="title">
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<string>&1st derivative</string>
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<string>&2nd derivative</string>
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</attribute>
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</widget>
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<widget class="MplWidget" name="tab_heatmap">
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@ -10,6 +10,7 @@ class MplCanvas(FigureCanvas):
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FigureCanvas.__init__(self, self.fig)
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FigureCanvas.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
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FigureCanvas.updateGeometry(self)
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self.setFocusPolicy(QtCore.Qt.StrongFocus)
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def clear(self):
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self.ax.clear()
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@ -18,7 +19,6 @@ class MplCanvas(FigureCanvas):
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class MplWidget(QtWidgets.QWidget):
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def __init__(self, parent = None):
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QtWidgets.QWidget.__init__(self, parent)
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self.canvas = MplCanvas()
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self.ntb = NavigationToolbar(self.canvas, self)
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self.vbl = QtWidgets.QVBoxLayout()
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