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First implementation of parameter dependency analysis

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in additions, averaging over rows was added
This commit is contained in:
Alexander Minges 2015-09-21 15:39:52 +02:00
parent 455f715e37
commit b8c67a13ed
6 changed files with 4357 additions and 136 deletions
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2
instruments/analytikJenaqTower2.py
View file

@ -11,6 +11,8 @@ class AnalytikJenaqTower2:
self.name = "Analytik Jena qTower 2.0/2.2"
self.providesTempRange = False
self.providesDeltaT = False
self.wells_horizontal = 12
self.wells_vertical = 8
def loadData(self, filename, reads, wells):
with open(filename, 'r') as f:

331
pydsf.py
View file

@ -47,7 +47,12 @@ class Well:
Owned by an object of type 'Plate'.
"""
def __init__(self, owner, name=None):
def __init__(self,
owner,
name=None,
concentration=None,
well_id=None,
empty=False):
self.owner = owner
self.name = name
self.raw = np.zeros(self.owner.reads, dtype=np.float)
@ -58,6 +63,10 @@ class Well:
self.tm_sd = np.NaN
self.baseline_correction = owner.baseline_correction
self.baseline = None
self.concentration = concentration
self.id = well_id
self.empty = empty
self.denatured = True
def filter_raw(self):
"""
@ -110,7 +119,7 @@ class Well:
Checks if a given value is within the defined temperature cutoff.
"""
if (value >= self.owner.tm_cutoff_low and
value <= self.owner.tm_cutoff_high):
value <= self.owner.tm_cutoff_high):
return True
else:
return False
@ -123,11 +132,13 @@ class Well:
try:
# If tm is within cutoff, perform the interpolation
if (self.temp_within_cutoff(tm)):
tm = round(peakutils.interpolate(x, y,
tm = round(peakutils.interpolate(x,
y,
width=3,
ind=[max_i])[0], 2)
ind=[max_i])[0],
2)
# Remove the denatured flag
self.owner.denatured_wells.remove(self)
self.denatured = False
return tm # and return the Tm
else:
return np.NaN # otherwise, return NaN
@ -139,11 +150,15 @@ class Well:
Calculate the Tm of the well. Returns either the Tm or 'np.NaN'.
"""
# Check if the well has already been flagged as denatured
if self in self.owner.denatured_wells:
# if self.denatured:
# return np.NaN # Return 'NaN' if true
# Check if the well is empty
if self.empty:
return np.NaN # Return 'NaN' if true
# First assume that the well is denatured
self.owner.denatured_wells.append(self)
self.denatured = True
# Use the whole temperature range for x. We'll check the cutoff later
x = self.owner.temprange
@ -174,6 +189,7 @@ class Well:
# melting temperature
if max_y and max_i:
tm = x[max_i]
self.denatured = False
return self.interpolate_tm(x, y, max_i, tm)
# if no maximum is found, return NaN
else:
@ -188,21 +204,18 @@ class Well:
already flagged as denatured, no Tm was found, or if the initial
signal intensity is above a user definded threshold.
"""
denatured = True # Assumption is that the well is denatured
if self in self.owner.denatured_wells:
# check if the well is already flagged as denatured
return denatured # return true if it is
if self.denatured:
return self.denatured
if self.tm and (self.tm <= self.owner.tm_cutoff_low or
self.tm >= self.owner.tm_cutoff_high):
denatured = True
return denatured
self.tm >= self.owner.tm_cutoff_high):
self.denatured = True
return self.denatured
for i in self.derivatives[1]:
# Iterate over all points in the first derivative
if i > 0: # If a positive slope is found
denatured = False # set denatured flag to False
self.denatured = False # set denatured flag to False
reads = int(round(self.owner.reads / 10))
# How many values should be checked against the signal threshold:
@ -210,47 +223,48 @@ class Well:
read = 0
# Initialize running variable representing the current data point
if not denatured:
if not self.denatured:
for j in self.filtered: # Iterate over the filtered data
if self.owner.signal_threshold:
# If a signal threshold was defined
if j > self.owner.signal_threshold and read <= reads:
# iterate over 1/10 of all data points
# and check for values larger than the threshold.
denatured = True
self.denatured = True
# Set flag to True if a match is found
print("{}: {}".format(self.name, j))
return denatured # and return
return self.denatured # and return
read += 1
return denatured
return self.denatured
def analyze(self):
"""
Analyse data of the well. Takes care of the calculation of derivatives,
fitting of splines to derivatives and calculation of melting point.
"""
# apply signal filter to raw data to filter out some noise
self.filter_raw()
# fit a spline to unfiltered and filtered raw data
self.splines["raw"] = self.calc_spline(self.raw)
self.splines["filtered"] = self.calc_spline(self.filtered)
# calculate derivatives of filtered data
self.calc_derivatives()
# if baseline correction is requested, calculate baseline
if self.baseline_correction:
self.baseline = self.calc_baseline(self.derivatives[1])
# do an initial check if data suggest denaturation
if self.is_denatured():
# if appropriate, append well to denatured wells of the plate
self.owner.denatured_wells.append(self)
# fit a spline to the first derivative
self.splines["derivative1"] = self.calc_spline(self.derivatives[1])
# calculate and set melting point
self.tm = self.calc_tm()
# fallback: set melting point to NaN
if self.tm is None:
self.tm = np.NaN
if not self.empty:
# apply signal filter to raw data to filter out some noise
self.filter_raw()
# fit a spline to unfiltered and filtered raw data
self.splines["raw"] = self.calc_spline(self.raw)
self.splines["filtered"] = self.calc_spline(self.filtered)
# calculate derivatives of filtered data
self.calc_derivatives()
# if baseline correction is requested, calculate baseline
if self.baseline_correction:
self.baseline = self.calc_baseline(self.derivatives[1])
# do an initial check if data suggest denaturation
# if self.is_denatured():
# if appropriate, append well to denatured wells of the plate
# self.owner.denatured_wells.append(self)
# fit a spline to the first derivative
self.splines["derivative1"] = self.calc_spline(self.derivatives[1])
# calculate and set melting point
self.tm = self.calc_tm()
# fallback: set melting point to NaN
if self.tm is None:
self.tm = np.NaN
class Experiment:
@ -268,7 +282,9 @@ class Experiment:
cutoff_high=None,
signal_threshold=None,
color_range=None,
baseline_correction=False):
baseline_correction=False,
concentrations=None,
average_rows=None):
self.replicates = replicates
self.cols = cols
self.rows = rows
@ -287,6 +303,8 @@ class Experiment:
self.signal_threshold = signal_threshold
self.avg_plate = None
self.baseline_correction = baseline_correction
self.concentrations = concentrations
self.average_rows = average_rows
# use cuttoff if provided, otherwise cut at edges
if cutoff_low:
self.tm_cutoff_low = cutoff_low
@ -322,9 +340,10 @@ class Experiment:
plate.id = i
self.plates.append(plate)
i += 1
# if more than one file is provied, assume that those are replicates
# and add a special plate representing the average results
if len(files) > 1:
# if more than one file is provided or average over rows is requested,
# assume that those are replicates and add a special plate
# representing the average results
if len(files) > 1 or self.average_rows:
self.avg_plate = Plate(owner=self,
filename=None,
t1=self.t1,
@ -338,6 +357,70 @@ class Experiment:
color_range=self.color_range)
self.avg_plate.id = 'average'
def average_by_plates(self):
# iterate over all wells in a plate
for i in range(self.wellnum):
tmp = []
# iterate over all plates
for plate in self.plates:
tm = plate.wells[i].tm
self.avg_plate.wells[i].name = plate.wells[i].name
if not plate.wells[i].denatured:
# if well is not denatured, add to collection of tm
# values
tmp.append(tm)
if len(tmp) > 0:
# if at least one tm is added, calculate average
# and standard deviation
self.avg_plate.wells[i].tm = np.nanmean(tmp)
self.avg_plate.wells[i].tm_sd = np.nanstd(tmp)
self.avg_plate.wells[
i].concentration = plate.wells[i].concentration
else:
# otherwise add to denatured wells
self.avg_plate.wells[i].denatured = True
def average_by_rows(self):
for plate in self.plates:
for well in self.avg_plate.wells:
well.empty = True
i = 0
for column in range(plate.cols):
equivalent_wells = []
for row in range(plate.rows):
w = row * plate.cols + column
mod = (row + 1) % self.average_rows
print("Merging well {} with Tm of {}".format(
plate.wells[w].id, plate.wells[w].tm))
equivalent_wells.append(plate.wells[w].tm)
if mod == 0:
print(equivalent_wells)
mean = np.nanmean(equivalent_wells)
std = np.nanstd(equivalent_wells)
equivalent_wells = []
self.avg_plate.wells[i].empty = False
self.avg_plate.wells[i].tm = mean
self.avg_plate.wells[i].tm_sd = std
self.avg_plate.wells[i].name = plate.wells[i].name
self.avg_plate.wells[
i].concentration = plate.wells[i].concentration
if np.isnan(mean):
self.avg_plate.wells[i].denatured = True
print("Well {} is denatured!".format(i))
else:
self.avg_plate.wells[i].denatured = False
print(
"Adding new well with ID {}, TM {}, SD {}".format(
i, mean, std))
if len(equivalent_wells) == 0:
# i = w
i += 1
def analyze(self):
"""
Triggers analyzation of plates.
@ -347,31 +430,15 @@ class Experiment:
# if more than one plate is present, calculate average values for the
# merged average plate
if len(self.plates) > 1:
# iterate over all wells in a plate
for i in range(self.wellnum):
tmp = []
# iterate over all plates
for plate in self.plates:
tm = plate.wells[i].tm
self.avg_plate.wells[i].name = plate.wells[i].name
if plate.wells[i] not in plate.denatured_wells:
# if well is not denatured, add to collection of tm
# values
tmp.append(tm)
if len(tmp) > 0:
# if at least one tm is added, calculate average
# and standard deviation
self.avg_plate.wells[i].tm = np.mean(tmp)
self.avg_plate.wells[i].tm_sd = np.std(tmp)
else:
# otherwise add to denatured wells
append_well = self.avg_plate.wells[i]
self.avg_plate.denatured_wells.append(append_well)
self.average_by_plates()
elif self.average_rows:
self.average_by_rows()
class Plate:
def __init__(self, owner,
def __init__(self,
owner,
plate_id=None,
filename=None,
replicates=None,
@ -383,7 +450,8 @@ class Plate:
cutoff_low=None,
cutoff_high=None,
signal_threshold=None,
color_range=None):
color_range=None,
concentrations=None):
self.cols = cols
self.rows = rows
self.owner = owner
@ -411,6 +479,10 @@ class Plate:
self.signal_threshold = signal_threshold
self.id = plate_id
self.baseline_correction = owner.baseline_correction
if concentrations is None:
self.concentrations = self.owner.concentrations
else:
self.concentrations = concentrations
if cutoff_low:
self.tm_cutoff_low = cutoff_low
else:
@ -424,34 +496,21 @@ class Plate:
else:
self.color_range = None
self.denatured_wells = []
self.tms = []
# TODO: Adapt for vertical concentrations
conc_id = 0
for i in range(self.wellnum):
well = Well(owner=self)
if self.concentrations:
if conc_id == self.cols:
conc_id = 0
concentration = self.concentrations[conc_id]
conc_id += 1
else:
concentration = None
well = Well(owner=self, well_id=i, concentration=concentration)
self.wells.append(well)
def analytikJena(self):
"""
Data processing for Analytik Jena qTower 2.0 export files
"""
with open(self.filename, 'r') as f:
reader = csv.reader(f, delimiter=';', quoting=csv.QUOTE_NONE)
i = 0
for row in reader:
temp = np.zeros(self.reads, dtype=float)
for read in range(self.reads + 1):
if read > 0:
try:
temp[read - 1] = row[read]
except (IndexError, ValueError):
temp[read - 1] = 0.0
elif read == 0:
self.wells[i].name = row[read]
self.wells[i].raw = temp
i += 1
def analyze(self):
try:
# Try to access data file in the given path
@ -461,8 +520,7 @@ class Plate:
# If the file is not found, or not accessible: abort
print('Error accessing file: {}'.format(e))
self.wells = self.instrument.loadData(self.filename,
self.reads,
self.wells = self.instrument.loadData(self.filename, self.reads,
self.wells)
for well in self.wells:
@ -540,10 +598,12 @@ class PlotResults():
c_values = [] # Array holding the color values aka Tm
dx_values = []
dy_values = []
ex_values = []
ey_values = []
canvas = widget.canvas
canvas.clear()
for well in plate.wells: # Iterate over all wells
if well not in plate.denatured_wells:
if not well.denatured and not well.empty:
# Check if well is denatured (no Tm found)
c = well.tm # If not, set color to Tm
if c < plate.tm_cutoff_low:
@ -554,6 +614,9 @@ class PlotResults():
# Check if Tm is higher that the cutoff
c = plate.tm_cutoff_high
# If it is, set color to cutoff
elif well.empty:
ex_values.append(x)
ey_values.append(y)
else: # If the plate is denatured
c = plate.tm_cutoff_low
# Set its color to the low cutoff
@ -576,7 +639,8 @@ class PlotResults():
# n rows
if plate.color_range:
# plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values,
cax = ax1.scatter(x_values,
y_values,
s=305,
c=c_values,
marker='s',
@ -584,20 +648,27 @@ class PlotResults():
vmax=plate.color_range[1])
else:
# plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values,
cax = ax1.scatter(x_values,
y_values,
s=305,
c=c_values,
marker='s')
ax1.scatter(dx_values, dy_values,
ax1.scatter(dx_values, dy_values, s=305, c='white', marker='s')
ax1.scatter(dx_values,
dy_values,
s=80,
c='white',
c='red',
marker='x',
linewidths=(1.5, ))
ax1.scatter(ex_values, ey_values, s=305, c='white', marker='s')
ax1.invert_yaxis() # invert y axis to math plate layout
cbar = fig1.colorbar(cax) # show colorbar
ax1.set_xlabel(_translate('pydsf',
'Columns')) # set axis and colorbar label
# set axis and colorbar label
ax1.set_xlabel(_translate('pydsf', 'Columns'))
ax1.set_ylabel(_translate('pydsf', 'Rows'))
if str(plate.id) == 'average':
@ -621,7 +692,8 @@ class PlotResults():
fig.suptitle(title + str(plate.id) + ')')
grid = mpl_toolkits.axes_grid1.Grid(
fig, 111,
fig,
111,
nrows_ncols=(plate.rows, plate.cols),
axes_pad=(0.15, 0.25),
add_all=True,
@ -641,22 +713,24 @@ class PlotResults():
ax = grid[i]
# set title of current subplot to well identifier
ax.set_title(well.name, size=6)
if well in plate.denatured_wells:
if well.denatured:
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))
# check if well is denatured (without determined Tm)
if well not in plate.denatured_wells:
if not well.denatured:
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,
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,
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
@ -681,7 +755,8 @@ class PlotResults():
fig.suptitle(title + str(plate.id) + ')')
grid = mpl_toolkits.axes_grid1.Grid(
fig, 111,
fig,
111,
nrows_ncols=(plate.rows, plate.cols),
axes_pad=(0.15, 0.25),
add_all=True,
@ -695,15 +770,17 @@ class PlotResults():
ax = grid[i]
# set title of current subplot to well identifier
ax.set_title(well.name, size=6)
if well in plate.denatured_wells:
if well.denatured:
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,
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,
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
@ -712,3 +789,41 @@ class PlotResults():
ax.plot(x, y)
fig.tight_layout()
canvas.draw()
def plot_concentration_dependency(self,
plate,
widget,
direction='horizontal',
parameter_label='Parameter [au]',
error_bars=False):
canvas = widget.canvas
canvas.clear()
fig = canvas.fig
title = _translate('pydsf', "Melting point vs Parameter (plate #")
fig.suptitle(title + str(plate.id) + ')')
ax1 = fig.add_subplot(111)
ax1.set_xlabel(parameter_label)
ax1.set_ylabel(_translate('pydsf', 'Melting point [°C]'))
for row in range(plate.rows):
x_values = []
y_values = []
if error_bars:
errors = []
for col in range(plate.cols):
well = plate.wells[row * col - 1]
x = well.concentration
y = well.tm
x_values.append(x)
y_values.append(y)
if error_bars:
errors.append(well.tm_sd)
if error_bars:
ax1.errorbar(x_values, y_values, yerr=errors, fmt='o')
else:
ax1.plot(x_values, y_values, 'o')
fig.tight_layout()
canvas.draw()

3905
ui/Ui_mainwindow.py
View file

File diff suppressed because it is too large Load diff

98
ui/mainwindow.py
View file

@ -57,6 +57,15 @@ class Worker(QRunnable):
files = []
for item in items:
files.append(item.text())
replicates = self.owner.groupBox_replicates.isChecked()
row_replicates = self.owner.radioButton_rep_rows.isChecked()
if replicates and row_replicates:
average_rows = self.owner.spinBox_avg_rows.value()
else:
average_rows = None
self.exp = Experiment(instrument=self.owner.instrument,
files=files,
t1=self.owner.doubleSpinBox_tmin.value(),
@ -67,7 +76,9 @@ class Worker(QRunnable):
cutoff_low=c_lower,
cutoff_high=c_upper,
signal_threshold=signal_threshold,
color_range=cbar_range)
color_range=cbar_range,
concentrations=self.owner.concentrations,
average_rows=average_rows)
self.exp.analyze()
self.signals.finished.emit()
@ -77,7 +88,6 @@ class TaskSignals(QObject):
class Tasks(QObject):
def __init__(self):
super(Tasks, self).__init__()
@ -116,7 +126,6 @@ class Tasks(QObject):
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
@ -141,10 +150,13 @@ class MainWindow(QMainWindow, Ui_MainWindow):
QDialogButtonBox.AcceptRole)
self.tasks = Tasks()
self.tasks.signals.finished.connect(self.on_processing_finished)
self.lineEdit_conc.textChanged.connect(
self.on_lineEdit_conc_textChanged)
self.worker = None
self.outputPath = None
self.instrument = None
self.concentrations = None
self.populateInstrumentList()
self.instrument = self.getSelectedInstrument()
def populateInstrumentList(self):
self.instruments = [AnalytikJenaqTower2()]
@ -152,6 +164,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
instrument = self.instruments[i]
self.comboBox_instrument.setItemText(i, instrument.name)
@pyqtSlot()
def getInstrumentFromName(self, name):
for instrument in self.instruments:
if instrument.name == name:
@ -178,7 +191,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.groupBox_replicates.setChecked(True)
self.radioButton_rep_files.setEnabled(True)
elif button == self.buttonBox_open_reset.button(
QDialogButtonBox.Reset):
QDialogButtonBox.Reset):
self.listWidget_data.clear()
@pyqtSlot("QAbstractButton*")
@ -202,8 +215,11 @@ class MainWindow(QMainWindow, Ui_MainWindow):
else:
self.groupBox_temp.setEnabled(True)
def generate_plot_tab(self, name):
tab = MplWidget(parent=self.tabWidget)
def generate_plot_tab(self, name, mouse_event=False):
if mouse_event:
tab = MplWidget(parent=self.tabWidget, mouse_event=True)
else:
tab = MplWidget(parent=self.tabWidget)
tab.setObjectName(name)
return tab
@ -220,7 +236,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
plotter = PlotResults()
if plate.id != 'average':
tab = self.generate_plot_tab("tab_heatmap_{}".format(plate.id))
tab = self.generate_plot_tab("tab_heatmap_{}".format(plate.id),
mouse_event=True)
title = _translate("MainWindow", "Heatmap #")
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab)
@ -243,8 +260,26 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.checkBox_saveplots.isChecked():
tab.canvas.save(
"{}/derivatives_{}.svg".format(self.outputPath, plate.id))
if self.groupBox_conc.isChecked():
tab = self.generate_plot_tab("tab_derivative_{}".format(
plate.id))
title = _translate("MainWindow", "Parameter Dependency #")
self.tabWidget.addTab(tab, title + str(plate.id))
if self.lineEdit_par_label.text():
par_label = self.lineEdit_par_label.text()
plotter.plot_concentration_dependency(
plate,
tab,
parameter_label=par_label)
else:
plotter.plot_concentration_dependency(plate, tab)
if self.checkBox_saveplots.isChecked():
tab.canvas.save(
"{}/para_{}.svg".format(self.outputPath, plate.id))
else:
tab = self.generate_plot_tab("tab_heatmap_{}".format(plate.id))
tab = self.generate_plot_tab("tab_heatmap_{}".format(plate.id),
mouse_event=True)
title = _translate("MainWindow", "Heatmap ")
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab)
@ -252,6 +287,26 @@ class MainWindow(QMainWindow, Ui_MainWindow):
tab.canvas.save(
"{}/heatmap_{}.svg".format(self.outputPath, plate.id))
if self.groupBox_conc.isChecked():
tab = self.generate_plot_tab("tab_derivative_{}".format(
plate.id))
title = _translate("MainWindow", "Parameter Dependency #")
self.tabWidget.addTab(tab, title + str(plate.id))
if self.lineEdit_par_label.text():
par_label = self.lineEdit_par_label.text()
plotter.plot_concentration_dependency(
plate,
tab,
parameter_label=par_label,
error_bars=True)
else:
plotter.plot_concentration_dependency(plate,
tab,
error_bars=True)
if self.checkBox_saveplots.isChecked():
tab.canvas.save(
"{}/para_{}.svg".format(self.outputPath, plate.id))
@pyqtSlot()
def on_buttonBox_process_accepted(self):
"""
@ -267,8 +322,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
_translate("MainWindow", "No data file loaded!"),
QMessageBox.Close, QMessageBox.Close)
return
if self.groupBox_conc.isChecked():
self.concentrations = self.lineEdit_conc.text().split(',')
if (self.groupBox_output.isChecked() and
self.lineEdit_output.text().strip() == ''):
self.lineEdit_output.text().strip() == ''):
QMessageBox.critical(
self, _translate("MainWindow", "Error"),
_translate("MainWindow", "No output path set!"),
@ -323,8 +380,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.checkBox_savetables.isChecked():
for plate in exp.plates:
plate.write_tm_table(
'{}/plate_{}_tm.csv'.format(self.outputPath,
str(plate.id)))
'{}/plate_{}_tm.csv'.format(self.outputPath, str(
plate.id)))
plate.write_data_table(
'{}/plate_{}_dI_dT.csv'.format(self.outputPath,
str(plate.id)),
@ -380,10 +437,25 @@ class MainWindow(QMainWindow, Ui_MainWindow):
dialog.ui.setupUi(dialog)
dialog.exec_()
@pyqtSlot()
def on_actionAbout_Qt_triggered(self):
"""
Slot documentation goes here.
"""
QApplication.aboutQt()
@pyqtSlot()
def on_lineEdit_conc_textChanged(self):
"""
Slot documentation goes here.
"""
num_conc = len(self.lineEdit_conc.text().split(','))
self.spinBox_num_conc.setValue(num_conc)
if self.comboBox_direction.currentIndex() == 0:
max_wells = self.instrument.wells_horizontal
else:
max_wells = self.instrument.wells_vertical
if num_conc > max_wells:
self.spinBox_num_conc.setStyleSheet("QSpinBox { color : red; }")
else:
self.spinBox_num_conc.setStyleSheet("QSpinBox { color : black; }")

134
ui/mainwindow.ui
View file

@ -79,7 +79,7 @@
<item row="0" column="0">
<widget class="QLabel" name="label_instrument">
<property name="text">
<string>Instrument</string>
<string>I&amp;nstrument</string>
</property>
<property name="buddy">
<cstring>comboBox_instrument</cstring>
@ -150,6 +150,13 @@
<bool>false</bool>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<item row="1" column="0">
<widget class="QRadioButton" name="radioButton_rep_rows">
<property name="text">
<string>Rows</string>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QRadioButton" name="radioButton_rep_files">
<property name="enabled">
@ -163,6 +170,23 @@
</property>
</widget>
</item>
<item row="1" column="2">
<widget class="QSpinBox" name="spinBox_avg_rows">
<property name="minimum">
<number>2</number>
</property>
<property name="value">
<number>3</number>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="label_rows">
<property name="text">
<string>Rows to average</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
@ -465,7 +489,7 @@
</layout>
</widget>
</item>
<item row="2" column="0" colspan="2">
<item row="3" column="0" colspan="2">
<widget class="QGroupBox" name="groupBox_output">
<property name="title">
<string>Sa&amp;ve processing results</string>
@ -477,14 +501,14 @@
<bool>false</bool>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<item row="1" column="0">
<widget class="QCheckBox" name="checkBox_saveplots">
<property name="text">
<string>Save plots</string>
</property>
</widget>
</item>
<item row="2" column="1">
<item row="3" column="1">
<widget class="QDialogButtonBox" name="buttonBox_output">
<property name="sizePolicy">
<sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
@ -500,14 +524,14 @@
</property>
</widget>
</item>
<item row="2" column="0">
<item row="3" column="0">
<widget class="QLineEdit" name="lineEdit_output">
<property name="toolTip">
<string>Output results to this path</string>
</property>
</widget>
</item>
<item row="1" column="0">
<item row="2" column="0">
<widget class="QCheckBox" name="checkBox_savetables">
<property name="text">
<string>Save tabular results</string>
@ -517,6 +541,102 @@
</layout>
</widget>
</item>
<item row="2" column="0" colspan="2">
<widget class="QGroupBox" name="groupBox_conc">
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="title">
<string>Parameter Dependency</string>
</property>
<property name="checkable">
<bool>true</bool>
</property>
<property name="checked">
<bool>false</bool>
</property>
<layout class="QFormLayout" name="formLayout_5">
<item row="0" column="0">
<widget class="QLabel" name="label_direction">
<property name="text">
<string>Direction</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QComboBox" name="comboBox_direction">
<property name="sizePolicy">
<sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<item>
<property name="text">
<string>Horizontal</string>
</property>
</item>
<item>
<property name="text">
<string>Vertical</string>
</property>
</item>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="label_conc">
<property name="text">
<string>Parameter Values</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QLineEdit" name="lineEdit_conc">
<property name="toolTip">
<string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Comma-seperated list of concentrations. This has to match the number of wells in either horizontal or vertical dimension. If a well is unused, either leave blank or use &amp;quot;NaN&amp;quot; as input.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_conc_num">
<property name="text">
<string>Number of wells</string>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QSpinBox" name="spinBox_num_conc">
<property name="toolTip">
<string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Displays the number of wells specified above.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property>
<property name="readOnly">
<bool>true</bool>
</property>
<property name="buttonSymbols">
<enum>QAbstractSpinBox::NoButtons</enum>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_par">
<property name="text">
<string>Parameter Label</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLineEdit" name="lineEdit_par_label">
<property name="placeholderText">
<string>Parameter [au]</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
@ -601,7 +721,7 @@
<x>0</x>
<y>0</y>
<width>4095</width>
<height>28</height>
<height>30</height>
</rect>
</property>
<property name="locale">

23
ui/mplwidget.py
View file

@ -19,12 +19,6 @@ class MplCanvas(FigureCanvas):
QtWidgets.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
# override mouseMoveEvent with non-functional dummy
# this will prevent the gui thread to hang while moving the mouse
# while a large number of plots is shown simultaniously
def mouseMoveEvent(self, event):
pass
def clear(self):
self.ax.clear()
self.fig.clear()
@ -40,6 +34,16 @@ class MplCanvas(FigureCanvas):
QtWidgets.QMessageBox.Close, QtWidgets.QMessageBox.Close)
class MplCanvasNoMouse(MplCanvas):
# override mouseMoveEvent with non-functional dummy
# this will prevent the gui thread to hang while moving the mouse
# while a large number of plots is shown simultaniously
def mouseMoveEvent(self, event):
pass
class CustomNavigationToolbar(NavigationToolbar):
toolitems = (
@ -60,9 +64,12 @@ class CustomNavigationToolbar(NavigationToolbar):
class MplWidget(QtWidgets.QGraphicsView):
def __init__(self, parent=None):
def __init__(self, parent=None, mouse_event=False):
QtWidgets.QGraphicsView.__init__(self, parent)
self.canvas = MplCanvas()
if mouse_event:
self.canvas = MplCanvas()
else:
self.canvas = MplCanvasNoMouse()
self.ntb = CustomNavigationToolbar(self.canvas, self,
coordinates=False)
self.vbl = QtWidgets.QVBoxLayout()