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

331
pydsf.py
View file

@ -47,7 +47,12 @@ class Well:
Owned by an object of type 'Plate'. 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.owner = owner
self.name = name self.name = name
self.raw = np.zeros(self.owner.reads, dtype=np.float) self.raw = np.zeros(self.owner.reads, dtype=np.float)
@ -58,6 +63,10 @@ class Well:
self.tm_sd = np.NaN self.tm_sd = np.NaN
self.baseline_correction = owner.baseline_correction self.baseline_correction = owner.baseline_correction
self.baseline = None self.baseline = None
self.concentration = concentration
self.id = well_id
self.empty = empty
self.denatured = True
def filter_raw(self): def filter_raw(self):
""" """
@ -110,7 +119,7 @@ class Well:
Checks if a given value is within the defined temperature cutoff. Checks if a given value is within the defined temperature cutoff.
""" """
if (value >= self.owner.tm_cutoff_low and if (value >= self.owner.tm_cutoff_low and
value <= self.owner.tm_cutoff_high): value <= self.owner.tm_cutoff_high):
return True return True
else: else:
return False return False
@ -123,11 +132,13 @@ class Well:
try: try:
# If tm is within cutoff, perform the interpolation # If tm is within cutoff, perform the interpolation
if (self.temp_within_cutoff(tm)): if (self.temp_within_cutoff(tm)):
tm = round(peakutils.interpolate(x, y, tm = round(peakutils.interpolate(x,
y,
width=3, width=3,
ind=[max_i])[0], 2) ind=[max_i])[0],
2)
# Remove the denatured flag # Remove the denatured flag
self.owner.denatured_wells.remove(self) self.denatured = False
return tm # and return the Tm return tm # and return the Tm
else: else:
return np.NaN # otherwise, return NaN 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'. Calculate the Tm of the well. Returns either the Tm or 'np.NaN'.
""" """
# Check if the well has already been flagged as denatured # 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 return np.NaN # Return 'NaN' if true
# First assume that the well is denatured # 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 # Use the whole temperature range for x. We'll check the cutoff later
x = self.owner.temprange x = self.owner.temprange
@ -174,6 +189,7 @@ class Well:
# melting temperature # melting temperature
if max_y and max_i: if max_y and max_i:
tm = x[max_i] tm = x[max_i]
self.denatured = False
return self.interpolate_tm(x, y, max_i, tm) return self.interpolate_tm(x, y, max_i, tm)
# if no maximum is found, return NaN # if no maximum is found, return NaN
else: else:
@ -188,21 +204,18 @@ class Well:
already flagged as denatured, no Tm was found, or if the initial already flagged as denatured, no Tm was found, or if the initial
signal intensity is above a user definded threshold. signal intensity is above a user definded threshold.
""" """
denatured = True # Assumption is that the well is denatured if self.denatured:
return self.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.tm and (self.tm <= self.owner.tm_cutoff_low or if self.tm and (self.tm <= self.owner.tm_cutoff_low or
self.tm >= self.owner.tm_cutoff_high): self.tm >= self.owner.tm_cutoff_high):
denatured = True self.denatured = True
return denatured return self.denatured
for i in self.derivatives[1]: for i in self.derivatives[1]:
# Iterate over all points in the first derivative # Iterate over all points in the first derivative
if i > 0: # If a positive slope is found 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)) reads = int(round(self.owner.reads / 10))
# How many values should be checked against the signal threshold: # How many values should be checked against the signal threshold:
@ -210,47 +223,48 @@ class Well:
read = 0 read = 0
# Initialize running variable representing the current data point # 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 for j in self.filtered: # Iterate over the filtered data
if self.owner.signal_threshold: if self.owner.signal_threshold:
# If a signal threshold was defined # If a signal threshold was defined
if j > self.owner.signal_threshold and read <= reads: if j > self.owner.signal_threshold and read <= reads:
# iterate over 1/10 of all data points # iterate over 1/10 of all data points
# and check for values larger than the threshold. # and check for values larger than the threshold.
denatured = True self.denatured = True
# Set flag to True if a match is found # Set flag to True if a match is found
print("{}: {}".format(self.name, j)) print("{}: {}".format(self.name, j))
return denatured # and return return self.denatured # and return
read += 1 read += 1
return denatured return self.denatured
def analyze(self): def analyze(self):
""" """
Analyse data of the well. Takes care of the calculation of derivatives, Analyse data of the well. Takes care of the calculation of derivatives,
fitting of splines to derivatives and calculation of melting point. fitting of splines to derivatives and calculation of melting point.
""" """
# apply signal filter to raw data to filter out some noise if not self.empty:
self.filter_raw() # apply signal filter to raw data to filter out some noise
# fit a spline to unfiltered and filtered raw data self.filter_raw()
self.splines["raw"] = self.calc_spline(self.raw) # fit a spline to unfiltered and filtered raw data
self.splines["filtered"] = self.calc_spline(self.filtered) self.splines["raw"] = self.calc_spline(self.raw)
# calculate derivatives of filtered data self.splines["filtered"] = self.calc_spline(self.filtered)
self.calc_derivatives() # calculate derivatives of filtered data
# if baseline correction is requested, calculate baseline self.calc_derivatives()
if self.baseline_correction: # if baseline correction is requested, calculate baseline
self.baseline = self.calc_baseline(self.derivatives[1]) if self.baseline_correction:
# do an initial check if data suggest denaturation self.baseline = self.calc_baseline(self.derivatives[1])
if self.is_denatured(): # do an initial check if data suggest denaturation
# if appropriate, append well to denatured wells of the plate # if self.is_denatured():
self.owner.denatured_wells.append(self) # if appropriate, append well to denatured wells of the plate
# fit a spline to the first derivative # self.owner.denatured_wells.append(self)
self.splines["derivative1"] = self.calc_spline(self.derivatives[1]) # fit a spline to the first derivative
# calculate and set melting point self.splines["derivative1"] = self.calc_spline(self.derivatives[1])
self.tm = self.calc_tm() # calculate and set melting point
# fallback: set melting point to NaN self.tm = self.calc_tm()
if self.tm is None: # fallback: set melting point to NaN
self.tm = np.NaN if self.tm is None:
self.tm = np.NaN
class Experiment: class Experiment:
@ -268,7 +282,9 @@ class Experiment:
cutoff_high=None, cutoff_high=None,
signal_threshold=None, signal_threshold=None,
color_range=None, color_range=None,
baseline_correction=False): baseline_correction=False,
concentrations=None,
average_rows=None):
self.replicates = replicates self.replicates = replicates
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
@ -287,6 +303,8 @@ class Experiment:
self.signal_threshold = signal_threshold self.signal_threshold = signal_threshold
self.avg_plate = None self.avg_plate = None
self.baseline_correction = baseline_correction self.baseline_correction = baseline_correction
self.concentrations = concentrations
self.average_rows = average_rows
# use cuttoff if provided, otherwise cut at edges # use cuttoff if provided, otherwise cut at edges
if cutoff_low: if cutoff_low:
self.tm_cutoff_low = cutoff_low self.tm_cutoff_low = cutoff_low
@ -322,9 +340,10 @@ class Experiment:
plate.id = i plate.id = i
self.plates.append(plate) self.plates.append(plate)
i += 1 i += 1
# if more than one file is provied, assume that those are replicates # if more than one file is provided or average over rows is requested,
# and add a special plate representing the average results # assume that those are replicates and add a special plate
if len(files) > 1: # representing the average results
if len(files) > 1 or self.average_rows:
self.avg_plate = Plate(owner=self, self.avg_plate = Plate(owner=self,
filename=None, filename=None,
t1=self.t1, t1=self.t1,
@ -338,6 +357,70 @@ class Experiment:
color_range=self.color_range) color_range=self.color_range)
self.avg_plate.id = 'average' 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): def analyze(self):
""" """
Triggers analyzation of plates. Triggers analyzation of plates.
@ -347,31 +430,15 @@ class Experiment:
# if more than one plate is present, calculate average values for the # if more than one plate is present, calculate average values for the
# merged average plate # merged average plate
if len(self.plates) > 1: if len(self.plates) > 1:
# iterate over all wells in a plate self.average_by_plates()
for i in range(self.wellnum): elif self.average_rows:
tmp = [] self.average_by_rows()
# 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)
class Plate: class Plate:
def __init__(self, owner, def __init__(self,
owner,
plate_id=None, plate_id=None,
filename=None, filename=None,
replicates=None, replicates=None,
@ -383,7 +450,8 @@ class Plate:
cutoff_low=None, cutoff_low=None,
cutoff_high=None, cutoff_high=None,
signal_threshold=None, signal_threshold=None,
color_range=None): color_range=None,
concentrations=None):
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
self.owner = owner self.owner = owner
@ -411,6 +479,10 @@ class Plate:
self.signal_threshold = signal_threshold self.signal_threshold = signal_threshold
self.id = plate_id self.id = plate_id
self.baseline_correction = owner.baseline_correction self.baseline_correction = owner.baseline_correction
if concentrations is None:
self.concentrations = self.owner.concentrations
else:
self.concentrations = concentrations
if cutoff_low: if cutoff_low:
self.tm_cutoff_low = cutoff_low self.tm_cutoff_low = cutoff_low
else: else:
@ -424,34 +496,21 @@ class Plate:
else: else:
self.color_range = None self.color_range = None
self.denatured_wells = []
self.tms = [] self.tms = []
# TODO: Adapt for vertical concentrations
conc_id = 0
for i in range(self.wellnum): 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) 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): def analyze(self):
try: try:
# Try to access data file in the given path # 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 # If the file is not found, or not accessible: abort
print('Error accessing file: {}'.format(e)) print('Error accessing file: {}'.format(e))
self.wells = self.instrument.loadData(self.filename, self.wells = self.instrument.loadData(self.filename, self.reads,
self.reads,
self.wells) self.wells)
for well in self.wells: for well in self.wells:
@ -540,10 +598,12 @@ class PlotResults():
c_values = [] # Array holding the color values aka Tm c_values = [] # Array holding the color values aka Tm
dx_values = [] dx_values = []
dy_values = [] dy_values = []
ex_values = []
ey_values = []
canvas = widget.canvas canvas = widget.canvas
canvas.clear() canvas.clear()
for well in plate.wells: # Iterate over all wells 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) # Check if well is denatured (no Tm found)
c = well.tm # If not, set color to Tm c = well.tm # If not, set color to Tm
if c < plate.tm_cutoff_low: if c < plate.tm_cutoff_low:
@ -554,6 +614,9 @@ class PlotResults():
# Check if Tm is higher that the cutoff # Check if Tm is higher that the cutoff
c = plate.tm_cutoff_high c = plate.tm_cutoff_high
# If it is, set color to cutoff # If it is, set color to cutoff
elif well.empty:
ex_values.append(x)
ey_values.append(y)
else: # If the plate is denatured else: # If the plate is denatured
c = plate.tm_cutoff_low c = plate.tm_cutoff_low
# Set its color to the low cutoff # Set its color to the low cutoff
@ -576,7 +639,8 @@ class PlotResults():
# n rows # n rows
if plate.color_range: if plate.color_range:
# plot wells and color using the colormap # plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values, cax = ax1.scatter(x_values,
y_values,
s=305, s=305,
c=c_values, c=c_values,
marker='s', marker='s',
@ -584,20 +648,27 @@ class PlotResults():
vmax=plate.color_range[1]) vmax=plate.color_range[1])
else: else:
# plot wells and color using the colormap # plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values, cax = ax1.scatter(x_values,
y_values,
s=305, s=305,
c=c_values, c=c_values,
marker='s') 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, s=80,
c='white', c='red',
marker='x', marker='x',
linewidths=(1.5, )) 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 ax1.invert_yaxis() # invert y axis to math plate layout
cbar = fig1.colorbar(cax) # show colorbar cbar = fig1.colorbar(cax) # show colorbar
ax1.set_xlabel(_translate('pydsf', # set axis and colorbar label
'Columns')) # set axis and colorbar label ax1.set_xlabel(_translate('pydsf', 'Columns'))
ax1.set_ylabel(_translate('pydsf', 'Rows')) ax1.set_ylabel(_translate('pydsf', 'Rows'))
if str(plate.id) == 'average': if str(plate.id) == 'average':
@ -621,7 +692,8 @@ class PlotResults():
fig.suptitle(title + str(plate.id) + ')') fig.suptitle(title + str(plate.id) + ')')
grid = mpl_toolkits.axes_grid1.Grid( grid = mpl_toolkits.axes_grid1.Grid(
fig, 111, fig,
111,
nrows_ncols=(plate.rows, plate.cols), nrows_ncols=(plate.rows, plate.cols),
axes_pad=(0.15, 0.25), axes_pad=(0.15, 0.25),
add_all=True, add_all=True,
@ -641,22 +713,24 @@ class PlotResults():
ax = grid[i] ax = grid[i]
# set title of current subplot to well identifier # set title of current subplot to well identifier
ax.set_title(well.name, size=6) ax.set_title(well.name, size=6)
if well in plate.denatured_wells: if well.denatured:
ax.patch.set_facecolor('#FFD6D6') ax.patch.set_facecolor('#FFD6D6')
# only show three tickmarks on both axes # only show three tickmarks on both axes
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
ax.yaxis.set_major_locator(ticker.MaxNLocator(4)) ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
# check if well is denatured (without determined Tm) # 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 tm = well.tm # if not, grab its Tm
else: else:
tm = np.NaN # else set Tm to np.NaN tm = np.NaN # else set Tm to np.NaN
if tm: if tm:
ax.axvline(x=tm) # plot vertical line at the 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', facecolor='0.8',
alpha=0.5) # shade lower cutoff area 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', facecolor='0.8',
alpha=0.5) # shade higher cutoff area alpha=0.5) # shade higher cutoff area
# set fontsize for all tick labels to xx-small # set fontsize for all tick labels to xx-small
@ -681,7 +755,8 @@ class PlotResults():
fig.suptitle(title + str(plate.id) + ')') fig.suptitle(title + str(plate.id) + ')')
grid = mpl_toolkits.axes_grid1.Grid( grid = mpl_toolkits.axes_grid1.Grid(
fig, 111, fig,
111,
nrows_ncols=(plate.rows, plate.cols), nrows_ncols=(plate.rows, plate.cols),
axes_pad=(0.15, 0.25), axes_pad=(0.15, 0.25),
add_all=True, add_all=True,
@ -695,15 +770,17 @@ class PlotResults():
ax = grid[i] ax = grid[i]
# set title of current subplot to well identifier # set title of current subplot to well identifier
ax.set_title(well.name, size=6) ax.set_title(well.name, size=6)
if well in plate.denatured_wells: if well.denatured:
ax.patch.set_facecolor('#FFD6D6') ax.patch.set_facecolor('#FFD6D6')
# only show three tickmarks on both axes # only show three tickmarks on both axes
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
ax.yaxis.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', facecolor='0.8',
alpha=0.5) # shade lower cutoff area 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', facecolor='0.8',
alpha=0.5) # shade higher cutoff area alpha=0.5) # shade higher cutoff area
# set fontsize for all tick labels to xx-small # set fontsize for all tick labels to xx-small
@ -712,3 +789,41 @@ class PlotResults():
ax.plot(x, y) ax.plot(x, y)
fig.tight_layout() fig.tight_layout()
canvas.draw() 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
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File diff suppressed because it is too large Load diff

98
ui/mainwindow.py
View file

@ -57,6 +57,15 @@ class Worker(QRunnable):
files = [] files = []
for item in items: for item in items:
files.append(item.text()) 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, self.exp = Experiment(instrument=self.owner.instrument,
files=files, files=files,
t1=self.owner.doubleSpinBox_tmin.value(), t1=self.owner.doubleSpinBox_tmin.value(),
@ -67,7 +76,9 @@ class Worker(QRunnable):
cutoff_low=c_lower, cutoff_low=c_lower,
cutoff_high=c_upper, cutoff_high=c_upper,
signal_threshold=signal_threshold, signal_threshold=signal_threshold,
color_range=cbar_range) color_range=cbar_range,
concentrations=self.owner.concentrations,
average_rows=average_rows)
self.exp.analyze() self.exp.analyze()
self.signals.finished.emit() self.signals.finished.emit()
@ -77,7 +88,6 @@ class TaskSignals(QObject):
class Tasks(QObject): class Tasks(QObject):
def __init__(self): def __init__(self):
super(Tasks, self).__init__() super(Tasks, self).__init__()
@ -116,7 +126,6 @@ class Tasks(QObject):
class MainWindow(QMainWindow, Ui_MainWindow): class MainWindow(QMainWindow, Ui_MainWindow):
""" """
Class documentation goes here. Class documentation goes here.
""" """
@ -141,10 +150,13 @@ class MainWindow(QMainWindow, Ui_MainWindow):
QDialogButtonBox.AcceptRole) QDialogButtonBox.AcceptRole)
self.tasks = Tasks() self.tasks = Tasks()
self.tasks.signals.finished.connect(self.on_processing_finished) self.tasks.signals.finished.connect(self.on_processing_finished)
self.lineEdit_conc.textChanged.connect(
self.on_lineEdit_conc_textChanged)
self.worker = None self.worker = None
self.outputPath = None self.outputPath = None
self.instrument = None self.concentrations = None
self.populateInstrumentList() self.populateInstrumentList()
self.instrument = self.getSelectedInstrument()
def populateInstrumentList(self): def populateInstrumentList(self):
self.instruments = [AnalytikJenaqTower2()] self.instruments = [AnalytikJenaqTower2()]
@ -152,6 +164,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
instrument = self.instruments[i] instrument = self.instruments[i]
self.comboBox_instrument.setItemText(i, instrument.name) self.comboBox_instrument.setItemText(i, instrument.name)
@pyqtSlot()
def getInstrumentFromName(self, name): def getInstrumentFromName(self, name):
for instrument in self.instruments: for instrument in self.instruments:
if instrument.name == name: if instrument.name == name:
@ -178,7 +191,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.groupBox_replicates.setChecked(True) self.groupBox_replicates.setChecked(True)
self.radioButton_rep_files.setEnabled(True) self.radioButton_rep_files.setEnabled(True)
elif button == self.buttonBox_open_reset.button( elif button == self.buttonBox_open_reset.button(
QDialogButtonBox.Reset): QDialogButtonBox.Reset):
self.listWidget_data.clear() self.listWidget_data.clear()
@pyqtSlot("QAbstractButton*") @pyqtSlot("QAbstractButton*")
@ -202,8 +215,11 @@ class MainWindow(QMainWindow, Ui_MainWindow):
else: else:
self.groupBox_temp.setEnabled(True) self.groupBox_temp.setEnabled(True)
def generate_plot_tab(self, name): def generate_plot_tab(self, name, mouse_event=False):
tab = MplWidget(parent=self.tabWidget) if mouse_event:
tab = MplWidget(parent=self.tabWidget, mouse_event=True)
else:
tab = MplWidget(parent=self.tabWidget)
tab.setObjectName(name) tab.setObjectName(name)
return tab return tab
@ -220,7 +236,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
plotter = PlotResults() plotter = PlotResults()
if plate.id != 'average': 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 #") title = _translate("MainWindow", "Heatmap #")
self.tabWidget.addTab(tab, title + str(plate.id)) self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab) plotter.plot_tm_heatmap_single(plate, tab)
@ -243,8 +260,26 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.checkBox_saveplots.isChecked(): if self.checkBox_saveplots.isChecked():
tab.canvas.save( tab.canvas.save(
"{}/derivatives_{}.svg".format(self.outputPath, plate.id)) "{}/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: 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 ") title = _translate("MainWindow", "Heatmap ")
self.tabWidget.addTab(tab, title + str(plate.id)) self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab) plotter.plot_tm_heatmap_single(plate, tab)
@ -252,6 +287,26 @@ class MainWindow(QMainWindow, Ui_MainWindow):
tab.canvas.save( tab.canvas.save(
"{}/heatmap_{}.svg".format(self.outputPath, plate.id)) "{}/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() @pyqtSlot()
def on_buttonBox_process_accepted(self): def on_buttonBox_process_accepted(self):
""" """
@ -267,8 +322,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
_translate("MainWindow", "No data file loaded!"), _translate("MainWindow", "No data file loaded!"),
QMessageBox.Close, QMessageBox.Close) QMessageBox.Close, QMessageBox.Close)
return return
if self.groupBox_conc.isChecked():
self.concentrations = self.lineEdit_conc.text().split(',')
if (self.groupBox_output.isChecked() and if (self.groupBox_output.isChecked() and
self.lineEdit_output.text().strip() == ''): self.lineEdit_output.text().strip() == ''):
QMessageBox.critical( QMessageBox.critical(
self, _translate("MainWindow", "Error"), self, _translate("MainWindow", "Error"),
_translate("MainWindow", "No output path set!"), _translate("MainWindow", "No output path set!"),
@ -323,8 +380,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.checkBox_savetables.isChecked(): if self.checkBox_savetables.isChecked():
for plate in exp.plates: for plate in exp.plates:
plate.write_tm_table( plate.write_tm_table(
'{}/plate_{}_tm.csv'.format(self.outputPath, '{}/plate_{}_tm.csv'.format(self.outputPath, str(
str(plate.id))) plate.id)))
plate.write_data_table( plate.write_data_table(
'{}/plate_{}_dI_dT.csv'.format(self.outputPath, '{}/plate_{}_dI_dT.csv'.format(self.outputPath,
str(plate.id)), str(plate.id)),
@ -380,10 +437,25 @@ class MainWindow(QMainWindow, Ui_MainWindow):
dialog.ui.setupUi(dialog) dialog.ui.setupUi(dialog)
dialog.exec_() dialog.exec_()
@pyqtSlot() @pyqtSlot()
def on_actionAbout_Qt_triggered(self): def on_actionAbout_Qt_triggered(self):
""" """
Slot documentation goes here. Slot documentation goes here.
""" """
QApplication.aboutQt() 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"> <item row="0" column="0">
<widget class="QLabel" name="label_instrument"> <widget class="QLabel" name="label_instrument">
<property name="text"> <property name="text">
<string>Instrument</string> <string>I&amp;nstrument</string>
</property> </property>
<property name="buddy"> <property name="buddy">
<cstring>comboBox_instrument</cstring> <cstring>comboBox_instrument</cstring>
@ -150,6 +150,13 @@
<bool>false</bool> <bool>false</bool>
</property> </property>
<layout class="QGridLayout" name="gridLayout_3"> <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"> <item row="0" column="0">
<widget class="QRadioButton" name="radioButton_rep_files"> <widget class="QRadioButton" name="radioButton_rep_files">
<property name="enabled"> <property name="enabled">
@ -163,6 +170,23 @@
</property> </property>
</widget> </widget>
</item> </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> </layout>
</widget> </widget>
</item> </item>
@ -465,7 +489,7 @@
</layout> </layout>
</widget> </widget>
</item> </item>
<item row="2" column="0" colspan="2"> <item row="3" column="0" colspan="2">
<widget class="QGroupBox" name="groupBox_output"> <widget class="QGroupBox" name="groupBox_output">
<property name="title"> <property name="title">
<string>Sa&amp;ve processing results</string> <string>Sa&amp;ve processing results</string>
@ -477,14 +501,14 @@
<bool>false</bool> <bool>false</bool>
</property> </property>
<layout class="QGridLayout" name="gridLayout_2"> <layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0"> <item row="1" column="0">
<widget class="QCheckBox" name="checkBox_saveplots"> <widget class="QCheckBox" name="checkBox_saveplots">
<property name="text"> <property name="text">
<string>Save plots</string> <string>Save plots</string>
</property> </property>
</widget> </widget>
</item> </item>
<item row="2" column="1"> <item row="3" column="1">
<widget class="QDialogButtonBox" name="buttonBox_output"> <widget class="QDialogButtonBox" name="buttonBox_output">
<property name="sizePolicy"> <property name="sizePolicy">
<sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed"> <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
@ -500,14 +524,14 @@
</property> </property>
</widget> </widget>
</item> </item>
<item row="2" column="0"> <item row="3" column="0">
<widget class="QLineEdit" name="lineEdit_output"> <widget class="QLineEdit" name="lineEdit_output">
<property name="toolTip"> <property name="toolTip">
<string>Output results to this path</string> <string>Output results to this path</string>
</property> </property>
</widget> </widget>
</item> </item>
<item row="1" column="0"> <item row="2" column="0">
<widget class="QCheckBox" name="checkBox_savetables"> <widget class="QCheckBox" name="checkBox_savetables">
<property name="text"> <property name="text">
<string>Save tabular results</string> <string>Save tabular results</string>
@ -517,6 +541,102 @@
</layout> </layout>
</widget> </widget>
</item> </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> </layout>
</widget> </widget>
</item> </item>
@ -601,7 +721,7 @@
<x>0</x> <x>0</x>
<y>0</y> <y>0</y>
<width>4095</width> <width>4095</width>
<height>28</height> <height>30</height>
</rect> </rect>
</property> </property>
<property name="locale"> <property name="locale">

23
ui/mplwidget.py
View file

@ -19,12 +19,6 @@ class MplCanvas(FigureCanvas):
QtWidgets.QSizePolicy.Expanding) QtWidgets.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self) 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): def clear(self):
self.ax.clear() self.ax.clear()
self.fig.clear() self.fig.clear()
@ -40,6 +34,16 @@ class MplCanvas(FigureCanvas):
QtWidgets.QMessageBox.Close, QtWidgets.QMessageBox.Close) 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): class CustomNavigationToolbar(NavigationToolbar):
toolitems = ( toolitems = (
@ -60,9 +64,12 @@ class CustomNavigationToolbar(NavigationToolbar):
class MplWidget(QtWidgets.QGraphicsView): class MplWidget(QtWidgets.QGraphicsView):
def __init__(self, parent=None): def __init__(self, parent=None, mouse_event=False):
QtWidgets.QGraphicsView.__init__(self, parent) QtWidgets.QGraphicsView.__init__(self, parent)
self.canvas = MplCanvas() if mouse_event:
self.canvas = MplCanvas()
else:
self.canvas = MplCanvasNoMouse()
self.ntb = CustomNavigationToolbar(self.canvas, self, self.ntb = CustomNavigationToolbar(self.canvas, self,
coordinates=False) coordinates=False)
self.vbl = QtWidgets.QVBoxLayout() self.vbl = QtWidgets.QVBoxLayout()