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Code Issues Releases Wiki Activity

Embedded plots into GUI

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This commit is contained in:
Alexander Minges 2015-01-30 20:14:56 +01:00
parent 926fb01502
commit cf75c8ee09
7 changed files with 446 additions and 349 deletions
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2
.gitignore vendored
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@ -21,7 +21,7 @@ var/
*.egg-info/ *.egg-info/
.installed.cfg .installed.cfg
*.egg *.egg
.idea .idea/
# PyInstaller # PyInstaller
# Usually these files are written by a python script from a template # Usually these files are written by a python script from a template

583
pydsf.py
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@ -1,6 +1,7 @@
#! /usr/bin/env python2 #! /usr/bin/env python2
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import csv import csv
import multiprocessing as mp
try: try:
import matplotlib as mpl import matplotlib as mpl
@ -23,54 +24,56 @@ except ImportError:
raise ImportError('----- NumPy must be installed. -----') raise ImportError('----- NumPy must be installed. -----')
try: try:
from scipy.signal import filtfilt, butter from scipy.signal import filtfilt, butter
from scipy import interpolate from scipy import interpolate
from scipy import optimize from scipy import optimize
except ImportError: except ImportError:
raise ImportError('----- SciPy must be installed. -----') raise ImportError('----- SciPy must be installed. -----')
class Well: class Well:
def __init__(self, owner): def __init__(self, owner):
self.owner = owner self.owner = owner
self.name = None self.name = None
self.raw = np.zeros(self.owner.reads, dtype=np.float) self.raw = np.zeros(self.owner.reads, dtype=np.float)
self.filtered = np.zeros(self.owner.reads, dtype=np.float) self.filtered = np.zeros(self.owner.reads, dtype=np.float)
self.derivatives = np.zeros((4, self.owner.reads)) self.derivatives = np.zeros((4, self.owner.reads))
self.splines = {"raw": None, self.splines = {"raw": None,
"filtered": None, "filtered": None,
"derivative1": None} "derivative1": None}
self.tm = np.NaN self.tm = np.NaN
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
def filter_raw(self): def filter_raw(self):
""" """
Apply a filter to the raw data Apply a filter to the raw data
""" """
b, a = butter(3, 0.3) b, a = butter(3, 0.3)
self.filtered = filtfilt(b, a, self.raw) self.filtered = filtfilt(b, a, self.raw)
def calc_spline(self, y): def calc_spline(self, y):
""" """
Calculate a spline that represents the smoothed data points Calculate a spline that represents the smoothed data points
""" """
spline = interpolate.InterpolatedUnivariateSpline(self.owner.temprange, y) spline = interpolate.InterpolatedUnivariateSpline(self.owner.temprange, y)
return spline return spline
def calc_derivatives(self, spline='filtered'): def calc_derivatives(self, spline='filtered'):
for t in self.owner.temprange: for t in self.owner.temprange:
temp = self.splines[spline].derivatives(t) temp = self.splines[spline].derivatives(t)
for i in range(4): for i in range(4):
self.derivatives[i, t - self.owner.t1] = temp[i] self.derivatives[i, t - self.owner.t1] = temp[i]
def calc_baseline(self, y): @staticmethod
def calc_baseline(y):
try: try:
baseline = peakutils.baseline(y) baseline = peakutils.baseline(y)
return baseline return baseline
except: except:
return np.NaN return np.NaN
def calc_tm(self): def calc_tm(self):
""" """
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'.
@ -83,7 +86,7 @@ class Well:
self.owner.denatured_wells.append(self) self.owner.denatured_wells.append(self)
if self.owner.tm_cutoff_low != self.owner.t1 or self.owner.tm_cutoff_high != self.owner.t1: if self.owner.tm_cutoff_low != self.owner.t1 or self.owner.tm_cutoff_high != self.owner.t1:
x = np.arange(self.owner.tm_cutoff_low, self.owner.tm_cutoff_high + 1, self.owner.dt, dtype=float) x = np.arange(self.owner.tm_cutoff_low, self.owner.tm_cutoff_high + 1, self.owner.dt, dtype=float)
x = self.owner.temprange x = self.owner.temprange
y = self.derivatives[1] y = self.derivatives[1]
@ -93,83 +96,85 @@ class Well:
try: try:
peak_indexes = peakutils.indexes(y, min_dist=len(x)) # calculate a rough estimate of peaks; set min_dist peak_indexes = peakutils.indexes(y, min_dist=len(x)) # calculate a rough estimate of peaks; set min_dist
# temperature range to only find one/the highest peak # temperature range to only find one/the highest peak
tm = peakutils.interpolate(x, y, ind=peak_indexes)[0] # increase resolution by fitting gaussian function tm = peakutils.interpolate(x, y, ind=peak_indexes)[0] # increase resolution by fitting gaussian function
# to peak # to peak
except: except:
return np.NaN # In case of error, return no peak return np.NaN # In case of error, return no peak
try: try:
# Check if the peak is within cutoff range # Check if the peak is within cutoff range
if tm and tm >= self.owner.tm_cutoff_low and tm <= self.owner.tm_cutoff_high: if tm and tm >= self.owner.tm_cutoff_low and tm <= self.owner.tm_cutoff_high:
self.owner.denatured_wells.remove(self) # If everything is fine, remove the denatured flag self.owner.denatured_wells.remove(self) # If everything is fine, remove the denatured flag
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
except: except:
return np.NaN # In case of error, return NaN return np.NaN # In case of error, return NaN
def is_denatured(self): def is_denatured(self):
""" """
Check if the well is denatured. Returns true if the well has been already flagged as Check if the well is denatured. Returns true if the well has been already flagged as
denatured, no Tm was found, or if the initial signal intensity is above a user definded denatured, no Tm was found, or if the initial signal intensity is above a user definded
threshold. threshold.
""" """
denatured = True # Assumption is that the well is denatured 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 if self in self.owner.denatured_wells: # check if the well is already flagged as denatured
return denatured # return true if it is return denatured # return true if it is
if self.tm and (self.tm <= self.owner.tm_cutoff_low or self.tm >= self.owner.tm_cutoff_high): if self.tm and (self.tm <= self.owner.tm_cutoff_low or self.tm >= self.owner.tm_cutoff_high):
denatured = True denatured = True
return denatured return denatured
for i in self.derivatives[1]: # Iterate over all points in the first derivative for i in self.derivatives[1]: # 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 denatured = False # set denatured flag to False
reads = int(round(self.owner.reads/10)) # How many values should be checked against the signal threshold: reads = int(round(self.owner.reads / 10)) # How many values should be checked against the signal threshold:
# 1/10 of the total number of data point # 1/10 of the total number of data point
read = 0 # Initialize running variable representing the current data point read = 0 # Initialize running variable representing the current data point
if not denatured: if not 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 a signal threshold was defined 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 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. # and check for values larger than the threshold.
denatured = True # Set flag to True if a match is found denatured = True # Set flag to True if a match is found
print("{}: {}".format(self.name, j)) print("{}: {}".format(self.name, j))
return denatured # and return return denatured # and return
read += 1 read += 1
return denatured return denatured
def analyze(self): def analyze(self):
self.filter_raw() self.filter_raw()
self.splines["raw"] = self.calc_spline(self.raw) self.splines["raw"] = self.calc_spline(self.raw)
self.splines["filtered"] = self.calc_spline(self.filtered) self.splines["filtered"] = self.calc_spline(self.filtered)
self.calc_derivatives() self.calc_derivatives()
if self.baseline_correction: if self.baseline_correction:
self.baseline = self.calc_baseline(self.derivatives[1]) self.baseline = self.calc_baseline(self.derivatives[1])
if self.is_denatured(): if self.is_denatured():
self.owner.denatured_wells.append(self) self.owner.denatured_wells.append(self)
self.splines["derivative1"] = self.calc_spline(self.derivatives[1]) self.splines["derivative1"] = self.calc_spline(self.derivatives[1])
self.tm = self.calc_tm() self.tm = self.calc_tm()
if self.tm is None: if self.tm is None:
self.tm = np.NaN self.tm = np.NaN
class Experiment: class Experiment:
def __init__(self, type, gui=None, files=None, replicates=None, t1=25, t2=95, dt=1, cols=12, rows=8, cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None, baseline_correction=False): def __init__(self, type, gui=None, files=None, replicates=None, t1=25, t2=95, dt=1, cols=12, rows=8,
cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None, baseline_correction=False):
self.replicates = replicates self.replicates = replicates
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
self.t1 = t1 self.t1 = t1
self.t2 = t2 self.t2 = t2
self.dt = dt self.dt = dt
self.temprange = np.arange(self.t1, self.t2 + 1, self.dt, dtype=float) self.temprange = np.arange(self.t1, self.t2 + 1, self.dt, dtype=float)
self.reads = int(round((t2 + 1 - t1) / dt)) self.reads = int(round((t2 + 1 - t1) / dt))
self.wellnum = self.cols * self.rows self.wellnum = self.cols * self.rows
self.files = files self.files = files
@ -178,10 +183,10 @@ class Experiment:
self.max_tm = None self.max_tm = None
self.min_tm = None self.min_tm = None
self.replicates = None self.replicates = None
self.gui=gui self.gui = gui
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
if cutoff_low: if cutoff_low:
self.tm_cutoff_low = cutoff_low self.tm_cutoff_low = cutoff_low
else: else:
@ -193,48 +198,54 @@ class Experiment:
if color_range: if color_range:
self.color_range = color_range self.color_range = color_range
else: else:
self.color_range = (self.t1, self.t2) self.color_range = None
self.plates = [] self.plates = []
i = 1 i = 1
for file in files: for file in files:
plate = Plate(type=self.type, owner=self, filename=file, t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols, rows=self.rows, cutoff_low=self.tm_cutoff_low, cutoff_high=self.tm_cutoff_high, signal_threshold=self.signal_threshold, color_range=self.color_range) plate = Plate(type=self.type, owner=self, filename=file, t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols,
rows=self.rows, cutoff_low=self.tm_cutoff_low, cutoff_high=self.tm_cutoff_high,
signal_threshold=self.signal_threshold, color_range=self.color_range)
plate.id = i plate.id = i
self.plates.append(plate) self.plates.append(plate)
i += 1 i += 1
if len(files) > 1: if len(files) > 1:
self.avg_plate = Plate(type=self.type, owner=self, filename=None, t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols, rows=self.rows, cutoff_low=self.tm_cutoff_low, cutoff_high=self.tm_cutoff_high, signal_threshold=self.signal_threshold, color_range=self.color_range) self.avg_plate = Plate(type=self.type, owner=self, filename=None, t1=self.t1, t2=self.t2, dt=self.dt,
cols=self.cols, rows=self.rows, cutoff_low=self.tm_cutoff_low,
cutoff_high=self.tm_cutoff_high, signal_threshold=self.signal_threshold,
color_range=self.color_range)
self.avg_plate.id = 'average' self.avg_plate.id = 'average'
def analyze(self): def analyze(self):
for plate in self.plates: for plate in self.plates:
plate.analyze(gui=self.gui) plate.analyze(gui=self.gui)
if len(self.plates) > 1: if len(self.plates) > 1:
#self.tm_replicates = np.zeros( self.wellnum, dtype=float ) # self.tm_replicates = np.zeros( self.wellnum, dtype=float )
#self.tm_replicates_sd = np.zeros( self.wellnum, dtype=float ) # self.tm_replicates_sd = np.zeros( self.wellnum, dtype=float )
for i in range(self.wellnum): for i in range(self.wellnum):
tmp = [] tmp = []
for plate in self.plates: for plate in self.plates:
tm = plate.wells[i].tm tm = plate.wells[i].tm
self.avg_plate.wells[i].name = plate.wells[i].name self.avg_plate.wells[i].name = plate.wells[i].name
if plate.wells[i] not in plate.denatured_wells: if plate.wells[i] not in plate.denatured_wells:
tmp.append(tm) tmp.append(tm)
if len(tmp) > 0: if len(tmp) > 0:
#self.avg_plate.wells[i].tm = (sum(tmp)/len(tmp)) # self.avg_plate.wells[i].tm = (sum(tmp)/len(tmp))
self.avg_plate.wells[i].tm = np.mean(tmp) self.avg_plate.wells[i].tm = np.mean(tmp)
self.avg_plate.wells[i].tm_sd = np.std(tmp) self.avg_plate.wells[i].tm_sd = np.std(tmp)
#self.tm_replicates[i] = (sum(tmp)/len(tmp)) # self.tm_replicates[i] = (sum(tmp)/len(tmp))
else: else:
self.avg_plate.denatured_wells.append(self.avg_plate.wells[i]) self.avg_plate.denatured_wells.append(self.avg_plate.wells[i])
class Plate: class Plate:
def __init__(self, type, owner, id=None, filename=None, replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8, cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None): def __init__(self, type, owner, id=None, filename=None, replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8,
cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None):
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
self.owner = owner self.owner = owner
@ -250,7 +261,7 @@ class Plate:
self.dt = dt self.dt = dt
else: else:
self.dt = owner.dt self.dt = owner.dt
self.temprange = np.arange(self.t1, self.t2 + 1, self.dt, dtype=float) self.temprange = np.arange(self.t1, self.t2 + 1, self.dt, dtype=float)
self.reads = int(round((t2 + 1 - t1) / dt)) self.reads = int(round((t2 + 1 - t1) / dt))
self.wellnum = self.cols * self.rows self.wellnum = self.cols * self.rows
self.filename = filename self.filename = filename
@ -274,28 +285,26 @@ class Plate:
self.color_range = color_range self.color_range = color_range
else: else:
self.color_range = None self.color_range = None
self.denatured_wells = [] self.denatured_wells = []
self.tms = [] self.tms = []
for i in range(self.wellnum):
well = Well(owner = self)
self.wells.append(well)
#self.analyze()
for i in range(self.wellnum):
well = Well(owner=self)
self.wells.append(well)
def analytikJena(self): def analytikJena(self):
""" """
Data processing for Analytik Jena qTower 2.0 export files Data processing for Analytik Jena qTower 2.0 export files
""" """
with open(self.filename, 'r') as f: with open(self.filename, 'r') as f:
reader = csv.reader(f, delimiter=';', quoting=csv.QUOTE_NONE) reader = csv.reader(f, delimiter=';', quoting=csv.QUOTE_NONE)
i = 0 i = 0
for row in reader: for row in reader:
temp = np.zeros(self.reads, dtype=float) temp = np.zeros(self.reads, dtype=float)
for read in range(self.reads+1): for read in range(self.reads + 1):
if read > 0: if read > 0:
try: try:
temp[read - 1] = row[read] temp[read - 1] = row[read]
@ -306,15 +315,15 @@ class Plate:
self.wells[i].raw = temp self.wells[i].raw = temp
i += 1 i += 1
def analyze(self, gui=None): def analyze(self, gui=None):
try: try:
# Try to access data file in the given path # Try to access data file in the given path
with open(self.filename) as f: pass with open(self.filename) as f:
pass
except IOError as e: except IOError as e:
# 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))
if self.type == 'Analytik Jena qTOWER 2.0/2.2': if self.type == 'Analytik Jena qTOWER 2.0/2.2':
self.analytikJena() self.analytikJena()
if gui: if gui:
@ -322,23 +331,23 @@ class Plate:
else: else:
# Raise exception, if the instrument's name is unknown # Raise exception, if the instrument's name is unknown
raise NameError('Unknown instrument type: {}'.format(self.type)) raise NameError('Unknown instrument type: {}'.format(self.type))
for well in self.wells: for well in self.wells:
well.analyze() well.analyze()
if gui: if gui:
update_progress_bar(gui.pb, 15) update_progress_bar(gui.pb, 15)
self.tms.append(well.tm) self.tms.append(well.tm)
if self.replicates: if self.replicates:
if self.replicates == 'rows': if self.replicates == 'rows':
print("rows") print("rows")
if self.replicates == 'cols': if self.replicates == 'cols':
print("cols") print("cols")
#print(self.tms) # print(self.tms)
self.max_tm = max(self.tms) self.max_tm = max(self.tms)
self.min_tm = min(self.tms) self.min_tm = min(self.tms)
def write_tm_table(self, filename): def write_tm_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#{:<4s}{:>13s}\n'.format('ID', '"Tm [°C]"')) f.write('#{:<4s}{:>13s}\n'.format('ID', '"Tm [°C]"'))
@ -347,7 +356,7 @@ class Plate:
f.write('{:<5s}{:>12s}\n'.format(well.name, 'NaN')) f.write('{:<5s}{:>12s}\n'.format(well.name, 'NaN'))
else: else:
f.write('{:<5s}{:>12s}\n'.format(well.name, str(well.tm))) f.write('{:<5s}{:>12s}\n'.format(well.name, str(well.tm)))
def write_avg_tm_table(self, filename): def write_avg_tm_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', '"Tm [°C]"', '"SD"')) f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', '"Tm [°C]"', '"SD"'))
@ -356,7 +365,7 @@ class Plate:
f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, 'NaN', 'NaN')) f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, 'NaN', 'NaN'))
else: else:
f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, str(well.tm), str(well.tm_sd))) f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, str(well.tm), str(well.tm_sd)))
def write_raw_table(self, filename): def write_raw_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#"Raw data"\n') f.write('#"Raw data"\n')
@ -364,16 +373,16 @@ class Plate:
for well in self.wells: for well in self.wells:
f.write('{:>15s}'.format(well.name)) f.write('{:>15s}'.format(well.name))
f.write('\n') f.write('\n')
i = 0 i = 0
for t in self.temprange: for t in self.temprange:
f.write('{:<10s}'.format(str(t))) f.write('{:<10s}'.format(str(t)))
for well in self.wells: for well in self.wells:
d = well.raw[i] d = well.raw[i]
f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3)))) f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3))))
f.write('\n') f.write('\n')
i += 1 i += 1
def write_filtered_table(self, filename): def write_filtered_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#"Filtered data" \n') f.write('#"Filtered data" \n')
@ -381,16 +390,16 @@ class Plate:
for well in self.wells: for well in self.wells:
f.write('{:>15s}'.format(well.name)) f.write('{:>15s}'.format(well.name))
f.write('\n') f.write('\n')
i = 0 i = 0
for t in self.temprange: for t in self.temprange:
f.write('{:<10s}'.format(str(t))) f.write('{:<10s}'.format(str(t)))
for well in self.wells: for well in self.wells:
d = well.filtered[i] d = well.filtered[i]
f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3)))) f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3))))
f.write('\n') f.write('\n')
i += 1 i += 1
def write_derivative_table(self, filename): def write_derivative_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#"Derivative dI/dT"\n') f.write('#"Derivative dI/dT"\n')
@ -398,13 +407,13 @@ class Plate:
for well in self.wells: for well in self.wells:
f.write('{:>15s}'.format(well.name)) f.write('{:>15s}'.format(well.name))
f.write('\n') f.write('\n')
i = 0 i = 0
for t in self.temprange: for t in self.temprange:
f.write('{:<10s}'.format(str(t))) f.write('{:<10s}'.format(str(t)))
for well in self.wells: for well in self.wells:
d = well.derivatives[1][i] d = well.derivatives[1][i]
f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3)))) f.write('{:>-15.3f}'.format(float(np.round(d, decimals=3))))
f.write('\n') f.write('\n')
i += 1 i += 1
@ -412,209 +421,185 @@ class Plate:
def write_baseline_corrected_table(self, filename): def write_baseline_corrected_table(self, filename):
raise NotImplementedError raise NotImplementedError
def update_progress_bar(bar, value): def update_progress_bar(bar, value):
bar.setValue(value) bar.setValue(value)
def plot_tm_heatmap_average(experiment, gui=None):
"""
Plot Tm heatmap (Fig. 1)
"""
x = 1 # Position in columns
y = 1 # Position in rows
x_values = [] # Array holding the columns
y_values = [] # Array holding the rows
c_values = [] # Array holding the color values aka Tm
# c = well.tm # If not, set color to Tm class PlotResults():
# if c < experiment.tm_cutoff_low: # Check if Tm is lower that the cutoff
# c = experiment.tm_cutoff_low # If it is, set color to cutoff
# elif c > experiment.tm_cutoff_high: # Check if Tm is higher that the cutoff
# c = experiment.tm_cutoff_high # If it is, set color to cutoff
# else: # If the plate is denatured
# c = experiment.tm_cutoff_low # Set its color to the low cutoff
for c in experiment.tm_replicates:
x_values.append(x) # Add values to the respective arrays def __init__(self, experiment):
y_values.append(y) self.experiment = experiment
c_values.append(c)
x += 1 # Increase column by one
if x > experiment.cols: # If maximum column per row is reached
x = 1 # reset column to one
y += 1 # and increase row by one
fig1 = plt.figure() # new figure def plot_tm_heatmap_single(self, plate, widget):
ax1 = fig1.add_subplot(1, 1, 1) # A single canvas """
ax1.autoscale(tight=True) # Scale plate size Plot Tm heatmap (Fig. 1)
ax1.xaxis.set_major_locator(ticker.MaxNLocator(experiment.cols + 1)) # n columns """
ax1.yaxis.set_major_locator(ticker.MaxNLocator(experiment.rows + 1)) # n rows x = 1 # Position in columns
if experiment.color_range: y = 1 # Position in rows
cax = ax1.scatter(x_values, y_values, s=300, c=c_values, marker='s', vmin=experiment.color_range[0], vmax=experiment.color_range[1]) # plot wells and color using the colormap x_values = [] # Array holding the columns
else: y_values = [] # Array holding the rows
cax = ax1.scatter(x_values, y_values, s=300, c=c_values, marker='s') # plot wells and color using the colormap c_values = [] # Array holding the color values aka Tm
ax1.invert_yaxis() # invert y axis to math plate layout dx_values = []
cbar = fig1.colorbar(cax) # show colorbar dy_values = []
ax1.set_xlabel('Columns') # set axis and colorbar label dc_values = []
ax1.set_ylabel('Rows') canvas = widget.canvas
ax1.set_title('$T_m$ heatmap (average)') canvas.clear()
cbar.set_label(u"Temperature [°C]") for well in plate.wells: # Iterate over all wells
if well not in plate.denatured_wells: # Check if well is denatured (no Tm found)
c = well.tm # If not, set color to Tm
def plot_tm_heatmap_single(plate, gui=None): if c < plate.tm_cutoff_low: # Check if Tm is lower that the cutoff
""" c = plate.tm_cutoff_low # If it is, set color to cutoff
Plot Tm heatmap (Fig. 1) elif c > plate.tm_cutoff_high: # Check if Tm is higher that the cutoff
""" c = plate.tm_cutoff_high # If it is, set color to cutoff
x = 1 # Position in columns else: # If the plate is denatured
y = 1 # Position in rows c = plate.tm_cutoff_low # Set its color to the low cutoff
x_values = [] # Array holding the columns dx_values.append(x)
y_values = [] # Array holding the rows dy_values.append(y)
c_values = [] # Array holding the color values aka Tm x_values.append(x) # Add values to the respective arrays
dx_values = [] y_values.append(y)
dy_values = [] c_values.append(c)
dc_values = [] x += 1 # Increase column by one
for well in plate.wells: # Iterate over all wells if x > plate.cols: # If maximum column per row is reached
if well not in plate.denatured_wells: # Check if well is denatured (no Tm found) x = 1 # reset column to one
c = well.tm # If not, set color to Tm y += 1 # and increase row by one
if c < plate.tm_cutoff_low: # Check if Tm is lower that the cutoff
c = plate.tm_cutoff_low # If it is, set color to cutoff
elif c > plate.tm_cutoff_high: # Check if Tm is higher that the cutoff
c = plate.tm_cutoff_high # If it is, set color to cutoff
else: # If the plate is denatured
c = plate.tm_cutoff_low # Set its color to the low cutoff
dx_values.append(x)
dy_values.append(y)
x_values.append(x) # Add values to the respective arrays
y_values.append(y)
c_values.append(c)
x += 1 # Increase column by one
if x > plate.cols: # If maximum column per row is reached
x = 1 # reset column to one
y += 1 # and increase row by one
fig1 = plt.figure() # new figure fig1 = canvas.fig # new figure
ax1 = fig1.add_subplot(1, 1, 1) # A single canvas ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
ax1.autoscale(tight=True) # Scale plate size ax1.autoscale(tight=True) # Scale plate size
ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1)) # n columns ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1)) # n columns
ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1)) # n rows ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1)) # n rows
if plate.color_range: if plate.color_range:
cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s', vmin=plate.color_range[0], vmax=plate.color_range[1]) # plot wells and color using the colormap cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s', vmin=plate.color_range[0],
else: vmax=plate.color_range[1]) # plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s') # plot wells and color using the colormap
cax2 = ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x', linewidths=(1.5,))
ax1.invert_yaxis() # invert y axis to math plate layout
cbar = fig1.colorbar(cax) # show colorbar
ax1.set_xlabel('Columns') # set axis and colorbar label
ax1.set_ylabel('Rows')
if str(plate.id) == 'average':
title = '$T_m$ heatmap (average)'
else:
title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
ax1.set_title(title)
cbar.set_label(u"Temperature [°C]")
#magenta_patch = mpatches.Patch(color='magenta', label='Denatured')
#fig1.legend([magenta_patch], 'Denatured', loc='lower right', bbox_to_anchor=[0.5, 0.5])
# if gui:
# update_progress_bar(gui.pb, 50)
def plot_derivative(plate, gui=None):
"""
Plot derivatives (Fig. 2)
"""
fig2 = plt.figure() # new figure
fig2.suptitle('Individual Derivatives (plate #{})'.format(str(plate.id))) # set title
for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
well = plate.wells[plot_num - 1] # get single well based on current plot number
ax = fig2.add_subplot(plate.rows, plate.cols, plot_num) # add new subplot
ax.autoscale(tight=True) # scale to data
ax.set_title(well.name, size='xx-small') # set title of current subplot to well identifier
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
ax.set_xlabel(u'T [°C]', size='xx-small')
ax.set_ylabel('dI/dT', size='xx-small')
x = plate.temprange # set values for the x axis to the given temperature range
if well.baseline_correction:
print(well.baseline)
y = well.derivatives[1] - well.baseline
else: else:
y = well.derivatives[1] # grab y values from the first derivative of the well cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s') # plot wells and color using the colormap
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes cax2 = ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x', linewidths=(1.5,))
ax.yaxis.set_major_locator(ticker.MaxNLocator(4)) ax1.invert_yaxis() # invert y axis to math plate layout
if well not in plate.denatured_wells: # check if well is denatured (without determined Tm) cbar = fig1.colorbar(cax) # show colorbar
tm = well.tm # if not, grab its Tm ax1.set_xlabel('Columns') # set axis and colorbar label
ax1.set_ylabel('Rows')
if str(plate.id) == 'average':
title = '$T_m$ heatmap (average)'
else: else:
tm = np.NaN # else set Tm to np.NaN title = '$T_m$ heatmap (plate #{})'.format(str(plate.id))
if tm: ax1.set_title(title)
ax.axvline(x=tm) # plot vertical line at the Tm cbar.set_label(u"Temperature [°C]")
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
label.set_fontsize('xx-small')
cax = ax.plot(x, y) # plot data to the current subplot
# if gui:
# update_progress_bar(gui.pb, 75)
def plot_raw(plate, gui=None):
"""
Plot raw data (Fig. 3)
"""
fig3 = plt.figure() # new figure
fig3.suptitle('Raw Data (plate #{})'.format(str(plate.id))) # set title
for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
well = plate.wells[plot_num - 1] # get single well based on current plot number
ax = fig3.add_subplot(plate.rows, plate.cols, plot_num) # add new subplot
ax.autoscale(tight=True) # scale to data
ax.set_title(well.name, size='xx-small') # set title of current subplot to well identifier
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
ax.set_xlabel(u'T [°C]', size='xx-small')
ax.set_ylabel('I', size='xx-small')
x = plate.temprange # set values for the x axis to the given temperature range
y = well.raw # grab y values from the raw data of the well
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes
ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
label.set_fontsize('xx-small')
cax = ax.plot(x, y) # plot data to the current subplot
# if gui:
# update_progress_bar(gui.pb, 100)
# gui.pb.hide()
def plot(experiment, gui=None): canvas.draw()
for plate in experiment.plates:
plot_raw(plate) def plot_derivative(self, plate, widget):
plot_derivative(plate) """
plot_tm_heatmap_single(plate) Plot derivatives (Fig. 2)
"""
if len(experiment.plates) > 1: canvas = widget.canvas
plot_tm_heatmap_single(experiment.avg_plate) canvas.clear()
#plot_tm_heatmap_average(experiment) fig2 = canvas.fig # new figure
fig2.suptitle('Individual Derivatives (plate #{})'.format(str(plate.id))) # set title
plt.show()
for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
well = plate.wells[plot_num - 1] # get single well based on current plot number
ax = fig2.add_subplot(plate.rows, plate.cols, plot_num) # add new subplot
ax.autoscale(tight=True) # scale to data
ax.set_title(well.name, size='xx-small') # set title of current subplot to well identifier
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
ax.set_xlabel(u'T [°C]', size='xx-small')
ax.set_ylabel('dI/dT', size='xx-small')
x = plate.temprange # set values for the x axis to the given temperature range
if well.baseline_correction:
print(well.baseline)
y = well.derivatives[1] - well.baseline
else:
y = well.derivatives[1] # grab y values from the first derivative of the well
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes
ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
if well not in plate.denatured_wells: # check if well is denatured (without determined Tm)
tm = well.tm # if not, grab its Tm
else:
tm = np.NaN # else set Tm to np.NaN
if tm:
ax.axvline(x=tm) # plot vertical line at the Tm
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
label.set_fontsize('xx-small')
cax = ax.plot(x, y) # plot data to the current subplot
canvas.draw()
def plot_raw(self, plate, widget):
"""
Plot raw data (Fig. 3)
"""
canvas = widget.canvas
canvas.clear()
fig3 = canvas.fig # new figure
fig3.suptitle('Raw Data (plate #{})'.format(str(plate.id))) # set title
for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
well = plate.wells[plot_num - 1] # get single well based on current plot number
ax = fig3.add_subplot(plate.rows, plate.cols, plot_num) # add new subplot
ax.autoscale(tight=True) # scale to data
ax.set_title(well.name, size='xx-small') # set title of current subplot to well identifier
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
if plot_num == plate.wellnum - plate.cols + 1: # add axis label to the subplot in the bottom left corner of the figure
ax.set_xlabel(u'T [°C]', size='xx-small')
ax.set_ylabel('I', size='xx-small')
x = plate.temprange # set values for the x axis to the given temperature range
y = well.raw # grab y values from the raw data of the well
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) # only show three tickmarks on both axes
ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', alpha=0.5) # shade higher cutoff area
for label in ax.get_xticklabels() + ax.get_yticklabels(): # set fontsize for all tick labels to xx-small
label.set_fontsize('xx-small')
cax = ax.plot(x, y) # plot data to the current subplot
canvas.draw()
# def _plot_wrapper(self, plot, plate):
#
# if plot == 'raw':
# fig, ax = self._plot_raw(plate)
# elif plot == 'derivative':
# fig, ax = self._plot_derivative(plate)
# elif plot == 'tm_heatmap':
# fig, ax = self._plot_tm_heatmap_single(plate)
# else:
# raise NotImplementedError
# fig = None
# ax = None
# return (fig, ax)
#
# def plot_all(self):
#
# figures = []
#
# for plate in self.experiment.plates:
#
# figures.append(self._plot_wrapper('raw', plate))
# figures.append(self._plot_wrapper('derivative', plate))
# figures.append(self._plot_wrapper('tm_heatmap', plate))
#
# if len(self.experiment.plates) > 1:
# figures.append(self._plot_wrapper('tm_heatmap', self.experiment.avg_plate))
#
# return figures
#plate = Plate('/home/alex/Dokumente/Universitaet/Promotion/Denaturierung/26092012/26092012-MG.csv', type='analytikJena', cutoff_low=35.0, cutoff_high=60.0, signal_threshold=50000, color_range=(42, 50))
#plot(plate)

57
ui/Ui_mainwindow.py
View file

@ -2,7 +2,7 @@
# Form implementation generated from reading ui file 'mainwindow.ui' # Form implementation generated from reading ui file 'mainwindow.ui'
# #
# Created: Fri Jan 30 14:07:06 2015 # Created: Fri Jan 30 19:20:59 2015
# by: PyQt5 UI code generator 5.4 # by: PyQt5 UI code generator 5.4
# #
# WARNING! All changes made in this file will be lost! # WARNING! All changes made in this file will be lost!
@ -12,7 +12,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object): class Ui_MainWindow(object):
def setupUi(self, MainWindow): def setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow") MainWindow.setObjectName("MainWindow")
MainWindow.resize(388, 642) MainWindow.resize(808, 646)
MainWindow.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates)) MainWindow.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates))
self.centralWidget = QtWidgets.QWidget(MainWindow) self.centralWidget = QtWidgets.QWidget(MainWindow)
self.centralWidget.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates)) self.centralWidget.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates))
@ -24,11 +24,11 @@ class Ui_MainWindow(object):
self.groupBox_experiment.setFlat(False) self.groupBox_experiment.setFlat(False)
self.groupBox_experiment.setCheckable(False) self.groupBox_experiment.setCheckable(False)
self.groupBox_experiment.setObjectName("groupBox_experiment") self.groupBox_experiment.setObjectName("groupBox_experiment")
self.gridLayout = QtWidgets.QGridLayout(self.groupBox_experiment) self.formLayout_3 = QtWidgets.QFormLayout(self.groupBox_experiment)
self.gridLayout.setObjectName("gridLayout") self.formLayout_3.setObjectName("formLayout_3")
self.label_instrument = QtWidgets.QLabel(self.groupBox_experiment) self.label_instrument = QtWidgets.QLabel(self.groupBox_experiment)
self.label_instrument.setObjectName("label_instrument") self.label_instrument.setObjectName("label_instrument")
self.gridLayout.addWidget(self.label_instrument, 0, 0, 1, 1) self.formLayout_3.setWidget(0, QtWidgets.QFormLayout.LabelRole, self.label_instrument)
self.comboBox_instrument = QtWidgets.QComboBox(self.groupBox_experiment) self.comboBox_instrument = QtWidgets.QComboBox(self.groupBox_experiment)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed) sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0) sizePolicy.setHorizontalStretch(0)
@ -37,7 +37,7 @@ class Ui_MainWindow(object):
self.comboBox_instrument.setSizePolicy(sizePolicy) self.comboBox_instrument.setSizePolicy(sizePolicy)
self.comboBox_instrument.setObjectName("comboBox_instrument") self.comboBox_instrument.setObjectName("comboBox_instrument")
self.comboBox_instrument.addItem("") self.comboBox_instrument.addItem("")
self.gridLayout.addWidget(self.comboBox_instrument, 0, 1, 1, 1) self.formLayout_3.setWidget(0, QtWidgets.QFormLayout.FieldRole, self.comboBox_instrument)
self.groupBox_data = QtWidgets.QGroupBox(self.groupBox_experiment) self.groupBox_data = QtWidgets.QGroupBox(self.groupBox_experiment)
self.groupBox_data.setEnabled(True) self.groupBox_data.setEnabled(True)
self.groupBox_data.setObjectName("groupBox_data") self.groupBox_data.setObjectName("groupBox_data")
@ -72,7 +72,7 @@ class Ui_MainWindow(object):
self.listWidget_data.setAlternatingRowColors(True) self.listWidget_data.setAlternatingRowColors(True)
self.listWidget_data.setObjectName("listWidget_data") self.listWidget_data.setObjectName("listWidget_data")
self.gridLayout_4.addWidget(self.listWidget_data, 0, 0, 2, 1) self.gridLayout_4.addWidget(self.listWidget_data, 0, 0, 2, 1)
self.gridLayout.addWidget(self.groupBox_data, 1, 0, 1, 2) self.formLayout_3.setWidget(1, QtWidgets.QFormLayout.SpanningRole, self.groupBox_data)
self.groupBox_temp = QtWidgets.QGroupBox(self.groupBox_experiment) self.groupBox_temp = QtWidgets.QGroupBox(self.groupBox_experiment)
self.groupBox_temp.setEnabled(True) self.groupBox_temp.setEnabled(True)
self.groupBox_temp.setAutoFillBackground(False) self.groupBox_temp.setAutoFillBackground(False)
@ -108,7 +108,7 @@ class Ui_MainWindow(object):
self.doubleSpinBox_dt.setProperty("value", 1.0) self.doubleSpinBox_dt.setProperty("value", 1.0)
self.doubleSpinBox_dt.setObjectName("doubleSpinBox_dt") self.doubleSpinBox_dt.setObjectName("doubleSpinBox_dt")
self.formLayout.setWidget(2, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_dt) self.formLayout.setWidget(2, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_dt)
self.gridLayout.addWidget(self.groupBox_temp, 2, 0, 1, 1) self.formLayout_3.setWidget(2, QtWidgets.QFormLayout.LabelRole, self.groupBox_temp)
self.groupBox_cutoff = QtWidgets.QGroupBox(self.groupBox_experiment) self.groupBox_cutoff = QtWidgets.QGroupBox(self.groupBox_experiment)
self.groupBox_cutoff.setEnabled(True) self.groupBox_cutoff.setEnabled(True)
self.groupBox_cutoff.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter) self.groupBox_cutoff.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignVCenter)
@ -135,7 +135,7 @@ class Ui_MainWindow(object):
self.doubleSpinBox_lower.setDecimals(1) self.doubleSpinBox_lower.setDecimals(1)
self.doubleSpinBox_lower.setObjectName("doubleSpinBox_lower") self.doubleSpinBox_lower.setObjectName("doubleSpinBox_lower")
self.formLayout_2.setWidget(1, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_lower) self.formLayout_2.setWidget(1, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_lower)
self.gridLayout.addWidget(self.groupBox_cutoff, 2, 1, 1, 1) self.formLayout_3.setWidget(2, QtWidgets.QFormLayout.FieldRole, self.groupBox_cutoff)
self.groupBox_signal_threshold = QtWidgets.QGroupBox(self.groupBox_experiment) self.groupBox_signal_threshold = QtWidgets.QGroupBox(self.groupBox_experiment)
self.groupBox_signal_threshold.setEnabled(True) self.groupBox_signal_threshold.setEnabled(True)
self.groupBox_signal_threshold.setCheckable(True) self.groupBox_signal_threshold.setCheckable(True)
@ -147,7 +147,7 @@ class Ui_MainWindow(object):
self.spinBox_signal_threshold.setMaximum(1000000) self.spinBox_signal_threshold.setMaximum(1000000)
self.spinBox_signal_threshold.setObjectName("spinBox_signal_threshold") self.spinBox_signal_threshold.setObjectName("spinBox_signal_threshold")
self.verticalLayout.addWidget(self.spinBox_signal_threshold) self.verticalLayout.addWidget(self.spinBox_signal_threshold)
self.gridLayout.addWidget(self.groupBox_signal_threshold, 3, 0, 1, 1) self.formLayout_3.setWidget(3, QtWidgets.QFormLayout.LabelRole, self.groupBox_signal_threshold)
self.groupBox_cbar = QtWidgets.QGroupBox(self.groupBox_experiment) self.groupBox_cbar = QtWidgets.QGroupBox(self.groupBox_experiment)
self.groupBox_cbar.setEnabled(True) self.groupBox_cbar.setEnabled(True)
self.groupBox_cbar.setCheckable(True) self.groupBox_cbar.setCheckable(True)
@ -170,15 +170,31 @@ class Ui_MainWindow(object):
self.doubleSpinBox_cbar_end.setDecimals(1) self.doubleSpinBox_cbar_end.setDecimals(1)
self.doubleSpinBox_cbar_end.setObjectName("doubleSpinBox_cbar_end") self.doubleSpinBox_cbar_end.setObjectName("doubleSpinBox_cbar_end")
self.formLayout_4.setWidget(2, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_cbar_end) self.formLayout_4.setWidget(2, QtWidgets.QFormLayout.FieldRole, self.doubleSpinBox_cbar_end)
self.gridLayout.addWidget(self.groupBox_cbar, 3, 1, 1, 1) self.formLayout_3.setWidget(3, QtWidgets.QFormLayout.FieldRole, self.groupBox_cbar)
self.gridLayout_2.addWidget(self.groupBox_experiment, 0, 0, 1, 1) self.buttonBox_process = QtWidgets.QDialogButtonBox(self.groupBox_experiment)
self.buttonBox_process = QtWidgets.QDialogButtonBox(self.centralWidget)
self.buttonBox_process.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok) self.buttonBox_process.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
self.buttonBox_process.setObjectName("buttonBox_process") self.buttonBox_process.setObjectName("buttonBox_process")
self.gridLayout_2.addWidget(self.buttonBox_process, 1, 0, 1, 1) self.formLayout_3.setWidget(4, QtWidgets.QFormLayout.FieldRole, self.buttonBox_process)
self.gridLayout_2.addWidget(self.groupBox_experiment, 0, 0, 1, 1)
self.tabWidget = QtWidgets.QTabWidget(self.centralWidget)
self.tabWidget.setObjectName("tabWidget")
self.tab_raw = MplWidget()
self.tab_raw.setObjectName("tab_raw")
self.tabWidget.addTab(self.tab_raw, "")
self.tab_derivative = MplWidget()
self.tab_derivative.setObjectName("tab_derivative")
self.tabWidget.addTab(self.tab_derivative, "")
self.tab_heatmap = MplWidget()
self.tab_heatmap.setObjectName("tab_heatmap")
self.tabWidget.addTab(self.tab_heatmap, "")
self.tab_heatmap_avg = MplWidget()
self.tab_heatmap_avg.setEnabled(False)
self.tab_heatmap_avg.setObjectName("tab_heatmap_avg")
self.tabWidget.addTab(self.tab_heatmap_avg, "")
self.gridLayout_2.addWidget(self.tabWidget, 0, 1, 1, 1)
MainWindow.setCentralWidget(self.centralWidget) MainWindow.setCentralWidget(self.centralWidget)
self.menuBar = QtWidgets.QMenuBar(MainWindow) self.menuBar = QtWidgets.QMenuBar(MainWindow)
self.menuBar.setGeometry(QtCore.QRect(0, 0, 388, 29)) self.menuBar.setGeometry(QtCore.QRect(0, 0, 808, 29))
self.menuBar.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates)) self.menuBar.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates))
self.menuBar.setObjectName("menuBar") self.menuBar.setObjectName("menuBar")
self.menuFile = QtWidgets.QMenu(self.menuBar) self.menuFile = QtWidgets.QMenu(self.menuBar)
@ -215,6 +231,7 @@ class Ui_MainWindow(object):
self.label_cbar_end.setBuddy(self.doubleSpinBox_cbar_end) self.label_cbar_end.setBuddy(self.doubleSpinBox_cbar_end)
self.retranslateUi(MainWindow) self.retranslateUi(MainWindow)
self.tabWidget.setCurrentIndex(3)
QtCore.QMetaObject.connectSlotsByName(MainWindow) QtCore.QMetaObject.connectSlotsByName(MainWindow)
def retranslateUi(self, MainWindow): def retranslateUi(self, MainWindow):
@ -236,7 +253,7 @@ class Ui_MainWindow(object):
self.label_dt.setText(_translate("MainWindow", "<html><head/><body><p>&Delta;T</p></body></html>")) self.label_dt.setText(_translate("MainWindow", "<html><head/><body><p>&Delta;T</p></body></html>"))
self.doubleSpinBox_dt.setSuffix(_translate("MainWindow", " °C")) self.doubleSpinBox_dt.setSuffix(_translate("MainWindow", " °C"))
self.groupBox_cutoff.setToolTip(_translate("MainWindow", "<html><head/><body><p>Only T<span style=\" vertical-align:sub;\">m</span> values within this limit are considered valid.</p></body></html>")) self.groupBox_cutoff.setToolTip(_translate("MainWindow", "<html><head/><body><p>Only T<span style=\" vertical-align:sub;\">m</span> values within this limit are considered valid.</p></body></html>"))
self.groupBox_cutoff.setTitle(_translate("MainWindow", "Cutoff")) self.groupBox_cutoff.setTitle(_translate("MainWindow", "&Cutoff"))
self.label_cutoff_high.setText(_translate("MainWindow", "&Upper")) self.label_cutoff_high.setText(_translate("MainWindow", "&Upper"))
self.doubleSpinBox_upper.setSuffix(_translate("MainWindow", " °C")) self.doubleSpinBox_upper.setSuffix(_translate("MainWindow", " °C"))
self.label_cutoff_low.setText(_translate("MainWindow", "Lower")) self.label_cutoff_low.setText(_translate("MainWindow", "Lower"))
@ -249,8 +266,14 @@ class Ui_MainWindow(object):
self.doubleSpinBox_cbar_start.setSuffix(_translate("MainWindow", " °C")) self.doubleSpinBox_cbar_start.setSuffix(_translate("MainWindow", " °C"))
self.label_cbar_end.setText(_translate("MainWindow", "En&d")) self.label_cbar_end.setText(_translate("MainWindow", "En&d"))
self.doubleSpinBox_cbar_end.setSuffix(_translate("MainWindow", " °C")) self.doubleSpinBox_cbar_end.setSuffix(_translate("MainWindow", " °C"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_raw), _translate("MainWindow", "Raw Data"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_derivative), _translate("MainWindow", "&1st derivative"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap), _translate("MainWindow", "Heatmap"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_heatmap_avg), _translate("MainWindow", "Heatmap average"))
self.menuFile.setTitle(_translate("MainWindow", "Fi&le")) self.menuFile.setTitle(_translate("MainWindow", "Fi&le"))
self.menuHelp.setTitle(_translate("MainWindow", "Help")) self.menuHelp.setTitle(_translate("MainWindow", "Hel&p"))
self.actionQuit.setText(_translate("MainWindow", "&Quit")) self.actionQuit.setText(_translate("MainWindow", "&Quit"))
self.actionAbout.setText(_translate("MainWindow", "&About")) self.actionAbout.setText(_translate("MainWindow", "&About"))
self.actionAbout_Qt.setText(_translate("MainWindow", "About &Qt")) self.actionAbout_Qt.setText(_translate("MainWindow", "About &Qt"))
from .mplwidget import MplWidget

4
ui/icons.qrc
View file

@ -1,5 +1,3 @@
<RCC> <RCC>
<qresource prefix="/"> <qresource prefix="/"/>
<file>qtlogo.svg</file>
</qresource>
</RCC> </RCC>

64
ui/mainwindow.py
View file

@ -17,6 +17,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
""" """
Class documentation goes here. Class documentation goes here.
""" """
def __init__(self, parent=None): def __init__(self, parent=None):
""" """
Constructor Constructor
@ -33,6 +34,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.statusBar.showMessage("Welcome to PyDSF") self.statusBar.showMessage("Welcome to PyDSF")
@pyqtSlot("QAbstractButton*") @pyqtSlot("QAbstractButton*")
def on_buttonBox_open_reset_clicked(self, button): def on_buttonBox_open_reset_clicked(self, button):
""" """
@ -47,8 +49,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
elif button == self.buttonBox_open_reset.button(QDialogButtonBox.Reset): elif button == self.buttonBox_open_reset.button(QDialogButtonBox.Reset):
self.listWidget_data.clear() self.listWidget_data.clear()
print("Data cleared") print("Data cleared")
# self.radioButton_rep_rows.setEnabled(False) # self.radioButton_rep_rows.setEnabled(False)
# self.radioButton_rep_columns.setEnabled(False) # self.radioButton_rep_columns.setEnabled(False)
@pyqtSlot("QString") @pyqtSlot("QString")
@ -61,10 +63,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.groupBox_temp.setEnabled(True) self.groupBox_temp.setEnabled(True)
else: else:
self.groupBox_temp.setEnabled(False) self.groupBox_temp.setEnabled(False)
# self.groupBox_data.setEnabled(True) # self.groupBox_data.setEnabled(True)
# self.groupBox_cutoff.setEnabled(True) # self.groupBox_cutoff.setEnabled(True)
# self.groupBox_cbar.setEnabled(True) # self.groupBox_cbar.setEnabled(True)
# self.groupBox_signal_threshold.setEnabled(True) # self.groupBox_signal_threshold.setEnabled(True)
@pyqtSlot() @pyqtSlot()
def on_buttonBox_process_accepted(self): def on_buttonBox_process_accepted(self):
@ -76,7 +78,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
QMessageBox.critical(self, 'Error', "No data file loaded!", QMessageBox.Close, QMessageBox.Close) QMessageBox.critical(self, 'Error', "No data file loaded!", QMessageBox.Close, QMessageBox.Close)
return return
if self.spinBox_signal_threshold.value() == 0 and self.groupBox_signal_threshold.isChecked(): if self.spinBox_signal_threshold.value() == 0 and self.groupBox_signal_threshold.isChecked():
QMessageBox.warning(self, 'Warning', "Signal threshold is currently set to zero.", QMessageBox.Ok, QMessageBox.Ok) QMessageBox.warning(self, 'Warning', "Signal threshold is currently set to zero.", QMessageBox.Ok,
QMessageBox.Ok)
self.progressBar.setEnabled(True) self.progressBar.setEnabled(True)
self.statusBar.showMessage("Processing...") self.statusBar.showMessage("Processing...")
@ -90,7 +93,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
c_lower = self.doubleSpinBox_lower.value() c_lower = self.doubleSpinBox_lower.value()
c_upper = self.doubleSpinBox_upper.value() c_upper = self.doubleSpinBox_upper.value()
if self.groupBox_cbar.isChecked(): if self.groupBox_cbar.isChecked():
cbar_range = (self.doubleSpinBox_cbar_start, self.doubleSpinBox_cbar_end) cbar_range = (self.doubleSpinBox_cbar_start, self.doubleSpinBox_cbar_end)
if self.groupBox_signal_threshold.isChecked(): if self.groupBox_signal_threshold.isChecked():
signal_threshold = self.spinBox_signal_threshold.value() signal_threshold = self.spinBox_signal_threshold.value()
@ -99,29 +102,53 @@ class MainWindow(QMainWindow, Ui_MainWindow):
files = [] files = []
for item in items: for item in items:
files.append(item.text()) files.append(item.text())
exp = Experiment(type=type, files=files, t1=self.doubleSpinBox_tmin.value(), t2=self.doubleSpinBox_tmax.value(), dt=self.doubleSpinBox_dt.value(), cols=12, rows=8, cutoff_low=c_lower, cutoff_high=c_upper, signal_threshold=signal_threshold, color_range=cbar_range) exp = Experiment(type=type, files=files, t1=self.doubleSpinBox_tmin.value(), t2=self.doubleSpinBox_tmax.value(),
dt=self.doubleSpinBox_dt.value(), cols=12, rows=8, cutoff_low=c_lower, cutoff_high=c_upper,
signal_threshold=signal_threshold, color_range=cbar_range)
exp.analyze() exp.analyze()
# plate = Plate(type=type, filename=self.lineEdit_data_file.text(), t1=self.doubleSpinBox_tmin.value(), t2=self.doubleSpinBox_tmax.value(), dt=self.doubleSpinBox_dt.value(), cols=12, rows=8, cutoff_low=c_lower, cutoff_high=c_upper, signal_threshold=signal_threshold, color_range=cbar_range) # plate = Plate(type=type, filename=self.lineEdit_data_file.text(), t1=self.doubleSpinBox_tmin.value(), t2=self.doubleSpinBox_tmax.value(), dt=self.doubleSpinBox_dt.value(), cols=12, rows=8, cutoff_low=c_lower, cutoff_high=c_upper, signal_threshold=signal_threshold, color_range=cbar_range)
# self.statusBar.addWidget(self.pb, 100) # self.statusBar.addWidget(self.pb, 100)
#plate.analyze(gui=self) # plate.analyze(gui=self)
save_data = QMessageBox.question(self, 'Save data', "Calculations are finished. Save results?", save_data = QMessageBox.question(self, 'Save data', "Calculations are finished. Save results?",
QMessageBox.Yes|QMessageBox.No, QMessageBox.Yes) QMessageBox.Yes | QMessageBox.No, QMessageBox.Yes)
if save_data == QMessageBox.Yes: if save_data == QMessageBox.Yes:
dialog = QFileDialog() dialog = QFileDialog()
dialog.setFileMode(QFileDialog.Directory) dialog.setFileMode(QFileDialog.Directory)
folder = dialog.getExistingDirectory(self, 'Choose path for results') folder = dialog.getExistingDirectory(self, 'Choose path for results')
for plate in exp.plates: for plate in exp.plates:
plate.write_tm_table('{}/plate_{}_04_tm.csv'.format(folder, str(plate.id))) plate.write_tm_table('{}/plate_{}_04_tm.csv'.format(folder, str(plate.id)))
plate.write_derivative_table('{}/plate_{}_03_dI_dT.csv'.format(folder, str(plate.id))) plate.write_derivative_table('{}/plate_{}_03_dI_dT.csv'.format(folder, str(plate.id)))
plate.write_filtered_table('{}/plate_{}_02_filtered_data.csv'.format(folder, str(plate.id))) plate.write_filtered_table('{}/plate_{}_02_filtered_data.csv'.format(folder, str(plate.id)))
plate.write_raw_table('{}/plate_{}_01_raw_data.csv'.format(folder, str(plate.id))) plate.write_raw_table('{}/plate_{}_01_raw_data.csv'.format(folder, str(plate.id)))
if exp.avg_plate: if exp.avg_plate:
exp.avg_plate.write_avg_tm_table('{}/plate_{}_05_tm_avg.csv'.format(folder, str(exp.avg_plate.id))) exp.avg_plate.write_avg_tm_table('{}/plate_{}_05_tm_avg.csv'.format(folder, str(exp.avg_plate.id)))
#plot(plate, self) #plot(plate, self)
plot(exp) plotter = PlotResults(exp)
for i in range(self.tabWidget.count()):
for plate in exp.plates:
if i == 0:
plotter.plot_raw(plate, self.tabWidget.widget(i))
elif i == 1:
plotter.plot_derivative(plate, self.tabWidget.widget(i))
elif i == 2:
plotter.plot_tm_heatmap_single(plate, self.tabWidget.widget(i))
elif exp.avg_plate and i == 3:
plotter.plot_tm_heatmap_single(exp.avg_plate, self.tabWidget.widget(i))
self.tabWidget.setTabEnabled(i, True)
else:
self.tabWidget.setTabEnabled(i, False)
#for i in range(self.tabWidget.count()):
# self.tabWidget.widget(i).canvas.clear()
#fig, ax = figures[0]
#self.tabWidget.widget(0).canvas.fig = fig
#self.tabWidget.widget(0).canvas.ax = ax
#self.tabWidget.widget(0).canvas.draw()
self.progressBar.setEnabled(False) self.progressBar.setEnabled(False)
self.statusBar.showMessage("Finished!") self.statusBar.showMessage("Finished!")
@ -135,6 +162,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
QApplication.quit() QApplication.quit()
pyqtSlot() pyqtSlot()
def on_actionQuit_triggered(self): def on_actionQuit_triggered(self):
""" """
Slot documentation goes here. Slot documentation goes here.

60
ui/mainwindow.ui
View file

@ -6,8 +6,8 @@
<rect> <rect>
<x>0</x> <x>0</x>
<y>0</y> <y>0</y>
<width>388</width> <width>808</width>
<height>642</height> <height>646</height>
</rect> </rect>
</property> </property>
<property name="windowTitle"> <property name="windowTitle">
@ -35,7 +35,7 @@
<property name="checkable"> <property name="checkable">
<bool>false</bool> <bool>false</bool>
</property> </property>
<layout class="QGridLayout" name="gridLayout"> <layout class="QFormLayout" name="formLayout_3">
<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">
@ -247,7 +247,7 @@
<string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Only T&lt;span style=&quot; vertical-align:sub;&quot;&gt;m&lt;/span&gt; values within this limit are considered valid.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string> <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Only T&lt;span style=&quot; vertical-align:sub;&quot;&gt;m&lt;/span&gt; values within this limit are considered valid.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
</property> </property>
<property name="title"> <property name="title">
<string>Cutoff</string> <string>&amp;Cutoff</string>
</property> </property>
<property name="alignment"> <property name="alignment">
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set> <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
@ -406,14 +406,44 @@
</layout> </layout>
</widget> </widget>
</item> </item>
<item row="4" column="1">
<widget class="QDialogButtonBox" name="buttonBox_process">
<property name="standardButtons">
<set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
</property>
</widget>
</item>
</layout> </layout>
</widget> </widget>
</item> </item>
<item row="1" column="0"> <item row="0" column="1">
<widget class="QDialogButtonBox" name="buttonBox_process"> <widget class="QTabWidget" name="tabWidget">
<property name="standardButtons"> <property name="currentIndex">
<set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set> <number>3</number>
</property> </property>
<widget class="MplWidget" name="tab_raw">
<attribute name="title">
<string>Raw Data</string>
</attribute>
</widget>
<widget class="MplWidget" name="tab_derivative">
<attribute name="title">
<string>&amp;1st derivative</string>
</attribute>
</widget>
<widget class="MplWidget" name="tab_heatmap">
<attribute name="title">
<string>Heatmap</string>
</attribute>
</widget>
<widget class="MplWidget" name="tab_heatmap_avg">
<property name="enabled">
<bool>false</bool>
</property>
<attribute name="title">
<string>Heatmap average</string>
</attribute>
</widget>
</widget> </widget>
</item> </item>
</layout> </layout>
@ -423,7 +453,7 @@
<rect> <rect>
<x>0</x> <x>0</x>
<y>0</y> <y>0</y>
<width>388</width> <width>808</width>
<height>29</height> <height>29</height>
</rect> </rect>
</property> </property>
@ -444,7 +474,7 @@
<locale language="English" country="UnitedStates"/> <locale language="English" country="UnitedStates"/>
</property> </property>
<property name="title"> <property name="title">
<string>Help</string> <string>Hel&amp;p</string>
</property> </property>
<addaction name="actionAbout"/> <addaction name="actionAbout"/>
<addaction name="actionAbout_Qt"/> <addaction name="actionAbout_Qt"/>
@ -465,7 +495,7 @@
</action> </action>
<action name="actionAbout_Qt"> <action name="actionAbout_Qt">
<property name="icon"> <property name="icon">
<iconset resource="icons.qrc"> <iconset>
<normaloff>:/qtlogo.svg</normaloff>:/qtlogo.svg</iconset> <normaloff>:/qtlogo.svg</normaloff>:/qtlogo.svg</iconset>
</property> </property>
<property name="text"> <property name="text">
@ -473,6 +503,14 @@
</property> </property>
</action> </action>
</widget> </widget>
<customwidgets>
<customwidget>
<class>MplWidget</class>
<extends>QWidget</extends>
<header>mplwidget</header>
<container>1</container>
</customwidget>
</customwidgets>
<resources> <resources>
<include location="icons.qrc"/> <include location="icons.qrc"/>
</resources> </resources>

25
ui/mplwidget.py Normal file
View file

@ -0,0 +1,25 @@
from PyQt5 import QtWidgets
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QTAgg as NavigationToolbar
from matplotlib.figure import Figure
class MplCanvas(FigureCanvas):
def __init__(self):
self.fig = Figure()
self.ax = self.fig.add_subplot(111)
FigureCanvas.__init__(self, self.fig)
FigureCanvas.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def clear(self):
self.ax.clear()
self.fig.clear()
class MplWidget(QtWidgets.QWidget):
def __init__(self, parent = None):
QtWidgets.QWidget.__init__(self, parent)
self.canvas = MplCanvas()
self.vbl = QtWidgets.QVBoxLayout()
self.vbl.addWidget(self.canvas)
self.setLayout(self.vbl)