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Embedded plots into GUI
This commit is contained in:
parent
926fb01502
commit
cf75c8ee09
7 changed files with 446 additions and 349 deletions
2
.gitignore
vendored
2
.gitignore
vendored
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@ -21,7 +21,7 @@ var/
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*.egg-info/
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.installed.cfg
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*.egg
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.idea
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.idea/
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# PyInstaller
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# Usually these files are written by a python script from a template
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173
pydsf.py
173
pydsf.py
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@ -1,6 +1,7 @@
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#! /usr/bin/env python2
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# -*- coding: utf-8 -*-
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import csv
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import multiprocessing as mp
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try:
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import matplotlib as mpl
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@ -29,6 +30,7 @@ try:
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except ImportError:
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raise ImportError('----- SciPy must be installed. -----')
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class Well:
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def __init__(self, owner):
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self.owner = owner
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@ -64,7 +66,8 @@ class Well:
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for i in range(4):
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self.derivatives[i, t - self.owner.t1] = temp[i]
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def calc_baseline(self, y):
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@staticmethod
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def calc_baseline(y):
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try:
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baseline = peakutils.baseline(y)
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return baseline
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@ -128,7 +131,7 @@ class Well:
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if i > 0: # If a positive slope is found
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denatured = False # set denatured flag to False
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reads = int(round(self.owner.reads/10)) # How many values should be checked against the signal threshold:
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reads = int(round(self.owner.reads / 10)) # How many values should be checked against the signal threshold:
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# 1/10 of the total number of data point
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read = 0 # Initialize running variable representing the current data point
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@ -161,8 +164,10 @@ class Well:
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if self.tm is None:
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self.tm = np.NaN
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class Experiment:
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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):
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def __init__(self, type, gui=None, files=None, replicates=None, t1=25, t2=95, dt=1, cols=12, rows=8,
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cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None, baseline_correction=False):
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self.replicates = replicates
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self.cols = cols
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self.rows = rows
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@ -178,10 +183,10 @@ class Experiment:
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self.max_tm = None
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self.min_tm = None
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self.replicates = None
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self.gui=gui
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self.gui = gui
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self.signal_threshold = signal_threshold
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self.avg_plate = None
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self.baseline_correction=baseline_correction
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self.baseline_correction = baseline_correction
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if cutoff_low:
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self.tm_cutoff_low = cutoff_low
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else:
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@ -193,18 +198,23 @@ class Experiment:
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if color_range:
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self.color_range = color_range
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else:
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self.color_range = (self.t1, self.t2)
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self.color_range = None
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self.plates = []
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i = 1
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for file in files:
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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)
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plate = Plate(type=self.type, owner=self, filename=file, t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols,
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rows=self.rows, cutoff_low=self.tm_cutoff_low, cutoff_high=self.tm_cutoff_high,
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signal_threshold=self.signal_threshold, color_range=self.color_range)
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plate.id = i
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self.plates.append(plate)
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i += 1
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if len(files) > 1:
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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)
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self.avg_plate = Plate(type=self.type, owner=self, filename=None, t1=self.t1, t2=self.t2, dt=self.dt,
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cols=self.cols, rows=self.rows, cutoff_low=self.tm_cutoff_low,
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cutoff_high=self.tm_cutoff_high, signal_threshold=self.signal_threshold,
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color_range=self.color_range)
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self.avg_plate.id = 'average'
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def analyze(self):
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@ -213,8 +223,8 @@ class Experiment:
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if len(self.plates) > 1:
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#self.tm_replicates = np.zeros( self.wellnum, dtype=float )
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#self.tm_replicates_sd = np.zeros( self.wellnum, dtype=float )
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# self.tm_replicates = np.zeros( self.wellnum, dtype=float )
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# self.tm_replicates_sd = np.zeros( self.wellnum, dtype=float )
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for i in range(self.wellnum):
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@ -225,16 +235,17 @@ class Experiment:
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if plate.wells[i] not in plate.denatured_wells:
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tmp.append(tm)
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if len(tmp) > 0:
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#self.avg_plate.wells[i].tm = (sum(tmp)/len(tmp))
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# self.avg_plate.wells[i].tm = (sum(tmp)/len(tmp))
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self.avg_plate.wells[i].tm = np.mean(tmp)
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self.avg_plate.wells[i].tm_sd = np.std(tmp)
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#self.tm_replicates[i] = (sum(tmp)/len(tmp))
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# self.tm_replicates[i] = (sum(tmp)/len(tmp))
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else:
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self.avg_plate.denatured_wells.append(self.avg_plate.wells[i])
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class Plate:
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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):
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def __init__(self, type, owner, id=None, filename=None, replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8,
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cutoff_low=None, cutoff_high=None, signal_threshold=None, color_range=None):
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self.cols = cols
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self.rows = rows
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self.owner = owner
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@ -279,11 +290,9 @@ class Plate:
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self.tms = []
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for i in range(self.wellnum):
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well = Well(owner = self)
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well = Well(owner=self)
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self.wells.append(well)
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#self.analyze()
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def analytikJena(self):
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"""
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@ -295,7 +304,7 @@ class Plate:
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i = 0
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for row in reader:
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temp = np.zeros(self.reads, dtype=float)
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for read in range(self.reads+1):
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for read in range(self.reads + 1):
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if read > 0:
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try:
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temp[read - 1] = row[read]
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@ -309,12 +318,12 @@ class Plate:
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def analyze(self, gui=None):
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try:
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# Try to access data file in the given path
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with open(self.filename) as f: pass
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with open(self.filename) as f:
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pass
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except IOError as e:
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# If the file is not found, or not accessible: abort
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print('Error accessing file: {}'.format(e))
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if self.type == 'Analytik Jena qTOWER 2.0/2.2':
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self.analytikJena()
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if gui:
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@ -335,7 +344,7 @@ class Plate:
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print("rows")
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if self.replicates == 'cols':
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print("cols")
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#print(self.tms)
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# print(self.tms)
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self.max_tm = max(self.tms)
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self.min_tm = min(self.tms)
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@ -417,51 +426,12 @@ class Plate:
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def update_progress_bar(bar, value):
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bar.setValue(value)
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def plot_tm_heatmap_average(experiment, gui=None):
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"""
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Plot Tm heatmap (Fig. 1)
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"""
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x = 1 # Position in columns
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y = 1 # Position in rows
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x_values = [] # Array holding the columns
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y_values = [] # Array holding the rows
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c_values = [] # Array holding the color values aka Tm
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class PlotResults():
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# c = well.tm # If not, set color to Tm
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# if c < experiment.tm_cutoff_low: # Check if Tm is lower that the cutoff
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# c = experiment.tm_cutoff_low # If it is, set color to cutoff
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# elif c > experiment.tm_cutoff_high: # Check if Tm is higher that the cutoff
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# c = experiment.tm_cutoff_high # If it is, set color to cutoff
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# else: # If the plate is denatured
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# c = experiment.tm_cutoff_low # Set its color to the low cutoff
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for c in experiment.tm_replicates:
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def __init__(self, experiment):
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self.experiment = experiment
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x_values.append(x) # Add values to the respective arrays
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y_values.append(y)
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c_values.append(c)
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x += 1 # Increase column by one
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if x > experiment.cols: # If maximum column per row is reached
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x = 1 # reset column to one
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y += 1 # and increase row by one
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fig1 = plt.figure() # new figure
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ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
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ax1.autoscale(tight=True) # Scale plate size
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ax1.xaxis.set_major_locator(ticker.MaxNLocator(experiment.cols + 1)) # n columns
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ax1.yaxis.set_major_locator(ticker.MaxNLocator(experiment.rows + 1)) # n rows
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if experiment.color_range:
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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
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else:
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cax = ax1.scatter(x_values, y_values, s=300, c=c_values, marker='s') # plot wells and color using the colormap
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ax1.invert_yaxis() # invert y axis to math plate layout
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cbar = fig1.colorbar(cax) # show colorbar
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ax1.set_xlabel('Columns') # set axis and colorbar label
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ax1.set_ylabel('Rows')
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ax1.set_title('$T_m$ heatmap (average)')
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cbar.set_label(u"Temperature [°C]")
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def plot_tm_heatmap_single(plate, gui=None):
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def plot_tm_heatmap_single(self, plate, widget):
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"""
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Plot Tm heatmap (Fig. 1)
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"""
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@ -473,6 +443,8 @@ def plot_tm_heatmap_single(plate, gui=None):
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dx_values = []
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dy_values = []
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dc_values = []
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canvas = widget.canvas
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canvas.clear()
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for well in plate.wells: # Iterate over all wells
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if well not in plate.denatured_wells: # Check if well is denatured (no Tm found)
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c = well.tm # If not, set color to Tm
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@ -492,13 +464,14 @@ def plot_tm_heatmap_single(plate, gui=None):
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x = 1 # reset column to one
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y += 1 # and increase row by one
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fig1 = plt.figure() # new figure
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fig1 = canvas.fig # new figure
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ax1 = fig1.add_subplot(1, 1, 1) # A single canvas
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ax1.autoscale(tight=True) # Scale plate size
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ax1.xaxis.set_major_locator(ticker.MaxNLocator(plate.cols + 1)) # n columns
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ax1.yaxis.set_major_locator(ticker.MaxNLocator(plate.rows + 1)) # n rows
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if plate.color_range:
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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
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s', vmin=plate.color_range[0],
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vmax=plate.color_range[1]) # plot wells and color using the colormap
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else:
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values, marker='s') # plot wells and color using the colormap
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@ -515,17 +488,15 @@ def plot_tm_heatmap_single(plate, gui=None):
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ax1.set_title(title)
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cbar.set_label(u"Temperature [°C]")
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#magenta_patch = mpatches.Patch(color='magenta', label='Denatured')
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#fig1.legend([magenta_patch], 'Denatured', loc='lower right', bbox_to_anchor=[0.5, 0.5])
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canvas.draw()
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# if gui:
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# update_progress_bar(gui.pb, 50)
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def plot_derivative(plate, gui=None):
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def plot_derivative(self, plate, widget):
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"""
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Plot derivatives (Fig. 2)
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"""
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fig2 = plt.figure() # new figure
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canvas = widget.canvas
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canvas.clear()
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fig2 = canvas.fig # new figure
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fig2.suptitle('Individual Derivatives (plate #{})'.format(str(plate.id))) # set title
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for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
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@ -562,14 +533,16 @@ def plot_derivative(plate, gui=None):
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label.set_fontsize('xx-small')
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cax = ax.plot(x, y) # plot data to the current subplot
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# if gui:
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# update_progress_bar(gui.pb, 75)
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canvas.draw()
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def plot_raw(plate, gui=None):
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def plot_raw(self, plate, widget):
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"""
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Plot raw data (Fig. 3)
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"""
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fig3 = plt.figure() # new figure
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canvas = widget.canvas
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canvas.clear()
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fig3 = canvas.fig # new figure
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fig3.suptitle('Raw Data (plate #{})'.format(str(plate.id))) # set title
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for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
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@ -596,25 +569,37 @@ def plot_raw(plate, gui=None):
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label.set_fontsize('xx-small')
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cax = ax.plot(x, y) # plot data to the current subplot
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# if gui:
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# update_progress_bar(gui.pb, 100)
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# gui.pb.hide()
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def plot(experiment, gui=None):
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for plate in experiment.plates:
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plot_raw(plate)
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plot_derivative(plate)
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plot_tm_heatmap_single(plate)
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if len(experiment.plates) > 1:
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plot_tm_heatmap_single(experiment.avg_plate)
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#plot_tm_heatmap_average(experiment)
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plt.show()
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canvas.draw()
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#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))
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#plot(plate)
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# def _plot_wrapper(self, plot, plate):
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#
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# if plot == 'raw':
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# fig, ax = self._plot_raw(plate)
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# elif plot == 'derivative':
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# fig, ax = self._plot_derivative(plate)
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# elif plot == 'tm_heatmap':
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# fig, ax = self._plot_tm_heatmap_single(plate)
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# else:
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# raise NotImplementedError
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# fig = None
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# ax = None
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# return (fig, ax)
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#
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# def plot_all(self):
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#
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# figures = []
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#
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# for plate in self.experiment.plates:
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#
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# figures.append(self._plot_wrapper('raw', plate))
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# figures.append(self._plot_wrapper('derivative', plate))
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# figures.append(self._plot_wrapper('tm_heatmap', plate))
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#
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# if len(self.experiment.plates) > 1:
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# figures.append(self._plot_wrapper('tm_heatmap', self.experiment.avg_plate))
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#
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# return figures
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'mainwindow.ui'
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#
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# Created: Fri Jan 30 14:07:06 2015
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# Created: Fri Jan 30 19:20:59 2015
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# by: PyQt5 UI code generator 5.4
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#
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# WARNING! All changes made in this file will be lost!
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@ -12,7 +12,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
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class Ui_MainWindow(object):
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def setupUi(self, MainWindow):
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MainWindow.setObjectName("MainWindow")
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MainWindow.resize(388, 642)
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MainWindow.resize(808, 646)
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MainWindow.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates))
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self.centralWidget = QtWidgets.QWidget(MainWindow)
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self.centralWidget.setLocale(QtCore.QLocale(QtCore.QLocale.English, QtCore.QLocale.UnitedStates))
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@ -24,11 +24,11 @@ class Ui_MainWindow(object):
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self.groupBox_experiment.setFlat(False)
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self.groupBox_experiment.setCheckable(False)
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self.groupBox_experiment.setObjectName("groupBox_experiment")
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self.gridLayout = QtWidgets.QGridLayout(self.groupBox_experiment)
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self.gridLayout.setObjectName("gridLayout")
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self.formLayout_3 = QtWidgets.QFormLayout(self.groupBox_experiment)
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self.formLayout_3.setObjectName("formLayout_3")
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self.label_instrument = QtWidgets.QLabel(self.groupBox_experiment)
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self.label_instrument.setObjectName("label_instrument")
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self.gridLayout.addWidget(self.label_instrument, 0, 0, 1, 1)
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self.formLayout_3.setWidget(0, QtWidgets.QFormLayout.LabelRole, self.label_instrument)
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self.comboBox_instrument = QtWidgets.QComboBox(self.groupBox_experiment)
|
||||
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
|
||||
sizePolicy.setHorizontalStretch(0)
|
||||
|
|
@ -37,7 +37,7 @@ class Ui_MainWindow(object):
|
|||
self.comboBox_instrument.setSizePolicy(sizePolicy)
|
||||
self.comboBox_instrument.setObjectName("comboBox_instrument")
|
||||
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.setEnabled(True)
|
||||
self.groupBox_data.setObjectName("groupBox_data")
|
||||
|
|
@ -72,7 +72,7 @@ class Ui_MainWindow(object):
|
|||
self.listWidget_data.setAlternatingRowColors(True)
|
||||
self.listWidget_data.setObjectName("listWidget_data")
|
||||
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.setEnabled(True)
|
||||
self.groupBox_temp.setAutoFillBackground(False)
|
||||
|
|
@ -108,7 +108,7 @@ class Ui_MainWindow(object):
|
|||
self.doubleSpinBox_dt.setProperty("value", 1.0)
|
||||
self.doubleSpinBox_dt.setObjectName("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.setEnabled(True)
|
||||
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.setObjectName("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.setEnabled(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.setObjectName("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.setEnabled(True)
|
||||
self.groupBox_cbar.setCheckable(True)
|
||||
|
|
@ -170,15 +170,31 @@ class Ui_MainWindow(object):
|
|||
self.doubleSpinBox_cbar_end.setDecimals(1)
|
||||
self.doubleSpinBox_cbar_end.setObjectName("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.gridLayout_2.addWidget(self.groupBox_experiment, 0, 0, 1, 1)
|
||||
self.buttonBox_process = QtWidgets.QDialogButtonBox(self.centralWidget)
|
||||
self.formLayout_3.setWidget(3, QtWidgets.QFormLayout.FieldRole, self.groupBox_cbar)
|
||||
self.buttonBox_process = QtWidgets.QDialogButtonBox(self.groupBox_experiment)
|
||||
self.buttonBox_process.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
|
||||
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)
|
||||
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.setObjectName("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.retranslateUi(MainWindow)
|
||||
self.tabWidget.setCurrentIndex(3)
|
||||
QtCore.QMetaObject.connectSlotsByName(MainWindow)
|
||||
|
||||
def retranslateUi(self, MainWindow):
|
||||
|
|
@ -236,7 +253,7 @@ class Ui_MainWindow(object):
|
|||
self.label_dt.setText(_translate("MainWindow", "<html><head/><body><p>ΔT</p></body></html>"))
|
||||
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.setTitle(_translate("MainWindow", "Cutoff"))
|
||||
self.groupBox_cutoff.setTitle(_translate("MainWindow", "&Cutoff"))
|
||||
self.label_cutoff_high.setText(_translate("MainWindow", "&Upper"))
|
||||
self.doubleSpinBox_upper.setSuffix(_translate("MainWindow", " °C"))
|
||||
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.label_cbar_end.setText(_translate("MainWindow", "En&d"))
|
||||
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.menuHelp.setTitle(_translate("MainWindow", "Help"))
|
||||
self.menuHelp.setTitle(_translate("MainWindow", "Hel&p"))
|
||||
self.actionQuit.setText(_translate("MainWindow", "&Quit"))
|
||||
self.actionAbout.setText(_translate("MainWindow", "&About"))
|
||||
self.actionAbout_Qt.setText(_translate("MainWindow", "About &Qt"))
|
||||
|
||||
from .mplwidget import MplWidget
|
||||
|
|
|
|||
|
|
@ -1,5 +1,3 @@
|
|||
<RCC>
|
||||
<qresource prefix="/">
|
||||
<file>qtlogo.svg</file>
|
||||
</qresource>
|
||||
<qresource prefix="/"/>
|
||||
</RCC>
|
||||
|
|
|
|||
|
|
@ -17,6 +17,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
"""
|
||||
Class documentation goes here.
|
||||
"""
|
||||
|
||||
def __init__(self, parent=None):
|
||||
"""
|
||||
Constructor
|
||||
|
|
@ -33,6 +34,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
self.statusBar.showMessage("Welcome to PyDSF")
|
||||
|
||||
|
||||
|
||||
@pyqtSlot("QAbstractButton*")
|
||||
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):
|
||||
self.listWidget_data.clear()
|
||||
print("Data cleared")
|
||||
# self.radioButton_rep_rows.setEnabled(False)
|
||||
# self.radioButton_rep_columns.setEnabled(False)
|
||||
# self.radioButton_rep_rows.setEnabled(False)
|
||||
# self.radioButton_rep_columns.setEnabled(False)
|
||||
|
||||
|
||||
@pyqtSlot("QString")
|
||||
|
|
@ -61,10 +63,10 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
self.groupBox_temp.setEnabled(True)
|
||||
else:
|
||||
self.groupBox_temp.setEnabled(False)
|
||||
# self.groupBox_data.setEnabled(True)
|
||||
# self.groupBox_cutoff.setEnabled(True)
|
||||
# self.groupBox_cbar.setEnabled(True)
|
||||
# self.groupBox_signal_threshold.setEnabled(True)
|
||||
# self.groupBox_data.setEnabled(True)
|
||||
# self.groupBox_cutoff.setEnabled(True)
|
||||
# self.groupBox_cbar.setEnabled(True)
|
||||
# self.groupBox_signal_threshold.setEnabled(True)
|
||||
|
||||
@pyqtSlot()
|
||||
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)
|
||||
return
|
||||
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.statusBar.showMessage("Processing...")
|
||||
|
|
@ -99,14 +102,16 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
files = []
|
||||
for item in items:
|
||||
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()
|
||||
|
||||
# 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)
|
||||
#plate.analyze(gui=self)
|
||||
# plate.analyze(gui=self)
|
||||
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:
|
||||
dialog = QFileDialog()
|
||||
dialog.setFileMode(QFileDialog.Directory)
|
||||
|
|
@ -121,7 +126,29 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
exp.avg_plate.write_avg_tm_table('{}/plate_{}_05_tm_avg.csv'.format(folder, str(exp.avg_plate.id)))
|
||||
#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.statusBar.showMessage("Finished!")
|
||||
|
|
@ -135,6 +162,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
|
|||
QApplication.quit()
|
||||
|
||||
pyqtSlot()
|
||||
|
||||
def on_actionQuit_triggered(self):
|
||||
"""
|
||||
Slot documentation goes here.
|
||||
|
|
|
|||
|
|
@ -6,8 +6,8 @@
|
|||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>388</width>
|
||||
<height>642</height>
|
||||
<width>808</width>
|
||||
<height>646</height>
|
||||
</rect>
|
||||
</property>
|
||||
<property name="windowTitle">
|
||||
|
|
@ -35,7 +35,7 @@
|
|||
<property name="checkable">
|
||||
<bool>false</bool>
|
||||
</property>
|
||||
<layout class="QGridLayout" name="gridLayout">
|
||||
<layout class="QFormLayout" name="formLayout_3">
|
||||
<item row="0" column="0">
|
||||
<widget class="QLabel" name="label_instrument">
|
||||
<property name="text">
|
||||
|
|
@ -247,7 +247,7 @@
|
|||
<string><html><head/><body><p>Only T<span style=" vertical-align:sub;">m</span> values within this limit are considered valid.</p></body></html></string>
|
||||
</property>
|
||||
<property name="title">
|
||||
<string>Cutoff</string>
|
||||
<string>&Cutoff</string>
|
||||
</property>
|
||||
<property name="alignment">
|
||||
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
|
||||
|
|
@ -406,10 +406,7 @@
|
|||
</layout>
|
||||
</widget>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
</item>
|
||||
<item row="1" column="0">
|
||||
<item row="4" column="1">
|
||||
<widget class="QDialogButtonBox" name="buttonBox_process">
|
||||
<property name="standardButtons">
|
||||
<set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
|
||||
|
|
@ -418,12 +415,45 @@
|
|||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
</item>
|
||||
<item row="0" column="1">
|
||||
<widget class="QTabWidget" name="tabWidget">
|
||||
<property name="currentIndex">
|
||||
<number>3</number>
|
||||
</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>&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>
|
||||
</item>
|
||||
</layout>
|
||||
</widget>
|
||||
<widget class="QMenuBar" name="menuBar">
|
||||
<property name="geometry">
|
||||
<rect>
|
||||
<x>0</x>
|
||||
<y>0</y>
|
||||
<width>388</width>
|
||||
<width>808</width>
|
||||
<height>29</height>
|
||||
</rect>
|
||||
</property>
|
||||
|
|
@ -444,7 +474,7 @@
|
|||
<locale language="English" country="UnitedStates"/>
|
||||
</property>
|
||||
<property name="title">
|
||||
<string>Help</string>
|
||||
<string>Hel&p</string>
|
||||
</property>
|
||||
<addaction name="actionAbout"/>
|
||||
<addaction name="actionAbout_Qt"/>
|
||||
|
|
@ -465,7 +495,7 @@
|
|||
</action>
|
||||
<action name="actionAbout_Qt">
|
||||
<property name="icon">
|
||||
<iconset resource="icons.qrc">
|
||||
<iconset>
|
||||
<normaloff>:/qtlogo.svg</normaloff>:/qtlogo.svg</iconset>
|
||||
</property>
|
||||
<property name="text">
|
||||
|
|
@ -473,6 +503,14 @@
|
|||
</property>
|
||||
</action>
|
||||
</widget>
|
||||
<customwidgets>
|
||||
<customwidget>
|
||||
<class>MplWidget</class>
|
||||
<extends>QWidget</extends>
|
||||
<header>mplwidget</header>
|
||||
<container>1</container>
|
||||
</customwidget>
|
||||
</customwidgets>
|
||||
<resources>
|
||||
<include location="icons.qrc"/>
|
||||
</resources>
|
||||
|
|
|
|||
25
ui/mplwidget.py
Normal file
25
ui/mplwidget.py
Normal 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)
|
||||
Loading…
Add table
Reference in a new issue