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Coding style
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parent
86b5090b49
commit
11e480037a
2 changed files with 54 additions and 26 deletions
73
pydsf.py
73
pydsf.py
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@ -34,15 +34,14 @@ class Well:
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Represents a well in a microtiter plate.
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Owned by an object of type 'Plate'.
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"""
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def __init__(self, owner, name=None):
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self.owner = owner
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self.name = name
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self.raw = np.zeros(self.owner.reads, dtype=np.float)
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self.filtered = np.zeros(self.owner.reads, dtype=np.float)
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self.derivatives = np.zeros((4, self.owner.reads))
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self.splines = {"raw": None,
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"filtered": None,
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"derivative1": None}
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self.splines = {"raw": None, "filtered": None, "derivative1": None}
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self.tm = np.NaN
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self.tm_sd = np.NaN
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self.baseline_correction = owner.baseline_correction
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@ -111,8 +110,7 @@ class Well:
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if (self.owner.tm_cutoff_low != self.owner.t1 or
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self.owner.tm_cutoff_high != self.owner.t1):
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x = np.arange(self.owner.tm_cutoff_low,
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self.owner.tm_cutoff_high + 1,
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self.owner.dt,
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self.owner.tm_cutoff_high + 1, self.owner.dt,
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dtype=np.dtype(np.float))
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# Otherwise use the whole temperature range of the data
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else:
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@ -154,7 +152,8 @@ class Well:
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try:
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if (tm and tm >= self.owner.tm_cutoff_low and
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tm <= self.owner.tm_cutoff_high):
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tm = round(peakutils.interpolate(x, y, width=3,
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tm = round(peakutils.interpolate(x, y,
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width=3,
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ind=[max_i])[0], 2)
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self.owner.denatured_wells.remove(self)
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# If everything is fine, remove the denatured flag
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@ -236,9 +235,19 @@ class Well:
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class Experiment:
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def __init__(self, exp_type, gui=None, files=None, replicates=None, t1=25,
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t2=95, dt=1, cols=12, rows=8, cutoff_low=None,
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cutoff_high=None, signal_threshold=None, color_range=None,
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def __init__(self, exp_type,
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gui=None,
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files=None,
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replicates=None,
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t1=25,
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t2=95,
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dt=1,
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cols=12,
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rows=8,
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cutoff_low=None,
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cutoff_high=None,
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signal_threshold=None,
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color_range=None,
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baseline_correction=False):
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self.replicates = replicates
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self.cols = cols
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@ -280,9 +289,15 @@ class Experiment:
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# populate self.plates with data in provided files list
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i = 1
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for file in files:
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plate = Plate(plate_type=self.type, owner=self, filename=file,
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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,
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plate = Plate(plate_type=self.type,
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owner=self,
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filename=file,
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t1=self.t1,
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t2=self.t2,
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dt=self.dt,
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cols=self.cols,
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rows=self.rows,
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cutoff_low=self.tm_cutoff_low,
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cutoff_high=self.tm_cutoff_high,
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signal_threshold=self.signal_threshold,
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color_range=self.color_range)
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@ -292,9 +307,14 @@ class Experiment:
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# if more than one file is provied, assume that those are replicates
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# and add a special plate representing the average results
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if len(files) > 1:
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self.avg_plate = Plate(plate_type=self.type, owner=self,
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filename=None, t1=self.t1, t2=self.t2,
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dt=self.dt, cols=self.cols, rows=self.rows,
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self.avg_plate = Plate(plate_type=self.type,
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owner=self,
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filename=None,
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t1=self.t1,
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t2=self.t2,
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dt=self.dt,
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cols=self.cols,
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rows=self.rows,
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cutoff_low=self.tm_cutoff_low,
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cutoff_high=self.tm_cutoff_high,
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signal_threshold=self.signal_threshold,
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@ -333,9 +353,18 @@ class Experiment:
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class Plate:
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def __init__(self, plate_type, owner, plate_id=None, filename=None,
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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,
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def __init__(self, plate_type, owner,
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plate_id=None,
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filename=None,
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replicates=None,
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t1=None,
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t2=None,
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dt=None,
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cols=12,
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rows=8,
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cutoff_low=None,
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cutoff_high=None,
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signal_threshold=None,
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color_range=None):
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self.cols = cols
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self.rows = rows
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@ -449,13 +478,11 @@ class Plate:
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def write_avg_tm_table(self, filename):
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with open(filename, 'w') as f:
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f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"',
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'"Tm [°C]"',
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f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', '"Tm [°C]"',
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'"SD"'))
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for well in self.wells:
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if np.isnan(well.tm) or well in self.denatured_wells:
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name,
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'NaN',
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, 'NaN',
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'NaN'))
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else:
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name,
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@ -527,7 +554,6 @@ def update_progress_bar(bar, value):
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class PlotResults():
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def plot_raw(self, plate, widget):
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n = 0
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for i in range(plate.wellnum):
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@ -544,7 +570,6 @@ class PlotResults():
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n += 1
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p1 = widget.addPlot(title=well.name, x=x, y=well.raw)
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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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@ -20,7 +20,10 @@ from .Ui_mainwindow import Ui_MainWindow
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import ui.libs.pyqtgraph as pg
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from pydsf import Experiment, PlotResults
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pg.setConfigOptions(antialias=True)
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# pg.setConfigOptions(antialias=True)
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# Switch to using white background and black foreground
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pg.setConfigOption('background', 'w')
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pg.setConfigOption('foreground', 'k')
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VERSION = "1.0"
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@ -157,7 +160,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
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def generate_plot_tab(self, name):
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tab = QScrollArea()
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tab.setObjectName(name)
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tab.setWidgetResizable(True)
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tab.setWidgetResizable(False)
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return tab
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def generate_plate_tabs(self, plate):
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