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Code Issues Releases Wiki Activity

Move Instrument specific code to class (WIP)

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This commit is contained in:
Alexander Minges 2015-07-09 00:49:25 +02:00
parent 71c25f902b
commit 5e275d57e5
4 changed files with 79 additions and 48 deletions
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31
instruments/analytikJenaqTower2.py Normal file
View file

@ -0,0 +1,31 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import csv
import numpy as np
class AnalytikJenaqTower2:
def __init__(self):
self.name = "Analytik Jena qTower 2.0/2.2"
self.providesTempRange = False
self.providesDeltaT = False
def loadData(self, filename, reads, wells):
with open(filename, 'r') as f:
reader = csv.reader(f, delimiter=';', quoting=csv.QUOTE_NONE)
i = 0
for row in reader:
temp = np.zeros(reads, dtype=float)
for read in range(reads + 1):
if read > 0:
try:
temp[read - 1] = row[read]
except (IndexError, ValueError):
temp[read - 1] = 0.0
elif read == 0:
wells[i].name = row[read]
wells[i].raw = temp
i += 1
return wells

57
pydsf.py
View file

@ -34,13 +34,20 @@ except ImportError:
try:
from PyQt5.QtCore import QCoreApplication
except:
except ImportError:
raise ImportError('----- PyQt5 must be installed -----')
# Import available instruments
try:
from instruments.analytikJenaqTower2 import AnalytikJenaqTower2
except ImportError as err:
raise ImportError('Error while loading instrument plugins:', err)
_translate = QCoreApplication.translate
class Well:
"""
Represents a well in a microtiter plate.
Owned by an object of type 'Plate'.
@ -137,23 +144,10 @@ class Well:
# Run peak finding; return NaN in case of error
try:
peak_indexes = peakutils.indexes(y, thres=0.3)
peaks_x = peakutils.interpolate(x, y, width=3, ind=peak_indexes)
# loop over results to find maximum value for peak candidates
max_y = None # current maximum
max_i = None # index of current maximum
for peak in peak_indexes:
# if current peak is larger than old maximum and its
# second derivative is positive, replace maximum with
# current peak
if (not max_y or y[peak] > max_y) and y[peak] > 0:
max_y = y[peak]
max_i = peak
# If a global maximum is identified, return use its x value as
# melting temperature
if max_y and max_i:
tm = x[max_i]
# if no maximum is found, return NaN
if len(peaks_x) > 0:
tm = max(peaks_x)
else:
return np.NaN
@ -163,9 +157,6 @@ class Well:
try:
if (tm and tm >= self.owner.tm_cutoff_low and
tm <= self.owner.tm_cutoff_high):
tm = round(peakutils.interpolate(x, y,
width=3,
ind=[max_i])[0], 2)
self.owner.denatured_wells.remove(self)
# If everything is fine, remove the denatured flag
return tm # and return the Tm
@ -246,8 +237,8 @@ class Well:
class Experiment:
def __init__(self, exp_type,
gui=None,
files=None,
replicates=None,
t1=25,
@ -275,7 +266,6 @@ class Experiment:
self.max_tm = None
self.min_tm = None
self.replicates = None
self.gui = gui
self.signal_threshold = signal_threshold
self.avg_plate = None
self.baseline_correction = baseline_correction
@ -337,7 +327,7 @@ class Experiment:
Triggers analyzation of plates.
"""
for plate in self.plates:
plate.analyze(gui=self.gui)
plate.analyze()
# if more than one plate is present, calculate average values for the
# merged average plate
if len(self.plates) > 1:
@ -364,6 +354,7 @@ class Experiment:
class Plate:
def __init__(self, plate_type, owner,
plate_id=None,
filename=None,
@ -445,7 +436,7 @@ class Plate:
self.wells[i].raw = temp
i += 1
def analyze(self, gui=None):
def analyze(self):
try:
# Try to access data file in the given path
with open(self.filename) as f:
@ -455,17 +446,16 @@ class Plate:
print('Error accessing file: {}'.format(e))
if self.type == 'Analytik Jena qTOWER 2.0/2.2':
self.analytikJena()
if gui:
update_progress_bar(gui.pb, 1)
instrument = AnalytikJenaqTower2()
else:
# Raise exception, if the instrument's name is unknown
raise NameError('Unknown instrument type: {}'.format(self.type))
self.wells = instrument.loadData(self.filename, self.reads, self.wells)
for well in self.wells:
well.analyze()
if gui:
update_progress_bar(gui.pb, 15)
self.tms.append(well.tm)
@ -511,7 +501,9 @@ class Plate:
elif dataType == 'derivative':
d = well.derivatives[1][i]
else:
raise ValueError('Valid dataTypes are "raw", "filtered", and "derivative"! dataType provided was:{}'.format(dataType))
raise ValueError("Valid dataTypes are raw,"
"filtered, and derivative! dataType"
"provided was:{}".format(dataType))
d_rounded = float(np.round(d, decimals=3))
row.append(d_rounded)
writer.writerow(row)
@ -524,11 +516,8 @@ class Plate:
raise NotImplementedError
def update_progress_bar(bar, value):
bar.setValue(value)
class PlotResults():
def plot_tm_heatmap_single(self, plate, widget):
"""
Plot Tm heatmap (Fig. 1)

20
ui/mainwindow.py
View file

@ -72,6 +72,7 @@ class TaskSignals(QObject):
class Tasks(QObject):
def __init__(self):
super(Tasks, self).__init__()
@ -100,6 +101,7 @@ class Tasks(QObject):
class MainWindow(QMainWindow, Ui_MainWindow):
"""
Class documentation goes here.
"""
@ -150,7 +152,8 @@ class MainWindow(QMainWindow, Ui_MainWindow):
@pyqtSlot("QAbstractButton*")
def on_buttonBox_output_clicked(self, button):
if button == self.buttonBox_output.button(QDialogButtonBox.Open):
path = QFileDialog.getExistingDirectory(parent=self, caption=_translate('MainWindow', 'Choose output path'), options=QFileDialog.ShowDirsOnly)
path = QFileDialog.getExistingDirectory(parent=self, caption=_translate(
'MainWindow', 'Choose output path'), options=QFileDialog.ShowDirsOnly)
self.lineEdit_output.setText(path.strip())
@pyqtSlot("QString")
@ -186,29 +189,32 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab)
if self.checkBox_saveplots.isChecked():
tab.canvas.save("{}/heatmap_{}.svg".format(self.outputPath, plate.id))
tab.canvas.save(
"{}/heatmap_{}.svg".format(self.outputPath, plate.id))
tab = self.generate_plot_tab("tab_raw_{}".format(plate.id))
title = _translate("MainWindow", "Raw Data #")
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_raw(plate, tab)
if self.checkBox_saveplots.isChecked():
tab.canvas.save("{}/raw_{}.svg".format(self.outputPath, plate.id))
tab.canvas.save(
"{}/raw_{}.svg".format(self.outputPath, plate.id))
tab = self.generate_plot_tab("tab_derivative_{}".format(plate.id))
title = _translate("MainWindow", "Derivatives #")
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_derivative(plate, tab)
if self.checkBox_saveplots.isChecked():
tab.canvas.save("{}/derivatives_{}.svg".format(self.outputPath, plate.id))
tab.canvas.save(
"{}/derivatives_{}.svg".format(self.outputPath, plate.id))
else:
tab = self.generate_plot_tab("tab_heatmap_{}".format(plate.id))
title = _translate("MainWindow", "Heatmap ")
self.tabWidget.addTab(tab, title + str(plate.id))
plotter.plot_tm_heatmap_single(plate, tab)
if self.checkBox_saveplots.isChecked():
tab.canvas.save("{}/heatmap_{}.svg".format(self.outputPath, plate.id))
tab.canvas.save(
"{}/heatmap_{}.svg".format(self.outputPath, plate.id))
@pyqtSlot()
def on_buttonBox_process_accepted(self):
@ -279,7 +285,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
'{}/plate_{}_dI_dT.csv'.format(self.outputPath, str(plate.id)), dataType='derivative')
plate.write_data_table(
'{}/plate_{}_filtered_data.csv'.format(self.outputPath,
str(plate.id)), dataType='filtered')
str(plate.id)), dataType='filtered')
plate.write_data_table('{}/plate_{}_raw_data.csv'.format(
self.outputPath, str(plate.id)))

19
ui/mplwidget.py
View file

@ -9,6 +9,7 @@ _translate = QCoreApplication.translate
class MplCanvas(FigureCanvas):
def __init__(self, parent=None, width=4, height=5, dpi=100):
self.fig = Figure(figsize=(width, height), dpi=dpi)
self.ax = self.fig.add_subplot(111)
@ -34,20 +35,23 @@ class MplCanvas(FigureCanvas):
except IOError:
QtWidgets.QMessageBox.critical(
self, _translate("MainWindow", "Error"),
_translate("MainWindow", "Error saving figure! Please check permissions/free space of target path!"),
_translate("MainWindow", "Error saving figure! Please check "
"permissions/free space of target path!"),
QtWidgets.QMessageBox.Close, QtWidgets.QMessageBox.Close)
class CustomNavigationToolbar(NavigationToolbar):
toolitems = (
(_translate("CustomNavigationToolbar", 'Save'),
(_translate("CustomNavigationToolbar", "Save"),
_translate("CustomNavigationToolbar",
'Save the figure'), 'filesave',
'save_figure'),
(_translate("CustomNavigationToolbar", 'Subplots'),
"Save the figure"), "filesave",
"save_figure"),
(_translate("CustomNavigationToolbar", "Subplots"),
_translate("CustomNavigationToolbar",
'Configure subplots'), 'subplots',
'configure_subplots'), (None, None, None, None), )
"Configure subplots"), "subplots",
"configure_subplots"),
(None, None, None, None), )
def __init__(self, canvas, parent, coordinates=True):
NavigationToolbar.__init__(self, canvas, parent,
@ -55,6 +59,7 @@ class CustomNavigationToolbar(NavigationToolbar):
class MplWidget(QtWidgets.QGraphicsView):
def __init__(self, parent=None):
QtWidgets.QGraphicsView.__init__(self, parent)
self.canvas = MplCanvas()