From 5e275d57e55c395238020be3d51ad05af3e40e7a Mon Sep 17 00:00:00 2001
From: Alexander Minges <alexander.minges@gmail.com>
Date: Thu, 9 Jul 2015 00:49:25 +0200
Subject: [PATCH] Move Instrument specific code to class (WIP)
---
instruments/analytikJenaqTower2.py | 31 ++++++++++++++++
pydsf.py | 57 ++++++++++++------------------
ui/mainwindow.py | 20 +++++++----
ui/mplwidget.py | 19 ++++++----
4 files changed, 79 insertions(+), 48 deletions(-)
create mode 100644 instruments/analytikJenaqTower2.py
diff --git a/instruments/analytikJenaqTower2.py b/instruments/analytikJenaqTower2.py
new file mode 100644
index 0000000..44146e3
--- /dev/null
+++ b/instruments/analytikJenaqTower2.py
@@ -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
diff --git a/pydsf.py b/pydsf.py
index 62fe33a..4a6a4f3 100644
--- a/pydsf.py
+++ b/pydsf.py
@@ -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)
diff --git a/ui/mainwindow.py b/ui/mainwindow.py
index 72bbbf3..69e503c 100644
--- a/ui/mainwindow.py
+++ b/ui/mainwindow.py
@@ -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)))
diff --git a/ui/mplwidget.py b/ui/mplwidget.py
index b90694f..1620186 100644
--- a/ui/mplwidget.py
+++ b/ui/mplwidget.py
@@ -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()