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Code Issues Releases Wiki Activity

Populate instrument list dynamically; Fixes

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Populate instrument list dynamically from a given set of instrument
objects; Fix a bug when doing mutliple analysis in a row.
This commit is contained in:
Alexander Minges 2015-07-09 15:42:25 +02:00
parent b85c58018c
commit 342ed3b3d1
3 changed files with 81 additions and 42 deletions
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26
pydsf.py
View file

@ -238,7 +238,8 @@ class Well:
class Experiment: class Experiment:
def __init__(self, exp_type, def __init__(self,
instrument,
files=None, files=None,
replicates=None, replicates=None,
t1=25, t1=25,
@ -261,7 +262,7 @@ class Experiment:
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
self.type = exp_type self.instrument = instrument
self.wells = [] self.wells = []
self.max_tm = None self.max_tm = None
self.min_tm = None self.min_tm = None
@ -290,8 +291,7 @@ class Experiment:
# populate self.plates with data in provided files list # populate self.plates with data in provided files list
i = 1 i = 1
for file in files: for file in files:
plate = Plate(plate_type=self.type, plate = Plate(owner=self,
owner=self,
filename=file, filename=file,
t1=self.t1, t1=self.t1,
t2=self.t2, t2=self.t2,
@ -308,8 +308,7 @@ class Experiment:
# if more than one file is provied, assume that those are replicates # if more than one file is provied, assume that those are replicates
# and add a special plate representing the average results # and add a special plate representing the average results
if len(files) > 1: if len(files) > 1:
self.avg_plate = Plate(plate_type=self.type, self.avg_plate = Plate(owner=self,
owner=self,
filename=None, filename=None,
t1=self.t1, t1=self.t1,
t2=self.t2, t2=self.t2,
@ -355,7 +354,7 @@ class Experiment:
class Plate: class Plate:
def __init__(self, plate_type, owner, def __init__(self, owner,
plate_id=None, plate_id=None,
filename=None, filename=None,
replicates=None, replicates=None,
@ -387,7 +386,7 @@ class Plate:
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
self.type = plate_type self.instrument = owner.instrument
self.wells = [] self.wells = []
self.max_tm = None self.max_tm = None
self.min_tm = None self.min_tm = None
@ -445,14 +444,9 @@ class Plate:
# 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': self.wells = self.instrument.loadData(self.filename,
instrument = AnalytikJenaqTower2() self.reads,
self.wells)
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: for well in self.wells:
well.analyze() well.analyze()

2
ui/Ui_mainwindow.py
View file

@ -302,7 +302,7 @@ class Ui_MainWindow(object):
MainWindow.setWindowTitle(_translate("MainWindow", "PyDSF")) MainWindow.setWindowTitle(_translate("MainWindow", "PyDSF"))
self.groupBox_experiment.setTitle(_translate("MainWindow", "Experimental Setup")) self.groupBox_experiment.setTitle(_translate("MainWindow", "Experimental Setup"))
self.label_instrument.setText(_translate("MainWindow", "Instrument")) self.label_instrument.setText(_translate("MainWindow", "Instrument"))
self.comboBox_instrument.setItemText(0, _translate("MainWindow", "Analytik Jena qTOWER 2.0/2.2")) #self.comboBox_instrument.setItemText(0, _translate("MainWindow", "Analytik Jena qTOWER 2.0/2.2"))
self.groupBox_data.setToolTip(_translate("MainWindow", "<html><head/><body><p>Add data files to the experiment. If multiple files are loaded, they are treated as replicates.</p></body></html>")) self.groupBox_data.setToolTip(_translate("MainWindow", "<html><head/><body><p>Add data files to the experiment. If multiple files are loaded, they are treated as replicates.</p></body></html>"))
self.groupBox_data.setTitle(_translate("MainWindow", "Data File")) self.groupBox_data.setTitle(_translate("MainWindow", "Data File"))
self.groupBox_replicates.setTitle(_translate("MainWindow", "Replicates")) self.groupBox_replicates.setTitle(_translate("MainWindow", "Replicates"))

95
ui/mainwindow.py
View file

@ -12,6 +12,12 @@ from .mplwidget import MplWidget
from pydsf import Experiment, PlotResults from pydsf import Experiment, PlotResults
import os import os
# Import available instruments
try:
from instruments.analytikJenaqTower2 import AnalytikJenaqTower2
except ImportError as err:
raise ImportError('Error while loading instrument plugins:', err)
VERSION = "1.0" VERSION = "1.0"
_translate = QCoreApplication.translate _translate = QCoreApplication.translate
@ -25,7 +31,7 @@ class Worker(QRunnable):
finished = pyqtSignal(int) finished = pyqtSignal(int)
def __init__(self, owner): def __init__(self, owner):
super(Worker, self).__init__() super().__init__()
self.exp = None self.exp = None
self.owner = owner self.owner = owner
self.signals = WorkerSignals() self.signals = WorkerSignals()
@ -35,7 +41,7 @@ class Worker(QRunnable):
c_upper = None c_upper = None
cbar_range = None cbar_range = None
signal_threshold = None signal_threshold = None
instrument_type = self.owner.comboBox_instrument.currentText() #instrument_type = self.owner.comboBox_instrument.currentText()
if self.owner.groupBox_cutoff.isChecked(): if self.owner.groupBox_cutoff.isChecked():
c_lower = self.owner.doubleSpinBox_lower.value() c_lower = self.owner.doubleSpinBox_lower.value()
c_upper = self.owner.doubleSpinBox_upper.value() c_upper = self.owner.doubleSpinBox_upper.value()
@ -51,7 +57,7 @@ class Worker(QRunnable):
files = [] files = []
for item in items: for item in items:
files.append(item.text()) files.append(item.text())
self.exp = Experiment(exp_type=instrument_type, self.exp = Experiment(instrument=self.owner.instrument,
files=files, files=files,
t1=self.owner.doubleSpinBox_tmin.value(), t1=self.owner.doubleSpinBox_tmin.value(),
t2=self.owner.doubleSpinBox_tmax.value(), t2=self.owner.doubleSpinBox_tmax.value(),
@ -84,6 +90,12 @@ class Tasks(QObject):
def add_task(self, task): def add_task(self, task):
self.tasks.append(task) self.tasks.append(task)
def remove_task(self, task):
self.tasks.remove(task)
def clear(self):
self.tasks.clear()
def get_data(self): def get_data(self):
self.pool.waitForDone() self.pool.waitForDone()
return self.data return self.data
@ -95,6 +107,7 @@ class Tasks(QObject):
for task in self.tasks: for task in self.tasks:
self.data.append(task.exp) self.data.append(task.exp)
self.remove_task(task)
self.signals.finished.emit(self.data) self.signals.finished.emit(self.data)
@ -120,25 +133,42 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.statusBar.addPermanentWidget(self.progressBar) self.statusBar.addPermanentWidget(self.progressBar)
self.statusBar.showMessage(_translate("MainWindow", self.statusBar.showMessage(_translate("MainWindow",
"Welcome to PyDSF")) "Welcome to PyDSF"))
self.buttonBox_process.addButton( self.buttonBox_process.addButton(
_translate("MainWindow", "&Start Processing"), _translate("MainWindow", "&Start Processing"),
QDialogButtonBox.AcceptRole) QDialogButtonBox.AcceptRole)
self.tasks = Tasks() self.tasks = Tasks()
self.worker = Worker(self) self.tasks.signals.finished.connect(self.on_processing_finished)
self.worker = None
self.outputPath = None self.outputPath = None
self.instrument = None
self.populateInstrumentList()
def populateInstrumentList(self):
self.instruments = [AnalytikJenaqTower2()]
for i in range(len(self.instruments)):
instrument = self.instruments[i]
self.comboBox_instrument.setItemText(i, instrument.name)
def getInstrumentFromName(self, name):
for instrument in self.instruments:
if instrument.name == name:
return instrument
raise IndexError("Requested instrument not")
def getSelectedInstrument(self):
name = str(self.comboBox_instrument.currentText())
instrument = self.getInstrumentFromName(name)
return instrument
@pyqtSlot("QAbstractButton*") @pyqtSlot("QAbstractButton*")
def on_buttonBox_open_reset_clicked(self, button): def on_buttonBox_open_reset_clicked(self, button):
""" """
Slot documentation goes here. Triggered when either the open or reset button in the data file
dialog is clicked. Spawns an open file dialog or resets the listview.
""" """
if button == self.buttonBox_open_reset.button(QDialogButtonBox.Open): if button == self.buttonBox_open_reset.button(QDialogButtonBox.Open):
filenames = QFileDialog.getOpenFileNames( filenames = QFileDialog.getOpenFileNames(
self, self, _translate("MainWindow", "Open data file"), '',
_translate("MainWindow", "Open data file"), '',
_translate("MainWindow", "Text files (*.txt *.csv)")) _translate("MainWindow", "Text files (*.txt *.csv)"))
self.listWidget_data.addItems(filenames[0]) self.listWidget_data.addItems(filenames[0])
if self.listWidget_data.count() > 1: if self.listWidget_data.count() > 1:
@ -151,19 +181,23 @@ class MainWindow(QMainWindow, Ui_MainWindow):
@pyqtSlot("QAbstractButton*") @pyqtSlot("QAbstractButton*")
def on_buttonBox_output_clicked(self, button): def on_buttonBox_output_clicked(self, button):
if button == self.buttonBox_output.button(QDialogButtonBox.Open): if button == self.buttonBox_output.button(QDialogButtonBox.Open):
path = QFileDialog.getExistingDirectory(parent=self, caption=_translate( caption = _translate('MainWindow', 'Choose output path')
'MainWindow', 'Choose output path'), options=QFileDialog.ShowDirsOnly) path = QFileDialog.getExistingDirectory(
parent=self,
caption=caption,
options=QFileDialog.ShowDirsOnly)
self.lineEdit_output.setText(path.strip()) self.lineEdit_output.setText(path.strip())
@pyqtSlot("QString") @pyqtSlot("QString")
def on_comboBox_instrument_currentIndexChanged(self, p0): def on_comboBox_instrument_currentIndexChanged(self, p0):
""" """
Slot documentation goes here. Triggered when another instrument is selected from the combobox.
""" """
if p0 == 'Analytik Jena qTOWER 2.0/2.2': self.instrument = self.getInstrumentFromName(p0)
self.groupBox_temp.setEnabled(True) if self.instrument.providesTempRange:
else:
self.groupBox_temp.setEnabled(False) self.groupBox_temp.setEnabled(False)
else:
self.groupBox_temp.setEnabled(True)
def generate_plot_tab(self, name): def generate_plot_tab(self, name):
tab = MplWidget(parent=self.tabWidget) tab = MplWidget(parent=self.tabWidget)
@ -221,19 +255,23 @@ class MainWindow(QMainWindow, Ui_MainWindow):
Slot documentation goes here. Slot documentation goes here.
""" """
self.instrument = self.getSelectedInstrument()
if self.listWidget_data.count() < 1: if self.listWidget_data.count() < 1:
QMessageBox.critical( QMessageBox.critical(
self, _translate("MainWindow", "Error"), self, _translate("MainWindow", "Error"),
_translate("MainWindow", "No data file loaded!"), _translate("MainWindow", "No data file loaded!"),
QMessageBox.Close, QMessageBox.Close) QMessageBox.Close, QMessageBox.Close)
return return
if self.groupBox_output.isChecked() and self.lineEdit_output.text().strip() == '': if (self.groupBox_output.isChecked() and
self.lineEdit_output.text().strip() == ''):
QMessageBox.critical( QMessageBox.critical(
self, _translate("MainWindow", "Error"), self, _translate("MainWindow", "Error"),
_translate("MainWindow", "No output path set!"), _translate("MainWindow", "No output path set!"),
QMessageBox.Close, QMessageBox.Close) QMessageBox.Close, QMessageBox.Close)
return return
elif self.groupBox_output.isChecked() and self.lineEdit_output.text().strip() != '': elif (self.groupBox_output.isChecked() and
self.lineEdit_output.text().strip() != ''):
path = self.lineEdit_output.text().strip() path = self.lineEdit_output.text().strip()
if os.path.isdir(path): if os.path.isdir(path):
self.outputPath = self.lineEdit_output.text().strip() self.outputPath = self.lineEdit_output.text().strip()
@ -246,8 +284,7 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.spinBox_signal_threshold.value( if self.spinBox_signal_threshold.value(
) == 0 and self.groupBox_signal_threshold.isChecked(): ) == 0 and self.groupBox_signal_threshold.isChecked():
QMessageBox.warning( QMessageBox.warning(
self, _translate("MainWindow", "Warning"), self, _translate("MainWindow", "Warning"), _translate(
_translate(
"MainWindow", "MainWindow",
"Signal threshold is currently set to zero."), "Signal threshold is currently set to zero."),
QMessageBox.Ok, QMessageBox.Ok) QMessageBox.Ok, QMessageBox.Ok)
@ -256,12 +293,14 @@ class MainWindow(QMainWindow, Ui_MainWindow):
self.progressBar.setEnabled(True) self.progressBar.setEnabled(True)
self.statusBar.showMessage(_translate("MainWindow", "Processing...")) self.statusBar.showMessage(_translate("MainWindow", "Processing..."))
self.tasks.signals.finished.connect(self.on_processing_finished) self.worker = Worker(self)
self.tasks.add_task(self.worker) self.tasks.add_task(self.worker)
self.tasks.start() self.tasks.start()
@pyqtSlot() @pyqtSlot()
def on_processing_finished(self): def on_processing_finished(self):
# Clear all jobs from task list
# self.tasks.clear()
# For now, only read the first entry # For now, only read the first entry
exp = self.tasks.data[0] exp = self.tasks.data[0]
@ -279,19 +318,25 @@ class MainWindow(QMainWindow, Ui_MainWindow):
if self.checkBox_savetables.isChecked(): if self.checkBox_savetables.isChecked():
for plate in exp.plates: for plate in exp.plates:
plate.write_tm_table( plate.write_tm_table(
'{}/plate_{}_tm.csv'.format(self.outputPath, str(plate.id))) '{}/plate_{}_tm.csv'.format(self.outputPath,
str(plate.id)))
plate.write_data_table( plate.write_data_table(
'{}/plate_{}_dI_dT.csv'.format(self.outputPath, str(plate.id)), dataType='derivative') '{}/plate_{}_dI_dT.csv'.format(self.outputPath,
str(plate.id)),
dataType='derivative')
plate.write_data_table( plate.write_data_table(
'{}/plate_{}_filtered_data.csv'.format(self.outputPath, '{}/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( plate.write_data_table('{}/plate_{}_raw_data.csv'.format(
self.outputPath, str(plate.id))) self.outputPath, str(plate.id)))
if exp.avg_plate: if exp.avg_plate:
exp.avg_plate.write_tm_table( exp.avg_plate.write_tm_table(
'{}/plate_{}_tm_avg.csv'.format( '{}/plate_{}_tm_avg.csv'.format(
self.outputPath, str(self.worker.exp.avg_plate.id)), avg=True) self.outputPath,
str(self.worker.exp.avg_plate.id)),
avg=True)
self.progressBar.setEnabled(False) self.progressBar.setEnabled(False)
self.statusBar.showMessage(_translate("MainWindow", "Finished!")) self.statusBar.showMessage(_translate("MainWindow", "Finished!"))