def load_new_file_db(self, file_loc):
#TODO: this should be called by init too so opening a new file_db
# will load all the preferences from that file_db (like what happens in
# init now
#load everything
if file_loc is None:
return
self.directory = op.expanduser(file_loc)
file_db = quick_sqlite(op.join(self.directory, 'aston.sqlite'))
def_group = simple_auth(file_db)
read_directory(self.directory, file_db, group=def_group)
self.pal_tab = PaletteTreeModel(file_db, self.ui.paletteTreeView, self)
self.file_tab = FileTreeModel(file_db, self.ui.fileTreeView, self)
## add settings widget in
#TODO: this will happen multiple times
self.settings = SettingsWidget(self, db=file_db)
self.ui.verticalLayout_settings.addWidget(self.settings)
class AstonWindow(QtWidgets.QMainWindow):
state = {}
def __init__(self, parent=None):
QtWidgets.QWidget.__init__(self, parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# my icon!
icn_path = resfile('aston/qtgui', 'icons/logo.png')
self.setWindowIcon(QtGui.QIcon(icn_path))
# quick fix for Mac OS menus
self.ui.actionSettings.setMenuRole(QtWidgets.QAction.NoRole)
# set up the list of files in the current directory
fdir = get_pref('Default.FILE_DIRECTORY')
self.load_new_file_db(fdir)
# connect the menu logic
self.ui.actionOpen.triggered.connect(self.open_folder)
self.ui.actionExportChromatogram.triggered.connect(
self.exportChromatogram
)
self.ui.actionExportSpectra.triggered.connect(self.exportSpectrum)
self.ui.actionExportSelectedItems.triggered.connect(self.exportItems)
self.ui.actionIntegrate.triggered.connect(self.integrate)
self.ui.actionEditFilters.triggered.connect(self.showFilterWindow)
self.ui.actionRevert.triggered.connect(self.revertChromChange)
self.ui.actionQuit.triggered.connect(QtWidgets.qApp.quit)
self.ui.loadPeakList.triggered.connect(self.load_peaks)
# hook up the windows to the menu
for ac in [self.ui.actionFiles, self.ui.actionSettings,
self.ui.actionSpectra, self.ui.actionMethods,
self.ui.actionCompounds, self.ui.actionPalette]:
ac.triggered.connect(self.updateWindows)
# set up the grouping for the dock widgets and
# hook the menus up to the windows
for ac in [self.ui.filesDockWidget, self.ui.paletteDockWidget,
self.ui.spectraDockWidget, self.ui.settingsDockWidget,
self.ui.methodDockWidget, self.ui.compoundDockWidget]:
if ac is not self.ui.filesDockWidget:
self.tabifyDockWidget(self.ui.filesDockWidget, ac)
ac.visibilityChanged.connect(self.updateWindowsMenu)
self.ui.filesDockWidget.raise_()
self.ui.settingsDockWidget.setVisible(False)
self.ui.compoundDockWidget.setVisible(False)
self.ui.methodDockWidget.setVisible(False)
# create the things that keep track of how the plots should look
self.plotter = Plotter(self)
self.specplotter = SpecPlotter(self)
# FIXME
# hook up the search box
# self.ui.lineEdit.textChanged.connect(self.updateSearch)
# make integrator options
def set_peak_find(x):
self.state['peak_finder'] = x
peak_find_menu = QtWidgets.QMenu(self.ui.menuChromatogram)
v = list(aston.qtgui.MenuOptions.peak_finders.keys())[0]
set_peak_find(v)
add_opts_to_menu(peak_find_menu,
aston.qtgui.MenuOptions.peak_finders.keys(),
set_peak_find, v)
self.ui.actionPeak_Finder.setMenu(peak_find_menu)
def set_integrator(x):
self.state['integrator'] = x
integrator_menu = QtWidgets.QMenu(self.ui.menuChromatogram)
v = list(aston.qtgui.MenuOptions.integrators.keys())[0]
set_integrator(v)
add_opts_to_menu(integrator_menu,
aston.qtgui.MenuOptions.integrators.keys(),
set_integrator, v)
self.ui.actionIntegrator.setMenu(integrator_menu)
menu_gp = QtWidgets.QActionGroup(self)
for ac in self.ui.menuIntegrand.actions():
menu_gp.addAction(ac)
## hook up spectrum menu
#for m in [self.ui.actionSpecLibDisp, self.ui.actionSpecLibLabel,\
# self.ui.actionSpecMainDisp, self.ui.actionSpecMainLabel, \
# self.ui.actionSpecPrevDisp, self.ui.actionSpecPrevLabel]:
# m.triggered.connect(self.specplotter.plot)
#self.ui.actionSpecMainSave.triggered.connect( \
# self.specplotter.save_main_spec)
#self.ui.actionSpecPrevSave.triggered.connect( \
# self.specplotter.save_prev_spec)
#flesh out the settings menu
color_menu = QtWidgets.QMenu(self.ui.menuSettings)
v_cs = self.settings.get_key('color_scheme', dflt='Spectral')
v = aston_field_opts['color-2d'][v_cs]
c_opts = list(aston_field_opts['color-2d'].values())
add_opts_to_menu(color_menu, c_opts, self.set_color_scheme, v)
self.ui.actionColor_Scheme.setMenu(color_menu)
self.ui.actionLegend.triggered.connect(self.set_legend)
self.ui.actionGraphGrid.triggered.connect(self.set_legend)
self.ui.actionGraphLogYAxis.triggered.connect(self.set_legend)
#self.ui.actionGraphFxnCollection.triggered.connect(self.set_legend)
#self.ui.actionGraphFIA.triggered.connect(self.set_legend)
#self.ui.actionGraphIRMS.triggered.connect(self.set_legend)
#self.ui.actionGraph_Peaks_Found.triggered.connect(self.set_legend)
#style_menu = QtWidgets.QMenu(self.ui.menuSettings)
#v_gs = self.settings.get_key('graph_style', dflt='default')
#v = self.plotter._styles[v_gs]
#self.plotter.setStyle(v)
#add_opts_to_menu(style_menu, \
# self.plotter.availStyles(), self.set_graph_style, v)
#self.ui.actionGraph_Style.setMenu(style_menu)
# plot data
self.plot_data()
##set up the compound database
#cmpd_loc = self.settings.get_key('db_compound', dflt='')
#if cmpd_loc != '':
# cmpd_db = get_compound_db(cmpd_loc)
# self.cmpd_tab = FileTreeModel(cmpd_db, self.ui.compoundTreeView, \
# self)
def updateWindows(self):
"""
Update the tab windows to match the menu.
"""
self.ui.filesDockWidget.setVisible(self.ui.actionFiles.isChecked())
self.ui.settingsDockWidget.setVisible(
self.ui.actionSettings.isChecked()
)
self.ui.spectraDockWidget.setVisible(self.ui.actionSpectra.isChecked())
self.ui.methodDockWidget.setVisible(self.ui.actionMethods.isChecked())
self.ui.compoundDockWidget.setVisible(
self.ui.actionCompounds.isChecked()
)
self.ui.paletteDockWidget.setVisible(self.ui.actionPalette.isChecked())
def updateWindowsMenu(self):
"""
Update the windows menu to match the tab.
"""
self.ui.actionFiles.setChecked(self.ui.filesDockWidget.isVisible())
self.ui.actionSettings.setChecked(
self.ui.settingsDockWidget.isVisible()
)
self.ui.actionSpectra.setChecked(self.ui.spectraDockWidget.isVisible())
self.ui.actionMethods.setChecked(self.ui.methodDockWidget.isVisible())
self.ui.actionCompounds.setChecked(
self.ui.compoundDockWidget.isVisible()
)
self.ui.actionPalette.setChecked(self.ui.paletteDockWidget.isVisible())
def show_status(self, msg):
self.statusBar().showMessage(msg, 2000)
def open_folder(self):
folder = str(QtWidgets.QFileDialog.getExistingDirectory(self, tr("Open Folder"))) # noqa
if folder == '':
return
#need to discard old connections
#self.ui.fileTreeView.clicked.disconnect()
#self.ui.fileTreeView.selectionModel().currentChanged.disconnect()
#self.ui.fileTreeView.customContextMenuRequested.disconnect()
#self.ui.fileTreeView.header().customContextMenuRequested.disconnect()
#self.ui.fileTreeView.header().sectionMoved.disconnect()
#self.ui.paletteTreeView.clicked.disconnect()
self.ui.paletteTreeView.selectionModel().currentChanged.disconnect()
#self.ui.paletteTreeView.customContextMenuRequested.disconnect()
#self.ui.paletteTreeView.header().customContextMenuRequested.disconnect()
#self.ui.paletteTreeView.header().sectionMoved.disconnect()
self.load_new_file_db(folder)
def load_new_file_db(self, file_loc):
#TODO: this should be called by init too so opening a new file_db
# will load all the preferences from that file_db (like what happens in
# init now
#load everything
if file_loc is None:
return
self.directory = op.expanduser(file_loc)
file_db = quick_sqlite(op.join(self.directory, 'aston.sqlite'))
def_group = simple_auth(file_db)
read_directory(self.directory, file_db, group=def_group)
self.pal_tab = PaletteTreeModel(file_db, self.ui.paletteTreeView, self)
self.file_tab = FileTreeModel(file_db, self.ui.fileTreeView, self)
## add settings widget in
#TODO: this will happen multiple times
self.settings = SettingsWidget(self, db=file_db)
self.ui.verticalLayout_settings.addWidget(self.settings)
#self.plot_data()
#cmpd_loc = file_db.get_key('db_compound', dflt='')
#if cmpd_loc != '':
# cmpd_db = get_compound_db(cmpd_loc)
# self.cmpd_tab = FileTreeModel(cmpd_db, self.ui.compoundTreeView, \
# self)
def load_peaks(self):
ftypes = 'AMDIS (*.*);;Isodat (*.*)'
fname = QtWidgets.QFileDialog.getOpenFileName(self, tr("Open File"),
'', ftypes)
if str(fname) == '':
return
from aston.peaks.PeakReader import read_peaks
read_peaks(self.obj_tab.db, str(fname))
self.plot_data(updateBounds=False)
def set_color_scheme(self):
v = self.plotter.setColorScheme(self.sender().data())
self.obj_tab.db.set_key('color_scheme', v)
self.plot_data(updateBounds=False)
def set_legend(self):
self.plotter.legend = self.ui.actionLegend.isChecked()
self.plot_data(updateBounds=False)
def set_graph_style(self):
v = self.plotter.setStyle(self.sender().data())
self.obj_tab.db.set_key('graph_style', v)
self.plot_data()
def exportChromatogram(self):
fopts = tr('PNG Image (*.png);;PGF Image (*.pgf);;RAW Image (*.raw);;'
'RGBA Image (*.rgba);;SVG Image (*.svg);;'
'EMF Image (*.emf);;EPS Image (*.eps);;'
'Portable Document Format (*.pdf);;'
'Postscript Image (*.ps);;Compressed SVG File (*.svgz);;'
'Comma-Delimited Text (*.csv)')
fname = str(QtWidgets.QFileDialog.getSaveFileNameAndFilter(
self, tr("Save As..."), filter=fopts
)[0])
if fname == '':
return
elif fname[-4:].lower() == '.csv':
dt = self.obj_tab.active_file()
ts = None
for ion in dt.info['traces'].split(','):
if ts is None:
ts = dt.trace(ion)
else:
ts &= dt.trace(ion)
with open(fname, 'w') as f:
f.write(tr('Time') + ',' + ','.join(ts.ions) + ',\n')
for t, d in zip(ts.times, ts.data):
f.write(str(t) + ',' + ','.join(str(i) for i in d) + '\n')
else:
self.plotter.plt.get_figure().savefig(fname, transparent=True)
def exportSpectrum(self):
# TODO: this needs to be updated when SpecPlot becomes better
fopts = tr('PNG Image (*.png);;PGF Image (*.pgf);;RAW Image (*.raw);;'
'RGBA Image (*.rgba);;SVG Image (*.svg);;'
'EMF Image (*.emf);;EPS Image (*.eps);;'
'Portable Document Format (*.pdf);;'
'Postscript Image (*.ps);;Compressed SVG File (*.svgz);;'
'Comma-Delimited Text (*.csv)')
fname = str(QtWidgets.QFileDialog.getSaveFileNameAndFilter(
self, tr("Save As..."), filter=fopts
)[0])
if fname == '':
return
elif fname[-4:].lower() == '.csv':
if '' not in self.specplotter.scans:
return
with open(fname, 'w') as f:
scan = self.specplotter.scans['']
f.write(tr('mz') + ',' + tr('abun') + '\n')
for mz, abun in scan.T:
f.write(str(mz) + ',' + str(abun) + '\n')
else:
self.specplotter.plt.get_figure().savefig(fname, transparent=True)
def exportItems(self):
#TODO: options for exporting different delimiters (e.g. tab) or
#exporting select items as pictures (e.g. selected spectra)
fopts = tr('Comma-Delimited Text (*.csv)')
fname = str(QtWidgets.QFileDialog.getSaveFileNameAndFilter(self, \
tr("Save As..."), filter=fopts)[0])
if fname == '':
return
sel = self.obj_tab.returnSelFiles()
with codecs.open(fname, 'w', encoding='utf-8') as f:
f.write(self.obj_tab.items_as_csv(sel))
def get_f_opts(self, f):
gf = lambda k, df: float(self.settings.get_key(k, dflt=str(df)))
gv = lambda k, df: str(self.settings.get_key(k, dflt=str(df)))
p = {}
fname = f.__name__
if fname == 'simple_peak_find':
p['init_slope'] = gf('peakfind_simple_initslope', 500)
p['start_slope'] = gf('peakfind_simple_startslope', 500)
p['end_slope'] = gf('peakfind_simple_endslope', 200)
p['min_peak_height'] = gf('peakfind_simple_minheight', 50)
p['max_peak_width'] = gf('peakfind_simple_maxwidth', 1.5)
elif fname == 'wavelet_peak_find':
p['min_snr'] = gf('peakfind_wavelet_minsnr', 1)
p['assume_sig'] = gf('peakfind_wavelet_asssig', 4)
elif fname == 'event_peak_find':
p['adjust_times'] = gv('peakfind_event_adjust', False)
elif fname == 'leastsq_integrate':
p['f'] = gv('integrate_leastsq_f', 'gaussian')
elif fname == 'periodic_integrate':
p['offset'] = gf('integrate_periodic_offset', 0.)
p['period'] = gf('integrate_periodic_period', 1.)
return p
def find_peaks(self, tss, plot, isomode=False, mp=False):
opt = self.state['peak_finder']
pf_f = aston.qtgui.MenuOptions.peak_finders[opt]
pf_fopts = self.get_f_opts(pf_f)
#TODO: this should be smarter?
if pf_f.__name__ == 'event_peak_find':
evts = []
for n in ('fia', 'fxn', 'refgas'):
evts += plot.events(n)
pf_fopts['events'] = evts
if isomode:
return find_peaks_as_first(tss, pf_f, pf_fopts, mp)
else:
return find_peaks(tss, pf_f, pf_fopts, mp)
def integrate_peaks(self, tss, found_peaks, isomode=False, mp=False):
opt = self.state['integrator']
int_f = aston.qtgui.MenuOptions.integrators[opt]
int_fopts = self.get_f_opts(int_f)
return integrate_peaks(tss, found_peaks, int_f, int_fopts, isomode, mp)
def integrate(self):
plot = self.pal_tab.active_plot()
mp = self.settings.get_key('multiprocessing', dflt=True)
mp = False
isomode = False
if self.ui.actionIntegrandActiveTrace.isChecked():
tss = [plot.trace()]
elif self.ui.actionIntegrandAsFirst.isChecked():
#plot.frame
tss = plot.frame().traces
isomode = True
elif self.ui.actionIntegrandIndependent.isChecked():
#plot.frame
tss = plot.frame().traces
else:
tss = []
#TODO: all traces in palette?
found_peaks = self.find_peaks(tss, plot, isomode, mp)
mrg_pks = self.integrate_peaks(tss, found_peaks, isomode, mp)
with self.pal_tab.add_rows(plot, len(mrg_pks)):
for pk in mrg_pks:
pk.dbplot = plot
self.pal_tab.db.add_all(mrg_pks)
self.pal_tab.db.commit()
self.plot_data(update_bounds=False)
def showFilterWindow(self):
if self.obj_tab.active_file() is not None:
self.dlg = FilterWindow(self)
self.dlg.show()
def revertChromChange(self):
"""
Delete all of the info keys related to display transformations.
"""
for dt in self.obj_tab.returnSelFiles('file'):
dt.info.del_items('t-')
self.plot_data()
def plot_data(self, **kwargs):
plots = []
for pr in self.pal_tab._children:
plots += [t for t in pr.plots if t.vis > 0 and t.is_valid]
if 'update_bounds' in kwargs:
self.plotter.plot_data(plots, kwargs['update_bounds'])
else:
self.plotter.plot_data(plots)
def updateSearch(self, text):
"""
If the search box changes, update the file table.
"""
self.obj_tab.proxyMod.setFilterFixedString(text)