def data(self, index, role):
fld = self.fields[index.column()]
obj = index.internalPointer()
rslt = None
if type(obj) is Project:
if role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
if fld == 'name':
rslt = obj.name
elif role == QtCore.Qt.DecorationRole and index.column() == 0:
#TODO: icon for projects
pass
elif type(obj) is Run:
if fld == 'sel' and role == QtCore.Qt.CheckStateRole:
if self.master_window.pal_tab.has_run(obj, enabled=True):
rslt = QtCore.Qt.Checked
else:
rslt = QtCore.Qt.Unchecked
elif role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
if fld == 'name':
rslt = obj.name
else:
rslt = obj.info.get(fld, '')
elif role == QtCore.Qt.DecorationRole and index.column() == 0:
loc = resfile('aston/qtgui', 'icons/file.png')
rslt = QtGui.QIcon(loc)
elif type(obj) is Analysis:
if role == QtCore.Qt.DisplayRole:
if fld == 'name':
return obj.name
#elif role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
# if fld == 'p-model' and f.db_type == 'peak':
# rpeakmodels = {peak_models[k]: k for k in peak_models}
# rslt = rpeakmodels.get(f.info[fld], 'None')
# else:
# rslt = f.info[fld]
#elif role == QtCore.Qt.DecorationRole and index.column() == 0:
# #TODO: icon for method, compound
# fname = {'file': 'file.png', 'peak': 'peak.png', \
# 'spectrum': 'spectrum.png'}
# loc = resfile('aston/ui', 'icons/' + fname.get(f.db_type, ''))
# rslt = QtGui.QIcon(loc)
return rslt
def __init__(self, canvas, parent=None):
NavigationToolbar2QTAgg.__init__(self, canvas, parent, False)
self.parent = parent
self.ev_time = 0
self._xypress = []
#quick function to return icon locs
icon = lambda l: resfile('aston/qtgui', 'icons/' + l + '.png')
#remove the plot adjustment buttons
self.removeAction(self.actions()[-1])
self.removeAction(self.actions()[-1])
self.removeAction(self.actions()[-1])
#add the alignment tool
if not hasattr(self, '_actions'):
self._actions = {}
self._actions['align'] = QtGui.QAction(QtGui.QIcon(icon('align')), \
self.parent.tr('Align Chromatogram'), self)
self._actions['align'].setCheckable(True)
self.addAction(self._actions['align'])
self._actions['align'].triggered.connect(self.align)
self.addSeparator()
#add the peak tool
self._actions['peak'] = QtGui.QAction(QtGui.QIcon(icon('peak')), \
self.parent.tr('Add/Delete Peak'), self)
self._actions['peak'].setCheckable(True)
self.addAction(self._actions['peak'])
self._actions['peak'].triggered.connect(self.peak)
#add the spectra tool
self._actions['spectrum'] = QtGui.QAction( \
QtGui.QIcon(icon('spectrum')), self.parent.tr('Get Spectrum'), self)
self._actions['spectrum'].setCheckable(True)
self.addAction(self._actions['spectrum'])
self._actions['spectrum'].triggered.connect(self.spec)
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()
def data(self, index, role):
fld = self.fields[index.column()]
obj = index.internalPointer()
rslt = None
if type(obj) is PaletteRun:
if role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
if fld == 'name':
rslt = obj.run.name
elif role == QtCore.Qt.DecorationRole and fld == 'name':
loc = resfile('aston/qtgui', 'icons/file.png')
rslt = QtGui.QIcon(loc)
elif type(obj) is Plot:
if fld == 'vis' and role == QtCore.Qt.CheckStateRole:
#TODO: allow vis to be a plot number instead?
if obj.vis > 0:
rslt = QtCore.Qt.Checked
else:
rslt = QtCore.Qt.Unchecked
elif role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
if fld == 'name':
rslt = obj.name
elif fld == 'style':
rslt = aston_field_opts[fld][obj.style]
elif fld == 'color':
if obj.style in {'heatmap', 'colors'}:
rslt = aston_field_opts['color-2d'][obj.color]
else:
rslt = aston_field_opts['color-1d'][obj.color]
elif role == QtCore.Qt.FontRole and fld == 'name':
# strike out invalid plot names
if not obj.is_valid:
rslt = QtGui.QFont()
rslt.setStrikeOut(True)
#elif role == QtCore.Qt.DecorationRole and index.column() == 0:
# if not obj.is_valid:
# loc = resfile('aston/qtgui', 'icons/x.png')
# rslt = QtGui.QIcon(loc)
elif type(obj) is Peak:
if fld == 'vis' and role == QtCore.Qt.CheckStateRole:
if obj.vis:
rslt = QtCore.Qt.Checked
else:
rslt = QtCore.Qt.Unchecked
elif role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
if fld == 'name':
rslt = obj.name
elif fld == 'color':
rslt = aston_field_opts['color-1d'][obj.color]
elif fld in {'p-model'}:
v = obj.components[0].info.get(fld, None)
if v is not None:
rslt = aston_field_opts[fld][v]
elif fld in {'p-model-fit'}:
fmt = lambda x: '{:.3f}'.format(x)
rslt = ','.join(fmt(c.info.get('p-model-fit', '')) \
for c in obj.components \
if c.info.get('p-model') is not None)
elif fld in {'p-type'}:
rslt = aston_field_opts[fld][obj.info.get(fld, '')]
elif fld in {'p-d13c'}:
rslt = str(obj.info.get(fld, ''))
elif fld in {'s-mz-names'}:
rslt = ','.join(str(c._trace.name) for c in obj.components)
elif fld in {'p-area', 'p-length', 'p-height', 'p-width', \
'p-pwhm', 'p-time'}:
rslt = str(getattr(obj, fld[2:])())
#elif role == QtCore.Qt.DisplayRole or role == QtCore.Qt.EditRole:
# if fld == 'p-model' and f.db_type == 'peak':
# rpeakmodels = {peak_models[k]: k for k in peak_models}
# rslt = rpeakmodels.get(f.info[fld], 'None')
# else:
# rslt = f.info[fld]
#elif role == QtCore.Qt.DecorationRole and index.column() == 0:
# #TODO: icon for method, compound
# fname = {'file': 'file.png', 'peak': 'peak.png', \
# 'spectrum': 'spectrum.png'}
# loc = resfile('aston/ui', 'icons/' + fname.get(f.db_type, ''))
# rslt = QtGui.QIcon(loc)
return rslt
warnings.simplefilter('ignore', sqlalchemy.exc.SAWarning)
# for multiprocessing to work on Windows
import multiprocessing
multiprocessing.freeze_support()
#all the other imports
import sys
import PyQt4
from aston.qtgui.MainWindow import AstonWindow
qt = PyQt4.QtGui.QApplication(sys.argv)
# translation stuff
import locale
import pkg_resources
from aston.resources import resfile
try:
locale.setlocale(locale.LC_ALL, '')
if locale.getlocale()[0] is not None:
lang = locale.getlocale()[0]
tlate = PyQt4.QtCore.QTranslator(qt)
tlate.load('aston_' + lang + '.qm', resfile('aston/qtgui', 'i18n'))
qt.installTranslator(tlate)
except locale.Error:
pass
# set up the main window and start
aston = AstonWindow()
aston.show()
sys.exit(qt.exec_())