def initalize_dialog(self, config, massdat):
"""
Initilizes dialog and the layout. Calls run_autocorr.
:param config: UniDecConfig object
:param massdat: Array of mass distribution (N x 2)
:return: None
"""
self.config = config
self.massdat = massdat
panel = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
hbox = wx.BoxSizer(wx.HORIZONTAL)
sb = wx.StaticBox(panel, label='Autocorrelation')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
self.plot1 = plot1d.Plot1d(panel)
sbs.Add(self.plot1)
hbox.Add(sbs)
self.listpanel = CorrListCtrlPanel(panel)
hbox.Add(self.listpanel)
panel.SetSizer(hbox)
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
# closebutton = wx.Button(self, label='Cancel')
hboxend.Add(okbutton)
# hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(panel, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
# closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
self.CenterOnParent()
self.run_autocorr(0)
def __init__(self,
parent,
data_list,
config=None,
yvals=None,
mode="1D",
pks=None,
pksmode="mz",
*args,
**kwargs):
"""
A simple window for animating mulitple 1D or 2D plots in a sequence.
:param parent: Parent window. Passed to wx.Frame.
:param data_list: List of data to be plotted
:param config: UniDecConfig object
:param yvals: Titles for the plots.
:param mode: 1 = 1D plots, 2 = 2D plots
:param args:
:param kwargs:
:return: None
"""
wx.Frame.__init__(self, parent, title="Plot Animations", size=(-1, -1))
# Initialize parameters
if mode == "2D":
self.mode = 2
else:
self.mode = 1
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
else:
self.config = config
self.datalist = data_list
self.pks = pks
self.pksmode = pksmode
if self.pksmode == "mz":
self.xlabel = "m/z (Th)"
self.testkda = False
elif self.pksmode == "CCS":
self.xlabel = "CCS"
self.testkda = False
else:
self.xlabel = "Mass (Da)"
self.testkda = True
self.yvals = yvals
if self.yvals is None:
self.yvals = list(range(0, len(data_list)))
self.dim = 1
self.pos = -1
self.play = False
self.animation = None
# Create GUI
# Make the menu
filemenu = wx.Menu()
menu_save_fig = filemenu.Append(wx.ID_ANY, "Save Figures",
"Save all figures at selected path")
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig)
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
self.SetMenuBar(menu_bar)
self.CreateStatusBar(2)
panel = wx.Panel(self)
sizer = wx.BoxSizer(wx.VERTICAL)
if self.mode == 1:
self.plot = plot1d.Plot1d(panel)
else:
self.plot = plot2d.Plot2d(panel)
sizer.Add(self.plot, 0, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
sb = wx.StaticBox(panel, label='Frame Rate (ms/frame)')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
frmax = 2000
frmin = 1
self.frslider = wx.Slider(
panel, wx.ID_ANY, 500, frmin, frmax, (30, 60), (250, -1),
wx.SL_HORIZONTAL | wx.SL_AUTOTICKS | wx.SL_LABELS)
self.frslider.SetTickFreq(100)
sbs.Add(self.frslider, 0, wx.EXPAND)
self.Bind(wx.EVT_COMMAND_SCROLL_THUMBRELEASE, self.update_framerate,
self.frslider)
controlsizer.Add(sbs, 0, wx.EXPAND)
self.playbutton = wx.ToggleButton(panel, label="Play")
self.nextbutton = wx.Button(panel, label="Next")
self.backbutton = wx.Button(panel, label="Back")
controlsizer.Add(self.backbutton, 0, wx.EXPAND)
controlsizer.Add(self.playbutton, 0, wx.EXPAND)
controlsizer.Add(self.nextbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_TOGGLEBUTTON, self.on_play, self.playbutton)
self.Bind(wx.EVT_BUTTON, self.on_next, self.nextbutton)
self.Bind(wx.EVT_BUTTON, self.on_back, self.backbutton)
self.ctlautoscale = wx.CheckBox(panel, label="Autoscale")
controlsizer.Add(self.ctlautoscale, 0, wx.EXPAND)
if self.mode == 2:
self.ctlautoscale.SetValue(True)
sizer.Add(controlsizer, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close, self)
self.init()
self.Centre()
self.Show(True)
def __init__(self, parent, datalist, xarray, yarray, config=None, xtype=0):
wx.Frame.__init__(self, parent,
title="Mass Defect Extractor") # ,size=(-1,-1))
self.xtype = xtype
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
self.config.discreteplot = 0
self.config.cmap = u"jet"
self.config.peakcmap = u"rainbow"
self.config.separation = 0.025
else:
self.config = config
# Setup initial values
try:
self.directory = parent.directory
except:
self.directory = os.getcwd()
self.outfname = os.path.splitext(self.config.filename)[0]
if self.outfname != "":
self.outfname += "_"
self.window = 0.05
self.data = datalist
self.xdat = xarray
self.ydat = yarray
defaultexchoice = "Local Max"
self.totgrid = []
self.grid = []
self.fitdats = None
self.fits = None
# Make the menu
filemenu = wx.Menu()
menu_oligomer_tools = filemenu.Append(wx.ID_ANY,
"Generate from Masses",
"Oligomer and Mass Tools")
filemenu.AppendSeparator()
menu_save_fig_png = filemenu.Append(
wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
menu_save_fig_pdf = filemenu.Append(
wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_oligomer_tools, menu_oligomer_tools)
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig_png)
self.Bind(wx.EVT_MENU, self.on_save_fig_pdf, menu_save_fig_pdf)
self.plotmenu = wx.Menu()
self.menuaddline = self.plotmenu.Append(
wx.ID_ANY, "Add Horizontal Line",
"Add Horizontal Line at Specific Y Value")
self.plotmenu.AppendSeparator()
self.menutotal = self.plotmenu.Append(
wx.ID_ANY, "Plot Total Bound vs. Unbound",
"Assumes the first value is the unbound and each other is 1, 2, 3, and so on bound ligands."
)
self.Bind(wx.EVT_MENU, self.on_add_line, self.menuaddline)
self.Bind(wx.EVT_MENU, self.on_total, self.menutotal)
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
menu_bar.Append(self.plotmenu, "Plot")
self.SetMenuBar(menu_bar)
# Setup the GUI
panel = wx.Panel(self)
self.plot1 = plot1d.Plot1d(panel)
self.plot2 = plot2d.Plot2d(panel)
self.plot5 = plot1d.Plot1d(panel)
self.plot6 = plot2d.Plot2d(panel)
sizer = wx.BoxSizer(wx.VERTICAL)
hbox = wx.BoxSizer(wx.HORIZONTAL)
sb = wx.StaticBox(panel, label='Set the Mass Defect Values to Extract')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
importbutton = wx.Button(panel, label="Import from File")
self.Bind(wx.EVT_BUTTON, self.on_import_masses, importbutton)
clearbutt = wx.Button(panel, label="Clear List")
self.Bind(wx.EVT_BUTTON, self.on_clear_masslist, clearbutt)
addbutton = wx.Button(panel, label="Add Species")
self.Bind(wx.EVT_BUTTON, self.on_add_mass, addbutton)
sbs.Add(importbutton, 0, wx.EXPAND)
sbs.Add(addbutton, 0, wx.EXPAND)
self.masslistbox = masstools.MassListCtrlPanel(
panel, columntitle="Mass Defect Value", size=(210, 320))
sbs.Add(wx.StaticText(panel, label="Mass Defect List"))
sbs.Add(self.masslistbox)
sbs.Add(clearbutt, 0, wx.EXPAND)
# hbox.Add(sbs, 0, wx.EXPAND)
plotsizer1 = wx.BoxSizer(wx.VERTICAL)
plotsizer2 = wx.BoxSizer(wx.VERTICAL)
plotsizer1.Add(self.plot1, 2, wx.EXPAND)
plotsizer1.Add(self.plot2, 2, wx.EXPAND)
plotsizer2.Add(self.plot5, 0, wx.EXPAND)
plotsizer2.Add(self.plot6, 0, wx.EXPAND)
hbox.Add(sbs, 0)
hbox.Add(plotsizer1, 1, wx.EXPAND)
hbox.Add(plotsizer2, 1, wx.EXPAND)
sizer.Add(hbox, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
totalbutton = wx.Button(panel, label="Extract")
controlsizer.Add(totalbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_extract, totalbutton)
controlsizer.Add(wx.StaticText(panel, label=" How to extract: "), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctlextract = wx.ComboBox(panel,
value=defaultexchoice,
choices=list(extractchoices.values()),
style=wx.CB_READONLY
| wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlextract, 0,
wx.EXPAND | wx.ALIGN_CENTER_VERTICAL)
self.ctlwindow = wx.TextCtrl(panel,
value=str(self.window),
size=(60, 23))
controlsizer.Add(wx.StaticText(panel, label="Window:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlwindow, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlnorm = wx.RadioBox(
panel,
label="Extract Normalization",
choices=["None", "Max", "Sum", "Peak Max", "Peak Sum"])
self.ctlnorm.SetSelection(2)
# , majorDimension=3,style=wx.RA_SPECIFY_COLS)
self.ctlnorm.SetSelection(2)
controlsizer.Add(self.ctlnorm, 0, wx.ALIGN_CENTER_VERTICAL)
fitbutton = wx.Button(panel, label="Fit")
controlsizer.Add(fitbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_fit, fitbutton)
self.ctlmaxshift = wx.TextCtrl(panel, value=str(0.05), size=(40, 23))
controlsizer.Add(wx.StaticText(panel, label="Max MD Shift:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlmaxshift, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlshiftguess = wx.TextCtrl(panel,
value=str("None"),
size=(40, 23))
controlsizer.Add(wx.StaticText(panel, label="Shift Guess:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlshiftguess, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlwidthguess = wx.TextCtrl(panel, value=str(0.05), size=(40, 23))
controlsizer.Add(wx.StaticText(panel, label="Width Guess:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlwidthguess, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.Add(controlsizer, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close)
self.Centre()
# self.MakeModal(True)
self.Show(True)
self.Raise()
self.make_list_plots()
def __init__(self,
parent,
title,
config=None,
iconfile="logo.ico",
*args,
**kwargs):
mainwindow_base.MainwindowBase.__init__(self, parent, title, config,
iconfile)
# wx.Frame.__init__(self, None, title=title) # ,size=(200,-1))
self.pres = parent
if config is None:
self.config = self.pres.eng.config
else:
self.config = config
self.icon_path = iconfile
self.datachoices = {
0: "Raw Data",
1: "Processed Data",
2: "Zero Charge Mass Spectrum"
}
self.extractchoices = {
0: "Height",
1: "Local Max",
2: "Area",
3: "Center of Mass",
4: "Local Max Position"
}
self.extractlabels = {
0: "Intensity",
1: "Intensity",
2: "Area",
3: "Mass",
4: "Mass"
}
self.CreateStatusBar(7)
self.SetStatusWidths([-1, 200, 120, 200, 230, 250, 130])
pub.subscribe(self.on_motion, 'newxy')
pub.subscribe(self.pres.on_selection, 'scans_selected')
self.menu = meta_menu(self, self.config, self.pres, type="Chrom")
self.SetMenuBar(self.menu.menuBar)
self.panel = wx.Panel(self)
self.panel.SetDropTarget(ChromDropTarget(self))
self.mainsizer = wx.BoxSizer(wx.HORIZONTAL)
self.leftsizer = wx.BoxSizer(wx.VERTICAL)
labelfont = wx.Font(16, wx.DECORATIVE, wx.ITALIC, wx.NORMAL)
self.ctlsizer = wx.BoxSizer(wx.VERTICAL)
label = wx.StaticText(self.panel,
label="Chromatogram Parsing Tools",
size=(300, 30))
label.SetFont(labelfont)
self.ctlsizer.Add(label, 0)
self.manual_add_button = wx.Button(self.panel,
label="Add From Manual Selection")
self.Bind(wx.EVT_BUTTON, self.pres.on_manual_add,
self.manual_add_button)
self.ctlsizer.Add(self.manual_add_button)
tsizer0 = wx.BoxSizer(wx.HORIZONTAL)
self.cpeaksbutton = wx.Button(self.panel,
label="Find Chrom. Peaks Near Width:")
self.Bind(wx.EVT_BUTTON, self.pres.on_chrom_peaks, self.cpeaksbutton)
tsizer0.Add(self.cpeaksbutton)
self.ctlcpeaks_param1 = wx.TextCtrl(self.panel,
value=str(
self.config.chrom_peak_width),
size=(50, 20))
tsizer0.Add(self.ctlcpeaks_param1, 0, wx.ALIGN_CENTER_VERTICAL)
tsizer0.Add(wx.StaticText(self.panel, label="min"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctlsizer.Add(tsizer0)
tsizer1 = wx.BoxSizer(wx.HORIZONTAL)
self.timepartbutton = wx.Button(self.panel,
label="Partition in Time Steps of:")
self.Bind(wx.EVT_BUTTON, self.pres.on_timepart, self.timepartbutton)
tsizer1.Add(self.timepartbutton)
self.ctlmin = wx.TextCtrl(self.panel,
value=str(self.config.time_window),
size=(50, 20))
tsizer1.Add(self.ctlmin, 0, wx.ALIGN_CENTER_VERTICAL)
tsizer1.Add(wx.StaticText(self.panel, label="min"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctlsizer.Add(tsizer1)
tsizer2 = wx.BoxSizer(wx.HORIZONTAL)
self.swbutton = wx.Button(self.panel, label="Sliding Window (min):")
self.Bind(wx.EVT_BUTTON, self.pres.on_sliding_window, self.swbutton)
tsizer2.Add(self.swbutton)
self.ctlswwin = wx.TextCtrl(self.panel,
value=str(self.config.sw_time_window),
size=(50, 20))
tsizer2.Add(self.ctlswwin, 0, wx.ALIGN_CENTER_VERTICAL)
tsizer2.Add(wx.StaticText(self.panel, label="Offset (#):"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctlswoffset = wx.TextCtrl(self.panel,
value=str(
int(self.config.sw_scan_offset)),
size=(50, 20))
tsizer2.Add(self.ctlswoffset, 0, wx.ALIGN_CENTER_VERTICAL)
tsizer2.Add(wx.StaticText(self.panel, label="min"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctlsizer.Add(tsizer2)
tsizer2 = wx.BoxSizer(wx.HORIZONTAL)
tsizer2.Add(wx.StaticText(self.panel, label="Time Start:"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctltmin = wx.TextCtrl(self.panel,
value=str(self.config.time_start),
size=(50, 20))
tsizer2.Add(self.ctltmin, 0, wx.ALIGN_CENTER_VERTICAL)
tsizer2.Add(wx.StaticText(self.panel, label="End:"), 0,
wx.ALIGN_CENTER_VERTICAL)
self.ctltmax = wx.TextCtrl(self.panel,
value=str(self.config.time_end),
size=(50, 20))
tsizer2.Add(self.ctltmax, 0, wx.ALIGN_CENTER_VERTICAL)
# tsizer2.Add(wx.StaticText(self.panel, label="min. Offset:"), 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlsizer.Add(tsizer2)
self.clear_button = wx.Button(self.panel, label="Clear All Spectra")
self.Bind(wx.EVT_BUTTON, self.pres.on_clear_spectra, self.clear_button)
self.ctlsizer.Add(self.clear_button)
label = wx.StaticText(self.panel,
label="Parsed Spectra",
size=(300, 30))
label.SetFont(labelfont)
self.ctlsizer.Add(label, 0)
self.leftsizer.Add(self.ctlsizer)
self.ypanel = ListCtrlPanel(self.panel, self.pres, size=(300, 300))
self.leftsizer.Add(self.ypanel, 1, wx.EXPAND)
self.ctlsizer2 = wx.BoxSizer(wx.VERTICAL)
label = wx.StaticText(self.panel,
label="UniDec of Manual Selection",
size=(300, 30))
label.SetFont(labelfont)
self.ctlsizer2.Add(label, 0)
self.run_ud_button = wx.Button(self.panel,
label="Run UniDec On Selection")
self.Bind(wx.EVT_BUTTON, self.pres.on_unidec_run, self.run_ud_button)
self.ctlsizer2.Add(self.run_ud_button)
self.pick_peaks_button_individual = wx.Button(
self.panel, label="Pick Peaks On Selection")
self.Bind(wx.EVT_BUTTON, self.pres.on_pick_peaks_individual,
self.pick_peaks_button_individual)
self.ctlsizer2.Add(self.pick_peaks_button_individual)
self.open_ud_button = wx.Button(self.panel,
label="Open Selection in UniDec GUI")
self.Bind(wx.EVT_BUTTON, self.pres.on_open_ud, self.open_ud_button)
self.ctlsizer2.Add(self.open_ud_button)
label = wx.StaticText(self.panel,
label="Peaks for Manual Selection",
size=(300, 30))
label.SetFont(labelfont)
self.ctlsizer2.Add(label, 0)
self.singlepeakpanel = peaklistsort.PeakListCtrlPanel(self.panel,
meta=False,
size=(300, 300))
self.Bind(self.singlepeakpanel.EVT_DELETE_SELECTION_2,
self.pres.on_single_delete, self.singlepeakpanel)
self.Bind(self.singlepeakpanel.EVT_CHARGE_STATE,
self.pres.on_single_charge_states, self.singlepeakpanel)
self.Bind(self.singlepeakpanel.EVT_DIFFERENCES,
self.pres.on_single_differences, self.singlepeakpanel)
self.Bind(self.singlepeakpanel.EVT_MASSES,
self.pres.on_single_label_masses, self.singlepeakpanel)
self.ctlsizer2.Add(self.singlepeakpanel, 0, wx.EXPAND)
self.leftsizer.Add(self.ctlsizer2, 0, wx.EXPAND)
self.mainsizer.Add(self.leftsizer, 0, wx.EXPAND)
plotwindow = scrolled.ScrolledPanel(self.panel)
sizerplot = wx.GridBagSizer()
figsize = (4.9, 3.5)
self.plotc = plot1d.Plot1d(plotwindow, figsize=figsize) # Chromatogram
self.plotm = plot1d.Plot1d(
plotwindow, figsize=figsize) # Selection from chromatogram
self.plot1 = plot1d.Plot1d(plotwindow, smash=1,
figsize=figsize) # MUD Plot 1 m/z cascade
self.plot2 = plot1d.Plot1d(plotwindow,
figsize=figsize) # MUD Deconvolved Data
self.plot7 = plot1d.Plot1d(plotwindow,
figsize=figsize) # MUD Extraction
self.plot2s = plot1d.Plot1d(plotwindow,
figsize=figsize) # Selection mass
self.plot3 = plot2d.Plot2d(plotwindow,
figsize=figsize) # MUD 2D m/z vs. time
self.plot5 = plot2d.Plot2d(plotwindow,
figsize=figsize) # MUD 2D mass vs. time
sizerplot.Add(self.plotc, (0, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plotm, (1, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot1, (0, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot2, (1, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot7, (2, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot2s, (2, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot3, (3, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot5, (3, 1), span=(1, 1), flag=wx.EXPAND)
self.plots = [
self.plotc, self.plotm, self.plot1, self.plot2, self.plot7,
self.plot2s, self.plot3, self.plot5
]
self.plotnames = [
"Chrom_TIC", "Chrom_mz_selected", "ChromFigure_mz",
"ChromFigure_mass", "ChromFigure_XIC", "Chrom_mass_selected",
"Chrom2Dmz", "Chrom2Dmass"
]
plotwindow.SetSizerAndFit(sizerplot)
plotwindow.SetupScrolling()
self.mainsizer.Add(plotwindow, 1, wx.EXPAND)
self.sizer3 = wx.BoxSizer(wx.VERTICAL)
label = wx.StaticText(self.panel,
label=" Peaks for Parsed Spectra",
size=(300, 30))
label.SetFont(labelfont)
self.sizer3.Add(label, 0)
self.peakpanel = peaklistsort.PeakListCtrlPanel(self.panel, meta=True)
self.Bind(self.peakpanel.EVT_DELETE_SELECTION_2, self.pres.on_delete,
self.peakpanel)
self.Bind(self.peakpanel.EVT_CHARGE_STATE,
self.pres.on_charge_states_mud, self.peakpanel)
self.Bind(self.peakpanel.EVT_DIFFERENCES, self.pres.on_differences,
self.peakpanel)
self.Bind(self.peakpanel.EVT_MASSES, self.pres.on_label_masses,
self.peakpanel)
self.sizer3.Add(self.peakpanel, 0, wx.EXPAND)
self.mainsizer.Add(self.sizer3, 0, wx.EXPAND)
self.controls = main_controls(self, self.config, self.pres, self.panel,
self.icon_path)
self.mainsizer.Add(self.controls, 0, wx.EXPAND)
self.panel.SetSizer(self.mainsizer)
self.mainsizer.Fit(self)
keys = [
["E", self.pres.on_auto, self.controls.autobutton],
# ["G", self.pres.on_paste_spectrum, self.menu.menupastespectrum],
["R", self.pres.on_unidec_button, self.controls.udbutton],
["D", self.pres.on_dataprep_button, self.controls.dataprepbutton],
["O", self.pres.on_open,
self.menu.openmenu], # ["I", self.pres.on_integrate],
["P", self.pres.on_pick_peaks,
self.controls.plotbutton], # ["K", self.pres.on_plot_peaks],
# ["C", self.pres.on_plot_composite, self.controls.compositebutton],
# ["N", self.pres.on_wizard, self.menu.wizardmenu],
# ["F", self.pres.on_plot_offsets], # ["Z", self.pres.on_charge_plot],
# ["L", self.pres.on_load_state], ["S", self.pres.on_save_state],
# ["B", self.pres.on_batch_run, self.menu.menubatchrun],
["Q", self.on_exit, self.menu.menuExit],
["T", self.pres.on_mass_tools, self.menu.menuMassFile],
["M", self.pres.on_match, self.menu.menumatch],
["W", self.pres.on_auto_peak_width, self.menu.menuAutoWidth],
# ["Z", self.pres.on_undo, self.menu.menuundo],
# ["Y", self.pres.on_redo, self.menu.menuredo],
["K", self.pres.on_kendrick, self.menu.menukendrick]
]
self.setup_shortcuts(keys)
self.Centre()
self.Show(True)
def __init__(self,
parent,
title,
config,
iconfile="logo.ico",
tabbed=None):
"""
initialize window and feed in links to presenter and config.
:param parent: GUniDec Presenter -> self.pres
:param title: Window title (string)
:param config: UniDecConfig object ->self.config
:return: None
"""
MainwindowBase.__init__(self, parent, title, config, iconfile, tabbed)
self.CreateStatusBar(4)
self.SetStatusWidths([-1, 150, 150, 150])
pub.subscribe(self.on_motion, 'newxy')
# pub.subscribe(self.on_selection, 'scans_selected')
self.filemenu = wx.Menu()
self.menuOpen = self.filemenu.Append(wx.ID_SAVE, "Open File Set",
"Open File Set")
# self.Bind(wx.EVT_MENU, self.on_open, self.menuOpen)
self.menuSave = self.filemenu.Append(wx.ID_SAVE, "Save File Set",
"Save File Set")
# self.Bind(wx.EVT_MENU, self.on_open, self.menuOpen)
self.menuAdd = self.filemenu.Append(wx.ID_SAVE, "Add Files To Set",
"Add Files To Set")
self.Bind(wx.EVT_MENU, self.pres.on_add, self.menuAdd)
self.menuBar = wx.MenuBar()
self.menuBar.Append(self.filemenu, "&File")
self.SetMenuBar(self.menuBar)
self.panel = wx.Panel(self)
# self.panel.SetDropTarget(ChromDropTarget(self))
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.inputsizer = wx.BoxSizer(wx.HORIZONTAL)
self.filelist = UDListCtrlPanel(self.panel)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.on_click, self.filelist.list)
self.inputsizer.Add(self.filelist)
self.plotsizer = wx.BoxSizer(wx.VERTICAL)
self.plot4 = plot1d.Plot1d(self.panel)
self.plot2 = plot1d.Plot1d(self.panel)
self.insetplot = plot1d.Plot1d(self.panel)
self.multiplot = plot1d.Plot1d(self.panel)
self.plotsizer.Add(self.multiplot)
self.plotsizer.Add(self.insetplot)
self.plotsizer.Add(self.plot4)
self.plotsizer.Add(self.plot2)
self.inputsizer.Add(self.plotsizer)
self.peakpanel = peaklistsort.PeakListCtrlPanel(self.panel)
self.Bind(self.peakpanel.EVT_DELETE_SELECTION_2, self.pres.on_replot,
self.peakpanel)
self.Bind(self.peakpanel.EVT_CHARGE_STATE, self.pres.on_charge_states,
self.peakpanel)
self.Bind(self.peakpanel.EVT_DIFFERENCES, self.pres.on_differences,
self.peakpanel)
self.Bind(self.peakpanel.EVT_MASSES, self.pres.on_label_masses,
self.peakpanel)
self.inputsizer.Add(self.peakpanel, 0, wx.EXPAND)
self.sizer.Add(self.inputsizer, 1, wx.EXPAND)
self.panel.SetSizer(self.sizer)
self.sizer.Fit(self)
self.Centre()
self.Show(True)
def initiate_dialog(self, config, data):
"""
Initiate the dialog window, lay everything out, and plot the intial results
:param config: UniDecConfig object
:param data: Data to plot (either MS or IM-MS)
:return: None
"""
self.data = data
self.SetSize((550 + config.imflag * 50, 650))
self.config = config
panel = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
size = (7, 4)
vbox2 = wx.BoxSizer(wx.VERTICAL)
if self.config.imflag == 0:
self.plot1 = plot1d.Plot1d(panel, figsize=size)
else:
self.plot1 = plot2d.Plot2d(panel, figsize=size)
vbox2.Add(self.plot1, 0, wx.EXPAND)
hbox = wx.BoxSizer(wx.HORIZONTAL)
sb = wx.StaticBox(panel, label='Manually Set Masses')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
importbutton = wx.Button(panel, label="Import from File")
self.Bind(wx.EVT_BUTTON, self.on_import, importbutton)
clearbutt = wx.Button(panel, label="Clear List")
self.Bind(wx.EVT_BUTTON, self.on_clear, clearbutt)
addbutton = wx.Button(panel, label="Manual Add Species")
self.Bind(wx.EVT_BUTTON, self.on_add, addbutton)
addbutton2 = wx.Button(panel, label="Add from Plot Zoom Range")
self.Bind(wx.EVT_BUTTON, self.on_add_from_plot, addbutton2)
plotbutton = wx.Button(panel, label="Plot Manual Assignments")
self.Bind(wx.EVT_BUTTON, self.on_plot, plotbutton)
sbs.Add(importbutton, 0, wx.EXPAND)
sbs.Add(addbutton, 0, wx.EXPAND)
sbs.Add(addbutton2, 0, wx.EXPAND)
sbs.Add(clearbutt, 0, wx.EXPAND)
sbs.Add(plotbutton, 0, wx.EXPAND)
hbox.Add(sbs)
sb2 = wx.StaticBox(panel, label='Manual List')
sbs2 = wx.StaticBoxSizer(sb2, orient=wx.VERTICAL)
self.masslistbox = ManualListCtrlPanel(panel,
imflag=self.config.imflag)
# sbs2.Add(wx.StaticText(panel, label="Manual List"))
sbs2.Add(self.masslistbox)
hbox.Add(sbs2)
vbox2.Add(hbox, 1)
panel.SetSizer(vbox2)
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
closebutton = wx.Button(self, label='Cancel')
hboxend.Add(okbutton)
hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(panel, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
self.masslistbox.list.populate(self.config.manuallist)
self.on_plot(0)
self.CenterOnParent()
def initialize_interface(self, massaxis, chargeaxis, igrid, config, pks):
"""
Initialize the parameters, setup the GUI, and plot the intial results.
:param massaxis: Mass axis values
:param chargeaxis: Charge axis value
:param igrid: Intensities at each mass and charge point
:param config: UniDecConfig object
:param pks: Peaks object
:return: None
"""
# Initialize the parameters
self.config = config
self.pks = pks
self.massaxis = np.array(massaxis)
self.chargeaxis = np.array(chargeaxis)
self.igrid = np.reshape(igrid, (len(massaxis), len(chargeaxis)))
# Setup the GUI
pnl = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
sb = wx.StaticBox(pnl, label='Set Parameters to Plot Native Z')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
self.plot1 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot2 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot3 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot4 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot5 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot6 = plot1d.Plot1d(pnl, figsize=self.figsize)
self.plot7 = plot2d.Plot2d(pnl, figsize=self.figsize)
hbox0 = wx.BoxSizer(wx.HORIZONTAL)
hbox0.Add(self.plot1, 0, wx.EXPAND)
hbox0.Add(self.plot3, 0, wx.EXPAND)
hbox0.Add(self.plot4, 0, wx.EXPAND)
hbox2 = wx.BoxSizer(wx.HORIZONTAL)
hbox2.Add(self.plot2, 0, wx.EXPAND)
hbox2.Add(self.plot5, 0, wx.EXPAND)
hbox2.Add(self.plot6, 0, wx.EXPAND)
sbs.Add(hbox0, 0, wx.EXPAND)
sbs.Add(hbox2, 0, wx.EXPAND)
hbox1 = wx.BoxSizer(wx.HORIZONTAL)
addbutton = wx.Button(pnl, label="Add Line")
fitbutton = wx.Button(pnl, label="Fit")
resetbutton = wx.Button(pnl, label="Reset to Default")
extractbutton = wx.Button(pnl, label="Extract")
self.ctlmassoffset = wx.TextCtrl(pnl,
value=str(self.config.massoffset),
size=(50, -1))
self.ctlfilt = wx.RadioBox(pnl,
label="Extract Shape",
choices=["Box", "Gaussian"])
self.ctlfilt.SetSelection(self.config.extractshape)
savefigbutton = wx.Button(pnl, label="Save Figures")
replotbutton = wx.Button(pnl, label="Replot")
hbox1.Add(addbutton, 0)
hbox1.Add(replotbutton, 0)
hbox1.Add(resetbutton, 0)
hbox1.Add(wx.StaticText(pnl, label=" "), 0,
wx.ALIGN_CENTER_VERTICAL)
hbox1.Add(fitbutton, 0)
hbox1.Add(extractbutton, 0)
hbox1.Add(wx.StaticText(pnl, label=" Monomer Mass: "),
0) # , wx.ALIGN_CENTER_VERTICAL)
hbox1.Add(self.ctlmassoffset, 0)
hbox1.Add(self.ctlfilt, 0)
hbox1.Add(savefigbutton, 0)
sbs.Add(hbox1, 0, wx.EXPAND)
hbox3 = wx.BoxSizer(wx.HORIZONTAL)
self.zlistctrl = ColorList(pnl)
hbox3.Add(self.zlistctrl, 1, wx.EXPAND)
hbox3.Add(self.plot7, 0, wx.EXPAND)
sbs.Add(hbox3, 0, wx.EXPAND)
pnl.SetSizer(sbs)
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
closebutton = wx.Button(self, label='Cancel')
hboxend.Add(okbutton)
hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(pnl, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
self.Center()
# Bind events
self.zlistctrl.ultimateList.Bind(wx.EVT_BUTTON, self.on_delete)
self.zlistctrl.ultimateList.Bind(wx.EVT_LIST_ITEM_DESELECTED,
self.update)
fitbutton.Bind(wx.EVT_BUTTON, self.fit)
addbutton.Bind(wx.EVT_BUTTON, self.on_add)
resetbutton.Bind(wx.EVT_BUTTON, self.on_reset)
extractbutton.Bind(wx.EVT_BUTTON, self.extract)
savefigbutton.Bind(wx.EVT_BUTTON, self.save_figures)
replotbutton.Bind(wx.EVT_BUTTON, self.on_replot)
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
# Set Range Here and plot the initial results
tstart = time.perf_counter()
self.make_f_array(-50, 15)
tend = time.perf_counter()
print("F Array Time: %.2gs" % (tend - tstart))
if self.config.zoffs == []:
self.get_maxima()
else:
self.zoffs = self.config.zoffs
self.plot_zoffs()
self.populate_list(0)
def setup_main_panel(self):
"""
Lays Out Main Panel. Binds some functions to presenter.
:return: None
"""
# Create Status Bar
self.CreateStatusBar(7)
self.SetStatusWidths([-1, 300, 200, 200, 250, 150, 130])
# Sizers to develop layout
# s1 = (min(self.displaysize[0], 1851), self.displaysize[1])
# s2 = (550, self.displaysize[1])
splitterwindow = wx.SplitterWindow(self,
-1,
style=wx.SP_3D | wx.SP_BORDER)
splitterwindow2 = wx.SplitterWindow(splitterwindow,
-1,
style=wx.SP_3D | wx.SP_BORDER)
panelp = wx.Panel(splitterwindow2, -1)
panel = scrolled.ScrolledPanel(splitterwindow2,
-1) # wx.Panel(splitterwindow2, -1)
splitterwindow2.SplitVertically(panelp,
panel,
sashPosition=-250 -
self.config.imflag * 20)
splitterwindow2.SetMinimumPaneSize(175)
splitterwindow.SetMinimumPaneSize(175)
# splitterwindow.SetMinSize((0,0))
# splitterwindow2.SetMinSize((0,0))
file_drop_target = MyFileDropTarget(self)
splitterwindow.SetDropTarget(file_drop_target)
# .................................
#
# Layout the Plots
#
# ...................................
# Tabbed view of plots
if self.tabbed == 1:
figsize = (6, 5)
plotwindow = wx.Notebook(splitterwindow)
splitterwindow.SplitVertically(plotwindow,
splitterwindow2,
sashPosition=-550)
tab1 = wx.Panel(plotwindow)
tab2 = wx.Panel(plotwindow)
tab3 = wx.Panel(plotwindow)
tab4 = wx.Panel(plotwindow)
tab5 = wx.Panel(plotwindow)
tab6 = wx.Panel(plotwindow)
self.plot1 = plot1d.Plot1d(tab1, smash=1, figsize=figsize)
self.plot2 = plot1d.Plot1d(tab2, integrate=1, figsize=figsize)
self.plot3 = plot2d.Plot2d(tab3, figsize=figsize)
self.plot4 = plot1d.Plot1d(tab4, figsize=figsize)
self.plot5 = plot2d.Plot2d(tab5, figsize=figsize)
self.plot6 = plot1d.Plot1d(tab6, figsize=figsize)
miscwindows.setup_tab_box(tab1, self.plot1)
miscwindows.setup_tab_box(tab2, self.plot2)
miscwindows.setup_tab_box(tab3, self.plot3)
miscwindows.setup_tab_box(tab4, self.plot4)
miscwindows.setup_tab_box(tab5, self.plot5)
miscwindows.setup_tab_box(tab6, self.plot6)
if self.config.imflag == 1:
tab1im = wx.Panel(plotwindow)
tab1fit = wx.Panel(plotwindow)
tab2ccs = wx.Panel(plotwindow)
tab3color = wx.Panel(plotwindow)
tab5mccs = wx.Panel(plotwindow)
tab5ccsz = wx.Panel(plotwindow)
tab9 = wx.Panel(plotwindow)
tab10 = wx.Panel(plotwindow)
self.plot1im = plot2d.Plot2d(tab1im, figsize=figsize)
self.plot1fit = plot2d.Plot2d(tab1fit, figsize=figsize)
self.plot2ccs = plot1d.Plot1d(tab2ccs, figsize=figsize)
self.plot5mccs = plot2d.Plot2d(tab5mccs, figsize=figsize)
self.plot5ccsz = plot2d.Plot2d(tab5ccsz, figsize=figsize)
self.plot3color = ColorPlot.ColorPlot2D(tab3color,
figsize=figsize)
self.plot9 = plot3d.CubePlot(tab9, figsize=figsize)
self.plot10 = plot3d.CubePlot(tab10, figsize=figsize)
miscwindows.setup_tab_box(tab1im, self.plot1im)
miscwindows.setup_tab_box(tab1fit, self.plot1fit)
miscwindows.setup_tab_box(tab2ccs, self.plot2ccs)
miscwindows.setup_tab_box(tab3color, self.plot3color)
miscwindows.setup_tab_box(tab5mccs, self.plot5mccs)
miscwindows.setup_tab_box(tab5ccsz, self.plot5ccsz)
miscwindows.setup_tab_box(tab9, self.plot9)
miscwindows.setup_tab_box(tab10, self.plot10)
plotwindow.AddPage(tab1, "MS Data v. Fit")
if self.config.imflag == 1:
plotwindow.AddPage(tab1im, "IM-MS Data")
plotwindow.AddPage(tab1fit, "IM-MS Fit")
plotwindow.AddPage(tab3color, "IM-MS Charges")
plotwindow.AddPage(tab9, "m/z Cube")
plotwindow.AddPage(tab3, "m/z Grid")
plotwindow.AddPage(tab2, "Mass Distribution")
if self.config.imflag == 1:
plotwindow.AddPage(tab2ccs, "CCS Distribution")
plotwindow.AddPage(tab4, "Individual Peaks")
plotwindow.AddPage(tab5, "Mass vs. Charge")
if self.config.imflag == 1:
plotwindow.AddPage(tab5mccs, "Mass vs. CCS ")
plotwindow.AddPage(tab5ccsz, "CCS vs. Charge")
plotwindow.AddPage(tab10, "Mass Cube")
plotwindow.AddPage(tab6, "Bar Chart")
# Scrolled panel view of plots
else:
# TODO: Line up plots on left hand side so that they share an m/z axis
plotwindow = scrolled.ScrolledPanel(splitterwindow)
splitterwindow.SplitVertically(plotwindow,
splitterwindow2,
sashPosition=-550)
sizerplot = wx.GridBagSizer()
figsize = self.config.figsize
self.plot1 = plot1d.Plot1d(plotwindow, smash=1, figsize=figsize)
self.plot2 = plot1d.Plot1d(plotwindow,
integrate=1,
figsize=figsize)
self.plot3 = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot4 = plot1d.Plot1d(plotwindow, figsize=figsize)
self.plot5 = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot6 = plot1d.Plot1d(plotwindow, figsize=figsize)
if self.config.imflag == 1:
self.plot1im = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot1fit = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot2ccs = plot1d.Plot1d(plotwindow, figsize=figsize)
self.plot5mccs = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot5ccsz = plot2d.Plot2d(plotwindow, figsize=figsize)
self.plot3color = ColorPlot.ColorPlot2D(plotwindow,
figsize=figsize)
self.plot9 = plot3d.CubePlot(plotwindow, figsize=figsize)
self.plot10 = plot3d.CubePlot(plotwindow, figsize=figsize)
if self.config.imflag == 0:
sizerplot.Add(self.plot1, (0, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot2, (0, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot3, (1, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot4, (1, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot5, (2, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot6, (2, 1), span=(1, 1), flag=wx.EXPAND)
else:
sizerplot.Add(self.plot1, (0, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot1im, (0, 1),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot1fit, (1, 1),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot3color, (1, 0),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot2, (2, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot2ccs, (3, 0),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot3, (2, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot4, (4, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot5, (3, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot5mccs, (4, 1),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot5ccsz, (5, 1),
span=(1, 1),
flag=wx.EXPAND)
sizerplot.Add(self.plot6, (5, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot9, (6, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot10, (6, 1), span=(1, 1), flag=wx.EXPAND)
# plotwindow.SetScrollbars(1, 1,1,1)
if self.system == "Linux":
plotwindow.SetSizer(sizerplot)
sizerplot.Fit(self)
else:
plotwindow.SetSizerAndFit(sizerplot)
plotwindow.SetupScrolling()
self.plots = [
self.plot1, self.plot2, self.plot3, self.plot4, self.plot5,
self.plot6
]
if self.config.imflag == 1:
self.plots = self.plots + [
self.plot1im, self.plot1fit, self.plot2ccs, self.plot5mccs,
self.plot5ccsz, self.plot3color, self.plot9, self.plot10
]
self.plotnames = [
"Figure1", "Figure2", "Figure3", "Figure4", "Figure5", "Figure6"
]
if self.config.imflag == 1:
self.plotname = self.plotnames + [
"Figure1im", "Figure1fit", "Figure2ccs", "Figure3color",
"Figure5ccsz", "Figure5massccs", "mzCube", "massCube"
]
# ...........................
#
# Sizer for Peaks
#
# ...........................
sizerpeaks = wx.BoxSizer(wx.VERTICAL)
self.peakpanel = peaklistsort.PeakListCtrlPanel(panelp)
self.Bind(self.peakpanel.EVT_DELETE_SELECTION_2, self.pres.on_delete,
self.peakpanel)
self.Bind(self.peakpanel.EVT_CHARGE_STATE, self.pres.on_charge_states,
self.peakpanel)
self.Bind(self.peakpanel.EVT_DIFFERENCES, self.pres.on_differences,
self.peakpanel)
sizerpeaks.Add(self.peakpanel, 0, wx.EXPAND)
panelp.SetSizer(sizerpeaks)
sizerpeaks.Fit(self)
# ..........................
#
# Setup Control Panel
#
# .............................
sizercontrols = wx.BoxSizer(wx.VERTICAL)
self.controls = ud_controls.main_controls(self, self.config, self.pres,
panel, self.icon_path)
sizercontrols.Add(self.controls, 1, wx.EXPAND)
panel.SetSizer(sizercontrols)
sizercontrols.Fit(self)
# panel.SetAutoLayout(1)
# panel.SetupScrolling(scroll_x=False, scroll_y=True)
if self.system == "Linux" and self.tabbed != 1:
sizerplot.Fit(splitterwindow)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(splitterwindow, 1, wx.EXPAND)
# Set everything up
self.SetSizer(sizer)
sizer.Fit(self)
pass
def initialize_interface(self, config, data):
"""
Create the GUI, import the paramters, and plot the intial data.
:param config: UniDecConfig Object
:param data: Data array (N x 2)
:return: None
"""
# Initialize parameters
self.config = config
self.data = data
self.psfun = config.psfun
# Create the GUI
pnl = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
sb = wx.StaticBox(pnl, label='Peak Shape Tool')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
self.plot1 = plot1d.Plot1d(pnl)
self.plot1.plotrefreshtop(self.data[:, 0],
self.data[:, 1],
title="Data",
xlabel="m/z (Th)",
ylabel="Normalized Intensity",
zoom="span")
sbs.Add(self.plot1, 1, wx.EXPAND)
hbox11 = wx.BoxSizer(wx.HORIZONTAL)
hbox10 = wx.BoxSizer(wx.VERTICAL)
centerbutton = wx.Button(pnl, label='Reset Range')
centerbutton.Bind(wx.EVT_BUTTON, self.on_reset)
hbox10.Add(centerbutton, 0, wx.ALIGN_LEFT)
hbox11.Add(hbox10, 0, wx.ALIGN_LEFT)
hbox9 = wx.BoxSizer(wx.VERTICAL)
self.ctlpsfun = wx.RadioBox(
pnl,
label="Peak Shape Fit Function",
choices=["Gaussian", "Lorentzian", "Split G/L"])
self.ctlpsfun.SetSelection(self.psfun)
fitbutton = wx.Button(pnl, label='Fit Peak Shape')
plotbutton = wx.Button(pnl, label='Plot Guess')
hbox9.Add(self.ctlpsfun, 0, wx.ALIGN_RIGHT)
hbox8 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlmzsig = wx.TextCtrl(pnl, value=str(self.config.mzsig))
hbox8.Add(wx.StaticText(pnl, label='Guess for Peak FWHM: '),
wx.ALIGN_CENTER_VERTICAL)
hbox8.Add(self.ctlmzsig,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox9.Add(hbox8, 0, wx.ALIGN_RIGHT)
hbox9.Add(plotbutton, 0, wx.ALIGN_RIGHT)
hbox9.Add(fitbutton, 0, wx.ALIGN_RIGHT)
hbox6 = wx.BoxSizer(wx.HORIZONTAL)
self.errorbox = wx.TextCtrl(pnl, value="", style=wx.TE_READONLY)
hbox6.Add(wx.StaticText(pnl, label='Error in Fit: '),
wx.ALIGN_CENTER_VERTICAL)
hbox6.Add(self.errorbox,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox9.Add(hbox6, 0, wx.ALIGN_RIGHT)
hbox7 = wx.BoxSizer(wx.HORIZONTAL)
self.resbox = wx.TextCtrl(pnl, value=str(""))
hbox7.Add(wx.StaticText(pnl, label='Resolution (M/FWHM): '),
wx.ALIGN_CENTER_VERTICAL)
hbox7.Add(self.resbox,
flag=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox9.Add(hbox7, 0, wx.ALIGN_RIGHT)
hbox11.Add(hbox9, 1, wx.ALIGN_RIGHT)
sbs.Add(hbox11, 0, wx.EXPAND)
pnl.SetSizer(sbs)
# Create the bottom buttons
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
closebutton = wx.Button(self, label='Cancel')
hboxend.Add(okbutton)
hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(pnl, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
# Bind some things
plotbutton.Bind(wx.EVT_BUTTON, self.on_plot)
fitbutton.Bind(wx.EVT_BUTTON, self.on_fit)
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
self.CenterOnParent()
def initialize_interface(self, data3, data2, config):
"""
Initialize the parameters, create the interface, plot the initial data.
:param data3: 2D IM-MS data
:param data2: 1D MS data
:param config: UniDecConfig Object
:return: None
"""
# Initialize the parameters
self.mz = np.unique(data3[:, 0])
self.dt = np.unique(data3[:, 1])
self.C = data3[:, 2].reshape((len(self.mz), len(self.dt)))
self.data = data2
self.config = config
self.psfun = config.psfun
# Create the interface
pnl = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
sb = wx.StaticBox(pnl, label='Peak Shape Tool')
sbs = wx.StaticBoxSizer(sb, orient=wx.VERTICAL)
self.plot1 = plot1d.Plot1d(pnl)
sbs.Add(self.plot1, 1, wx.EXPAND)
hbox11 = wx.BoxSizer(wx.HORIZONTAL)
hbox10 = wx.BoxSizer(wx.VERTICAL)
centerbutton = wx.Button(pnl, label='Reset Range')
self.flipbutton = wx.Button(pnl, label='Flip m/z and AT')
centerbutton.Bind(wx.EVT_BUTTON, self.on_reset)
self.flipbutton.Bind(wx.EVT_BUTTON, self.on_flip)
hboxsigs = wx.BoxSizer(wx.HORIZONTAL)
self.outmzsig = wx.TextCtrl(pnl, value="")
hboxsigs.Add(wx.StaticText(pnl, label='m/z Width Fit: '),
wx.ALIGN_CENTER_VERTICAL)
hboxsigs.Add(self.outmzsig,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hboxsigs2 = wx.BoxSizer(wx.HORIZONTAL)
self.outdtsig = wx.TextCtrl(pnl, value="")
hboxsigs2.Add(wx.StaticText(pnl, label='A.T. Width Fit: '),
wx.ALIGN_CENTER_VERTICAL)
hboxsigs2.Add(self.outdtsig,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox10.Add(centerbutton, 0, wx.ALIGN_LEFT)
hbox10.Add(self.flipbutton, 0, wx.ALIGN_LEFT)
hbox10.Add(hboxsigs, 0, wx.ALIGN_LEFT)
hbox10.Add(hboxsigs2, 0, wx.ALIGN_LEFT)
hbox11.Add(hbox10, 0, wx.ALIGN_LEFT)
hbox9 = wx.BoxSizer(wx.VERTICAL)
self.ctlpsfun = wx.RadioBox(
pnl,
label="Peak Shape Fit Function",
choices=["Gaussian", "Lorentzian", "Split G/L"])
self.ctlpsfun.SetSelection(self.psfun)
fitbutton = wx.Button(pnl, label='Fit Peak Shape')
plotbutton = wx.Button(pnl, label='Plot Guess')
hbox9.Add(self.ctlpsfun, 0, wx.ALIGN_RIGHT)
hbox8 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlsigguess = wx.TextCtrl(pnl, value=str(self.config.mzsig))
hbox8.Add(wx.StaticText(pnl, label='Guess for Peak Width: '),
wx.ALIGN_CENTER_VERTICAL)
hbox8.Add(self.ctlsigguess,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox9.Add(hbox8, 0, wx.ALIGN_RIGHT)
hbox9.Add(plotbutton, 0, wx.ALIGN_RIGHT)
hbox9.Add(fitbutton, 0, wx.ALIGN_RIGHT)
hbox6 = wx.BoxSizer(wx.HORIZONTAL)
self.errorbox = wx.TextCtrl(pnl, value="", style=wx.TE_READONLY)
hbox6.Add(wx.StaticText(pnl, label='Error in Fit: '),
wx.ALIGN_CENTER_VERTICAL)
hbox6.Add(self.errorbox,
flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox7 = wx.BoxSizer(wx.HORIZONTAL)
self.resbox = wx.TextCtrl(pnl, value=str(""))
hbox7.Add(wx.StaticText(pnl, label='Resolution (M/FWHM): '),
wx.ALIGN_CENTER_VERTICAL)
hbox7.Add(self.resbox,
flag=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL,
border=5)
hbox9.Add(hbox6, 0, wx.ALIGN_RIGHT)
hbox9.Add(hbox7, 0, wx.ALIGN_RIGHT)
hbox11.Add(hbox9, 1, wx.ALIGN_RIGHT)
sbs.Add(hbox11, 0, wx.EXPAND)
pnl.SetSizer(sbs)
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
closebutton = wx.Button(self, label='Cancel')
hboxend.Add(okbutton)
hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(pnl, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
plotbutton.Bind(wx.EVT_BUTTON, self.on_plot)
fitbutton.Bind(wx.EVT_BUTTON, self.on_fit)
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
self.CenterOnParent()
# Plot the result
self.plot1.plotrefreshtop(self.data[:, 0],
self.data[:, 1],
title="Data",
xlabel="m/z (Th)",
ylabel="Normalized Intensity",
zoom="span")
def __init__(self, parent, data, pks, config=None):
wx.Frame.__init__(self, parent, title="Subtract and Divide Tools", size=(1100, 600)) # ,size=(-1,-1))
self.parent = parent
self.div = 760
self.sub = 44088
self.data = data
self.pks = pks
self.avgs = None
self.nums = None
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
else:
self.config = config
self.sub = config.molig
try:
self.masses = []
for p in self.pks.peaks:
if p.ignore == 0:
self.masses.append(p.mass)
defaultsub = np.amin(self.masses)
except:
self.masses = None
defaultsub = 44088
self.sub = defaultsub
self.panel = wx.Panel(self)
self.plot1 = plot1d.Plot1d(self.panel)
self.plot2 = plot1d.Plot1d(self.panel)
self.ctlsub = wx.TextCtrl(self.panel, value=str(self.sub))
self.ctldiv = wx.TextCtrl(self.panel, value=str(self.div))
self.ctlresult = wx.TextCtrl(self.panel, value="")
self.ctltype = wx.RadioBox(self.panel, label="X-axis", choices=["Mass", "Number"])
self.replotbutton = wx.Button(self.panel, -1, "Replot")
self.sizer = wx.BoxSizer(wx.VERTICAL)
s1 = wx.BoxSizer(wx.HORIZONTAL)
s1.Add(self.plot1, 1, wx.GROW)
s1.Add(self.plot2, 1, wx.GROW)
self.sizer.Add(s1, 1)
s2 = wx.BoxSizer(wx.HORIZONTAL)
s2.Add(wx.StaticText(self.panel, label=" Subtract (Da): "), flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(self.ctlsub, 0, flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(wx.StaticText(self.panel, label=" Divide (Da): "), flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(self.ctldiv, 0, flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(self.ctltype, 0, flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(self.replotbutton, 0, flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(wx.StaticText(self.panel, label=" Result (Da): "), flag=wx.ALIGN_CENTER_VERTICAL)
s2.Add(self.ctlresult, 0, flag=wx.ALIGN_CENTER_VERTICAL)
self.sizer.Add(s2, 0)
self.Bind(wx.EVT_BUTTON, self.replot, self.replotbutton)
self.Bind(wx.EVT_RADIOBOX, self.change_type, self.ctltype)
self.panel.SetSizer(self.sizer)
self.panel.Fit()
self.Show(True)
self.replot()
def __init__(self, parent, data_list, config=None, yvals=None, directory=None, header=None, params=None):
"""
Create wx.Frame and initialzie components
:param parent: Parent window or panel passed to wx.Frame
:param data_list: Input data for extraction in a list of arrays (N x 2)
:param config: UniDecConfig object. If None, will use defaults.
:param yvals: Position values for corresponding data_list elements.
For plots, these become the titles. For the Weighted-Average-of-Position (WAP) these are the position values.
:param directory: Directory for saving files. Default is current working directory.
:param header: Header for files that are written. Default is "Extract"
:param params: List of 8 values that define the parameters for extraction.
0=mass 0
1=mass 1
2=mass 2
3=minimum oligomeric state of mass 1
4=maximum oligomeric state of mass 1
5=minimum oligomeric state of mass 2
6=maximum oligomeric state of mass 2
7=Error window for finding intensity value
masses = m0 + m1 * range(min m1, max m1 +1) + m2 * range(min m2, max m2 +1)
:return: None
"""
wx.Frame.__init__(self, parent, title="2D Grid Extraction", size=(-1, -1))
# Make Menu
self.filemenu = wx.Menu()
self.menuSaveFigPNG = self.filemenu.Append(wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
self.menuSaveFigPDF = self.filemenu.Append(wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_save_fig, self.menuSaveFigPNG)
self.Bind(wx.EVT_MENU, self.on_save_figPDF, self.menuSaveFigPDF)
self.plotmenu = wx.Menu()
self.menufit = self.plotmenu.Append(wx.ID_ANY, "Fit Gaussians",
"Fit total distribution to a series of Gaussians")
self.menufit2 = self.plotmenu.Append(wx.ID_ANY, "Fit Poisson",
"Fit total distribution to a Poisson Distribution")
self.menufit3 = self.plotmenu.Append(wx.ID_ANY, "Fit Binomial",
"Fit total distribution to a Binomial Distribution")
self.menufit4 = self.plotmenu.Append(wx.ID_ANY, "Fit Multiple Poissons",
"Fit total distribution to multiple Poisson distributions")
self.Bind(wx.EVT_MENU, self.on_fit, self.menufit)
self.Bind(wx.EVT_MENU, self.on_fit2, self.menufit2)
self.Bind(wx.EVT_MENU, self.on_fit3, self.menufit3)
self.Bind(wx.EVT_MENU, self.on_fit4, self.menufit4)
self.menuBar = wx.MenuBar()
self.menuBar.Append(self.filemenu, "&File")
self.menuBar.Append(self.plotmenu, "Plot")
self.SetMenuBar(self.menuBar)
# Initialize Parameters
if config is None:
# Default UniDecConfig object
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
else:
self.config = config
if directory is None:
self.directory = os.getcwd()
else:
self.directory = directory
if header is None:
self.header = "Extract"
else:
self.header = header
if params is None:
self.params = [98868, 760.076, 22044, 0, 90, 0, 2, 0]
self.params = [0, 4493, 678, 1, 20, 0, 30, 10]
else:
self.params = params
self.datalist = data_list
self.dlen = len(data_list)
self.pos = -1
self.yvals = np.array(yvals).astype(np.float)
if ud.isempty(yvals):
self.yvals = np.arange(0, len(data_list))
self.storediscrete = deepcopy(self.config.discreteplot)
# Setup GUI
panel = wx.Panel(self)
sizer = wx.BoxSizer(wx.VERTICAL)
self.plot1 = plot1d.Plot1d(panel)
self.plot2 = plot2d.Plot2d(panel)
sizer.Add(self.plot1, 1, wx.EXPAND)
sizer.Add(self.plot2, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
controlsizer1 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlm0 = wx.TextCtrl(panel, value=str(self.params[0]))
self.ctlm1 = wx.TextCtrl(panel, value=str(self.params[1]))
self.ctlm2 = wx.TextCtrl(panel, value=str(self.params[2]))
self.ctlm1min = wx.TextCtrl(panel, value=str(self.params[3]))
self.ctlm1max = wx.TextCtrl(panel, value=str(self.params[4]))
self.ctlm2min = wx.TextCtrl(panel, value=str(self.params[5]))
self.ctlm2max = wx.TextCtrl(panel, value=str(self.params[6]))
self.ctlwindow = wx.TextCtrl(panel, value=str(self.params[7]))
controlsizer.Add(wx.StaticText(panel, label="Mass 0"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlm0, 0, wx.EXPAND)
controlsizer.Add(wx.StaticText(panel, label="Mass 1"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlm1, 0, wx.EXPAND)
controlsizer.Add(wx.StaticText(panel, label="Mass 2"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlm2, 0, wx.EXPAND)
controlsizer.Add(wx.StaticText(panel, label="Mass Window"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlwindow, 0, wx.EXPAND)
if self.dlen > 1:
self.ctlnorm = wx.CheckBox(panel, label="Normalize")
controlsizer.Add(self.ctlnorm, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass 1 Min #"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm1min, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass 1 Max #"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm1max, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass 2 Min #"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm2min, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass 2 Max #"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm2max, 0, wx.EXPAND)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
backbutton = wx.Button(panel, label="Back")
nextbutton = wx.Button(panel, label="Next")
if self.dlen > 1:
totalbutton = wx.Button(panel, label="Total")
else:
totalbutton = wx.Button(panel, label="Replot")
#wapbutton = wx.Button(panel, label="WAP")
if self.dlen > 1:
controlsizer2.Add(backbutton, 0, wx.EXPAND)
controlsizer2.Add(nextbutton, 0, wx.EXPAND)
controlsizer2.Add(totalbutton, 0, wx.EXPAND)
#if self.dlen > 1:
#controlsizer2.Add(wapbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_back, backbutton)
self.Bind(wx.EVT_BUTTON, self.on_next, nextbutton)
self.Bind(wx.EVT_BUTTON, self.on_total, totalbutton)
#self.Bind(wx.EVT_BUTTON, self.on_wap, wapbutton)
sizer.Add(controlsizer, 0, wx.EXPAND)
sizer.Add(controlsizer1, 0, wx.EXPAND)
sizer.Add(controlsizer2, 0, wx.EXPAND)
self.Bind(wx.EVT_CLOSE, self.on_close, self)
panel.SetSizer(sizer)
sizer.Fit(self)
# Run initial extraction
try:
self.on_total(0)
except Exception as e:
try:
self.on_next(0)
except:
pass
print(e)
self.Centre()
self.Show(True)
self.normflag = 1
def __init__(self, parent, data, config=None, directory=None):
"""
masses = m0 + m1 * range(min m1, max m1 +1)
:return: None
"""
wx.Frame.__init__(self,
parent,
title="2D Grid Extraction",
size=(-1, -1))
# Make Menu
self.filemenu = wx.Menu()
self.menuSaveFigPNG = self.filemenu.Append(
wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
self.menuSaveFigPDF = self.filemenu.Append(
wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_save_fig, self.menuSaveFigPNG)
self.Bind(wx.EVT_MENU, self.on_save_figPDF, self.menuSaveFigPDF)
self.menuBar = wx.MenuBar()
self.menuBar.Append(self.filemenu, "&File")
self.SetMenuBar(self.menuBar)
# Initialize Parameters
self.data = data
self.config = config
if self.config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
self.config.cmap = u"viridis"
if directory is None:
self.directory = os.getcwd()
else:
if directory is None:
self.directory = self.config.dirname
if self.config.griddecon is None:
self.params = [98868, 760.076, 0, 120, 1, 25, 0, 20, 3, 1]
else:
self.params = self.config.griddecon
if config is not None:
self.params[0] = self.config.oligomerlist[0][0]
self.params[1] = self.config.oligomerlist[0][1]
self.params[2] = self.config.oligomerlist[0][2]
self.params[3] = self.config.oligomerlist[0][3]
self.params[4] = self.config.startz
self.params[5] = self.config.endz
self.params[7] = self.config.mzsig
self.params[8] = self.config.msig
self.params[9] = self.config.zzsig
self.storediscrete = deepcopy(self.config.discreteplot)
else:
self.storediscrete = 1
# Setup GUI
panel = wx.Panel(self)
topsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer = wx.BoxSizer(wx.VERTICAL)
self.plot1 = plot1d.Plot1d(panel)
self.plot2 = plot2d.Plot2d(panel)
sizer.Add(self.plot1, 1, wx.EXPAND)
sizer.Add(self.plot2, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.VERTICAL)
controlsizer1 = wx.BoxSizer(wx.VERTICAL)
self.ctlm0 = wx.TextCtrl(panel, value=str(self.params[0]))
self.ctlm1 = wx.TextCtrl(panel, value=str(self.params[1]))
self.ctlm1min = wx.TextCtrl(panel, value=str(self.params[2]))
self.ctlm1max = wx.TextCtrl(panel, value=str(self.params[3]))
self.ctlm2min = wx.TextCtrl(panel, value=str(self.params[4]))
self.ctlm2max = wx.TextCtrl(panel, value=str(self.params[5]))
self.ctlwindow = wx.TextCtrl(panel, value=str(self.params[6]))
self.ctlfwhm = wx.TextCtrl(panel, value=str(self.params[7]))
self.ctlmsig = wx.TextCtrl(panel, value=str(self.params[8]))
self.ctlzzsig = wx.TextCtrl(panel, value=str(self.params[9]))
controlsizer1.Add(wx.StaticText(panel, label="Base Mass"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm0, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Monomer Mass"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm1, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass Window"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlwindow, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Monomer Min #"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm1min, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Monomer Max #"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm1max, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Minimum Charge State"),
0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm2min, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Maximum Charge State"),
0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlm2max, 0, wx.EXPAND)
controlsizer1.Add(
wx.StaticText(panel, label="Peak Full Width at Half Max"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlfwhm, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Mass Filter Width"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlmsig, 0, wx.EXPAND)
controlsizer1.Add(wx.StaticText(panel, label="Charge Filter Width"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlzzsig, 0, wx.EXPAND)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
extractbutton = wx.Button(panel, label="Extract")
deconbutton = wx.Button(panel, label="Deconvolute")
controlsizer2.Add(extractbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.extract, extractbutton)
controlsizer2.Add(deconbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.deconvolve, deconbutton)
controlsizer.Add(controlsizer1, 0, wx.EXPAND)
controlsizer.Add(controlsizer2, 0, wx.EXPAND)
topsizer.Add(sizer, 0, wx.EXPAND)
topsizer.Add(controlsizer, 1, wx.EXPAND)
self.Bind(wx.EVT_CLOSE, self.on_close, self)
panel.SetSizer(topsizer)
topsizer.Fit(self)
# Run initial extraction
self.extract(0)
#self.deconvolve(0)
self.Centre()
self.Show(True)
def initialize_interface(self, massdat, ccsdat, mccsgrid, config, pks):
"""
Initilizes the interface and plots the intial results.
:param massdat: Mass distribution array (N x 2)
:param ccsdat: CCS distribution array (M x 2)
:param mccsgrid: Array of intensity values for corresponding mass and CCS values (N x M) array
:param config: UniDecConfig object
:param pks: Peaks object
:return: None
"""
self.config = config
self.massdat = massdat
self.ccsdat = ccsdat
self.totalgrid = mccsgrid
self.pks = pks
self.ztab = np.arange(float(self.config.startz),
float(self.config.endz + 1))
zstrings = [str(int(z)) for z in self.ztab]
zstrings.append("All")
pnl = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
sb = wx.StaticBox(pnl, label='Ion Mobility Extraction Tool')
sbs = wx.StaticBoxSizer(sb, orient=wx.HORIZONTAL)
figsize = (6, 5)
self.plot1 = plot2d.Plot2d(pnl, figsize=figsize)
self.plot2 = plot1d.Plot1d(pnl, figsize=figsize)
plotsizer = wx.BoxSizer(wx.VERTICAL)
plotsizer.Add(self.plot1, 0, wx.EXPAND)
plotsizer.Add(self.plot2, 0, wx.EXPAND)
sbs.Add(plotsizer, 0, wx.EXPAND)
sb2 = wx.StaticBox(pnl, label='Extraction Parameters')
sbs2 = wx.StaticBoxSizer(sb2, orient=wx.VERTICAL)
gbox1c = wx.GridBagSizer(wx.VERTICAL)
size1 = (75, -1)
self.ctlzout = wx.ComboBox(pnl, value="", size=size1, choices=zstrings)
gbox1c.Add(self.ctlzout, (0, 1), span=(1, 1))
gbox1c.Add(wx.StaticText(pnl, label="Charge State: "), (0, 0),
flag=wx.ALIGN_CENTER_VERTICAL)
sbs2.Add(gbox1c, 0, wx.EXPAND)
self.masspanel = IMListCtrlPanel(pnl, size=(200, 700))
addbutton = wx.Button(pnl, label="Add Species")
plotbutton = wx.Button(pnl, label="Plot Species")
sbs2.Add(plotbutton, 0, wx.EXPAND)
sbs2.Add(self.masspanel, 0, wx.EXPAND)
sbs2.Add(addbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_add, addbutton)
self.Bind(wx.EVT_BUTTON, self.on_plot, plotbutton)
sbs.Add(sbs2, 0, wx.EXPAND)
pnl.SetSizer(sbs)
hboxend = wx.BoxSizer(wx.HORIZONTAL)
okbutton = wx.Button(self, label='Ok')
closebutton = wx.Button(self, label='Cancel')
okbutton.Bind(wx.EVT_BUTTON, self.on_close)
closebutton.Bind(wx.EVT_BUTTON, self.on_close_cancel)
hboxend.Add(okbutton)
hboxend.Add(closebutton, flag=wx.LEFT, border=5)
vbox.Add(pnl, proportion=1, flag=wx.ALL | wx.EXPAND, border=5)
vbox.Add(hboxend, flag=wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, border=10)
self.SetSizer(vbox)
vbox.Fit(self)
self.CenterOnParent()
self.loadpeaks(0)
self.on_plot(0)
self.ctlzout.SetSelection(len(zstrings) - 1)
def setupmainpanel(self):
sizer = wx.BoxSizer(wx.HORIZONTAL)
panel = wx.Panel(self)
file_drop_target = MyFileDropTarget(self)
panel.SetDropTarget(file_drop_target)
self.ypanel = ListCtrlPanel(panel, self.pres, size=(300, 300))
sizer.Add(self.ypanel, 0, wx.EXPAND)
# Tabbed view of plots
if self.tabbed == 1:
figsize = (6, 5)
plotwindow = wx.Notebook(panel)
tab1 = wx.Panel(plotwindow)
tab2 = wx.Panel(plotwindow)
tab3 = wx.Panel(plotwindow)
tab5 = wx.Panel(plotwindow)
tab6 = wx.Panel(plotwindow)
tab7 = wx.Panel(plotwindow)
tab8 = wx.Panel(plotwindow)
tab9 = wx.Panel(plotwindow)
self.plot1 = plot1d.Plot1d(tab1, smash=1, figsize=figsize)
self.plot2 = plot1d.Plot1d(tab2, integrate=1, figsize=figsize)
self.plot3 = plot2d.Plot2d(tab3, figsize=figsize)
self.plot5 = plot2d.Plot2d(tab5, figsize=figsize)
self.plot6 = plot1d.Plot1d(tab6, figsize=figsize)
self.plot7 = plot1d.Plot1d(tab7, figsize=figsize)
self.plot8 = plot2d.Plot2d(tab8, figsize=figsize)
self.plot9 = plot1d.Plot1d(tab9, figsize=figsize)
miscwindows.setup_tab_box(tab1, self.plot1)
miscwindows.setup_tab_box(tab2, self.plot2)
miscwindows.setup_tab_box(tab3, self.plot3)
miscwindows.setup_tab_box(tab5, self.plot5)
miscwindows.setup_tab_box(tab6, self.plot6)
miscwindows.setup_tab_box(tab7, self.plot7)
miscwindows.setup_tab_box(tab8, self.plot8)
miscwindows.setup_tab_box(tab9, self.plot9)
plotwindow.AddPage(tab1, "MS Data")
plotwindow.AddPage(tab9, "Charge Distributions")
plotwindow.AddPage(tab2, "Mass Distribution")
plotwindow.AddPage(tab7, "Extracts Line Plot")
plotwindow.AddPage(tab8, "Extracts Grid Plot")
plotwindow.AddPage(tab6, "Bar Chart")
plotwindow.AddPage(tab3, "m/z Grid")
plotwindow.AddPage(tab5, "Mass vs. Charge")
sizer.Add(plotwindow, 1, wx.EXPAND)
else:
self.plotpanel = scrolled.ScrolledPanel(panel)
sizerplot = wx.GridBagSizer()
figsize = self.config.figsize
self.plot1 = plot1d.Plot1d(self.plotpanel, smash=1, figsize=figsize)
self.plot2 = plot1d.Plot1d(self.plotpanel, integrate=1, figsize=figsize)
self.plot3 = plot2d.Plot2d(self.plotpanel, figsize=figsize)
self.plot5 = plot2d.Plot2d(self.plotpanel, figsize=figsize)
self.plot6 = plot1d.Plot1d(self.plotpanel, figsize=figsize)
self.plot7 = plot1d.Plot1d(self.plotpanel, figsize=figsize)
self.plot8 = plot2d.Plot2d(self.plotpanel, figsize=figsize)
self.plot9 = plot1d.Plot1d(self.plotpanel, figsize=figsize)
sizerplot.Add(self.plot1, (0, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot9, (0, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot2, (1, 0), span=(1, 2), flag=wx.EXPAND)
sizerplot.Add(self.plot6, (3, 0), span=(1, 2), flag=wx.EXPAND)
sizerplot.Add(self.plot7, (2, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot8, (2, 1), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot3, (4, 0), span=(1, 1), flag=wx.EXPAND)
sizerplot.Add(self.plot5, (4, 1), span=(1, 1), flag=wx.EXPAND)
self.plotpanel.SetSizerAndFit(sizerplot)
self.plotpanel.SetupScrolling()
sizer.Add(self.plotpanel, 1, wx.EXPAND)
self.plots = [self.plot1, self.plot2, self.plot6, self.plot7, self.plot8, self.plot9, self.plot3, self.plot5]
self.plotnames = ["MetaFigure1", "MetaFigure2", "MetaFigure3", "MetaFigure4", "MetaFigure5", "MetaFigure6",
"MeatFigure7", "MetaFigure8"]
self.peakpanel = peaklistsort.PeakListCtrlPanel(panel, meta=True)
self.Bind(self.peakpanel.EVT_DELETE_SELECTION_2, self.pres.on_delete, self.peakpanel)
self.Bind(self.peakpanel.EVT_CHARGE_STATE, self.pres.on_charge_states_mud, self.peakpanel)
self.Bind(self.peakpanel.EVT_DIFFERENCES, self.pres.on_differences, self.peakpanel)
self.Bind(self.peakpanel.EVT_MASSES, self.pres.on_label_masses, self.peakpanel)
sizer.Add(self.peakpanel, 0, wx.EXPAND)
self.controls = main_controls(self, self.config, self.pres, panel, self.icon_path)
sizer.Add(self.controls, 0, wx.EXPAND)
# Set everything up
panel.SetSizer(sizer)
sizer.Fit(self)
self.CreateStatusBar(7)
self.SetStatusWidths([-1, 600, 120, 0, 230, 250, 130])
def __init__(self, parent, inputdata=None, config=None, directory=""):
wx.Frame.__init__(self, parent, title="iFAMS") # ,size=(-1,-1))
self.parent = parent
self.directory = directory
# Set up the config file
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
else:
self.config = config
# Make the menu
filemenu = wx.Menu()
menu_load_data = filemenu.Append(wx.ID_ANY, "Load Spectrum", "Loads the Mass Spectrum from a .txt file")
menu_save_fig_png = filemenu.Append(wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
menu_save_fig_pdf = filemenu.Append(wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_load_spectrum, menu_load_data)
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig_png)
self.Bind(wx.EVT_MENU, self.on_save_fig_pdf, menu_save_fig_pdf)
self.plotmenu = wx.Menu()
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
menu_bar.Append(self.plotmenu, "Plot")
self.SetMenuBar(menu_bar)
# Setup the Plots
panel = wx.Panel(self)
self.plot1 = plot1d.Plot1d(panel)
self.plot2 = plot1d.Plot1d(panel)
self.plot3 = plot1d.Plot1d(panel)
self.plot4 = plot1d.Plot1d(panel)
sizer = wx.BoxSizer(wx.VERTICAL)
plotsizer1 = wx.BoxSizer(wx.HORIZONTAL)
plotsizer2 = wx.BoxSizer(wx.HORIZONTAL)
plotsizer1.Add(self.plot1, 2, wx.EXPAND)
plotsizer1.Add(self.plot4, 0, wx.EXPAND)
plotsizer2.Add(self.plot2, 2, wx.EXPAND)
plotsizer2.Add(self.plot3, 0, wx.EXPAND)
sizer.Add(plotsizer1, 1, wx.EXPAND)
sizer.Add(plotsizer2, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
controlsizer3 = wx.BoxSizer(wx.HORIZONTAL)
controlsizer4 = wx.BoxSizer(wx.HORIZONTAL)
controlsizer5 = wx.BoxSizer(wx.HORIZONTAL)
# Set up the controls
self.ctlm0 = wx.TextCtrl(panel, value=str(0))
self.ctlwindow = wx.TextCtrl(panel, value=str(0))
self.ctlwindow1 = wx.TextCtrl(panel, value=str(0))
self.zerodata = wx.TextCtrl(panel, value=str(0))
self.overtone = wx.TextCtrl(panel, value=str(0))
self.harmavg = wx.TextCtrl(panel, value=str(0))
self.lowcharge = wx.TextCtrl(panel, value=str(0))
self.highcharge = wx.TextCtrl(panel, value=str(0))
self.mansub = wx.TextCtrl(panel, value=str(0))
controlsizer2.Add(wx.StaticText(panel, label="Minimum Frequency"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlm0, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(wx.StaticText(panel, label="Minimum Height"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlwindow, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(wx.StaticText(panel, label="Delta"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlwindow1, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer4.Add(wx.StaticText(panel, label="# of zero frequency data"), 0, wx.ALIGN_RIGHT)
controlsizer4.Add(self.zerodata, 0, wx.ALIGN_RIGHT)
controlsizer4.Add(wx.StaticText(panel, label="# of harmonics for filter"), 0, wx.ALIGN_RIGHT)
controlsizer4.Add(self.overtone, 0, wx.ALIGN_RIGHT)
controlsizer3.Add(wx.StaticText(panel, label="# of harmonics for average"), 0, wx.ALIGN_RIGHT)
controlsizer3.Add(self.harmavg, 0, wx.ALIGN_RIGHT)
controlsizer5.Add(wx.StaticText(panel, label="lowest charge state"), 0, wx.ALIGN_RIGHT)
controlsizer5.Add(self.lowcharge, 0, wx.ALIGN_RIGHT)
controlsizer5.Add(wx.StaticText(panel, label="highest charge state"), 0, wx.ALIGN_RIGHT)
controlsizer5.Add(self.highcharge, 0, wx.ALIGN_RIGHT)
controlsizer5.Add(wx.StaticText(panel, label="subunit mass"), 0, wx.ALIGN_RIGHT)
controlsizer5.Add(self.mansub, 0, wx.ALIGN_RIGHT)
recalcbutton = wx.Button(panel, label="Recalc. Maxima Finder")
controlsizer2.Add(recalcbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_calc, recalcbutton)
iFAMSbutton = wx.Button(panel, label="Run iFAMS analysis")
controlsizer.Add(iFAMSbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_SubAndCharCalc, iFAMSbutton)
Filbutton = wx.Button(panel, label="Fourier Filter")
controlsizer4.Add(Filbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_fourier_fil, Filbutton)
havgbutton = wx.Button(panel, label="Harmonic Average")
controlsizer3.Add(havgbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_harm_average, havgbutton)
self.realdatasel = wx.CheckBox(panel, label="plot real data")
controlsizer.Add(self.realdatasel, 0, wx.EXPAND)
self.Bind(wx.EVT_CHECKBOX, self.onChecked)
mancalcbutton = wx.Button(panel, label="Man Calc Subunit and Charge")
controlsizer5.Add(mancalcbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_man_calc, mancalcbutton)
sizer.Add(controlsizer, 0, wx.EXPAND)
sizer.Add(controlsizer2, 0, wx.EXPAND)
sizer.Add(controlsizer3, 0, wx.EXPAND)
sizer.Add(controlsizer4, 0, wx.EXPAND)
sizer.Add(controlsizer5, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close)
self.Centre()
# self.MakeModal(True)
self.Show(True)
self.Raise()
if inputdata is not None:
self.data = inputdata
self.makeplot()
def __init__(self, parent, data, config=None, directory=None):
wx.Frame.__init__(self, parent, title="FFT Analysis")
# Setup initial values
if directory is None:
self.directory = os.getcwd()
else:
self.directory = directory
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
self.config.discreteplot = 0
else:
self.config = config
self.config.publicationmode = 0
self.window_fwhm = 500
self.binsize = 0.5
self.wbin = 200
self.diffrange = [700, 800]
self.rawdata = data
self.rawdata[:, 1] /= np.amax(self.rawdata[:, 1])
self.xlims = [min(data[:, 0]), max(data[:, 0])]
# Make the menu
filemenu = wx.Menu()
menu_save_fig_png = filemenu.Append(wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
menu_save_fig_pdf = filemenu.Append(wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig_png)
self.Bind(wx.EVT_MENU, self.on_save_fig_pdf, menu_save_fig_pdf)
self.plotmenu = wx.Menu()
self.menuaddline = self.plotmenu.Append(wx.ID_ANY, "Add Horizontal Line",
"Add Horizontal Line at Specific Y Value")
self.Bind(wx.EVT_MENU, self.on_add_line, self.menuaddline)
self.menupeaks = self.plotmenu.Append(wx.ID_ANY, "Get Peaks",
"Get Peaks from Spectrum")
self.Bind(wx.EVT_MENU, self.on_get_peaks, self.menupeaks)
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
menu_bar.Append(self.plotmenu, "Plot")
self.SetMenuBar(menu_bar)
# Setup the GUI
displaysize = wx.GetDisplaySize()
panel = wx.Panel(self)
sizer = wx.BoxSizer(wx.VERTICAL)
plotpanel1 = wx.BoxSizer(wx.HORIZONTAL)
plotpanel2 = wx.BoxSizer(wx.HORIZONTAL)
if displaysize[0] < 1700:
figsize = (4, 3)
else:
figsize = (5, 4)
self.plot1 = plot1d.Plot1d(panel, figsize=figsize)
self.plot2 = plot2d.Plot2d(panel, figsize=figsize)
self.plot3 = plot1d.Plot1d(panel, figsize=figsize)
self.plot4 = plot1d.Plot1d(panel, figsize=figsize)
plotpanel1.Add(self.plot1, 1, flag=wx.EXPAND)
plotpanel2.Add(self.plot2, 1, flag=wx.EXPAND)
plotpanel1.Add(self.plot3, 1, flag=wx.EXPAND)
plotpanel2.Add(self.plot4, 1, flag=wx.EXPAND)
self.plot1._axes = [0.1, 0.1, 0.64, 0.8]
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlfwhm = wx.TextCtrl(panel, value=str(self.window_fwhm))
self.ctlwbin = wx.TextCtrl(panel, value=str(self.wbin))
self.ctlbinsize = wx.TextCtrl(panel, value=str(self.binsize))
controlsizer.Add(wx.StaticText(panel, label=" Window FWHM:"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlfwhm, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(wx.StaticText(panel, label=" Window every:"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlwbin, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(wx.StaticText(panel, label=" Linearization Bin Size:"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlbinsize, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlmin = wx.TextCtrl(panel, value=str(self.diffrange[0]))
self.ctlmax = wx.TextCtrl(panel, value=str(self.diffrange[1]))
controlsizer2.Add(wx.StaticText(panel, label=" Min Difference:"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlmin, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(wx.StaticText(panel, label=" Max Difference:"), 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlmax, 0, wx.ALIGN_CENTER_VERTICAL)
label = "Replot"
replotbutton = wx.Button(panel, label=label)
controlsizer2.Add(replotbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.makeplot, replotbutton)
comparebutton = wx.Button(panel, label="Compare")
controlsizer2.Add(comparebutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_compare_regions, comparebutton)
self.compareclicks = 0
self.comparetext = wx.StaticText(panel, label="Click to activate compare mode")
controlsizer2.Add(self.comparetext, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.Add(plotpanel1, 0, wx.EXPAND)
sizer.Add(plotpanel2, 0, wx.EXPAND)
sizer.Add(controlsizer, 0, wx.EXPAND)
sizer.Add(controlsizer2, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close)
self.makeplot()
self.Centre()
# self.MakeModal(True)
self.Show(True)
def __init__(self,
parent,
datalist,
xvals=None,
config=None,
directory=None):
wx.Frame.__init__(self, parent, title="FFT Analysis")
# Setup initial values
if directory is None:
self.directory = os.getcwd()
else:
self.directory = directory
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
self.config.discreteplot = 0
else:
self.config = config
self.config.publicationmode = 0
self.binsize = 0.5
self.diffrange = [740, 770]
if xvals is None:
xvals = np.arange(0, len(datalist))
self.xvals = xvals
self.datalist = np.array(datalist)
mins = []
maxes = []
for d in self.datalist:
d[:, 1] /= np.amax(d[:, 1])
mins.append(np.amin(d[:, 0]))
maxes.append(np.amax(d[:, 0]))
self.xlims = [min(mins), max(maxes)]
self.colors = self.config.get_colors(len(self.datalist))
# Make the menu
filemenu = wx.Menu()
menu_save_fig_png = filemenu.Append(
wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
menu_save_fig_pdf = filemenu.Append(
wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig_png)
self.Bind(wx.EVT_MENU, self.on_save_fig_pdf, menu_save_fig_pdf)
self.plotmenu = wx.Menu()
self.menuaddline = self.plotmenu.Append(
wx.ID_ANY, "Add Horizontal Line",
"Add Horizontal Line at Specific Y Value")
self.Bind(wx.EVT_MENU, self.on_add_line, self.menuaddline)
#self.menupeaks = self.plotmenu.Append(wx.ID_ANY, "Get Peaks",
# "Get Peaks from Spectrum")
#self.Bind(wx.EVT_MENU, self.on_get_peaks, self.menupeaks)
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
menu_bar.Append(self.plotmenu, "Plot")
self.SetMenuBar(menu_bar)
# Setup the GUI
displaysize = wx.GetDisplaySize()
panel = wx.Panel(self)
sizer = wx.BoxSizer(wx.VERTICAL)
plotpanel1 = wx.BoxSizer(wx.HORIZONTAL)
plotpanel2 = wx.BoxSizer(wx.HORIZONTAL)
if displaysize[0] < 1700:
figsize = (4, 3)
else:
figsize = (5, 4)
self.plot1 = plot1d.Plot1d(panel, figsize=figsize)
self.plot2 = plot2d.Plot2d(panel, figsize=figsize)
self.plot3 = plot1d.Plot1d(panel, figsize=figsize)
self.plot4 = plot1d.Plot1d(panel, figsize=figsize)
plotpanel1.Add(self.plot1, 1, flag=wx.EXPAND)
plotpanel2.Add(self.plot2, 1, flag=wx.EXPAND)
plotpanel1.Add(self.plot3, 1, flag=wx.EXPAND)
plotpanel2.Add(self.plot4, 1, flag=wx.EXPAND)
self.plot1._axes = [0.1, 0.1, 0.64, 0.8]
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlminmz = wx.TextCtrl(panel, value=str(self.xlims[0]))
self.ctlmaxmz = wx.TextCtrl(panel, value=str(self.xlims[1]))
self.ctlbinsize = wx.TextCtrl(panel, value=str(self.binsize))
controlsizer.Add(wx.StaticText(panel, label=" Min m/z:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlminmz, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(wx.StaticText(panel, label=" Max m/z:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlmaxmz, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(
wx.StaticText(panel, label=" Linearization Bin Size:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlbinsize, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlmin = wx.TextCtrl(panel, value=str(self.diffrange[0]))
self.ctlmax = wx.TextCtrl(panel, value=str(self.diffrange[1]))
controlsizer2.Add(wx.StaticText(panel, label=" Min Difference:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlmin, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(wx.StaticText(panel, label=" Max Difference:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlmax, 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlsep = wx.TextCtrl(panel, value=str(self.config.separation))
controlsizer2.Add(wx.StaticText(panel, label=" Plot Separation:"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer2.Add(self.ctlsep, 0, wx.ALIGN_CENTER_VERTICAL)
label = "Replot"
replotbutton = wx.Button(panel, label=label)
controlsizer2.Add(replotbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.makeplot, replotbutton)
sizer.Add(plotpanel1, 0, wx.EXPAND)
sizer.Add(plotpanel2, 0, wx.EXPAND)
sizer.Add(controlsizer, 0, wx.EXPAND)
sizer.Add(controlsizer2, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close)
self.makeplot()
self.Centre()
# self.MakeModal(True)
self.Show(True)
def __init__(self,
parent,
data_list,
config=None,
yvals=None,
pks=None,
value=None,
directory=None):
"""
Creates a window for visualizing high-mass mass defects.
:param parent: Passed to wx.Frame
:param data_list: List of mass distribution data.
:param config: UniDecConfig object
:param yvals: List of titles for each mass distribution in data_list
:param pks: Peaks object
:param value: Kendrick reference mass (default is 760.076, the mass of POPC)
:param directory: Directory to save files to (default is os.getcwd())
:return: None
"""
wx.Frame.__init__(self, parent, title="Mass Defect") # ,size=(-1,-1))
# Setup initial values
if directory is None:
self.directory = os.getcwd()
else:
self.directory = directory
self.parent = parent
self.m0 = deepcopy(value)
if self.m0 is None:
self.m0 = 760.076
if config is None:
self.config = unidecstructure.UniDecConfig()
self.config.initialize()
self.config.discreteplot = 0
self.config.cmap = u"jet"
self.config.peakcmap = u"rainbow"
self.config.separation = 0.025
else:
self.config = config
self.config.publicationmode = 0
self.pos = -1
self.yvals = yvals
self.ylab = "Normalized Mass Defect"
if self.config.defectparams is not None:
p = self.config.defectparams
self.nbins = p[0]
self.transformmode = p[1]
self.centermode = p[2]
self.xtype = p[3]
else:
self.nbins = 50
self.transformmode = 1
self.centermode = 1
self.xtype = 0
self.factor = 1
self.xlab = ""
self.outfname = os.path.splitext(self.config.filename)[0]
if self.outfname is not "":
self.outfname += "_"
try:
self.datalist = [data_list[0]]
except:
self.datalist = data_list[0]
for i in range(1, len(data_list)):
self.datalist.append(ud.mergedata(data_list[0], data_list[i]))
self.datalist = np.array(self.datalist)
if self.yvals is not None:
try:
self.yvals = np.array(self.yvals, dtype="float")
except:
self.yvals = np.arange(0, len(self.datalist))
self.datasum = np.transpose(
[self.datalist[0, :, 0],
np.sum(self.datalist[:, :, 1], axis=0)])
print("Data list shape:", self.datalist.shape)
# Make the menu
filemenu = wx.Menu()
if self.datalist.shape[0] > 1:
extractwindow = filemenu.Append(
wx.ID_ANY, "Extract Mass Defect Values",
"Open Window to Extract Mass Defect Values")
self.Bind(wx.EVT_MENU, self.on_extract_window, extractwindow)
filemenu.AppendSeparator()
menu_save_fig_png = filemenu.Append(
wx.ID_ANY, "Save Figures as PNG",
"Save all figures as PNG in central directory")
menu_save_fig_pdf = filemenu.Append(
wx.ID_ANY, "Save Figures as PDF",
"Save all figures as PDF in central directory")
self.Bind(wx.EVT_MENU, self.on_save_fig, menu_save_fig_png)
self.Bind(wx.EVT_MENU, self.on_save_fig_pdf, menu_save_fig_pdf)
self.plotmenu = wx.Menu()
self.menuaddline = self.plotmenu.Append(
wx.ID_ANY, "Add Horizontal Line",
"Add Horizontal Line at Specific Y Value")
self.menufit = self.plotmenu.Append(wx.ID_ANY, "Fit Peaks",
"Fit total mass defect peaks")
self.menupeaks = self.plotmenu.Append(wx.ID_ANY, "Label Peaks",
"Label peaks")
self.Bind(wx.EVT_MENU, self.on_add_line, self.menuaddline)
self.Bind(wx.EVT_MENU, self.on_fit, self.menufit)
self.Bind(wx.EVT_MENU, self.on_label_peaks, self.menupeaks)
menu_bar = wx.MenuBar()
menu_bar.Append(filemenu, "&File")
menu_bar.Append(self.plotmenu, "Plot")
self.SetMenuBar(menu_bar)
# Setup the GUI
panel = wx.Panel(self)
self.plot1 = plot1d.Plot1d(panel)
self.plot2 = plot2d.Plot2d(panel)
self.plot3 = plot1d.Plot1d(panel)
self.plot4 = plot1d.Plot1d(panel)
if self.datalist.shape[0] > 1:
self.flag2 = True
self.plot5 = plot1d.Plot1d(panel)
self.plot6 = plot2d.Plot2d(panel)
else:
self.flag2 = False
self.plot5 = None
self.plot6 = None
sizer = wx.BoxSizer(wx.VERTICAL)
plotsizer1 = wx.BoxSizer(wx.HORIZONTAL)
plotsizer2 = wx.BoxSizer(wx.HORIZONTAL)
plotsizer1.Add(self.plot1, 2, wx.EXPAND)
plotsizer1.Add(self.plot4, 0, wx.EXPAND)
plotsizer2.Add(self.plot2, 2, wx.EXPAND)
plotsizer2.Add(self.plot3, 0, wx.EXPAND)
if self.flag2:
plotsizer1.Add(self.plot5, 0, wx.EXPAND)
plotsizer2.Add(self.plot6, 0, wx.EXPAND)
sizer.Add(plotsizer1, 1, wx.EXPAND)
sizer.Add(plotsizer2, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
self.ctlm0 = wx.TextCtrl(panel, value=str(self.m0))
self.ctlwindow = wx.TextCtrl(panel, value=str(self.nbins))
controlsizer.Add(wx.StaticText(panel, label="Kendrick Mass"), 0,
wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlm0, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(wx.StaticText(panel, label="Number of Defect Bins"),
0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlwindow, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
if len(data_list) > 1:
label = "Back"
else:
label = "Replot"
backbutton = wx.Button(panel, label=label)
controlsizer2.Add(backbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_back, backbutton)
if len(data_list) > 1:
nextbutton = wx.Button(panel, label="Next")
controlsizer2.Add(nextbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_next, nextbutton)
totalbutton = wx.Button(panel, label="Total")
controlsizer2.Add(totalbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.makeplottotal, totalbutton)
else:
if not ud.isempty(pks):
self.pks = pks
peaksbutton = wx.Button(panel, label="Plot Peaks")
controlsizer2.Add(peaksbutton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_peaks, peaksbutton)
self.radiobox = wx.RadioBox(panel,
choices=["Integrate", "Interpolate"],
label="Type of Transform")
controlsizer.Add(self.radiobox, 0, wx.EXPAND)
self.radiobox.SetSelection(self.transformmode)
self.radiobox2 = wx.RadioBox(panel,
choices=["-0.5:0.5", "0:1"],
label="Range")
controlsizer.Add(self.radiobox2, 0, wx.EXPAND)
self.radiobox2.SetSelection(self.centermode)
self.radiobox3 = wx.RadioBox(panel,
choices=["Normalized", "Mass (Da)"],
label="Mass Defect Units")
controlsizer.Add(self.radiobox3, 0, wx.EXPAND)
self.radiobox3.SetSelection(self.xtype)
sizer.Add(controlsizer, 0, wx.EXPAND)
sizer.Add(controlsizer2, 0, wx.EXPAND)
panel.SetSizer(sizer)
sizer.Fit(self)
self.Bind(wx.EVT_CLOSE, self.on_close)
try:
self.makeplottotal(0)
except Exception as e:
self.on_next(0)
self.Centre()
# self.MakeModal(True)
self.Show(True)
self.Raise()
def __init__(self, parent, title, path=None, *args, **kwargs):
wx.Frame.__init__(self, parent, title=title) # ,size=(200,-1))
self.CreateStatusBar(4)
self.SetStatusWidths([-1, 150, 150, 150])
pub.subscribe(self.on_motion, 'newxy')
pub.subscribe(self.on_selection, 'scans_selected')
self.filemenu = wx.Menu()
self.menuOpen = self.filemenu.Append(wx.ID_SAVE, "Open File", "Open File")
self.Bind(wx.EVT_MENU, self.on_open, self.menuOpen)
self.menuBar = wx.MenuBar()
self.menuBar.Append(self.filemenu, "&File")
self.SetMenuBar(self.menuBar)
self.panel = wx.Panel(self)
self.panel.SetDropTarget(ChromDropTarget(self))
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.inputsizer = wx.BoxSizer(wx.HORIZONTAL)
self.plotc = plot1d.Plot1d(self.panel)
self.plotm = plot1d.Plot1d(self.panel)
self.inputsizer.Add(self.plotc)
self.inputsizer.Add(self.plotm)
self.sizer.Add(self.inputsizer, 1, wx.EXPAND)
self.ctlsizer = wx.BoxSizer(wx.HORIZONTAL)
self.runbutton = wx.Button(self.panel, label="Run UniDec")
self.Bind(wx.EVT_BUTTON, self.on_unidec_run, self.runbutton)
self.ctlsizer.Add(self.runbutton)
self.exportbutton = wx.Button(self.panel, label="Export m/z data as:")
self.Bind(wx.EVT_BUTTON, self.export_mz_file, self.exportbutton)
self.ctlsizer.Add(self.exportbutton)
self.ctlfname = wx.TextCtrl(self.panel, value="", size=(100, 20))
self.ctlsizer.Add(self.ctlfname, 1, wx.EXPAND)
self.autobutton = wx.Button(self.panel, label="Autoexport in steps of:")
self.Bind(wx.EVT_BUTTON, self.on_autoexport, self.autobutton)
self.ctlsizer.Add(self.autobutton)
self.ctlmin = wx.TextCtrl(self.panel, value="2", size=(100, 20))
self.ctlsizer.Add(self.ctlmin, 0)
self.ctlsizer.Add(wx.StaticText(self.panel, label="minutes. Start label at:"), 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlstart = wx.TextCtrl(self.panel, value="40", size=(100, 20))
self.ctlsizer.Add(self.ctlstart, 0)
self.ctlsizer.Add(wx.StaticText(self.panel, label=" and increment label by:"), 0, wx.ALIGN_CENTER_VERTICAL)
self.ctlincr = wx.TextCtrl(self.panel, value="10", size=(100, 20))
self.ctlsizer.Add(self.ctlincr, 0)
self.sizer.Add(self.ctlsizer, 0, wx.EXPAND)
self.panel.SetSizer(self.sizer)
self.sizer.Fit(self)
self.Centre()
self.Show(True)
self.eng = ChromEngine()
self.outputfile = None
self.udwin = None
self.scans = None
self.autoparams = None
if path is not None:
self.open_file(path)
