def initialize(self):
"""
Initialize Config, DataContainer, and Peaks
:return: None
"""
self.config = unidecstructure.UniDecConfig()
self.clear_history()
self.config.initialize_system_paths()
self.reset_config()
self.data = unidecstructure.DataContainer()
self.pks = peakstructure.Peaks()
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, 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=None,
filelist=None,
config=None,
):
"""
"""
wx.Frame.__init__(self, parent,
title="Mass Defect Comparison") # ,size=(-1,-1))
file1 = None
file2 = None
if datalist is None:
if filelist is None:
if config is None:
print(
"ERROR: No data supplied to Mass Defect Compare Window"
)
return
else:
self.config = config
file1 = self.config.defectcomparefiles[0]
file2 = self.config.defectcomparefiles[1]
else:
file1 = filelist[0]
file2 = filelist[1]
self.get_data(file1, file2)
self.file1 = file1
self.file2 = file2
self.parent = parent
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.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 = self.config.outfname
if self.outfname != "":
self.outfname += "_"
self.total = False
self.notchanged = False
'''
# 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.menuaddmultiline = self.plotmenu.Append(wx.ID_ANY, "Add Multiple Lines",
"Add Multiple Horizontal Lines at Specific Y Values")
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.menulinreg = self.plotmenu.Append(wx.ID_ANY, "Linear Regression",
"Linear Regression")
self.menucom = self.plotmenu.Append(wx.ID_ANY, "Center of Mass", "Center of Mass")
self.Bind(wx.EVT_MENU, self.on_add_line, self.menuaddline)
self.Bind(wx.EVT_MENU, self.on_add_multilines, self.menuaddmultiline)
self.Bind(wx.EVT_MENU, self.on_fit, self.menufit)
self.Bind(wx.EVT_MENU, self.on_label_peaks, self.menupeaks)
self.Bind(wx.EVT_MENU, self.on_linear_regression, self.menulinreg)
self.Bind(wx.EVT_MENU, self.on_com, self.menucom)
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 = plot2d.Plot2d(panel)
self.plot2 = plot2d.Plot2d(panel)
self.plot3 = ColorPlot.ColorPlot2D(panel)
# self.plot4 = plot1d.Plot1d(panel)
sizer = wx.BoxSizer(wx.VERTICAL)
# plotsizer1 = wx.BoxSizer(wx.HORIZONTAL)
plotsizer2 = wx.BoxSizer(wx.HORIZONTAL)
# plotsizer1.Add(self.plot4, 0, wx.EXPAND)
plotsizer2.Add(self.plot1, 2, wx.EXPAND)
plotsizer2.Add(self.plot2, 2, wx.EXPAND)
plotsizer2.Add(self.plot3, 2, wx.EXPAND)
# sizer.Add(plotsizer1, 1, wx.EXPAND)
sizer.Add(plotsizer2, 1, wx.EXPAND)
controlsizer = wx.BoxSizer(wx.HORIZONTAL)
self.ctlf1 = wx.TextCtrl(panel, value=str(self.file1), size=(1500, 25))
self.f1button = wx.Button(panel, label="File 1: ")
self.Bind(wx.EVT_BUTTON, self.on_f1button, self.f1button)
controlsizer.Add(self.f1button, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer.Add(self.ctlf1, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1 = wx.BoxSizer(wx.HORIZONTAL)
self.ctlf2 = wx.TextCtrl(panel, value=str(self.file2), size=(1500, 25))
self.f2button = wx.Button(panel, label="File 2: ")
self.Bind(wx.EVT_BUTTON, self.on_f2button, self.f2button)
controlsizer1.Add(self.f2button, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer1.Add(self.ctlf2, 0, wx.ALIGN_CENTER_VERTICAL)
controlsizer2 = wx.BoxSizer(wx.HORIZONTAL)
label = "Replot"
ReplotButton = wx.Button(panel, label=label)
controlsizer2.Add(ReplotButton, 0, wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.on_replot, ReplotButton)
'''
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(controlsizer1, 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(0)
self.Centre()
# self.MakeModal(True)
self.Show(True)
self.Raise()
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,
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, 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, 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)