UniDec
Universal Deconvolution of Mass and Ion Mobility Spectra
Public Member Functions | Public Attributes | List of all members
UniDec.unidec_modules.nativez.NativeZ Class Reference
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Public Member Functions

def __init__ (self, args, kwargs)
 
def initialize_interface (self, massaxis, chargeaxis, igrid, config, pks)
 
def update (self, e)
 
def on_replot (self, e)
 
def plot_zoffs (self)
 
def make_plot_7 (self, e)
 
def on_delete (self, event)
 
def fit (self, e)
 
def on_reset (self, e)
 
def update_list (self)
 
def populate_list (self, e)
 
def on_add (self, e)
 
def make_f_array
 
def fast_extract (self, f, width, eshape)
 
def get_maxima (self)
 
def extract (self, e)
 
def peak_extract (self)
 
def save_figures (self, e)
 
def on_close (self, e)
 
def on_close_cancel (self, e)
 

Public Attributes

 figsize
 
 config
 
 pks
 
 zoffs
 
 massoffset
 
 massaxis
 
 chargeaxis
 
 igrid
 
 offset_totals
 
 offset_grid
 
 plot1
 
 plot2
 
 plot3
 
 plot4
 
 plot5
 
 plot6
 
 plot7
 
 zlistctrl
 
 ctlmassoffset
 
 ctlfilt
 

Constructor & Destructor Documentation

def UniDec.unidec_modules.nativez.NativeZ.__init__ (   self,
  args,
  kwargs 
)
Create a dialog for examining the native charge/mass relationship and extraction specific CID states.
Tries to create a big window, but will rescale to smaller if the screen is too small.
:param args: Passed to wx.Dialog
:param kwargs: Passed to wx.Dialog
:return: None

Member Function Documentation

def UniDec.unidec_modules.nativez.NativeZ.extract (   self,
  e 
)
Extract the mass distribution at each offset value, plot it, and write the outputs.
Call self.peak_extract
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.fast_extract (   self,
  f,
  width,
  eshape 
)
Extract the intensity data for a specific charge offset from self.igrid. Mask all of the other data.
:param f: Charge offset
:param width: Width of the extraction (+/- from charge offset)
:param eshape: Shape of the extraction
0 = Box (+/- is a hard cutoff)
1 = Gaussian (+/- is std deviation of Gaussian)
:return: masked intensity values from self.igrid for a specific charge offset

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def UniDec.unidec_modules.nativez.NativeZ.fit (   self,
  e 
)
Fit the offset totals to a series of overlapping Gaussians.
Update the plots and listctrl from the result.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.get_maxima (   self)
Detect peaks in self.offset_totals (the total extracted intensitites) and set default parameters.
Plot the results.
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.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

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def UniDec.unidec_modules.nativez.NativeZ.make_f_array (   self,
  minval,
  maxval,
  zwidth = 1 
)
Get the global offset parameters for the massaxis and chargeaxis.
Create a grid of mass and charge value.
Calculate the charge offset at each point and store it at self.offset_grid.
Calculate the total intensity for each charge offset value +/- zwidth (default is 1).
:param minval: Minimum charge offset value
:param maxval: Maximum charge offset value
:param zwidth: Tolerance window for the offset to be summed.
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.make_plot_7 (   self,
  e 
)
Plot the 2D mass v. charge plot.
Add colored charge offset bands on top of the plot.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.on_add (   self,
  e 
)
Add a blank line to self.zlistctrl.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.on_close (   self,
  e 
)
Close the window and update the parameters
:param e:
:return:

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def UniDec.unidec_modules.nativez.NativeZ.on_close_cancel (   self,
  e 
)
Close the window but do not update the parameters.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.on_delete (   self,
  event 
)
Delete item from the list ctrl.
:param event: wx.Button event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.on_replot (   self,
  e 
)
Update the parameters and replot the results.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.on_reset (   self,
  e 
)
Reset the listctrl and plots to the default states.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.peak_extract (   self)
Extract the values for local max (height) and area for peaks in pks from each zoff.extract.
Plot the results.
Write the results to files.
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.plot_zoffs (   self)
Plot the total charge offsets along with fits. Call self.make_plot_7.
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.populate_list (   self,
  e 
)
Add data from self.zoffs to self.zlistctrl.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.save_figures (   self,
  e 
)
Save the figures as pdfs in the unidec folder.
:param e: Unused event
:return: None

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def UniDec.unidec_modules.nativez.NativeZ.update (   self,
  e 
)
Update self.zoffs from the self.zlistctrl. Update the intensities for each zoffset value.
:param e:
:return:

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def UniDec.unidec_modules.nativez.NativeZ.update_list (   self)
Update self.zlistctrl from self.zoffs.
:return: None

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Member Data Documentation

UniDec.unidec_modules.nativez.NativeZ.chargeaxis
UniDec.unidec_modules.nativez.NativeZ.config
UniDec.unidec_modules.nativez.NativeZ.ctlfilt
UniDec.unidec_modules.nativez.NativeZ.ctlmassoffset
UniDec.unidec_modules.nativez.NativeZ.figsize
UniDec.unidec_modules.nativez.NativeZ.igrid
UniDec.unidec_modules.nativez.NativeZ.massaxis
UniDec.unidec_modules.nativez.NativeZ.massoffset
UniDec.unidec_modules.nativez.NativeZ.offset_grid
UniDec.unidec_modules.nativez.NativeZ.offset_totals
UniDec.unidec_modules.nativez.NativeZ.pks
UniDec.unidec_modules.nativez.NativeZ.plot1
UniDec.unidec_modules.nativez.NativeZ.plot2
UniDec.unidec_modules.nativez.NativeZ.plot3
UniDec.unidec_modules.nativez.NativeZ.plot4
UniDec.unidec_modules.nativez.NativeZ.plot5
UniDec.unidec_modules.nativez.NativeZ.plot6
UniDec.unidec_modules.nativez.NativeZ.plot7
UniDec.unidec_modules.nativez.NativeZ.zlistctrl
UniDec.unidec_modules.nativez.NativeZ.zoffs

The documentation for this class was generated from the following file: