spike.Interactive package

Submodules

spike.Interactive.FTICR_INTER copy module

spike.Interactive.FTICR_INTER module

A tool to display 2D FT-ICR data-sets

to be embedded in jupyter notebook

First version MAD jan 2019 preliminary and not fully tested !

class spike.Interactive.FTICR_INTER.Calib(data)

Bases: object

a simple tool to show and modify calibration cste

back(event)

update(event)

class spike.Interactive.FTICR_INTER.MR(name, report=True, Debug=False)

Bases: object

this class handles multiresolution datasets

col(i)

return a column with coordinate in index

colmz(i)

return a column with coordinate in m/z

compute_absmax()

computes largest point from smaller resolution, and propagates

load()

load from file

report()

report object content

row(i)

return a row with coordinate in index

rowmz(i)

return a row with coordinate in m/z

to_display(zoom=((0, 10000000.0), (0, 10000000.0)), verbose=False)

computes and return which dataset to display at a given zoom and scale level” in: zoom = ((F1low, F1up), (F2low,F2up)) - in m/z

out: a tuple (data, zoomwindow), where data is a NPKData and zoomwindow an eventually recalibrated zoom window

so, if DATA is an MR() object and Zoom a defined window in m/z ((F1low, F1up), (F2low,F2up)) the sequence:

datasel, zz = DATA.to_display(Zoom) datasel.display(zoom=zz, scale=…)

will display the selected zone with the best possible resolution

class spike.Interactive.FTICR_INTER.MR2(name, figsize=None, report=True, show=True, Debug=False)

Bases: spike.Interactive.FTICR_INTER.MR_interact

back(*arg)

forw(*arg)

class spike.Interactive.FTICR_INTER.MR_interact(name, figsize=None, report=True, show=True, Debug=False)

Bases: spike.Interactive.FTICR_INTER.MR

I1D()

back(*arg)

bb(name, desc, action, layout=None, tooltip='')

build button

check_fig()

check_fig1D()

display(zoom=None, scale=None, redraw=None)

display1D()

down(b, factor=1.44)

ext_box()

forw(*arg)

fullzoom()

left(b, factor=1.44)

reset(b)

reset_track()

right(b, factor=1.44)

scale1(b)

scaledown(b)

scaleup(b)

show()

actually show the graphical tool and the interactive spectrum

up(b, factor=1.44)

update()

zoom

zoom_box()

zoom_in(b, factor=1.44)

z_in: waft = wbef/factor => waft*factor = wbef

dw = wbef/factor-wbef = wbef*(1-factor) dw = waft*factor*(1-factor)

zoom_out(b, factor=1.44)

z_in: dw = waft*factor*(1-factor) z_out:dw = wbef*(factor*(1-factor))

zoomwidth()

class spike.Interactive.FTICR_INTER.MSPeaker(npkd, pkname)

Bases: object

a peak-picker for MS experiments

display(event={'name': 'value'})

display spectrum and peaks

done(event)

exit GUI

pickpeak(event)

interactive wrapper to peakpick

pkexport(event)

exports the peaklist to file

pklist()

creates peaklist

pkprint(event)

pp()

do the peak-picking calling pp().centroid()

class spike.Interactive.FTICR_INTER.SpforSuper(i, name)

Bases: object

a holder for SuperImpose

display()

class spike.Interactive.FTICR_INTER.SuperImpose(base=None, filetype='*.msh5', N=None)

Bases: object

a tool to superimpose spectra

Show()

copy(event)

display(event)

spike.Interactive.INTER module

A set of utilities to use spike in NMR or FTMS within jupyter

First version MAD june 2017 preliminary and not fully tested !

class spike.Interactive.INTER.AvProc1D(filename='')

Bases: object

Detailed 1D NMR Processing

apmin_select(e)

apod()

apod_select(e)

display()

load()

process(e)

show()

show_apod(e)

class spike.Interactive.INTER.FileChooser(base=None, filetype=['fid', 'ser'], mode='r', show=True)

Bases: object

a simple file chooser for Jupyter - obsolete - not used

basename

the basename of the chosen file

dirlist()

dirname

the final dirname containing the chosen file

file

the chosen complete filename

filelist()

nmrname

the final dirname containing the chosen file for TopSpin files

setdir(e)

show()

updir(e)

wob(e)

class spike.Interactive.INTER.NMRIntegrate(npkd)

Bases: object

an integrator for NMR experiments

display(event)

refresh display from event

int()

do the integration

integrate(event)

integrate from event

on_Apply(b)

on_cancel(b)

print(event)

set_value(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER.NMRPeaker(npkd)

Bases: object

a peak-picker for NMR experiments

display(event)

interactive wrapper to peakpick

on_Apply(b)

on_cancel(b)

pickpeak(event)

interactive wrapper to peakpick

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp()

do the peak-picking calling pp().centroid()

zm

returns the zoom window in ppm

class spike.Interactive.INTER.Phaser1D(data)

Bases: object

An interactive phaser in 1D NMR

Phaser1D(spectrum)

best when in %matplotlib inline

close_all()

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

apply phase and display

ppivot()

converts from pivot values to centered ones

class spike.Interactive.INTER.Phaser2D(data)

Bases: object

An interactive phaser in 2D NMR

Phaser2D(spec)

best when in %matplotlib inline

close()

display(todisplay=None)

display either the current data or the one provided - red and blue

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

compute phase and display

class spike.Interactive.INTER.Show1D(data, title=None, figsize=None)

Bases: object

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

close()

disp()

ob(event)

observe events and display

on_done(b)

class spike.Interactive.INTER.Show1Dplus(data, title=None)

Bases: object

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

ob(event)

observe events and display

on_done(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER.Show2D(data, title=None, figsize=None)

Bases: object

A display for 2D NMR with a scale cursor Show2D(spectrum) where spectrum is a NPKData object - special display for DOSY.

disp(new=False)

ob(event)

observe events and display

on_done(b)

class spike.Interactive.INTER.Show2Dplus(data, title=None)

Bases: object

A VERY preliminary minimimum interactive display for 2D NMR

Show2D(spectrum)

disp(new=False)

fullzoom()

ob(event)

observe events and display

on_done(b)

zoom_box()

class spike.Interactive.INTER.SimpleZoom(**kwargs)

Bases: ipywidgets.widgets.widget_box.HBox

ob(event)

observe changes and set values

zfull(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER.baseline1D(data, figsize=None)

Bases: spike.Interactive.INTER.Show1D

close()

corrected()

correction()

returns the correction to apply as a numpy array

disp()

on_auto(e)

automatically set baseline points

on_cancel(e)

on_done(e)

on_set(e)

add baseline points at selector

on_unset(e)

remove baseline points closest from selector

selpos()

returns selector pos in ppm

class spike.Interactive.INTER.baseline2D_F2(data, figsize=None)

Bases: spike.Interactive.INTER.baseline1D

on_done(e)

spike.Interactive.INTER.hidecode(initial='show', message=True)

this func adds a button to hide/show the code on a jupyter page initial is either ‘show’ or ‘hide’ see: https://stackoverflow.com/questions/27934885/how-to-hide-code-from-cells-in-ipython-notebook-visualized-with-nbviewer/28073228#28073228

spike.Interactive.INTER.jsalert(msg)

send a javascript alert

spike.Interactive.INTER_res module

A set of utilities to use spike in NMR or FTMS within jupyter

First version MAD june 2017 preliminary and not fully tested !

class spike.Interactive.INTER_res.AvProc1D(filename='')

Bases: object

Detailed 1D NMR Processing

apmin_select(e)

apod()

apod_select(e)

display()

load()

process(e)

show()

show_apod(e)

class spike.Interactive.INTER_res.FileChooser(base=None, filetype=['fid', 'ser'], mode='r', show=True)

Bases: object

a simple file chooser for Jupyter - obsolete - not used

basename

the basename of the chosen file

dirlist()

dirname

the final dirname containing the chosen file

file

the chosen complete filename

filelist()

nmrname

the final dirname containing the chosen file for TopSpin files

setdir(e)

show()

updir(e)

wob(e)

class spike.Interactive.INTER_res.NMRIntegrate(npkd)

Bases: object

an integrator for NMR experiments

display(event)

refresh display from event

int()

do the integration

integrate(event)

integrate from event

on_Apply(b)

on_cancel(b)

print(event)

set_value(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_res.NMRPeaker(npkd)

Bases: object

a peak-picker for NMR experiments

display(event)

interactive wrapper to peakpick

on_Apply(b)

on_cancel(b)

pickpeak(event)

interactive wrapper to peakpick

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp()

do the peak-picking calling pp().centroid()

zm

returns the zoom window in ppm

class spike.Interactive.INTER_res.Phaser1D(data)

Bases: object

An interactive phaser in 1D NMR

Phaser1D(spectrum)

best when in %matplotlib inline

close_all()

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

apply phase and display

ppivot()

converts from pivot values to centered ones

zfull(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_res.Phaser2D(data)

Bases: object

An interactive phaser in 2D NMR

Phaser2D(spec)

best when in %matplotlib inline

close()

display(todisplay=None)

display either the current data or the one provided - red and blue

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

compute phase and display

class spike.Interactive.INTER_res.Show1D(data, title=None)

Bases: object

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

ob(event)

observe events and display

on_done(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_res.Show2D(data, title=None)

Bases: object

A display for 2D NMR with a scale cursor Show2D(spectrum) where spectrum is a NPKData object

disp(new=False)

ob(event)

observe events and display

on_done(b)

class spike.Interactive.INTER_res.Show2Dplus(data, title=None)

Bases: object

A VERY preliminary minimimum interactive display for 2D NMR

Show2D(spectrum)

disp(new=False)

fullzoom()

ob(event)

observe events and display

on_done(b)

zoom_box()

class spike.Interactive.INTER_res.SimpleZoom(**kwargs)

Bases: ipywidgets.widgets.widget_box.HBox

ob(event)

observe changes and set values

zfull(b)

zm

returns the zoom window in ppm

spike.Interactive.INTER_res.hidecode(initial='show', message=True)

this func adds a button to hide/show the code on a jupyter page initial is either ‘show’ or ‘hide’ see: https://stackoverflow.com/questions/27934885/how-to-hide-code-from-cells-in-ipython-notebook-visualized-with-nbviewer/28073228#28073228

spike.Interactive.INTER_vrai module

A set of utilities to use spike in NMR or FTMS within jupyter

First version MAD june 2017 preliminary and not fully tested !

class spike.Interactive.INTER_vrai.AvProc1D(filename='')

Bases: object

Detailed 1D NMR Processing

apmin_select(e)

apod()

apod_select(e)

display()

load()

process(e)

show()

show_apod(e)

class spike.Interactive.INTER_vrai.FileChooser(base=None, filetype=['fid', 'ser'], mode='r', show=True)

Bases: object

a simple file chooser for Jupyter - obsolete - not used

basename

the basename of the chosen file

dirlist()

dirname

the final dirname containing the chosen file

file

the chosen complete filename

filelist()

nmrname

the final dirname containing the chosen file for TopSpin files

setdir(e)

show()

updir(e)

wob(e)

class spike.Interactive.INTER_vrai.NMRIntegrate(npkd)

Bases: object

an integrator for NMR experiments

display(event)

refresh display from event

int()

do the integration

integrate(event)

integrate from event

on_Apply(b)

on_cancel(b)

print(event)

set_value(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_vrai.NMRPeaker(npkd)

Bases: object

a peak-picker for NMR experiments

display(event)

interactive wrapper to peakpick

on_Apply(b)

on_cancel(b)

pickpeak(event)

interactive wrapper to peakpick

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp()

do the peak-picking calling pp().centroid()

zm

returns the zoom window in ppm

class spike.Interactive.INTER_vrai.Phaser1D(data)

Bases: object

An interactive phaser in 1D NMR

Phaser1D(spectrum)

best when in %matplotlib inline

close_all()

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

apply phase and display

ppivot()

converts from pivot values to centered ones

zfull(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_vrai.Phaser2D(data)

Bases: object

An interactive phaser in 2D NMR

Phaser2D(spec)

best when in %matplotlib inline

close()

display(todisplay=None)

display either the current data or the one provided - red and blue

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

phase()

compute phase and display

class spike.Interactive.INTER_vrai.Show1D(data, title=None)

Bases: object

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

ob(event)

observe events and display

on_done(b)

zm

returns the zoom window in ppm

class spike.Interactive.INTER_vrai.Show2D(data, title=None)

Bases: object

A display for 2D NMR with a scale cursor Show2D(spectrum) where spectrum is a NPKData object - special display for DOSY.

disp(new=False)

ob(event)

observe events and display

on_done(b)

class spike.Interactive.INTER_vrai.Show2Dplus(data, title=None)

Bases: object

A VERY preliminary minimimum interactive display for 2D NMR

Show2D(spectrum)

disp(new=False)

fullzoom()

ob(event)

observe events and display

on_done(b)

zoom_box()

class spike.Interactive.INTER_vrai.SimpleZoom(**kwargs)

Bases: ipywidgets.widgets.widget_box.HBox

ob(event)

observe changes and set values

zfull(b)

zm

returns the zoom window in ppm

spike.Interactive.INTER_vrai.hidecode(initial='show', message=True)

this func adds a button to hide/show the code on a jupyter page initial is either ‘show’ or ‘hide’ see: https://stackoverflow.com/questions/27934885/how-to-hide-code-from-cells-in-ipython-notebook-visualized-with-nbviewer/28073228#28073228

spike.Interactive.INTER_vrai.jsalert(msg)

send a javascript alert

spike.Interactive.ipyfilechooser module

class spike.Interactive.ipyfilechooser.FileChooser(path='/Users/mad/spike/spike_make_sphinx', filename='', show_hidden=False, **kwargs)

Bases: ipywidgets.widgets.widget_box.VBox

default

Get the default value

default_filename

Get the default_filename value

default_path

Get the default_path value

nmrname

refresh()

Re-render the form

reset(path=None, filename=None)

Reset the form to the default path and filename

rows

Get current number of rows

selected

Get selected value

selected_filename

Get the selected_filename

selected_path

Get selected_path value

show_hidden

Get current number of rows

spike.Interactive.ipyfilechooser.get_dir_contents(path, hidden=False)

Get directory contents

spike.Interactive.ipyfilechooser.get_subpaths(path)

Walk a path and return a list of subpaths

spike.Interactive.ipyfilechooser.has_parent(path)

Check if a path has a parent folder

spike.Interactive.ipyfilechooser.update_path(path, item)

Update path with new item

Module contents