spike.Interactive package

Submodules

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.MR_interact(name, figsize=None, report=True, show=True, Debug=False)

Bases: spike.Interactive.FTICR_INTER.MR

I1D()

show the 1D selector

back(*arg)

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

build button

check_fig()

check_fig1D()

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

display1D()

display the selected 1D

down(b, factor=1.44)

ext_box()

defines the interactive tools for 1D

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()

property 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.FTICR_INTER_v2 module

A tool to display FT-ICR data-sets

to be embedded in jupyter notebook

MAD Sept 2019

This version requires ipympl (see: https://github.com/matplotlib/jupyter-matplotlib ) and the notebook to be opened with %matplotlib widget

class spike.Interactive.FTICR_INTER_v2.Calib(data)

Bases: object

a simple tool to show and modify calibration cste

back(event)

update(event)

class spike.Interactive.FTICR_INTER_v2.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_v2.MR_interact(name, figsize=None, report=True, show=True, Debug=False)

Bases: spike.Interactive.FTICR_INTER_v2.MR

I1D()

show the 1D selector

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

build a button into self

check_fig()

create figure if missing

check_fig1D()

display(zoom=None, scale=None)

computes pictures (display in the SPIKE sense - not ipywidget one)

display1D()

display the selected 1D

ext_box()

defines the interactive tools for 1D

fullzoom()

ob(event)

observe events and display

reset(b)

reset_track()

scale_up(step)

set_on_redraw()

show()

actually show the graphical tool and the interactive spectrum

spec_box()

defines the spectral box widget

update(e)

update internal zoom coordinates

zoom_box()

defines the zoom box widget

class spike.Interactive.FTICR_INTER_v2.MS2Dscene(show=True, root='/')

Bases: ipywidgets.widgets.widget_box.HBox

a widget to set all MS tools into one screen

load2D(e)

create 2D object and display

class spike.Interactive.FTICR_INTER_v2.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_v2.SpforSuper(i, name)

Bases: object

a holder for SuperImpose

display()

class spike.Interactive.FTICR_INTER_v2.SuperImpose(base=None, filetype='*.msh5', N=None)

Bases: object

a tool to superimpose spectra

Show()

copy(event)

display(event)

spike.Interactive.INTER (copy) module

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

First version MAD june 2017 definitive ? version MAD october 2019

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

property basename

the basename of the chosen file

dirlist()

property dirname

the final dirname containing the chosen file

property file

the chosen complete filename

filelist()

property nmrname

the final dirname containing the chosen file for TopSpin files

setdir(e)

show()

updir(e)

wob(e)

class spike.Interactive.INTER.NMRIntegrate(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

an integrator for NMR experiments

disp(zoom=False)

refresh display from event - if zoom is True, display only in xbound

int()

do the automatic integration from peaks and parameters

integrate(event)

ob(event)

observe events and display

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

peak_and_integrate(event)

print(event)

set_value(b)

show()

class spike.Interactive.INTER.NMRPeaker1D(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

a peak-picker for NMR experiments

disp()

interactive wrapper to peakpick

ob(event)

observe events and display

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

on_setcalib(e)

pickpeak(event)

interactive wrapper to peakpick

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp()

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

show()

class spike.Interactive.INTER.Phaser1D(data, figsize=None, title=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

An interactive phaser in 1D NMR

Phaser1D(spectrum)

requires %matplotlib widget

ctopivot(p0, p1)

convert from centered to pivot values

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

on_movepivot(event)

phase()

apply phase and display

ppivot()

converts from pivot values to centered ones

show()

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, reverse_scroll=False, show=True)

Bases: ipywidgets.widgets.widget_box.HBox

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

disp()

ob(event)

observe events and display

on_done(b)

on_reset(b)

scale_up(step)

set_on_redraw()

class spike.Interactive.INTER.Show1Dplus(data, base='/DATA', N=9, figsize=None, title=None, reverse_scroll=False)

Bases: spike.Interactive.INTER.Show1D

copy(event)

disp(zoom=False)

refresh display - if zoom is True, display only in xbound

on_done(e)

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.SpforSuper(i, name)

Bases: object

a holder for SuperImpose

display(unit='ppm')

class spike.Interactive.INTER.baseline1D(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

close()

close all widget

corrected()

correction()

returns the correction to apply as a numpy array

disp()

compute and display the spectrum

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

show()

create the widget and display the spectrum

smoothed()

returns a smoothed version of the data

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’ inspired from: 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 VIEUX module

spike.Interactive.INTER module

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

First version MAD june 2017 definitive ? version MAD october 2019

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

property basename

the basename of the chosen file

dirlist()

property dirname

the final dirname containing the chosen file

property file

the chosen complete filename

filelist()

property nmrname

the final dirname containing the chosen file for TopSpin files

setdir(e)

show()

updir(e)

wob(e)

class spike.Interactive.INTER.NMRIntegrate(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

an integrator for NMR experiments

disp(zoom=False)

refresh display from event - if zoom is True, display only in xbound

int()

do the automatic integration from peaks and parameters

integrate(event)

ob(event)

observe events and display

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

peak_and_integrate(event)

print(event)

set_value(b)

show()

class spike.Interactive.INTER.NMRPeaker1D(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

a peak-picker for NMR experiments

disp()

interactive wrapper to peakpick

ob(event)

observe events and display

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

on_setcalib(e)

pickpeak(event)

interactive wrapper to peakpick

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp()

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

show()

class spike.Interactive.INTER.Phaser1D(data, figsize=None, title=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

An interactive phaser in 1D NMR

Phaser1D(spectrum)

requires %matplotlib widget

ctopivot(p0, p1)

convert from centered to pivot values

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

on_movepivot(event)

phase()

apply phase and display

ppivot()

converts from pivot values to centered ones

show()

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, reverse_scroll=False, show=True)

Bases: ipywidgets.widgets.widget_box.HBox

An interactive display, 1D NMR

Show1D(spectrum)

to be developped for peaks and integrals

disp()

ob(event)

observe events and display

on_done(b)

on_reset(b)

scale_up(step)

set_on_redraw()

class spike.Interactive.INTER.Show1Dplus(data, base='/DATA', N=9, figsize=None, title=None, reverse_scroll=False)

Bases: spike.Interactive.INTER.Show1D

copy(event)

disp(zoom=False)

refresh display - if zoom is True, display only in xbound

on_done(e)

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.SpforSuper(i, name)

Bases: object

a holder for SuperImpose

display(unit='ppm')

class spike.Interactive.INTER.baseline1D(data, figsize=None, reverse_scroll=False, show=True)

Bases: spike.Interactive.INTER.Show1D

close()

close all widget

corrected()

correction()

returns the correction to apply as a numpy array

disp()

compute and display the spectrum

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

show()

create the widget and display the spectrum

smoothed()

returns a smoothed version of the data

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’ inspired from: 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.ipyfilechooser module

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

Bases: ipywidgets.widgets.widget_box.VBox

property default

Get the default value

property default_filename

Get the default_filename value

property default_path

Get the default_path value

property nmrname

refresh()

Re-render the form

reset(path=None, filename=None)

Reset the form to the default path and filename

property rows

Get current number of rows

property selected

Get selected value

property selected_filename

Get the selected_filename

property selected_path

Get selected_path value

property 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