spike.Interactive package

Submodules

spike.Interactive.FTICR_INTER module

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

to be embedded in jupyter notebook

class spike.Interactive.FTICR_INTER.Calib(data)

Bases: object

a simple tool to show and modify calibration cste

back(event)

setref(e=None)

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()

resetzoom(b)

class spike.Interactive.FTICR_INTER.Show1D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

on_reset(b=None)

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(**kwargs)

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

spike.Interactive.INTER module

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

First version MAD june 2017 Intermediate version MAD october 2019 Improvements MAD spring - summer - automn 2021 - winter 2022

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)

spike.Interactive.INTER.Logo(width=150)

display the Logo

spike.Interactive.INTER.Logofile()

return the address on disk of the Logo file

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

Bases: spike.Interactive.INTER.Show1D

an integrator for NMR experiments

disp()

draw()

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 redraw

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

peak_and_integrate(event)

print(event)

set_value(b)

class spike.Interactive.INTER.NMRPeaker1D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

a peak-picker for NMR experiments

disp()

draw()

interactive wrapper to peakpick

ob(event)

observe events and redraw

on_add(b)

on_cancel(b)

on_done(b)

on_rem(b)

on_reset(b=None)

on_setcalib(e)

pickpeak(event)

interactive wrapper to pp

pklist()

creates peaklist for printing or exporting

pkprint(event)

pp(**kwargs)

class spike.Interactive.INTER.Phaser1D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

An interactive phaser in 1D NMR

Phaser1D(spectrum, …)

ctopivot(p0, p1)

convert from centered to pivot values

disconnect_press()

should be called before close()

disp()

update display and display pivot

draw()

copied from super() as it does not display the spectrum !

ob(event)

observe changes and start phasing

on_Apply(b)

on_cancel(b)

on_movepivot(event)

phase()

phase_n_disp()

apply phase and disp

ppivot()

converts from pivot values to centered ones

rescale_p1(**kwargs)

class spike.Interactive.INTER.Show1D(**kwargs)

Bases: ipywidgets.widgets.widget_box.HBox

An interactive display, 1D NMR

Show1D(spectrum)

disp()

draw()

builds and display the picture

ob(event)

observe events and redraw

obdisp(event)

observe events and display

on_done(b)

on_reset(b=None)

scale_up(**kwargs)

set_on_redraw()

set-up mouse scroll control and click

class spike.Interactive.INTER.Show1Dplus(**kwargs)

Bases: spike.Interactive.INTER.Show1D

copy(event)

draw(zoom=False)

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

on_done(e)

class spike.Interactive.INTER.SpforSuper(i, filename='None', axref=False, ref=None)

Bases: object

a holder for one spectrum to SuperImpose

B(text, size='auto')

bold HTML widget

I(text, size='auto')

Italic HTML widget

activate(e)

called when state changes

disp()

refresh

draw(unit='ppm')

injectobserve(method)

used to to observe form outer object for draw

move_xdata()

adapt self.xdata to offset and stretching, then return the value

move_ydata()

adapt self.ydata to direct, scale, and offset and return the value

property mult

nactivate(e)

called to check name validity, when name is entered

property nmrname

ob(event)

observe events and display

simpledisplay()

a simplified widget

class spike.Interactive.INTER.Timer(timeout, callback)

Bases: object

cancel()

start()

spike.Interactive.INTER.UserLogofile()

return the address on disk of the User Logo file - located in $HOME/Spike/Logo.png

class spike.Interactive.INTER.baseline1D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

An interactive baseline for 1D NMR

baseline1D(spectrum, …)

clear()

remove artists created by draw()

corrected()

correction()

returns the correction to apply as a numpy array

disconnect_press()

should be called before close()

disp()

used to refresh view

draw()

used to create the view with additional artists

itoc3(value)

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

spike.Interactive.INTER.debounce(wait)

Decorator that will postpone a function’s execution until after wait seconds have elapsed since the last time it was invoked.

spike.Interactive.INTER.hidecode(initial='show', message='<i>useful to show/print a clean screen when processing is finished</i>')

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.hidedoc(initial='show', message='<i>useful to show/print a clean screen when processing is finished</i>')

this func adds a button to hide/show the doc 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.initCSS()

adapt some CSS

spike.Interactive.INTER.initialize(verb=1)

initialize notebook interface for Spike

spike.Interactive.INTER.jsalert(msg='Alert text')

send a javascript alert

spike.Interactive.INTER.param_line(acqus, paramlist=None, output='string')

given a acqus dictionary, and a list of parameters to extract, this functions return either a plain text or a HTML table depending on output value either “string” or “HTML” )

spike.Interactive.INTER.param_table(data, output='string')

return the complete parameter table held into data output is either “string” or “HTML

spike.Interactive.INTER.popup_param_table(data)

spike.Interactive.INTER.readplist(paramtoadd, paramdict)

parse lists from acqus files - only that ones defined in arraynames

spike.Interactive.INTER.space(width='80px')

defines a layout of width, width should be a string in CSS syntax

spike.Interactive.INTER.spacer(width='80px')

defines a spacer to be used in widgets.Box - width should be a string in CSS syntax

spike.Interactive.INTER.summary(data, param=True, output='string')

produces a summary of the data set if param is True, a short list of 1D parameters is given, using the globally defined Paramlist output is either “string” or “HTML”

spike.Interactive.INTER_2D 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_2D.Phaser2D(**kwargs)

Bases: spike.Interactive.INTER_2D.Show2D

An interactive phaser in 2D NMR

Phaser2D(spec)

ctopivot(F1p0, F1p1, F2p0, F2p1)

convert from centered to pivot values

draw(todisplay=None, new=True)

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)

on_movepivot(event)

phase()

compute phase and display

phdisp(todisplay=None)

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

ppivot()

converts from pivot values to centered ones

class spike.Interactive.INTER_2D.Show2D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

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

disp(**kwargs)

draw(**kwargs)

builds and display the picture

on_reset(e=None)

class spike.Interactive.INTER_2D.baseline2D_F2(**kwargs)

Bases: spike.Interactive.INTER.baseline1D

on_done(e)

spike.Interactive.INTER_2D.sidedisplay(dt1d, ax)

spike.Interactive.INTER_MS (copy) module

spike.Interactive.INTER_MS module

spike.Interactive.INTER_MS_turn 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_MS_turn.FloatButt(**kwargs)

Bases: ipywidgets.widgets.widget_box.HBox

a float text with buttons rounds is a list on power of 10 to set

decrem(e)

increm(e)

property value

class spike.Interactive.INTER_MS_turn.Phaser1D(**kwargs)

Bases: spike.Interactive.INTER.Show1D

An interactive phaser in 1D MS

Phaser1D(spectrum)

requires %matplotlib widget

ctopivot(p0, p1, p2, pv)

convert from centered to pivot values - not used in PHASEQUAD

ob(event)

observe changes and start phasing

on_Apply(b)

on_addlist(b)

on_cancel(b)

on_clearlist(b)

on_movepivot(event)

on_printlist(b)

phase()

apply phase and display

ppivot()

converts current pivot values to centered ones - not used in PHASEQUAD

show()

spike.Interactive.ipyfilechooser module

class spike.Interactive.ipyfilechooser.FileChooser(**kwargs)

Bases: ipywidgets.widgets.widget_box.VBox

# FileChooser code is from # https://github.com/crahan/ipyfilechooser

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