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)[source]
Bases: object
a simple tool to show and modify calibration cste
-
back
(event)[source]
-
setref
(e=None)[source]
-
update
(event)[source]
-
class
spike.Interactive.FTICR_INTER.
MR
(name, report=True, Debug=False)[source]
Bases: object
this class handles multiresolution datasets
-
col
(i)[source]
return a column with coordinate in index
-
colmz
(i)[source]
return a column with coordinate in m/z
-
compute_absmax
()[source]
computes largest point from smaller resolution, and propagates
-
load
()[source]
load from file
-
report
()[source]
report object content
-
row
(i)[source]
return a row with coordinate in index
-
rowmz
(i)[source]
return a row with coordinate in m/z
-
to_display
(zoom=0, 10000000.0, 0, 10000000.0, verbose=False)[source]
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)[source]
Bases: spike.Interactive.FTICR_INTER.MR
-
I1D
()[source]
show the 1D selector
-
back
(*arg)[source]
-
bb
(name, desc, action, layout=None, tooltip='')[source]
build button
-
check_fig
()[source]
-
check_fig1D
()[source]
-
display
(zoom=None, scale=None, redraw=None)[source]
-
display1D
()[source]
display the selected 1D
-
down
(b, factor=1.44)[source]
-
ext_box
()[source]
defines the interactive tools for 1D
-
forw
(*arg)[source]
-
fullzoom
()[source]
-
left
(b, factor=1.44)[source]
-
reset
(b)[source]
-
reset_track
()[source]
-
right
(b, factor=1.44)[source]
-
scale1
(b)[source]
-
scaledown
(b)[source]
-
scaleup
(b)[source]
-
show
()[source]
actually show the graphical tool and the interactive spectrum
-
up
(b, factor=1.44)[source]
-
update
()[source]
-
property
zoom
-
zoom_box
()[source]
-
zoom_in
(b, factor=1.44)[source]
- 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)[source]
z_in: dw = waft*factor*(1-factor)
z_out:dw = wbef*(factor*(1-factor))
-
zoomwidth
()[source]
-
class
spike.Interactive.FTICR_INTER.
MSPeaker
(npkd, pkname)[source]
Bases: object
a peak-picker for MS experiments
-
display
(event={'name': 'value'})[source]
display spectrum and peaks
-
done
(event)[source]
exit GUI
-
pickpeak
(event)[source]
interactive wrapper to peakpick
-
pkexport
(event)[source]
exports the peaklist to file
-
pklist
()[source]
creates peaklist
-
pkprint
(event)[source]
-
pp
()[source]
do the peak-picking calling pp().centroid()
-
resetzoom
(b)[source]
-
class
spike.Interactive.FTICR_INTER.
Show1D
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
-
on_reset
(b=None)[source]
-
class
spike.Interactive.FTICR_INTER.
SpforSuper
(i, name)[source]
Bases: object
a holder for SuperImpose
-
display
()[source]
-
class
spike.Interactive.FTICR_INTER.
SuperImpose
(base=None, filetype='*.msh5', N=None)[source]
Bases: object
a tool to superimpose spectra
-
Show
()[source]
-
copy
(event)[source]
-
display
(event)[source]
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)[source]
Bases: object
a simple tool to show and modify calibration cste
-
back
(event)[source]
-
update
(event)[source]
-
class
spike.Interactive.FTICR_INTER_v2.
MR
(name, report=True, Debug=False)[source]
Bases: object
this class handles multiresolution datasets
-
col
(i)[source]
return a column with coordinate in index
-
colmz
(i)[source]
return a column with coordinate in m/z
-
compute_absmax
()[source]
computes largest point from smaller resolution, and propagates
-
load
()[source]
load from file
-
report
()[source]
report object content
-
row
(i)[source]
return a row with coordinate in index
-
rowmz
(i)[source]
return a row with coordinate in m/z
-
to_display
(zoom=0, 10000000.0, 0, 10000000.0, verbose=False)[source]
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)[source]
Bases: spike.Interactive.FTICR_INTER_v2.MR
-
I1D
()[source]
show the 1D selector
-
bb
(name, desc, action, layout=None, tooltip='')[source]
build a button into self
-
check_fig
()[source]
create figure if missing
-
check_fig1D
()[source]
-
display
(zoom=None, scale=None)[source]
computes pictures (display in the SPIKE sense - not ipywidget one)
-
display1D
()[source]
display the selected 1D
-
ext_box
()[source]
defines the interactive tools for 1D
-
fullzoom
()[source]
-
ob
(event)[source]
observe events and display
-
reset
(b)[source]
-
reset_track
()[source]
-
scale_up
(step)[source]
-
set_on_redraw
()[source]
-
show
()[source]
actually show the graphical tool and the interactive spectrum
-
spec_box
()[source]
defines the spectral box widget
-
update
(e)[source]
update internal zoom coordinates
-
zoom_box
()[source]
defines the zoom box widget
-
class
spike.Interactive.FTICR_INTER_v2.
MS2Dscene
(**kwargs)[source]
Bases: ipywidgets.widgets.widget_box.HBox
a widget to set all MS tools into one screen
-
load2D
(e)[source]
create 2D object and display
-
class
spike.Interactive.FTICR_INTER_v2.
MSPeaker
(npkd, pkname)[source]
Bases: object
a peak-picker for MS experiments
-
display
(event={'name': 'value'})[source]
display spectrum and peaks
-
done
(event)[source]
exit GUI
-
pickpeak
(event)[source]
interactive wrapper to peakpick
-
pkexport
(event)[source]
exports the peaklist to file
-
pklist
()[source]
creates peaklist
-
pkprint
(event)[source]
-
pp
()[source]
do the peak-picking calling pp().centroid()
-
class
spike.Interactive.FTICR_INTER_v2.
SpforSuper
(i, name)[source]
Bases: object
a holder for SuperImpose
-
display
()[source]
-
class
spike.Interactive.FTICR_INTER_v2.
SuperImpose
(base=None, filetype='*.msh5', N=None)[source]
Bases: object
a tool to superimpose spectra
-
Show
()[source]
-
copy
(event)[source]
-
display
(event)[source]
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='')[source]
Bases: object
Detailed 1D NMR Processing
-
apmin_select
(e)[source]
-
apod
()[source]
-
apod_select
(e)[source]
-
display
()[source]
-
load
()[source]
-
process
(e)[source]
-
show
()[source]
-
show_apod
(e)[source]
-
spike.Interactive.INTER.
Logo
(width=150)[source]
display the Logo
-
spike.Interactive.INTER.
Logofile
()[source]
return the address on disk of the Logo file
-
class
spike.Interactive.INTER.
NMRIntegrate
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
an integrator for NMR experiments
-
disp
()[source]
-
draw
()[source]
refresh display from event - if zoom is True, display only in xbound
-
int
()[source]
do the automatic integration from peaks and parameters
-
integrate
(event)[source]
-
ob
(event)[source]
observe events and redraw
-
on_add
(b)[source]
-
on_cancel
(b)[source]
-
on_done
(b)[source]
-
on_rem
(b)[source]
-
peak_and_integrate
(event)[source]
-
print
(event)[source]
-
set_value
(b)[source]
-
class
spike.Interactive.INTER.
NMRPeaker1D
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
a peak-picker for NMR experiments
-
disp
()[source]
-
draw
()[source]
interactive wrapper to peakpick
-
ob
(event)[source]
observe events and redraw
-
on_add
(b)[source]
-
on_cancel
(b)[source]
-
on_done
(b)[source]
-
on_rem
(b)[source]
-
on_reset
(b=None)[source]
-
on_setcalib
(e)[source]
-
pickpeak
(event)[source]
interactive wrapper to pp
-
pklist
()[source]
creates peaklist for printing or exporting
-
pkprint
(event)[source]
-
pp
(**kwargs)[source]
-
class
spike.Interactive.INTER.
Phaser1D
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
An interactive phaser in 1D NMR
-
ctopivot
(p0, p1)[source]
convert from centered to pivot values
-
disconnect_press
()[source]
should be called before close()
-
disp
()[source]
update display and display pivot
-
draw
()[source]
copied from super() as it does not display the spectrum !
-
ob
(event)[source]
observe changes and start phasing
-
on_Apply
(b)[source]
-
on_cancel
(b)[source]
-
on_movepivot
(event)[source]
-
phase
()[source]
-
phase_n_disp
()[source]
apply phase and disp
-
ppivot
()[source]
converts from pivot values to centered ones
-
rescale_p1
(**kwargs)[source]
-
class
spike.Interactive.INTER.
Show1D
(**kwargs)[source]
Bases: ipywidgets.widgets.widget_box.HBox
- An interactive display, 1D NMR
Show1D(spectrum)
-
disp
()[source]
-
draw
()[source]
builds and display the picture
-
ob
(event)[source]
observe events and redraw
-
obdisp
(event)[source]
observe events and display
-
on_done
(b)[source]
-
on_reset
(b=None)[source]
-
scale_up
(**kwargs)[source]
-
set_on_redraw
()[source]
set-up mouse scroll control and click
-
class
spike.Interactive.INTER.
Show1Dplus
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
-
copy
(event)[source]
-
draw
(zoom=False)[source]
refresh display - if zoom is True, display only in xbound
-
on_done
(e)[source]
-
class
spike.Interactive.INTER.
SpforSuper
(i, filename='None', axref=False, ref=None)[source]
Bases: object
a holder for one spectrum to SuperImpose
-
B
(text, size='auto')[source]
bold HTML widget
-
I
(text, size='auto')[source]
Italic HTML widget
-
activate
(e)[source]
called when state changes
-
disp
()[source]
refresh
-
draw
(unit='ppm')[source]
-
injectobserve
(method)[source]
used to to observe form outer object for draw
-
move_xdata
()[source]
adapt self.xdata to offset and stretching, then return the value
-
move_ydata
()[source]
adapt self.ydata to direct, scale, and offset and return the value
-
property
mult
-
nactivate
(e)[source]
called to check name validity, when name is entered
-
property
nmrname
-
ob
(event)[source]
observe events and display
-
simpledisplay
()[source]
a simplified widget
-
class
spike.Interactive.INTER.
Timer
(timeout, callback)[source]
Bases: object
-
cancel
()[source]
-
start
()[source]
-
spike.Interactive.INTER.
UserLogofile
()[source]
return the address on disk of the User Logo file - located in $HOME/Spike/Logo.png
-
class
spike.Interactive.INTER.
baseline1D
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
An interactive baseline for 1D NMR
-
clear
()[source]
remove artists created by draw()
-
corrected
()[source]
-
correction
()[source]
returns the correction to apply as a numpy array
-
disconnect_press
()[source]
should be called before close()
-
disp
()[source]
used to refresh view
-
draw
()[source]
used to create the view with additional artists
-
itoc3
(value)[source]
-
on_auto
(e)[source]
automatically set baseline points
-
on_cancel
(e)[source]
-
on_done
(e)[source]
-
on_set
(e)[source]
add baseline points at selector
-
on_unset
(e)[source]
remove baseline points closest from selector
-
spike.Interactive.INTER.
debounce
(wait)[source]
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>')[source]
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>')[source]
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
()[source]
adapt some CSS
-
spike.Interactive.INTER.
initialize
(verb=1)[source]
initialize notebook interface for Spike
-
spike.Interactive.INTER.
jsalert
(msg='Alert text')[source]
send a javascript alert
-
spike.Interactive.INTER.
param_line
(acqus, paramlist=None, output='string')[source]
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')[source]
return the complete parameter table held into data
output is either “string” or “HTML
-
spike.Interactive.INTER.
readplist
(paramtoadd, paramdict)[source]
parse lists from acqus files - only that ones defined in arraynames
-
spike.Interactive.INTER.
space
(width='80px')[source]
defines a layout of width, width should be a string in CSS syntax
-
spike.Interactive.INTER.
spacer
(width='80px')[source]
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')[source]
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)[source]
Bases: spike.Interactive.INTER_2D.Show2D
An interactive phaser in 2D NMR
-
ctopivot
(F1p0, F1p1, F2p0, F2p1)[source]
convert from centered to pivot values
-
draw
(todisplay=None, new=True)[source]
display either the current data or the one provided - red and blue
-
ob
(event)[source]
observe changes and start phasing
-
on_Apply
(b)[source]
-
on_cancel
(b)[source]
-
on_movepivot
(event)[source]
-
phase
()[source]
compute phase and display
-
phdisp
(todisplay=None)[source]
display either the current data or the one provided - red and blue
-
ppivot
()[source]
converts from pivot values to centered ones
-
class
spike.Interactive.INTER_2D.
Show2D
(**kwargs)[source]
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)[source]
-
class
spike.Interactive.INTER_2D.
baseline2D_F2
(**kwargs)[source]
Bases: spike.Interactive.INTER.baseline1D
-
on_done
(e)[source]
-
spike.Interactive.INTER_2D.
sidedisplay
(dt1d, ax)[source]
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)[source]
Bases: ipywidgets.widgets.widget_box.HBox
a float text with buttons
rounds is a list on power of 10 to set
-
decrem
(e)[source]
-
increm
(e)[source]
-
property
value
-
class
spike.Interactive.INTER_MS_turn.
Phaser1D
(**kwargs)[source]
Bases: spike.Interactive.INTER.Show1D
An interactive phaser in 1D MS
requires %matplotlib widget
-
ctopivot
(p0, p1, p2, pv)[source]
convert from centered to pivot values - not used in PHASEQUAD
-
ob
(event)[source]
observe changes and start phasing
-
on_Apply
(b)[source]
-
on_addlist
(b)[source]
-
on_cancel
(b)[source]
-
on_clearlist
(b)[source]
-
on_movepivot
(event)[source]
-
on_printlist
(b)[source]
-
phase
()[source]
apply phase and display
-
ppivot
()[source]
converts current pivot values to centered ones - not used in PHASEQUAD
-
show
()[source]
spike.Interactive.ipyfilechooser module
-
class
spike.Interactive.ipyfilechooser.
FileChooser
(**kwargs)[source]
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
()[source]
Re-render the form
-
reset
(path=None, filename=None)[source]
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)[source]
Get directory contents
-
spike.Interactive.ipyfilechooser.
get_subpaths
(path)[source]
Walk a path and return a list of subpaths
-
spike.Interactive.ipyfilechooser.
has_parent
(path)[source]
Check if a path has a parent folder
-
spike.Interactive.ipyfilechooser.
update_path
(path, item)[source]
Update path with new item
Module contents