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)[source]
Bases: object
a simple tool to show and modify calibration cste
-
back
(event)[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
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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
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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.
MR2
(name, figsize=None, report=True, show=True, Debug=False)[source]
Bases: spike.Interactive.FTICR_INTER.MR_interact
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back
(*arg)[source]
-
forw
(*arg)[source]
-
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]
-
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]
-
down
(b, factor=1.44)[source]
-
ext_box
()[source]
-
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]
-
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
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display
(event={'name': 'value'})[source]
display spectrum and peaks
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done
(event)[source]
exit GUI
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pickpeak
(event)[source]
interactive wrapper to peakpick
-
pkexport
(event)[source]
exports the peaklist to file
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pklist
()[source]
creates peaklist
-
pkprint
(event)[source]
-
pp
()[source]
do the peak-picking calling pp().centroid()
-
class
spike.Interactive.FTICR_INTER.
SpforSuper
(i, name)[source]
Bases: object
a holder for SuperImpose
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display
()[source]
-
class
spike.Interactive.FTICR_INTER.
SuperImpose
(base=None, filetype='*.msh5', N=None)[source]
Bases: object
a tool to superimpose spectra
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Show
()[source]
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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
preliminary and not fully tested !
-
class
spike.Interactive.INTER.
AvProc1D
(filename='')[source]
Bases: object
Detailed 1D NMR Processing
-
apmin_select
(e)[source]
-
apod
()[source]
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apod_select
(e)[source]
-
display
()[source]
-
load
()[source]
-
process
(e)[source]
-
show
()[source]
-
show_apod
(e)[source]
-
class
spike.Interactive.INTER.
FileChooser
(base=None, filetype=['fid', 'ser'], mode='r', show=True)[source]
Bases: object
a simple file chooser for Jupyter - obsolete - not used
-
basename
the basename of the chosen file
-
dirlist
()[source]
-
dirname
the final dirname containing the chosen file
-
file
the chosen complete filename
-
filelist
()[source]
-
nmrname
the final dirname containing the chosen file for TopSpin files
-
setdir
(e)[source]
-
show
()[source]
-
updir
(e)[source]
-
wob
(e)[source]
-
class
spike.Interactive.INTER.
NMRIntegrate
(npkd)[source]
Bases: object
an integrator for NMR experiments
-
display
()[source]
refresh display from event
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int
()[source]
do the integration
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integrate
(event)[source]
integrate from event
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ob
(event)[source]
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on_Apply
(b)[source]
-
on_cancel
(b)[source]
-
print
(event)[source]
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set_value
(b)[source]
-
class
spike.Interactive.INTER.
NMRPeaker1D
(data, figsize=None)[source]
Bases: spike.Interactive.INTER.Show1D
a peak-picker for NMR experiments
-
display
()[source]
interactive wrapper to peakpick
-
ob
(event)[source]
-
on_cancel
(b)[source]
-
on_done
(b)[source]
-
pickpeak
(event)[source]
interactive wrapper to peakpick
-
pklist
()[source]
creates peaklist for printing or exporting
-
pkprint
(event)[source]
-
pp
()[source]
do the peak-picking calling pp().centroid()
-
class
spike.Interactive.INTER.
Phaser1D
(data)[source]
Bases: object
An interactive phaser in 1D NMR
Phaser1D(spectrum)
best when in %matplotlib inline
-
close_all
()[source]
-
ob
(event)[source]
observe changes and start phasing
-
on_Apply
(b)[source]
-
on_cancel
(b)[source]
-
phase
()[source]
apply phase and display
-
ppivot
()[source]
converts from pivot values to centered ones
-
class
spike.Interactive.INTER.
Phaser2D
(data)[source]
Bases: object
An interactive phaser in 2D NMR
Phaser2D(spec)
best when in %matplotlib inline
-
close
()[source]
-
display
(todisplay=None)[source]
display either the current data or the one provided - red and blue
-
ob
(event)[source]
observe changes and start phasing
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on_Apply
(b)[source]
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on_cancel
(b)[source]
-
phase
()[source]
compute phase and display
-
class
spike.Interactive.INTER.
Show1D
(data, title=None, figsize=None)[source]
Bases: object
- An interactive display, 1D NMR
- Show1D(spectrum)
to be developped for peaks and integrals
-
close
()[source]
-
disp
()[source]
-
ob
(event)[source]
observe events and display
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on_done
(b)[source]
-
class
spike.Interactive.INTER.
Show1Dplus
(data, figsize=None, title=None)[source]
Bases: spike.Interactive.INTER.Show1D
-
disp
()[source]
-
on_done
(e)[source]
-
class
spike.Interactive.INTER.
Show2D
(data, title=None, figsize=None)[source]
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)[source]
-
ob
(event)[source]
observe events and display
-
on_done
(b)[source]
-
class
spike.Interactive.INTER.
baseline1D
(data, figsize=None)[source]
Bases: spike.Interactive.INTER.Show1D
-
close
()[source]
-
corrected
()[source]
-
correction
()[source]
returns the correction to apply as a numpy array
-
disp
()[source]
-
on_auto
(e)[source]
automatically set baseline points
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on_cancel
(e)[source]
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on_done
(e)[source]
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on_set
(e)[source]
add baseline points at selector
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on_unset
(e)[source]
remove baseline points closest from selector
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selpos
()[source]
returns selector pos in ppm
-
class
spike.Interactive.INTER.
baseline2D_F2
(data, figsize=None)[source]
Bases: spike.Interactive.INTER.baseline1D
-
on_done
(e)[source]
-
spike.Interactive.INTER.
hidecode
(initial='show', message=True)[source]
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)[source]
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)[source]
Bases: ipywidgets.widgets.widget_box.VBox
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default
Get the default value
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default_filename
Get the default_filename value
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default_path
Get the default_path value
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nmrname
-
refresh
()[source]
Re-render the form
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reset
(path=None, filename=None)[source]
Reset the form to the default path and filename
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rows
Get current number of rows
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selected
Get selected value
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selected_filename
Get the selected_filename
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selected_path
Get selected_path value
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show_hidden
Get current number of rows
-
spike.Interactive.ipyfilechooser.
get_dir_contents
(path, hidden=False)[source]
Get directory contents
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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