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 !
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class
spike.Interactive.FTICR_INTER.
Calib
(data)[source]¶ Bases:
object
a simple tool to show and modify calibration cste
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class
spike.Interactive.FTICR_INTER.
MR
(name, report=True, Debug=False)[source]¶ Bases:
object
this class handles multiresolution datasets
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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
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class
spike.Interactive.FTICR_INTER.
MR_interact
(name, figsize=None, report=True, show=True, Debug=False)[source]¶ Bases:
spike.Interactive.FTICR_INTER.MR
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property
zoom
¶
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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)
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property
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class
spike.Interactive.FTICR_INTER.
MSPeaker
(npkd, pkname)[source]¶ Bases:
object
a peak-picker for MS experiments
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
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class
spike.Interactive.FTICR_INTER_v2.
Calib
(data)[source]¶ Bases:
object
a simple tool to show and modify calibration cste
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class
spike.Interactive.FTICR_INTER_v2.
MR
(name, report=True, Debug=False)[source]¶ Bases:
object
this class handles multiresolution datasets
-
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
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class
spike.Interactive.FTICR_INTER_v2.
MR_interact
(name, figsize=None, report=True, show=True, Debug=False)[source]¶
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class
spike.Interactive.FTICR_INTER_v2.
MS2Dscene
(show=True, root='/')[source]¶ Bases:
ipywidgets.widgets.widget_box.HBox
a widget to set all MS tools into one screen
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class
spike.Interactive.FTICR_INTER_v2.
MSPeaker
(npkd, pkname)[source]¶ Bases:
object
a peak-picker for MS experiments
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
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class
spike.Interactive.INTER.
AvProc1D
(filename='')[source]¶ Bases:
object
Detailed 1D NMR Processing
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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
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property
basename
¶ the basename of the chosen file
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property
dirname
¶ the final dirname containing the chosen file
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property
file
¶ the chosen complete filename
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property
nmrname
¶ the final dirname containing the chosen file for TopSpin files
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property
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class
spike.Interactive.INTER.
NMRIntegrate
(data, figsize=None, reverse_scroll=False, show=True)[source]¶ Bases:
spike.Interactive.INTER.Show1D
an integrator for NMR experiments
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class
spike.Interactive.INTER.
NMRPeaker1D
(data, figsize=None, reverse_scroll=False, show=True)[source]¶ Bases:
spike.Interactive.INTER.Show1D
a peak-picker for NMR experiments
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class
spike.Interactive.INTER.
Phaser1D
(data, figsize=None, title=None, reverse_scroll=False, show=True)[source]¶ Bases:
spike.Interactive.INTER.Show1D
An interactive phaser in 1D NMR
Phaser1D(spectrum)
requires %matplotlib widget
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class
spike.Interactive.INTER.
Phaser2D
(data)[source]¶ Bases:
object
An interactive phaser in 2D NMR
Phaser2D(spec)
best when in %matplotlib inline
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class
spike.Interactive.INTER.
Show1D
(data, title=None, figsize=None, reverse_scroll=False, show=True)[source]¶ Bases:
ipywidgets.widgets.widget_box.HBox
- An interactive display, 1D NMR
Show1D(spectrum)
to be developped for peaks and integrals
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class
spike.Interactive.INTER.
Show1Dplus
(data, base='/DATA', N=9, figsize=None, title=None, reverse_scroll=False)[source]¶
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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.
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class
spike.Interactive.INTER.
baseline1D
(data, figsize=None, reverse_scroll=False, show=True)[source]¶
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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’ inspired from: https://stackoverflow.com/questions/27934885/how-to-hide-code-from-cells-in-ipython-notebook-visualized-with-nbviewer/28073228#28073228
spike.Interactive.ipyfilechooser module¶
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class
spike.Interactive.ipyfilechooser.
FileChooser
(path='/home/mad/Documents/spike/spike_make_sphinx', filename='', show_hidden=False, **kwargs)[source]¶ Bases:
ipywidgets.widgets.widget_box.VBox
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property
default
¶ Get the default value
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property
default_filename
¶ Get the default_filename value
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property
default_path
¶ Get the default_path value
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property
nmrname
¶
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property
rows
¶ Get current number of rows
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property
selected
¶ Get selected value
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property
selected_filename
¶ Get the selected_filename
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property
selected_path
¶ Get selected_path value
Get current number of rows
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property
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spike.Interactive.ipyfilechooser.
get_dir_contents
(path, hidden=False)[source]¶ Get directory contents