This little utility allows to interactively explore large 2D FTICR-MS datasets.
You find here a simple interface the reads and displays the multiresolution 2D files created by SPIKE
when processing 2D data-sets (usually called xxx_mr.msh5
).
It is based on the capabilities of both the SPIKE
library and the jupyter notebook
interface.
Thanks to the technology behind, these extremely large files can be accessed rapidly, even on a laptop computer.
This program supersedes the old Visu2D
program, developped in Qt
, which could no longer be maintained.\ables\
In addition to a regular anaconda python 3 distribution, it requires pytables
and ipympl
- to be installed with conda.
This is a work inprogress - additional utilities should come soon !
In[x]
) and run it by cliking on the â–¶Run
icon on the top of the window (the python code should be hidden after this).scale
slider, you can select the display level.
Think to this as an archipelago viewed on the map; the slider changes the sea level, raising the scale raises the floor (or lower the sea level)Redraw
button, or change the scale.
The smaller the zoom box, the better the resolution.### Initialization of the environment
### the following cell should be run only once *(but no harm if you run it twice)* .
from IPython.display import display, HTML, Markdown, Image
display(Markdown('## STARTING Environment...'))
%matplotlib widget
import spike
from spike.Interactive.INTER import hidecode
import spike.Interactive.FTICR_INTER_v2 as IF2
display(Markdown('## ... program is ready'))
from importlib import reload # the two following lines are debugging help
reload(IF2) # and can be removed safely when in production
hidecode(initial='hide', message=False)
ms = IF2.MS2Dscene(root='/home/mad/Documents/DATA')
import matplotlib.pyplot as plt
with ms.out2D:
plt.plot([1,2,3],[2,4,0])
with ms.out2D:
IF2.MR_interact(ms.FC.selected, show=True, figsize=(8,8), Debug=False)
IF2.MR_interact(ms.FC.selected, show=True, figsize=(8,8), Debug=False)