Display utility for 2D FTICR Spectra

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 !

To use it,

  • Select the executable cell below (marked with the 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).
  • select the file you want look at, and Load, it will show-up as a full width 2D image. ignore eventual warnings about missing attributes
    • the F2/horizontal axis is the high resolution, direct axis. You find fragments along this line
    • the F1/vertical axis is the low resolution, indirect axis. You have parents along this axis.
  • with the zoom tool (the square below the spectrum) you can select the region you want to display, you can also dial it in on the top box.
  • with the 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)
  • The data have a hierarchical multiresolution structure. Zooming does not change the resolution, to force it, either click on the Redraw button, or change the scale. The smaller the zoom box, the better the resolution.
In [5]:
### 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')

STARTING Environment...

... program is ready

to come

  • calibration
  • peak detection
  • superimposition
  • extraction of arbitrary 1D
  • locate/remove artifacts due to harmonics
In [ ]:
import matplotlib.pyplot as plt
with ms.out2D:
    plt.plot([1,2,3],[2,4,0])
In [ ]:
with ms.out2D:
    IF2.MR_interact(ms.FC.selected,  show=True, figsize=(8,8), Debug=False)
In [ ]:
IF2.MR_interact(ms.FC.selected,  show=True, figsize=(8,8), Debug=False)
In [ ]: