Quick intro

timsdata is a module that wraps Bruker's tdf-sdk into a module, for convenience of not having to copy it in all possible projects.

Requirements

Linux or Windows only for now. Python3.6 or higher.

Installation

From terminal (assuming you have python and pip included in the system PATH:

pip3 install timsdata

For fresher versions:

pip3 install git+https://github.com/MatteoLacki/timsdata

For development:

github clone https://github.com/MatteoLacki/timsdata
cd timsdata
pip3 install -e .

Usage

from timsdata.timsdata import TimsData

D = TimsData('path_to_your_data')

# choose some frame and scan limits
frame_no, min_scan, max_scan = 100, 0, 918

# lists of numpy arrays
D.readScans(frame_no, min_scan, max_scan)

## THIS RESULTS IN ARRAYS WITH TIME OF FLIGHTS AND INTENSITIES
## EACH ONE CORRESPONDS TO ONE SCAN, PER ONE FRAME (ONE RETENTION-TIME UNIT)
# [...
# (array([], dtype=uint32), array([], dtype=uint32)),
# (array([], dtype=uint32), array([], dtype=uint32)),
# (array([], dtype=uint32), array([], dtype=uint32)),
# (array([389679, 394578], dtype=uint32), array([9, 9], dtype=uint32)),
# (array([], dtype=uint32), array([], dtype=uint32)),
# (array([ 78036, 210934, 211498, 351984], dtype=uint32),
#  array([9, 9, 9, 9], dtype=uint32)),
#  ...]


D.frame_array(frame_no, min_scan, max_scan)
# one 4-dimensional numpy array
# columns corresponds to:
# frame_number, scan_number, mass_index (time of flight), intensity
# array([[   100,     35, 389679,      9],
#        [   100,     35, 394578,      9],
#        [   100,     37,  78036,      9],
#        ...,
#        [   100,    911, 294204,      9],
#        [   100,    913, 248788,      9],
#        [   100,    915, 100120,    120]])

Do observe, that you must know which values: to put there. If you don't, consider TimsPy.

Plans for future

We will gradually introduce cppyy to the project and fill up numpy arrays in C++.

Law

Please read LICENCE.txt for legal aspects of using the software.

Special thanks

We would like to thank Michael Krause, Sascha Winter, and Sven Brehmer, all from Bruker Daltonik GmbH, for their magnificent work in developing tfd-sdk.