brukerapi

brukerapi-python

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A Python package providing I/O interface for Bruker data sets.

tl;dr

Install using pip:

pip install brukerapi

Load any data set:

from brukerapi.dataset import Dataset
dataset = Dataset('{path}/2dseq')    # create data set, works for fid, 2dseq, rawdata.x
dataset.data                         # access data array
dataset.VisuCoreSize                 # get a value of a single parameter

Load an entire study:

from brukerapi.folders import Study
study = Study('{path_to_study_folder}')
dataset = study.get_dataset(exp_id='1', proc_id='1')

# get_dataset returns an empty dataset
# in order to load data into the data set, you can either use the context manager:

with dataset as d:
    d.data                         # access data array
    d.VisuCoreSize                 # get a value of a parameter

# or the load function
dataset.load()
dataset.data                       # access data array
dataset.VisuCoreSize               # get a value of a single parameter

Load a parametric file:

from brukerapi.jcampdx import JCAMPDX

parameters = JCAMPDX('path_to_scan/method')

TR = data.params["PVM_RepetitionTime"].value # This way
TR = data.get_value("PVM_RepetitionTime") # Or this way

Features

I/O interface for fid data sets
I/O interface for 2dseq data sets
I/O interface for rawdata data sets
Random access for fid and 2dseq data sets
Split operation implemented over 2dseq data sets
Filter operation implemented over Bruker folders (allowing you to work with a subset of your study only)

Examples

How to read a Bruker fid, 2dseq, or rawdata file
How to split slice packages of a 2dseq data set
How to split FG_ECHO of a 2dseq data set
How to split FG_ISA of a 2dseq data set

Documentation

Online documentation of the API is available at Read The Docs.

Install

Using pip:

pip install brukerapi

From source:

git clone https://github.com/isi-nmr/brukerapi-python.git
cd brukerapi-python
python setup.py build
python setup.py install

Testing

To ensure reliability, every commit to this repository is tested against the following, publicly available data sets:

Compatibility

The API was tested using various data sets obtained by ParaVision 5.1, 6.0.1 and 360. It it is compatible with the following data set types from individual ParaVision versions.

ParaVision v5.1

Compatible data set types:

fid
2dseq
rawdata.job0
rawdata.Navigator

Compatible pulse sequences for fid data sets:

FLASH.ppg
MGE.ppg
MSME.ppg
RARE.ppg
FAIR_RARE.ppg
RAREVTR.ppg
RAREst.ppg
MDEFT.ppg
FISP.ppg
FLOWMAP.ppg
DtiStandard.ppg
EPI.ppg
FAIR_EPI.ppg
DtiEpi.ppg
T1_EPI.ppg
T2_EPI.ppg
T2S_EPI.ppg
SPIRAL.ppg
DtiSpiral.ppg
UTE.ppg
UTE3D.ppg
ZTE.ppg
CSI.ppg
FieldMap.ppg
NSPECT.ppg
PRESS.ppg
STEAM.ppg
igFLASH.ppg

ParaVision v6.0.1 and v7.0.0

Compatible data set types:

fid
2dseq
rawdata.job0
rawdata.Navigator

Compatible pulse sequences for fid data sets:

FLASH.ppg,
FLASHAngio.ppg
IgFLASH.ppg
MGE.ppg
MSME.ppg
RARE.ppg
FAIR_RARE.ppg
RAREVTR.ppg
RAREst.ppg
MDEFT.ppg
FISP.ppg
FLOWMAP.ppg
DtiStandard.ppg
EPI.ppg
FAIR_EPI.ppg
CASL_EPI.ppg
DtiEpi.ppg
T1_EPI.ppg
T2_EPI.ppg
T2S_EPI.ppg
SPIRAL.ppg
DtiSpiral.ppg
UTE.ppg
UTE3D.ppg
ZTE.ppg
CSI.ppg
FieldMap.ppg
SINGLEPULSE.ppg
NSPECT.ppg
EPSI.ppg
PRESS.ppg
STEAM.ppg
ISIS.ppg
CPMG.ppg
RfProfile.ppg

ParaVision 360 v1.1 v3.0-v3.7

Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment. Compatible data set types:

2dseq
rawdata.job0
rawdata.Navigator

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