Command line interface (CLI)

Together with the API a bruker command line tool is installed. It can be used with the following sub-commands:

It is also possible to create command line pipelines using our api

Data used in examples on this page are freely available at Zenodo:

It is possible to run examples in this section by setting an environment variable DATA_PATH to contain a path to the downloaded dataset:

export DATA_PATH={path_to_20200612_094625_lego_phantom_3_1_2}

report

For each data set contained in a folder specified by the -i argument, the report sub-command saves properties individual data sets into a JSON, or a YAML file located in the dataset folder, or a folder, or file specified using the -o argument. It is also possible to only export properties defined by the -p argument.

Save properties of all data sets contained within the 20200612_094625_lego_phantom_3_1_2 folder:

bruker report -i 20200612_094625_lego_phantom_3_1_2/3/pdata/1/2dseq

The following is the content of the resulting report.json file located in the same folder as the 2dseq file:

{
    "TE": 4,
    "dim_type": [
        "spatial",
        "spatial",
        "<FG_SLICE>"
    ],
    "encoded_dim": 2,
    "shape_final": [
        256,
        256,
        3
    ],
    "is_single_slice": false,
    "shape_fg": [
        3
    ],
    "numpy_dtype": "int16",
    "shape_block": [
        256,
        256
    ],
    "pv_version": "6.0.1",
    "date": "<class 'datetime.datetime'>",
    "shape_frames": [
        3
    ],
    "offset": [
        0,
        0,
        0
    ],
    "TR": 100,
    "slope": [
        0.00176479209428005,
        0.00176479209428005,
        0.00176479209428005
    ],
    "shape_storage": [
        256,
        256,
        3
    ],
    "num_slice_packages": 3
}

The reporting sub-command can be used in one of five possible cases:

  • folder in-place

  • folder to folder

  • dataset in-place

  • dataset to file

  • dataset to folder

Each of these cases is described in the examples section.

usage:

bruker report [-h] -i INPUT [-f {json,yml}] [-p PROPS [PROPS ...]]
arguments:

  • -h, –help show help message and exit

  • -i –input path to a Bruker data set, or a folder containing Bruker data sets

  • -o –output path to a folder, or a file to report to

  • -f, –format format of report files, one of {json,yml}, default value is json

  • -p, –props list of properties to export, if undefined, all properties are exported

examples:

The following list of scenarios is avaliable for the report subcommand:

  • Folder in-place – for every dataset within the folder (recursively) save its report file to the same folder where the dataset is located. It is possible to choose format using the -f argument.:

    bruker report -i ${DATA_PATH}/20200612_094625_lego_phantom_3_1_2/ -f yml

  • Folder to folder – for every dataset within the folder (recursively) save all report files to a folder specified by the -o argument. It is possible to choose format using the -f argument.:

    bruker report -i ${DATA_PATH}/20200612_094625_lego_phantom_3_1_2/ -o ${DATA_PATH}/tmp/ -f yml

  • Dataset in-place – for a dataset within the folder (recursively) save all report files to a folder specified by the -o argument. It is possible to choose format using the -f argument.:

    bruker report -i ${DATA_PATH}/20200612_094625_lego_phantom_3_1_2/3/pdata/1/2dseq  -f yml

  • Dataset to file – for every dataset within the folder (recursively) save all report files to a folder specified by the -o argument. It is possible to choose format using the -f argument.:

    bruker report -i 20200612_094625_lego_phantom_3_1_2/3/pdata/1/2dseq -o ${DATA_PATH}/tmp/report.json

  • Dataset to folder – for every dataset within the folder (recursively) save all report files to a folder specified by the -o argument. It is possible to choose format using the -f argument.:

    bruker report -i 20200612_094625_lego_phantom_3_1_2/ -o ${DATA_PATH}/tmp  -f yml

  • Say we are only interested in TE and TR properties and we want to specify name of the report file, to achieve this, we can use the -p argument.:

    bruker report -i 20200612_094625_lego_phantom_3_1_2/3/pdata/1/2dseq -p TE TR

split

Usage:

bruker report [-h] -i INPUT [-f {json,yml}] [-p PROPS [PROPS ...]]
arguments:

  • -h, –help show help message and exit

  • -i –input path to a Bruker data set, or a folder containing Bruker data sets

  • -f, –format format of report files, one of {json,yml}

  • -p, –props list of properties to export, if undefined, all properties are exported

Split by slice package:

bruker split -i 20200612_094625_lego_phantom_3_1_2/43/pdata/2/2dseq -s

Split by `FG_ISA`:

bruker split -i 20200612_094625_lego_phantom_3_1_2/43/pdata/2/2dseq -f FG_ISA

Split by `FG_ECHO`:

bruker split -i 20200612_094625_lego_phantom_3_1_2/43/pdata/2/2dseq -f FG_ECHO

filter

The filter sub-command provides an option to make various queries on folders containing Bruker data. It is possible to list all data sets measured with the same pulse sequence, data sets measured during the last month,etc.

List all data sets measured using the EPI pulse sequence:

bruker filter -i ${DATA_PATH}/20200612_094625_lego_phantom_3_1_2 -q "#PULPROG=='<EPI.ppg>'"

pipelines

It is possible to assemble pipelines using the Bruker API and xargs. Let us see some examples:

Using filter and report subcommands to only report datasets measured by the MGE sequence:

bruker filter -i /home/tomas/data/20200612_094625_lego_phantom_3_1_2/ -q "#PULPROG=='<MGE.ppg>'" | xargs -I {} bruker report -i {} -o /home/tomas/data/reports