LSMTool: the LOFAR Sky Model Tool

LSMTool allows the manipulation of LOFAR sky models (in the makesourcedb format).

Author:

• David Rafferty

Based on contributed scripts by:

• Bjoern Adebahr
• Francesco de Gasperin
• Reinout van Weeren

Contents:

• docs/: documentation
• tests/: contains test sky models and scripts useful for validation
• bin/: contains lsmtool executable
• lsmtool/: contains the main LSMTool scripts
• lsmtool/operations/: contains the modules for operations
• parsets/: some example parsets

The following operations are available:

• SELECT: Select sources by source or patch properties
• REMOVE: Remove sources by source or patch properties
• TRANSFER: Transfer a patch scheme from one sky model to another
• GROUP: Group sources into patches
• UNGROUP: Remove patches
• MOVE: Move a source or patch position
• MERGE: Merge two or more patches into one
• CONCATENATE: Concatenate two sky models
• ADD: Add a source
• SETPATCHPOSITIONS: Calculate and set patch positions
• PLOT: Plot the sky model
• COMPARE: Compare source fluxes and positions of two sky models

For details, please see the full documentation.

Dependencies

LSMTool depends on the following packages:

• Astropy (version 3.2 or later)
• EveryBeam (version 0.6.1 or later)
• Matplotlib
• NumPy
• Pillow (any version except 10.x)
• PyBDSF
• Python-Casacore
• PyVO
• Scipy (version 0.11 or later)
• Shapely

These packages will normally be installed automatically.

Downloading and Installing

LSMTool uses PyBDSF as default source finder. If you wish, you can use SoFiA-2 instead, which can be installed as extra.

Install the latest release from PyPI

    pip install lsmtool

or with SoFiA-2 as extra:

    pip install lsmtool[sofia]

Install the latest developer version

    pip install git+https://git.astron.nl/RD/LSMTool.git

or with SoFiA-2 as extra:

    pip install lsmtool[sofia] git+https://git.astron.nl/RD/LSMTool.git

Install a faster mean-shift grouping algorithm

If you have a C++11-compliant compiler, you can build a faster version of the mean shift grouping algorithm by compiling it yourself:

    git clone https://git.astron.nl/RD/LSMTool.git
    cd LSMTool
    sed -Ei 's/^(BUILD_EXTENSIONS = ).*/\1"ON"/' pyproject.toml
    pip install .

Note that the C++ version will give slightly different results compared to the Python version, but such differences are not expected to be important in practice.

Testing

If you've cloned the repository, and installed the software from source, you can test that the installation works as expected:

    pip install pytest
    pytest

If no errors occur, LSMTool is installed correctly.

Usage

The LSMTool executable can be used from the command line with a parset that defines the steps to be done. E.g.:

$ lsmtool model.sky lsmtool.parset

The parset follows the usual DP3 format. E.g.:

# Select individual sources with Stokes I fluxes above 1 Jy
LSMTool.Steps.select.Operation = SELECT
LSMTool.Steps.select.FilterExpression = I > 1.0 Jy
LSMTool.Steps.select.OutFile = out_model.sky

LSMTool can also be used in Python scripts by importing the lsmtool module. E.g.:

>>> import lsmtool
>>> skymod = lsmtool.load('model.sky')
>>> skymod.select('I > 1.0 Jy')
>>> skymod.write('out_model.sky')

For further details, please see the full documentation.