Most of the programs require a working OpenCL environment and the installation of pyOpenCL (see https://mathema.tician.de/software/pyopencl/).
Programs assume that the source tree exists under one's own home directory, in ~/GITHUB. If the files are elsewhere, one can set an environmental variable ISM_DIRECTORY. ISM_DIRECTORY should point to the directory that contains ISM as a subdirectory (which then contains Defs.py and further subdirectories FITS, TM, etc.). If ISM_DIRECTORY is not set, that is the same as having ISM_DIRECTORY equal to ~/GITHUB.
Note: radiative transfer programs SOC and LOC now reside in separate repositories: https://github.com/mjuvela/SOC and https://github.com/mjuvela/LOC .
The directory TM contains scripts for template matching (TM) and Rolling Hough Transform -type (RHT) analysis of images. As an example of these, the script test_TM.py will run both routines on the provided FITS image. The expected output is shown in the included test_TM.png. For further information, see
- http://www.interstellarmedium.org/numerical_tools/template_matching
- Juvela M. 2016, A&A 593, A56: Pattern matching methods for the analysis of interstellar cloud structure
- www.interstellarmedium.org/numerical_tools/rht/
The directory Extinction includes some routines for the calculation of extinction maps based on the (near-infrared) reddening of background stars. The sample script test_Nicer.py should download input data (photometry for 2Mass stars) from the web, calculate an extinction map for a region specified in the script, and write the results to a FITS files. The programs again require a working OpenCL environment.
For further information, see *www.interstellarmedium.org/extinction' and the references mentioned there.
The directory FITS contains programs related to the handling of FITS images. At the moment there is a draft program for the resampling of FITS images using the Drizzle algorithm (for example the optional shrinking of input-image pixels is not yet implemented). The execution of
python test_drizzle.py
should run a series of tests, comparing the run times of Montage.reproject (assuming that one has installed montage_wrapper) and the OpenCL routine that is run on CPU and on GPU (assuming one has those available). Furthermore, the call
ResampleImage.py g.fits A.fits B.fits
will resample the FITS image g.fits onto the pixels defined by the header of the file A.fits, writing the result as a new file B.fits. If one has successfully run test_drizzle.py, g.fits and A.fits should already exist. A.fits was there produced from g.fits with the Montage program so that A.fits and the file B.fits, created by the above ResampleImage call, should be similar (except for the borders, see the first link below).
For more information,see
- http://www.interstellarmedium.org/numerical_tools/fits_images/, including a discussion on convolution with OpenCL
- http://www.interstellarmedium.org/numerical_tools/mad/ discusses the implementation of the median absolute deviation (MAD) algorithm with OpenCL
- the original publication on the Drizzle algorithm: Fruchter & Hook, 2002, PASP 112, 144; https://ui.adsabs.harvard.edu/abs/2002PASP..114..144F
The directory contains comparisons between modified blackbody fits with Scipy leastsq and a simplistic OpenCL routine. There are further examples of modified blackbody fits with Markov chain Monte Carlo. The results are discussed at
Ocfile directory contains a Python/pyOpenCL program that tries to identify filaments from a FITS image, trace the filaments, and produce 2D of them (one dimension running along the filament, the other being perpendicular). The current GitHub version relies on scipy.ndimage routine label(), which may not scale well for large images (>1000x1000 pixels). The (simple) program will be described in more detail at
SPIF can fit individual spectral lines with Gaussian (one or multiple velocity components) or as hyperfine lines consisting of several components. The input and output files are FITS cubes. The program is described in Juvela, M., Tharakkal, D., 2024, A&A, "Fast fitting of spectral lines with Gaussian and hyperfine structure models" in arXiv
Program handles currently only spherical models (cells are spherical shells), computes dust temperatures (equilibrium temperatures only), and returns spectra for different impact parameters. The program uses OpenCL libraries and is recommended to be run on GPUs. The paper Juvela M., "DIES: parallel dust radiative transfer program with the immediate re-emission method" has been submitted. Further information will be provided at