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Mohammad Akhlaghi authored
Some cosmetic changes were made in the pipeline to prepare it for the public release. In particular the following: - The `README' file was updated to be more clear and follow the same format as that of the photometry and astrometry pipeline (with the necessary corrections). - A `configure' script was added to greatly simply the processing of setting the input directories. The version controlled `DIRECTORIES.mk.in' file is now the base file. After running `./configure', a copy of it is put into `DIRECTORIES.mk' and an editor is opened so the user can set them easily. - The acceptable version of Gnuastro was changed from the unofficial and not-released version `0.2.52-f620' to `0.2.51-bc56-bugfix'. The only necessary correction was in a single file (`bin/mkcatalog/upperlimit.c'), so that file is now included in this pipeline to allow easy correction to the main Gnuastro branch if it is necessary to fetch this snapshot from Gnuastro's history directly. The instructions to do this are available in `README'. - In the version of the pipeline that was used to publish the paper, we had 13 extra objects that were not specificly detected by ORIGIN, making a total of 173 objects. However, only 160 objects have an ORIGIN-only flag in the final catalog (the extra objects were not used). So to keep things clean, the 13 extra objects are removed from the input table and the whole input table is now available in the repository. The file `reproduce/input/input-positions.txt' also describes how to generate this table from the released catalog. Since the input catalog is no longer a user-specified parameter, the file and variable names were changed to an all-small-caps format. - A small Perl `flock' script is added to the pipeline so if it is not available on the system, it can easily be copied from here. - One of the objects (MUSE ID 6512) that was mistakenly classified as `RP' (existing/present in Rafelski catalog) is now correctly classified as `RC'. The reason was an visual mistake: there was another brighter source near the large galaxy, so I had thought that is the main target. But zooming into the FITS file, I noticed that the main object of interest is actually part of the brigher galaxy. - A typo of `Ns' (instead of `NS') was corrected in the classification table. To avoid such mistakes the checks of the codes are now in an `if-else' conditional, not independent `if's. - To allow more clarity in the percentages of the classification, they are now reported to two decimals in the internal description. - The demonstration cutout codes were corrected for the new list (that is now only 160 objects, instead of the old 173). - Removed the extra `subsection.tex' file since the the contents of the main PDF weren't included in the main paper either. - Removed the version number from the final output files, so they aren't need-lessly created on every change in the Git repo. The version is alrady present within the files. - Added section describing the small differences between the classsifications of this pipeline and those reported in the paper. - Corrected the copyright information and my email.
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