- 24 Jul, 2018 1 commit
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Mohammad Akhlaghi authored
Gnuastro 0.2.51 only builds with CFITSIO 3.41 or earlier. But this was not described in the README file. With this commit, a note has been added regarding the CFITSIO version. This issue was raised by Alejandro Serrano Borlaff.
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- 01 Feb, 2018 4 commits
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Mohammad Akhlaghi authored
A link to the page where I have described reproducible science has been added to the README to help people unfamiliar with the concept understand the purpose of this reproduction pipeline.
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Mohammad Akhlaghi authored
The link describing where to get the necessary version of Gnuastro was changed to point directly to the file in Zenodo. Also, the README file was slightly edited.
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Mohammad Akhlaghi authored
The copyright information on the files were not in a unified format. They are now all in a single format and mention the years that work has been done on them (2016-2018).
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Mohammad Akhlaghi authored
The main input dataset (the MUSE pseudo-broad-band images) and the whole pipeline in general (along with the HST images and throughputs, and also the necessary version of Gnuastro) will be uploaded to Zenodo for easy access in the future. With this commit, if the MUSE images are not in the given directory, they will also be downloaded and unpacked for use (similar to the HST images). The README file is also updated to account for this change. The contents of this commit will also be uploaded to Zenodo.
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- 31 Jan, 2018 1 commit
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Mohammad Akhlaghi authored
This commit does not affect the processing. Some final touches were made to the pipeline to make it easier and more stable for reproduction. The most important changes are: - The configuration files now have the specific version of Gnuastro in them so the pipeline doesn't run with any other version. - A README file was added to explain how to run the pipeline and also the dependencies. - Since the `flock' program might not be available on some systems, a Perl script was put in `reproduce/scripts/flock' so people can use it instead. - Some corrections were made in the downloaded file names. - Until now, the pipeline used a separate version of Gnuastro for its Table program which could write output into a FITS table (version 0.2.51-bc56 which is used in the pipeline can't do that). But the format of the output is irrelevant, for the purpose here, the contents are important. So this step was removed and the final tarball output of the pipeline is now fully reproducible with the single 0.2.51-bc56 version of Gnuastro. - The final tarball is placed in the `reproduce/output' directory, because it may be necessary later (when the intermediate files are deleted).
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- 30 Jun, 2017 1 commit
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Mohammad Akhlaghi authored
The `data-products' target was defined under the comments for the BibLaTeX target. So to make it more clear, some comments were specifically written for it and it was placed separtely in that file. This change has no effect on the results, only helps in readability.
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- 05 Jan, 2017 3 commits
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Mohammad Akhlaghi authored
The comments on the final tables were corrected to fit the new Gnuastro plain text table format. So using the Table program from new Gnuastro (currently under development) datastruct branch, the plain text tables were converted to FITS tables. They are then packed into a `.tar.gz' file to be easily communicated.
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Mohammad Akhlaghi authored
The plots for the difference in RA and Dec as a function of magnitude for the mosaic and the UDF10 have been created in the final PDF.
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Mohammad Akhlaghi authored
Until now NoiseChisel was ran on the HST images and the segmentation map was used for the comparisons of both magitude and astrometry. While this is accurate for the former, it is not so good for the latter, especially as the targets become fainter. The shape of the segmentation map (from HST) will bias the shallower MUSE astrometry. So for astrometry, we done the opposite: doing detection on MUSE and using its segmentation map on both MUSE and HST. The final comparison catalogs are now made with this commit and we can go onto the statistics.
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- 03 Jan, 2017 2 commits
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Mohammad Akhlaghi authored
The difference in distance plots are now also plotted in a similar way to the differences in magnitude. To do this generically and easily, the $(two-d-hists) rule in `statistics.mk' was slightly modified, so all the two-d histograms are generated with separate invokations of a single AWK command. This greatly helps later corrections/additions.
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Mohammad Akhlaghi authored
The source files have been separated: with the Make (`.mk') files now in `reproduce/make' and the scripts (for the time being only AWK) in `reproduce/scripts'. Also work has started on deriving the statistics of each field, but is not yet complete (it isn't a prerequisite of the final PDF for now in this commit).
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- 27 Dec, 2016 1 commit
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Mohammad Akhlaghi authored
Until now, NoiseChisel was run on the degraded HST images only for the segmentation map. However, because of the bad Sky subtraction in the HST images (as shown in the previous commit), the F814W result was strongly affected. So we now run NoiseChisel on the degraded HST images first, save the segments, and then subtract the Sky value from the degraded image. The result in the F814W image is now reasonable.
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- 26 Dec, 2016 3 commits
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Mohammad Akhlaghi authored
A first draft of a description has been written to explain the process. Since the F814W results are so significantly offset/different, a cutout was also included as PDF in the paper to display the possible cause.
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Mohammad Akhlaghi authored
Until now, the segmentation maps were created from the original resolution HST image, then warped to the grid of MUSE. However, the mixed pixels that were created would bias the position measurements of the objects, so now, we are using NoiseChisel on the degraded HST image. But since there is practically no noise left in those images, we use very lax NoiseChisel parameters. Also, the Sky value of the HST images is subtracted before convolution.
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Mohammad Akhlaghi authored
The ranges of the 2D histograms were corrected to more reasonable/descriptive values for better comparison.
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- 25 Dec, 2016 2 commits
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Mohammad Akhlaghi authored
PDF plots of the magnitude differences are now made and included in the description. Currently, the description doesn't have any text, but tha will be added when everything is thoroughly checked.
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Mohammad Akhlaghi authored
Catalogs with HST and MUSE magnitudes and positions are now created for the full UDF Mosaic and the UDF-10 field. The comments above the rules are descriptive enough.
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- 24 Dec, 2016 2 commits
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Mohammad Akhlaghi authored
Due to very small WCS differences, we might be having one column or row difference between the warped HST images and the MUSE images. To generate the catalog, the two images need to be the same size, so this was a problem. To solve it, the MUSE images are now cutout from the input image in a new directory (`muse-cutouts'). Then, after the HST images are warped, the MUSE and HST-warped image sizes are compared and if they are different, the MUSE image corrected (by one row or column of pixels along the respective dimension). Then it is put into the old `cutouts' directory. If the sizes are the same, then a copy is just put there.
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Mohammad Akhlaghi authored
Magnitude and position catalogs are now generated for both the HST images and the MUSE images. Using GNU Make's Secondary expansion, we don't need the `-h' or `-m' suffixes for the segmentation maps any more. Since the instrument name will be removed from the output filename during secondary expansion. The Sky and Sky standard deviation images are now also created. Note that since the purpose of this study is calibration, they are set to all 0 and all 1 valued images. Finally, using the filters and instrument the zeropoint magnitudes are calculated and used for MakeCatalog. Currently the catalogs are only used for similarly sized original cutouts. But the cutouts can be differently sized (due to sub-pixel differences in the WCS). So when the images have a different size, it currently stops.
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- 23 Dec, 2016 1 commit
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Mohammad Akhlaghi authored
NoiseChisel is now run on the original HST images and the object labeled image is then warped to the MUSE resolution and prepared to derive the segmentation maps. To make the prerequisite management of the final catalog much more easier, the final cutouts of both MUSE and HST are now in the same directory, only differing with a `-m.fits' or `-h.fits' suffix. The segmentation maps also follow the same naming convention, however, since the segmentation map is identical, the `-m.fits' file is actually a symbolic link to the `-h.fits' file.
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- 22 Dec, 2016 2 commits
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Mohammad Akhlaghi authored
The model MUSE PSFs were incorrectly calculated until now! I was mistakenly assuming that the `FSF01FWA' was the FWHM. However, the FWHM must be calculated from `b*lambda+a' where `b' is the value to `FSF01FWB' keyword and `a' is the value of `FSF01FWA'. The effective `lambda' (or wavelength) to use for each broad-band filter is the throughput-weighted average wavelength of the filter. So, the pipeline now uses the HST filter throughputs to find `lambda' and then uses the values of these keywords to generate the proper FWHM for the Moffat function. The throughputs will be downloaded if not already available. The FWHMs decreased from around 14 pixels to around 10 pixels. After implementing this correction, a test run of the deconvolution gave a better result. The reason was that the image crop to feed into the deconvolution algorithm was larger and so lower frequencies could be sampled. After seeing this trend, I increased the truncation radius of the model MUSE PSFs and also the deconvolution image size and saw that the deconvolution output kernel is becoming better and better. I finally stopped at 6 times the FWHM since it was apparently not making much more change. So, now the proper kernel to convolve with the HST images is created and we can directly compare the results with the MUSE images without worrying about a larger PSF. After convolution, the HST images are now also sampled to the same pixel size as MUSE.
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Mohammad Akhlaghi authored
The directories directly under the build directory are now built by one rule in the top level `Makefile' to avoid the confusion and Make errors that can be caused by doing it every time. This can also encourage building more of these directories for easy checking. The size of the kernel was also increased because in the MUSE PSF, 21 pixels was too small. The problem with the deconvolution is certainly more fundamental than that and must be solved separately. So for the time being we are ignoring the steps in generating the HST PSF.
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- 21 Dec, 2016 2 commits
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Mohammad Akhlaghi authored
The aligned UDF (not UDF10) images were in the same directory as the cutouts of each subfield. They are now saved in a separate directory of the top build directory to make the cutouts directory more easily understandable/managable. Especially since the HST images will be coming in too soon.
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Mohammad Akhlaghi authored
The MUSE PSFs were given as parameters to a Moffat function fit. So they were created using Gnuastro's MakeProfiles. The HST PSF was also generated from one of the bright stars in the UDF. It isn't the brightest, but so far we haven't checked if it was saturated or not. However, apparently, Gnuastro's convolve had problems in finding the kernel to convolve with the HST image to get to the MUSE resolution. So for now, we have kept the rules (to work on them later), but they are currently ignored in the pipeline (they aren't a prerequisite to anything). Since the MUSE PSF is much wider than the HST, for now, we will just convolve the HST image with the MUSE PSF. Later, when the problem above is solved, we will find the proper kernel more accurately.
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- 18 Dec, 2016 2 commits
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Mohammad Akhlaghi authored
The UDF1 to UDF9 regions of the MUSE UDF-Mosiac image have been defined and cropped from the main input image. However, the input image was not aligned with the celestial coordinates (which ImageCrop currently needs), so it was first aligned and then the regions were cut.
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Mohammad Akhlaghi authored
The UDF10 region cutouts are now made.
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