Package: astro-reduce
astro_reduce: A simple CCD-image reducer for theObservatoire de Paris-Meudon, applied to OHP T120 telescope.What does astro_reduce do?astro_reducecarries out the cosmetic and astrometric reduction of astronomical CCD images read in FITS format. The cosmetic reduction is done in a standard fashion with dark and flat field images. The astrometric reduction is done via calling either theAstromatic Software Suiteor theastrometry.neton the images obtained from the cosmetic reduction.Optionally, it can interpolate dark fields for exposure times missing in the available data and can also convert the intermediate and reduced images to PNG format for easy inspection. The astrometric reduction can be carried out anywhere from simply extracting sources to catalogs up to updating the image headers with astrometric output such as the linear projection matrix coefficients. For this, the relevant programs--eithersex,psfexorscampaccordingly with the specified options--must be installed on your system. The configuration files for these commands are handled internally byastro_reduce, you do not need to provide them.To operate,astro_reduceis to be launched from a directory containing three folders:ADARKfolder, containing all the dark field images,AFLATfolder, containing all flat field images,AORIGINALfolder, containing all the images of objects.All files must be in FITS format, with correct filter, exposure time and object header keywords wherever relevant.The flowchart below illustrates howastro_reduceruns. The boxes describe the content of folders found after the run, with directory names and name formats for files therein. The lines describe the flow of data during the run: solid lines indicate the standard run of the program, while dashed lines can be realized optionally.When launched for the first time in a directory, use the--setupoption. This will copy all data files to working folders (thereby backing up the original data). Then, runastro_reduceagain with relevant options to run the cosmetic and astrometric reductions; see details below on usage.During cosmetic reduction, intermediate images such as master dark fields or non-stacked object images are safe-kept in thear_masters/andar_tmp/folders. The final stacked images can be found in thestacked/folder. The cosmetic reduction process and the nomenclature for the naming of the files in thear_masters/,ar_tmp/andstacked/folders are given in theCosmetic reduction methodparagraph below. If options to perform the astrometric reduction were used, the results (such as source catalogs) can be found after running in theSEXRES,PSFRESandSCAMPRESfolders. The images with updated astrometric header data can be found in thereduced/folder, seeAstrometric reduction methodbelow.Note:It is highly recommended to inspect the intermediate images produced byastro_reducebefore considering the final reduced images. Also, we highly recommend you inspect your raw images and eliminate any bad ones before launching the software.InstallingTheastro_reduceprogram can be installed from the PyPI under the nameastro-reduce. This package provides the command with all options.Alternatively, use thesetup.pyfile in the project directory withpython3 setup.py install --userto install the program locally. You should then include~/.local/bin(or~/Library/Python/3.x/binfor Mac users) to your path in order to invokeastro_reducefrom the console.Dependenciesastro_reduceis written in Python 3.astro_reducedepends on theclick,astropy,astroquery,numpy,scipyandmatplotlibPython packages, which are all available through the PyPI.UsageWhen used for the first time in a directory, or when the data has been modified since the last use ofastro_reduce, the program should be invoked with the--setupoption:astro_reduce --setup [--verbose]This will setup the reduction by copying all the raw data toastro_reduce's working folders whilst changing the file names to standardized formats, as seen in the flowchart. Also, during this phase, a configuration file in the JSON format will be written. It summarizes the objects, filters and exposures times present in the original data and is used byastro_reducein the reduction process. This file should be left in the directory for further reference or for later rerunning of the program.Note:This first setup step is effectively a back-up of your data, as the data left in theDARK,FLATandORIGINALfolders are no longer touched during the subsequent reduction process.If the original data has changed or your are not sure when the--setupoption was used last, you can remove allastro_reduceworking data with the--clearoption.If the setup has already been done in the directory by prior use of the--setupoption,astro_reduceshould be used without this option:astro_reduce [OPTIONS]astro_reducehas been tested on Linux and Mac platforms, and has yet to be tested on Windows.Options--version          Show the version and exit.-s, --setup        Set up the directory for reduction. Use this option the first time astro_reduce is run in the directory or after the '--clear' option was used.-c, --clear        Remove all astro_reduce-related files and folders in current directory and exit.-i, --interpolate  Interpolate existing dark fields if some are missing.-v, --verbose      Enables verbose mode (recommended).-t, --tmppng       Write PNG format of auxiliary and master images after cosmetic reduction.-r, --stkpng       Write PNG format of stacked images after cosmetic reduction.-m, --astromatic   Performs all the astromatic suite commands (sextractor, psfex and scamp) for astrometry reduction purpose. This is equivalent to setting all the --sex --psfex --sexagain --scamp options.-n, --astrometrynet Performs the astrometry reduction with the astrometry.net tool. Note that by default the astromatic sextractor software is run and only the sources are sent to the astrometry.net server. If this operation fails, the whole image is sent, which increases the user exectution time but also increases the chances of convergence success. Setting -n erases the -m option.--sex              Run the 'sex' Astromatic command on all auxiliary images after the cosmetic reduction.--psfex            Run the 'psfex' Astromatic command with the 'sex'-determined sources in all auxiliary images.--sexagain         Run the 'sex' Astromatic command a second time, using the 'psfex'-determined PSF data.--scamp            Run the 'scamp' Astromatic command on all auxiliary images after cosmetic reduction.--nomaster         If set, do not calculate the master darks and flats (and assume they are already there!).--nostack          If set, skip the stacking process.--help             Show this message and exit.Cosmetic reduction methodMaster dark imagesFor a given exposure time, themaster darkis calculated as the pixel-wisemedianof all the dark fields of that exposure. This allows to eliminate cosmic ray traces.Dark field interpolationIn the case where dark fields for some exposure times are missing,astro_reducecan interpolate from the available master darks to obtain master darks for all the exposures necessary to reduce the object or flat images. This is done by specifying the--interpolateoption.The interpolation isleast-square linear, i.e., two images A and B are determined from the available master dark images such as tominimize the square erroron the linear interpolation (master dark) = (exposure time) x A + B.Using these A and B, the missing master darks are calculated according to this equation.The FITS files for all the master dark images (deduced from dark fields or interpolated) can be found after run in thear_masters/directory under the namesmdark_[exposure].fits.Master transmission (flat) imagesThemaster transmissionimage for a given filter is an image which encompasses the relative transmission of each pixel in the optical setup (telescope optics through filters to CCD matrix). It is calculated for every filter as themedianover all flat field images, aftersubtraction of corresponding master dark imagesandnormalization.The FITS files for all the master transmission images can be found after reduction in thear_masters/directory under the namesmtrans_[filter].fits.If you have already runastro_reduceor have your own master dark and flat images, you can skip these two last steps with the--nomasteroption. Beware that, in this case, you must place your custom master files in thear_masters/folder before running.Individual image reductionAn object image of given exposure and filter is cosmetically reduced bysubtractingthe corresponding exposure master dark image, anddividingby the corresponding filter master transmission image. We refer to these images as theauxiliaryimages, as in the flowchart.The FITS files for objectobj, with filterfiltand exposure timeexpare found in thear_tmp/folder after reduction, under the name[obj]_[filt]_[exp]_*_aux.fits(forauxiliary), which contains anastro_reduce-internal reference number.Realignment and stackingFinally, for each series of same exposure and filter for each object, the auxiliary images stacked: they are realigned through optimization of theirmutual cross-correlations, and then their pixel-wisemedianimage is calculated. Using the median rather than the mean allows to efficiently remove hot pixels. This will be all the more effective as dithering has been used in acquiring the images of a series.During the realignment, images are rolled to superimpose themselves. Therefore, if the images were too misaligned to begin with, objects that roll beyond the edge can end up in odd places, potentially producing ghost images of objects. Duringastro_reduce's run, a warning is issued to the user if any image is rolled by more than 15% of the field size during the realignment. In this case, it may be useful to remove the offending image from the dataset. If there are many such images and they are aligned amongst themselves, it is advised to change their headerOBJECTs in order to process them together as a separate batch.These stacked images are the final cosmetically reduced images and can be found in thestacked/folder after reduction, with the same names as in the preceding step, save the_auxsuffix and the internal image reference number.This stacking step can be altogether skipped using the--nostack, as appropriate for, e.g., fast moving objects.Some things to knowAs mentioned earlier, the original files in theDARK,FLATandORIGINALfolders are not used during the reduction process. Only their copies in thear_*working folders are used.In copying the original files during the setup process,astro_reducein effect backs up your data.astro_reducewill deduce the object captured in a given field from theOBJECTkeyword entry in the file's header. In the reduction, all files of a same object, filter and exposure time are cosmetically reduced and stacked together. Therefore, in order to keep different series of images of a same object separate, it is recommended to append a tag to the object name in acquiring the images of the series. For example NGC4993-1, NGC4993-2, etc.During the cosmetic reduction, the headers of synthetic images are filled in with the correctOBJECT,FILTER,EXPOSURE,EXPTIMEandIMAGETYPkeyword values. The other keyword values (such as the time of acquisition) are inherited from the parent images (raw darks and flats for master dark and master transmission images; raw object images for final reduced object fields).The cosmetically reduced images found inar_cosmetic/and thenstacked/are more voluminous (typically 4 times) than the original images, because they are encoded as floats following the dark-flat manipulations.fitand other derivatives can be used as extensions for the FITS files.Remaining hot pixels in the reduced images can be the result of insufficient dithering.Astrometric reduction methodThe astrometric reduction is launched either with the-m(or--astromatic),-n(or--astrometrynet), or--sex,--psfex,--sexagainand--scamp`) options, depending on how far you would like to take the reduction:Using-m(or--astromatic) is equivalent to setting all options--sex,--psfex,--sexagainand--scampUsing--sexruns theSExtractorprogram on all auxiliary files and places the results (source catalogs, etc.) in theSEXRES/folder, as in the flowchart.Using--psfex(which implies--sex) runs thePSFExprogram on the auxiliary images withSExtractor's results to produce PSF-related data in thePSFRES/folder.Using--sexagain(which implies--psfex) runsSExtractora second time on the auxiliary images, but using the PSF data from thePSFExrun. This updates the results inSEXRES/.Finally, using--scamp(which implies--sex) runsSCAMPto perform the astrometric reduction on the auxiliary images, using the source catalogs fromSEXRES/and data on remote servers.Alternatively to the Astromatic suite, you may use the astrometry.net capabilities by using the-n(or `--astrometrynet) option. This will run first the SExtractor software and send the sources found to the astrometry.net server for astrometric reduction. The resulting header is put into the output images.If the--scampoption was used, the final astrometrically reduced files with updated headers can be found inreduced/after run.Alternatively to the Astromatic suite, you may use the astrometry.net capabilities by using the-n(or--astrometrynet) option. This will run first the SExtractor software and send the sources found to the astrometry.net server for astrometric reduction. The resulting header is put into the output images, found in thereduced/directory.Note:astro_reduceships with all configuration files for the astrometric reduction of the OHP T120 telescope camera, you need not provide them. Astrometry is also performed on the stacked images.Enhancingastro_reduceHow can I add an option toastro_reduce?The project uses theClickPython package to handle the CLI options. To add an option, follow these steps:Add a@click.optiondecorator to theclifunction defined inastro_reduce.py. This allows to define the option's command-line flag, its short version and its help sentence. You can take inspiration from the existing options;The previous step will define a argument to theclifunction, with exactly the spelling of the CLI's flag; You must add this argument to the signature of theclifunction;So that the listing of current options in the welcome message continues to work properly, you must add the option to theOPT_LISTinhelpers.py;If the option extends the astrometric reduction capabilities ofastro_reduce, please also add the option to theASTROMATIC_LISTinhelpers.py.For more information on defining options, see theClick documentation.Making releases to the PyPiWe use the PyPi to distributeastro_reduce. To make a release, follow these steps:Define the version number of your release in thex.y.zform insetup.py. This version must not already exist in the PyPi, or else you will run into trouble down the line. We usesemantic versioning:Changexwhen you make backwards-incompatible changes, such as changing an existing option or the output format;Changeywhen you make backwards-compatible changes, such as introducing new functionality through a new option or new documentation;Changezwhen you fix minor bugs without noteworthy functionality improvement.Make sure you have updated the documentation (i.e., thisREADME) such that it fits the new version;Make a commit to the git repository where you indicate the number of the new version;Runpython3 setup.py bdist_wheeland thentwine upload dist/*.This last step will prompt you for your PyPi credentials. Naturally, it will only work if you have maintainer or owner status on the project's PyPi repository.Adding or changing a data fileWe also use the PyPi to distribute data files forastro_reduce. To include a new file to the distribution, do the following:Add the file to thedata/folder in the project repository;To make sure it is distributed with the rest of the project, list it in thedata_filesoption insetup.py;To retrieve the path to the file in theastro_reduce.pyscript in order to use the file, we use
theresource_filenamefunction of thepkg_resourcespackage: If you addedmy_new_file.txttodata/in the repo, the path to filemy_new_file.txtin the user's system will be the result of the call topkg_resources.resource_filenamewith argumentsastro_reduceanddata/my_new_file.txt. For example, see how we retrieve the paths to the Astromatic configuration files around line 570 inastro_reduce.py.Potential improvementsAllow the user to specify their own configuration file for the Astromatic programs (thus overriding the ones distributed throughpip).Allow the user to run the Astromatic suite on the stacked images as well, not only on the auxiliary images.