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1. prefix string will be prepended to the column names of the astropy table that I return writelog if True I save the sextractor command line input and output into a dedicated log file in the workdir Returns a dict containing the keys catfilepath the path to the sextractor output catalog file table the astropy table of the output catalog if returncat was not set to False e workdir the path to the workdir all my internal files are there logfilepath the path to the SExtractor log file in the workdir Everything related to this particular image stays within this method the SExtractor instance in particular config is not modified fullparamtxt n NUMBER Running object number n EXT_NUMBER FITS extension number n FLUX_ISO ls fullparamlist NUMBER EXT_NUMBER FLUX_ISO FLUXERR_ISO MAG _ISO MAGERR_ISO E 1 4 How to generate this documentation This documentation is generated using http sphinx doc org To build these pages go into the sewpy sphinx directory and run make html no need for apidoc The result is in build html index html 1 4 How to generate this documentation 7 sewpy Documentation Release 1 0dev 8 Chapter 1 Contents CHAPTER 2 Indices and tables e genindex e modindex s search Last build of this documentation May 24 2015 sewpy Documentation Release 1 0dev 10 Chapter 2 Indices and tables Pyt2. as the output astropy table catfilepath workdir and logfilepath 4 Chapter 1 Contents gging DEBUG sewpy Documentation Release 1 0dev now also works with vector parameters such as MAG_APER 4 possibility to nice SExtractor a log file is written for every run if not told otherwise filenames change according to FITS image file name where required but you can also pass an imgname argument to run and this will be used instead params and config files are written only once as discussed appropriate warnings and behaviour when a workdir already exists or when you rerun on the same file possibility to use existing param config conv nnw files run returns either the catalog or the filepath to the catalog To do e move config to run e check that all masked columns of ASSOC do indeed share the same mask e implement _check_config e better detection of SExtractor failures e implement raising Exceptions when SExtractor fails e implement CHECK IMAGE helper e give access to several conv and nnw settings if needed class sewpy sewpy SEW workdir None sexpath sex params None config None config filepath None nice None loglevel None Holds together all the settings to run SExtractor executable on one or several images _ init__ workdir None sexpath sex params None config None configfilepath None nice None loglevel None All arguments have default values and ar
3. Your are viewing the documentation of sewpy The code including the sources of the present documentation is hosted on github com megalut sewpy Contents 1 sewpy Documentation Release 1 0dev 2 Contents CHAPTER 1 Contents 1 1 Installing sewpy The requirements are astropy version 0 4 2 or later and obviously SExtractor sewpy does not require a specific version To get sewpy clone the project on github or click here to get a tarball of the latest version You now have at least two options to install the module 1 1 1 Method 1 if you just want to use the module Extract the tarball if required cd into it and python setup py install user For a system wide install remove the user More information about how to install python modules with distutil can be found in the official Distutils documentation 1 1 2 Method 2 if you intend to develop the module A simple solution is to add your local clone of sewpy to your python path for instance by modifying your bash_profile or equivalent export PYTHONPATH PYTHONPATH path to megalut sewpy 1 0 1 2 User manual 1 2 1 General philosophy to be rewritten e If you do not specify a workdir I 1l write all my required internal files somewhere in tmp and you don t have to bother about this this is done using the tempfile module params a list refers to the features that you want SExtractor to measure e g settings y
4. e optional Parameters e workdir where I ll write my files Specify this e g test if you care about the output files If None I create a unique temporary directory myself usually in tmp sexpath path to the sextractor executable e g sex or sextractor if in your PATH params list of strings the parameters you want SExtractor to measure i e what you would write in the default param file config dict config settings that will supersede the default config e g what you would change in the default sex file configfilepath specify this if you want me to use an existing SExtractor config file as default instead of the sextractor d one nice int niceness with which I should run SExtractor Use e g 19 for set lowest priority loglevel string or int or logging level verbosity e g the python level logging threshold for the sewpy module logger For example set this to WARNING and sewpy will no longer log simple INFOs Choices are DEBUG INFO WARNING ER ROR CRITICAL To disable logging set loglevel CRITICAL 1 3 API documentation of the sewpy module 5 sewpy Documentation Release 1 0dev To use an existing SExtractor param conv or nnw file simply specify these in the config dict using the appropriate SExtractor keys PARAMETERS_NAME FILTER_NAME Warning When using vector type params resulting
5. hon Module Index S sewpy sewpy 4 11 sewpy Documentation Release 1 0dev 12 Python Module Index Index Symbols __call__ sewpy sewpy SEW method 7 __init__ sewpy sewpy SEW method 5 __module__ sewpy sewpy SEW attribute 7 __str__ sewpy sewpy SEW method 6 _add_prefix sewpy sewpy SEW method 7 _check_config sewpy sewpy SEW method 6 _check_params sewpy sewpy SEW method 6 _clean_workdir sewpy sewpy SEW method 6 _get_assoc_filepath sewpy sewpy SEW method 6 _get_cat_filepath sewpy sewpy SEW method 6 _get_config_filepath sewpy sewpy SEW method 6 _get_conv_filepath sewpy sewpy SEW method 6 _get_log_filepath sewpy sewpy SEW method 6 _get_params_filepath sewpy sewpy SEW method 6 _set_instance_config sewpy sewpy SEW method 6 _write_assoc sewpy sewpy SEW method 6 _write_default_config sewpy sewpy SEW method 6 _write_default_conv sewpy sewpy SEW method 6 _write_params sewpy sewpy SEW method 6 F fullparamlist sewpy sewpy SEW attribute 7 fullparamtxt sewpy sewpy SEW attribute 7 G get_version sewpy sewpy SEW method 6 S SEW class in sewpy sewpy 5 sewpy sewpy module 4 13
6. in multiple columns such as FLUX_RADIUS 3 in the example above do not put these in the last position of the params list otherwise astropy fails reading the catalog This is probably due to the fact that the SExtractor header doesn t give a hint that multiple columns are expected when a vector type param comes last A workaround would be way too complicated get_version To find the SExtractor version we call it without arguments and parse the stdout Returns a string e g 2 4 4 __str__ A string summary representing the instance _check_params Compares the params to a list of known params and spits out a useful warning if something seems fishy _check_config Not yet implemented _set_instance_config Sets config parameters that remain fixed for this instance Called by __init__ If needed you could still mess with this config after __init__ has run _get_params_filepath Stays the same for a given instance _get_config_filepath Idem stays the same for a given instance Might return the non default configfilepath if set _get_conv_filepath Stays the same for a given instance _get_cat_filepath imgname This changes from image to image _get_assoc_filepath imgname Changes from image to image _get_log_filepath imgname Changes from image to image _write_params force False Writes the parameters to the file if needed Parameters force if True I overwrite any exis
7. input catalog instead of just making a new catalog of all sources In summary you pass an existing input catalog and you ll get this same catalog as output but with the new columns corresponding to the SExtractor params appended To use the ASSOC helper e Add VECTOR_ASSOC 3 to your params at the beginning not at the end of the params list e Add for instance ASSOC_RADIUS 10 0 ASSOC_TYPE ues are the defaults used if you don t specify anything NEAREST to your config These val e Give the relevant arguments assoc_cat assoc_xname assoc_yname when calling The output will contain an astropy table with the same rows as assoc_cat but to which the new SExtractor columns will be appended Those SExtractor columns might be masked columns leading to a masked table as some of your sources might not have been found by SExtractor Note that the attribute mytable masked tells you if an astropy table mytable is masked To make it even more foolproof I systematically add a boolean column named prefix assoc_flag True means that the source was found 1 3 API documentation of the sewpy module sewpy Source Extractor Wrapper for Python Recent improvements latest on top new loglevel option to adjust sewpy s overall verbosity on instantiation e better verbosity about masked output of ASSOC procedure e ASSOC helper implemented e run now returns a dict containing several objects such
8. ou find in de fault param config a dict refers to the settings e g stuff you find in default sex sewpy Documentation Release 1 0dev e A SEW instance can well be reused for different images that you want to analyse with the same params but a different config Indeed you usually don t want to change params from image to image but you might have to change the config e g gain seeing In the params list you have to specify all the parameters that you want to be measured On the other hand in the config dict you only have to give those settings that deviate from the default We take as default the output of sextractor d if not told otherwise When repeatedly calling run we avoid writing the SExtractor input files to disk over and over again Instead param is written only once and config settings are passed as command line arguments to the SExtractor exe cutable superseding the default config So to change config from image to image simply edit se config between calls of run There is special helper functionality for using ASSOC see note below 1 2 2 Logging Sewpy uses the logging module To see a detailed log of what is going on insert this into your script import logging logging basicConfig format levelname s name s funcName s message s level lq 1 2 3 The ASSOC helper The ASSOC helper assists you in measuring galaxies from an existing
9. sewpy Documentation Release 1 0dev The MegaLUT developers May 24 2015 Contents 1 Contents 3 J Installing sewpy sin 2 250040054 2H db Ge ee R 3 1 2 ser manual 2 Sc eee u oo ERAGE ES E AO A ee DR es 3 1 3 API documentation of the sewpy module LL LL e e nun 4 14 How to generate this documentation s s o e ecne e pece e e nn 7 2 Indices and tables 9 Python Module Index 11 sewpy Documentation Release 1 0dev The tiny sewpy module let s you run SExtractor as if it would all be native python import sewpy sew sewpy SEW params X_IMAGE Y_IMAGE FLUX_RADIUS 3 FLAGS config DETECT_MINAREA 10 PHOT_FLUXFRAC 0 3 0 5 0 8 out sew myimage fits print out table this is an astropy table but also allows for a more sophisticated use for instance if you want to use existing SExtractor input files Why yet another SExtractor wrapper Because we needed one that e is based on astropy in particular ast ropy table e uses standard Logging and also logs SExtractor s stdout amp stderr to file e uses tempfile to hide all input and output files except if you want to see them e has some convenience functionality to use SExtractor s ASSOC process give me an input catalog and I append columns with SExtractor measurements to it The demos in the examples directory can be run without installing sewpy and provide a quick overview
10. ting file _write_default_config force False Writes the default config file if needed I don t write this file if a specific config file is set Parameters force if True I overwrite any existing file _write_default_conv Writes the default convolution matrix if needed _clean_workdir Removes the config param files related to this instance to allow for a fresh restart Files related to specific images are not removed 6 Chapter 1 Contents sewpy Documentation Release 1 0dev _write_assoc cat xname yname imgname Writes a plain text file which can be used as sextractor input for the ASSOC identification And index for each source is generated it gets used to identify galaxies __module__ sewpy sewpy _add_prefix table prefix Modifies the column names of a table by prepending the prefix in place Skips the VECTOR_ASSOC stuff __call__ imgfilepath imgname None assoc_cat None assoc_xname x assoc_yname y re turncat True prefix writelog True Runs SExtractor on a given image Parameters imgfilepath Path to the input FITS image I should run on assoc_cat optional input catalog astropy table if you want to use the ASSOC helper assoc_xname x coordinate name I should use in the ASSOC helper assoc_yname idem returncat by default I read the SExtractor output catalog and return it as an astropy table If set to False I do not attempt to read it
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