Contents:
legacypipe.runbrick module¶Main “pipeline” script for the Legacy Survey (DECaLS, MzLS, BASS) data reductions.
For calling from other scripts, see:
Or for much more fine-grained control, see the individual stages:
stage_tims()stage_image_coadds()stage_srcs()stage_fitblobs()stage_coadds()stage_wise_forced()stage_writecat()To see the code we run on each “blob” of pixels, see “oneblob.py”.
one_blob()legacypipe.runbrick.collapse_unwise_bitmask(bitmask, band)[source]¶
Converts WISE mask bits (in the unWISE data products) into the more compact codes reported in the tractor files as WISEMASK_W[12], and the “maskbits” WISE extensions.
output bits : # 2^0 = bright star core and wings # 2^1 = PSF-based diffraction spike # 2^2 = optical ghost # 2^3 = first latent # 2^4 = second latent # 2^5 = AllWISE-like circular halo # 2^6 = bright star saturation # 2^7 = geometric diffraction spike
legacypipe.runbrick.read_gaia(targetwcs)[source]¶
margin in degrees
legacypipe.runbrick.read_star_clusters(targetwcs)[source]¶
Code to regenerate the NGC-star-clusters-fits catalog:
wget https://raw.githubusercontent.com/mattiaverga/OpenNGC/master/NGC.csv
import os import numpy as np import numpy.ma as ma from astropy.io import ascii from astrometry.util.starutil_numpy import hmsstring2ra, dmsstring2dec import desimodel.io import desimodel.footprint
NGC = ascii.read(‘NGC.csv’, delimiter=’;’, names=names)
objtype = np.char.strip(ma.getdata(NGC[‘type’])) keeptype = (‘PN’, ‘OCl’, ‘GCl’, ‘Cl+N’) keep = np.zeros(len(NGC), dtype=bool) for otype in keeptype:
ww = [otype == tt for tt in objtype] keep = np.logical_or(keep, ww)
clusters = NGC[keep]
ra, dec = [], [] for _ra, _dec in zip(ma.getdata(clusters[‘ra_hms’]), ma.getdata(clusters[‘dec_dms’])):
ra.append(hmsstring2ra(_ra.replace(‘h’, ‘:’).replace(‘m’, ‘:’).replace(‘s’,’‘))) dec.append(dmsstring2dec(_dec.replace(‘d’, ‘:’).replace(‘m’, ‘:’).replace(‘s’,’‘)))
clusters[‘ra’] = ra clusters[‘dec’] = dec
tiles = desimodel.io.load_tiles(onlydesi=True) indesi = desimodel.footprint.is_point_in_desi(tiles, ma.getdata(clusters[‘ra’]),
ma.getdata(clusters[‘dec’]))
print(np.sum(indesi)) clusters.write(‘NGC-star-clusters.fits’, overwrite=True)
legacypipe.runbrick.run_brick(brick, survey, radec=None, pixscale=0.262, width=3600, height=3600, zoom=None, bands=None, allbands=None, depth_cut=False, nblobs=None, blob=None, blobxy=None, blobradec=None, blobid=None, max_blobsize=None, nsigma=6, simul_opt=False, wise=True, lanczos=True, early_coadds=False, blob_image=False, do_calibs=True, write_metrics=True, gaussPsf=False, pixPsf=False, hybridPsf=False, normalizePsf=False, apodize=False, rgb_kwargs=None, rex=False, splinesky=True, subsky=True, constant_invvar=False, gaia_stars=False, min_mjd=None, max_mjd=None, unwise_coadds=False, bail_out=False, ceres=True, wise_ceres=True, unwise_dir=None, unwise_tr_dir=None, threads=None, plots=False, plots2=False, coadd_bw=False, plot_base=None, plot_number=0, record_event=None, pickle_pat='pickles/runbrick-%(brick)s-%%(stage)s.pickle', stages=['writecat'], force=[], forceall=False, write_pickles=True, checkpoint_filename=None, checkpoint_period=None, prereqs_update=None, stagefunc=None)[source]¶
Run the full Legacy Survey data reduction pipeline.
The pipeline is built out of “stages” that run in sequence. By default, this function will cache the result of each stage in a (large) pickle file. If you re-run, it will read from the prerequisite pickle file rather than re-running the prerequisite stage. This can yield faster debugging times, but you almost certainly want to turn it off (with writePickles=False, forceall=True) in production.
Parameters:Brick name such as ‘2090m065’. Can be None if radec is given.
charge of the list of bricks and CCDs to be handled, and where output files should be written.
RA,Dec center of the custom region to run.
Brick pixel scale, in arcsec/pixel. Default = 0.262
Brick size in pixels. Default of 3600 pixels (with the default pixel scale of 0.262) leads to a slight overlap between bricks.
Pixel coordinates [xlo,xhi, ylo,yhi] of the brick subimage to run.
Filter (band) names to include; default is “grz”.
If an invalid brick name is given.
If no CCDs, or no photometric CCDs, overlap the given brick or region.
Notes
You must specify the region of sky to work on, via one of:
If radec is given, brick should be None. If brick is given, that brick`s RA,Dec center will be looked up in the survey-bricks.fits file.
You can also change the size of the region to reduce:
If you want to measure only a subset of the astronomical objects, you can use:
Other options:
Plotting options:
Options regarding the “stages”:
legacypipe.runbrick.stage_coadds(survey=None, bands=None, version_header=None, targetwcs=None, tims=None, ps=None, brickname=None, ccds=None, custom_brick=False, T=None, cat=None, pixscale=None, plots=False, coadd_bw=False, brick=None, W=None, H=None, lanczos=True, saturated_pix=None, brightblobmask=None, bailout_mask=None, mp=None, record_event=None, **kwargs)[source]¶
After the stage_fitblobs fitting stage, we have all the source model fits, and we can create coadds of the images, model, and residuals. We also perform aperture photometry in this stage.
legacypipe.runbrick.stage_fitblobs(T=None, brickname=None, brickid=None, brick=None, version_header=None, blobsrcs=None, blobslices=None, blobs=None, cat=None, targetwcs=None, W=None, H=None, bands=None, ps=None, tims=None, survey=None, plots=False, plots2=False, nblobs=None, blob0=None, blobxy=None, blobradec=None, blobid=None, max_blobsize=None, simul_opt=False, use_ceres=True, mp=None, checkpoint_filename=None, checkpoint_period=600, write_pickle_filename=None, write_metrics=True, get_all_models=False, refstars=None, rex=False, bailout=False, record_event=None, custom_brick=False, **kwargs)[source]¶
This is where the actual source fitting happens. The one_blob function is called for each “blob” of pixels with the sources contained within that blob.
legacypipe.runbrick.stage_mask_junk(tims=None, targetwcs=None, W=None, H=None, bands=None, mp=None, nsigma=None, plots=None, ps=None, record_event=None, **kwargs)[source]¶
This pipeline stage tries to detect artifacts in the individual exposures, by running a detection step and removing blobs with large axis ratio (long, thin objects, often satellite trails).
legacypipe.runbrick.stage_srcs(targetrd=None, pixscale=None, targetwcs=None, W=None, H=None, bands=None, ps=None, tims=None, plots=False, plots2=False, brickname=None, mp=None, nsigma=None, survey=None, brick=None, gaia_stars=False, star_clusters=True, record_event=None, **kwargs)[source]¶
In this stage we run SED-matched detection to find objects in the images. For each object detected, a tractor source object is created, initially a tractor.PointSource. In this stage, the sources are also split into “blobs” of overlapping pixels. Each of these blobs will be processed independently.
legacypipe.runbrick.stage_tims(W=3600, H=3600, pixscale=0.262, brickname=None, survey=None, ra=None, dec=None, plots=False, ps=None, target_extent=None, program_name='runbrick.py', bands=['g', 'r', 'z'], do_calibs=True, splinesky=True, subsky=True, gaussPsf=False, pixPsf=False, hybridPsf=False, normalizePsf=False, apodize=False, constant_invvar=False, depth_cut=True, read_image_pixels=True, min_mjd=None, max_mjd=None, mp=None, record_event=None, unwise_dir=None, unwise_tr_dir=None, **kwargs)[source]¶
This is the first stage in the pipeline. It determines which CCD images overlap the brick or region of interest, runs calibrations for those images if necessary, and then reads the images, creating tractor.Image (“tractor image” or “tim”) objects for them.
PSF options:
Sky:
legacypipe.runbrick.stage_wise_forced(survey=None, cat=None, T=None, targetwcs=None, W=None, H=None, pixscale=None, brickname=None, unwise_dir=None, unwise_tr_dir=None, brick=None, wise_ceres=True, unwise_coadds=False, version_header=None, mp=None, record_event=None, **kwargs)[source]¶
After the model fits are finished, we can perform forced photometry of the unWISE coadds.
legacypipe.runbrick.stage_writecat(survey=None, version_header=None, T=None, WISE=None, WISE_T=None, maskbits=None, maskbits_header=None, wise_mask_maps=None, AP=None, apertures_arcsec=None, cat=None, pixscale=None, targetwcs=None, W=None, H=None, bands=None, ps=None, plots=False, brickname=None, brickid=None, brick=None, invvars=None, gaia_stars=False, allbands='ugrizY', record_event=None, **kwargs)[source]¶
Final stage in the pipeline: format results for the output catalog.
legacypipe.detection.run_sed_matched_filters(SEDs, bands, detmaps, detivs, omit_xy, targetwcs, nsigma=5, saturated_pix=None, plots=False, ps=None, mp=None)[source]¶
Runs a given set of SED-matched filters.
Parameters:The SEDs to run. The sed values are lists the same length as bands.
The band names of detmaps and detivs.
Detection maps for each of the listed bands.
Inverse-variances of the detmaps.
Existing sources to avoid: x, y, radius.
WCS object to use to convert pixel values into RA,Decs for the returned Tractor PointSource objects.
Detection threshold
Passed through to sed_matched_detection. A map of pixels that are always considered “hot” when determining whether a new source touches hot pixels of an existing source.
Create plots?
Create plots?
Multiprocessing
Table of new sources detected
Newly detected objects, with positions and fluxes, as Tractor PointSource objects.
“Hot pixels” containing sources.
legacypipe.detection.sed_matched_detection(sedname, sed, detmaps, detivs, bands, xomit, yomit, romit, nsigma=5.0, saturated_pix=None, saddle=2.0, cutonaper=True, ps=None)[source]¶
Runs a single SED-matched detection filter.
Avoids creating sources close to existing sources.
Parameters:Name of this SED; only used for plots.
The SED – a list of floats, one per band, of this SED.
The per-band detection maps. These must all be the same size, the brick image size.
The inverse-variance maps associated with detmaps.
The band names of the detmaps and detivs images.
Previously known sources that are to be avoided; x,y +- radius
Detection threshold.
A map of pixels that are always considered “hot” when determining whether a new source touches hot pixels of an existing source.
Saddle-point depth from existing sources down to new sources.
Apply a cut that the source’s detection strength must be greater than nsigma above the 16th percentile of the detection strength in an annulus (from 10 to 20 pixels) around the source.
Create plots?
A map of the blobs yielding sources in this SED.
The new sources found.
The detection strength in the annulus around the source, if cutonaper is set; else -1.
The detection strength.
legacypipe.detection.sed_matched_filters(bands)[source]¶
Determines which SED-matched filters to run based on the available bands.
Returns:legacypipe.detection.segment_and_group_sources(image, T, name=None, ps=None, plots=False)[source]¶
image: binary image that defines “blobs” T: source table; only “.ibx” and “.iby” elements are used (x,y integer pix pos). Note: “.blob” field is added. name: for debugging only
Returns: (blobs, blobsrcs, blobslices)
blobs: image, values -1 = no blob, integer blob indices blobsrcs: list of np arrays of integers, elements in T within each blob blobslices: list of slice objects for blob bounding-boxes.
legacypipe.catalog.read_fits_catalog(T, hdr=None, invvars=False, bands='grz', allbands=None, ellipseClass=<Mock id='140636938539536'>, unpackShape=True, fluxPrefix='')[source]¶
This is currently a weird hybrid of dynamic and hard-coded.
Return list of tractor Sources.
If invvars=True, return sources,invvars where invvars is a list matching sources.getParams()
If ellipseClass is set, assume that type for galaxy shapes; if None, read the type from the header.
If unpackShapes is True and ellipseClass is EllipseE, read catalog entries “shapeexp_r”, “shapeexp_e1”, “shapeexp_e2” rather than “shapeExp”, and similarly for “dev”.
legacypipe.survey.BrickDuck(ra, dec, brickname)[source]¶
Bases: object
A little duck-typing class when running on a custom RA,Dec center rather than a brick center.
legacypipe.survey.LegacySurveyData(survey_dir=None, cache_dir=None, output_dir=None, version=None, ccds=None, verbose=False)[source]¶
Bases: object
A class describing the contents of a LEGACY_SURVEY_DIR directory – tables of CCDs and of bricks, and calibration data. Methods for dealing with the CCDs and bricks tables.
This class is also responsible for creating LegacySurveyImage objects (eg, DecamImage objects), which then allow data to be read from disk.
Methods
add_hashcode(fn, hashcode) Callback to be called in the write_output routine. bricks_touching_radec_box(bricks, ralo, …) Returns an index vector of the bricks that touch the given RA,Dec box. ccds_touching_wcs(wcs, **kwargs) Returns a table of the CCDs touching the given wcs region. drop_cache() Clears all cached data contained in this object. filter_ccds_files(fns) When reading the list of CCDs, we find all files named survey-ccds-*.fits.gz, then filter that list using this function. find_ccds([expnum, ccdname, camera]) Returns a table of CCDs matching the given expnum (exposure number, integer), ccdname (string), and camera (string), if given. find_file(filetype[, brick, brickpre, band, …]) Returns the filename of a Legacy Survey file. get_annotated_ccds() Returns the annotated table of CCDs. get_brick(brickid) Returns a brick (as one row in a table) by brickid (integer). get_brick_by_name(brickname) Returns a brick (as one row in a table) by name (string). get_bricks() Returns a table of bricks. get_bricks_near(ra, dec, radius) Returns a set of bricks near the given RA,Dec and radius (all in degrees). get_bricks_readonly() Returns a read-only (shared) copy of the table of bricks. get_calib_dir() Returns the directory containing calibration data. get_ccds(**kwargs) Returns the table of CCDs. get_ccds_readonly() Returns a shared copy of the table of CCDs. get_image_dir() Returns the directory containing image data. get_image_object(t, **kwargs) Returns a DecamImage or similar object for one row of the CCDs table. get_se_dir() Returns the directory containing SourceExtractor config files, used during calibration. get_survey_dir() Returns the base LEGACY_SURVEY_DIR directory. read_intermediate_catalog(brick, **kwargs) Reads the intermediate tractor catalog for the given brickname. tims_touching_wcs(targetwcs, mp[, bands]) Creates tractor.Image objects for CCDs touching the given targetwcs region. try_expnum_kdtree(expnum) # By creating a kd-tree from the ‘expnum’ column, search for expnums # can be sped up: from astrometry.libkd.spherematch import * from astrometry.util.fits import fits_table T=fits_table(‘/global/cscratch1/sd/dstn/dr7-depthcut/survey-ccds-dr7.kd.fits’, columns=[‘expnum’]) ekd = tree_build(np.atleast_2d(T.expnum.copy()).T.astype(float), nleaf=60, bbox=False, split=True) ekd.set_name(‘expnum’) ekd.write(‘ekd.fits’) write_output(filetype[, hashsum]) Returns a context manager for writing an output file; use like: ccds_for_fitting check_cache cleanup_ccds_table debug filter_ccd_kd_files get_approx_wcs get_ccd_kdtrees get_compression_string image_class_for_camera index_of_band sed_matched_filters
add_hashcode(fn, hashcode)[source]¶
Callback to be called in the write_output routine.
bricks_touching_radec_box(bricks, ralo, rahi, declo, dechi)[source]¶
Returns an index vector of the bricks that touch the given RA,Dec box.
ccds_touching_wcs(wcs, **kwargs)[source]¶
Returns a table of the CCDs touching the given wcs region.
drop_cache()[source]¶
Clears all cached data contained in this object. Useful for pickling / multiprocessing.
filter_ccds_files(fns)[source]¶
When reading the list of CCDs, we find all files named survey-ccds-*.fits.gz, then filter that list using this function.
find_ccds(expnum=None, ccdname=None, camera=None)[source]¶
Returns a table of CCDs matching the given expnum (exposure number, integer), ccdname (string), and camera (string), if given.
find_file(filetype, brick=None, brickpre=None, band='%(band)s', output=False, **kwargs)[source]¶
Returns the filename of a Legacy Survey file.
brick : string, brick name such as “0001p000”
output: True if we are about to write this file; will use self.outdir as the base directory rather than self.survey_dir.
Returns: path to the specified file (whether or not it exists).
get_annotated_ccds()[source]¶
Returns the annotated table of CCDs.
get_brick(brickid)[source]¶
Returns a brick (as one row in a table) by brickid (integer).
get_brick_by_name(brickname)[source]¶
Returns a brick (as one row in a table) by name (string).
get_bricks()[source]¶
Returns a table of bricks. The caller owns the table.
For read-only purposes, see get_bricks_readonly(), which uses a cached version.
get_bricks_near(ra, dec, radius)[source]¶
Returns a set of bricks near the given RA,Dec and radius (all in degrees).
get_bricks_readonly()[source]¶
Returns a read-only (shared) copy of the table of bricks.
get_calib_dir()[source]¶
Returns the directory containing calibration data.
get_ccds(**kwargs)[source]¶
Returns the table of CCDs.
get_ccds_readonly()[source]¶
Returns a shared copy of the table of CCDs.
get_image_dir()[source]¶
Returns the directory containing image data.
get_image_object(t, **kwargs)[source]¶
Returns a DecamImage or similar object for one row of the CCDs table.
get_se_dir()[source]¶
Returns the directory containing SourceExtractor config files, used during calibration.
get_survey_dir()[source]¶
Returns the base LEGACY_SURVEY_DIR directory.
read_intermediate_catalog(brick, **kwargs)[source]¶
Reads the intermediate tractor catalog for the given brickname.
kwargs: passed to self.find_file()
Returns (T, hdr, primhdr)
tims_touching_wcs(targetwcs, mp, bands=None, **kwargs)[source]¶
Creates tractor.Image objects for CCDs touching the given targetwcs region.
mp: multiprocessing object
kwargs are passed to LegacySurveyImage.get_tractor_image() and may include:
try_expnum_kdtree(expnum)[source]¶
# By creating a kd-tree from the ‘expnum’ column, search for expnums # can be sped up: from astrometry.libkd.spherematch import * from astrometry.util.fits import fits_table T=fits_table(‘/global/cscratch1/sd/dstn/dr7-depthcut/survey-ccds-dr7.kd.fits’,
columns=[‘expnum’])
ekd.set_name(‘expnum’) ekd.write(‘ekd.fits’)
> fitsgetext -i $CSCRATCH/dr7-depthcut/survey-ccds-dr7.kd.fits -o dr7-%02i -a -M > fitsgetext -i ekd.fits -o ekd-%02i -a -M > cat dr7-0* ekd-0[123456] > $CSCRATCH/dr7-depthcut+/survey-ccds-dr7.kd.fits
write_output(filetype, hashsum=True, **kwargs)[source]¶
Returns a context manager for writing an output file; use like:
For FITS output, out.fits is a fitsio.FITS object. The file contents will actually be written in memory, and then a sha256sum computed before the file contents are written out to the real disk file. The ‘out.fn’ member variable is NOT set.
Does the following on entry: - calls self.find_file() to determine which filename to write to - ensures the output directory exists - appends a “.tmp” to the filename
Does the following on exit: - moves the “.tmp” to the final filename (to make it atomic) - computes the sha256sum
legacypipe.survey.brick_catalog_for_radec_box(ralo, rahi, declo, dechi, survey, catpattern, bricks=None)[source]¶
Merges multiple Tractor brick catalogs to cover an RA,Dec bounding-box.
No cleverness with RA wrap-around; assumes ralo < rahi.
survey: LegacySurveyData object
bricks: table of bricks, eg from LegacySurveyData.get_bricks()
legacypipe.survey.bricks_touching_wcs(targetwcs, survey=None, B=None, margin=20)[source]¶
Finds LegacySurvey bricks touching a given WCS header object.
Parameters:The region of sky to search
From which the brick table will be retrieved
The table of brick objects to search
Margin in pixels around the outside of the WCS
legacypipe.survey.ccd_map_image(valmap, empty=0.0)[source]¶
valmap: { ‘N7’ : 1., ‘N8’ : 17.8 }
Returns: a numpy image (shape (12,14)) with values mapped to their CCD locations.
legacypipe.survey.ccds_touching_wcs(targetwcs, ccds, ccdrad=None, polygons=True)[source]¶
targetwcs: wcs object describing region of interest ccds: fits_table object of CCDs
ccdrad: radius of CCDs, in degrees. If None (the default), compute from the CCDs table. (0.17 for DECam)
Returns: index array I of CCDs within range.
legacypipe.survey.get_git_version(dir=None)[source]¶
Runs ‘git describe’ in the current directory (or given dir) and returns the result as a string.
Parameters:If non-None, “cd” to the given directory before running ‘git describe’
legacypipe.survey.get_rgb(imgs, bands, mnmx=None, arcsinh=None, scales=None, clip=True)[source]¶
Given a list of images in the given bands, returns a scaled RGB image.
imgs a list of numpy arrays, all the same size, in nanomaggies bands a list of strings, eg, [‘g’,’r’,’z’] mnmx = (min,max), values that will become black/white after scaling. Default is (-3,10) arcsinh use nonlinear scaling as in SDSS scales
Returns a (H,W,3) numpy array with values between 0 and 1.
Creates a fitsio header describing a DECaLS data product.
legacypipe.survey.imsave_jpeg(jpegfn, img, **kwargs)[source]¶
Saves a image in JPEG format. Some matplotlib installations (notably at NERSC) don’t support jpeg, so we write to PNG and then convert to JPEG using the venerable netpbm tools.
jpegfn: JPEG filename img: image, in the typical matplotlib formats (see plt.imsave)
legacypipe.survey.radec_at_mjd(ra, dec, ref_year, pmra, pmdec, parallax, mjd)[source]¶
Units: - matches Gaia DR1/DR2 - pmra,pmdec are in mas/yr. pmra is in angular speed (ie, has a cos(dec) factor) - parallax is in mas.
NOTE: does not broadcast completely correctly – all params vectors or all motion params vector + scalar mjd work fine. Other combos: not certain.
Returns RA,Dec
legacypipe.survey.switch_to_soft_ellipses(cat)[source]¶
Converts our softened-ellipticity EllipseESoft parameters into normal EllipseE ellipses.
legacypipe.survey.wcs_for_brick(b, W=3600, H=3600, pixscale=0.262)[source]¶
Returns an astrometry.net style Tan WCS object for a given brick object.
b: row from survey-bricks.fits file W,H: size in pixels pixscale: pixel scale in arcsec/pixel.
Returns: Tan wcs object
legacypipe.oneblob.SourceModels[source]¶
Bases: object
This class maintains a list of the model patches for a set of sources in a set of images.
Methods
add(i, tims) Adds the models for source i back into the tims. create(tims, srcs[, subtract]) Note that this modifies the tims if subtract=True. model_masks restore_images save_images update_and_subtract
add(i, tims)[source]¶
Adds the models for source i back into the tims.
create(tims, srcs, subtract=False)[source]¶
Note that this modifies the tims if subtract=True.
legacypipe.oneblob.one_blob(X)[source]¶
Fits sources contained within a “blob” of pixels.
legacypipe.image.LegacySurveyImage(survey, ccd)[source]¶
Bases: object
A base class containing common code for the images we handle.
You probably shouldn’t need to directly instantiate this class, but rather use the recipe described in the __init__ method.
Objects of this class represent the metadata we have on an image, and are used to handle some of the details of going from an entry in the CCDs table to a tractor Image object.
Attributes:shape
Returns the full shape of the image, (H,W).
Methods
funpack_files(imgfn, maskfn, hdu, todelete) Source Extractor can’t handle .fz files, so unpack them. get_cacheable_filename_variables() These are names of self.X variables that are filenames that could be cached. get_good_image_slice(extent[, get_extent]) extent = None or extent = [x0,x1,y0,y1] get_good_image_subregion() Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good. get_image_extent([wcs, slc, radecpoly]) Returns x0,x1,y0,y1,slc get_image_shape() Returns image shape H,W. get_sky_sig1([splinesky]) Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. get_tractor_image([slc, radecpoly, …]) Returns a tractor.Image (“tim”) object for this image. read_dq(**kwargs) Reads the Data Quality (DQ) mask image. read_image(**kwargs) Reads the image file from disk. read_image_header(**kwargs) Reads the FITS image header from self.imgfn HDU self.hdu. read_image_primary_header(**kwargs) Reads the FITS primary (HDU 0) header from self.imgfn. read_invvar(**kwargs) Reads the inverse-variance (weight) map image. read_invvar_clipped([clip, clipThresh]) A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero. read_primary_header(fn) Reads the FITS primary header (HDU 0) from the given filename. read_sky_model([splinesky, slc]) Reads the sky model, returning a Tractor Sky object. remap_dq(dq, header) Called by get_tractor_image() to map the results from read_dq into a bitmask. remap_invvar_shotnoise(invvar, primhdr, img, dq) run_calibs([psfex, sky, se, fcopy, …]) Run calibration pre-processing steps. check_for_cached_files check_image_header compute_filenames galaxy_norm get_sig1 get_tractor_wcs get_wcs psf_norm read_psf_model remap_dq_cp_codes remap_invvar run_psfex run_se run_sky
funpack_files(imgfn, maskfn, hdu, todelete)[source]¶
Source Extractor can’t handle .fz files, so unpack them.
get_cacheable_filename_variables()[source]¶
These are names of self.X variables that are filenames that could be cached.
get_good_image_slice(extent, get_extent=False)[source]¶
extent = None or extent = [x0,x1,y0,y1]
If get_extent = True, returns the new [x0,x1,y0,y1] extent.
Returns a new pair of slices, or extent if the whole image is good.
get_good_image_subregion()[source]¶
Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good.
This cut is applied in addition to any masking in the mask or invvar map.
get_image_extent(wcs=None, slc=None, radecpoly=None)[source]¶
Returns x0,x1,y0,y1,slc
get_image_shape()[source]¶
Returns image shape H,W.
get_sky_sig1(splinesky=False)[source]¶
Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. NOTE that this is in image pixel counts, NOT calibrated nanomaggies.
get_tractor_image(slc=None, radecpoly=None, gaussPsf=False, pixPsf=False, hybridPsf=False, normalizePsf=False, splinesky=False, apodize=False, nanomaggies=True, subsky=True, tiny=10, dq=True, invvar=True, pixels=True, no_remap_invvar=False, constant_invvar=False)[source]¶
Returns a tractor.Image (“tim”) object for this image.
Options describing a subimage to return:
Options determining the PSF model to use:
Options determining the sky model to use:
Options determining the units of the image:
read_dq(**kwargs)[source]¶
Reads the Data Quality (DQ) mask image.
read_image(**kwargs)[source]¶
Reads the image file from disk.
The image is read from FITS file self.imgfn HDU self.hdu.
Parameters:2-dimensional slice of the subimage to read.
Return the image header also, as tuple (image, header) ?
The image pixels.
If header = True.
Reads the FITS image header from self.imgfn HDU self.hdu.
Returns:The FITS header
Reads the FITS primary (HDU 0) header from self.imgfn.
Returns:The FITS header
read_invvar(**kwargs)[source]¶
Reads the inverse-variance (weight) map image.
read_invvar_clipped(clip=True, clipThresh=0.01, **kwargs)[source]¶
A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero.
Reads the FITS primary header (HDU 0) from the given filename. This is just a faster version of fitsio.read_header(fn).
read_sky_model(splinesky=False, slc=None, **kwargs)[source]¶
Reads the sky model, returning a Tractor Sky object.
remap_dq(dq, header)[source]¶
Called by get_tractor_image() to map the results from read_dq into a bitmask.
run_calibs(psfex=True, sky=True, se=False, fcopy=False, use_mask=True, force=False, git_version=None, splinesky=False)[source]¶
Run calibration pre-processing steps.
shape¶
Returns the full shape of the image, (H,W).
legacypipe.image.remap_dq_cp_codes(dq)[source]¶
Some versions of the CP use integer codes, not bit masks. This converts them.
legacypipe.decam.DecamImage(survey, t)[source]¶
Bases: legacypipe.image.LegacySurveyImage
A LegacySurveyImage subclass to handle images from the Dark Energy Camera, DECam, on the Blanco telescope.
Attributes:shape
Returns the full shape of the image, (H,W).
Methods
funpack_files(imgfn, maskfn, hdu, todelete) Source Extractor can’t handle .fz files, so unpack them. get_cacheable_filename_variables() These are names of self.X variables that are filenames that could be cached. get_good_image_slice(extent[, get_extent]) extent = None or extent = [x0,x1,y0,y1] get_image_extent([wcs, slc, radecpoly]) Returns x0,x1,y0,y1,slc get_image_shape() Returns image shape H,W. get_sky_sig1([splinesky]) Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. get_tractor_image([slc, radecpoly, …]) Returns a tractor.Image (“tim”) object for this image. read_dq(**kwargs) Reads the Data Quality (DQ) mask image. read_image(**kwargs) Reads the image file from disk. read_image_header(**kwargs) Reads the FITS image header from self.imgfn HDU self.hdu. read_image_primary_header(**kwargs) Reads the FITS primary (HDU 0) header from self.imgfn. read_invvar_clipped([clip, clipThresh]) A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero. read_primary_header(fn) Reads the FITS primary header (HDU 0) from the given filename. read_sky_model([splinesky, slc]) Reads the sky model, returning a Tractor Sky object. remap_dq(dq, hdr) Called by get_tractor_image() to map the results from read_dq into a bitmask. remap_invvar_shotnoise(invvar, primhdr, img, dq) run_calibs([psfex, sky, se, fcopy, …]) Run calibration pre-processing steps. check_for_cached_files check_image_header compute_filenames galaxy_norm get_good_image_subregion get_sig1 get_tractor_wcs get_wcs glowmjd psf_norm read_invvar read_psf_model remap_dq_cp_codes remap_invvar run_psfex run_se run_sky
get_good_image_subregion()[source]¶
Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good.
This cut is applied in addition to any masking in the mask or invvar map.
read_invvar(**kwargs)[source]¶
Reads the inverse-variance (weight) map image.
remap_dq(dq, hdr)[source]¶
Called by get_tractor_image() to map the results from read_dq into a bitmask.
legacypipe.bok.BokImage(survey, t)[source]¶
Bases: legacypipe.image.LegacySurveyImage
Class for handling images from the 90prime camera processed by the NOAO Community Pipeline.
Attributes:shape
Returns the full shape of the image, (H,W).
Methods
funpack_files(imgfn, maskfn, hdu, todelete) Source Extractor can’t handle .fz files, so unpack them. get_cacheable_filename_variables() These are names of self.X variables that are filenames that could be cached. get_good_image_slice(extent[, get_extent]) extent = None or extent = [x0,x1,y0,y1] get_good_image_subregion() Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good. get_image_extent([wcs, slc, radecpoly]) Returns x0,x1,y0,y1,slc get_image_shape() Returns image shape H,W. get_sky_sig1([splinesky]) Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. get_tractor_image([slc, radecpoly, …]) Returns a tractor.Image (“tim”) object for this image. read_image(**kwargs) Reads the image file from disk. read_image_header(**kwargs) Reads the FITS image header from self.imgfn HDU self.hdu. read_image_primary_header(**kwargs) Reads the FITS primary (HDU 0) header from self.imgfn. read_invvar_clipped([clip, clipThresh]) A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero. read_primary_header(fn) Reads the FITS primary header (HDU 0) from the given filename. read_sky_model([splinesky, slc]) Reads the sky model, returning a Tractor Sky object. remap_dq(dq, header) Called by get_tractor_image() to map the results from read_dq into a bitmask. remap_invvar_shotnoise(invvar, primhdr, img, dq) run_calibs([psfex, sky, se, fcopy, …]) Run calibration pre-processing steps. check_for_cached_files check_image_header compute_filenames galaxy_norm get_sig1 get_tractor_wcs get_wcs psf_norm read_dq read_invvar read_psf_model remap_dq_cp_codes remap_invvar run_psfex run_se run_sky
read_dq(slice=None, header=False, **kwargs)[source]¶
Reads the Data Quality (DQ) mask image.
read_invvar(**kwargs)[source]¶
Reads the inverse-variance (weight) map image.
legacypipe.ptf.PtfImage(survey, t)[source]¶
Bases: legacypipe.image.LegacySurveyImage
A LegacySurveyImage subclass to handle images from the Dark Energy Camera, DECam, on the Blanco telescope.
Attributes:shape
Returns the full shape of the image, (H,W).
Methods
funpack_files(imgfn, maskfn, hdu, todelete) Source Extractor can’t handle .fz files, so unpack them. get_cacheable_filename_variables() These are names of self.X variables that are filenames that could be cached. get_good_image_slice(extent[, get_extent]) extent = None or extent = [x0,x1,y0,y1] get_image_extent([wcs, slc, radecpoly]) Returns x0,x1,y0,y1,slc get_image_shape() Returns image shape H,W. get_sky_sig1([splinesky]) Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. get_tractor_image([slc, radecpoly, …]) Returns a tractor.Image (“tim”) object for this image. get_wcs() read_image(**kwargs) returns tuple of img,hdr read_image_header(**kwargs) Reads the FITS image header from self.imgfn HDU self.hdu. read_image_primary_header(**kwargs) Reads the FITS primary (HDU 0) header from self.imgfn. read_invvar_clipped([clip, clipThresh]) A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero. read_primary_header(fn) Reads the FITS primary header (HDU 0) from the given filename. read_pv_wcs() extract wcs from fits header directly remap_dq(dq, header) Called by get_tractor_image() to map the results from read_dq into a bitmask. remap_invvar_shotnoise(invvar, primhdr, img, dq) check_for_cached_files check_image_header compute_filenames galaxy_norm get_good_image_subregion get_sig1 get_tractor_wcs psf_norm read_dq read_invvar read_psf_model read_sky_model remap_dq_cp_codes remap_invvar run_calibs run_psfex run_se run_sky
get_good_image_subregion()[source]¶
Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good.
This cut is applied in addition to any masking in the mask or invvar map.
get_tractor_image(slc=None, radecpoly=None, gaussPsf=False, const2psf=False, pixPsf=False, splinesky=False, nanomaggies=True, subsky=True, tiny=5, dq=True, invvar=True, pixels=True)[source]¶
Returns a tractor.Image (“tim”) object for this image.
Options describing a subimage to return:
Options determining the PSF model to use:
Options determining the sky model to use:
Options determining the units of the image:
read_dq(**kwargs)[source]¶
Reads the Data Quality (DQ) mask image.
read_image(**kwargs)[source]¶
returns tuple of img,hdr
read_invvar(clip=False, clipThresh=0.2, **kwargs)[source]¶
Reads the inverse-variance (weight) map image.
read_pv_wcs()[source]¶
extract wcs from fits header directly
read_sky_model(**kwargs)[source]¶
Reads the sky model, returning a Tractor Sky object.
run_calibs(psfex=True, sky=True, funpack=False, git_version=None, force=False, **kwargs)[source]¶
Run calibration pre-processing steps.
legacypipe.ptf.read_dq(dqfn, hdu)[source]¶
return bit mask which Tractor calls “data quality” image PTF DMASK BIT DEFINITIONS BIT00 = 0 / AIRCRAFT/SATELLITE TRACK BIT01 = 1 / OBJECT (detected by SExtractor) BIT02 = 2 / HIGH DARK-CURRENT BIT03 = 3 / RESERVED FOR FUTURE USE BIT04 = 4 / NOISY BIT05 = 5 / GHOST BIT06 = 6 / CCD BLEED BIT07 = 7 / RAD HIT BIT08 = 8 / SATURATED BIT09 = 9 / DEAD/BAD BIT10 = 10 / NAN (not a number) BIT11 = 11 / DIRTY (10-sigma below coarse local median) BIT12 = 12 / HALO BIT13 = 13 / RESERVED FOR FUTURE USE BIT14 = 14 / RESERVED FOR FUTURE USE BIT15 = 15 / RESERVED FOR FUTURE USE INFOBITS= 0 / Database infobits (2^2 and 2^3 excluded)
legacypipe.ptf.read_image(imgfn, hdu)[source]¶
return gain*pixel DN as numpy array
legacypipe.mosaic.MosaicImage(survey, t)[source]¶
Bases: legacypipe.image.LegacySurveyImage
Class for handling images from the Mosaic3 camera processed by the NOAO Community Pipeline.
Attributes:shape
Returns the full shape of the image, (H,W).
Methods
funpack_files(imgfn, maskfn, hdu, todelete) Source Extractor can’t handle .fz files, so unpack them. get_cacheable_filename_variables() These are names of self.X variables that are filenames that could be cached. get_good_image_slice(extent[, get_extent]) extent = None or extent = [x0,x1,y0,y1] get_good_image_subregion() Returns x0,x1,y0,y1 of the good region of this chip, or None if no cut should be applied to that edge; returns (None,None,None,None) if the whole chip is good. get_image_extent([wcs, slc, radecpoly]) Returns x0,x1,y0,y1,slc get_image_shape() Returns image shape H,W. get_sky_sig1([splinesky]) Returns the per-pixel noise estimate, which (for historical reasons) is stored in the sky model. get_tractor_image([slc, radecpoly, …]) Returns a tractor.Image (“tim”) object for this image. read_dq(**kwargs) Reads the Data Quality (DQ) mask image. read_image(**kwargs) Reads the image file from disk. read_image_header(**kwargs) Reads the FITS image header from self.imgfn HDU self.hdu. read_image_primary_header(**kwargs) Reads the FITS primary (HDU 0) header from self.imgfn. read_invvar(**kwargs) Reads the inverse-variance (weight) map image. read_invvar_clipped([clip, clipThresh]) A function that can optionally be called by subclassers for read_invvar, clipping fpack artifacts to zero. read_primary_header(fn) Reads the FITS primary header (HDU 0) from the given filename. read_sky_model([splinesky, slc]) Reads the sky model, returning a Tractor Sky object. remap_dq(dq, header) Called by get_tractor_image() to map the results from read_dq into a bitmask. remap_invvar_shotnoise(invvar, primhdr, img, dq) run_calibs([psfex, sky, se, fcopy, …]) Run calibration pre-processing steps. check_for_cached_files check_image_header compute_filenames galaxy_norm get_sig1 get_tractor_wcs get_wcs psf_norm read_psf_model remap_dq_cp_codes remap_invvar run_psfex run_se run_sky
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