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[NEW FEATURE] Third-party catalogue for tile objects #650

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[NEW FEATURE] Third-party catalogue for tile objects #650

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4b9bf26
Added get_image config files to download catalogues; expanded error m…
martinkilbinger May 16, 2023
6595390
Clarified error messages in file_io; added code to read cat in sextra…
martinkilbinger May 17, 2023
4e49080
Clarified error messages in file_io; added code to read cat in sextra…
martinkilbinger May 17, 2023
ffb388b
testing int columns for output
martinkilbinger May 17, 2023
d327cc4
sextractor_runner restored to develop
martinkilbinger May 17, 2023
6c16d82
testing minimal SExtractor param file
martinkilbinger Jun 5, 2023
bf10760
Merge remote-tracking branch 'upstream/develop' into detect_third
martinkilbinger Oct 18, 2023
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sextractor_runner restored to develop
  • Loading branch information
@martinkilbinger
martinkilbinger committed May 17, 2023
commit d327cc4f0540332928c4d80cb94d90b0c89fc2bf
69 changes: 69 additions & 0 deletions example/cfis/default_cat.param
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@@ -0,0 +1,69 @@
NUMBER #Running object number
EXT_NUMBER #FITS extension number

FLUX_AUTO #Flux within a Kron-like elliptical aperture [count]
FLUXERR_AUTO #RMS error for AUTO flux [count]
MAG_AUTO #Kron-like elliptical aperture magnitude [mag]
MAGERR_AUTO #RMS error for AUTO magnitude [mag]
FLUX_WIN #Gaussian-weighted flux [count]
FLUXERR_WIN #RMS error for WIN flux [count]
MAG_WIN #Gaussian-weighted magnitude [mag]
MAGERR_WIN #RMS error for MAG_WIN [mag]
FLUX_APER(1)
FLUXERR_APER(1)

FLUX_RADIUS #Fraction-of-light radii [pixel]

SNR_WIN #Gaussian-weighted SNR

BACKGROUND #Background at centroid position [count]
THRESHOLD #Detection threshold above background [count]

X_IMAGE #Object position along x [pixel]
Y_IMAGE #Object position along y [pixel]

X_WORLD #Barycenter position along world x axis [deg]
Y_WORLD #Barycenter position along world y axis [deg]

X2_IMAGE #Variance along x [pixel**2]
Y2_IMAGE #Variance along y [pixel**2]
XY_IMAGE #Covariance between x and y [pixel**2]
ERRX2_IMAGE #Variance of position along x [pixel**2]
ERRY2_IMAGE #Variance of position along y [pixel**2]
ERRXY_IMAGE #Covariance of position between x and y [pixel**2]

XWIN_IMAGE #Windowed position estimate along x [pixel]
YWIN_IMAGE #Windowed position estimate along y [pixel]

XWIN_WORLD #Windowed position along world x axis [deg]
YWIN_WORLD #Windowed position along world y axis [deg]

X2WIN_IMAGE #Windowed variance along x [pixel**2]
Y2WIN_IMAGE #Windowed variance along y [pixel**2]
XYWIN_IMAGE #Windowed covariance between x and y [pixel**2]
ERRX2WIN_IMAGE #Variance of windowed pos along x [pixel**2]
ERRY2WIN_IMAGE #Variance of windowed pos along y [pixel**2]
ERRXYWIN_IMAGE #Covariance of windowed pos between x and y [pixel**2]

MU_THRESHOLD #Analysis threshold above background [mag * arcsec**(-2)]
MU_MAX #Peak surface brightness above background [mag * arcsec**(-2)]

FLAGS #Extraction flags
FLAGS_WIN #Flags for WINdowed parameters

#!!! REQUIRE FLAG_IMAGE !!!
IMAFLAGS_ISO #FLAG-image flags OR'ed over the iso. profile !!! REQUIRE FLAG_IMAGE !!!

FWHM_IMAGE #FWHM assuming a gaussian core [pixel]
FWHM_WORLD #FWHM assuming a gaussian core [deg]
ELONGATION #A_IMAGE/B_IMAGE
ELLIPTICITY #1 - B_IMAGE/A_IMAGE

VIGNET(51,51) #Pixel data around detection [count]

#VECTOR_ASSOC #ASSOCiated parameter vector
NUMBER_ASSOC #Number of ASSOCiated IDs

#SPREAD_MODEL
#SPREADERR_MODEL
#FWHMPSF_IMAGE
141 changes: 58 additions & 83 deletions shapepipe/modules/sextractor_runner.py
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Expand Up @@ -36,93 +36,68 @@ def sextractor_runner(
else:
exec_path = 'sex'

if exec_path != 'None':

# Get SExtractor config options
dot_sex = config.getexpanded(module_config_sec, 'DOT_SEX_FILE')
dot_param = config.getexpanded(module_config_sec, 'DOT_PARAM_FILE')
dot_conv = config.getexpanded(module_config_sec, 'DOT_CONV_FILE')
weight_file = config.getboolean(module_config_sec, 'WEIGHT_IMAGE')
flag_file = config.getboolean(module_config_sec, 'FLAG_IMAGE')
psf_file = config.getboolean(module_config_sec, 'PSF_FILE')
detection_image = config.getboolean(module_config_sec, 'DETECTION_IMAGE')
detection_weight = config.getboolean(module_config_sec, 'DETECTION_WEIGHT')

zp_from_header = config.getboolean(module_config_sec, 'ZP_FROM_HEADER')
if zp_from_header:
zp_key = config.get(module_config_sec, 'ZP_KEY')
else:
zp_key = None

bkg_from_header = config.getboolean(module_config_sec, 'BKG_FROM_HEADER')
if bkg_from_header:
bkg_key = config.get(module_config_sec, 'BKG_KEY')
else:
bkg_key = None

if config.has_option(module_config_sec, 'CHECKIMAGE'):
check_image = config.getlist(module_config_sec, 'CHECKIMAGE')
else:
check_image = ['']

if config.has_option(module_config_sec, 'PREFIX'):
prefix = config.get(module_config_sec, 'PREFIX')
else:
prefix = None

# Create sextractor caller class instance
ss_inst = ss.SExtractorCaller(
input_file_list,
run_dirs['output'],
file_number_string,
dot_sex,
dot_param,
dot_conv,
weight_file,
flag_file,
psf_file,
detection_image,
detection_weight,
zp_from_header,
bkg_from_header,
zero_point_key=zp_key,
background_key=bkg_key,
check_image=check_image,
output_prefix=prefix,
)

# Generate sextractor command line
command_line = ss_inst.make_command_line(exec_path)
w_log.info(f'Calling command: {command_line}')

# Execute command line
stderr, stdout = execute(command_line)

# Parse SExtractor errors
stdout, stderr = ss_inst.parse_errors(stderr, stdout)
# Get SExtractor config options
dot_sex = config.getexpanded(module_config_sec, 'DOT_SEX_FILE')
dot_param = config.getexpanded(module_config_sec, 'DOT_PARAM_FILE')
dot_conv = config.getexpanded(module_config_sec, 'DOT_CONV_FILE')
weight_file = config.getboolean(module_config_sec, 'WEIGHT_IMAGE')
flag_file = config.getboolean(module_config_sec, 'FLAG_IMAGE')
psf_file = config.getboolean(module_config_sec, 'PSF_FILE')
detection_image = config.getboolean(module_config_sec, 'DETECTION_IMAGE')
detection_weight = config.getboolean(module_config_sec, 'DETECTION_WEIGHT')

zp_from_header = config.getboolean(module_config_sec, 'ZP_FROM_HEADER')
if zp_from_header:
zp_key = config.get(module_config_sec, 'ZP_KEY')
else:
zp_key = None

bkg_from_header = config.getboolean(module_config_sec, 'BKG_FROM_HEADER')
if bkg_from_header:
bkg_key = config.get(module_config_sec, 'BKG_KEY')
else:
bkg_key = None

# Read input catalogue
if config.has_option(module_config_sec, 'CHECKIMAGE'):
check_image = config.getlist(module_config_sec, 'CHECKIMAGE')
else:
check_image = ['']
ss_inst = ss.SExtractorCaller(
input_file_list,
run_dirs['output'],
file_number_string,
None,
None,
None,
True,
False,
False,
False,
False,
False,
False,
check_image=check_image,
)
data = ss_inst.read_from_ascii()
ss_inst.write_to_fits(data)

if config.has_option(module_config_sec, 'PREFIX'):
prefix = config.get(module_config_sec, 'PREFIX')
else:
prefix = None

# Create sextractor caller class instance
ss_inst = ss.SExtractorCaller(
input_file_list,
run_dirs['output'],
file_number_string,
dot_sex,
dot_param,
dot_conv,
weight_file,
flag_file,
psf_file,
detection_image,
detection_weight,
zp_from_header,
bkg_from_header,
zero_point_key=zp_key,
background_key=bkg_key,
check_image=check_image,
output_prefix=prefix,
)

# Generate sextractor command line
command_line = ss_inst.make_command_line(exec_path)
w_log.info(f'Calling command: {command_line}')

# Execute command line
stderr, stdout = execute(command_line)

# Parse SExtractor errors
stdout, stderr = ss_inst.parse_errors(stderr, stdout)

# Run sextractor post processing
if config.getboolean(module_config_sec, 'MAKE_POST_PROCESS'):
Expand Down