Stardice dev

.github/workflows/build.yaml

@@ -26,7 +26,7 @@ jobs:
         # Might be quicker to install rubin-env plus any necessary additions.
         shell: bash -l {0}
         run: |
-          mamba install -y  "numpy>1.15" scipy "matplotlib>3.1" pandas llvmlite numba "astropy>=3.2" "photutils>=1.7" astroquery coloredlogs scikit-image>=0.20 h5py emcee tqdm mpi4py schwimmbad "iminuit>=2" "coverage>=3.6" configparser coveralls deprecated pyyaml pytest pytest-cov rubin-libradtran "getCalspec>=2.0.0"
+          mamba install -y  "numpy>1.15" scipy "matplotlib>3.1" pandas llvmlite numba "astropy>=3.2" "photutils>=1.7" astroquery coloredlogs scikit-image>=0.20 h5py emcee tqdm mpi4py schwimmbad "iminuit>=2" "coverage>=3.6" configparser coveralls deprecated pyyaml "pytest==8.0.0" pytest-cov rubin-libradtran "getCalspec>=2.0.0"
           # python -c "from getCalspec.rebuild import rebuild_tables; rebuild_tables()"
           pip install lsst.utils
           pip install git+https://github.com/LSSTDESC/getObsAtmo.git@main

config/auxtel.ini

@@ -20,7 +20,9 @@ SPECTRACTOR_FIT_TIMEOUT_PER_ITER = 1200
 # maximum time per gradient descent before TimeoutError in seconds
 SPECTRACTOR_FIT_TIMEOUT = 7200
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
-SPECTRACTOR_ATMOSPHERE_SIM = getobstamo
+SPECTRACTOR_ATMOSPHERE_SIM = getobsatmo
+# simulate star field with Gaia catalog: False, True
+SPECTRACTOR_SIMULATE_STARFIELD = False
 
 [instrument]
 # instrument name
@@ -55,7 +57,7 @@ CCD_PIXEL2ARCSEC = 0.0952
 # approximate maximum ADU output of the CCD
 CCD_MAXADU = 170000
 # electronic gain : elec/ADU
-CCD_GAIN = 1.1
+CCD_GAIN = 1.3
 # rebinning of the image in pixel
 CCD_REBIN = 2
 
@@ -107,7 +109,7 @@ PIXWIDTH_BACKGROUND = 40
 PIXWIDTH_BOXSIZE = 20
 
 [PSF]
-# the PSF model: Gauss, Moffat or MoffatGauss
+# the PSF model: Gauss, Moffat, DoubleMoffat or MoffatGauss
 PSF_TYPE = Moffat
 # the order of the polynomials to model wavelength dependence of the PSF shape parameters
 PSF_POLY_ORDER = 2

config/ctio.ini

@@ -17,6 +17,8 @@ SPECTRACTOR_DECONVOLUTION_PSF2D = True
 SPECTRACTOR_DECONVOLUTION_FFM = True
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
 SPECTRACTOR_ATMOSPHERE_SIM = none
+# simulate star field with Gaia catalog: False, True
+SPECTRACTOR_SIMULATE_STARFIELD = True
 
 [instrument]
 # instrument name
@@ -99,10 +101,10 @@ PIXWIDTH_BACKGROUND = 100
 PIXWIDTH_BOXSIZE = 40
 
 [PSF]
-# the PSF model: Gauss, Moffat or MoffatGauss
+# the PSF model: Gauss, Moffat, DoubleMoffat, or MoffatGauss
 PSF_TYPE = Moffat
 # the order of the polynomials to model wavelength dependence of the PSF shape parameters
-PSF_POLY_ORDER = 4
+PSF_POLY_ORDER = 2
 # regularisation parameter for the chisq minimisation to extract the spectrum
 PSF_FIT_REG_PARAM = 0.04
 # step size in pixels for the first transverse PSF1D fit

config/default.ini

@@ -21,6 +21,8 @@ SPECTRACTOR_FIT_TIMEOUT_PER_ITER = 600
 SPECTRACTOR_FIT_TIMEOUT = 3600
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
 SPECTRACTOR_ATMOSPHERE_SIM = none
+# simulate star field with Gaia catalog: False, True
+SPECTRACTOR_SIMULATE_STARFIELD = False
 
 [instrument]
 # instrument name
@@ -113,12 +115,14 @@ PIXWIDTH_BACKGROUND = 40
 PIXWIDTH_BOXSIZE = 20
 
 [PSF]
-# the PSF model: Gauss, Moffat or MoffatGauss
+# the PSF model: Gauss, Moffat, DoubleMoffat or MoffatGauss
 PSF_TYPE = Moffat
 # the order of the polynomials to model wavelength dependence of the PSF shape parameters
 PSF_POLY_ORDER = 2
 # regularisation parameter for the chisq minimisation to extract the spectrum
 PSF_FIT_REG_PARAM = 0.01
+# polynomial type: must be polynomial or legendre
+PSF_POLY_TYPE = polynomial
 
 [detection line algorithm parameters]
 # order of the background polynome to fit

config/stardice.ini

@@ -6,7 +6,7 @@ THROUGHPUT_DIR = simulation/StarDiceThroughput/
 
 [pipeline]
 # method to get target centroid, choose among: guess, fit, WCS
-SPECTRACTOR_FIT_TARGET_CENTROID = WCS
+SPECTRACTOR_FIT_TARGET_CENTROID = fit
 # method to get image rotation angle: False, disperser, hessian
 SPECTRACTOR_COMPUTE_ROTATION_ANGLE = disperser
 # parameter to prevent from background subtraction
@@ -19,6 +19,8 @@ SPECTRACTOR_DECONVOLUTION_FFM = True
 SPECTRACTOR_DECONVOLUTION_SIGMA_CLIP = 100
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
 SPECTRACTOR_ATMOSPHERE_SIM = getobsatmo
+# simulate star field with Gaia catalog: False, True
+SPECTRACTOR_SIMULATE_STARFIELD = False
 
 [instrument]
 # instrument name
@@ -59,9 +61,9 @@ CCD_REBIN = 1
 
 [spectrograph]
 # distance between hologram and CCD in mm
-DISTANCE2CCD = 33.3
+DISTANCE2CCD = 33.5
 # uncertainty on distance between hologram and CCD in mm
-DISTANCE2CCD_ERR = 0.1
+DISTANCE2CCD_ERR = 0.06
 # default value for order 2 over order 1 transmission ratio
 GRATING_ORDER_2OVER1 = 0.1
 
@@ -75,7 +77,7 @@ XWINDOW_ROT = 30
 # window y size to search for the targeted object
 YWINDOW_ROT = 30
 # prior on the reliability of the centroid estimate in pixels
-PIXSHIFT_PRIOR = 0.5
+PIXSHIFT_PRIOR = 0.2
 
 [rotation parameters]
 # must be set to true, otherwise create residuals and correlated noise
@@ -96,21 +98,21 @@ SPEC_ORDER = 1
 
 [background subtraction parameters]
 # half transverse width of the signal rectangular window in pixels
-PIXWIDTH_SIGNAL = 10
+PIXWIDTH_SIGNAL = 30
 # distance from dispersion axis to analyse the background in pixels
-PIXDIST_BACKGROUND = 20
+PIXDIST_BACKGROUND = 30
 # transverse width of the background rectangular window in pixels
 PIXWIDTH_BACKGROUND = 80
 # box size for sextractor evaluation of the background
-PIXWIDTH_BOXSIZE = 40
+PIXWIDTH_BOXSIZE = 80
 
 [PSF]
 # the PSF model: Gauss, Moffat or MoffatGauss
 PSF_TYPE = Moffat
 # the order of the polynomials to model wavelength dependence of the PSF shape parameters
-PSF_POLY_ORDER = 4
+PSF_POLY_ORDER = 2
 # regularisation parameter for the chisq minimisation to extract the spectrum
-PSF_FIT_REG_PARAM = 0.1
+PSF_FIT_REG_PARAM = 1
 # step size in pixels for the first transverse PSF1D fit
 PSF_PIXEL_STEP_TRANSVERSE_FIT = 1
 # PSF is not evaluated outside a region larger than max(PIXWIDTH_SIGNAL, PSF_FWHM_CLIP*fwhm) pixels
@@ -120,9 +122,9 @@ PSF_FWHM_CLIP = 2
 # order of the background polynome to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
-CALIB_PEAK_WIDTH = 7
+CALIB_PEAK_WIDTH = 3
 # size of the peak sides to use to fit spectrum base line
-CALIB_BGD_WIDTH = 15
+CALIB_BGD_WIDTH = 5
 # window size for the savgol filter in pixels
 CALIB_SAVGOL_WINDOW = 5
 # polynom order for the savgol filter

runAstrometry.py

@@ -2,6 +2,7 @@
 from spectractor.astrometry import Astrometry
 from spectractor.logbook import LogBook
 from spectractor.config import load_config, apply_rebinning_to_parameters
+from spectractor.extractor.images import Image
 
 
 if __name__ == "__main__":
@@ -50,7 +51,6 @@
 
     logbook = LogBook(logbook=args.logbook)
     for file_name in file_names:
-        disperser_label = args.disperser_label
         if parameters.OBS_NAME == "CTIO":
             tag = file_name.split('/')[-1]
             tag = tag.replace('sim_', 'reduc_')
@@ -66,8 +66,8 @@
                 ypos = float(ypos)
                 guess = [xpos, ypos]
             target_label = args.target_label
-        a = Astrometry(file_name, target_label=target_label, disperser_label=disperser_label,
-                       output_directory=args.output_directory)
+        image = Image(file_name, config=args.config)
+        a = Astrometry(image, output_directory=args.output_directory)
         extent = ((int(max(0, xpos - radius)), int(min(xpos + radius, parameters.CCD_IMSIZE))),
                   (int(max(0, ypos - radius)), int(min(ypos + radius, parameters.CCD_IMSIZE))))
         gaia_min_residuals = a.run_full_astrometry(extent=extent, maxiter=int(args.maxiter))

runImageSim.py

@@ -49,4 +49,4 @@
             continue
 
         image = ImageSim(file_name, spectrum_file_name, args.output_directory, A2=1,
-                         psf_poly_params=psf_poly_params, with_stars=False)
+                         psf_poly_params=psf_poly_params, with_starfield=False)

runSimulator.py

@@ -43,6 +43,6 @@
         atmgrid = AtmosphereGrid(file_name)
         image = ImageSim(file_name, spectrum_file_name, args.output_directory, A1=1, A2=1,
                          pwv=5, ozone=300, aerosols=0.03,
-                         psf_poly_params=None, with_stars=True)
+                         psf_poly_params=None, with_starfield=True)
         sim_file_name = args.output_directory + tag.replace('reduc_', 'sim_')
         Spectractor(sim_file_name, args.output_directory, target, [xpos, ypos], disperser_label, args.config)

setup.cfg

@@ -1,5 +1,5 @@
 [tool:pytest]
-exclude=test_(extractor_ctio_planetary_nebula|astrometry|mcmc|multispectra)
+addopts = --ignore=tests/test_astrometry.py --ignore=tests/test_mcmc.py --ignore=tests/test_extractor_ctio_planetary_nebula.py
 
 [coverage:run]
 omit=spectractor/fit/mcmc.py

setup.py

@@ -30,8 +30,6 @@
     version=current_version,
     packages=['spectractor', 'spectractor.extractor', 'spectractor.simulation', 'spectractor.fit'],
     install_requires=reqs,
-    test_suite='nose.collector',
-    tests_require=['nose'],
     package_dir={'spectractor': './spectractor'},
     package_data={'spectractor': ['../config/*.ini'],
                   'spectractor.extractor': ['dispersers/HoloPhAg/*.txt', 'dispersers/HoloPhP/*.txt',

spectractor/_version.py

@@ -28,5 +28,5 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = '3.0.3'
+__version__ = '3.1.0'
 __version_info__ = tuple(map(int, __version__.split('.')))

spectractor/astrometry.py

@@ -323,7 +323,7 @@ def __init__(self, image, wcs_file_name="", gaia_file_name="", output_directory=
         self.gaia_radec_positions_after_pm = None
         if os.path.isfile(self.gaia_file_name):
             self.my_logger.info(f"\n\tLoad Gaia catalog from {self.gaia_file_name}.")
-            self.gaia_catalog = ascii.read(self.gaia_file_name, format="ecsv")
+            self.gaia_catalog = Table(ascii.read(self.gaia_file_name, format="ecsv"), masked=True)
             self.gaia_radec_positions_after_pm = get_gaia_coords_after_proper_motion(self.gaia_catalog, self.image.date_obs)
         self.sources = None
         self.sources_radec_positions = None

spectractor/config.py

@@ -116,6 +116,10 @@ def load_config(config_filename, rebin=True):
     if parameters.PIXWIDTH_BOXSIZE > parameters.PIXWIDTH_BACKGROUND:
         raise ValueError(f'parameters.PIXWIDTH_BOXSIZE must be smaller than parameters.PIXWIDTH_BACKGROUND (or equal).')
 
+    # check consistency
+    if parameters.PSF_POLY_TYPE not in ["polynomial", "legendre"]:
+        raise ValueError(f'parameters.PSF_POLY_TYPE must be either "polynomial" or "legendre". Got {parameters.PSF_POLY_TYPE=}')
+
     # check presence of atmospheric simulation packages
     if parameters.SPECTRACTOR_ATMOSPHERE_SIM.lower() not in ["none", "libradtran", "getobsatmo"]:
         raise ValueError(f'parameters.SPECTRACTOR_ATMOSPHERE_SIM must be either ["none", "libradtran", "getobsatmo"]. '

spectractor/extractor/background.py

@@ -54,7 +54,7 @@ def make_source_mask(data, nsigma, npixels, mask=None, sigclip_sigma=3.0,
 
     Parameters
     ----------
-    data : 2D `~numpy.ndarray`
+    data : np.ndarray
         The 2D array of the image.
     nsigma : float
         The number of standard deviations per pixel above the ``background``
@@ -236,7 +236,7 @@ def extract_spectrogram_background_sextractor(data, err, ws=(20, 30), mask_signa
     >>> from spectractor import parameters
     >>> parameters.DEBUG = True
     >>> psf = MoffatGauss()
-    >>> s0 = ChromaticPSF(psf, Nx=100, Ny=200, saturation=1000)
+    >>> s0 = ChromaticPSF(psf, Nx=100, Ny=300, saturation=1000)
     >>> params = s0.generate_test_poly_params()
     >>> saturation = params[-1]
     >>> data = s0.evaluate(s0.set_pixels(mode="1D"), poly_params=params)
@@ -275,7 +275,7 @@ def extract_spectrogram_background_sextractor(data, err, ws=(20, 30), mask_signa
     bkg = Background2D(data, (parameters.PIXWIDTH_BOXSIZE, parameters.PIXWIDTH_BOXSIZE),
                        filter_size=(filter_size, filter_size),
                        sigma_clip=sigma_clip, bkg_estimator=bkg_estimator,
-                       mask=mask)
+                       mask=mask, exclude_percentile=80)
     # reset at zero the edges
     bkg.background[data == 0] = 0
     bgd_model_func_interp = RegularGridInterpolator((np.arange(Nx), np.arange(Ny)), bkg.background.T, method='linear',