DM-38745: Resync with upstream

.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>=0.7" astroquery coloredlogs scikit-image h5py emcee tqdm mpi4py schwimmbad "iminuit>=2" "coverage>=3.6" coveralls deprecated pyyaml nose 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 nose rubin-libradtran "getCalspec>=2.0.0"
           # python -c "from getCalspec.rebuild import rebuild_tables; rebuild_tables()"
           mamba install astrometry
 
@@ -62,7 +62,7 @@ jobs:
       - name: Run doctests and coverage
         shell: bash -l {0}
         run: |
-          ./coverage_and_test.sh
+          .github/workflows/coverage_and_test.sh
 
       - name: Coveralls
         env:

config/stardice.ini

@@ -12,11 +12,11 @@ SPECTRACTOR_COMPUTE_ROTATION_ANGLE = disperser
 # parameter to prevent from background subtraction
 SPECTRACTOR_BACKGROUND_SUBTRACTION = True
 # deconvolve spectrogram with simple 2D PSF analysis: False, True
-SPECTRACTOR_DECONVOLUTION_PSF2D = True
+SPECTRACTOR_DECONVOLUTION_PSF2D = False
 # deconvolve spectrogram with full forward model: False, True
 SPECTRACTOR_DECONVOLUTION_FFM = False
 # value of sigma clip parameter for the spectractor deconvolution process PSF2D and FFM
-SPECTRACTOR_DECONVOLUTION_SIGMA_CLIP = 8
+SPECTRACTOR_DECONVOLUTION_SIGMA_CLIP = 100
 
 
 [instrument]
@@ -28,6 +28,8 @@ OBS_ALTITUDE = 0.650
 OBS_LATITUDE = 43.930832
 # diameter of the telescope in meter
 OBS_DIAMETER = 0.4
+#diameter of the telescope secondary mirror in meter
+OBS_SECONDARY_DIAMETER = 0.11
 # observation epoch
 OBS_EPOCH = J2000.0
 # systematics on the instrument transmission

docs/conf.py

@@ -32,8 +32,8 @@ def __getattr__(cls, name):
         return MagicMock()
 
 
-MOCK_MODULES = ['mpi4py']
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+# MOCK_MODULES = ['mpi4py']
+# sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 # -- General configuration ------------------------------------------------
 

requirements.txt

@@ -8,11 +8,10 @@ astropy>=3.2
 photutils>=1.7.0
 astroquery
 coloredlogs
-scikit-image
+scikit-image>=0.20
 h5py #==2.8.0
 emcee #==3.0rc2
 tqdm
-#mpi4py
 schwimmbad
 iminuit>=2
 coverage>=3.6 # <5

runFitter.py

@@ -1,4 +1,5 @@
 from spectractor import parameters
+from spectractor.extractor.spectrum import Spectrum
 from spectractor.fit.fit_spectrogram import SpectrogramFitWorkspace, run_spectrogram_minimisation
 from spectractor.fit.fit_spectrum import SpectrumFitWorkspace, run_spectrum_minimisation
 from spectractor.config import load_config
@@ -16,10 +17,8 @@
                         help="Enter verbose (print more stuff).", default=False)
     parser.add_argument("-o", "--output_directory", dest="output_directory", default="outputs/",
                         help="Write results in given output directory (default: ./outputs/).")
-    parser.add_argument("-l", "--logbook", dest="logbook", default="ctiofulllogbook_jun2017_v5.csv",
-                        help="CSV logbook file. (default: ctiofulllogbook_jun2017_v5.csv).")
-    parser.add_argument("-c", "--config", dest="config", default="config/ctio.ini",
-                        help="INI config file. (default: config/ctio.ini).")
+    parser.add_argument("-c", "--config", dest="config", default="",
+                        help="config file to be given for spectra extracted with Spectractor<2.4. (default: ''.")
     args = parser.parse_args()
 
     parameters.VERBOSE = args.verbose
@@ -29,13 +28,13 @@
 
     file_names = args.input
 
-    load_config(args.config)
+    if args.config != '':
+        load_config(args.config)
 
     for file_name in file_names:
-        atmgrid_filename = '' #file_name.replace('sim', 'reduc').replace('spectrum', 'atmsim')
-        w = SpectrumFitWorkspace(file_name, atmgrid_file_name=atmgrid_filename, nsteps=1000,
-                                 burnin=200, nbins=10, verbose=1, plot=True, live_fit=False)
+        atmgrid_filename = ''  # file_name.replace('sim', 'reduc').replace('spectrum', 'atmsim')
+        spec = Spectrum(file_name)
+        w = SpectrumFitWorkspace(spec, atmgrid_file_name=atmgrid_filename, verbose=True, plot=True, live_fit=False, fit_angstrom_exponent=True)
         run_spectrum_minimisation(w, method="newton")
-        w = SpectrogramFitWorkspace(file_name, atmgrid_file_name=atmgrid_filename, nsteps=2000,
-                                    burnin=1000, nbins=10, verbose=1, plot=True, live_fit=False)
+        w = SpectrogramFitWorkspace(spec, atmgrid_file_name=atmgrid_filename, verbose=True, plot=True, live_fit=False, fit_angstrom_exponent=True)
         run_spectrogram_minimisation(w, method="newton")

runSimulator.py

@@ -41,7 +41,6 @@
             continue
         spectrum_file_name = args.output_directory + '/' + tag.replace('.fits', '_spectrum.fits')
         atmgrid = AtmosphereGrid(file_name)
-        SpectrumSimulatorSimGrid(spectrum_file_name, args.output_directory)
         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)

setup.cfg

@@ -1,2 +1,2 @@
 [nosetests]
-exclude=test_(extractor_ctio_planetary_nebula|atmosphere|astrometry)
+exclude=test_(extractor_ctio_planetary_nebula|astrometry)

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__ = '2.4'
+__version__ = '2.5'
 __version_info__ = tuple(map(int, __version__.split('.')))