Merge pull request #147 from LSSTDESC/v3.0.3

v3.0.3: small corrections

.github/workflows/build.yaml

@@ -63,6 +63,7 @@ jobs:
           pytest tests/test_simulator.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
           pytest tests/test_utils.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
           pytest tests/test_fitter.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
+          pytest tests/test_multispectra.py --log-cli-level=INFO --cov --cov-append --cov-report lcov
 
       - name: Run doctests and coverage
         shell: bash -l {0}

config/ctio.ini

@@ -16,7 +16,7 @@ SPECTRACTOR_DECONVOLUTION_PSF2D = True
 # deconvolve spectrogram with full forward model: False, True
 SPECTRACTOR_DECONVOLUTION_FFM = True
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
-SPECTRACTOR_ATMOSPHERE_SIM = getobsatmo
+SPECTRACTOR_ATMOSPHERE_SIM = none
 
 [instrument]
 # instrument name

spectractor/fit/fit_multispectra.py

@@ -39,6 +39,7 @@ def _build_sim_sample(spectra, aerosols=0.05, ozone=300, pwv=5, angstrom_exponen
 
     Examples
     --------
+    >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
     >>> spectra = _build_sim_sample([Spectrum("./tests/data/reduc_20170530_134_spectrum.fits")])
     >>> len(spectra)
     1
@@ -76,6 +77,7 @@ def _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3), aerosols
 
     Examples
     --------
+    >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
     >>> _build_test_sample(targets=["HD111980"]*3, zs=[1, 1.5, 2])  #doctest: +ELLIPSIS
     CTIO site name validated...
     """
@@ -135,6 +137,7 @@ def __init__(self, output_file_name, spectra, fixed_A1s=True, fixed_deltas=True,
 
         Examples
         --------
+        >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
         >>> spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3))
         >>> w = MultiSpectraFitWorkspace("./outputs/test", spectra, bin_width=5, verbose=True)
         >>> w.output_file_name
@@ -173,7 +176,7 @@ def __init__(self, output_file_name, spectra, fixed_A1s=True, fixed_deltas=True,
             for ip in range(self.deltas_first_index, self.nspectra + self.deltas_first_index):
                 fixed[ip] = True
         labels = ["VAOD", "angstrom_exp", "ozone [db]", "PWV [mm]", "reso"] + [f"delta_{k}" for k in range(self.nspectra)] + [f"A1_{k}" for k in range(self.nspectra)]
-        axis_names = ["VAOD", r'$\"a$', "ozone [db]", "PWV [mm]", "reso"] + [f"$\delta_{k}$" for k in range(self.nspectra)] + ["$A_1^{(" + str(k) + ")}$" for k in range(self.nspectra)]
+        axis_names = ["VAOD", r'$\"a$', "ozone [db]", "PWV [mm]", "reso"] + [rf"$\delta_{k}$" for k in range(self.nspectra)] + ["$A_1^{(" + str(k) + ")}$" for k in range(self.nspectra)]
         bounds = [(0, 1), (0, 3), (100, 700), (0, 20), (0.1, 100)] + [(-20, 20)] * self.nspectra + [(1e-3, 2)] * self.nspectra
         if fixed[4]:  # reso
             bounds[4] = (-1, 0)
@@ -488,6 +491,7 @@ def simulate(self, aerosols, angstrom_exponent, ozone, pwv, reso, *A1s):
 
         Examples
         --------
+        >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
         >>> spectra = spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3))
         >>> w = MultiSpectraFitWorkspace("./outputs/test", spectra, bin_width=5, verbose=True)
         >>> lambdas, model, model_err = w.simulate(*w.params.values)
@@ -589,6 +593,7 @@ def plot_fit(self):  # pragma: no cover
 
         Examples
         --------
+        >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
         >>> spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3))
         >>> w = MultiSpectraFitWorkspace("./outputs/test", spectra, bin_width=5, verbose=True)
         >>> w.simulate(*w.params.values)  #doctest: +ELLIPSIS
@@ -668,6 +673,7 @@ def plot_transmissions(self):  # pragma: no cover
 
         Examples
         --------
+        >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
         >>> spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3))
         >>> w = MultiSpectraFitWorkspace("./outputs/test", spectra, bin_width=5, verbose=True)
         >>> _ = w.simulate(*w.params.values)
@@ -743,6 +749,7 @@ def plot_A1s(self):  # pragma: no cover
         """
         Examples
         --------
+        >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
         >>> spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3))
         >>> w = MultiSpectraFitWorkspace("./outputs/test", spectra, bin_width=5, verbose=True)
         >>> w.cov = np.eye(3 + w.nspectra - 1)
@@ -864,6 +871,7 @@ def run_multispectra_minimisation(fit_workspace, method="newton", verbose=False,
 
     Examples
     --------
+    >>> parameters.SPECTRACTOR_ATMOSPHERE_SIM = "getobsatmo"
     >>> spectra = _build_test_sample(targets=["HD111980"]*10, zs=np.linspace(1, 2, 10),
     ... aerosols=0.05, angstrom_exponent=1.5, ozone=300, pwv=3)
     >>> parameters.VERBOSE = True

spectractor/tools.py

@@ -2365,14 +2365,14 @@ def set_sources_file_name(file_name, output_directory=""):
     Examples
     --------
     >>> set_sources_file_name("image.fits", output_directory="")
-    'image_wcs/image.xyls'
+    'image_wcs/image.axy'
     >>> set_sources_file_name("image.png", output_directory="outputs")
-    'outputs/image_wcs/image.xyls'
+    'outputs/image_wcs/image.axy'
 
     """
     output_directory = set_wcs_output_directory(file_name, output_directory=output_directory)
     tag = set_wcs_tag(file_name)
-    return os.path.join(output_directory, f"{tag}.xyls")
+    return os.path.join(output_directory, f"{tag}.axy")
 
 
 def set_gaia_catalog_file_name(file_name, output_directory=""):

tests/test_fullchain.py

@@ -103,6 +103,7 @@ def make_image():
 def test_ctio_fullchain():
     parameters.VERBOSE = True
     parameters.DEBUG = False
+    parameters.SPECTRACTOR_ATMOSPHERE_SIM = "libradtran"
     sim_image = "./tests/data/sim_20170530_134.fits"
 
     # load test and make image simulation
@@ -120,6 +121,7 @@ def test_ctio_fullchain():
     logbook = LogBook(logbook="./tests/data/ctiofulllogbook_jun2017_v5.csv")
     disperser_label, target, xpos, ypos = logbook.search_for_image(tag)
     load_config("./config/ctio.ini")
+    parameters.SPECTRACTOR_ATMOSPHERE_SIM = "libradtran"
     parameters.PSF_POLY_ORDER = PSF_POLY_ORDER
     parameters.CCD_REBIN = 1
     #  JN: > 1 not working well for now: I guess CTIO spectra are too narrow
@@ -191,6 +193,7 @@ def test_ctio_fullchain():
     assert np.isclose(np.abs(w.params.values[9]), 0, atol=1e-3)  # B
 
     parameters.DEBUG = False
+    parameters.SPECTRACTOR_ATMOSPHERE_SIM = "libradtran"
     w = SpectrogramFitWorkspace(spectrum, atmgrid_file_name=atmgrid_filename, fit_angstrom_exponent=False,
                                 verbose=True, plot=True, live_fit=False)
     run_spectrogram_minimisation(w, method="newton")

tests/test_multispectra.py

@@ -1,24 +1,30 @@
 import matplotlib as mpl
 mpl.use('Agg')  # must be run first! But therefore requires noqa E402 on all other imports
 
-from spectractor.fit.fit_multispectra import _build_test_sample, MultiSpectraFitWorkspace, run_multispectra_minimisation
-from spectractor import parameters
-import numpy as np
+from spectractor.fit.fit_multispectra import _build_test_sample, MultiSpectraFitWorkspace, run_multispectra_minimisation  # noqa: E402
+from spectractor import parameters  # noqa: E402
+from spectractor.tools import uvspec_available  # noqa: E402
+import numpy as np  # noqa: E402
+import os  # noqa: E402
+import unittest  # noqa: E402
+import astropy.config  # noqa: E402
 
 
-NSPECTRA = 4
 OZONE = 300
 PWV = 5
-AEROSOLS = 0.05
-LOG10A = -2
+VAOD = 0.05
+ANGEXP = 1.2
 
+@unittest.skipIf(uvspec_available() is False, 'Skipping to avoid libradtran dependency')
+@astropy.config.set_temp_cache(os.path.join(os.path.abspath(os.path.dirname(__file__)), "data", "cache"))
 def test_multispectra():
-    spectra = _build_test_sample(NSPECTRA, aerosols=AEROSOLS, ozone=OZONE, pwv=PWV, angstrom_exponent=10**LOG10A)
+    spectra = _build_test_sample(targets=["HD111980"]*3, zs=np.linspace(1, 2, 3),
+                                 aerosols=VAOD, ozone=OZONE, pwv=PWV, angstrom_exponent=ANGEXP)
     parameters.VERBOSE = True
 
-    nsigma = 3
-    labels = ["VAOD", "LOG10A", "OZONE", "PWV"]
-    truth = [AEROSOLS, LOG10A, OZONE, PWV]
+    nsigma = 5
+    labels = ["VAOD", "ANGEXP", "OZONE", "PWV"]
+    truth = [VAOD, ANGEXP, OZONE, PWV]
     indices = [0, 1, 2, 3]
     for method in ["noprior", "spectrum"]:
         w = MultiSpectraFitWorkspace("./tests/data/multispectra_test", spectra, bin_width=10, verbose=True, fixed_deltas=True,

tests/test_simulator.py

@@ -56,6 +56,7 @@ def test_simulator():
     parameters.VERBOSE = True
     parameters.DEBUG = False
     load_config('config/ctio.ini')
+    parameters.SPECTRACTOR_ATMOSPHERE_SIM = "libradtran"
 
     for file_name in file_names:
         spectrum = Spectrum(file_name)