pyreduce-astro 0.6.0b2__py3-none-any.whl → 0.6.0b3__py3-none-any.whl

pyreduce/__init__.py

@@ -60,6 +60,7 @@ def __getattr__(name):
     """Lazy load submodules on first access."""
     if name in ("configuration", "datasets", "reduce", "util"):
         import importlib
+
         module = importlib.import_module(f".{name}", __name__)
         globals()[name] = module
         return module

pyreduce/extract.py

@@ -405,6 +405,8 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
     -------
     column_range : array[nord, 2]
         updated column range
+    orders : array[nord, degree]
+        order tracing coefficients (may have rows removed if no valid pixels)
     """
 
     ix = np.arange(ncol)
@@ -426,7 +428,7 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
 
         if len(points_in_image) == 0:
             # print(y_bot, y_top,nrow, ncol, points_in_image)
-            logger.warn(
+            logger.warning(
                 f"No pixels are completely within the extraction width for order {i}, removing it."
             )
             to_remove += [i]
@@ -452,9 +454,9 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
     column_range[0] = column_range[1]
     column_range[-1] = column_range[-2]
 
-    for i in to_remove:
-        np.delete(column_range, i, axis=0)
-        np.delete(orders, i, axis=0)
+    if to_remove:
+        column_range = np.delete(column_range, to_remove, axis=0)
+        orders = np.delete(orders, to_remove, axis=0)
 
     return column_range, orders
 

pyreduce/instruments/andes.json

@@ -8,8 +8,10 @@
     "date_format": "fits",
     "id_mode": "ESO INS MODE",
     "id_band": "ESO INS WLEN ID",
+    "id_decker": "ESO INS OPTI8 ID",
     "id_lamp": "ESO INS1 LAMP? ID",
     "modes": ["SL", "IFU"],
+    "deckers": ["Open", "pos1", "pos2"],
     "bands": ["UBV", "RIZ", "YJH", "K"],
     "settings": ["B", "V", "R", "IZ", "Y", "J", "H", "K"],
     "chips": ["det1"],

pyreduce/instruments/andes.py

@@ -45,8 +45,10 @@ class ANDES(Instrument):
         return modes
 
     def parse_mode(self, mode):
-        pattern = r"([YJHKLM]\d{4})(_(Open|pos1|pos2))?_det(\d)"
+        pattern = r"([A-Z]+)(_(Open|pos1|pos2))?_det(\d)"
         match = re.match(pattern, mode, flags=re.IGNORECASE)
+        if not match:
+            raise ValueError(f"Invalid mode format: {mode}")
         band = match.group(1).upper()
         if match.group(3) is not None:
             decker = match.group(3).lower().capitalize()

pyreduce/reduce.py

@@ -562,7 +562,7 @@ class Bias(Step):
         hdus.writeto(
             self.savefile,
             overwrite=True,
-            output_verify="fix",  # "silentfix+ignore",
+            output_verify="silentfix+ignore",
         )
         logger.info("Created master bias file: %s", self.savefile)
 

pyreduce/settings/settings_ANDES.json

@@ -0,0 +1,89 @@
+{
+    "__instrument__": "ANDES",
+    "instrument": {},
+    "bias": {
+        "degree": 1
+    },
+    "flat": {
+        "bias_scaling": "exposure_time"
+    },
+    "orders": {
+        "degree": 3,
+        "degree_before_merge": 1,
+        "filter_size": 100,
+        "min_cluster": 200000,
+        "border_width": 0,
+        "noise": 0,
+        "manual": false,
+        "auto_merge_threshold": 1,
+        "merge_min_threshold": 0.9,
+        "bias_scaling": "exposure_time"
+    },
+    "scatter": {
+        "extraction_width": 0.45,
+        "border_width": 50,
+        "bias_scaling": "exposure_time"
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0,
+        "extraction_width": 100,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "wavecal_master": {
+        "extraction_method": "optimal",
+        "extraction_width": 100,
+        "oversampling": 5,
+        "swath_width": 2000,
+        "smooth_slitfunction": 1,
+        "smooth_spectrum": 1e-7,
+        "extraction_cutoff": 20,
+        "bias_scaling": "exposure_time"
+    },
+    "wavecal_init": {
+        "element": "UNe",
+        "medium": "vac",
+        "cutoff": 5,
+        "smoothing": 1
+    },
+    "wavecal": {
+        "threshold": 100,
+        "closing": 0,
+        "dimensionality": "2D",
+        "element": null,
+        "degree": [5,5],
+        "manual": false
+    },
+    "freq_comb_master": {
+        "extraction_width": 10,
+        "bias_scaling": "exposure_time"
+    },
+    "freq_comb": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "degree": [8, 8]
+    },
+    "curvature": {
+        "peak_threshold": 1,
+        "window_width": 15,
+        "extraction_width": 100,
+        "dimensionality": "2D",
+        "degree": [
+            1,
+            1
+        ],
+        "curv_degree": 1,
+        "peak_function": "lorentzian",
+        "bias_scaling": "exposure_time"
+    },
+    "science": {
+        "oversampling": 1,
+        "extraction_width": 10,
+        "swath_width": 300,
+        "smooth_slitfunction": 0.1,
+        "smooth_spectrum": 0,
+        "bias_scaling": "exposure_time"
+    }
+}

{pyreduce_astro-0.6.0b2.dist-info → pyreduce_astro-0.6.0b3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.6.0b2
+Version: 0.6.0b3
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce.readthedocs.io
@@ -41,6 +41,7 @@ Requires-Dist: pre-commit>=3.5.0; extra == 'dev'
 Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
 Requires-Dist: pytest>=7.4.0; extra == 'dev'
 Requires-Dist: ruff>=0.8.0; extra == 'dev'
+Requires-Dist: setuptools; extra == 'dev'
 Requires-Dist: sphinx>=7.2.0; extra == 'dev'
 Description-Content-Type: text/markdown
 

{pyreduce_astro-0.6.0b2.dist-info → pyreduce_astro-0.6.0b3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-pyreduce/__init__.py,sha256=dA7KPdGmKFRPu5B-FOnslWTQLHVEkZlO0hySwWh_AGY,1729
+pyreduce/__init__.py,sha256=MgaO38bC9mwKHkrcAu5cyRHyfSMbCbYKy635-GDZyyo,1730
 pyreduce/__main__.py,sha256=x59nq52i35-56M-4crL97XNnpCsMD6HwbWwUni4SXfI,3095
 pyreduce/clipnflip.py,sha256=yL_ESobmpVopzEG_jGXeXu63MKnQGSyEW1uAGl7inFE,5557
 pyreduce/combine_frames.py,sha256=xPG-k_Z5Bf7bL6Io3OuHHlsVVlb95wU-QKggXB7RpJo,29196
@@ -8,25 +8,25 @@ pyreduce/cwrappers.py,sha256=_LHLMxPvWDigkcgJIY-U1_NY021ElK9VyN6vrHYnPuw,13590
 pyreduce/datasets.py,sha256=RpP9kSGDlih0jvXvz6ab8Otad74IzmGW5Q44wwa3mPc,5105
 pyreduce/echelle.py,sha256=JgSex9nW3pl9h73qy8jcr0rE6FEK_O9oVjn8HfceHoo,12275
 pyreduce/estimate_background_scatter.py,sha256=QVY1kpqirdZQr_tKWhbVocX2LnvDkVj30iAz7hQRpy0,3871
-pyreduce/extract.py,sha256=K8e_XMRtw7CEQHDFZ-0vvqvNBTkB64yrhKlzx6Dy0uY,44883
+pyreduce/extract.py,sha256=wDj3l-P8UCaM4KqM1yyQTRWqrB69Q8uQerU-0EIoVh8,45031
 pyreduce/extraction_width.py,sha256=71_wRtXJ5WaCR48WWemGS-FgDtrFCf1HGIPQskT3LI0,2308
 pyreduce/make_shear.py,sha256=hIiNKBkAgUiT29lO9xT5KA2PwCmE75J7ToeZYB8GFtw,20129
 pyreduce/rectify.py,sha256=2l8h8tU0dFD4uv5o4SlqrrIIxVj-RU2Q4aQj7yRNvkk,5025
-pyreduce/reduce.py,sha256=A8icegJtJyqAbM4Oj2_hQe1Gvmysz6V4sXQcESSM-vc,76294
+pyreduce/reduce.py,sha256=smXUX89Ta9NnSFNR7EcUyDo8fckj3v6q0aDV2VfglQQ,76284
 pyreduce/trace_orders.py,sha256=DxSvWA2rMjxYhyxwtF1AFmKcUGarsZ0ic0Sq-gqMExg,20672
 pyreduce/util.py,sha256=xu41l56zMVjuP9129dU45L05UHGXph9DtpIdUyB7VYY,37188
 pyreduce/wavelength_calibration.py,sha256=GNHTOUoGjk5l0TJ7ggaPX5fxZLBPJxuXEjcV3sTJuRs,68564
 pyreduce/clib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyreduce/clib/_slitfunc_2d.cpython-313-darwin.so,sha256=DI56HNhl66l-r3_8X_O8tKORd_C3SRUGat_FqZh9IF8,69872
-pyreduce/clib/_slitfunc_bd.cpython-313-darwin.so,sha256=mJxoOp_7M9DguObQkClGAM-_iREQOH4BkDKHOrPseC8,52240
+pyreduce/clib/_slitfunc_2d.cpython-313-darwin.so,sha256=Ea6I-KFM2rbdnNcu3Jaq3rPChevnoMcpy5rFLmL6D0k,69872
+pyreduce/clib/_slitfunc_bd.cpython-313-darwin.so,sha256=jBann6sSRkp97jEMgx9ZFViaOIMA1NdmGdo4Mu8CAt4,52240
 pyreduce/clib/build_extract.py,sha256=Jf1nqWUIR_fnlnUrwpiWJd-sNP6Yq2WZPC5mKqCOUbY,1945
 pyreduce/clib/slit_func_2d_xi_zeta_bd.c,sha256=o_R_3hq0tX2ZdaCRxJjY2mXQf4RaYENcVKVn2OZR_Rk,51279
 pyreduce/clib/slit_func_2d_xi_zeta_bd.h,sha256=vQkOPIzNzOa32D-iW1_qoQDp4jtaKjSHUYCiDMIIcq4,1512
 pyreduce/clib/slit_func_bd.c,sha256=i_nLyO-5PDZdNZyJKUk3oR_tCYZqVsYKrvQmhwQBxTg,11466
 pyreduce/clib/slit_func_bd.h,sha256=Dx9dBmk4xYiqK44Ak5lxI9JJTkxagKdKa-rOItiTpCE,1326
 pyreduce/instruments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyreduce/instruments/andes.json,sha256=7qVfw54J3f95JGNkVF0NSWafST-Yp-OMWNgu3rqttgw,1826
-pyreduce/instruments/andes.py,sha256=J5G_-D659FHSrDiQf12Rn2gjddXZqCYtEHJDzYsvOr4,3363
+pyreduce/instruments/andes.json,sha256=sk3pIuYYdty6r8_ihbTuJXpFAw2ZOLP5wUWLFESYBZs,1904
+pyreduce/instruments/andes.py,sha256=0Z9lACgBPI8KT7bRE_m_daqQzzfl6GcZVud6_hZGClk,3439
 pyreduce/instruments/common.json,sha256=ypTnKwF5ZT629RUwJa4zXQuBH5DXk2asSGcttQHwzGM,1134
 pyreduce/instruments/common.py,sha256=IE7R67gWA2BFRzu_akdqkUpC6scvoK0A2_hEsOES3E4,22316
 pyreduce/instruments/crires_plus.json,sha256=6WBw8hOkYvvAftxrC31tKHFKd5gUsmOAhctfgh-b1cI,2137
@@ -94,6 +94,7 @@ pyreduce/masks/mask_uves_red_2x2.fits.gz,sha256=rE-DhRuGKshYFpmjYDO9H6_7JHOb4GGU
 pyreduce/masks/mask_uves_red_2x2_split.fits.gz,sha256=dJ7XlP_VHF_s6mlaG-vFc4o9mhlt29B6lLpkRb085jM,9959
 pyreduce/masks/mask_uves_red_binned_2_2.fits.gz,sha256=rKmu5FQx2H-h7PDRg36sQJd20kVfiz4igP-5nqy32tE,13277
 pyreduce/masks/mask_xshooter_nir.fits.gz,sha256=ZyG6yKkYLb3FnOWlmTvbKzjEhv2PctvBGyq2TkfuiF4,28155
+pyreduce/settings/settings_ANDES.json,sha256=ej6Kx2fLFvGGiSoWzJvYsw15bcfnKLeGr4n6Cl7V9rE,2155
 pyreduce/settings/settings_CRIRES_PLUS.json,sha256=JEf1Ja5yv2boCuZx__XlNoBVSli-oKudRb4hix5Io00,2161
 pyreduce/settings/settings_HARPN.json,sha256=37Ya6unViL5Pocgih9FCRZ4VtlnQ-n-LScqzwMEHtds,1579
 pyreduce/settings/settings_HARPS.json,sha256=WcizGTYG5Tw5UQSuUB8MDbUPs909eDPtvCtefIWB7uI,1445
@@ -145,7 +146,7 @@ pyreduce/wavecal/xshooter_nir.npz,sha256=0Fu5wxWutc8072n8Hk2AZAWSlyT4WdhJuhh0OzU
 pyreduce/wavecal/atlas/thar.fits,sha256=nPPNStZ281iPUNsOXu3YJfHNlnHBd1CWMLwTuZL8vvo,1529218
 pyreduce/wavecal/atlas/thar_list.txt,sha256=saK3YW1slxlXGeulZDdILWf952XOWToJcUULVSHMe6k,63515
 pyreduce/wavecal/atlas/une.fits,sha256=egHlchdM4AN9MSksEI5MlHkmB3g1G1VhEdzhUG3XU8I,2949057
-pyreduce_astro-0.6.0b2.dist-info/METADATA,sha256=mmpbNGsvx1yf0JShQF3IWn4MoamokSrhrgLF-2SMhKQ,5267
-pyreduce_astro-0.6.0b2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pyreduce_astro-0.6.0b2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-pyreduce_astro-0.6.0b2.dist-info/RECORD,,
+pyreduce_astro-0.6.0b3.dist-info/METADATA,sha256=OuWiEn2E11TSmdlK-O9ART_g6DyYdsmqyA5dFm8DV1Y,5309
+pyreduce_astro-0.6.0b3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+pyreduce_astro-0.6.0b3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pyreduce_astro-0.6.0b3.dist-info/RECORD,,