Add support for mwmVisit files (#68)

* adding mwmvisit to spectra model

* adding mwmvisit to file return path

* bumping specutils version

* updating solara deps

* updating poetry lock file

* relocking

pyproject.toml

@@ -36,7 +36,7 @@ Sphinx = {version="^3.0.0", optional=true}
 fastapi = {extras = ["all"], version = "^0.104.0"}
 uvicorn = "^0.22.0"
 gunicorn = "^20.1.0"
-astropy = "^5.2.0"
+astropy = "^6.1.0"
 aiofiles = "^0.5.0"
 orjson = "^3.9.0"
 fastapi-restful = {extras = ["all"], version = "^0.5.0"}

python/valis/db/models.py

@@ -248,7 +248,7 @@ class PipeFiles(BaseModel):
     """ Pydantic model for lists of files """
     boss: Optional[str] = None
     apogee: Optional[str] = None
-    astra: Optional[str] = None
+    astra: Optional[list[str]] = None
 
 
 class PipesModel(PeeweeBase):

python/valis/db/queries.py

@@ -547,7 +547,8 @@ def get_pipe_meta(sdss_id: int, release: str, pipeline: str) -> dict:
     # get astra pipeline target
     elif pipeline == 'astra' and (qq := get_astra_target(sdss_id, release)):
         res = qq.dicts().first()
-        return {pipeline: res, 'files': {pipeline: build_astra_path(res, release)}}
+        return {pipeline: res, 'files': {pipeline: [build_astra_path(res, release),
+                                                    build_astra_path(res, release, name='mwmVisit')]}}
 
 
 def get_target_pipeline(sdss_id: int, release: str, pipeline: str = 'all') -> dict:

python/valis/io/model_spectra_info.json

@@ -35,5 +35,18 @@
             "error": {"extension": 1, "type": "table", "column": "ivar"},
             "mask": {"extension": 1, "type": "table", "column": "pixel_flags"}
         }
+    },
+    {
+        "product": "mwmVisit",
+        "aliases": ["mwmvisit"],
+        "pipeline": "astra",
+        "multi_spectra": true,
+        "spectral_extensions": ["BOSS/APO", "BOSS/LCO", "APOGEE/APO", "APOGEE/LCO"],
+        "parameters": {
+            "flux": {"extension": 1, "type": "table", "column": "flux", "units": "1e-17 * erg / (s * cm**2 * Angstrom)"},
+            "wavelength": {"extension": 1, "type": "wcscon", "column": "LOGLIN", "nwave": "NPIXELS", "units": "Angstrom", "crval": "CRVAL", "cdelt": "CDELT"},
+            "error": {"extension": 1, "type": "table", "column": "ivar"},
+            "mask": {"extension": 1, "type": "table", "column": "pixel_flags"}
+        }
     }
 ]

python/valis/io/spectra.py

@@ -106,6 +106,13 @@ def extract_data(product: str, filepath: str, multispec: Union[int, str] = None)
                     vals = vals.value
 
                 data[param] = vals
+            elif info['type'] == "wcscon":
+                # extract the correct wcs header column
+                npixels = hdulist[extension].header[info['nwave']]
+                cdelt = hdulist[extension].header[info['cdelt']]
+                crval = hdulist[extension].header[info['crval']]
+
+                data[param] = 10 ** (np.arange(npixels) * cdelt + crval)
             else:
                 data[param] = hdulist[extension].data
 

python/valis/utils/paths.py

@@ -156,7 +156,8 @@ def build_apogee_path(values: dict, release: str, ignore_existence: bool = False
                            ignore_existence=ignore_existence)
 
 
-def build_astra_path(values: dict, release: str, ignore_existence: bool = False) -> str:
+def build_astra_path(values: dict, release: str, name: str = 'mwmStar',
+                     ignore_existence: bool = False) -> str:
     """ Build an Astra mwmStar file path
 
     Builds an Astra file path to the mwmStar file.  It sets a default
@@ -168,6 +169,8 @@ def build_astra_path(values: dict, release: str, ignore_existence: bool = False)
         the input data values to give to the path template
     release : str
         the data release
+    name : str
+        the name of the file product
     ignore_existence : bool, optional
         flag to ignore file existence and return path, by default False
 
@@ -176,5 +179,5 @@ def build_astra_path(values: dict, release: str, ignore_existence: bool = False)
     str
         the output file path
     """
-    return build_file_path(values, 'mwmStar', release, defaults={'component': ''},
+    return build_file_path(values, name, release, defaults={'component': ''},
                            ignore_existence=ignore_existence)