Move source catalog reader to lib (#9994)

Author: emolter

jwst/assign_wcs/util.py

@@ -7,7 +7,6 @@
 from astropy.constants import c
 from astropy.coordinates import SkyCoord
 from astropy.modeling import models as astmodels
-from astropy.table import QTable
 from gwcs import WCS
 from gwcs import utils as gwutils
 from gwcs.wcstools import grid_from_bounding_box
@@ -16,7 +15,7 @@
 from stdatamodels.jwst.transforms.models import GrismObject
 from stpipe.exceptions import StpipeExitException
 
-from jwst.lib.catalog_utils import SkyObject
+from jwst.lib.catalog_utils import SkyObject, read_source_catalog
 
 log = logging.getLogger(__name__)
 
@@ -32,7 +31,6 @@
     "calc_rotation_matrix",
     "wrap_ra",
     "update_fits_wcsinfo",
-    "read_source_catalog",
 ]
 
 
@@ -219,47 +217,6 @@ def not_implemented_mode(input_model, ref, slit_y_range=None):  # noqa: ARG001
     log.critical(message)
 
 
-def read_source_catalog(catalog_name):
-    """
-    Read a source catalog from file or validate an existing QTable.
-
-    Parameters
-    ----------
-    catalog_name : str or `~astropy.table.QTable`
-        Either the filename of a source catalog in ECSV format, or an
-        existing Astropy QTable containing the catalog data.
-
-    Returns
-    -------
-    catalog : `~astropy.table.QTable`
-        The source catalog as a table.
-
-    Raises
-    ------
-    ValueError
-        If an empty filename string is provided.
-    FileNotFoundError
-        If the specified catalog file cannot be found.
-    TypeError
-        If the input is neither a string filename nor a QTable instance.
-    """
-    if isinstance(catalog_name, str):
-        if len(catalog_name) == 0:
-            err_text = "Empty catalog filename"
-            log.error(err_text)
-            raise ValueError(err_text)
-        try:
-            return QTable.read(catalog_name, format="ascii.ecsv")
-        except FileNotFoundError as e:
-            log.error(f"Could not find catalog file: {e}")
-            raise FileNotFoundError(f"Could not find catalog: {e}") from None
-    elif isinstance(catalog_name, QTable):
-        return catalog_name
-    err_text = "Need to input string name of catalog or astropy.table.table.QTable instance"
-    log.error(err_text)
-    raise TypeError(err_text)
-
-
 def get_object_info(catalog_name=None):
     """
     Return a list of SkyObjects from the direct image.

jwst/extract_2d/grisms.py

@@ -16,6 +16,7 @@
 from stdatamodels.jwst.transforms.models import IdealToV2V3
 
 from jwst.assign_wcs import util
+from jwst.lib.catalog_utils import read_source_catalog
 
 log = logging.getLogger(__name__)
 
@@ -750,7 +751,7 @@ def radec_to_source_ids(catalog, source_ids=None, source_ra=None, source_dec=Non
     source_ids : np.ndarray or None
         List of unique source IDs to extract.
     """
-    catalog = util.read_source_catalog(catalog)
+    catalog = read_source_catalog(catalog)
     catalog_coord = catalog["sky_centroid"]
     if source_ids is None:
         source_ids = []

jwst/lib/catalog_utils.py

@@ -1,10 +1,56 @@
 """Utilities for naming source catalogs."""
 
+import logging
 import re
 from collections import namedtuple
 from pathlib import Path
 
-__all__ = ["replace_suffix_ext", "SkyObject"]
+from astropy.table import QTable
+
+log = logging.getLogger(__name__)
+
+__all__ = ["replace_suffix_ext", "SkyObject", "read_source_catalog"]
+
+
+def read_source_catalog(catalog_name):
+    """
+    Read a source catalog from file or validate an existing QTable.
+
+    Parameters
+    ----------
+    catalog_name : str or `~astropy.table.QTable`
+        Either the filename of a source catalog in ECSV format, or an
+        existing Astropy QTable containing the catalog data.
+
+    Returns
+    -------
+    catalog : `~astropy.table.QTable`
+        The source catalog as a table.
+
+    Raises
+    ------
+    ValueError
+        If an empty filename string is provided.
+    FileNotFoundError
+        If the specified catalog file cannot be found.
+    TypeError
+        If the input is neither a string filename nor a QTable instance.
+    """
+    if isinstance(catalog_name, str):
+        if len(catalog_name) == 0:
+            err_text = "Empty catalog filename"
+            log.error(err_text)
+            raise ValueError(err_text)
+        try:
+            return QTable.read(catalog_name, format="ascii.ecsv")
+        except FileNotFoundError as e:
+            log.error(f"Could not find catalog file: {e}")
+            raise FileNotFoundError(f"Could not find catalog: {e}") from None
+    elif isinstance(catalog_name, QTable):
+        return catalog_name
+    err_text = "Need to input string name of catalog or astropy.table.table.QTable instance"
+    log.error(err_text)
+    raise TypeError(err_text)
 
 
 def replace_suffix_ext(filename, old_suffix_list, new_suffix, output_ext="ecsv", output_dir=None):

jwst/lib/tests/test_catalog_utils.py

@@ -0,0 +1,50 @@
+import pytest
+from astropy.utils.diff import report_diff_values
+
+from jwst.lib.catalog_utils import read_source_catalog
+from jwst.source_catalog import SourceCatalogStep
+from jwst.source_catalog.tests.helpers import make_nircam_model
+
+
+@pytest.fixture
+def nircam_model():
+    return make_nircam_model()
+
+
+def test_read_source_catalog(nircam_model, tmp_path):
+    """Ensure read_source_catalog can read a real source catalog file."""
+
+    step = SourceCatalogStep(
+        snr_threshold=0.5, npixels=10, bkg_boxsize=50, kernel_fwhm=2.0, save_results=False
+    )
+    cat = step.run(nircam_model)
+
+    # in memory
+    cat_in_memory = read_source_catalog(cat)
+    assert len(cat_in_memory) > 0
+
+    # from file
+    catpath = tmp_path / "test.ecsv"
+    catstr = str(catpath)
+    cat.write(catpath, format="ascii.ecsv", overwrite=True)
+    cat_from_str = read_source_catalog(catstr)
+    identical = report_diff_values(cat_in_memory, cat_from_str)
+    assert identical, f"Catalogs read in memory and from file str differ: {identical}"
+
+
+def test_read_source_catalog_invalid_input():
+    """Test that read_source_catalog raises appropriate errors for invalid inputs."""
+
+    # Test empty string
+    with pytest.raises(ValueError, match="Empty catalog filename"):
+        read_source_catalog("")
+
+    # Test file not found
+    with pytest.raises(FileNotFoundError, match="Could not find catalog"):
+        read_source_catalog("nonexistent_catalog.ecsv")
+
+    # Test invalid type
+    with pytest.raises(
+        TypeError, match="Need to input string name of catalog or astropy.table.table.QTable"
+    ):
+        read_source_catalog(12345)

jwst/source_catalog/tests/helpers.py

@@ -0,0 +1,119 @@
+import numpy as np
+import stdatamodels.jwst.datamodels as dm
+from photutils.datasets import make_gwcs
+
+
+def make_nircam_model():
+    """
+    Create a NIRCam ImageModel with synthetic data for testing.
+
+    Returns
+    -------
+    model : dm.ImageModel
+        NIRCam image model with data, error, and weight arrays.
+    """
+    rng = np.random.default_rng(seed=123)
+    data = rng.normal(0, 0.5, size=(101, 101))
+    data[20:80, 10:20] = 1.4
+    data[20:30, 20:45] = 1.4
+    data[20:80, 55:65] = 7.2
+    data[70:80, 65:87] = 7.2
+    data[45:55, 65:87] = 7.2
+    data[20:30, 65:87] = 7.2
+    data[55:75, 82:92] = 7.2
+    data[25:45, 82:92] = 7.2
+
+    wht = np.ones(data.shape)
+    wht[0:10, :] = 0.0
+    err = np.abs(data) / 10.0
+    model = dm.ImageModel(data, wht=wht, err=err)
+    model.meta.bunit_data = "MJy/sr"
+    model.meta.bunit_err = "MJy/sr"
+    model.meta.photometry.pixelarea_steradians = 1.0e-13
+    model.meta.wcs = make_gwcs(data.shape)
+    model.meta.wcsinfo = {
+        "ctype1": "RA---TAN",
+        "ctype2": "DEC--TAN",
+        "dec_ref": 11.99875540218638,
+        "ra_ref": 22.02351763251896,
+        "roll_ref": 0.005076934167039675,
+        "v2_ref": 86.039011,
+        "v3_ref": -493.385704,
+        "v3yangle": -0.07385127,
+        "vparity": -1,
+        "wcsaxes": 2,
+        "crpix1": 50,
+        "crpix2": 50,
+    }
+    model.meta.instrument = {
+        "channel": "LONG",
+        "detector": "NRCALONG",
+        "filter": "F444W",
+        "lamp_mode": "NONE",
+        "module": "A",
+        "name": "NIRCAM",
+        "pupil": "CLEAR",
+    }
+    model.meta.exposure.type = "NRC_IMAGE"
+    model.meta.observation.date = "2021-01-01"
+    model.meta.observation.time = "00:00:00"
+
+    return model
+
+
+def make_nircam_model_without_apcorr():
+    """
+    Create a NIRCam ImageModel without aperture correction.
+
+    Returns
+    -------
+    model : dm.ImageModel
+        NIRCam image model with data, error, and weight arrays.
+    """
+    rng = np.random.default_rng(seed=123)
+    data = rng.normal(0, 0.5, size=(101, 101))
+    data[20:80, 10:20] = 1.4
+    data[20:30, 20:45] = 1.4
+    data[20:80, 55:65] = 7.2
+    data[70:80, 65:87] = 7.2
+    data[45:55, 65:87] = 7.2
+    data[20:30, 65:87] = 7.2
+    data[55:75, 82:92] = 7.2
+    data[25:45, 82:92] = 7.2
+
+    wht = np.ones(data.shape)
+    wht[0:10, :] = 0.0
+    err = np.abs(data) / 10.0
+    model = dm.ImageModel(data, wht=wht, err=err)
+    model.meta.bunit_data = "MJy/sr"
+    model.meta.bunit_err = "MJy/sr"
+    model.meta.photometry.pixelarea_steradians = 1.0e-13
+    model.meta.wcs = make_gwcs(data.shape)
+    model.meta.wcsinfo = {
+        "ctype1": "RA---TAN",
+        "ctype2": "DEC--TAN",
+        "dec_ref": 11.99875540218638,
+        "ra_ref": 22.02351763251896,
+        "roll_ref": 0.005076934167039675,
+        "v2_ref": 86.039011,
+        "v3_ref": -493.385704,
+        "v3yangle": -0.07385127,
+        "vparity": -1,
+        "wcsaxes": 2,
+        "crpix1": 50,
+        "crpix2": 50,
+    }
+    model.meta.instrument = {
+        "channel": "LONG",
+        "detector": "NRCALONG",
+        "filter": "F2550WR",
+        "lamp_mode": "NONE",
+        "module": "A",
+        "name": "NIRCAM",
+        "pupil": "CLEAR",
+    }
+    model.meta.exposure.type = "NRC_IMAGE"
+    model.meta.observation.date = "2021-01-01"
+    model.meta.observation.time = "00:00:00"
+
+    return model