Merge branch 'master' into release/1.12.x

CHANGES.rst

@@ -1,4 +1,19 @@
-1.12.3 (unreleased)
+1.12.4 (2023-10-12)
+===================
+
+cube_build
+----------
+
+- Keep data models opened by cube build open until the step completes. [#7998]
+
+general
+-------
+
+- Fix numpy 2.0 deprecation warnings in cube_build, photom and wfs_combine. [#7999]
+
+- pinned dependencies for several in-development packages below their next versions to maintain compatibility
+
+1.12.3 (2023-10-03)
 ===================
 
 documentation
@@ -41,7 +56,7 @@ extract_1d
 flat_field
 ----------
 
-- Update the ``combine_fast_slow`` function for NIRSpec spectroscopic flats 
+- Update the ``combine_fast_slow`` function for NIRSpec spectroscopic flats
   to use 1D error values provided by F-flat reference files. [#7978]
 
 - For NIRSpec modes, set all DO_NOT_USE pixels to NaN after flat
@@ -65,7 +80,7 @@ straylight
 extract_1d
 ----------
 
-- For MIRS MRS IFU data allow the user to set the src_type and allow 
+- For MIRS MRS IFU data allow the user to set the src_type and allow
   the user to scale the extraction radius between 0.5 to 3.0 FWHM. [#7883]
 
 - Bug fix for #7883. The input model type is checked to see if the input is
@@ -245,7 +260,7 @@ pathloss
 - Fix interpolation error for point source corrections. [#7799]
 
 - Update the MIRI LRS fixed-slit correction to default to the center of the slit
-  when the computed target location is outside the slit. Add the parameter 
+  when the computed target location is outside the slit. Add the parameter
   "user_slit_loc" to allow specifying the source location to use. [#7806]
 
 photom

CITATION.cff

@@ -75,7 +75,7 @@ authors:
   given-names: "Maria"
   orcid: "https://orcid.org/0000-0003-2314-3453"
 title: "JWST Calibration Pipeline"
-version: 1.12.2
+version: 1.12.4
 doi: 10.5281/zenodo.7038885
-date-released: 2023-10-02
+date-released: 2023-10-12
 url: "https://github.com/spacetelescope/jwst"

README.md

@@ -210,10 +210,12 @@ the specified context and less than the context for the next release.
 
 | jwst tag            | DMS build | SDP_VER  | CRDS_CONTEXT | Released   | Ops Install | Notes                                         |
 |---------------------|-----------|----------|--------------|------------|-------------|-----------------------------------------------|
-| 1.12.2              | B10.0rc3  | 2023.3.x | 1135         | 2023-10-02 |             | Third release candidate for B10.0             |
-| 1.12.1              | B10.0rc2  | 2023.3.x | 1132         | 2023-09-26 |             | Second release candidate for B10.0            |
-| 1.12.0              | B10.0rc1  | 2023.3.x | 1130         | 2023-09-18 |             | First release candidate for B10.0             |
-| 1.11.4              | B9.3.1    | 2023.2.1 | 1107         | 2023-08-14 |             | Final release for B9.3.1 patch                |
+| 1.12.4              |           | 2023.3.0 | 1135         | 2023-10-12 |             | Pinning dependencies for external users       |
+| 1.12.3              | B10.0     | 2023.3.0 | 1135         | 2023-10-03 | 2023-12-05  | Final release candidate for B10.0             |
+| 1.12.2              | B10.0rc3  |          | 1135         | 2023-10-02 | (tentative) | Third release candidate for B10.0             |
+| 1.12.1              | B10.0rc2  |          | 1132         | 2023-09-26 |             | Second release candidate for B10.0            |
+| 1.12.0              | B10.0rc1  |          | 1130         | 2023-09-18 |             | First release candidate for B10.0             |
+| 1.11.4              | B9.3.1    | 2023.2.1 | 1107         | 2023-08-14 | 2023-08-24  | Final release for B9.3.1 patch                |
 | 1.11.3              | B9.3      | 2023.2.0 | 1097         | 2023-07-17 |             | Final release candidate for B9.3              |
 | 1.11.2              | B9.3rc3   |          | 1097         | 2023-07-12 |             | Third release candidate for B9.3              |
 | 1.11.1              | B9.3rc2   |          | 1094         | 2023-06-29 |             | Second release candidate for B9.3             |

jwst/cube_build/cube_build_step.py

@@ -241,6 +241,7 @@ def process(self, input):
         # Check for a valid reference file
         if par_filename == 'N/A':
             self.log.warning('No default cube parameters reference file found')
+            input_table.close()
             return
 # ________________________________________________________________________________
 # shove the input parameters in to pars to pull out in general cube_build.py
@@ -299,6 +300,7 @@ def process(self, input):
         if instrument == 'MIRI' and self.coord_system == 'internal_cal':
             self.log.warning('The output coordinate system of internal_cal is not valid for MIRI')
             self.log.warning('use output_coord = ifualign instead')
+            input_table.close()
             return
         filenames = master_table.FileMap['filename']
 
@@ -402,6 +404,7 @@ def process(self, input):
         if status_cube == 1:
             self.skip = True
 
+        input_table.close()
         return cube_container
 # ******************************************************************************
 

jwst/cube_build/data_types.py

@@ -69,30 +69,34 @@ def __init__(self, input, single, output_file, output_dir):
 
         self.input_models = []
         self.output_name = None
-        
+
         # open the input with datamodels
         # if input is filename or model when it is opened it is a model
         # if input if an association name or ModelContainer then it is opened as a container
 
-        with datamodels.open(input) as input_models:
-
-            if isinstance(input_models, datamodels.IFUImageModel):
-                # It's a single image that's been passed in as a model
-                # input is a model
-                filename = input_models.meta.filename
-                self.input_models.append(input_models)
-                self.output_name = self.build_product_name(filename)
-
-            elif isinstance(input_models, ModelContainer):
-                self.output_name = 'Temp'
-                self.input_models = input_models
-                if not single:  # find the name of the output file from the association
-                    self.output_name = input_models.meta.asn_table.products[0].name
-            else:
-                raise TypeError("Failed to process file type {}".format(type(input_models)))
-            # if the user has set the output name - strip out *.fits
-            # later suffixes will be added to this name to designate the
-            # channel, subchannel or grating,filter the data is covers.
+        input_models = datamodels.open(input)
+        # if input is a filename, we will need to close the opened file 
+        self._opened = [input_models]
+
+        if isinstance(input_models, datamodels.IFUImageModel):
+            # It's a single image that's been passed in as a model
+            # input is a model
+            filename = input_models.meta.filename
+            self.input_models.append(input_models)
+            self.output_name = self.build_product_name(filename)
+
+        elif isinstance(input_models, ModelContainer):
+            self.output_name = 'Temp'
+            self.input_models = input_models
+            if not single:  # find the name of the output file from the association
+                self.output_name = input_models.meta.asn_table.products[0].name
+        else:
+            # close files opened above
+            self.close()
+            raise TypeError("Failed to process file type {}".format(type(input_models)))
+        # If the user has set the output name, strip off *.fits.
+        # Suffixes will be added to this name later, to designate the
+        # channel+subchannel (MIRI MRS) or grating+filter (NRS IFU) the output cube covers.
 
 
         if output_file is not None:
@@ -102,6 +106,12 @@ def __init__(self, input, single, output_file, output_dir):
         if output_dir is not None:
             self.output_name = output_dir + '/' + self.output_name
 
+    def close(self):
+        """
+        Close any files opened by this instance
+        """
+        [f.close() for f in self._opened]
+
 # _______________________________________________________________________________
     def build_product_name(self, filename):
         """ Determine the base of output name if an input data is a fits filename.

jwst/cube_build/file_table.py

@@ -113,7 +113,6 @@ def set_file_table(self,
 # ________________________________________________________________________________
 # Loop over input list of files and assign fill in the MasterTable with filename
 # for the correct (channel-subchannel) or (grating-subchannel)
-
         for model in input_models:
             instrument = model.meta.instrument.name.upper()
             assign_wcs = model.meta.cal_step.assign_wcs
@@ -143,9 +142,6 @@ def set_file_table(self,
                 log.info('Instrument not valid for cube')
                 pass
 
-            model.close()
-            del model
-
         return instrument
 
 

jwst/cube_build/ifu_cube.py

@@ -294,13 +294,13 @@ def set_geometry(self, corner_a, corner_b, lambda_min, lambda_max):
         xilimit = max(np.abs(xi_min), np.abs(xi_max))
         etalimit = max(np.abs(eta_min), np.abs(eta_max))
 
-        na = math.ceil(xilimit / self.cdelt1) + 1
-        nb = math.ceil(etalimit / self.cdelt2) + 1
+        na = math.ceil((xilimit / self.cdelt1).item()) + 1
+        nb = math.ceil((etalimit / self.cdelt2).item()) + 1
 
         # if the user set the nspax_x or nspax_y then redefine na, nb
         # it is assumed that both values are ODD numbers
         # We want the central pixel to be the tangent point with na/nb pixels on either
-        # side of central pixel. 
+        # side of central pixel.
         if self.nspax_x is not None:
             na = int(self.nspax_x/2)
         if self.nspax_y is not None:

jwst/cube_build/tests/test_cube_build_step.py

@@ -6,8 +6,10 @@
 import pytest
 from astropy.io import fits
 
+from gwcs import WCS
 from stdatamodels.jwst.datamodels import IFUImageModel
 
+from jwst import assign_wcs
 from jwst.cube_build import CubeBuildStep
 from jwst.cube_build.file_table import ErrorNoAssignWCS
 from jwst.cube_build.cube_build import ErrorNoChannels
@@ -100,8 +102,15 @@ def miri_image():
     return image
 
 
-def test_call_cube_build(_jail, miri_cube_pars, miri_image):
+@pytest.mark.parametrize("as_filename", [True, False])
+def test_call_cube_build(_jail, miri_cube_pars, miri_image, tmp_path, as_filename):
     """ test defaults of step are set up and user input are defined correctly """
+    if as_filename:
+        fn = tmp_path / 'miri.fits'
+        miri_image.save(fn)
+        step_input = fn
+    else:
+        step_input = miri_image
 
     # we do not want to run the CubeBuild through to completion because
     # the image needs to be a full image and this take too much time
@@ -112,7 +121,7 @@ def test_call_cube_build(_jail, miri_cube_pars, miri_image):
         step = CubeBuildStep()
         step.override_cubepar = miri_cube_pars
         step.channel = '3'
-        step.run(miri_image)
+        step.run(step_input)
 
     # Test some defaults to step are setup correctly and
     # is user specifies channel is set up correctly
@@ -121,7 +130,7 @@ def test_call_cube_build(_jail, miri_cube_pars, miri_image):
     step.channel = '1'
 
     try:
-        step.run(miri_image)
+        step.run(step_input)
     except ErrorNoAssignWCS:
         pass
 
@@ -132,8 +141,53 @@ def test_call_cube_build(_jail, miri_cube_pars, miri_image):
 
     # Set Assign WCS has been run but the user input to channels is wrong
     miri_image.meta.cal_step.assign_wcs = 'COMPLETE'
+    # save file with modifications
+    if as_filename:
+        miri_image.save(step_input)
     with pytest.raises(ErrorNoChannels):
         step = CubeBuildStep()
         step.override_cubepar = miri_cube_pars
         step.channel = '3'
-        step.run(miri_image)
+        step.run(step_input)
+
+
+@pytest.fixture(scope='function')
+def nirspec_data():
+    image = IFUImageModel((2048, 2048))
+    image.data = np.random.random((2048, 2048))
+    image.meta.instrument.name = 'NIRSPEC'
+    image.meta.instrument.detector = 'NRS1'
+    image.meta.exposure.type = 'NRS_IFU'
+    image.meta.filename = 'test_nirspec.fits'
+    image.meta.observation.date = '2023-10-06'
+    image.meta.observation.time = '00:00:00.000'
+    # below values taken from regtest using file
+    # jw01249005001_03101_00004_nrs1_cal.fits
+    image.meta.instrument.filter = 'F290LP'
+    image.meta.instrument.grating = 'G395H'
+    image.meta.wcsinfo.v2_ref = 299.83548
+    image.meta.wcsinfo.v3_ref = -498.256805
+    image.meta.wcsinfo.ra_ref = 358.0647567841019
+    image.meta.wcsinfo.dec_ref = -2.167207258876695
+    image.meta.cal_step.assign_wcs = 'COMPLETE'
+    step = assign_wcs.assign_wcs_step.AssignWcsStep()
+    refs = {}
+    for reftype in assign_wcs.assign_wcs_step.AssignWcsStep.reference_file_types:
+        refs[reftype] = step.get_reference_file(image, reftype)
+    pipe = assign_wcs.nirspec.create_pipeline(image, refs, slit_y_range=[-.5, .5])
+    image.meta.wcs = WCS(pipe)
+    return image
+
+
+@pytest.mark.parametrize("as_filename", [True, False])
+def test_call_cube_build_nirspec(_jail, nirspec_data, tmp_path, as_filename):
+    if as_filename:
+        fn = tmp_path / 'test_nirspec.fits'
+        nirspec_data.save(fn)
+        step_input = fn
+    else:
+        step_input = nirspec_data
+    step = CubeBuildStep()
+    step.channel = '1'
+    step.coord_system = 'internal_cal'
+    step.run(step_input)

jwst/cube_build/tests/test_wcs.py

@@ -84,8 +84,8 @@ def test_coord_trans1():
     # and an eta close to diff_dec
 
     xi, eta = coord.radec2std(crval1, crval2, ra, dec)
-    assert math.isclose(xi, 0.0, abs_tol=0.001)
-    assert math.isclose(eta, diff_ra, abs_tol=0.001)
+    assert math.isclose(xi.item(), 0.0, abs_tol=0.001)
+    assert math.isclose(eta.item(), diff_ra, abs_tol=0.001)
 
 
 def test_coord_trans2():
@@ -101,8 +101,8 @@ def test_coord_trans2():
     # and an eta close to diff_dec
 
     xi, eta = coord.radec2std(crval1, crval2, ra, dec)
-    assert math.isclose(xi, -3.535, abs_tol=0.001)
-    assert math.isclose(eta, diff_ra, abs_tol=0.001)
+    assert math.isclose(xi.item(), -3.535, abs_tol=0.001)
+    assert math.isclose(eta.item(), diff_ra, abs_tol=0.001)
 
 
 def test_coord_trans3():
@@ -120,8 +120,8 @@ def test_coord_trans3():
 
     xi, eta = coord.radec2std(crval1, crval2, ra, dec)
     ra_test, dec_test = coord.std2radec(crval1, crval2, xi, eta)
-    assert math.isclose(ra, ra_test, abs_tol=0.00001)
-    assert math.isclose(dec, dec_test, abs_tol=0.00001)
+    assert math.isclose(ra, ra_test.item(), abs_tol=0.00001)
+    assert math.isclose(dec, dec_test.item(), abs_tol=0.00001)
 
 
 def test_wrap_ra():

jwst/photom/photom.py

@@ -511,7 +511,7 @@ def calc_miri(self, ftab):
                 # Old style ref file; skip the correction
                 log.info("Skipping MRS MIRI time correction. Extensions not found in the reference file.")
                 self.mrs_time_correction = False
-            
+
             #if np.any(ftab.timecoeff_ch1['binwave']) and self.mrs_time_correction:
             if self.mrs_time_correction:
                 log.info("Applying MRS IFU time dependent correction.")
@@ -1151,7 +1151,7 @@ def save_area_nirspec(self, pix_area):
                     slit.meta.photometry.pixelarea_arcsecsq = 1.
                     slit.meta.photometry.pixelarea_steradians = 1.
                 else:
-                    slit.meta.photometry.pixelarea_arcsecsq = float(pixarea[match])
+                    slit.meta.photometry.pixelarea_arcsecsq = float(pixarea[match].item())
                     slit.meta.photometry.pixelarea_steradians = \
                         slit.meta.photometry.pixelarea_arcsecsq * A2_TO_SR
             if n_failures > 0: