keep cube build input models open to allow reading wcs (spacetelescop…

…e#7998)

Co-authored-by: Howard Bushouse <[email protected]>

CHANGES.rst

@@ -1,7 +1,11 @@
 1.12.4 (unreleased)
 ===================
 
-- 
+cube_build
+----------
+
+- Keep data models opened by cube build open until the step completes. [#7998] 
+
 
 1.12.3 (2023-10-03)
 ===================

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/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)