adding tests for changes in JP-3311 and minor fixes (#8481)

Co-authored-by: Howard Bushouse <bushouse@stsci.edu>

CHANGES.rst

@@ -99,6 +99,8 @@ outlier_detection
   finished, unless save_intermediate_results is True. This PR also addressed
   the _i2d files not being saved in the specified output directory. [#8464]
 
+- Added tests for changes made in #8464. [#8481]
+
 photom
 ------
 

jwst/outlier_detection/outlier_detection.py

@@ -351,7 +351,7 @@ def detect_outliers(self, blot_models):
 def _remove_file(fn):
     if isinstance(fn, str) and os.path.isfile(fn):
         os.remove(fn)
-        log.debug(f"    {fn}")
+        log.info(f"Removing file {fn}")
 
 
 def flag_cr(sci_image, blot_image, snr="5.0 4.0", scale="1.2 0.7", backg=0,

jwst/outlier_detection/outlier_detection_spec.py

@@ -110,6 +110,7 @@ def do_detection(self):
             if not pars['in_memory']:
                 for fn in drizzled_models._models:
                     _remove_file(fn)
+                    log.info(f"Removing file {fn}")
 
         if pars['resample_data'] is True:
             # Blot the median image back to recreate each input image specified
@@ -130,4 +131,5 @@ def do_detection(self):
         if not pars['save_intermediate_results']:
             for fn in blot_models._models:
                 _remove_file(fn)
+                log.info(f"Removing file {fn}")
         del median_model, blot_models

jwst/outlier_detection/outlier_detection_step.py

@@ -167,8 +167,6 @@ def process(self, input_data):
 
             state = 'COMPLETE'
             if self.input_container:
-                if not self.save_intermediate_results:
-                    self.log.debug("The following files will be deleted since save_intermediate_results=False:")
                 for model in self.input_models:
                     model.meta.cal_step.outlier_detection = state
             else:

jwst/outlier_detection/tests/test_outlier_detection.py

@@ -1,6 +1,8 @@
 import pytest
 import numpy as np
 from scipy.ndimage import gaussian_filter
+from glob import glob
+import os
 
 from stdatamodels.jwst import datamodels
 
@@ -15,7 +17,6 @@
 )
 from jwst.assign_wcs.pointing import create_fitswcs
 
-
 OUTLIER_DO_NOT_USE = np.bitwise_or(
     datamodels.dqflags.pixel["DO_NOT_USE"], datamodels.dqflags.pixel["OUTLIER"]
 )
@@ -184,6 +185,15 @@ def test_outlier_step(we_three_sci, tmp_cwd):
     # Drop a CR on the science array
     container[0].data[12, 12] += 1
 
+    # Verify that intermediary files are removed
+    OutlierDetectionStep.call(container)
+    i2d_files = glob(os.path.join(tmp_cwd, '*i2d.fits'))
+    median_files = glob(os.path.join(tmp_cwd, '*median.fits'))
+    blot_files = glob(os.path.join(tmp_cwd, '*blot.fits'))
+    assert len(i2d_files) == 0
+    assert len(median_files) == 0
+    assert len(blot_files) == 0
+
     result = OutlierDetectionStep.call(
         container, save_results=True, save_intermediate_results=True
     )
@@ -199,6 +209,14 @@ def test_outlier_step(we_three_sci, tmp_cwd):
     # Verify CR is flagged
     assert result[0].dq[12, 12] == OUTLIER_DO_NOT_USE
 
+    # Verify that intermediary files are saved at the specified location
+    i2d_files = glob(os.path.join(tmp_cwd, '*i2d.fits'))
+    median_files = glob(os.path.join(tmp_cwd, '*median.fits'))
+    blot_files = glob(os.path.join(tmp_cwd, '*blot.fits'))
+    assert len(i2d_files) != 0
+    assert len(median_files) != 0
+    assert len(blot_files) != 0
+
 
 def test_outlier_step_on_disk(we_three_sci, tmp_cwd):
     """Test whole step with an outlier including saving intermediate and results files"""

jwst/regtest/test_miri_lrs_slit_spec3.py

@@ -79,7 +79,7 @@ def test_miri_lrs_slit_spec3(run_pipeline, rtdata_module, fitsdiff_default_kwarg
     diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
     assert diff.identical, diff.report()
 
-    if "s2d" in output:
+    if output == "s2d":
         # Compare the calculated wavelengths
         tolerance = 1e-03
         dmt = datamodels.open(rtdata.truth)

jwst/regtest/test_nirspec_fs_spec3.py

@@ -46,7 +46,7 @@ def test_nirspec_fs_spec3(run_pipeline, rtdata_module, fitsdiff_default_kwargs,
     diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
     assert diff.identical, diff.report()
 
-    if "s2d" in output:
+    if output == "s2d":
         # Compare the calculated wavelengths
         tolerance = 1e-03
         dmt = datamodels.open(rtdata.truth)

jwst/resample/resample.py

@@ -72,7 +72,7 @@ def __init__(self, input_models, output=None, single=False, blendheaders=True,
         self.input_models = input_models
         self.output_dir = None
         self.output_filename = output
-        if output is not None and '.fits' not in output:
+        if output is not None and '.fits' not in str(output):
             self.output_dir = output
             self.output_filename = None
 

jwst/resample/resample_spec.py

@@ -64,7 +64,7 @@ def __init__(self, input_models, output=None, single=False, blendheaders=False,
 
         self.output_filename = output
         self.output_dir = None
-        if output is not None and '.fits' not in output:
+        if output is not None and '.fits' not in str(output):
             self.output_dir = output
             self.output_filename = None
         self.pscale_ratio = pscale_ratio