dkist-processing-cryonirsp 0.0.56rc1__tar.gz → 0.0.58rc1__tar.gz

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+v0.0.56 (2024-04-26)
+====================
+
+Documentation
+-------------
+
+- Update online documentation for Cryo-NIRSP bad pixel correction, beam angle calculation, and beam boundary calculation. (`#117 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/117>`__)
+
+
 v0.0.55 (2024-04-12)
 ====================
 

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dkist_processing_cryonirsp
-Version: 0.0.56rc1
+Version: 0.0.58rc1
 Summary: Science processing code for the Cryo-NIRSP instrument on DKIST
 Home-page: https://bitbucket.org/dkistdc/dkist_processing_cryonirsp/src/main/
 Author: NSO / AURA

dkist_processing_cryonirsp-0.0.58rc1/changelog/116.misc.rst

@@ -0,0 +1 @@
+Reduce flakyness in bad px correction test by contriving bad px neighborhood to give a known result.

dkist_processing_cryonirsp-0.0.58rc1/changelog/119.bugfix.rst

@@ -0,0 +1,2 @@
+Some Cryo-NIRSP CI movies were far too large (>1GB).
+This fix made the movies smaller by scaling down the size of the movies.

dkist_processing_cryonirsp-0.0.58rc1/changelog/120.misc.rst

@@ -0,0 +1 @@
+Rename non-FITS L1 products to better manage namespace.

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp/tasks/assemble_movie.py

@@ -42,7 +42,16 @@ class AssembleCryonirspMovieBase(AssembleMovie):
         raw_L1_shape = random_frame.shape
         flipped_shape = raw_L1_shape[::-1]
 
-        return flipped_shape
+        standard_HD_num_pix = 1920 * 1080
+        frame_num_pix = np.prod(flipped_shape)
+        scale_factor = (
+            np.sqrt(standard_HD_num_pix / frame_num_pix)
+            if frame_num_pix > standard_HD_num_pix
+            else 1.0
+        )
+        scaled_shape = tuple(int(i * scale_factor) for i in flipped_shape)
+
+        return scaled_shape
 
     def pre_run(self) -> None:
         """Set the movie frame shape prior to running."""

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp/tests/test_assemble_movie.py

@@ -13,13 +13,23 @@ from dkist_processing_cryonirsp.tests.conftest import generate_214_l1_fits_frame
 from dkist_processing_cryonirsp.tests.header_models import Cryonirsp122ObserveFrames
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(
+    scope="function", params=[pytest.param(True, id="shrink"), pytest.param(False, id="noshrink")]
+)
 def assemble_movie_task_with_tagged_movie_frames(
-    tmp_path, recipe_run_id, init_cryonirsp_constants_db
+    request,
+    tmp_path,
+    recipe_run_id,
+    init_cryonirsp_constants_db,
 ):
     num_map_scans = 10
     num_scan_steps = 1
-    frame_shape = (100, 200)
+    if request.param:
+        frame_shape = (1080 * 2, 1920 * 2)  # Intentionally "backward" from normal
+        expected_shape = (1080, 1920)[::-1]
+    else:
+        frame_shape = (100, 235)  # Weird aspect ratio
+        expected_shape = (100, 235)[::-1]
     init_cryonirsp_constants_db(recipe_run_id, CryonirspConstantsDb(NUM_MAP_SCANS=num_map_scans))
     with AssembleCryonirspMovie(
         recipe_run_id=recipe_run_id,
@@ -53,7 +63,7 @@ def assemble_movie_task_with_tagged_movie_frames(
                         ],
                         encoder=fits_hdulist_encoder,
                     )
-            yield task, frame_shape
+            yield task, frame_shape, expected_shape
         finally:
             task._purge()
 
@@ -62,7 +72,7 @@ def test_assemble_movie(assemble_movie_task_with_tagged_movie_frames, mocker):
     mocker.patch(
         "dkist_processing_common.tasks.mixin.metadata_store.GraphQLClient", new=FakeGQLClient
     )
-    task, _ = assemble_movie_task_with_tagged_movie_frames
+    task, _, _ = assemble_movie_task_with_tagged_movie_frames
     task()
     movie_file = list(task.read(tags=[CryonirspTag.movie()]))
     assert len(movie_file) == 1
@@ -75,15 +85,15 @@ def test_compute_frame_shape(assemble_movie_task_with_tagged_movie_frames):
     When: Computing the size of the final movie
     Then: The correct size is computed: the size of an L1 output frame
     """
-    task, frame_shape = assemble_movie_task_with_tagged_movie_frames
+    task, frame_shape, expected_shape = assemble_movie_task_with_tagged_movie_frames
 
     # Task starts as polarimetric from fixture constants
-    assert task._compute_frame_shape() == tuple(np.array(frame_shape)[::-1])
+    assert task._compute_frame_shape() == tuple(expected_shape)
 
     # Update constants to be non-polarimetric
     del task.constants._db_dict[CryonirspBudName.num_modstates.value]
     task.constants._db_dict[CryonirspBudName.num_modstates.value] = 1
-    assert task._compute_frame_shape() == tuple(np.array(frame_shape)[::-1])
+    assert task._compute_frame_shape() == tuple(expected_shape)
 
 
 @pytest.fixture(scope="function")

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp/tests/test_corrections.py

@@ -1,3 +1,5 @@
+from typing import Literal
+
 import numpy as np
 import pytest
 from dkist_processing_common._util.scratch import WorkflowFileSystem
@@ -63,6 +65,25 @@ def bad_pixel_mask_task(
             task._purge()
 
 
+def contrive_bad_px_neighborhood(
+    array: np.ndarray, bad_px_location: tuple[int, int], kernel_size: int, desired_median: float
+) -> np.array:
+    """
+    Adjust array values so the neighborhood around a bad pixel results in a known value being used to replace that pixel.
+    """
+    # Sticking with the y, x convention used by `corrections_correct_bad_pixels`.
+    y, x = bad_px_location
+    half_kernel_size = kernel_size // 2
+    num_y, num_x = array.shape
+
+    y_slice = slice(max(y - half_kernel_size, 0), min(y + half_kernel_size + 1, num_y))
+    x_slice = slice(max(x - half_kernel_size, 0), min(x + half_kernel_size + 1, num_x))
+
+    array[y_slice, x_slice] = desired_median
+
+    return array
+
+
 @pytest.mark.parametrize(
     "bad_pixel_map, algorithm_type",
     [
@@ -74,19 +95,32 @@ def test_corrections_correct_bad_pixels(bad_pixel_map, algorithm_type, bad_pixel
     t = bad_pixel_mask_task
     bad_pixel_x = 1
     bad_pixel_y = 6
-    array_to_fix = np.random.random(size=(10, 10))
+
+    # Create a data array. Adding 10 ensures that 0 will be a valid sentinel value of bad-ness
+    rng = np.random.default_rng()
+    array_to_fix = rng.random((10, 10), dtype=float) * 100 + 10.0
+
     # Assign a single bad pixel to check against
+    if algorithm_type == "normal":
+        expected_corrected_value = rng.random() * 100 + 10
+        array_to_fix = contrive_bad_px_neighborhood(
+            array=array_to_fix,
+            bad_px_location=(1, 6),
+            kernel_size=t.parameters.corrections_bad_pixel_median_filter_size,
+            desired_median=expected_corrected_value,
+        )
     array_to_fix[bad_pixel_x, bad_pixel_y] = 0
+
     corrected_array = t.corrections_correct_bad_pixels(
         array_to_fix=array_to_fix, bad_pixel_map=bad_pixel_map
     )
     if algorithm_type == "fast":
         for val in corrected_array[:, bad_pixel_y]:
             assert val == np.nanmedian(array_to_fix)
-        assert corrected_array[bad_pixel_x, bad_pixel_y] != 0
+        assert corrected_array[bad_pixel_x, bad_pixel_y] == np.nanmedian(array_to_fix)
+
     if algorithm_type == "normal":
         x, y = np.meshgrid(np.arange(10), np.arange(10))
         idx = np.where((x != bad_pixel_x) | (y != bad_pixel_y))
         np.testing.assert_array_equal(corrected_array[idx], array_to_fix[idx])
-        assert corrected_array[bad_pixel_x, bad_pixel_y] != np.nanmedian(array_to_fix)
-        assert corrected_array[bad_pixel_x, bad_pixel_y] != 0
+        assert corrected_array[bad_pixel_x, bad_pixel_y] == expected_corrected_value

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dkist-processing-cryonirsp
-Version: 0.0.56rc1
+Version: 0.0.58rc1
 Summary: Science processing code for the Cryo-NIRSP instrument on DKIST
 Home-page: https://bitbucket.org/dkistdc/dkist_processing_cryonirsp/src/main/
 Author: NSO / AURA

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp.egg-info/SOURCES.txt

@@ -12,7 +12,9 @@ setup.cfg
 setup.py
 towncrier_science.toml
 changelog/.gitempty
-changelog/117.doc.rst
+changelog/116.misc.rst
+changelog/119.bugfix.rst
+changelog/120.misc.rst
 dkist_processing_cryonirsp/__init__.py
 dkist_processing_cryonirsp.egg-info/PKG-INFO
 dkist_processing_cryonirsp.egg-info/SOURCES.txt

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/dkist_processing_cryonirsp.egg-info/requires.txt

@@ -2,7 +2,7 @@ Pillow==10.2.0
 astropy==5.3.2
 dkist-fits-specifications==4.1.1
 dkist-header-validator==5.1.0
-dkist-processing-common==6.1.2
+dkist-processing-common==6.2.1
 dkist-processing-math==2.0.0
 dkist-processing-pac==3.0.1
 dkist-spectral-lines==2.0.0
@@ -18,7 +18,7 @@ sunpy==5.0.0
 
 [asdf]
 dkist-processing-common[asdf]
-dkist-inventory[asdf]==1.3.0
+dkist-inventory[asdf]==1.3.1
 
 [docs]
 sphinx
@@ -32,11 +32,11 @@ dkist-sphinx-theme
 [grogu]
 dkist
 pyparsing
-dkist-inventory>=1.3.0
+dkist-inventory>=1.3.1
 
 [inventory]
 dkist-processing-common[inventory]
-dkist-inventory==1.3.0
+dkist-inventory==1.3.1
 
 [test]
 pytest
@@ -47,6 +47,6 @@ hypothesis
 towncrier
 dkist-data-simulator>=5.1.1
 dkist-processing-common[inventory]
-dkist-inventory==1.3.0
+dkist-inventory==1.3.1
 dkist-processing-common[asdf]
-dkist-inventory[asdf]==1.3.0
+dkist-inventory[asdf]==1.3.1

{dkist_processing_cryonirsp-0.0.56rc1 → dkist_processing_cryonirsp-0.0.58rc1}/setup.cfg

@@ -21,7 +21,7 @@ install_requires =
 	astropy == 5.3.2
 	dkist-fits-specifications == 4.1.1
 	dkist-header-validator == 5.1.0
-	dkist-processing-common == 6.1.2
+	dkist-processing-common == 6.2.1
 	dkist-processing-math == 2.0.0
 	dkist-processing-pac == 3.0.1
 	dkist-spectral-lines == 2.0.0
@@ -48,14 +48,14 @@ test =
 	%(asdf)s  # identify pip conflicts in test
 inventory = 
 	dkist-processing-common[inventory]
-	dkist-inventory==1.3.0
+	dkist-inventory==1.3.1
 asdf = 
 	dkist-processing-common[asdf]
-	dkist-inventory[asdf]==1.3.0
+	dkist-inventory[asdf]==1.3.1
 grogu = 
 	dkist
 	pyparsing
-	dkist-inventory >= 1.3.0
+	dkist-inventory >= 1.3.1
 docs = 
 	sphinx
 	sphinx-astropy

dkist_processing_cryonirsp-0.0.56rc1/changelog/117.doc.rst

@@ -1 +0,0 @@
-Update online documentation for Cryo-NIRSP bad pixel correction, beam angle calculation, and beam boundary calculation.