chore: Update output data validations for frames and ctf

ingestion_tools/scripts/data_validation/shared/helper/tiltseries_helper.py

@@ -10,6 +10,17 @@
 TILT_AXIS_ANGLE_REGEX = re.compile(r".*tilt\s*axis\s*angle\s*=\s*([-+]?(?:\d*\.*\d+))")
 
 
+
+@pytest.fixture
+def mdoc_tilt_axis_angle(mdoc_data: pd.DataFrame) -> float:
+    # To convert the data from the mdoc into a data frame, all the global records are added to each section's data
+    titles = mdoc_data["titles"][0]
+    for title in titles:
+        if result := re.match(TILT_AXIS_ANGLE_REGEX, title.lower()):
+            return float(result[1])
+    pytest.fail("No Tilt axis angle found")
+
+
 class TiltSeriesHelper(HelperTestMRCZarrHeader):
 
     @pytest.fixture(autouse=True)
@@ -25,15 +36,6 @@ def tiltseries_metadata_range(self, tiltseries_metadata: dict) -> list[float]:
             tiltseries_metadata["tilt_step"],
         ).tolist()
 
-    @pytest.fixture
-    def mdoc_tilt_axis_angle(self, mdoc_data: pd.DataFrame) -> float:
-        # To convert the data from the mdoc into a data frame, all the global records are added to each section's data
-        titles = mdoc_data["titles"][0]
-        for title in titles:
-            if result := re.match(TILT_AXIS_ANGLE_REGEX, title.lower()):
-                return float(result[1])
-        pytest.fail("No Tilt axis angle found")
-
     @allure.title("Tiltseries: tilt axis angle in mdoc file matches that in tilt series metadata (+/- 10 deg).")
     def test_tilt_axis_angle(self, mdoc_tilt_axis_angle: float, tiltseries_metadata: dict[str, Any]):
         metadata_tilt_axis = tiltseries_metadata["tilt_axis"]

ingestion_tools/scripts/data_validation/standardized/fixtures/path.py

@@ -99,7 +99,7 @@ def frames_meta_file(frames_dir: str, filesystem: FileSystemApi) -> str:
     if filesystem.exists(dst):
         return dst
     else:
-        pytest.fail(f"Frames metadata file not found: {dst}")
+        pytest.fail(f"The frames directory exists, but frames_metadata.json is not found: {dst}")
 
 
 @pytest.fixture(scope="session")

ingestion_tools/scripts/data_validation/standardized/tests/test_alignments.py

@@ -7,6 +7,29 @@
 from data_validation.shared.helper.angles_helper import helper_angles_injection_errors
 
 
+def matrix_to_angle(matrix: list[list[float]]) -> float:
+    """
+    Converts a 2x2 rotation matrix into an angle in degrees.
+
+    Args:
+        matrix: A 2x2 list of floats representing the rotation matrix.
+
+    Returns:
+        The rotation angle in degrees.
+    """
+    # Extract the elements of the matrix
+    r00, r01 = matrix[0]
+    r10, r11 = matrix[1]
+
+    # Calculate the angle in radians using atan2
+    angle_radians = np.arctan2(r10, r00)
+
+    # Convert the angle to degrees
+    angle_degrees = np.rad2deg(angle_radians)
+
+    return angle_degrees
+
+
 @pytest.mark.alignment
 @pytest.mark.parametrize("dataset, run_name, aln_dir", pytest.cryoet.dataset_run_alignment_combinations, scope="session")
 class TestAlignments:
@@ -91,19 +114,18 @@ def test_tilt_tiltseries_range(
             + f"\nRange: {alignment_tiltseries_metadata['tilt_range']['min']} to {alignment_tiltseries_metadata['tilt_range']['max']}, with step {alignment_tiltseries_metadata['tilt_step']}"
         )
 
-    @allure.title("Alignment: tilt axis angle in mdoc file matches that in the alignment metadata [per_section_alignment_parameters.in_plane_rotation] (+/- 10 deg)")
-    def test_mdoc_tilt_axis_angle_in_alignment_per_section_alignment_parameters(self, mdoc_data: pd.DataFrame, alignment_tiltseries_metadata: dict[str, dict]):
-        per_section_alignment_parameters = alignment_tiltseries_metadata.get("per_section_alignment_parameters")
+    @allure.title("Alignment: tilt angle in mdoc file matches that in the alignment metadata [per_section_alignment_parameters.in_plane_rotation] (+/- 10 deg)")
+    def test_mdoc_tilt_axis_angle_in_alignment_per_section_alignment_parameters(self, mdoc_tilt_axis_angle: float, alignment_metadata: dict[str, dict]):
+        per_section_alignment_parameters = alignment_metadata.get("per_section_alignment_parameters")
         if not per_section_alignment_parameters:
             pytest.skip("Alignment metadata missing per_section_alignment_parameters.")
-        errors = []
-        for i, psap in enumerate(per_section_alignment_parameters):
-            if (in_plane_rotation := psap.get("in_plane_rotation")) is not None:
-                try:
-                    assert abs(mdoc_data["TiltAxisAngle"].iloc[0] - in_plane_rotation) < 10, \
-                        f"Tilt axis angle in mdoc file {mdoc_data['TiltAxisAngle'].iloc[0]} does not match alignment metadata['per_section_alignment_parameter'][{i}]['tilt_angle']: {in_plane_rotation}"
-                except AssertionError as e:
-                    errors.append(str(e))
-        assert not errors, "\n".join(errors)
+        # convert all in_plane_rotation angles to degrees and sort them in ascending order
+        in_plane_rotations = [matrix_to_angle(psap["in_plane_rotation"]) for psap in per_section_alignment_parameters]
+        # check that all in_plane_rotation angles are equal
+        assert len(set(in_plane_rotations)) == 1, "in_plane_rotation angles are not all equal."
+        # check that in_plane_roation against mdoc_tilt_axis_angle
+        in_plane_rotation = in_plane_rotations[0]
+        assert in_plane_rotation == pytest.approx(mdoc_tilt_axis_angle, rel=10), f"Mdoc tilt axis angle {mdoc_tilt_axis_angle} does not match alignment metadata['per_section_alignment_parameters'][*]['in_plane_rotation']: {in_plane_rotation}"
+
 
     ### END Tiltseries consistency tests ###

ingestion_tools/scripts/data_validation/standardized/tests/test_frame.py

@@ -15,13 +15,13 @@ def test_is_gain_corrected_false(self,
                          frame_metadata: Dict,
                          gain_headers: Dict[str, Union[List[tifffile.TiffPage], MrcInterpreter]], # this is skipped if it is not found
                          ):
-        if frame_metadata.get("is_gain_corrected") is False: # todo is none considered false?
+        if not frame_metadata.get("is_gain_corrected"):
             assert len(gain_headers) > 0
 
     @allure.title("Frames: max(acquisitionOrder) <= number of frames -1")
     def test_max_acquisition_order(self, frame_metadata: Dict):
         acquisition_order_max = max(f.get("acquisition_order", 0) for f in frame_metadata["frames"])
-        assert acquisition_order_max <= len(frame_metadata["frames"]) -1
+        assert acquisition_order_max <= len(frame_metadata["frames"]) - 1
 
     @allure.title("Frames: Sorting acquisitionOrder low-to-high and accumulatedDose low-to-high results in the same order")
     def test_sorting_acquisition_order_and_accumulated_dose(self, frame_metadata: Dict):