dkist-processing-visp 5.1.2rc2__py3-none-any.whl → 5.2.0rc1__py3-none-any.whl

dkist_processing_visp/tests/local_trial_workflows/l0_solar_gain_as_science.py

@@ -28,6 +28,7 @@ from dkist_processing_visp.tasks.geometric import GeometricCalibration
 from dkist_processing_visp.tasks.instrument_polarization import InstrumentPolarizationCalibration
 from dkist_processing_visp.tasks.lamp import LampCalibration
 from dkist_processing_visp.tasks.solar import SolarCalibration
+from dkist_processing_visp.tasks.wavelength_calibration import WavelengthCalibration
 from dkist_processing_visp.tests.conftest import VispInputDatasetParameterValues
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadBackgroundCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadCalibratedData
@@ -37,6 +38,9 @@ from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers impor
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadInstPolCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadLampCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadSolarCal
+from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
+    LoadWavelengthCalibration,
+)
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
     ParseCalOnlyL0InputData,
 )
@@ -51,6 +55,9 @@ from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers impor
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
     SaveSolarGainAsScience,
 )
+from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
+    SaveWavelengthCalibration,
+)
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SetAxesTypes
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
     SetCadenceConstants,
@@ -158,6 +165,7 @@ def main(
     load_lamp: bool = False,
     load_geometric: bool = False,
     load_solar: bool = False,
+    load_wavelength_calibration: bool = False,
     load_inst_pol: bool = False,
     load_solar_gain_as_science: bool = False,
     load_calibrated_data: bool = False,
@@ -223,6 +231,11 @@ def main(
         else:
             manual_processing_run.run_task(task=SolarCalibration)
             manual_processing_run.run_task(task=SaveSolarCal)
+        if load_wavelength_calibration:
+            manual_processing_run.run_task(task=LoadWavelengthCalibration)
+        else:
+            manual_processing_run.run_task(task=WavelengthCalibration)
+            manual_processing_run.run_task(task=SaveWavelengthCalibration)
 
         if load_inst_pol:
             manual_processing_run.run_task(task=LoadInstPolCal)
@@ -349,6 +362,12 @@ if __name__ == "__main__":
         help="Load solar calibration from previously saved run",
         action="store_true",
     )
+    parser.add_argument(
+        "-W",
+        "--load-wavelength-calibration",
+        help="Load wavelength calibration solution from previously saved run",
+        action="store_true",
+    )
     parser.add_argument(
         "-P",
         "--load-inst-pol",
@@ -378,6 +397,7 @@ if __name__ == "__main__":
             load_lamp=args.load_lamp,
             load_geometric=args.load_geometric,
             load_solar=args.load_solar,
+            load_wavelength_calibration=args.load_wavelength_calibration,
             load_inst_pol=args.load_inst_pol,
             load_solar_gain_as_science=args.load_solar_gain_as_science,
             load_calibrated_data=args.load_calibrated_data,

dkist_processing_visp/tests/local_trial_workflows/l0_to_l1.py

@@ -32,6 +32,7 @@ from dkist_processing_visp.tasks.quality_metrics import VispL1QualityMetrics
 from dkist_processing_visp.tasks.science import ScienceCalibration
 from dkist_processing_visp.tasks.solar import SolarCalibration
 from dkist_processing_visp.tasks.visp_base import VispTaskBase
+from dkist_processing_visp.tasks.wavelength_calibration import WavelengthCalibration
 from dkist_processing_visp.tasks.write_l1 import VispWriteL1Frame
 from dkist_processing_visp.tests.conftest import VispInputDatasetParameterValues
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadBackgroundCal
@@ -41,6 +42,9 @@ from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers impor
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadInstPolCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadLampCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import LoadSolarCal
+from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
+    LoadWavelengthCalibration,
+)
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveBackgroundCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveDarkCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveGeometricCal
@@ -48,6 +52,9 @@ from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers impor
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveInstPolCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveLampCal
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import SaveSolarCal
+from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
+    SaveWavelengthCalibration,
+)
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import tag_inputs_task
 from dkist_processing_visp.tests.local_trial_workflows.local_trial_helpers import (
     transfer_trial_data_locally_task,
@@ -178,6 +185,7 @@ def main(
     load_lamp: bool = False,
     load_geometric: bool = False,
     load_solar: bool = False,
+    load_wavelength_calibration: bool = False,
     load_inst_pol: bool = False,
     transfer_trial_data: str | None = None,
 ):
@@ -236,6 +244,12 @@ def main(
             manual_processing_run.run_task(task=SolarCalibration)
             manual_processing_run.run_task(task=SaveSolarCal)
 
+        if load_wavelength_calibration:
+            manual_processing_run.run_task(task=LoadWavelengthCalibration)
+        else:
+            manual_processing_run.run_task(task=WavelengthCalibration)
+            manual_processing_run.run_task(task=SaveWavelengthCalibration)
+
         if load_inst_pol:
             manual_processing_run.run_task(task=LoadInstPolCal)
         else:
@@ -345,6 +359,12 @@ if __name__ == "__main__":
         help="Load solar calibration from previously saved run",
         action="store_true",
     )
+    parser.add_argument(
+        "-W",
+        "--load-wavelength-calibration",
+        help="Load wavelength calibration solution from previously saved run",
+        action="store_true",
+    )
     parser.add_argument(
         "-P",
         "--load-inst-pol",
@@ -365,6 +385,7 @@ if __name__ == "__main__":
             load_lamp=args.load_lamp,
             load_geometric=args.load_geometric,
             load_solar=args.load_solar,
+            load_wavelength_calibration=args.load_wavelength_calibration,
             load_inst_pol=args.load_inst_pol,
             transfer_trial_data=args.transfer_trial_data,
         )

dkist_processing_visp/tests/local_trial_workflows/local_trial_helpers.py

@@ -11,6 +11,7 @@ from dkist_processing_common.codecs.fits import fits_array_decoder
 from dkist_processing_common.codecs.fits import fits_hdulist_encoder
 from dkist_processing_common.models.constants import BudName
 from dkist_processing_common.models.fits_access import MetadataKey
+from dkist_processing_common.models.metric_code import MetricCode
 from dkist_processing_common.models.task_name import TaskName
 from dkist_processing_common.parsers.cs_step import CSStepFlower
 from dkist_processing_common.parsers.cs_step import NumCSStepBud
@@ -270,6 +271,7 @@ class SaveSolarCal(SaveTaskTags):
     @property
     def tag_lists_to_save(self) -> list[list[str]]:
         return super().tag_lists_to_save + [
+            [VispTag.intermediate_frame(beam=1), VispTag.task_characteristic_spectra()],
             [VispTag.quality("TASK_TYPES"), VispTag.workflow_task("SolarCalibration")],
             [VispTag.quality(VispMetricCode.solar_first_vignette)],
             [VispTag.quality(VispMetricCode.solar_final_vignette)],
@@ -280,6 +282,31 @@ class SaveSolarCal(SaveTaskTags):
         return "solar_cal.asdf"
 
 
+class SaveWavelengthCalibration(SaveTaskTags):
+    @property
+    def task_str(self) -> str:
+        return VispTaskName.wavelength_calibration.value
+
+    @property
+    def relative_save_file(self) -> str:
+        return "wavelength_calibration.asdf"
+
+    @property
+    def tag_lists_to_save(self) -> list[list[str]]:
+        return super().tag_lists_to_save + [
+            [
+                VispTag.quality(MetricCode.wavecal_fit),
+                VispTag.workflow_task("WavelengthCalibration"),
+            ],
+        ]
+
+
+class LoadWavelengthCalibration(LoadTaskTags):
+    @property
+    def relative_save_file(self) -> str:
+        return "wavelength_calibration.asdf"
+
+
 class LoadSolarCal(LoadTaskTags):
     @property
     def relative_save_file(self) -> str:

dkist_processing_visp/tests/test_parameters.py

@@ -37,6 +37,8 @@ def unit_parameter_names_and_units() -> dict[str, u.Unit | list[u.Unit]]:
         "solar_vignette_crval_bounds_px": u.pix,
         "wavecal_camera_lens_parameters": [u.m, u.m / u.nm, u.m / u.nm**2],
         "wavecal_pixel_pitch_micron_per_pix": u.um / u.pix,
+        "wavecal_crval_bounds_px": u.pix,
+        "wavecal_incident_light_angle_bounds_deg": u.deg,
     }
 
 
@@ -106,7 +108,7 @@ def test_non_wave_parameters(
         if (
             parameter_name not in parse_parameter_names
             and not is_wavelength_param
-            and parameter_name != "solar_vignette_wavecal_fit_kwargs"
+            and parameter_name not in ["solar_vignette_wavecal_fit_kwargs", "wavecal_fit_kwargs"]
         ):
             param_obj_value = getattr(task_param_attr, parameter_name)
             if isinstance(pv, tuple):
@@ -197,22 +199,26 @@ class AnyInt:
         pytest.param(dict(), dict(), id="no_kwargs"),
     ],
 )
+@pytest.mark.parametrize(
+    "fit_kwarg_name", ["visp_solar_vignette_wavecal_fit_kwargs", "visp_wavecal_fit_kwargs"]
+)
 def test_fit_kwarg_parameters(
     basic_science_task_with_parameter_mixin,
     db_value,
     expected,
+    fit_kwarg_name,
 ):
     """
     Given: A Science task with the parameter mixin
     When: Accessing properties for parameters that do not depend on wavelength
     Then: The correct value is returned
     """
+    kwargs = {fit_kwarg_name: db_value}
+
     task, _ = next(
-        basic_science_task_with_parameter_mixin(
-            VispInputDatasetParameterValues(visp_solar_vignette_wavecal_fit_kwargs=db_value)
-        )
+        basic_science_task_with_parameter_mixin(VispInputDatasetParameterValues(**kwargs))
     )
-    kwarg_dict = task.parameters.solar_vignette_wavecal_fit_kwargs
+    kwarg_dict = getattr(task.parameters, fit_kwarg_name.removeprefix("visp_"))
     assert kwarg_dict.keys() == expected.keys()
     for k in expected.keys():
         if expected[k] is AnyInt:

dkist_processing_visp/tests/test_science.py

@@ -12,6 +12,7 @@ from dkist_header_validator import spec122_validator
 from dkist_processing_common._util.scratch import WorkflowFileSystem
 from dkist_processing_common.codecs.fits import fits_array_encoder
 from dkist_processing_common.codecs.fits import fits_hdu_decoder
+from dkist_processing_common.codecs.json import json_encoder
 from dkist_processing_common.models.fits_access import MetadataKey
 from dkist_processing_common.models.tags import Tag
 
@@ -65,6 +66,7 @@ def write_input_observe_frames_to_task(
     num_maps: int,
     data_shape: tuple[int, int],
     polarimeter_mode: Literal["observe_polarimetric", "obser_intensity"] = "observe_polarimetric",
+    swap_wcs_axes: bool = False,
 ):
     array_shape = (1, *data_shape)
     dataset = VispHeadersValidObserveFrames(
@@ -74,6 +76,7 @@ def write_input_observe_frames_to_task(
         num_raster_steps=num_raster_steps,
         num_maps=num_maps,
         polarimeter_mode=polarimeter_mode,
+        swap_wcs_axes=swap_wcs_axes,
     )
     write_frames_to_task(
         task=task,
@@ -100,6 +103,7 @@ def science_calibration_task(
     recipe_run_id,
     init_visp_constants_db,
     request,
+    swap_wcs_axes,
 ):
     num_map_scans = 2
     num_raster_steps = 2
@@ -117,6 +121,8 @@ def science_calibration_task(
         NUM_RASTER_STEPS=num_raster_steps,
         NUM_BEAMS=2,
         OBSERVE_READOUT_EXP_TIMES=(readout_exp_time,),
+        AXIS_1_TYPE="AWAV" if swap_wcs_axes else "HPLT-TAN",
+        AXIS_2_TYPE="HPLT-TAN" if swap_wcs_axes else "AWAV",
     )
     init_visp_constants_db(recipe_run_id, constants_db)
     with ScienceCalibration(
@@ -134,6 +140,23 @@ def science_calibration_task(
             task._purge()
 
 
+@pytest.fixture
+def dummy_wavelength_solution(swap_wcs_axes):
+    axis_num = 1 if swap_wcs_axes else 2
+    dummy_fit_solution = {
+        f"CTYPE{axis_num}": "AWAV-GRA",
+        f"CUNIT{axis_num}": "nm",
+        f"CRPIX{axis_num}": 5,
+        f"CRVAL{axis_num}": 9999.0,
+        f"CDELT{axis_num}": 4.56,
+        f"PV{axis_num}_0": 78.9,
+        f"PV{axis_num}_1": 51,
+        f"PV{axis_num}_2": 11121,
+    }
+
+    return dummy_fit_solution | {f"{k}A": v for k, v in dummy_fit_solution.items()}
+
+
 @pytest.fixture(scope="function")
 def dummy_calibration_collection():
     input_shape = (50, 20)
@@ -148,6 +171,7 @@ def dummy_calibration_collection():
     angle_dict = {VispTag.beam(beam): 0.0}
     spec_dict = {VispTag.beam(beam): np.zeros(intermediate_shape[1])}
     offset_dict = {VispTag.beam(beam): {VispTag.modstate(modstate): np.zeros(2)}}
+    wavecal_dict = dict()
 
     collection = CalibrationCollection(
         dark=dark_dict,
@@ -156,6 +180,7 @@ def dummy_calibration_collection():
         angle=angle_dict,
         spec_shift=spec_dict,
         state_offset=offset_dict,
+        wavelength_calibration_header=wavecal_dict,
         demod_matrices=None,
     )
 
@@ -209,6 +234,7 @@ def calibration_collection_with_geo_shifts(shifts) -> CalibrationCollection:
         angle=dict(),
         state_offset=geo_shifts,
         spec_shift=dict(),
+        wavelength_calibration_header=dict(),
         demod_matrices=None,
     )
 
@@ -246,13 +272,18 @@ def calibration_collection_with_full_overlap_slice() -> CalibrationCollection:
         angle=dict(),
         state_offset=geo_shifts,
         spec_shift=dict(),
+        wavelength_calibration_header=dict(),
         demod_matrices=None,
     )
 
 
 @pytest.mark.parametrize(
-    "background_on",
-    [pytest.param(True, id="background_on"), pytest.param(False, id="background_off")],
+    "background_on, swap_wcs_axes",
+    [
+        pytest.param(True, False, id="background_on-no_swap"),
+        pytest.param(False, False, id="background_off-no_swap"),
+        pytest.param(False, True, id="background_off-axes_swap"),
+    ],
 )
 def test_science_calibration_task(
     science_calibration_task,
@@ -260,6 +291,8 @@ def test_science_calibration_task(
     assign_input_dataset_doc_to_task,
     mocker,
     fake_gql_client,
+    dummy_wavelength_solution,
+    swap_wcs_axes,
 ):
     """
     Given: A ScienceCalibration task
@@ -290,7 +323,7 @@ def test_science_calibration_task(
         ),
     )
 
-    offsets = np.tile(np.array([-10.2, 5.1]), (2, num_modstates, 1))
+    offsets = np.tile(np.array([-10.2, -5.1]), (2, num_modstates, 1))
     offsets[0] = 0.0  # So beam 1 has zero offset
 
     write_intermediate_darks_to_task(
@@ -312,6 +345,11 @@ def test_science_calibration_task(
         data_shape=intermediate_shape,
     )
     write_demod_matrices_to_task(task=task, num_modstates=num_modstates)
+    task.write(
+        data=dummy_wavelength_solution,
+        tags=[VispTag.intermediate(), VispTag.task_wavelength_calibration()],
+        encoder=json_encoder,
+    )
     write_input_observe_frames_to_task(
         task=task,
         readout_exp_time=readout_exp_time,
@@ -319,6 +357,7 @@ def test_science_calibration_task(
         num_raster_steps=num_raster_steps,
         num_maps=num_maps,
         data_shape=input_shape,
+        swap_wcs_axes=swap_wcs_axes,
     )
 
     input_header = get_input_obs_frame_header(task=task)
@@ -365,10 +404,22 @@ def test_science_calibration_task(
         assert header["VSPMAP"] == map_scan
 
         # Check that WCS keys were updated
+        spec_axis_num = 1 if swap_wcs_axes else 2
+        spatial_axis_num = 2 if swap_wcs_axes else 1
         if offsets[1, 0, 0] < 0:
-            assert header["CRPIX2"] == input_header["CRPIX2"] - np.ceil(-offsets[1, 0, 0])
+            assert header[f"CRPIX{spec_axis_num}"] == dummy_wavelength_solution[
+                f"CRPIX{spec_axis_num}"
+            ] - np.ceil(-offsets[1, 0, 0])
+            assert header[f"CRPIX{spec_axis_num}A"] == dummy_wavelength_solution[
+                f"CRPIX{spec_axis_num}A"
+            ] - np.ceil(-offsets[1, 0, 0])
         if offsets[1, 0, 1] < 0:
-            assert header["CRPIX1"] == input_header["CRPIX1"] - np.ceil(-offsets[1, 0, 1])
+            assert header[f"CRPIX{spatial_axis_num}"] == input_header[
+                f"CRPIX{spatial_axis_num}"
+            ] - np.ceil(-offsets[1, 0, 1])
+            assert header[f"CRPIX{spatial_axis_num}A"] == input_header[
+                f"CRPIX{spatial_axis_num}A"
+            ] - np.ceil(-offsets[1, 0, 1])
 
     quality_files = task.read(tags=[Tag.quality("TASK_TYPES")])
     for file in quality_files:
@@ -380,6 +431,7 @@ def test_science_calibration_task(
             )
 
 
+@pytest.mark.parametrize("swap_wcs_axes", [pytest.param(False, id="no_swap")])
 def test_readout_normalization_correct(
     science_calibration_task, dummy_calibration_collection, assign_input_dataset_doc_to_task
 ):
@@ -550,6 +602,7 @@ def test_beam_overlap_slice(calibration_collection_with_geo_shifts, expected):
     assert y_slice == expected[1]
 
 
+@pytest.mark.parametrize("swap_wcs_axes", [pytest.param(False, id="no_swap")])
 def test_combine_beams(
     science_calibration_task,
     calibrated_array_and_header_dicts,
@@ -598,6 +651,7 @@ def test_combine_beams(
     ],
     ids=["Positive and negative"],
 )
+@pytest.mark.parametrize("swap_wcs_axes", [pytest.param(False, id="no_swap")])
 def test_combine_and_cut_nan_masks(
     science_calibration_task, calibration_collection_with_geo_shifts, shifts
 ):
@@ -649,6 +703,7 @@ def test_combine_and_cut_nan_masks(
     assert np.sum(combined_nan_mask) == 2  # only two NaN values are in the final mask
 
 
+@pytest.mark.parametrize("swap_wcs_axes", [pytest.param(False, id="no_swap")])
 def test_generate_nan_mask(science_calibration_task, dummy_calibration_collection):
     """
     Given: a calibration collection

dkist_processing_visp/tests/test_solar.py

@@ -9,7 +9,6 @@ import pytest
 from asdf.tags.core import NDArrayType
 from astropy import constants
 from astropy.coordinates import EarthLocation
-from astropy.io import fits
 from astropy.stats import gaussian_fwhm_to_sigma
 from astropy.time import Time
 from dkist_processing_common._util.scratch import WorkflowFileSystem