dkist-processing-cryonirsp 0.0.76rc1__tar.gz → 0.0.77rc1__tar.gz

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+v0.0.76 (2024-08-05)
+====================
+
+Documentation
+-------------
+
+- Add pre-commit hook for documentation, add missing workflow documentation and update README.rst. (`#139 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/139>`__)
+
+
 v0.0.75 (2024-07-31)
 ====================
 

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dkist_processing_cryonirsp
-Version: 0.0.76rc1
+Version: 0.0.77rc1
 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-0.0.77rc1/changelog/110.feature.rst

@@ -0,0 +1,6 @@
+Add calibration task to compute accurate header values for
+CTYPE1, CUNIT1, CRPIX1, PV1_0, PV1_1, PV1_2, CRVAL1, CDELT1, PV1_2,
+CTYPE1A, CUNIT1A, CRPIX1A, PV1_0A, PV1_1A, PV1_2A, CRVAL1A, CDELT1A, PV1_2A.
+
+This is done by shifting the raw wavelength value (CRVAL1/A) to align with the FTS atlas, and
+then fitting a model to infer and correct the values of the aforementioned headers.

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/models/constants.py

@@ -18,6 +18,11 @@ class CryonirspBudName(Enum):
     num_map_scans = "NUM_MAP_SCANS"
     num_modstates = "NUM_MODSTATES"
     wavelength = "WAVELENGTH"
+    wave_min = "WAVE_MIN"
+    wave_max = "WAVE_MAX"
+    grating_position_deg = "GRATING_POSITION_DEG"
+    grating_littrow_angle_deg = "GRATING_LITTROW_ANGLE_DEG"
+    grating_constant = "GRATING_CONSTANT"
     camera_readout_mode = "CAM_READOUT_MODE"
     num_meas = "NUM_MEAS"
     time_obs_list = "TIME_OBS_LIST"
@@ -40,6 +45,7 @@ class CryonirspBudName(Enum):
     roi_1_size_x = "ROI_1_SIZE_X"
     roi_1_size_y = "ROI_1_SIZE_Y"
     optical_density_filter_picky_bud = "OPTICAL_DENSITY_FILTER_PICKY_BUD"
+    solar_gain_ip_start_time = "SOLAR_GAIN_IP_START_TIME"
 
 
 class CryonirspConstants(ConstantsBase):
@@ -73,6 +79,36 @@ class CryonirspConstants(ConstantsBase):
         """Wavelength."""
         return self._db_dict[CryonirspBudName.wavelength.value]
 
+    @property
+    def wave_min(self) -> float:
+        """Wavelength minimum."""
+        return self._db_dict[CryonirspBudName.wave_min.value]
+
+    @property
+    def wave_max(self) -> float:
+        """Wavelength maximum."""
+        return self._db_dict[CryonirspBudName.wave_max.value]
+
+    @property
+    def solar_gain_ip_start_time(self) -> str:
+        """Solar gain IP start time."""
+        return self._db_dict[CryonirspBudName.solar_gain_ip_start_time.value]
+
+    @property
+    def grating_position_deg(self) -> float:
+        """Grating position angle (deg)."""
+        return self._db_dict[CryonirspBudName.grating_position_deg.value]
+
+    @property
+    def grating_littrow_angle_deg(self) -> float:
+        """Grating littrow angle (deg)."""
+        return self._db_dict[CryonirspBudName.grating_littrow_angle_deg.value]
+
+    @property
+    def grating_constant(self) -> float:
+        """Grating constant."""
+        return self._db_dict[CryonirspBudName.grating_constant.value]
+
     @property
     def camera_readout_mode(self) -> str:
         """Determine the readout mode of the camera."""

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/models/parameters.py

@@ -7,6 +7,7 @@ import numpy as np
 from dkist_processing_common.models.parameters import ParameterArmIdMixin
 from dkist_processing_common.models.parameters import ParameterBase
 from dkist_processing_common.models.parameters import ParameterWavelengthMixin
+from dkist_processing_common.tasks.mixin.input_dataset import InputDatasetMixin
 
 from dkist_processing_cryonirsp.models.exposure_conditions import AllowableOpticalDensityFilterNames
 
@@ -258,3 +259,38 @@ class CryonirspParameters(ParameterBase, ParameterWavelengthMixin, ParameterArmI
         """Return the CryoNIRSP mirror scan recalibration constant."""
         mirror_scan_recalibration_constant = 0.466 / 0.5
         return mirror_scan_recalibration_constant
+
+    @property
+    def camera_mirror_focal_length_mm(self) -> u.Quantity:
+        """Return the CryoNIRSP camera mirror focal length."""
+        return (
+            self._find_most_recent_past_value("cryonirsp_camera_mirror_focal_length_mm")
+            * u.millimeter
+        )
+
+    @property
+    def pixel_pitch_micron(self) -> u.Quantity:
+        """Return the CryoNIRSP pixel pitch."""
+        return self._find_most_recent_past_value("cryonirsp_pixel_pitch_micron") * u.micron
+
+    @cached_property
+    def solar_atlas(self) -> np.ndarray:
+        """Solar reference atlas.
+
+        Contains two arrays:
+        - wavelength in nanometers
+        - transmission at given wavelength
+        """
+        param_dict = self._find_most_recent_past_value("cryonirsp_solar_atlas")
+        return self._load_param_value_from_numpy_save(param_dict)
+
+    @cached_property
+    def telluric_atlas(self) -> np.ndarray:
+        """Telluric reference atlas.
+
+        Contains two arrays:
+        - wavelength in nanometers
+        - transmission at given wavelength
+        """
+        param_dict = self._find_most_recent_past_value("cryonirsp_telluric_atlas")
+        return self._load_param_value_from_numpy_save(param_dict)

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/models/tags.py

@@ -156,3 +156,13 @@ class CryonirspTag(Tag):
     def task_bad_pixel_map(cls) -> str:
         """Tags intermediate bad pixel map objects."""
         return cls.format_tag(StemName.task, CryonirspTaskName.bad_pixel_map.value)
+
+    @classmethod
+    def task_spectral_fit(cls) -> str:
+        """Tags spectral fit solution."""
+        return cls.format_tag(StemName.task, CryonirspTaskName.spectral_fit.value)
+
+    @classmethod
+    def task_characteristic_spectra(cls) -> str:
+        """Tags 1D intermediate characteristic spectra."""
+        return cls.format_tag(StemName.task, CryonirspTaskName.solar_char_spec.value)

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/models/task_name.py

@@ -10,3 +10,5 @@ class CryonirspTaskName(str, Enum):
     polcal_dark = "POLCAL_DARK"
     polcal_gain = "POLCAL_GAIN"
     spectral_corrected_solar_array = "SPECTRAL_CORRECTED_SOLAR_ARRAY"
+    spectral_fit = "SPECTRAL_FIT"
+    solar_char_spec = "SOLAR_CHAR_SPEC"

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/parsers/cryonirsp_l0_fits_access.py

@@ -86,12 +86,24 @@ class CryonirspL0FitsAccess(L0FitsAccess):
         self.axis_1_type: str = self.header["CTYPE1"]
         self.axis_2_type: str = self.header["CTYPE2"]
         self.axis_3_type: str = self.header["CTYPE3"]
+        self.wave_min: float = round(
+            self.header["CRVAL1"] - (self.header["CRPIX1"] * self.header["CDELT1"]), 1
+        )
+        self.wave_max: float = round(
+            self.header["CRVAL1"]
+            + ((self.header["NAXIS1"] - self.header["CRPIX1"]) * self.header["CDELT1"]),
+            1,
+        )
+        self.grating_position_deg: float = self.header["CNGRTPOS"]
+        self.grating_littrow_angle_deg: float = self.header["CNGRTLAT"]
+        self.grating_constant: float = self.header["CNGRTCON"]
         self.obs_ip_start_time = self.header["DKIST011"]
         # The ExposureConditions are a combination of the exposure time and the OD filter name:
         self.exposure_conditions = ExposureConditions(
             round(self.fpa_exposure_time_ms, CRYO_EXP_TIME_ROUND_DIGITS),
             self.header["CNFILTNP"].upper(),
         )
+        self.solar_gain_ip_start_time = self.header["DATE-OBS"]
 
     @property
     def cn1_scan_step(self):

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/parsers/time.py

@@ -1,12 +1,43 @@
 """Buds to parse exposure time."""
 from typing import Hashable
+from typing import Type
 
+from dkist_processing_common.models.flower_pot import SpilledDirt
 from dkist_processing_common.models.flower_pot import Stem
+from dkist_processing_common.models.task_name import TaskName
+from dkist_processing_common.parsers.task import parse_header_ip_task_with_gains
 
 from dkist_processing_cryonirsp.models.constants import CryonirspBudName
+from dkist_processing_cryonirsp.parsers.cryonirsp_l0_fits_access import CryonirspL0FitsAccess
 from dkist_processing_cryonirsp.parsers.cryonirsp_l0_fits_access import CryonirspRampFitsAccess
 
 
+class CryonirspSolarGainStartTimeBud(Stem):
+    """Bud for finding the start time of the solar gain."""
+
+    def __init__(self):
+        self.metadata_key = "time_obs"
+        super().__init__(stem_name=CryonirspBudName.solar_gain_ip_start_time.value)
+
+    def setter(self, fits_obj: CryonirspL0FitsAccess) -> Type[SpilledDirt] | int:
+        """
+        Setter for the bud.
+
+        Parameters
+        ----------
+        fits_obj:
+            A single FitsAccess object
+        """
+        if parse_header_ip_task_with_gains(fits_obj) != TaskName.solar_gain.value:
+            return SpilledDirt
+        return getattr(fits_obj, self.metadata_key)
+
+    def getter(self, key: Hashable):
+        """Return the first date-obs value."""
+        first_date_obs = min(list(self.key_to_petal_dict.values()))
+        return first_date_obs
+
+
 class CryonirspTimeObsBud(Stem):
     """
     Produce a tuple of all time_obs values present in the dataset.

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/tasks/__init__.py

@@ -11,6 +11,7 @@ from dkist_processing_cryonirsp.tasks.make_movie_frames import *
 from dkist_processing_cryonirsp.tasks.parse import *
 from dkist_processing_cryonirsp.tasks.quality_metrics import *
 from dkist_processing_cryonirsp.tasks.sp_beam_boundaries import *
+from dkist_processing_cryonirsp.tasks.sp_dispersion_axis_correction import *
 from dkist_processing_cryonirsp.tasks.sp_geometric import *
 from dkist_processing_cryonirsp.tasks.sp_science import *
 from dkist_processing_cryonirsp.tasks.sp_solar_gain import *

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/tasks/mixin/corrections.py

@@ -47,7 +47,7 @@ class CorrectionsMixin:
             array[np.where(array == -np.inf)] = np.min(array[np.isfinite(array)])
             array[np.isnan(array)] = np.nanmedian(array)
             translated = affine_transform_arrays(array, translation=-shift, mode="edge", order=1)
-            # TODO: rotate_arrays_about_point rotates the wrong way, so no negative sign here
+            # rotate_arrays_about_point rotates the wrong way, so no negative sign here
             yield next(rotate_arrays_about_point(translated, angle=angle, mode="edge", order=1))
 
     @staticmethod
@@ -85,7 +85,7 @@ class CorrectionsMixin:
             array[np.where(array == np.inf)] = np.max(array[np.isfinite(array)])
             array[np.where(array == -np.inf)] = np.min(array[np.isfinite(array)])
             array[np.isnan(array)] = np.nanmedian(array)
-            # TODO: rotate_arrays_about_point rotates the wrong way, so no negative sign here
+            # rotate_arrays_about_point rotates the wrong way, so no negative sign here
             rotated = rotate_arrays_about_point(array, angle=angle, mode="edge")
             yield next(affine_transform_arrays(rotated, translation=-shift, mode="edge"))
 

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/tasks/parse.py

@@ -13,6 +13,7 @@ from dkist_processing_common.parsers.task import parse_header_ip_task_with_gains
 from dkist_processing_common.parsers.task import PolcalTaskFlower
 from dkist_processing_common.parsers.task import TaskTypeFlower
 from dkist_processing_common.parsers.time import ObsIpStartTimeBud
+from dkist_processing_common.parsers.unique_bud import TaskUniqueBud
 from dkist_processing_common.parsers.unique_bud import UniqueBud
 from dkist_processing_common.tasks import default_constant_bud_factory
 from dkist_processing_common.tasks import default_tag_flower_factory
@@ -43,9 +44,11 @@ from dkist_processing_cryonirsp.parsers.optical_density_filters import OpticalDe
 from dkist_processing_cryonirsp.parsers.polarimetric_check import PolarimetricCheckingUniqueBud
 from dkist_processing_cryonirsp.parsers.scan_step import NumberOfScanStepsBud
 from dkist_processing_cryonirsp.parsers.scan_step import ScanStepNumberFlower
+from dkist_processing_cryonirsp.parsers.time import CryonirspSolarGainStartTimeBud
 from dkist_processing_cryonirsp.parsers.time import CryonirspTimeObsBud
 from dkist_processing_cryonirsp.parsers.wavelength import ObserveWavelengthBud
 
+
 __all__ = ["ParseL0CryonirspRampData", "ParseL0CryonirspLinearizedData"]
 S = TypeVar("S", bound=Stem)
 
@@ -169,7 +172,20 @@ class ParseL0CryonirspLinearizedData(ParseDataBase, InputDatasetMixin):
             NumMapScansBud(),
             NumberOfScanStepsBud(),
             NumberOfMeasurementsBud(),
+            CryonirspSolarGainStartTimeBud(),
             NumCSStepBud(self.parameters.max_cs_step_time_sec),
+            TaskUniqueBud(
+                constant_name=CryonirspBudName.wave_min.value,
+                metadata_key="wave_min",
+                ip_task_type=TaskName.solar_gain.value,
+                task_type_parsing_function=parse_header_ip_task_with_gains,
+            ),
+            TaskUniqueBud(
+                constant_name=CryonirspBudName.wave_max.value,
+                metadata_key="wave_max",
+                ip_task_type=TaskName.solar_gain.value,
+                task_type_parsing_function=parse_header_ip_task_with_gains,
+            ),
             CryonirspTaskExposureConditionsBud(
                 stem_name=CryonirspBudName.dark_frame_exposure_conditions_list.value,
                 ip_task_type=TaskName.dark.value,
@@ -203,6 +219,24 @@ class ParseL0CryonirspLinearizedData(ParseDataBase, InputDatasetMixin):
                 constant_name=CryonirspBudName.modulator_spin_mode.value,
                 metadata_key="modulator_spin_mode",
             ),
+            TaskUniqueBud(
+                constant_name=CryonirspBudName.grating_position_deg.value,
+                metadata_key="grating_position_deg",
+                ip_task_type=TaskName.solar_gain.value,
+                task_type_parsing_function=parse_header_ip_task_with_gains,
+            ),
+            TaskUniqueBud(
+                constant_name=CryonirspBudName.grating_littrow_angle_deg.value,
+                metadata_key="grating_littrow_angle_deg",
+                ip_task_type=TaskName.solar_gain.value,
+                task_type_parsing_function=parse_header_ip_task_with_gains,
+            ),
+            TaskUniqueBud(
+                constant_name=CryonirspBudName.grating_constant.value,
+                metadata_key="grating_constant",
+                ip_task_type=TaskName.solar_gain.value,
+                task_type_parsing_function=parse_header_ip_task_with_gains,
+            ),
         ]
 
     @property

{dkist_processing_cryonirsp-0.0.76rc1 → dkist_processing_cryonirsp-0.0.77rc1}/dkist_processing_cryonirsp/tasks/quality_metrics.py

@@ -237,7 +237,7 @@ class CryonirspL1QualityMetrics(CryonirspTaskBase, QualityMixin):
         median = np.nanmedian(frame.data)
         time_obs_mjd = Time(frame.time_obs).mjd
         mean = np.nanmean(frame.data)
-        average = median or mean  # TODO: Needs hardening for value of 0
+        average = median or mean
         result = _QualityDataPoint(value=average, datetime=time_obs_mjd)
         logger.info(f"Calculated intensity frame average as {result}")
         return result