dkist-processing-dlnirsp 0.32.2__tar.gz → 0.32.4__tar.gz

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/CHANGELOG.rst

@@ -1,3 +1,21 @@
+v0.32.4 (2025-12-01)
+====================
+
+Bugfixes
+--------
+
+- Fix bug in how the "SubFrame" camera readout mode has its ramps parsed and linearized. (`#115 <https://bitbucket.org/dkistdc/dkist-processing-dlnirsp/pull-requests/115>`__)
+
+
+v0.32.3 (2025-11-04)
+====================
+
+Misc
+----
+
+- Replace metadata key strings with members of the string enum DlnirspMetadataKey. (`#111 <https://bitbucket.org/dkistdc/dkist-processing-dlnirsp/pull-requests/111>`__)
+
+
 v0.32.2 (2025-11-03)
 ====================
 

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-dlnirsp
-Version: 0.32.2
+Version: 0.32.4
 Summary: Science processing code for the DLNIRSP instrument on DKIST
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause
@@ -76,6 +76,7 @@ Requires-Dist: Flask-Login==0.6.3; extra == "frozen"
 Requires-Dist: Flask-SQLAlchemy==2.5.1; extra == "frozen"
 Requires-Dist: Flask-Session==0.5.0; extra == "frozen"
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 Requires-Dist: charset-normalizer==3.4.4; extra == "frozen"
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 Requires-Dist: click-plugins==1.1.1.2; extra == "frozen"
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@@ -149,7 +150,7 @@ Requires-Dist: dill==0.4.0; extra == "frozen"
 Requires-Dist: dkist-header-validator==5.2.1; extra == "frozen"
 Requires-Dist: dkist-processing-common==11.8.0; extra == "frozen"
 Requires-Dist: dkist-processing-core==6.0.0; extra == "frozen"
-Requires-Dist: dkist-processing-dlnirsp==0.32.2; extra == "frozen"
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 Requires-Dist: dkist-processing-pac==3.1.1; extra == "frozen"
 Requires-Dist: dkist-service-configuration==4.1.7; extra == "frozen"
@@ -157,14 +158,15 @@ Requires-Dist: dkist-spectral-lines==3.0.0; extra == "frozen"
 Requires-Dist: dkist_fits_specifications==4.17.0; extra == "frozen"
 Requires-Dist: dnspython==2.8.0; extra == "frozen"
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+Requires-Dist: google-re2==1.1.20251105; extra == "frozen"
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 Requires-Dist: greenlet==3.2.4; extra == "frozen"
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 Requires-Dist: kiwisolver==1.4.9; extra == "frozen"
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 Requires-Dist: lazy_loader==0.4; extra == "frozen"
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 Requires-Dist: numba==0.61.2; extra == "frozen"
 Requires-Dist: numpy==2.2.5; extra == "frozen"
 Requires-Dist: object-clerk==1.0.0; extra == "frozen"
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-Requires-Dist: protobuf==6.33.0; extra == "frozen"
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 Requires-Dist: psutil==7.1.3; extra == "frozen"
 Requires-Dist: psycopg2-binary==2.9.11; extra == "frozen"
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-Requires-Dist: pydantic_core==2.41.4; extra == "frozen"
+Requires-Dist: pydantic==2.12.5; extra == "frozen"
+Requires-Dist: pydantic-settings==2.12.0; extra == "frozen"
+Requires-Dist: pydantic_core==2.41.5; extra == "frozen"
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 Requires-Dist: pyparsing==3.2.5; extra == "frozen"
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@@ -273,17 +274,16 @@ Requires-Dist: requests-toolbelt==1.0.0; extra == "frozen"
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-Requires-Dist: rpds-py==0.28.0; extra == "frozen"
-Requires-Dist: s3transfer==0.14.0; extra == "frozen"
+Requires-Dist: rpds-py==0.30.0; extra == "frozen"
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 Requires-Dist: scikit-image==0.25.2; extra == "frozen"
 Requires-Dist: scipy==1.15.3; extra == "frozen"
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 Requires-Dist: setproctitle==1.3.7; extra == "frozen"
 Requires-Dist: six==1.17.0; extra == "frozen"
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 Requires-Dist: solar-wavelength-calibration==1.0.1; extra == "frozen"
 Requires-Dist: sqids==0.5.1; extra == "frozen"
-Requires-Dist: sqlparse==0.5.3; extra == "frozen"
+Requires-Dist: sqlparse==0.5.4; extra == "frozen"
 Requires-Dist: sunpy==6.1.1; extra == "frozen"
 Requires-Dist: tabulate==0.9.0; extra == "frozen"
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@@ -297,16 +297,17 @@ Requires-Dist: traitlets==5.14.3; extra == "frozen"
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 Requires-Dist: typing_extensions==4.15.0; extra == "frozen"
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+Requires-Dist: tzlocal==5.3.1; extra == "frozen"
 Requires-Dist: uc-micro-py==1.0.3; extra == "frozen"
 Requires-Dist: uncertainties==3.2.3; extra == "frozen"
-Requires-Dist: universal_pathlib==0.3.4; extra == "frozen"
+Requires-Dist: universal_pathlib==0.3.6; extra == "frozen"
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 Requires-Dist: wrapt==1.17.3; extra == "frozen"
-Requires-Dist: yamale==6.0.0; extra == "frozen"
+Requires-Dist: yamale==6.1.0; extra == "frozen"
 Requires-Dist: yarl==1.22.0; extra == "frozen"
 Requires-Dist: zipp==3.23.0; extra == "frozen"
 

dkist_processing_dlnirsp-0.32.4/dkist_processing_dlnirsp/models/fits_access.py

@@ -0,0 +1,32 @@
+"""DLNIRSP control of FITS key names and values."""
+
+from enum import StrEnum
+
+from dkist_processing_common.models.fits_access import MetadataKey
+
+
+class DlnirspMetadataKey(StrEnum):
+    """Controlled list of names for FITS metadata header keys."""
+
+    crpix_1 = "CRPIX1"
+    crpix_2 = "CRPIX2"
+    modulator_spin_mode = "DLMOD"
+    camera_readout_mode = "DLCAMSMD"
+    num_frames_in_ramp = "DLCAMNS"
+    current_frame_in_ramp = "DLCAMCUR"
+    arm_id = "DLARMID"
+    camera_sample_sequence = "DLCAMSSQ"
+    polarimeter_mode = "DLPOLMD"
+    number_of_modulator_states = "DLNUMST"
+    modulator_state = "DLSTNUM"
+    num_mosaic_repeats = "DLMOSNRP"
+    mosaic_num = "DLCURMOS"
+    num_X_tiles = "DLNSSTPX"
+    X_tile_num = "DLCSTPX"
+    num_Y_tiles = "DLNSSTPY"
+    Y_tile_num = "DLCSTPY"
+    num_dither_steps = "DLDMODE"
+    dither_step = "DLCURSTP"
+    arm_position_mm = "DLARMPS"
+    grating_position_deg = "DLGRTAN"
+    grating_constant_inverse_mm = "DLGRTCN"

dkist_processing_dlnirsp-0.32.4/dkist_processing_dlnirsp/parsers/dlnirsp_l0_fits_access.py

@@ -0,0 +1,99 @@
+"""DLNIRSP FitsAccess classes for raw and linearized data."""
+
+from astropy.io import fits
+from dkist_processing_common.parsers.l0_fits_access import L0FitsAccess
+
+from dkist_processing_dlnirsp.models.fits_access import DlnirspMetadataKey
+
+
+class DlnirspRampFitsAccess(L0FitsAccess):
+    """
+    Class to provide easy access to L0 headers for non-linearized (raw) DLNIRSP data.
+
+    i.e. instead of <DlnirspL0FitsAccess>.header['weird_key'] this class lets us use <DlnirspL0FitsAccess>.nice_key instead
+
+    Parameters
+    ----------
+    hdu :
+        Fits L0 header object
+
+    name : str
+        The name of the file that was loaded into this FitsAccess object
+
+    auto_squeeze : bool
+        When set to True, dimensions of length 1 will be removed from the array
+    """
+
+    def __init__(
+        self,
+        hdu: fits.ImageHDU | fits.PrimaryHDU | fits.CompImageHDU,
+        name: str | None = None,
+        auto_squeeze: bool = True,
+    ):
+        super().__init__(hdu=hdu, name=name, auto_squeeze=auto_squeeze)
+
+        self.modulator_spin_mode: str = self.header[DlnirspMetadataKey.modulator_spin_mode]
+        self.camera_readout_mode: str = self.header.get(
+            DlnirspMetadataKey.camera_readout_mode, "DEFAULT_VISIBLE_CAMERA"
+        )
+        self.num_frames_in_ramp: int = self.header.get(DlnirspMetadataKey.num_frames_in_ramp, -99)
+        self.current_frame_in_ramp: int = self.header.get(
+            DlnirspMetadataKey.current_frame_in_ramp, -88
+        )
+        self.arm_id: str = self.header[DlnirspMetadataKey.arm_id]
+        self.camera_sample_sequence: str = self.header.get(
+            DlnirspMetadataKey.camera_sample_sequence, "VISIBLE_CAMERA_SEQUENCE"
+        )
+
+
+class DlnirspL0FitsAccess(L0FitsAccess):
+    """
+    Class to provide easy access to L0 headers for linearized (ready for processing) DLNIRSP data.
+
+    i.e. instead of <DlnirspL0FitsAccess>.header['weird_key'] this class lets us use <DlnirspL0FitsAccess>.nice_key instead
+
+    Parameters
+    ----------
+    hdu :
+        Fits L0 header object
+
+    name : str
+        The name of the file that was loaded into this FitsAccess object
+
+    auto_squeeze : bool
+        When set to True, dimensions of length 1 will be removed from the array
+    """
+
+    def __init__(
+        self,
+        hdu: fits.ImageHDU | fits.PrimaryHDU | fits.CompImageHDU,
+        name: str | None = None,
+        auto_squeeze: bool = True,
+    ):
+        super().__init__(hdu=hdu, name=name, auto_squeeze=auto_squeeze)
+
+        self.crpix_1: float = self.header[DlnirspMetadataKey.crpix_1]
+        self.crpix_2: float = self.header[DlnirspMetadataKey.crpix_2]
+        self.arm_id: str = self.header[DlnirspMetadataKey.arm_id]
+        self.polarimeter_mode: str = self.header[DlnirspMetadataKey.polarimeter_mode]
+        self.number_of_modulator_states: int = self.header[
+            DlnirspMetadataKey.number_of_modulator_states
+        ]
+        self.modulator_state: int = self.header[DlnirspMetadataKey.modulator_state]
+        self.num_mosaic_repeats: int = self.header[DlnirspMetadataKey.num_mosaic_repeats]
+        self.mosaic_num: int = self.header[DlnirspMetadataKey.mosaic_num]
+        self.num_X_tiles: int = self.header[DlnirspMetadataKey.num_X_tiles]
+        self.X_tile_num: int = self.header[DlnirspMetadataKey.X_tile_num]
+        self.num_Y_tiles: int = self.header[DlnirspMetadataKey.num_Y_tiles]
+        self.Y_tile_num: int = self.header[DlnirspMetadataKey.Y_tile_num]
+        # DLDMODE is a bool in the header; the number of dither steps is either 1 or 2, corresponding to dither
+        # mode being True or False, respectively
+        self.num_dither_steps: int = int(self.header[DlnirspMetadataKey.num_dither_steps]) + 1
+        # Same with DLCURSTP. We'll index the dither loop at 0 so `False` is the first step and `True` is the second
+        # Use `get` because this key only exists if DLDMODE is `True`
+        self.dither_step: int = int(self.header.get(DlnirspMetadataKey.dither_step, False))
+        self.arm_position_mm: float = self.header[DlnirspMetadataKey.arm_position_mm]
+        self.grating_position_deg: float = self.header[DlnirspMetadataKey.grating_position_deg]
+        self.grating_constant_inverse_mm: float = self.header[
+            DlnirspMetadataKey.grating_constant_inverse_mm
+        ]

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/dkist_processing_dlnirsp/parsers/task.py

@@ -1,15 +1,11 @@
 """Custom parsers to identify task sub-groupings not captured by a single header key."""
 
-from typing import Callable
-
-from dkist_processing_common.models.flower_pot import SpilledDirt
+from dkist_processing_common.models.fits_access import MetadataKey
 from dkist_processing_common.models.tags import StemName
 from dkist_processing_common.models.task_name import TaskName
-from dkist_processing_common.parsers.near_bud import NearFloatBud
 from dkist_processing_common.parsers.single_value_single_key_flower import (
     SingleValueSingleKeyFlower,
 )
-from dkist_processing_common.parsers.unique_bud import UniqueBud
 
 from dkist_processing_dlnirsp.parsers.dlnirsp_l0_fits_access import DlnirspL0FitsAccess
 
@@ -41,7 +37,7 @@ class DlnirspTaskTypeFlower(SingleValueSingleKeyFlower):
     """Flower to find the DLNIRSP task type."""
 
     def __init__(self):
-        super().__init__(tag_stem_name=StemName.task.value, metadata_key="ip_task_type")
+        super().__init__(tag_stem_name=StemName.task.value, metadata_key=MetadataKey.ip_task_type)
 
     def setter(self, fits_obj: DlnirspL0FitsAccess):
         """

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/dkist_processing_dlnirsp/parsers/time.py

@@ -2,6 +2,7 @@
 
 from typing import Hashable
 
+from dkist_processing_common.models.fits_access import MetadataKey
 from dkist_processing_common.models.flower_pot import Stem
 from dkist_processing_common.models.task_name import TaskName
 from dkist_processing_common.parsers.unique_bud import TaskUniqueBud
@@ -17,7 +18,7 @@ class DLnirspSolarGainIpStartTimeBud(TaskUniqueBud):
     def __init__(self):
         super().__init__(
             constant_name=DlnirspBudName.solar_gain_ip_start_time.value,
-            metadata_key="ip_start_time",
+            metadata_key=MetadataKey.ip_start_time,
             ip_task_types=TaskName.solar_gain.value,
             task_type_parsing_function=parse_header_ip_task,
         )

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/dkist_processing_dlnirsp/parsers/wavelength.py

@@ -1,5 +1,6 @@
 """Bud to get the wavelength."""
 
+from dkist_processing_common.models.fits_access import MetadataKey
 from dkist_processing_common.models.flower_pot import SpilledDirt
 from dkist_processing_common.parsers.unique_bud import UniqueBud
 
@@ -11,7 +12,10 @@ class ObserveWavelengthBud(UniqueBud):
     """Bud to find the wavelength."""
 
     def __init__(self):
-        super().__init__(constant_name=DlnirspBudName.wavelength.value, metadata_key="wavelength")
+        super().__init__(
+            constant_name=DlnirspBudName.wavelength.value,
+            metadata_key=MetadataKey.wavelength,
+        )
 
     def setter(self, fits_obj: DlnirspL0FitsAccess):
         """

{dkist_processing_dlnirsp-0.32.2 → dkist_processing_dlnirsp-0.32.4}/dkist_processing_dlnirsp/tasks/linearity_correction.py

@@ -28,14 +28,32 @@ class LinearityCorrection(DlnirspTaskBase):
 
     record_provenance = True
 
-    camera_sequence_regex: re.Pattern = re.compile(r"(\d*)line,(\d*)read")
+    valid_camera_sequence_regex: re.Pattern = re.compile(
+        r"^(\d*subframe)?(?(1)|(?:\d*line,\d*read,?)+)(?:,\d*line)?$"
+    )
     """
-    regex pattern used to parse line-read-line values for a single coadd.
+    regex pattern that defines all valid camera-sample sequences.
+
+    It must start with either "Xline,Yread", which can repeat any number of times, or "Xsubframe" which must be by itself.
+    Either of these sequences may be padded with ",Zline" reset frames.
+    """
+
+    uptheramp_coadd_regex: re.Pattern = re.compile(r"(\d*)line,(\d*)read")
+    """
+    regex pattern used to parse line-read-line values for a single UpTheRamp coadd.
 
     This is where we decide that camera sequences are one or more coadd sequences, where each coadd sequence is
     "Xline,Yread". The total sequence may be padded with ",Zline" reset frames, which are not captured by this regex.
     """
 
+    subframe_sequence_regex: re.Pattern = re.compile(r"(\d*)subframe")
+    """
+    regex pattern used to parse coadds in SubFrame mode
+
+    Simply looks for "Xsubframe" and captures the "X". The sequence may be padded with ",Zline" reset frames, which are
+    not captured by this regex.
+    """
+
     def run(self):
         """
         Linearize IR camera frames or tag VIS camera frames as LINEARIZED.
@@ -110,17 +128,16 @@ class LinearityCorrection(DlnirspTaskBase):
         )
         num_coadds = len(coadd_sequence_nums_list)
 
-        line_read_line_indices = coadd_sequence_nums_list[0]
-        num_bias, num_read = line_read_line_indices[:2]
-
-        ndr_per_coadd = num_bias + num_read
-
         # In `is_ramp_valid` we already confirmed that all NDRs have the same values and that they are one of the
         # expected values
         camera_readout_mode = ramp_obj_list[0].camera_readout_mode
         modulator_spin_mode = ramp_obj_list[0].modulator_spin_mode
         match camera_readout_mode:
             case "UpTheRamp":
+                line_read_line_indices = coadd_sequence_nums_list[0]
+                num_bias, num_read = line_read_line_indices[:2]
+                ndr_per_coadd = num_bias + num_read
+
                 match modulator_spin_mode:
                     case "Continuous":
                         linearization_func = partial(
@@ -136,6 +153,11 @@ class LinearityCorrection(DlnirspTaskBase):
                         )
 
             case "SubFrame":
+                # `self.valid_camera_sequence_regex`, along with `parse_camera_sample_sequence`, provides assurance that
+                # by the time we get here these assumptions are valid
+                num_bias = 0
+                num_read = 1
+                ndr_per_coadd = 1
                 linearization_func = self.linearize_subframe_coadd
 
         coadd_stack = np.zeros((num_coadds, *ramp_obj_list[0].data.shape))
@@ -291,16 +313,25 @@ class LinearityCorrection(DlnirspTaskBase):
         "3line,45read,3line,45read,2line"
             `[[3, 45], [3, 45]]`
 
+        "4subframe,89line"
+            `[[1], [1], [1], [1]]`
+
         Returns
         -------
-        A list of lists. Top-level list contains an item for each coadd. These items are themselves lists of
-        length 2. The numbers in these inner lists correspond to the number of bias and read frames in that coadd,
-        respectively.
+        A list of lists. Top-level list contains an item for each coadd. In UpTheRamp mode these items are themselves
+        lists of length 2. The numbers in these inner lists correspond to the number of bias and read frames in that coadd,
+        respectively. In SubFrame mode the inner lists will always be length 1 and should be equal to `[1]`.
         """
-        coadd_matches = self.camera_sequence_regex.findall(camera_sample_sequence)
-        coadd_sequence_numbers = [
-            [int(num) for num in coadd_match] for coadd_match in coadd_matches
-        ]
+        if "subframe" in camera_sample_sequence:
+            coadd_matches = self.subframe_sequence_regex.findall(camera_sample_sequence)
+            # `is_ramp_valid` ensures we only have a single match here
+            num_coadd = int(coadd_matches[0])
+            coadd_sequence_numbers = [[1]] * num_coadd
+        else:
+            coadd_matches = self.uptheramp_coadd_regex.findall(camera_sample_sequence)
+            coadd_sequence_numbers = [
+                [int(num) for num in coadd_match] for coadd_match in coadd_matches
+            ]
 
         return coadd_sequence_numbers
 
@@ -310,15 +341,15 @@ class LinearityCorrection(DlnirspTaskBase):
 
         Current validity checks are:
 
-          1. All frames in the ramp have the same value for NUM_FRAMES_IN_RAMP
-          2. All frames in the ramp have the same value for CAMERA_READOUT_MODE
-          3. All frames in the ramp have the same value for MODULATOR_SPIN_MODE
-          4. The CAMERA_READOUT and MODULATOR_SPIN modes have expected values
-          5. The value of NUM_FRAMES_IN_RAMP equals the length of actual frames found
-          6. All frames in the ramp have the same value for CAMERA_SAMPLE_SEQUENCE
-          7. The camera sample sequence has the expected form ('(,?\d*line,\d*read)*(,\d*line)?')
-          8. All coadds in the ramp have the same camera sample sequence
-          9. The ramp length is equal to the expected length from the camera sample sequence
+        #. All frames in the ramp have the same value for NUM_FRAMES_IN_RAMP
+        #. All frames in the ramp have the same value for CAMERA_READOUT_MODE
+        #. All frames in the ramp have the same value for MODULATOR_SPIN_MODE
+        #. The CAMERA_READOUT and MODULATOR_SPIN modes have expected values
+        #. The value of NUM_FRAMES_IN_RAMP equals the length of actual frames found
+        #. All frames in the ramp have the same value for CAMERA_SAMPLE_SEQUENCE
+        #. The camera sample sequence has the expected form (`valid_camera_sequence_regex`)
+        #. All coadds in the ramp have the same camera sample sequence
+        #. The ramp length is equal to the expected length from the camera sample sequence
 
         If a ramp is not valid then the reason is logged and `False` is returned.
         """
@@ -382,7 +413,7 @@ class LinearityCorrection(DlnirspTaskBase):
             return False
 
         camera_sample_sequence = camera_sample_sequence_set.pop()
-        if re.search(r"\d*line,\d*line", camera_sample_sequence):
+        if not self.valid_camera_sequence_regex.search(camera_sample_sequence):
             logger.info(
                 f"Malformed camera sample sequence: '{camera_sample_sequence}'. "
                 f"{common_status_str}"