dkist-processing-common 10.6.3__py3-none-any.whl → 10.7.0__py3-none-any.whl

dkist_processing_common/tasks/write_l1.py

@@ -18,7 +18,7 @@ from dkist_fits_specifications import __version__ as spec_version
 from dkist_fits_specifications.utils.formatter import reformat_spec214_header
 from dkist_header_validator import spec214_validator
 from dkist_header_validator.translator import remove_extra_axis_keys
-from dkist_header_validator.translator import sanitize_to_spec214_level1
+from dkist_header_validator.translator import remove_spec_122_keys_and_spec_214_l0_keys
 from dkist_spectral_lines.search import get_closest_spectral_line
 from dkist_spectral_lines.search import get_spectral_lines
 from scipy.stats import kurtosis
@@ -102,7 +102,9 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
 
                 # Check that the written file passes spec 214 validation if requested
                 if self.validate_l1_on_write:
-                    spec214_validator.validate(self.scratch.absolute_path(relative_path))
+                    spec214_validator.validate(
+                        self.scratch.absolute_path(relative_path), extra=False
+                    )
 
     @cached_property
     def tile_size_param(self) -> int | None:
@@ -170,19 +172,21 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
     def add_stats_headers(header: fits.Header, data: np.ndarray) -> fits.Header:
         """Fill out the spec 214 statistics header table."""
         data = data.flatten()
-        percentiles = np.nanpercentile(data, [1, 10, 25, 75, 90, 95, 98, 99])
+        percentiles = np.nanpercentile(data, [1, 2, 5, 10, 25, 75, 90, 95, 98, 99])
         header["DATAMIN"] = np.nanmin(data)
         header["DATAMAX"] = np.nanmax(data)
         header["DATAMEAN"] = np.nanmean(data)
         header["DATAMEDN"] = np.nanmedian(data)
-        header["DATA01"] = percentiles[0]
-        header["DATA10"] = percentiles[1]
-        header["DATA25"] = percentiles[2]
-        header["DATA75"] = percentiles[3]
-        header["DATA90"] = percentiles[4]
-        header["DATA95"] = percentiles[5]
-        header["DATA98"] = percentiles[6]
-        header["DATA99"] = percentiles[7]
+        header["DATAP01"] = percentiles[0]
+        header["DATAP02"] = percentiles[1]
+        header["DATAP05"] = percentiles[2]
+        header["DATAP10"] = percentiles[3]
+        header["DATAP25"] = percentiles[4]
+        header["DATAP75"] = percentiles[5]
+        header["DATAP90"] = percentiles[6]
+        header["DATAP95"] = percentiles[7]
+        header["DATAP98"] = percentiles[8]
+        header["DATAP99"] = percentiles[9]
         header["DATARMS"] = np.sqrt(np.nanmean(data**2))
         header["DATAKURT"] = kurtosis(data, nan_policy="omit")
         header["DATASKEW"] = skew(data, nan_policy="omit")
@@ -214,11 +218,12 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
         header["CADMAX"] = self.constants.maximum_cadence
         header["CADVAR"] = self.constants.variance_cadence
         # Keywords to support reprocessing
-        if ids_par_id := self.metadata_store_input_dataset_parameters.inputDatasetPartId:
-            header["IDSPARID"] = ids_par_id
-        header["IDSOBSID"] = self.metadata_store_input_dataset_observe_frames.inputDatasetPartId
-        if ids_cal_id := self.metadata_store_input_dataset_calibration_frames.inputDatasetPartId:
-            header["IDSCALID"] = ids_cal_id
+        if parameters := self.metadata_store_input_dataset_parameters:
+            header["IDSPARID"] = parameters.inputDatasetPartId
+        if observe_frames := self.metadata_store_input_dataset_observe_frames:
+            header["IDSOBSID"] = observe_frames.inputDatasetPartId
+        if calibration_frames := self.metadata_store_input_dataset_calibration_frames:
+            header["IDSCALID"] = calibration_frames.inputDatasetPartId
         header["WKFLNAME"] = self.workflow_name
         header["WKFLVERS"] = self.workflow_version
         header = self.add_contributing_id_headers(header=header)
@@ -377,7 +382,7 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
         # Add the dataset headers (abstract - implement in instrument task)
         header = self.add_dataset_headers(header=header, stokes=stokes_param)
         # Remove any headers not contained in spec 214
-        header = sanitize_to_spec214_level1(input_headers=header)
+        header = remove_spec_122_keys_and_spec_214_l0_keys(input_headers=header)
         # Remove any keys referring to axes that don't exist
         header = remove_extra_axis_keys(input_headers=header)
         return header

dkist_processing_common/tests/conftest.py

@@ -113,7 +113,7 @@ class CommonDataset(Spec122Dataset):
         self.add_constant_key("TELEVATN", 6.28)
         self.add_constant_key("TAZIMUTH", 3.14)
         self.add_constant_key("TTBLANGL", 1.23)
-        self.add_constant_key("INST_FOO", "bar")
+        self.add_constant_key("VISP_012", "bar")
         self.add_constant_key("DKIST004", "observe")
         self.add_constant_key("ID___005", "ip id")
         self.add_constant_key("PAC__004", "Sapphire Polarizer")

dkist_processing_common/tests/test_fits_access.py

@@ -220,7 +220,7 @@ def test_as_subclass(hdu_with_complete_common_header):
     class InstFitsAccess(L0FitsAccess):
         def __init__(self, hdu, name):
             super().__init__(hdu, name)
-            self.foo: str = self.header["INST_FOO"]
+            self.foo: str = self.header["VISP_012"]
 
     fits_obj = InstFitsAccess(hdu_with_complete_common_header, name="foo")
     assert fits_obj.foo == "bar"

dkist_processing_common/tests/test_transfer_input_data.py

@@ -6,6 +6,7 @@ import pytest
 
 from dkist_processing_common._util.scratch import WorkflowFileSystem
 from dkist_processing_common.codecs.json import json_decoder
+from dkist_processing_common.models.graphql import InputDatasetRecipeRunResponse
 from dkist_processing_common.models.tags import Tag
 from dkist_processing_common.tasks.transfer_input_data import TransferL0Data
 from dkist_processing_common.tests.conftest import create_parameter_files
@@ -17,13 +18,14 @@ class TransferL0DataTask(TransferL0Data):
         ...
 
 
-class FakeGQLClientMissingPart(FakeGQLClient):
+class FakeGQLClientMissingInputDatasetPart(FakeGQLClient):
     """Same metadata mocker with calibration input dataset part missing."""
 
     def execute_gql_query(self, **kwargs):
         original_response = super().execute_gql_query(**kwargs)
-        # Remove calibration frames part
-        del original_response[0].recipeInstance.inputDataset.inputDatasetInputDatasetParts[2]
+        # Remove calibration frames part if getting InputDatasetRecipeRunResponse:
+        if kwargs.get("query_response_cls") == InputDatasetRecipeRunResponse:
+            del original_response[0].recipeInstance.inputDataset.inputDatasetInputDatasetParts[2]
         return original_response
 
 
@@ -53,7 +55,7 @@ def transfer_l0_data_task(recipe_run_id, tmp_path, mocker):
 @pytest.fixture
 def transfer_l0_data_task_missing_part(recipe_run_id, tmp_path, mocker):
     yield from _transfer_l0_data_task_with_client(
-        recipe_run_id, tmp_path, mocker, FakeGQLClientMissingPart
+        recipe_run_id, tmp_path, mocker, FakeGQLClientMissingInputDatasetPart
     )
 
 

dkist_processing_common/tests/test_write_l1.py

@@ -24,6 +24,9 @@ from dkist_processing_common.models.wavelength import WavelengthRange
 from dkist_processing_common.tasks.write_l1 import WriteL1Frame
 from dkist_processing_common.tests.conftest import FakeGQLClient
 from dkist_processing_common.tests.conftest import TILE_SIZE
+from dkist_processing_common.tests.test_transfer_input_data import (
+    FakeGQLClientMissingInputDatasetPart,
+)
 
 
 class FakeGQLClientDefaultRecipeConfiguration(FakeGQLClient):
@@ -132,6 +135,7 @@ def write_l1_task(request, recipe_run_id, tmp_path):
         stokes_params = ["I", "Q", "U", "V"]
         used_stokes_params = []
         hdu = fits.PrimaryHDU(data=np.random.random(size=(1, 128, 128)) * 10, header=header)
+        hdu.header["IPTASK"] = "level0_only key to be removed"
         hdul = fits.HDUList([hdu])
         for i in range(num_of_stokes_params):
             task.write(
@@ -276,6 +280,9 @@ def test_write_l1_frame(
             # Test that FRAMEVOL still has its comment
             assert hdu.header.comments["FRAMEVOL"]
 
+            # Test that 'level0_only' keys are being removed
+            assert "IPTASK" not in hdu.header.keys()
+
 
 def test_replace_header_values(write_l1_task):
     """
@@ -484,6 +491,29 @@ def test_reprocessing_keys(write_l1_task, mocker):
         assert header["PRODUCT"] == task.compute_product_id(header["IDSOBSID"], header["PROCTYPE"])
 
 
+def test_missing_input_dataset_part(write_l1_task, mocker):
+    """
+    :Given: a Write_L1 task with a missing calibration frames part
+    :When: running the task
+    :Then: the input dataset part keys are correctly written without throwing an exception
+    """
+    mocker.patch(
+        "dkist_processing_common.tasks.mixin.metadata_store.GraphQLClient",
+        new=FakeGQLClientMissingInputDatasetPart,
+    )
+    task, _, _ = write_l1_task
+    task()
+    files = list(task.read(tags=[Tag.frame(), Tag.output()]))
+    for file in files:
+        header = fits.open(file)[1].header
+        assert header["IDSPARID"] == task.metadata_store_input_dataset_parameters.inputDatasetPartId
+        assert (
+            header["IDSOBSID"]
+            == task.metadata_store_input_dataset_observe_frames.inputDatasetPartId
+        )
+        assert "IDSCALID" not in header
+
+
 @pytest.mark.parametrize(
     "ids_obs_id, proc_type",
     [

{dkist_processing_common-10.6.3.dist-info → dkist_processing_common-10.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-common
-Version: 10.6.3
+Version: 10.7.0
 Summary: Common task classes used by the DKIST science data processing pipelines
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause

{dkist_processing_common-10.6.3.dist-info → dkist_processing_common-10.7.0.dist-info}/RECORD

@@ -58,7 +58,7 @@ dkist_processing_common/tasks/teardown.py,sha256=e4LKnphJDYDVDAez2tH7MxpZgCmxYsK
 dkist_processing_common/tasks/transfer_input_data.py,sha256=afEW0glpCFMZRj90nFtQo_4XOQ4CuoOh86jahP6a-a0,5548
 dkist_processing_common/tasks/trial_catalog.py,sha256=Y3DKstRfMS8nWWtJFMB0MUVPlZ1jWS_2jhJGMWwxy50,8748
 dkist_processing_common/tasks/trial_output_data.py,sha256=aI_aRuu0qVO8zFGrr_9baxx9i3jUEHZSmsmbO6ytlkE,6960
-dkist_processing_common/tasks/write_l1.py,sha256=C5IRUX1JO_Wa7suv_tgE4tH1E2eAUkro0rtj9EHduqw,22429
+dkist_processing_common/tasks/write_l1.py,sha256=Jw8zQjlYjBQru3m1SB_ZDmicMkDRiUihy9VdwehvZc0,22683
 dkist_processing_common/tasks/mixin/__init__.py,sha256=-g-DQbU7m1bclJYuFe3Yh757V-35GIDTbstardKQ7nU,68
 dkist_processing_common/tasks/mixin/globus.py,sha256=QAV8VElxMAqxJ2KSB_bJaraceovYfjHXjOdocrTCkIA,6592
 dkist_processing_common/tasks/mixin/input_dataset.py,sha256=dkW5vf_QPgWedHO_Lf9GjBxr1QrUCKs6gIXufUTi7GE,6813
@@ -69,14 +69,14 @@ dkist_processing_common/tasks/mixin/quality/__init__.py,sha256=Bgu-DHW7yXLiehgll
 dkist_processing_common/tasks/mixin/quality/_base.py,sha256=nZ9IC-O-hsLXa5-tk29B13CZyQIdhJCv0eO9cdkAhWc,8303
 dkist_processing_common/tasks/mixin/quality/_metrics.py,sha256=WenTfa12guIUfm0GzkrK2gduKaOHs03e6RhE6j37Les,54304
 dkist_processing_common/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dkist_processing_common/tests/conftest.py,sha256=B4BtMYCStjy3zvqefwJB6-ntSNOicIyQwfE0YeapCEE,30160
+dkist_processing_common/tests/conftest.py,sha256=h_ObhpXb1S0-db0Je8XoHNLkrXxXW_0B0TMhbnbDjMo,30160
 dkist_processing_common/tests/test_assemble_movie.py,sha256=XY_ruXSYP5k6s2gUAwlFdnhJ81eyWLSd2O9IkX4RXeo,4165
 dkist_processing_common/tests/test_assemble_quality.py,sha256=fWSHK4UdVqgNjvxQuD40NBUnXrtmthUP7PUbISPV4MQ,16897
 dkist_processing_common/tests/test_base.py,sha256=4ST3__jEHitEQaQs9-0OcqtyEJfIjZsk_6PRYZFV2-U,7124
 dkist_processing_common/tests/test_codecs.py,sha256=9Ln8FJs319rbHpCukO9lKLk3aDrdyDREjA4nCHsxDCA,20796
 dkist_processing_common/tests/test_constants.py,sha256=Kc9k5TdYy5QkRRlGav6kfI2dy5HHKqtpf9qOuaAfDZU,5903
 dkist_processing_common/tests/test_cs_step.py,sha256=RA0QD3D8eaL3YSOL_gIJ9wkngy14RQ2jbD-05KAziW4,2408
-dkist_processing_common/tests/test_fits_access.py,sha256=e1B_N13vz6hFCBup6FlGItaH59dAmqXvox7jQuSyOB0,10946
+dkist_processing_common/tests/test_fits_access.py,sha256=aqJ2oBWxEP4PzKfe4fiaGxvfjB9Fvt2f0Owp9XFW-rw,10946
 dkist_processing_common/tests/test_flower_pot.py,sha256=X9_UI3maa3ZQncV3jYHgovWnawDsdEkEB5vw6EAB96o,3151
 dkist_processing_common/tests/test_input_dataset.py,sha256=AI5uqaDea4kOwpwAU5qQdzUbxMpBwD20YCAvB7nzD5o,18766
 dkist_processing_common/tests/test_interservice_bus.py,sha256=M_iv2CLmx5TnCB1VUN4YjkQ2LEUjfCKk7-ZlkV62XEQ,3000
@@ -95,12 +95,12 @@ dkist_processing_common/tests/test_tags.py,sha256=UwlOJ45rkvbfbd5L5m5YltvOxQc8kG
 dkist_processing_common/tests/test_task_name.py,sha256=kqFr59XX2K87xzfTlClzDV4-Je1dx72LvdaJ22UE8UU,1233
 dkist_processing_common/tests/test_task_parsing.py,sha256=QXt1X6DTO3_liBD2c-t84DToLeEn7B3J-eteIyN4HEM,4027
 dkist_processing_common/tests/test_teardown.py,sha256=w2sATQHkg2lMLvm6VFZF1mNGFYHwWj_SxvF9RQu-tuY,5362
-dkist_processing_common/tests/test_transfer_input_data.py,sha256=pys5JI-alVEsN4nFE6KDLrAfvLOAH5lSHHpkruLR6lE,6390
+dkist_processing_common/tests/test_transfer_input_data.py,sha256=kE-FQTcN9nft5bh2Rhtp-8ldCTvGXTvWFcsNm6DY7lk,6619
 dkist_processing_common/tests/test_transfer_l1_output_data.py,sha256=27PifkyH3RZg0nsM-AjmrFJ-hbYuCk5Tt_0Zx8PJBfM,2109
 dkist_processing_common/tests/test_trial_catalog.py,sha256=SZ-nyn0MXU9Lkg_94FbKER_cwiGoi06GYlzF_3AmvKg,6802
 dkist_processing_common/tests/test_trial_output_data.py,sha256=cBCj0kXyF5NEMzKh6zPVksdoXyE8ju1opJgWgjdcJWA,12790
 dkist_processing_common/tests/test_workflow_task_base.py,sha256=Z5aPW5LQtS0UWJiYho4X0r-2gPLfzpkmMwfmaoFLjMg,10517
-dkist_processing_common/tests/test_write_l1.py,sha256=bIQd95Dhb8aHxCtOXV7Az4Fy_OeEIlspoSktdUR5lRA,20794
+dkist_processing_common/tests/test_write_l1.py,sha256=R_ljJdSC4hCHS_mLV6rKE7PVfpDWCaMXoN6n45QJNWM,21951
 docs/Makefile,sha256=qnlVz6PuBqE39NfHWuUnHhNEA-EFgT2-WJNNNy9ttfk,4598
 docs/changelog.rst,sha256=S2jPASsWlQxSlAPqdvNrYvhk9k3FcFWNXFNDYXBSjl4,120
 docs/conf.py,sha256=FkX575cqTqZGCcLAjg2MlvE8Buj1Vt3CpHNgZxG256E,1890
@@ -109,7 +109,7 @@ docs/landing_page.rst,sha256=aPAuXFhBx73lEZ59B6E6JXxkK0LlxzD0n-HXqHrfumQ,746
 docs/make.bat,sha256=mBAhtURwhQ7yc95pqwJzlhqBSvRknr1aqZ5s8NKvdKs,4513
 docs/requirements.txt,sha256=Kbl_X4c7RQZw035YTeNB63We6I7pvXFU4T0Uflp2yDY,29
 licenses/LICENSE.rst,sha256=piZaQplkzOMmH1NXg6QIdo9wwo9pPCoHkvm2-DmH76E,1462
-dkist_processing_common-10.6.3.dist-info/METADATA,sha256=e_NApWqP_nEbasza1gENhO_v3h2w8yBNjcjbuk4HBWY,7154
-dkist_processing_common-10.6.3.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-dkist_processing_common-10.6.3.dist-info/top_level.txt,sha256=LJhd1W-Vn90K8HnQDIE4r52YDpUjjMWDnllAWHBByW0,48
-dkist_processing_common-10.6.3.dist-info/RECORD,,
+dkist_processing_common-10.7.0.dist-info/METADATA,sha256=4YcNp2PrDZuC5FpxD_2Wr9Zo92EqvXbUYr6GC9t-QEY,7154
+dkist_processing_common-10.7.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+dkist_processing_common-10.7.0.dist-info/top_level.txt,sha256=LJhd1W-Vn90K8HnQDIE4r52YDpUjjMWDnllAWHBByW0,48
+dkist_processing_common-10.7.0.dist-info/RECORD,,