dkist-processing-cryonirsp 1.9.0__py3-none-any.whl → 1.10.0rc1__py3-none-any.whl

{dkist_processing_cryonirsp-1.9.0.dist-info → dkist_processing_cryonirsp-1.10.0rc1.dist-info}/RECORD

@@ -1,18 +1,19 @@
 changelog/.gitempty,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+changelog/167.feature.rst,sha256=UDCWFhNjmut91SbtIICb3Y5_MiPJ4zSPc0chd6y8AJU,142
 dkist_processing_cryonirsp/__init__.py,sha256=Z6-kB7fXXUI-F7Vz1HnEaja2h8qgH9IZExRl1lUxvZg,350
-dkist_processing_cryonirsp/config.py,sha256=xNkUNJ1BeBxJX881mTCIEbirZlD5_5txpV1QqkbfRM0,507
+dkist_processing_cryonirsp/config.py,sha256=DlU2dr_oORrwytQVmEUSg3IRPXxE4vhAWiCiw7ykvzo,641
 dkist_processing_cryonirsp/codecs/__init__.py,sha256=du1iitvsudSSOMENSywXmXSLOlvIocJsPbvfEcyqFNc,159
 dkist_processing_cryonirsp/codecs/fits.py,sha256=EAdPcqWXMEWtWnRDLH_LX20giPoLVfmKBawb9J2z0wM,1718
 dkist_processing_cryonirsp/models/__init__.py,sha256=m6UekKftTahNJ3W5K3mZSz4Y4ZZpHRxF_ZAxuaKYL7o,12
 dkist_processing_cryonirsp/models/beam_boundaries.py,sha256=FyiLd2iCWA6TUojeGaqQ_ULxvakDY13VxqUJVlmYvV0,1159
-dkist_processing_cryonirsp/models/constants.py,sha256=aKhSu4Hp0kKRgO6muMli2W4DC3zP0sEm4TzK--hyJXQ,11062
+dkist_processing_cryonirsp/models/constants.py,sha256=rFCkE-bZhbCABKVtQom5iTfPgDqDzsKkrtTnngZExkM,11528
 dkist_processing_cryonirsp/models/exposure_conditions.py,sha256=slFq5-Qz4fRpJKDBabbm4evPWLQVYmT-Uf9rk7nI734,813
-dkist_processing_cryonirsp/models/parameters.py,sha256=icAnYJvVCSJiNoT9SuYTZfDx6imwcq7QwfCY3_qQAIY,13154
+dkist_processing_cryonirsp/models/parameters.py,sha256=Yn6GPEGnMiQyEL9n2BPx9LIVWPSdVXmcIX9OzzDOvPc,13144
 dkist_processing_cryonirsp/models/tags.py,sha256=ac0MnYlsn8-w7IioOvWeo7mBaDKE9o9TlRpxCH1OsRc,5743
 dkist_processing_cryonirsp/models/task_name.py,sha256=xK4AKwgOx2uANbjhr0Q5Q3R9iPxLfkVKxWYY8wWjKhE,439
 dkist_processing_cryonirsp/parsers/__init__.py,sha256=m6UekKftTahNJ3W5K3mZSz4Y4ZZpHRxF_ZAxuaKYL7o,12
 dkist_processing_cryonirsp/parsers/check_for_gains.py,sha256=v-eD1LG0dlFoZXz5Y-2ZyPvRL2TZ8gWfr5cN6YNYqvo,2341
-dkist_processing_cryonirsp/parsers/cryonirsp_l0_fits_access.py,sha256=HtkmVdhEZxasKQyxWQyrirmiDrzAVfr3QCC2ldzBdSk,5617
+dkist_processing_cryonirsp/parsers/cryonirsp_l0_fits_access.py,sha256=rMB4mrUGQnQ6nHEZVegkdGpnW4Q2iXG5YRAaAq9tOW4,5608
 dkist_processing_cryonirsp/parsers/cryonirsp_l1_fits_access.py,sha256=sc8MzxYMc8E1eFrL5KguAGHViCMJhaDfiBtZPml4ELg,886
 dkist_processing_cryonirsp/parsers/exposure_conditions.py,sha256=Mcud-0PQK0oJSxbqtQUtVk0t8b6YBEFSyGsGbG5UqGg,8445
 dkist_processing_cryonirsp/parsers/map_repeats.py,sha256=PjZ986bqkCdii-EOzU045cWqadxQC_nyyqwWYIpYdls,1566
@@ -23,7 +24,7 @@ dkist_processing_cryonirsp/parsers/polarimetric_check.py,sha256=HBzg9Zi9-M1M2jh4
 dkist_processing_cryonirsp/parsers/scan_step.py,sha256=7XNUq48qbdpV8GeaBeG9XFRDkYlgw8Fjd6ByFZ24OAc,18972
 dkist_processing_cryonirsp/parsers/time.py,sha256=dpajm3tfrih-8pjlOWOvZVJVP2FihR87HFQSjR_KPYI,2543
 dkist_processing_cryonirsp/parsers/wavelength.py,sha256=Ay5hZiDNV25-N_QXZINTCgn1ToiP2jvwumkbirBiJGk,883
-dkist_processing_cryonirsp/tasks/__init__.py,sha256=JyM9oA1A6t5sPsbaNmnK9_e6t00kUYzDZzqmSg0nVjE,1061
+dkist_processing_cryonirsp/tasks/__init__.py,sha256=iSODAESNU6zBZo_t44LeTmS1oj_l6EVF7k8xSNtppnk,1057
 dkist_processing_cryonirsp/tasks/assemble_movie.py,sha256=UrxfKSsT3mBkV2LYvnePzKr9nXlvjpoa5amY5C3ftFI,7350
 dkist_processing_cryonirsp/tasks/bad_pixel_map.py,sha256=z-ACCwHqiRANsR7gkkCIycPpgOdR04Mo85WLAPiAJno,3961
 dkist_processing_cryonirsp/tasks/beam_boundaries_base.py,sha256=-sKmBDuNq22QZBe6Vdu5aaiOxeikM6bICpkZ4lBP--g,9688
@@ -36,21 +37,21 @@ dkist_processing_cryonirsp/tasks/instrument_polarization.py,sha256=xS2jcngnibDCL
 dkist_processing_cryonirsp/tasks/l1_output_data.py,sha256=3RFt493MEJxdpF81gcp8FDlQ8vGZ0GXEDYQFWIufumI,1554
 dkist_processing_cryonirsp/tasks/linearity_correction.py,sha256=n9vK9cT7NWkpAM9J6wOYDj95Kh0va_ot-hdncd7ye0Y,24199
 dkist_processing_cryonirsp/tasks/make_movie_frames.py,sha256=I7s3Tml6AevHci0kTPF71mNjXNl3wlG57Jh7ghnndeg,13928
-dkist_processing_cryonirsp/tasks/parse.py,sha256=5nkCjKeCi6oKHzBXmqs81yZwyRPBmIMmL8Lh53CEv4E,13114
+dkist_processing_cryonirsp/tasks/parse.py,sha256=8efntsSPkNl_sokRU2SEStZBCRJvnXDsCelVumOUwH8,13824
 dkist_processing_cryonirsp/tasks/quality_metrics.py,sha256=jyx2YZzLb5sVxbJ_H6PaKQqZbyZy9QuuLqu18jsnncQ,11447
 dkist_processing_cryonirsp/tasks/science_base.py,sha256=YYUQUfLeuzDb6E5TecOH22orTN4-hWocoYaGOq6Zoro,18637
 dkist_processing_cryonirsp/tasks/sp_beam_boundaries.py,sha256=XI3iepNe04xaU4ilqxrlOgYDkv5I5rUc0RXEE1Rwt0o,10296
-dkist_processing_cryonirsp/tasks/sp_dispersion_axis_correction.py,sha256=w3DHEWEJwl3zuKuUB6kzG3vuBWJM84cZGbfeFQKWwJE,18279
 dkist_processing_cryonirsp/tasks/sp_geometric.py,sha256=_M_e_blz4mKDIUWSasonnOzbZ6EUbHp9pAZXQx4zY7U,24387
 dkist_processing_cryonirsp/tasks/sp_science.py,sha256=QWyAEkXYamAcWxi62-tVD6ptuQ6vt8yIzuCKzCIYW20,13643
 dkist_processing_cryonirsp/tasks/sp_solar_gain.py,sha256=d4UABsMxyzCMduVxptHY_TCGqS-l-W5iuhW7HJwVPkA,21024
-dkist_processing_cryonirsp/tasks/write_l1.py,sha256=nLAV0fx_bRFA7WAPrdxJQKogGSRj3pscDJXzhogrVuw,41476
+dkist_processing_cryonirsp/tasks/sp_wavelength_calibration.py,sha256=E9HBmlzvvUEgoAamlO-E0MngYKjuUVq3WwK0DRDLvPk,12843
+dkist_processing_cryonirsp/tasks/write_l1.py,sha256=Jzg09WUYi8uY5o6By7JOsFP0CHpfPCVC4M2UvLSO2PA,41169
 dkist_processing_cryonirsp/tasks/mixin/__init__.py,sha256=m6UekKftTahNJ3W5K3mZSz4Y4ZZpHRxF_ZAxuaKYL7o,12
 dkist_processing_cryonirsp/tasks/mixin/corrections.py,sha256=rcKmckBJkoExcX0XW1i3OZzuMu1i7tX5Hgwy15chU50,6566
 dkist_processing_cryonirsp/tasks/mixin/shift_measurements.py,sha256=EbU3VQ_1QLbENHO_SfhWc7d573UwbofKU-PpbfBPKI8,11620
 dkist_processing_cryonirsp/tests/__init__.py,sha256=m6UekKftTahNJ3W5K3mZSz4Y4ZZpHRxF_ZAxuaKYL7o,12
-dkist_processing_cryonirsp/tests/conftest.py,sha256=oeZw5KXlvm_UasgFc3uzxD2Z2uTg5-rJu7Do9wIKJKU,18131
-dkist_processing_cryonirsp/tests/header_models.py,sha256=klif5-UzTzvAqpj5cJCdLtyodJZS_awhy53NUHyucTw,20601
+dkist_processing_cryonirsp/tests/conftest.py,sha256=ThhhNZ61a-qRMiPEM7PgLwKTw9L4C5nh0IHLDnwtTRo,18016
+dkist_processing_cryonirsp/tests/header_models.py,sha256=eQWRwJzWCIK8-ak1oLWf88u7eo7ERxPMrmQHuphUfX8,21115
 dkist_processing_cryonirsp/tests/test_assemble_movie.py,sha256=YNZINIFXR9kZBlE1AIvjlVmwwhZJeVYOOPk7Q8IVkcI,6222
 dkist_processing_cryonirsp/tests/test_assemble_qualilty.py,sha256=upk-oUqVBHGK3F0eemshLpAPrnfh9mbeuZXow4E1Rmc,16859
 dkist_processing_cryonirsp/tests/test_bad_pixel_maps.py,sha256=TsUIaCWQolOJCU2YOhxxmXWby6j3NhCkB2W2jDgb9OM,4855
@@ -58,33 +59,33 @@ dkist_processing_cryonirsp/tests/test_ci_beam_boundaries.py,sha256=h-v79qi4VohcX
 dkist_processing_cryonirsp/tests/test_ci_science.py,sha256=PryW50DZaKiTcLaSvhfaolrosXObj7-O1jweCJeLM_Y,14403
 dkist_processing_cryonirsp/tests/test_corrections.py,sha256=Q_prvaXKdmpebEa5d05s86pcGB9VTjsGB0g5AfEB2Ks,4536
 dkist_processing_cryonirsp/tests/test_cryo_base.py,sha256=9dSQ_3j_n04NX-nbdAFWhdHGwMe720Vyx0Jxof9eySo,6647
-dkist_processing_cryonirsp/tests/test_cryo_constants.py,sha256=OanX9nPCvhFe9mBV0SRCsClqiSaHi8YxgG2HoESrzTk,2827
+dkist_processing_cryonirsp/tests/test_cryo_constants.py,sha256=WP3cHUF7g9urUt_BuchkbG6ldjM07QltClxRPLnmjsw,3008
 dkist_processing_cryonirsp/tests/test_dark.py,sha256=9WQDoVw1qwaqK-iaVfjOKbIusr4SJrR1rGiPZAWhNIU,11669
 dkist_processing_cryonirsp/tests/test_gain.py,sha256=KAkIXJnifVx7CHnKBY-7EhhUi5b8t5U8wBOL9F8M0gM,11260
 dkist_processing_cryonirsp/tests/test_instrument_polarization.py,sha256=COiopx4ueVPeyQO12eVP125nqBrgsnCa0ddo8y6Qrxs,19711
 dkist_processing_cryonirsp/tests/test_linearity_correction.py,sha256=r1EwZsW1yO0B0ERGn1kDciZKvjipN_LVHFXR-XIJmP0,9350
 dkist_processing_cryonirsp/tests/test_make_movie_frames.py,sha256=WznHp9dV2-jbJYzRniCAIbSHCGNc0SpSzyVDSrZkYd4,4904
-dkist_processing_cryonirsp/tests/test_parameters.py,sha256=yVyUmLst26Ws-_21lS727HkP08DcQh9kycZb9ICsHGY,10948
-dkist_processing_cryonirsp/tests/test_parse.py,sha256=qop-scwjeN70xdgFxDiHuPjDy4b4rnA11W8Q5BkcL9o,56006
+dkist_processing_cryonirsp/tests/test_parameters.py,sha256=hy0ssu2OJmkHFKlGd0_d6EW10YjWsqGb68rOFlPqGuo,11105
+dkist_processing_cryonirsp/tests/test_parse.py,sha256=Ejullo7r7vR0zYRCd714z4berKwXrwSnv8xMVRVqNd4,57090
 dkist_processing_cryonirsp/tests/test_quality.py,sha256=qrJBYjnZOhmQ4vjDcDV3FVSUAdktFgs-pRaHX4cf2G0,8129
 dkist_processing_cryonirsp/tests/test_sp_beam_boundaries.py,sha256=tLQToWStb4Yu2jEHkzv2FyifO_QPwegzttyNKjX8JPk,4880
-dkist_processing_cryonirsp/tests/test_sp_dispersion_axis_correction.py,sha256=Z0t_v85ATh9ntlngUa8v_hqs0ZCd4nkakpHNeCVRwiE,6141
 dkist_processing_cryonirsp/tests/test_sp_geometric.py,sha256=ZnusZvxsJ8YX-rg0R1azg7-DPr4vz5q2NE030bsuWXo,15691
 dkist_processing_cryonirsp/tests/test_sp_make_movie_frames.py,sha256=Kn8U_HzaaHW2bHmBxsotdjmpBhd_Ft6pLWhVsMWIJE8,5322
 dkist_processing_cryonirsp/tests/test_sp_science.py,sha256=fCmyXh27nxKU_N90yW1WqPGq1mZ6ODrw0UvtMB1elHI,19835
 dkist_processing_cryonirsp/tests/test_sp_solar.py,sha256=IdZZ2RvCwKk6_q_JKo93nFFk0HJ74yUxHxq9W1LppJE,10008
+dkist_processing_cryonirsp/tests/test_sp_wavelength_calibration.py,sha256=SZMixYxMnIksvQpTiXt8MiwLbyZiDyKE6CW2vjl4af8,5666
 dkist_processing_cryonirsp/tests/test_trial_create_quality_report.py,sha256=x8dRAMyawQVYZQGsuO36DMZxK4L13hZBUn86qbhJiNk,2805
 dkist_processing_cryonirsp/tests/test_workflows.py,sha256=2a-TUMbVEyNjHYNyzo2UQMLg5PSaEx6iV9hOsGp-Mck,291
-dkist_processing_cryonirsp/tests/test_write_l1.py,sha256=VDSRU7j4eylYlmYQYKn32Od751NmG7qzhpoaFYFWQDM,17729
+dkist_processing_cryonirsp/tests/test_write_l1.py,sha256=Ijf1Dxa-jCkMjEcPuSRbtCsFzfHH-nifn2AQ84qg1zg,17644
 dkist_processing_cryonirsp/tests/local_trial_workflows/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dkist_processing_cryonirsp/tests/local_trial_workflows/l0_cals_only.py,sha256=nWs3Qg3f4DHqN_6JBKDaR5q9TncgR_PeRWw3_bUBZWA,20110
-dkist_processing_cryonirsp/tests/local_trial_workflows/l0_to_l1.py,sha256=KaxxMeo_sOMWgekNVkPsTJt6XWU2Ov7rnMkBtG_sKcc,23938
+dkist_processing_cryonirsp/tests/local_trial_workflows/l0_cals_only.py,sha256=jUC6EnzBLwso7DBCtmhTdPJw3zlrIJYW0KTKNlWgGAM,20088
+dkist_processing_cryonirsp/tests/local_trial_workflows/l0_to_l1.py,sha256=Ab1IeXfys130jkRs0iNIPv2rZFXg-IDCNkK4Z_wdOuI,23909
 dkist_processing_cryonirsp/tests/local_trial_workflows/linearize_only.py,sha256=kl9yrE1EbgxNn__x4q0WYoZIvS8zefcOPbQQdxB4_ZE,3280
-dkist_processing_cryonirsp/tests/local_trial_workflows/local_trial_helpers.py,sha256=FteYoLXR6BW3MBb-Wc6-O8mRj26U2U6T95_itslDhEo,20966
+dkist_processing_cryonirsp/tests/local_trial_workflows/local_trial_helpers.py,sha256=DQDpjc6_I5o6dIPv5hK65oBKG0vksp9lY4k9A0hu1D4,20953
 dkist_processing_cryonirsp/workflows/__init__.py,sha256=iEbV3oiKmkfmdZjeNJxqw08IIZnYSroq-2b-ARpkLFQ,112
 dkist_processing_cryonirsp/workflows/ci_l0_processing.py,sha256=8-96ZWi_hnzsashkFaaK6YjO0CUk_2iO_gCoHTmGow8,3823
-dkist_processing_cryonirsp/workflows/sp_l0_processing.py,sha256=Afy8JTTKcjRHh7c-hjnbXy6iP16OafHiVivoLWhDBUg,4254
-dkist_processing_cryonirsp/workflows/trial_workflows.py,sha256=UvSvsho6gYWliJ_sRN_uYbt5jBdA68hVyLiyr6X5QTo,8088
+dkist_processing_cryonirsp/workflows/sp_l0_processing.py,sha256=TFycCbC_N3MhM0rEHpEPmKtfJLNaVY3csR6uDrRCKI4,4245
+dkist_processing_cryonirsp/workflows/trial_workflows.py,sha256=eLrROaZiyZwn8ta34oSO06aH_D9VPoqWinjDMN-9VN4,8079
 docs/Makefile,sha256=qnlVz6PuBqE39NfHWuUnHhNEA-EFgT2-WJNNNy9ttfk,4598
 docs/bad_pixel_calibration.rst,sha256=bHRclUItBA1QbGlek36B1yN5WHN53WkfjKUvZaq_j2I,2452
 docs/beam_angle_calculation.rst,sha256=-yUPFRl6SbPBIj-wOwylEymQDMQnkay7kAIAiubpQT8,2941
@@ -92,7 +93,7 @@ docs/beam_boundary_computation.rst,sha256=khyc_uW5zII6c0vN1lOvrwMAr5WO1XFFIou3QB
 docs/changelog.rst,sha256=S2jPASsWlQxSlAPqdvNrYvhk9k3FcFWNXFNDYXBSjl4,120
 docs/ci_science_calibration.rst,sha256=6HLt4ljL49sYH_iFU-Nz8KSWLyS8h_SSkzgUv-LsfqM,1704
 docs/conf.py,sha256=cv1Gct6NbY_kxJEKqw-mMIoauxtWVZeNzRLFqX1_GUw,2038
-docs/index.rst,sha256=FZY5WfJ16HQyslyaJxgTLs6XCD73_aFFdH4CjzagNjs,445
+docs/index.rst,sha256=l6vH2FhWpuz0X1SbgfaMBoCACMPRuhHCs9dTxW1Hcaw,472
 docs/l0_to_l1_cryonirsp_ci-full-trial.rst,sha256=-uhtnd51ttJYw9T5hs5A9HQWpXJkOJmvfXf1INFT3MI,582
 docs/l0_to_l1_cryonirsp_ci.rst,sha256=OhGTy9CBTqQJ04XhThTws8KBnGLFiP5vBX0DlX6NXKA,458
 docs/l0_to_l1_cryonirsp_sp-full-trial.rst,sha256=cKdRI7qVEVYsqqgYuL9nzqFP3uTR4cu305WfjmmyetY,582
@@ -104,8 +105,9 @@ docs/requirements.txt,sha256=Kbl_X4c7RQZw035YTeNB63We6I7pvXFU4T0Uflp2yDY,29
 docs/requirements_table.rst,sha256=FaqSag9kPi77gWPhzeo_tFEhRFjb3qUuNqqQe1K76NM,297
 docs/scientific_changelog.rst,sha256=01AWBSHg8zElnodCgAq-hMxhk9CkX5rtEENx4iz0sjI,300
 docs/sp_science_calibration.rst,sha256=XL-H_hyzqwPHYNW3j-muItX_hGqMi-gjFRQbHp60LlU,2997
+docs/wavelength_calibration.rst,sha256=s7ds_QKlVJ68fdONSY3DOBvHHaQC0JR_D4goG_VVKWw,3457
 licenses/LICENSE.rst,sha256=piZaQplkzOMmH1NXg6QIdo9wwo9pPCoHkvm2-DmH76E,1462
-dkist_processing_cryonirsp-1.9.0.dist-info/METADATA,sha256=ldY1xHkvAxyI_K4JmhwFjzAg4Tx73hxCqqjIuYSZINM,22052
-dkist_processing_cryonirsp-1.9.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dkist_processing_cryonirsp-1.9.0.dist-info/top_level.txt,sha256=Sm9b1ddKnsF9Bh3mqDOct1Sm7k8I9aN7vGHgpmu-MlQ,51
-dkist_processing_cryonirsp-1.9.0.dist-info/RECORD,,
+dkist_processing_cryonirsp-1.10.0rc1.dist-info/METADATA,sha256=aYUp1rzLQuMN0qnC4k9OdBurJb_iO0fLG_zfemf40hQ,22111
+dkist_processing_cryonirsp-1.10.0rc1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dkist_processing_cryonirsp-1.10.0rc1.dist-info/top_level.txt,sha256=Sm9b1ddKnsF9Bh3mqDOct1Sm7k8I9aN7vGHgpmu-MlQ,51
+dkist_processing_cryonirsp-1.10.0rc1.dist-info/RECORD,,

docs/index.rst

@@ -14,6 +14,7 @@
     bad_pixel_calibration
     beam_boundary_computation
     beam_angle_calculation
+    wavelength_calibration
     ci_science_calibration
     sp_science_calibration
     autoapi/index

docs/wavelength_calibration.rst

@@ -0,0 +1,62 @@
+Wavelength Calibration
+============================
+
+Overview
+--------
+
+The `~dkist_processing_cryonirsp.tasks.sp_wavelength_calibration` task provides an absolute wavelength calibration of
+Cryo-NIRSP solar spectra by using the routines provided by the
+`solar-wavelength-calibration <https://docs.dkist.nso.edu/projects/solar-wavelength-calibration/en/latest/>`_ library.
+
+Workflow
+--------
+
+#. **Input Spectrum**: Compute a spatially averaged input spectrum from solar gain images.
+#. **Initial Guess**: Use Level 0 headers to generate a first-guess wavelength solution.
+#. **Fitting**: Fit the representative spectrum using the `solar-wavelength-calibration <https://docs.dkist.nso.edu/projects/solar-wavelength-calibration/en/latest/>`_  library, refining the wavelength solution.
+#. **Header Encoding**: Save the fit results as FITS header keywords, parameterizing the solution for downstream use.
+
+Wavelength Solution Encoding
+----------------------------
+
+The wavelength solution is stored in FITS headers using the following keywords (see `Greisen et al (2006) <https://ui.adsabs.harvard.edu/abs/2006A%26A...446..747G/abstract>`_, Section 5 and Table 6):
+
++---------+--------------------------+----------------+
+| Keyword | Description              | Units          |
++=========+==========================+================+
+| `CTYPE1`| Spectral coordinate type | "AWAV-GRA"     |
++---------+--------------------------+----------------+
+| `CUNIT1`| Wavelength unit          | "nm"           |
++---------+--------------------------+----------------+
+| `CRPIX1`| Reference pixel          |                |
++---------+--------------------------+----------------+
+| `CRVAL1`| Reference wavelength     | nm             |
++---------+--------------------------+----------------+
+| `CDELT1`| Linear dispersion        | nm / px        |
++---------+--------------------------+----------------+
+| `PV1_0` | Grating constant         | 1 / m          |
++---------+--------------------------+----------------+
+| `PV1_1` | Spectral order           |                |
++---------+--------------------------+----------------+
+| `PV1_1` | Incident light angle     | deg            |
++---------+--------------------------+----------------+
+
+Note: The units of `PV1_0` are always 1 / m.
+
+Fitted Parameters
+-----------------
+
+The fitting process can optimize several parameters. The parameters that are free in Cryo-NIRSP fits are:
+
+- **crval**: Wavelength zero-point.
+- **dispersion**: Linear dispersion, allowed to vary within a few percent of the nominal value.
+- **opacity_factor**: Atmospheric absorption scaling, to match telluric line strengths.
+- **continuum_level**: Overall spectrum scaling, to match the observed continuum.
+- **straylight_fraction**: Fraction of stray or scattered light added to the observed spectrum, affecting line depths and continuum.
+- **resolving_power**: Spectral resolving power (:math:`R = \frac{\lambda}{\Delta\lambda}`), characterizing the instrument's ability to distinguish close spectral features.
+- **incident_light_angle**: Angle at which light enters the grating, influencing the wavelength solution through the grating equation.
+
+
+For more details on the fitting algorithms and parameterization, see the
+`solar-wavelength-calibration documentation <https://docs.dkist.nso.edu/projects/solar-wavelength-calibration/en/latest/>`_
+and `Greisen et al. (2006) <https://ui.adsabs.harvard.edu/abs/2006A%26A...446..747G/abstract>`_.

dkist_processing_cryonirsp/tasks/sp_dispersion_axis_correction.py

@@ -1,465 +0,0 @@
-"""Cryonirsp SP dispersion axis calibration task."""
-import warnings
-
-import numpy as np
-from astropy import constants as const
-from astropy import units as u
-from astropy.coordinates import EarthLocation
-from astropy.coordinates.spectral_coordinate import SpectralCoord
-from astropy.io import fits
-from astropy.time import Time
-from astropy.wcs import WCS
-from dkist_processing_common.codecs.asdf import asdf_encoder
-from dkist_processing_common.models.dkist_location import location_of_dkist
-from dkist_service_configuration.logging import logger
-from scipy.ndimage import gaussian_filter1d
-from scipy.optimize import differential_evolution
-from scipy.optimize import OptimizeResult
-from sunpy.coordinates import HeliocentricInertial
-
-from dkist_processing_cryonirsp.codecs.fits import cryo_fits_access_decoder
-from dkist_processing_cryonirsp.codecs.fits import cryo_fits_array_decoder
-from dkist_processing_cryonirsp.models.tags import CryonirspTag
-from dkist_processing_cryonirsp.parsers.cryonirsp_l0_fits_access import CryonirspL0FitsAccess
-from dkist_processing_cryonirsp.tasks.cryonirsp_base import CryonirspTaskBase
-
-__all__ = ["SPDispersionAxisCorrection"]
-
-
-class SPDispersionAxisCorrection(CryonirspTaskBase):
-    """Task class for correcting the dispersion axis wavelength values.
-
-    Parameters
-    ----------
-    recipe_run_id : int
-        id of the recipe run used to identify the workflow run this task is part of
-    workflow_name : str
-        name of the workflow to which this instance of the task belongs
-    workflow_version : str
-        version of the workflow to which this instance of the task belongs
-
-    """
-
-    record_provenance = True
-
-    def run(self):
-        """
-        Run method for the task.
-
-        For each beam
-            - Gather 1D characteristic spectrum.
-            - Compute the theoretical dispersion.
-            - Load the telluric and non-telluric FTS atlases and grab only the portion of the atlases that pertain to the current observation.
-            - Shift the preliminary wavelength vector (from the data) so that it generally aligns with the FTS atlas data.
-            - Account for the speed at which DKIST was moving relative to the sun's center at the time of observation.
-            - Define fitting bounds and fit the profile using scipy.optimize.differential_evolution.
-            - Write results to disk.
-
-
-        Returns
-        -------
-        None
-        """
-        spectrum = self.load_1d_char_spectrum()
-
-        solar_header = self.load_header()
-
-        dispersion, order, alpha = self.get_theoretical_dispersion()
-
-        expected_wavelength_vector = self.compute_expected_wavelength_vector(spectrum, solar_header)
-
-        (
-            telluric_atlas_wave,
-            telluric_atlas_trans,
-            solar_atlas_wave_air,
-            solar_atlas_trans_flipped,
-        ) = self.load_and_resample_fts_atlas(expected_wavelength_vector)
-
-        (fts_wave, fts_solar, fts_telluric) = self.initial_alignment(
-            spectrum,
-            expected_wavelength_vector,
-            solar_atlas_wave_air,
-            solar_atlas_trans_flipped,
-            telluric_atlas_wave,
-            telluric_atlas_trans,
-        )
-
-        doppler_shift = self.get_doppler_shift()
-
-        fit_result = self.fit_dispersion_axis_to_FTS(
-            fts_wave,
-            fts_telluric,
-            fts_solar,
-            dispersion,
-            alpha,
-            doppler_shift,
-            spectrum,
-            order,
-            self.constants.grating_constant,
-        )
-
-        self.write_fit_results(spectrum, order, fit_result)
-
-    def write_fit_results(
-        self, spectrum: np.ndarray, order: int, fit_result: OptimizeResult
-    ) -> None:
-        """Save the fit results to disk to later be used to update the l1 headers."""
-        updated_headers = {
-            "CRPIX1": np.size(spectrum) // 2 + 1,
-            "CRVAL1": fit_result.x[0],
-            "CDELT1": fit_result.x[1],
-            "PV1_0": self.constants.grating_constant,
-            "PV1_1": order,
-            "PV1_2": fit_result.x[2],
-            "CRPIX1A": np.size(spectrum) // 2 + 1,
-            "CRVAL1A": fit_result.x[0],
-            "CDELT1A": fit_result.x[1],
-            "PV1_0A": self.constants.grating_constant,
-            "PV1_1A": order,
-            "PV1_2A": fit_result.x[2],
-        }
-
-        self.write(
-            data=updated_headers,
-            tags=[CryonirspTag.task_spectral_fit(), CryonirspTag.intermediate()],
-            encoder=asdf_encoder,
-        )
-
-    def load_1d_char_spectrum(self) -> np.ndarray:
-        """Load intermediate 1d characteristic measured_spectra for beam 1."""
-        # Only fitting with the left beam.
-        beam = 1
-        array_generator = self.read(
-            tags=[CryonirspTag.intermediate_frame(beam=beam), CryonirspTag.task("SOLAR_CHAR_SPEC")],
-            decoder=cryo_fits_array_decoder,
-        )
-
-        return next(array_generator)
-
-    def load_header(self) -> fits.header.Header:
-        """Grab a header from a random solar gain frame to be used to find a rough initial wavelength estimate."""
-        # Only fitting with the left beam.
-        beam = 1
-        solar_tags = [CryonirspTag.linearized_frame(), CryonirspTag.task("SOLAR_GAIN")]
-        solar_obj = next(
-            self.read(
-                tags=solar_tags,
-                decoder=cryo_fits_access_decoder,
-                fits_access_class=CryonirspL0FitsAccess,
-            )
-        )
-        solar_header = solar_obj.header
-        return solar_header
-
-    def get_theoretical_dispersion(self) -> tuple[u.Quantity, int, float]:
-        """Compute theoretical dispersion value using the following grating equation.
-
-        m = d/lambda * (sin(alpha) + sin(beta))
-
-        where
-        m = order
-        d = grating spacing
-        lambda = wavelength
-        alpha = incident angle
-        beta = diffraction angle
-
-        """
-        wavelength = self.constants.wavelength * u.nanometer
-        grating_position_angle_phi = np.deg2rad(self.constants.grating_position_deg)
-        grating_littrow_angle_theta = np.deg2rad(self.constants.grating_littrow_angle_deg)
-        alpha = grating_position_angle_phi + grating_littrow_angle_theta
-        beta = grating_position_angle_phi - grating_littrow_angle_theta
-        grating_spacing_distance = (1.0 / self.constants.grating_constant) * u.m
-        order = int(grating_spacing_distance / wavelength * (np.sin(alpha) + np.sin(beta)))
-        camera_mirror_focal_length = self.parameters.camera_mirror_focal_length_mm
-        pixpitch = self.parameters.pixel_pitch_micron
-        linear_disp = order / (grating_spacing_distance * np.cos(beta)) * camera_mirror_focal_length
-        theoretical_dispersion = (pixpitch / linear_disp).to(u.nanometer)
-
-        return theoretical_dispersion, order, alpha
-
-    def compute_expected_wavelength_vector(
-        self, spectrum: np.ndarray, header: fits.header.Header
-    ) -> u.Quantity:
-        """Compute the expected wavelength vector based on the header information.""" ""
-        # resample atlases
-        number_of_wave_pix = np.size(spectrum)
-        header["CRPIX1"] = number_of_wave_pix // 2 + 1
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")  ## TO ELIMINATE datafix warnings
-            wcs = WCS(header)
-            # get wavelength based on header info (not fully accurate)
-            expected_wavelength_vector = wcs.spectral.pixel_to_world(
-                np.arange(number_of_wave_pix)
-            ).to(u.nm)
-
-        return expected_wavelength_vector
-
-    def load_and_resample_fts_atlas(
-        self, expected_wavelength_vector: u.Quantity
-    ) -> tuple[u.Quantity, np.ndarray, u.Quantity, np.ndarray]:
-        """Load telluric and non-telluric FTS atlas data, resample both atlases to be on the same, linear wavelength grid, select the portion of atlas that pertains to bandpass used."""
-        solar_atlas_wavelength, solar_atlas_transmission = self.parameters.solar_atlas
-        solar_atlas_wavelength = solar_atlas_wavelength * u.nm
-        telluric_atlas_wavelength, telluric_atlas_transmission = self.parameters.telluric_atlas
-        telluric_atlas_wavelength = telluric_atlas_wavelength * u.nm
-
-        expected_wavelength_range = (
-            expected_wavelength_vector.max() - expected_wavelength_vector.min()
-        )
-        min_wavelength = expected_wavelength_vector.min() - 0.25 * expected_wavelength_range
-        max_wavelength = expected_wavelength_vector.max() + 0.25 * expected_wavelength_range
-
-        cropped_telluric_mask = (telluric_atlas_wavelength > min_wavelength) * (
-            telluric_atlas_wavelength < max_wavelength
-        )
-        telluric_atlas_wavelength = telluric_atlas_wavelength[cropped_telluric_mask]
-        telluric_atlas_transmission = telluric_atlas_transmission[cropped_telluric_mask]
-
-        cropped_solar_mask = (solar_atlas_wavelength > min_wavelength) * (
-            solar_atlas_wavelength < max_wavelength
-        )
-        solar_atlas_wavelength = solar_atlas_wavelength[cropped_solar_mask]
-        solar_atlas_transmission = solar_atlas_transmission[cropped_solar_mask]
-
-        return (
-            telluric_atlas_wavelength,
-            telluric_atlas_transmission,
-            solar_atlas_wavelength,
-            solar_atlas_transmission,
-        )
-
-    def get_doppler_shift(self) -> u.Quantity:
-        """Find the speed at which DKIST is moving relative to the Sun's center.
-
-        Positive values refer to when DKIST is moving away from the sun.
-        """
-        coord = location_of_dkist.get_gcrs(obstime=Time(self.constants.solar_gain_ip_start_time))
-        heliocentric_coord = coord.transform_to(
-            HeliocentricInertial(obstime=Time(self.constants.solar_gain_ip_start_time))
-        )
-        obs_vr_kms = heliocentric_coord.d_distance
-        return obs_vr_kms
-
-    def initial_alignment(
-        self,
-        spectrum: np.ndarray,
-        expected_wavelength_vector: SpectralCoord,
-        solar_atlas_wave_air: u.Quantity,
-        solar_atlas_trans_flipped: np.ndarray,
-        telluric_atlas_wave: u.Quantity,
-        telluric_atlas_trans: np.ndarray,
-    ) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
-        """Determine a shift of the preliminary wavelength vector so that it generally aligns with the data itself."""
-        shifts = np.linspace(-2, 2, 550) * u.nm
-        merit = np.zeros(len(shifts))
-        for n, shift in enumerate(shifts):
-            preliminary_wavelength = expected_wavelength_vector + shift
-            fts_solar = np.interp(
-                preliminary_wavelength, solar_atlas_wave_air, solar_atlas_trans_flipped
-            )
-            fts_telluric = np.interp(
-                preliminary_wavelength, telluric_atlas_wave, telluric_atlas_trans
-            )
-            # calculate a merit value to be minimized
-            merit[n] = np.std(spectrum - fts_solar * fts_telluric)
-
-        # get minimum
-        shift = shifts[np.argmin(merit)]
-
-        # recalculate spectral axis and atlas spectrum for the best shift value
-        fts_wave = expected_wavelength_vector + shift
-        fts_solar = np.interp(fts_wave, solar_atlas_wave_air, solar_atlas_trans_flipped)
-        fts_telluric = np.interp(fts_wave, telluric_atlas_wave, telluric_atlas_trans)
-
-        return fts_wave.value, fts_solar, fts_telluric
-
-    @staticmethod
-    def fitness(
-        parameters: np.ndarray,
-        spectrum: np.ndarray,
-        fts_wave: np.ndarray,
-        fts_telluric: np.ndarray,
-        fts_solar: np.ndarray,
-        order: int,
-        grating_constant: float,
-        doppler_shift: float,
-    ) -> float:
-        """
-        Model function for profile fitting.
-
-        Parameters
-        ----------
-        crval1
-            Wavelength at crpix1
-
-        cdelt1
-            Spectral dispersion at crpix1
-
-        incident_light_angle
-            Incident angle in degrees
-
-        resolving_power
-            Resolving power -- used to estimate the line spread function (may not be correct off limb)
-
-        opacity
-            Opacity scaling applied to telluric absorption
-
-        stray_light_frac
-            Inferred straylight fraction in the spectrograph --> This scales the lines non-linearly.
-
-        continuum_amplitude
-            Amplitude of the scattered light continuum
-        """
-        (
-            crval1,
-            cdelt1,
-            incident_light_angle,
-            resolving_power,
-            opacity,
-            stray_light_frac,
-            continuum_amplitude,
-        ) = parameters
-
-        # calculate the spectral axis
-        # Representations of spectral coordinates in FITS
-        # https://ui.adsabs.harvard.edu/abs/2006A%26A...446..747G/abstract
-        # https://specreduce.readthedocs.io/en/latest/api/specreduce.utils.synth_data.make_2d_arc_image.html
-
-        number_of_wave_pix = np.size(spectrum)
-
-        non_linear_header = {
-            "CTYPE1": "AWAV-GRA",  # Grating dispersion function with air wavelengths
-            "CUNIT1": "nm",  # Dispersion units
-            "CRPIX1": number_of_wave_pix // 2 + 1,  # Reference pixel [pix]
-            "PV1_0": grating_constant,  # Grating density
-            "PV1_1": order,  # Diffraction order
-            "CRVAL1": crval1,  # Reference value [nm] (<<<< TO BE OPTMIZED <<<<<<)
-            "CDELT1": cdelt1,  # Linear dispersion [nm/pix] (<<<< TO BE OPTMIZED <<<<<<)
-            "PV1_2": incident_light_angle,  # Incident angle [deg] (<<<< TO BE OPTMIZED <<<<<<)
-        }
-
-        non_linear_wcs = WCS(non_linear_header)
-        wavelength_vector = (
-            (non_linear_wcs.spectral.pixel_to_world(np.arange(number_of_wave_pix))).to(u.nm).value
-        )
-
-        # Gaussian convolution of the FTS atlas
-        fwhm_wavelength = np.divide(crval1, resolving_power)
-        sigma_wavelength = fwhm_wavelength / (2.0 * np.sqrt(2.0 * np.log(2)))
-        kern_pix = sigma_wavelength / np.abs(cdelt1)
-
-        # interpolate the telluric spectral atlas onto the new wavelength axis and scale by the opacity value that is being optimized
-        fts_atmosphere_interp = np.interp(wavelength_vector, fts_wave, fts_telluric)
-        fts_telluric_interp = np.exp(opacity * np.log(fts_atmosphere_interp))
-
-        # interpolate the solar spectral atlas onto the new wavelength axis and apply a shift according to the Doppler shift due to orbital motions
-        fts_solar_interp = np.interp(
-            wavelength_vector,
-            fts_wave + doppler_shift / (const.c.to("km/s")).value * crval1,
-            fts_solar,
-        )
-
-        # apply telluric absorption spectrum to solar spectrum
-        fts_modulated = fts_telluric_interp * fts_solar_interp
-        # add flat value of straylight contamination
-        fts_modulated_with_straylight = (fts_modulated + stray_light_frac) / (
-            1.0 + stray_light_frac
-        )
-        # scale for total intensity of the continuum
-        fit_amplitude = fts_modulated_with_straylight * continuum_amplitude
-
-        # convolution for spectrograph line spread function
-        fit_amplitude = gaussian_filter1d(fit_amplitude, kern_pix)
-
-        # chisquare calculation for fit metric
-        res_amplitude = np.sum((spectrum - fit_amplitude) ** 2)
-
-        return res_amplitude
-
-    def fit_dispersion_axis_to_FTS(
-        self,
-        fts_wave: np.ndarray,
-        fts_telluric: np.ndarray,
-        fts_solar: np.ndarray,
-        dispersion: u.Quantity,
-        alpha: float,
-        doppler_shift: u.Quantity,
-        spectrum: np.ndarray,
-        order: int,
-        grating_constant: float,
-    ) -> OptimizeResult:
-        """Define the bounds and send the fitting model on its way."""
-        parameter_names = (
-            "crval1 (wavelength at crpix1)",
-            "cdelt1 (spectral dispersion at crpix1)",
-            "incident_light_angle",
-            "resolving_power",
-            "opacity",
-            "stray_light_frac",
-            "continuum_amplitude",
-        )
-        crpix1_updated = np.size(spectrum) // 2 + 1
-        crval1 = fts_wave[crpix1_updated]  # initial guess
-        bounds = [
-            # [nm[ +\- 0.5 nm range used for finding CRVAL1
-            (crval1 - 0.5, crval1 + 0.5),
-            # [nm/pix] 5% bounds on the dispersion at CRPIX1
-            (
-                dispersion.value - 0.05 * dispersion.value,
-                dispersion.value + 0.05 * dispersion.value,
-            ),
-            # [radian] Incident angle range is +/- 5 degree from value in header
-            (np.rad2deg(alpha) - 5, np.rad2deg(alpha) + 5),
-            # resolving power range
-            (20000, 125000),
-            # opacity factor bounds
-            (0.0, 10),
-            # straylight fraction
-            (0.0, 0.5),
-            # continuum intensity correction
-            (0.8 * np.nanpercentile(spectrum, 75), 1.2 * np.nanpercentile(spectrum, 75)),
-        ]
-
-        for repeat_fit in range(5):  # repeat just in case the fitting gets stuck in a local minimum
-            fit_result = differential_evolution(
-                SPDispersionAxisCorrection.fitness,
-                args=(
-                    spectrum,
-                    fts_wave,
-                    fts_telluric,
-                    fts_solar,
-                    order,
-                    grating_constant,
-                    doppler_shift.value,
-                ),
-                popsize=2,
-                maxiter=300,
-                bounds=bounds,
-                disp=True,
-                polish=True,
-                tol=1.0e-9,
-            )
-            if fit_result.fun < 0.03:
-                logger.info(" Convergence good based on fit func value")
-                break
-
-        logger.info("Fitted Values:")
-        logger.info(" ")
-        for p in range(len(parameter_names)):
-            logger.info(
-                f"Parameter: {parameter_names[p]},   Fit Result: {fit_result.x[p]},    Bounds: {bounds[p]}"
-            )
-
-        fit_amplitude = SPDispersionAxisCorrection.fitness(
-            fit_result.x,
-            spectrum,
-            fts_wave,
-            fts_telluric,
-            fts_solar,
-            order,
-            grating_constant,
-            doppler_shift.value,
-        )
-
-        return fit_result