dkist-processing-cryonirsp 0.0.23rc2__tar.gz → 0.0.25rc1__tar.gz

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/CHANGELOG.rst

@@ -1,3 +1,21 @@
+v0.0.24 (2024-01-03)
+====================
+
+Misc
+----
+
+- Bump version of `dkist-processing-pac` to v3.0.1. No change to pipeline behavior at all. (`#82 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/82>`__)
+
+
+v0.0.23 (2023-12-20)
+====================
+
+Misc
+----
+
+- Adding manual processing worker capabilities via dkist-processing-common update. (`#81 <https://bitbucket.org/dkistdc/dkist-processing-cryonirsp/pull-requests/81>`__)
+
+
 v0.0.22 (2023-12-01)
 ====================
 

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dkist_processing_cryonirsp
-Version: 0.0.23rc2
+Version: 0.0.25rc1
 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-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/bitbucket-pipelines.yml

@@ -123,6 +123,21 @@ pipelines:
       - step: *scan
       - step: *test
       - step: *docs
+  custom:
+    build_rc:  # I.e. skip the doc check (because we might have rc dependencies)
+      - variables:
+        - name: BITBUCKET_TAG
+          description: "Tag version to build (e.g., 'vX.Y.ZrcR')"
+      - parallel:
+        - step: *changelog
+        - step: *lint
+      - parallel:
+        - step: *scan
+        - step: *test
+      - parallel:
+        - step: *push_workflow
+        - step: *push_mpw
+      - step: *push_code
   tags:
     'v*':
       - parallel:
@@ -131,7 +146,7 @@ pipelines:
       - parallel:
         - step: *scan
         - step: *test
-        #- step: *docs
+        - step: *docs
       - parallel:
           - step: *push_workflow
           - step: *push_mpw

dkist_processing_cryonirsp-0.0.25rc1/changelog/84.bugfix.rst

@@ -0,0 +1,2 @@
+Compute polarimetric noise and sensitivity values and add to L1 headers (POL_NOIS, and POL_SENS, respectively). These
+keywords are now required by the fits-spec.

dkist_processing_cryonirsp-0.0.25rc1/changelog/84.misc.rst

@@ -0,0 +1 @@
+Update `dkist-fits-specifications` and associated (validator, simulator) to use new conditional requiredness framework.

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp/tasks/science_base.py

@@ -297,20 +297,28 @@ class ScienceCalibrationBase(CryonirspTaskBase, ABC):
         meas_num
             The current measurement number
         """
+        final_header = self._update_calibrated_header(calibrated_object.header, map_scan=map_scan)
         if self.constants.correct_for_polarization:
-            stokes_targets = self.constants.stokes_params
-        else:
-            stokes_targets = self.constants.stokes_I_list
+            stokes_I_data = calibrated_object.data[:, :, 0]
+            for s, stokes_param in enumerate(self.constants.stokes_params):
+                stokes_data = calibrated_object.data[:, :, s]
+                final_data = self._re_dummy_data(stokes_data)
+                pol_header = self._add_L1_pol_headers(final_header, stokes_data, stokes_I_data)
+                self._write_calibrated_array(
+                    data=final_data,
+                    header=pol_header,
+                    stokes=stokes_param,
+                    meas_num=meas_num,
+                    scan_step=scan_step,
+                    map_scan=map_scan,
+                )
 
-        for i, stokes_param in enumerate(stokes_targets):
-            final_data = self._re_dummy_data(calibrated_object.data[:, :, i])
-            final_header = self._update_calibrated_header(
-                calibrated_object.header, map_scan=map_scan
-            )
+        else:
+            final_data = self._re_dummy_data(calibrated_object.data[:, :, 0])
             self._write_calibrated_array(
                 data=final_data,
                 header=final_header,
-                stokes=stokes_param,
+                stokes="I",
                 meas_num=meas_num,
                 scan_step=scan_step,
                 map_scan=map_scan,
@@ -405,6 +413,52 @@ class ScienceCalibrationBase(CryonirspTaskBase, ABC):
 
         return header
 
+    def _add_L1_pol_headers(
+        self, input_header: fits.Header, stokes_data: np.ndarray, stokes_I_data: np.ndarray
+    ) -> fits.Header:
+        """Compute and add 214 header values specific to polarimetric datasets."""
+        # Probably not needed, but just to be safe
+        output_header = input_header.copy()
+
+        pol_noise = self.compute_polarimetric_noise(stokes_data, stokes_I_data)
+        pol_sensitivity = self.compute_polarimetric_sensitivity(stokes_I_data)
+        output_header["POL_NOIS"] = pol_noise
+        output_header["POL_SENS"] = pol_sensitivity
+
+        return output_header
+
+    def compute_polarimetric_noise(
+        self, stokes_data: np.ndarray, stokes_I_data: np.ndarray
+    ) -> float:
+        r"""
+        Compute the polarimetric noise for a single frame.
+
+        The polarimetric noise, :math:`N`, is defined as
+
+        .. math::
+
+            N = stddev(\frac{F_i}{F_I})
+
+        where :math:`F_i` is a full array of values for Stokes parameter :math:`i` (I, Q, U, V), and :math:`F_I` is the
+        full frame of Stokes-I. The stddev is computed across the entire frame.
+        """
+        return float(np.nanstd(stokes_data / stokes_I_data))
+
+    def compute_polarimetric_sensitivity(self, stokes_I_data: np.ndarray) -> float:
+        r"""
+        Compute the polarimetric sensitivity for a single frame.
+
+        The polarimetric sensitivity is the smallest signal that can be measured based on the values in the Stokes-I
+        frame. The sensitivity, :math:`S`, is computed as
+
+        .. math::
+
+            S = \frac{1}{\sqrt{\mathrm{max}(F_I)}}
+
+        where :math:`F_I` is the full frame of values for Stokes-I.
+        """
+        return float(1.0 / np.sqrt(np.nanmax(stokes_I_data)))
+
     def _write_calibrated_array(
         self,
         data: np.ndarray,

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp/tests/test_ci_science.py

@@ -257,6 +257,9 @@ def test_ci_science_calibration_task(ci_science_calibration_task, mocker):
         assert hdu.data.shape == expected_final_shape
         assert "DATE-BEG" in hdu.header.keys()
         assert "DATE-END" in hdu.header.keys()
+        if polarization_mode == "Full Stokes":
+            assert "POL_NOIS" in hdu.header.keys()
+            assert "POL_SENS" in hdu.header.keys()
 
         # Check that scan step keys were updated
         scan_step = [

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp/tests/test_sp_science.py

@@ -305,6 +305,9 @@ def test_sp_science_calibration_task(sp_science_calibration_task, mocker):
         assert hdu.data.shape == expected_final_shape
         assert "DATE-BEG" in hdu.header.keys()
         assert "DATE-END" in hdu.header.keys()
+        if polarization_mode == "Full Stokes":
+            assert "POL_NOIS" in hdu.header.keys()
+            assert "POL_SENS" in hdu.header.keys()
 
         # Check that scan step keys were updated
         scan_step = [

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp/tests/test_write_l1.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Literal
 
 import numpy as np
 import pytest
@@ -83,6 +82,20 @@ def write_l1_task(
             hdul[0].header["CTYPE1"] = axis_1_type
             hdul[0].header["CTYPE2"] = axis_2_type
             hdul[0].header["CTYPE3"] = axis_3_type
+            hdul[0].header["CNNMAPS"] = num_map_scans
+
+            # Set CNMODNST and CNSPINMD so the correct schema is loaded for validation
+            hdul[0].header["CNMODNST"] = num_modstates
+            if num_stokes_params > 1:
+                hdul[0].header["CNSPINMD"] = "Continuous"
+
+                # These headers are added to polarimetric frames in the science task
+                hdul[0].header["POL_NOIS"] = 0.1
+                hdul[0].header["POL_SENS"] = 0.2
+
+            else:
+                hdul[0].header["CNSPINMD"] = "None"
+
             for map_scan in range(1, num_map_scans + 1):
                 for scan_step in range(1, num_scan_steps + 1):
                     for meas_num in range(1, num_meas + 1):

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dkist-processing-cryonirsp
-Version: 0.0.23rc2
+Version: 0.0.25rc1
 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-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp.egg-info/SOURCES.txt

@@ -12,7 +12,8 @@ setup.cfg
 setup.py
 towncrier_science.toml
 changelog/.gitempty
-changelog/81.misc.rst
+changelog/84.bugfix.rst
+changelog/84.misc.rst
 dkist_processing_cryonirsp/__init__.py
 dkist_processing_cryonirsp.egg-info/PKG-INFO
 dkist_processing_cryonirsp.egg-info/SOURCES.txt

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/dkist_processing_cryonirsp.egg-info/requires.txt

@@ -1,10 +1,10 @@
 Pillow==10.0.1
 astropy==5.3.2
-dkist-fits-specifications==3.9.0
-dkist-header-validator==4.1.0
-dkist-processing-common==5.0.0rc1
+dkist-fits-specifications==4.0.0rc5
+dkist-header-validator==5.0.0rc6
+dkist-processing-common==5.0.1rc1
 dkist-processing-math==2.0.0
-dkist-processing-pac==3.0.0
+dkist-processing-pac==3.0.1
 dkist-spectral-lines==2.0.0
 largestinteriorrectangle==0.2.0
 dkist-service-configuration==1.1.0
@@ -28,7 +28,7 @@ dkist-sphinx-theme
 [grogu]
 dkist
 pyparsing
-dkist-inventory
+dkist-inventory==1.2.2rc3
 
 [test]
 pytest
@@ -37,4 +37,4 @@ pytest-xdist
 pytest-mock
 hypothesis
 towncrier
-dkist-data-simulator
+dkist-data-simulator==5.0.0rc5

{dkist_processing_cryonirsp-0.0.23rc2 → dkist_processing_cryonirsp-0.0.25rc1}/setup.cfg

@@ -19,11 +19,11 @@ include_package_data = True
 install_requires = 
 	Pillow == 10.0.1
 	astropy == 5.3.2
-	dkist-fits-specifications == 3.9.0
-	dkist-header-validator == 4.1.0
-	dkist-processing-common == 5.0.0rc1
+	dkist-fits-specifications == 4.0.0rc5
+	dkist-header-validator == 5.0.0rc6
+	dkist-processing-common == 5.0.1rc1
 	dkist-processing-math == 2.0.0
-	dkist-processing-pac == 3.0.0
+	dkist-processing-pac == 3.0.1
 	dkist-spectral-lines == 2.0.0
 	largestinteriorrectangle == 0.2.0
 	dkist-service-configuration == 1.1.0
@@ -43,11 +43,11 @@ test =
 	pytest-mock
 	hypothesis
 	towncrier
-	dkist-data-simulator
+	dkist-data-simulator == 5.0.0rc5
 grogu = 
 	dkist
 	pyparsing
-	dkist-inventory
+	dkist-inventory == 1.2.2rc3
 docs = 
 	sphinx
 	sphinx-astropy

dkist_processing_cryonirsp-0.0.23rc2/changelog/81.misc.rst

@@ -1 +0,0 @@
-Adding manual processing worker capabilities via dkist-processing-common update.