dkist-processing-cryonirsp 1.3.4__py3-none-any.whl

docs/bad_pixel_calibration.rst

@@ -0,0 +1,47 @@
+Bad Pixel Calibration
+============================
+
+Introduction
+------------
+
+Both of the Cryo-NIRSP instrument cameras are known to have significant numbers of bad pixels.
+The effects of these are made worse by the linearization algorithm, which can force some pixels
+to be exactly zero. The algorithm described below is used to identify bad pixels and create a map
+of their locations. The map is an integer array of the same size as the camera output array, with
+zeros for pixels that are good and ones for the pixels that are bad.
+
+The Bad Pixel Map Algorithm
+------------------------------
+
+Compute Average Solar Gain Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+First we will compute an average solar gain image. The solar gain is used because it has high flux
+and the beam illumination pattern is the same as during normal observing.
+
+Smooth the Average Gain Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We can remove the effects of any bad pixels by smoothing the average gain image using a median filter method,
+filtering only along the spatial axis of the slit for SP data so as to not broaden the spectral lines, and
+filtering along both the spatial and spectral axes for CI data. After the gain image has been smoothed,
+the bad pixel areas should no longer be visible.
+
+Threshold the Difference Image to Find Bad Pixels
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next, we subtract the smoothed image from the average gain image. Doing this allows us to identify all
+pixels in the difference image whose absolute value is larger than a set threshold value times the standard
+deviation of the average image (i.e., a difference larger than N standard deviations of the original image is
+considered a bad pixel). The threshold value is a pipeline settable parameter and was derived
+empirically. With a too-low threshold, we start to pick up the solar spectrum in the bad pixel image. With a
+too-large threshold, we start to miss bad pixels. Moreover, we currently use bad pixel corrections only for the
+gain images and not for the observe images, so any potential impacts are limited. This may change in the
+future.
+
+Apply Bad Pixel Map
+^^^^^^^^^^^^^^^^^^^
+
+This bad pixel map is then applied to the lamp gain and solar gain by replacing the identified
+bad pixels with the median value of the input image over a specified region. This prevents the
+gain image from causing “hot” or “cold” pixels in the resulting gain corrected input images.

docs/beam_angle_calculation.rst

@@ -0,0 +1,53 @@
+Beam Angle Computation
+============================
+
+Introduction
+------------
+
+As part of the geometric calibration, the angular rotation of the slit relative to the image axes
+must be computed and then corrected. There is no fiducial mark or hairline present in the Cryo-NIRSP
+images, so some other method must be used. The angular rotation is derived from the lamp gain images using
+the algorithm described below. It is described for only a single beam, but is equally applicable to use for both
+beams.
+
+The Beam Angle Algorithm
+------------------------------
+
+Compute Average Lamp Gain Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We start by using the normalized lamp gain image that is computed as part of the lamp gain calibration.
+The image has been corrected for bad pixels (hot or cold) using the bad pixel map derived from average
+solar gain images (See :doc:`bad pixel calibration <bad_pixel_calibration>`).
+
+Compute the Normalized Spatial Gradient Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The normalized lamp gain image contains some some faint horizontal (i.e. along the spectral axis) lines. These are the result of slight
+imperfections in the slit and in the grating optics, and they can be used to derive the rotation of the slit axis
+relative to the image axes. By computing a normalized spatial gradient along the spatial axis (along the slit),
+we can enhance the faint horizontal lines to make them more pronounced. The gradient is computed by shifting the
+image along the spatial axis in both the + and - directions, computing the difference of the two images, and
+normalizing by the sum of the two at each pixel position. The resulting gradient image contains horizontal
+lines that are more emphasized.
+
+Compute the Angular Rotation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next we identify two long, narrow regions, or strips along the spatial axis. The length of each of the strips
+is one half of the slit length in pixels and they are centered about the mid-point of the length of the slit
+as seen on the sensor.
+
+We then compute the median value along the spectral axis (or rows). This condenses each strip into a 1D signal
+that represents the static fluctuations in the image along the spatial axis. The next step is to compute the
+cross correlation of the right signal relative to the left signal (the reference). The result is the measured
+shift of the right signal relative to the left. Using the measured shift between the signals and the known
+separation along the spectral axis between the midpoints of the strips, we can then compute the angular
+rotation using a simple arc-tangent.
+
+Correcting the Rotational Offset
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Finally, we can remove this rotational offset. The slit axis is now aligned with the spatial axis of the image.
+The angular rotation measured here using the lamp gain image is then used to correct all of the
+observe images as part of the geometric corrections.

docs/beam_boundary_computation.rst

@@ -0,0 +1,88 @@
+Beam Boundary Computation
+============================
+
+Introduction
+------------
+
+Raw Cryo-NIRSP frames are not fully illuminated; in some areas, there is no illumination at all.
+These areas should not be used for science processing and
+must be accounted for. Moreover, the illuminated region(s) will change slightly depending
+on the optical alignment of the instrument. Hence, we cannot use a particular set
+of beam boundary constants from which to extract the illuminated regions. Instead we need to
+compute these regions as part of the calibration process.
+
+The Beam Boundary Algorithm
+------------------------------
+
+The basic idea of the algorithm is to use an average solar gain image and apply a segmentation
+algorithm to it that separates the image into illuminated pixels and non-illuminated pixels.
+(Note: We use solar gain images because they have larger flux than the lamp gain images
+and the lamp gain images do not have the same illumination pattern as the solar
+gain images. Therefore, in order to make sure the beam boundaries match the on-sky data,
+and are as correct as they can be, we must use solar gain images. We only use a single frame because the
+illuminated portion of the CCD is always constant.)
+The segmentation must be robust enough to have all pixels within a well defined outer boundary
+considered to be illuminated. This is sufficient to extract an illuminated region from a single
+beam for the Context Imager (CI). For the Spectropolarimeter (SP), however, we need to identify
+the separate beam regions and perform an initial alignment prior to computing the final individual
+beam boundaries.
+
+Compute the Average Solar Gain Image
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We start by computing an average solar gain image. Because we are interested only in identifying
+the regions of the sensor that are illuminated, we do not need to perform any dark correction.
+Simply averaging the input solar gain images is sufficient.
+
+
+Correct Bad Pixels Using the Median Filter
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The effects of the bad pixels must be corrected, otherwise they might be mistaken for non-illuminated
+regions. We correct these bad pixels using the :doc:`bad pixel calibration algorithm <bad_pixel_calibration>`
+and by applying a median filter to only those pixels that are flagged as bad. We use the masked array feature
+of numpy to achieve this filtering. For the SP, the correction algorithm is applied only in the spatial
+direction along the slit. For the CI, it is applied along both axes. For this application, the
+difference does not matter, as all we are doing is identifying illuminated pixels. However, later on when
+the solar gain array is computed, the correction must not broaden the spectral lines and so the restriction
+is important.
+
+
+Segment the Image Into Illuminated and Non-Illuminated Regions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next we smooth the entire array so the image segmentation algorithm does not recognize the absorption
+lines as part of the non-illuminated region. The smoothed solar gain array is then used as the input to an
+image segmentation algorithm. The `Scikit Image threshold minimum <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_minimum>`_
+method is used to find the threshold between light and dark and this threshold is then
+used to generate a boolean map describing which pixels are illuminated (True) and which pixels are non-illuminated
+(False). However, this map cannot be used to easily extract illuminated regions because it is not guaranteed to be
+contiguous. Ideally, we would like to be able to identify a slice that can be used to extract the illuminated
+region as a rectangular array.
+
+
+Split Into Two Separate beam Images
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Now that we know the illuminated boundaries, we can identify and extract the largest inscribed rectangular
+region within the illuminated map. This is done using the `largestinteriorrectangle package <https://pypi.org/project/largestinteriorrectangle/>`_.
+We split the image into two beam images, avoiding a 10% spectral region
+surrounding the beam boundary in the middle of the image.
+
+Compute Relative Horizontal Shift of Right Beam to Left Beam
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There is a relative shift between these two images, so we need to determine that shift and compute the
+boundaries of each so that they overlap properly to within a single horizontal pixel. Note that the rotational
+differences and any additional shifts required to align the images are computed later as part of the geometric
+calibration. The horizontal shift of the right beam relative to the left is computed using the
+`Scikit Image phase cross correlation <https://scikit-image.org/docs/stable/api/skimage.registration.html#skimage.registration.phase_cross_correlation>`_
+method.
+
+Compute Beam Boundaries for Identical Size Overlapping Regions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+The final step is to use the shift to adjust the boundaries of each beam image such that both images
+have the same horizontal dimension and represent essentially the same spatial and spectral regions
+(as mentioned above, final adjustments will come later in the geometric calibration). Moreover the beam
+boundaries must be defined so that they represent slices into the original image and can then be used
+later to extract each beam from any type of input image (dark, gain, polcal, observe).

docs/changelog.rst

@@ -0,0 +1,7 @@
+Changelog
+*********
+
+.. changelog::
+    :towncrier:
+    :towncrier-skip-if-empty:
+    :changelog_file: ../CHANGELOG.rst

docs/ci_science_calibration.rst

@@ -0,0 +1,33 @@
+CI L1 Science Calibration
+=========================
+
+Introduction
+------------
+
+The `~dkist_processing_cryonirsp.tasks.ci_science` module takes L0 input science frames and fully calibrates
+them into L1 science products. This page describes the basic steps in this processes as well as important
+features of the Cryo-NIRSP Context Imager (CI) algorithm that may not be obvious.
+
+L1 Coordinate System
+^^^^^^^^^^^^^^^^^^^^
+
+The final step of the science pipeline places L1 data into a coordinate frame that matches the coordinates used by
+SDO/HMI and HINDOE-SP. Namely, -Q and +Q will be aligned parallel and perpendicular to the central meridian of the Sun,
+respectively.
+
+Algorithm
+---------
+
+Input CI science data is processed into L1 science data via the following steps:
+
+
+#.  Dark signals are subtracted from linearized input data.
+
+#.  :doc:`Bad Pixel correction <bad_pixel_calibration>` is done.
+
+#.  A solar gain calibration frame is divided from the data.
+
+#.  If data is polarimetric, demodulation matricies are applied.
+
+#.  If data is polarimetric, the Telescope Polarization is removed. This removes the polarization effects of all DKIST mirrors upstream
+    of Cryo-NIRSP. This step also includes the rotation into the coordinate frame described above.

docs/conf.py

@@ -0,0 +1,52 @@
+"""Configuration file for the Sphinx documentation builder."""
+# -- stdlib imports ------------------------------------------------------------
+import importlib
+import sys
+import warnings
+from importlib.metadata import distribution
+
+from dkist_sphinx_theme.conf import *
+from dkist_sphinx_theme.create_intersphinx_mapping import create_intersphinx_mapping
+from packaging.version import Version
+
+# Need a name for the overall repo
+# __name__ where this code executes is "builtins" so that is no help
+repo_name = "dkist-processing-cryonirsp"
+package_name = repo_name.replace("-", "_")
+
+dist = distribution(package_name)
+package = importlib.import_module(package_name)
+
+# -- Check for docs dependencies ----------------------------------------------------
+missing_requirements = missing_dependencies_by_extra(package_name, extras=["docs"])
+if missing_requirements["docs"]:
+    print(
+        f"The {' '.join(missing_requirements['docs'])} package(s) could not be found and "
+        "is needed to build the documentation, please install the 'docs' requirements."
+    )
+    sys.exit(1)
+
+# auto api parameters that cannot be moved into the theme:
+autoapi_dirs = [Path(package.__file__).parent]
+# Uncomment this for debugging
+# autoapi_keep_files = True
+
+# -- Options for intersphinx extension -----------------------------------------
+intersphinx_mapping = create_intersphinx_mapping(repo_name)
+# Remaining sphinx settings are in dkist-sphinx-theme conf.py
+
+# -- Project information -------------------------------------------------------
+project = "DKIST-PROCESSING-CRYONIRSP"
+
+# The full version, including alpha/beta/rc tags
+dkist_version = Version(dist.version)
+is_release = not (dkist_version.is_prerelease or dkist_version.is_devrelease)
+# We want to ignore all warnings in a release version.
+if is_release:
+    warnings.simplefilter("ignore")
+
+# Extensions so we can create the reqmts table and the workflow diagram
+extensions += [
+    "dkist_sphinx_theme.create_requirements_table",
+    "dkist_sphinx_theme.create_workflow_diagram",
+]

docs/index.rst

@@ -0,0 +1,21 @@
+.. include:: ../README.rst
+
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    self
+    l0_to_l1_cryonirsp_ci
+    l0_to_l1_cryonirsp_sp
+    l0_to_l1_cryonirsp_ci-full-trial
+    l0_to_l1_cryonirsp_sp-full-trial
+    scientific_changelog
+    linearization
+    bad_pixel_calibration
+    beam_boundary_computation
+    beam_angle_calculation
+    ci_science_calibration
+    sp_science_calibration
+    autoapi/index
+    requirements_table
+    changelog

docs/l0_to_l1_cryonirsp_ci-full-trial.rst

@@ -0,0 +1,10 @@
+l0_to_l1_cryonirsp_ci-full-trial
+================================
+
+This trial workflow is designed for pipeline testing internal to the DKIST Data Center (DC). It runs the full science
+pipeline, but stops short of publishing the results or activating downstream DC services. The pipeline products
+are transferred to an internal location where they can be examined by DC personnel or DKIST scientists.
+
+For more detail on each workflow task, you can click on the task in the diagram.
+
+.. workflow_diagram:: dkist_processing_cryonirsp.workflows.trial_workflows.full_trial_ci_pipeline

docs/l0_to_l1_cryonirsp_ci.rst

@@ -0,0 +1,10 @@
+l0_to_l1_cryonirsp_ci
+=====================
+
+In the normal Cryo-NIRSP Context Imager (CI) operating mode, raw Cryo-NIRSP data are gathered at the summit and
+delivered to the Data Center. The Data Center then calibrates this data and prepares it for storage using the
+following workflow.
+
+For more detail on each workflow task, you can click on the task in the diagram.
+
+.. workflow_diagram:: dkist_processing_cryonirsp.workflows.ci_l0_processing.l0_pipeline

docs/l0_to_l1_cryonirsp_sp-full-trial.rst

@@ -0,0 +1,10 @@
+l0_to_l1_cryonirsp_sp-full-trial
+================================
+
+This trial workflow is designed for pipeline testing internal to the DKIST Data Center (DC). It runs the full science
+pipeline, but stops short of publishing the results or activating downstream DC services. The pipeline products
+are transferred to an internal location where they can be examined by DC personnel or DKIST scientists.
+
+For more detail on each workflow task, you can click on the task in the diagram.
+
+.. workflow_diagram:: dkist_processing_cryonirsp.workflows.trial_workflows.full_trial_sp_pipeline

docs/l0_to_l1_cryonirsp_sp.rst

@@ -0,0 +1,10 @@
+l0_to_l1_cryonirsp_sp
+=====================
+
+In the normal Cryo-NIRSP Spectropolarimetric (SP) operating mode, raw Cryo-NIRSP data are gathered at the summit
+and delivered to the Data Center. The Data Center then calibrates this data and prepares it for storage using
+the following workflow.
+
+For more detail on each workflow task, you can click on the task in the diagram.
+
+.. workflow_diagram:: dkist_processing_cryonirsp.workflows.sp_l0_processing.l0_pipeline

docs/linearization.rst

@@ -0,0 +1,43 @@
+Linearization
+=============
+
+Introduction
+------------
+
+The Cryo-NIRSP camera has an H2RG detector, which has a non-linear response to light with
+increasing exposure time. This can vary from pixel to pixel. Because of the non-linear response, the count
+values at the final exposure do not accurately represent the light falling on the chip and therefore need to
+be corrected. We call this correction ‘linearization’. During an exposure, the camera
+reads out multiple frames and saves them while it continues to expose. The accumulated charge on the chip is
+not erased when this happens, so they are referred to as Non-Destructive Readouts (NDRs). The NDRs are
+saved at a pre-selected rate that is a fraction of the overall desired exposure time for a
+complete NDR. A set of NDRs with exposure times varying from 0 to the final desired exposure time are
+called a ramp. The linearization process reads all of the NDRs associated with a particular ramp and then
+applies an algorithm to compute what the final count values at the desired exposure time should be if the
+response of the detector was linear. Basically it takes the ramp set and "linearizes" it to produce a single
+NDR that has the correct counts at each pixel.
+
+A ramp can have many frames (anywhere from 10 to as much as 100, or more), and the linearization
+algorithm is agnostic to just about everything except the final exposure time. So after linearization, we
+have over 10x fewer frames to process, and the pipeline proceeds as though the linearized frames are raw input frames.
+
+The Linearization Algorithm
+---------------------------
+
+The Algorithm
+^^^^^^^^^^^^^
+
+First, we identify all NDRs from a single exposure of the Cryo-NIRSP cameras (i.e., a ramp set). A ramp is
+identified as all the files having the same DATE-OBS value. Note: If a ramp set contains only a single frame,
+it is discarded.
+
+Next, we need to identify the NDRs that fall in the “linear” portion of the chip response. These are those
+NDRs whose pixel value is below a pre-computed threshold value. I.e., the threshold values define the upper-limit
+of the linear response of each pixel.
+
+Then, we linearize this ramp set by normalizing the measured raw flux by the final ramp exposure time of the ramp set.
+Essentially, this removes the non-linear response of each pixel in the array. The resulting ramp set is essentially
+linear in ADUs v exposure time.
+
+Finally, we normalize the array by converting to counts per second and correct the counts for the Optical Density
+filter used during observations.

docs/make.bat

@@ -0,0 +1,170 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\Astropy.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\Astropy.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+:end

docs/requirements.txt

@@ -0,0 +1 @@
+# git deps for read the docs

docs/requirements_table.rst

@@ -0,0 +1,8 @@
+Package Requirements
+====================
+
+This table shows the main Python packages and their respective
+versions that were used to build the calibration codes documented
+here. All of these packages are available on `PyPI <https://pypi.org>`_.
+
+.. requirements_table:: dkist-processing-cryonirsp

docs/scientific_changelog.rst

@@ -0,0 +1,10 @@
+Scientific Changelog
+####################
+
+This page distills the verbosity of the :doc:`full Changelog <changelog>` into only those changes that affect the
+scientific quality of the L1 data.
+
+.. changelog::
+    :towncrier:
+    :towncrier-skip-if-empty:
+    :changelog_file: ../SCIENCE_CHANGELOG.rst

docs/sp_science_calibration.rst

@@ -0,0 +1,59 @@
+SP L1 Science Calibration
+=========================
+
+Introduction
+------------
+
+The `~dkist_processing_cryonirsp.tasks.sp_science` module takes L0 input science frames and fully calibrates
+them into L1 science products. This page describes the basic steps in this processes as well as important
+features of the Cryo-NIRSP Spectropolarimetric (SP) algorithm that may not be obvious.
+
+Important Features
+------------------
+
+Beam Combination
+^^^^^^^^^^^^^^^^
+
+Apart from the order in which the basic corrections are applied (described below), it is important to state how the two
+polarimetric beams of Cryo-NIRSP are combined to produce a single L1 data frame. After demodulation the 4 Stokes components of
+the two beams are combined thusly:
+
+.. math::
+
+  I_{comb} &= (I_1 + I_2) / 2 \\
+  Q_{comb} &= I_{comb} \left(\frac{Q_1}{I_1} + \frac{Q_2}{I_2}\right) / 2 \\
+  U_{comb} &= I_{comb} \left(\frac{U_1}{I_1} + \frac{U_2}{I_2}\right) / 2 \\
+  V_{comb} &= I_{comb} \left(\frac{V_1}{I_1} + \frac{V_2}{I_2}\right) / 2,
+
+where numbered subscripts correspond to beam number. This combination scheme improves the signal-to-noise of the data
+and mitigates residual polarization artifacts caused by temporal-based modulation (e.g., atmospheric seeing).
+
+L1 Coordinate System
+^^^^^^^^^^^^^^^^^^^^
+
+The final step of the science pipeline places L1 data into a coordinate frame that matches the coordinates used by
+SDO/HMI and HINDOE-SP. Namely, -Q and +Q will be aligned parallel and perpendicular to the central meridian of the Sun,
+respectively.
+
+Algorithm
+---------
+
+Input SP science data is processed into L1 science data via the following steps:
+
+#.  Dark signals are subtracted from linearized input data.
+
+#.  :doc:`Bad Pixel correction <bad_pixel_calibration>` is done.
+
+#.  A solar gain calibration frame is divided from the data.
+
+#.  If data is polarimetric, demodulation matrices are applied.
+
+#.  Geometric distortions (spectral rotation, x/y shift, spectral curvature) are removed via interpolation.
+    This step aligns the dispersion axis with a pixel axis, places both beams on the same pixel grid, and
+    straightens the spectra so that a single spectral pixel corresponds to the same physical wavelength for
+    all locations along the slit.
+
+#.  The beams are combined as described above. For non-polarimetric data, the combination is a simple average.
+
+#.  If data is polarimetric, the Telescope Polarization is removed. This removes the polarization effects of all DKIST mirrors upstream
+    of Cryo-NIRSP. This step also includes the rotation into the coordinate frame described above.

licenses/LICENSE.rst

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