Adding stcal-alignment sub-package.

.github/workflows/ci.yml

@@ -5,11 +5,13 @@ on:
     branches:
       - main
       - '*x'
+      - stcal-alignment
     tags:
       - '*'
   pull_request:
     branches:
       - main
+      - stcal-alignment
   schedule:
     # Weekly Monday 9AM build
     - cron: "0 9 * * 1"

.gitignore

@@ -51,6 +51,8 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+coverage/
+cov.xml
 
 # Translations
 *.mo
@@ -86,7 +88,7 @@ ipython_config.py
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -143,4 +145,7 @@ src/stcal/_version.py
 
 # auto-generated API docs
 docs/source/api
-.DS_Store
+.DS_Store
+
+# VSCode stuff
+.vscode

CHANGES.rst

@@ -1,6 +1,8 @@
 1.4.3 (unreleased)
 ==================
 
+- Added ``alignment`` sub-package. [#179]
+
 Other
 -----
 
@@ -50,6 +52,17 @@ Bug Fixes
 jump
 ~~~~
 
+- Added setting of number_extended_events for non-multiprocessing
+  mode. This is the value that is put into the header keyword EXTNCRS. [#178]
+
+1.4.1 (2023-06-29)
+
+Bug Fixes
+---------
+
+jump
+~~~~
+
 - Added statement to prevent the number of cores used in multiprocessing from
   being larger than the number of rows. This was causing some CI tests to fail. [#176]
 

docs/Makefile

@@ -6,6 +6,7 @@
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 BUILDDIR      = _build
+APIDIR        = api
 
 # Internal variables
 ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
@@ -25,6 +26,7 @@ help:
 
 clean:
 	-rm -rf $(BUILDDIR)/*
+	-rm -rf $(APIDIR)/*
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

docs/api.rst

@@ -1,4 +1,4 @@
-stcall API
+stcal API
 ==========
 
 .. automodapi:: stcal

docs/conf.py

@@ -4,11 +4,12 @@
 from pathlib import Path
 
 import stsci_rtd_theme
+
 if sys.version_info < (3, 11):
     import tomli as tomllib
 else:
     import tomllib
-    
+
 
 def setup(app):
     try:
@@ -27,7 +28,7 @@ def setup(app):
 # values here:
 with open(REPO_ROOT / "pyproject.toml", "rb") as configuration_file:
     conf = tomllib.load(configuration_file)
-setup_metadata = conf['project']
+setup_metadata = conf["project"]
 
 project = setup_metadata["name"]
 primary_author = setup_metadata["authors"][0]
@@ -38,19 +39,41 @@ def setup(app):
 version = package.__version__.split("-", 1)[0]
 release = package.__version__
 
+# Configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/devdocs", None),
+    "scipy": ("http://scipy.github.io/devdocs", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "gwcs": ("https://gwcs.readthedocs.io/en/latest/", None),
+    "astropy": ("https://docs.astropy.org/en/stable/", None),
+    "stdatamodels": ("https://stdatamodels.readthedocs.io/en/latest/", None),
+}
+
 extensions = [
+    "pytest_doctestplus.sphinx.doctestplus",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
     "sphinx_automodapi.automodapi",
-    "numpydoc",
+    "sphinx_automodapi.automodsumm",
+    "sphinx_automodapi.autodoc_enhancements",
+    "sphinx_automodapi.smart_resolver",
+    "sphinx_asdf",
+    "sphinx.ext.mathjax",
 ]
 
 autosummary_generate = True
 numpydoc_show_class_members = False
 autoclass_content = "both"
 
 html_theme = "stsci_rtd_theme"
-html_theme_options = {
-    "collapse_navigation": True
-}
+html_theme_options = {"collapse_navigation": True}
 html_theme_path = [stsci_rtd_theme.get_html_theme_path()]
 html_domain_indices = True
 html_sidebars = {"**": ["globaltoc.html", "relations.html", "searchbox.html"]}

docs/stcal/alignment/description.rst

@@ -0,0 +1,4 @@
+Description
+============
+
+This sub-package contains all the modules common to all missions.

docs/stcal/alignment/index.rst

@@ -0,0 +1,12 @@
+.. _alignment:
+
+===============
+Alignment Utils
+===============
+
+.. toctree::
+   :maxdepth: 2
+
+   description.rst
+
+.. automodapi:: stcal.alignment

docs/stcal/package_index.rst

@@ -6,3 +6,4 @@ Package Index
 
    jump/index.rst
    ramp_fitting/index.rst
+   alignment/index.rst

pyproject.toml

@@ -16,18 +16,21 @@ dependencies = [
     'scipy >=1.6.0',
     'numpy >=1.20',
     'opencv-python-headless >=4.6.0.66',
+    'asdf >=2.15.0',
+    'gwcs >= 0.18.1',
 ]
 dynamic = ['version']
 
 [project.optional-dependencies]
 docs = [
     'numpydoc',
     'packaging >=17',
-    'sphinx',
+    'sphinx<7.0.0',
+    'sphinx-asdf',
     'sphinx-astropy',
     'sphinx-rtd-theme',
     'stsci-rtd-theme',
-    'tomli; python_version <"3.11"',
+    'tomli; python_version <="3.11"',
 ]
 test = [
     'psutil',

src/stcal/alignment/__init__.py

@@ -0,0 +1 @@
+from .util import *  # noqa: F403

src/stcal/alignment/reproject.py

@@ -0,0 +1,89 @@
+import gwcs
+import numpy as np
+from astropy import wcs as fitswcs
+from astropy.modeling import Model
+from typing import Union
+
+
+def reproject_coords(wcs1, wcs2):
+    """
+    Given two WCSs or transforms return a function which takes pixel
+    coordinates in the first WCS or transform and computes them in pixel coordinates
+    in the second one. It performs the forward transformation of ``wcs1`` followed by the
+    inverse of ``wcs2``.
+
+    Parameters
+    ----------
+    wcs1, wcs2 : `~astropy.wcs.WCS` or `~gwcs.wcs.WCS` or `~astropy.modeling.Model`
+        WCS objects.
+
+    Returns
+    -------
+    _reproject : func
+        Function to compute the transformations.  It takes x, y
+        positions in ``wcs1`` and returns x, y positions in ``wcs2``.
+    """
+
+    def _get_forward_transform_func(wcs1):
+        """Get the forward transform function from the input WCS. If the wcs is a
+        fitswcs.WCS object all_pix2world requres three inputs, the x (str, ndarrray),
+        y (str, ndarray), and origin (int). The origin should be between 0, and 1
+        https://docs.astropy.org/en/latest/wcs/index.html#loading-wcs-information-from-a-fits-file
+        )
+        """ # noqa : E501
+        if isinstance(wcs1, fitswcs.WCS):
+            forward_transform = wcs1.all_pix2world
+        elif isinstance(wcs1, gwcs.WCS):
+            forward_transform = wcs1.forward_transform
+        elif issubclass(wcs1, Model):
+            forward_transform = wcs1
+        else:
+            raise TypeError(
+                "Expected input to be astropy.wcs.WCS or gwcs.WCS "
+                "object or astropy.modeling.Model subclass"
+            )
+        return forward_transform
+
+    def _get_backward_transform_func(wcs2):
+        if isinstance(wcs2, fitswcs.WCS):
+            backward_transform = wcs2.all_world2pix
+        elif isinstance(wcs2, gwcs.WCS):
+            backward_transform = wcs2.backward_transform
+        elif issubclass(wcs2, Model):
+            backward_transform = wcs2.inverse
+        else:
+            raise TypeError(
+                "Expected input to be astropy.wcs.WCS or gwcs.WCS "
+                "object or astropy.modeling.Model subclass"
+            )
+        return backward_transform
+
+    def _reproject(x: Union[str, np.ndarray], y: Union[str, np.ndarray]) -> tuple:
+        """
+        Reprojects the input coordinates from one WCS to another.
+
+        Parameters:
+        -----------
+        x : str or np.ndarray
+            Array of x-coordinates to be reprojected.
+        y : str or np.ndarray
+            Array of y-coordinates to be reprojected.
+
+        Returns:
+        --------
+        tuple
+            Tuple of reprojected x and y coordinates.
+        """
+        # example inputs to resulting function (12, 13, 0) # third number is origin
+        if not isinstance(x, list):
+            x = [x]
+        if not isinstance(y, list):
+            y = [y]
+        if len(x) != len(y):
+            raise ValueError("x and y must be the same length")
+        sky = _get_forward_transform_func(wcs1)(x, y, 0)
+        sky_back = np.array(_get_backward_transform_func(wcs2)(sky[0], sky[1], 0))
+        new_sky = tuple(sky_back[:, :1].flatten())
+        return tuple(new_sky)
+
+    return _reproject

src/stcal/alignment/testing_reproject.ipynb

@@ -0,0 +1,79 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from reproject import reproject_coords\n",
+    "from stwcs.wcsutil import HSTWCS\n",
+    "from astropy.wcs import WCS\n",
+    "from astropy.io import fits\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(2999.9999999998668, 2999.9999999999286)"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "hdu1=fits.open('hst_12546_22_acs_wfc_f606w_jbt122x1_drc.fits')\n",
+    "hdu2=fits.open('hst_12546_22_acs_wfc_f814w_jbt122_drc.fits')\n",
+    "wcs1=WCS(hdu1[1].header)\n",
+    "wcs2=WCS(hdu2[1].header)\n",
+    "# wcs2 = HSTWCS('jcdm74guq_drc.fits', ext=1)\n",
+    "f = reproject_coords(wcs1, wcs2)\n",
+    "f([3000], [3000])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}