Merge branch 'main' into ci/separate_devdeps

.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 @@
 1.4.5 (unreleased)
 ==================
 
+- Added ``alignment`` sub-package. [#179]
+
 Changes to API
 --------------
 
@@ -88,6 +90,17 @@ 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 +39,40 @@ 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),
+}
+
 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/resample_utils.py

@@ -0,0 +1,40 @@
+import logging
+import numpy as np
+from stcal.alignment import util
+from gwcs.wcstools import grid_from_bounding_box
+
+log = logging.getLogger(__name__)
+log.setLevel(logging.DEBUG)
+
+
+def calc_pixmap(in_wcs, out_wcs, shape=None):
+    """Return a pixel grid map from input frame to output frame
+
+    Parameters
+    ----------
+    in_wcs : `~astropy.wcs.WCS`
+        Input WCS objects or transforms.
+    out_wcs : `~astropy.wcs.WCS` or `~gwcs.wcs.WCS`
+        output WCS objects or transforms.
+    shape : tuple, optional
+        Shape of grid in pixels. The default is None.
+
+    Returns
+    -------
+    pixmap : ndarray of shape (xdim, ydim, 2)
+        Reprojected pixel grid map. `pixmap[xin, yin]` returns `xout,
+        yout` indices in the output image.
+    """
+    if shape:
+        bb = util.wcs_bbox_from_shape(shape)
+        log.debug("Bounding box from data shape: {}".format(bb))
+    else:
+        bb = util.wcs_bbox_from_shape(in_wcs.pixel_shape)
+        log.debug("Bounding box from WCS: {}".format(bb))
+
+    # creates 2 grids, one with rows of all x values * len(y) rows,
+    # and the reverse for all y columns
+    grid = grid_from_bounding_box(bb)
+    transform_function = util.reproject(in_wcs, out_wcs)
+    pixmap = np.dstack(transform_function(grid[0], grid[1]))
+    return pixmap