Tweaks from Nabil

Author: nabobalis

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.13.3"
+    rev: "v0.14.0"
     hooks:
       - id: ruff
         args: ["--fix", "--unsafe-fixes"]
@@ -30,8 +30,8 @@ repos:
     hooks:
       - id: codespell
         args: [ "--write-changes" ]
-  - repo: https://github.com/crate-ci/typos
-    rev: v1
+  - repo: https://github.com/adhtruong/mirrors-typos
+    rev: v1.38.0
     hooks:
       - id: typos
   - repo: https://github.com/pre-commit/mirrors-mypy

changelog/290.breaking.rst

@@ -5,4 +5,4 @@ Increased the minimum required versions:
 - sunpy 7.0.0 (from 6.0.0)
 - NumPy 1.26.0 (from 1.23.5)
 - Astropy 6.1.0 (from 5.3.0)
-- SciPy 1.11.0 (from 1.10.1)
+- SciPy 1.12.0 (from 1.10.1)

docs/code_ref/coalignment.rst

@@ -11,6 +11,7 @@ The module supports various transformation methods registered via the `~sunkit_i
 .. automodapi:: sunkit_image.coalignment
 
 .. automodapi:: sunkit_image.coalignment.interface
+    :skip: coalign
 
 .. automodapi:: sunkit_image.coalignment.match_template
 

examples/aligning_aia_with_eis_maps.py

@@ -6,24 +6,19 @@
 This example shows how to coalign EIS rasters to AIA images in order correct for the pointing
 uncertainty in EIS.
 """
-# sphinx_gallery_thumbnail_number = 2
-
-
 import matplotlib.pyplot as plt
 
 import astropy.units as u
 from astropy.visualization import AsinhStretch, ImageNormalize
 
 import sunpy.map
-from sunpy.net import Fido
-from sunpy.net import attrs as a
 
 from sunkit_image.coalignment import coalign
 
 ###################################################################################
 # For this example, we will use a preprocessed EIS raster image of the Fe XII
-# 195.119 Å line. This raster image was prepared using the `eispac <https://eispac.readthedocs.io/en/latest/>`_ package.
-
+# 195.119 Å line.
+# This raster image was prepared using the `eispac <https://eispac.readthedocs.io/en/latest/>`__ package.
 
 eis_map = sunpy.map.Map("https://github.com/sunpy/data/raw/main/sunkit-image/eis_20140108_095727.fe_12_195_119.2c-0.int.fits")
 
@@ -33,13 +28,17 @@
 # 193 Å channel of AIA as it sees plasma at approximately the same temperature as
 # the 195.119 Å line in our EIS raster.
 
-query = Fido.search(
-    a.Time(start=eis_map.date-1*u.minute, near=eis_map.date, end=eis_map.date+1*u.minute),
-    a.Instrument.aia,
-    a.Wavelength(193*u.angstrom)
-)
-aia_file = Fido.fetch(query, site='NSO')
-aia_map = sunpy.map.Map(aia_file)
+# Below is the Fido query to search and download the AIA data.
+# from sunpy.net import Fido
+# from sunpy.net import attrs as a
+# query = Fido.search(
+#     a.Time(start=eis_map.date-1*u.minute, near=eis_map.date, end=eis_map.date+1*u.minute),
+#     a.Instrument.aia,
+#     a.Wavelength(193*u.angstrom)
+# )
+# aia_file = Fido.fetch(query, site='NSO')
+# For now though we have stored this file on Github so we can download it directly.
+aia_map = sunpy.map.Map("https://github.com/sunpy/data/raw/refs/heads/main/sunkit-image/aia.lev1.193A_2014_01_08T09_57_30.84Z.image_lev1.fits")
 
 ####################################################################################
 # Before coaligning the images, we first resample the AIA image to the same plate

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
   "astropy>=6.1.0",
   "numpy>=1.26.0",
   "matplotlib>=3.8.0",
-  "scipy>=1.11.0",
+  "scipy>=1.12.0",
   "scikit-image>=0.20.0",
   "sunpy[map]>=7.0.0",
 ]

sunkit_image/coalignment/__init__.py

@@ -1,6 +1,7 @@
 # Need to register the the coalignment functions
-import sunkit_image.coalignment.match_template
-import sunkit_image.coalignment.phase_cross_correlation
+from sunkit_image.coalignment.match_template import match_template_coalign  # isort:skip
+from sunkit_image.coalignment.phase_cross_correlation import phase_cross_correlation_coalign  # isort:skip
+
 from sunkit_image.coalignment.interface import coalign
 
 __all__ = ["coalign"]

sunkit_image/coalignment/interface.py

@@ -91,8 +91,6 @@ def _update_fits_wcs_metadata(target_map, reference_map, affine_params):
         new_reference_coordinate.Tx - target_map.reference_coordinate.Tx,
         new_reference_coordinate.Ty - target_map.reference_coordinate.Ty,
     )
-    # TODO: Support metadata updates to PCij/CDij and CDELT for non-unity scaling and
-    # rotation in the affine transform
 
 
 def _warn_user_of_separation(target_map, reference_map):
@@ -199,4 +197,4 @@ def coalign(target_map, reference_map, method='match_template', **kwargs):
 _coalignment_function_names = ", ".join([f"``'{name}'``" for name in REGISTERED_METHODS])
 # Insert into the docstring for coalign. We cannot use the add_common_docstring decorator
 # due to what would be a circular loop in definitions.
-coalign.__doc__ = coalign.__doc__.format(coalignment_function_names=_coalignment_function_names)  # type: ignore
+coalign.__doc__ = coalign.__doc__.format(coalignment_function_names=_coalignment_function_names)  # TYPE: IGNORE

sunkit_image/coalignment/phase_cross_correlation.py

@@ -38,13 +38,11 @@ def phase_cross_correlation_coalign(target_array, reference_array, **kwargs):
     """
     if target_array.shape != reference_array.shape:
         raise ValueError("Input and target arrays must be the same shape.")
-    if "upsample_factor" not in kwargs:
-        kwargs["upsample_factor"] = 20
     shift, _, _ = phase_cross_correlation(reference_array, target_array, **kwargs)
     # Shift has axis ordering which is consistent with the axis order of the input arrays, so y, x
-    # These are negative based on the example provided in the scikit-image documentation
+    # See the example here:
     # https://scikit-image.org/docs/stable/auto_examples/registration/plot_register_translation.html
-    x_shift, y_shift = -shift[1], -shift[0]
+    x_shift, y_shift = shift[1], shift[0]
     log.debug(f"Phase cross correlation shift: x: {x_shift}, y: {y_shift}")
     # Particularly for this method, there is no change in the rotation or scaling,
     # hence the hardcoded values of scale to 1.0 & rotation to identity matrix

sunkit_image/coalignment/tests/test_coalignment.py

@@ -7,16 +7,9 @@
 from astropy.io import fits
 
 import sunpy.map
-from sunpy.net import Fido
-from sunpy.net import attrs as a
 
 from sunkit_image.coalignment import coalign
-from sunkit_image.coalignment.interface import (
-    REGISTERED_METHODS,
-    AffineParams,
-    _update_fits_wcs_metadata,
-    register_coalignment_method,
-)
+from sunkit_image.coalignment.interface import AffineParams, _update_fits_wcs_metadata
 from sunkit_image.tests.helpers import figure_test
 
 
@@ -28,16 +21,12 @@ def eis_test_map():
 
 
 @pytest.fixture()
-def aia193_test_map(eis_test_map):
-    query = Fido.search(
-        a.Time(start=eis_test_map.date-1*u.minute,
-               end=eis_test_map.date+1*u.minute,
-               near=eis_test_map.date),
-        a.Instrument.aia,
-        a.Wavelength(193*u.angstrom),
-    )
-    file = Fido.fetch(query, site='NSO')
-    return sunpy.map.Map(file)
+def aia193_test_map():
+    # This is matched to the EIS observation time
+    url = "https://github.com/sunpy/data/raw/refs/heads/main/sunkit-image/aia.lev1.193A_2014_01_08T09_57_30.84Z.image_lev1.fits"
+    with fits.open(url) as hdul:
+        hdul.verify('silentfix')
+        return sunpy.map.Map(hdul[1].data, hdul[1].header)
 
 
 @pytest.mark.remote_data()
@@ -116,32 +105,18 @@ def test_coalignment_figure(incorrect_pointing_cutout_map, cutout_map, aia171_te
     return fig
 
 
-def test_register_coalignment_method():
-    @register_coalignment_method("test_method")
-    def test_func():
-        return "Test function"
-
-    assert "test_method" in REGISTERED_METHODS
-    assert REGISTERED_METHODS["test_method"] == test_func
-    assert test_func() == "Test function"
-
-
 def test_unsupported_affine_parameters(incorrect_pointing_cutout_map, aia171_test_map):
     affine_rot = AffineParams(
         scale=[1,1],
         rotation_matrix=2*np.eye(2),
         translation=[0,0],
     )
     with pytest.raises(NotImplementedError, match=r"Changes to the rotation metadata are currently not supported."):
-        _ = _update_fits_wcs_metadata(incorrect_pointing_cutout_map,
-                                      aia171_test_map,
-                                      affine_rot)
+        _update_fits_wcs_metadata(incorrect_pointing_cutout_map, aia171_test_map, affine_rot)
     affine_scale = AffineParams(
         scale=[2,3],
         rotation_matrix=np.eye(2),
         translation=[0,0],
     )
     with pytest.raises(NotImplementedError, match=r"Changes to the pixel scale metadata are currently not supported."):
-        _ = _update_fits_wcs_metadata(incorrect_pointing_cutout_map,
-                                      aia171_test_map,
-                                      affine_scale)
+        _update_fits_wcs_metadata(incorrect_pointing_cutout_map, aia171_test_map, affine_scale)

sunkit_image/coalignment/tests/test_interface.py

@@ -0,0 +1,11 @@
+from sunkit_image.coalignment.interface import REGISTERED_METHODS, register_coalignment_method
+
+
+def test_register_coalignment_method():
+    @register_coalignment_method("test_method")
+    def test_func():
+        return "Test function"
+
+    assert "test_method" in REGISTERED_METHODS
+    assert REGISTERED_METHODS["test_method"] == test_func
+    assert test_func() == "Test function"