refactor: drop sip_tpv dependency, rely on astropy for TPV WCS

cailmdaley · cailmdaley · commit 995921b0dabd · 2026-04-23T10:52:06.000+02:00
Closes #713. The only functional use of sip_tpv in shapepipe was `split_exp.create_hdus` calling `stp.pv_to_sip(h)` to rewrite each per-CCD header's TPV distortion keywords as SIP before saving. Modern astropy (>=5) parses TPV natively via WCSLIB, as do SExtractor, PSFEx, and every other downstream WCS consumer in the pipeline, so the keyword-level conversion was no longer buying us anything. Removing the conversion lets us drop sip_tpv entirely — an unmaintained 2017 package whose v1.1 imports `pkg_resources` at module load and is incompatible with setuptools>=81 (the underlying cause of the ModuleNotFoundError in #713; PR #714's setuptools<81 pin is a symptom workaround). Changes: - split_exp: remove sip_tpv import + pv_to_sip call; drop the now-dead `transf_coord` plumbing through `process` / `create_hdus`; update module docstring accordingly. - Remove sip_tpv from `depends=[...]` in split_exp_runner, python_example_runner, and find_exposures_runner (the last was a spurious declaration — find_exposures_package never imported it). - Drop sip_tpv from environment.yml, environment-dev.yml, Dockerfile, install_shapepipe, docs/source/dependencies.md, and the orphan shupe:12 BibTeX entry. - New: `src/shapepipe/tests/test_split_exp.py` — three unittests that build a synthetic multi-CCD FITS with TPV distortion, run SplitExposures, and verify (1) per-CCD header WCS matches the source for several pixel samples, (2) the saved headers .npy round-trips pixel→world→pixel, (3) flag output uses int16. `scripts/jupyter/wcs.ipynb` still imports sip_tpv; it's an exploratory notebook last touched ~2.5 years ago and left alone.
diff --git a/Dockerfile b/Dockerfile
@@ -80,7 +80,6 @@ RUN pip install --no-cache-dir --upgrade pip && \
     pytest-pydocstyle==2.4.0 \
     reproject==0.14.1 \
     sf_tools==2.0.4 \
-    sip_tpv==1.1 \
     skaha==1.7.0 \
     sqlitedict==2.0.0 \
     termcolor==1.1.0 \
diff --git a/docs/source/dependencies.md b/docs/source/dependencies.md
@@ -20,7 +20,6 @@ reproducibility of the results. Below we list the main packages used.
 | [Numpy](https://numpy.org/) | {cite:p}`harris:20` |
 | [Pandas](https://pandas.pydata.org/) | {cite:p}`pandas:10,pandas:20` |
 | [sf_tools](https://github.com/sfarrens/sf_tools) | |
-| [sip_tpv](https://github.com/stargaser/sip_tpv) | {cite:p}`shupe:12` |
 | [sqlitedict](https://github.com/RaRe-Technologies/sqlitedict) | |
 | [TreeCorr](https://rmjarvis.github.io/TreeCorr/_build/html/index.html) | {cite:p}`jarvis:04` |
 
diff --git a/docs/source/refs.bib b/docs/source/refs.bib
@@ -736,22 +736,6 @@ @MISC{sheldon:15
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@INPROCEEDINGS{shupe:12,
-       author = {{Shupe}, David L. and {Laher}, Russ R. and {Storrie-Lombardi}, Lisa and {Surace}, Jason and {Grillmair}, Carl and {Levitan}, David and {Sesar}, Branimir},
-        title = "{More flexibility in representing geometric distortion in astronomical images}",
-    booktitle = {Software and Cyberinfrastructure for Astronomy II},
-         year = 2012,
-       editor = {{Radziwill}, Nicole M. and {Chiozzi}, Gianluca},
-       series = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series},
-       volume = {8451},
-        month = sep,
-          eid = {84511M},
-        pages = {84511M},
-          doi = {10.1117/12.925460},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2012SPIE.8451E..1MS},
-      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
 @article{spitzer:21,
         author = {{Spitzer}, I. et al.},
         title = "{Galaxy group and cluster masses from weak lensing in UNIONS}",
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -31,7 +31,6 @@ dependencies:
     - cs_util==0.0.5
     - mccd==1.2.4
     - modopt==1.6.1
-    - sip_tpv==1.1
     - sf_tools==2.0.4
     - git+https://github.com/CEA-COSMIC/pysap@develop
     - git+https://github.com/aguinot/ngmix@stable_version
diff --git a/environment.yml b/environment.yml
@@ -36,7 +36,6 @@ dependencies:
     - reproject
     - shear_psf_leakage
     - skaha
-    - sip_tpv
     - sf_tools
     - sqlitedict
     - termcolor
diff --git a/install_shapepipe b/install_shapepipe
@@ -237,7 +237,6 @@ site-packages() {
   check_site_pkg "pysap"
   check_site_pkg "scipy"
   check_site_pkg "sf_tools"
-  check_site_pkg "sip_tpv"
   check_site_pkg "sqlitedict"
   check_site_pkg "treecorr"
 }
diff --git a/src/shapepipe/modules/find_exposures_runner.py b/src/shapepipe/modules/find_exposures_runner.py
@@ -14,7 +14,7 @@
     version="1.1",
     file_pattern=["image"],
     file_ext=".fits",
-    depends=["numpy", "astropy", "sip_tpv"],
+    depends=["numpy", "astropy"],
     numbering_scheme="_0",
 )
 def find_exposures_runner(
diff --git a/src/shapepipe/modules/python_example_runner.py b/src/shapepipe/modules/python_example_runner.py
@@ -25,7 +25,6 @@
         "pysap",
         "scipy",
         "sf_tools",
-        "sip_tpv",
         "sqlitedict",
         "treecorr",
     ],
diff --git a/src/shapepipe/modules/split_exp_package/__init__.py b/src/shapepipe/modules/split_exp_package/__init__.py
@@ -28,9 +28,7 @@
     ``image``:
 
     1. Header is saved to numpy binary file (``.npy``);
-    2. Header WCS is saved in output FITS file header;
-    3. Geader WCS coordinates are transformed from pv to sip using the
-       ``sip_tpv`` package
+    2. Header WCS is saved in output FITS file header
 
     ``flag``: data is save as ``int16``
 
diff --git a/src/shapepipe/modules/split_exp_package/split_exp.py b/src/shapepipe/modules/split_exp_package/split_exp.py
@@ -11,7 +11,6 @@
 """
 
 import numpy as np
-import sip_tpv as stp
 from astropy.io import fits
 from astropy.wcs import WCS
 
@@ -62,16 +61,11 @@ def process(self):
         ):
 
             transf_int = "flag" in output_suffix
-            transf_coord = "image" in output_suffix
             save_header = "image" in output_suffix
 
-            self.create_hdus(
-                exp_path, output_suffix, transf_coord, transf_int, save_header
-            )
+            self.create_hdus(exp_path, output_suffix, transf_int, save_header)
 
-    def create_hdus(
-        self, exp_path, output_suffix, transf_coord, transf_int, save_header
-    ):
+    def create_hdus(self, exp_path, output_suffix, transf_int, save_header):
         """Create HDUs.
 
         Split a single exposures CCDs into separate files.
@@ -82,8 +76,6 @@ def create_hdus(
             Path to the single exposure
         output_suffix : str
             Suffix for the output file
-        transf_coord : bool
-            Transform the WCS (``pv`` to ``sip``) if ``True``
         transf_int : bool
             Set data types to int if ``True``
         save_header : bool
@@ -101,10 +93,7 @@ def create_hdus(
 
         for idx in range(1, self._n_hdu + 1):
 
-            # h = fits.getheader(exp_path, idx)
             h = hdu_list[idx].header
-            if transf_coord:
-                stp.pv_to_sip(h)
 
             # d = fits.getdata(exp_path, idx)
             try:
diff --git a/src/shapepipe/modules/split_exp_runner.py b/src/shapepipe/modules/split_exp_runner.py
@@ -15,7 +15,7 @@
     input_module="get_images_runner",
     file_pattern=["image", "weight", "flag"],
     file_ext=[".fz", ".fz", ".fz"],
-    depends=["numpy", "astropy", "sip_tpv"],
+    depends=["numpy", "astropy"],
     run_method="parallel",
 )
 def split_exp_runner(
diff --git a/src/shapepipe/tests/test_split_exp.py b/src/shapepipe/tests/test_split_exp.py
@@ -0,0 +1,164 @@
+"""UNIT TESTS FOR SPLIT_EXP.
+
+Verify that SplitExposures writes per-CCD FITS files whose WCS (including
+TPV distortion) round-trips correctly via astropy without requiring the
+sip_tpv package.
+
+"""
+
+import os
+import tempfile
+from unittest import TestCase
+
+import numpy as np
+import numpy.testing as npt
+from astropy.io import fits
+from astropy.wcs import WCS
+
+from shapepipe.modules.split_exp_package.split_exp import SplitExposures
+
+
+def _make_tpv_header(crval1, crval2):
+    """Build a synthetic MegaCam-style header with TPV distortion."""
+    h = fits.Header()
+    h["NAXIS"] = 2
+    h["NAXIS1"] = 64
+    h["NAXIS2"] = 64
+    h["CTYPE1"] = "RA---TPV"
+    h["CTYPE2"] = "DEC--TPV"
+    h["CRPIX1"] = 32.0
+    h["CRPIX2"] = 32.0
+    h["CRVAL1"] = crval1
+    h["CRVAL2"] = crval2
+    h["CD1_1"] = -5.16e-5
+    h["CD1_2"] = 0.0
+    h["CD2_1"] = 0.0
+    h["CD2_2"] = 5.16e-5
+    h["PV1_0"] = 0.0
+    h["PV1_1"] = 1.0
+    h["PV1_2"] = 0.0
+    h["PV1_4"] = 1.0e-4
+    h["PV2_0"] = 0.0
+    h["PV2_1"] = 1.0
+    h["PV2_2"] = 0.0
+    h["PV2_4"] = 1.0e-4
+    return h
+
+
+class SplitExpWCSRoundTripTestCase(TestCase):
+    """Split a synthetic multi-CCD exposure and verify WCS fidelity."""
+
+    def setUp(self):
+        self.tmpdir = tempfile.mkdtemp()
+        self.n_hdu = 3
+        self.file_number_string = "-0000001"
+        self.crvals = [
+            (180.0, 30.0),
+            (180.1, 30.0),
+            (180.0, 30.1),
+        ]
+        self.test_pixels = np.array([[1.0, 1.0], [32.0, 32.0], [60.0, 50.0]])
+
+        self.exp_path = os.path.join(self.tmpdir, "exp.fits")
+        primary = fits.PrimaryHDU()
+        ccds = [
+            fits.ImageHDU(
+                data=np.zeros((64, 64), dtype=np.float32),
+                header=_make_tpv_header(*self.crvals[i]),
+            )
+            for i in range(self.n_hdu)
+        ]
+        fits.HDUList([primary] + ccds).writeto(self.exp_path)
+
+    def tearDown(self):
+        for name in os.listdir(self.tmpdir):
+            os.remove(os.path.join(self.tmpdir, name))
+        os.rmdir(self.tmpdir)
+
+    def test_per_ccd_wcs_matches_source(self):
+        splitter = SplitExposures(
+            input_file_list=[self.exp_path],
+            output_dir=self.tmpdir,
+            file_number_string=self.file_number_string,
+            output_suffix=["image"],
+            n_hdu=self.n_hdu,
+        )
+        splitter.process()
+
+        with fits.open(self.exp_path) as src:
+            for idx in range(self.n_hdu):
+                src_world = WCS(src[idx + 1].header).wcs_pix2world(
+                    self.test_pixels, 1
+                )
+                out_path = os.path.join(
+                    self.tmpdir, f"image{self.file_number_string}-{idx}.fits"
+                )
+                with fits.open(out_path) as out:
+                    out_wcs = WCS(out[0].header)
+                    out_world = out_wcs.wcs_pix2world(self.test_pixels, 1)
+                    npt.assert_allclose(
+                        out_world,
+                        src_world,
+                        err_msg=f"CCD {idx}: world coords diverge from source",
+                    )
+                    npt.assert_allclose(
+                        out_wcs.wcs_world2pix(out_world, 1),
+                        self.test_pixels,
+                        atol=1e-6,
+                        err_msg=f"CCD {idx}: WCS does not round-trip",
+                    )
+
+    def test_headers_npy_roundtrips(self):
+        splitter = SplitExposures(
+            input_file_list=[self.exp_path],
+            output_dir=self.tmpdir,
+            file_number_string=self.file_number_string,
+            output_suffix=["image"],
+            n_hdu=self.n_hdu,
+        )
+        splitter.process()
+
+        headers = np.load(
+            os.path.join(self.tmpdir, f"headers{self.file_number_string}.npy"),
+            allow_pickle=True,
+        )
+        self.assertEqual(len(headers), self.n_hdu)
+        for idx, entry in enumerate(headers):
+            w = entry["WCS"]
+            world = w.wcs_pix2world(self.test_pixels, 1)
+            npt.assert_allclose(
+                w.wcs_world2pix(world, 1),
+                self.test_pixels,
+                atol=1e-6,
+                err_msg=f"Stored WCS for CCD {idx} does not round-trip",
+            )
+
+    def test_flag_output_uses_int16(self):
+        flag_exp = os.path.join(self.tmpdir, "flag.fits")
+        fits.HDUList(
+            [fits.PrimaryHDU()]
+            + [
+                fits.ImageHDU(
+                    data=np.ones((64, 64), dtype=np.float32) * 7,
+                    header=_make_tpv_header(*self.crvals[i]),
+                )
+                for i in range(self.n_hdu)
+            ]
+        ).writeto(flag_exp)
+
+        splitter = SplitExposures(
+            input_file_list=[flag_exp],
+            output_dir=self.tmpdir,
+            file_number_string=self.file_number_string,
+            output_suffix=["flag"],
+            n_hdu=self.n_hdu,
+        )
+        splitter.process()
+
+        for idx in range(self.n_hdu):
+            out_path = os.path.join(
+                self.tmpdir, f"flag{self.file_number_string}-{idx}.fits"
+            )
+            with fits.open(out_path) as out:
+                self.assertEqual(out[0].data.dtype.kind, "i")
+                self.assertEqual(out[0].data.dtype.itemsize, 2)

Original file line number	Diff line number	Diff line change
`@@ -237,7 +237,6 @@ site-packages() {`
`237`	`237`	`check_site_pkg "pysap"`
`238`	`238`	`check_site_pkg "scipy"`
`239`	`239`	`check_site_pkg "sf_tools"`
`240`		`- check_site_pkg "sip_tpv"`
`241`	`240`	`check_site_pkg "sqlitedict"`
`242`	`241`	`check_site_pkg "treecorr"`
`243`	`242`	`}`
Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@`
`14`	`14`	`version="1.1",`
`15`	`15`	`file_pattern=["image"],`
`16`	`16`	`file_ext=".fits",`
`17`		`- depends=["numpy", "astropy", "sip_tpv"],`
	`17`	`+ depends=["numpy", "astropy"],`
`18`	`18`	`numbering_scheme="_0",`
`19`	`19`	`)`
`20`	`20`	`def find_exposures_runner(`