thuban 0.0.5__tar.gz → 0.0.6__tar.gz

thuban-0.0.6/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

thuban-0.0.6/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

{thuban-0.0.5 → thuban-0.0.6}/.github/workflows/ci_fixed.yaml

@@ -36,7 +36,7 @@ jobs:
         pip install ".[test]"
     - name: Test with pytest
       run: |
-        coverage run -m pytest
+        coverage run --branch --source=thuban/ -m pytest tests -m "not slow"
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       env:

{thuban-0.0.5 → thuban-0.0.6}/.pre-commit-config.yaml

@@ -3,14 +3,14 @@ repos:
   # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.3
+    rev: v0.11.4
     hooks:
       # Run the linter.
       - id: ruff
         types_or: [ python, pyi ]
         args: [ --fix ]
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunpy/extern)$"
@@ -29,3 +29,6 @@ repos:
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.json)$|^CITATION.rst$"
       - id: mixed-line-ending
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+ci:
+  autofix_prs: false
+  autoupdate_schedule: "quarterly"

thuban-0.0.6/CHANGELOG.md

@@ -0,0 +1,32 @@
+# Changelog
+
+[Also available through GitHub interface](https://github.com/punch-mission/thuban/releases)
+
+## Version 0.0.6: May 22, 2025
+
+* specify codecov path by @jmbhughes in https://github.com/punch-mission/thuban/pull/18
+* Update issue templates by @jmbhughes in https://github.com/punch-mission/thuban/pull/19
+* Support more PUNCH features in https://github.com/punch-mission/thuban/pull/25
+
+## Version 0.0.5: Nov 13, 2024
+
+- Fix version names in docs by @jmbhughes in #12
+- add tolerances by @jmbhughes in #13
+- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #14
+
+## Version 0.0.4: Nov 1, 2024
+
+- Add pinned environment ci by @jmbhughes in #10
+- Create .readthedocs.yaml by @jmbhughes in #11
+
+## Version 0.0.3: Aug 24, 2024
+
+- incorporates masking and pv by @jmbhughes in #8
+
+## Version 0.0.2: Aug 18, 2024
+
+- add file manifest by @jmbhughes in #7
+
+## Version 0.0.1: Aug 18, 2024
+
+Initial release

{thuban-0.0.5 → thuban-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: thuban
-Version: 0.0.5
+Version: 0.0.6
 Summary: High precision and accuracy astrometric image solving from a guess
 Author-email: "J. Marcus Hughes" <hughes.jmb@gmail.com>
 Maintainer-email: "J. Marcus Hughes" <hughes.jmb@gmail.com>
@@ -19,7 +19,7 @@ Requires-Dist: numpy
 Requires-Dist: astropy
 Requires-Dist: matplotlib
 Requires-Dist: pandas
-Requires-Dist: sep-pjw
+Requires-Dist: sep
 Requires-Dist: scipy
 Requires-Dist: scikit-learn
 Requires-Dist: lmfit
@@ -39,13 +39,14 @@ Requires-Dist: pydata-sphinx-theme; extra == "docs"
 Requires-Dist: sphinx-favicon; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: packaging; extra == "docs"
+Dynamic: license-file
 
 # thuban
 
 High precision astrometric image solving from a guess.
 
 > [!WARNING]
-> This package is not yet ready for production usage.
+> This package may still have significant changes until v1. 
 
 
 ## To-do

{thuban-0.0.5 → thuban-0.0.6}/README.md

@@ -3,7 +3,7 @@
 High precision astrometric image solving from a guess.
 
 > [!WARNING]
-> This package is not yet ready for production usage.
+> This package may still have significant changes until v1. 
 
 
 ## To-do

{thuban-0.0.5 → thuban-0.0.6}/pyproject.toml

@@ -10,7 +10,7 @@ dependencies = ["numpy",
     "astropy",
     "matplotlib",
     "pandas",
-    "sep-pjw",
+    "sep",
     "scipy",
     "scikit-learn",
     "lmfit",

{thuban-0.0.5 → thuban-0.0.6}/thuban/cli.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 import click
 import numpy as np
-import sep_pjw as sep
+import sep
 from astropy.io import fits
 from astropy.wcs import WCS
 from tqdm import tqdm
@@ -38,9 +38,8 @@ def open_files(paths: [Path], byte_swap=True) -> (np.ndarray, [fits.Header]):
     for filename in tqdm(paths):
         with fits.open(filename) as hdul:
             if byte_swap:
-                data = hdul[data_hdu_num].data.byteswap().newbyteorder().astype(float)
-            else:
-                data = hdul[data_hdu_num].data.astype(float)
+                raise NotImplementedError()
+            data = hdul[data_hdu_num].data.astype(float)
             head = hdul[data_hdu_num].header
             all_wcses.append(WCS(head, hdul, key=celestial_wcs_key))
         all_data.append(data)
@@ -79,8 +78,6 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
     # data[:, :edge, :] = 0.0
     # data[:, -edge:, :] = 0.0
     # data[:, :, -edge:] = 0.0
-
-    print(headers)
     current_wcses = [convert_cd_matrix_to_pc_matrix(w) for w in all_wcses]
 
     # remove any SIP distortion model and make an empty table
@@ -91,7 +88,6 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
         wcs.sip = None
         wcs.cpdis1 = cpdis1
         wcs.cpdis2 = cpdis2
-    print(current_wcses[0].wcs.cunit)
 
     counts = []
     for iteration in range(iterations):
@@ -110,13 +106,18 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
                                 current_wcses[file_index],
                                 file_index,
                                 detection_threshold=threshold,
-                                max_trials=5,
+                                max_trials=10,
                                 dimmest_magnitude=magnitude,
                                 num_stars=num_stars,
                                 background_width=background,
                                 background_height=background,
-                                chisqr_threshold=0.05,
-                                method='least_squares'))
+                                chisqr_threshold=0.1,
+                                max_error=150,
+                                method='least_squares',
+                                fix_crota=False,
+                                fix_crval=False,
+                                fix_pv=iteration == 0 or iteration == iterations - 1,
+                                fix_cdelt=True or iteration == iterations - 1 or iteration % 2 == 1))
 
         print("\tprocessing")
         with tqdm(total=len(futures)) as pbar:
@@ -124,21 +125,28 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
 
                 updated_wcs, _, solution, num_trials, file_index = future.result()
                 current_wcses[file_index] = updated_wcs
+                pbar.update(1)
 
+        global_pv = np.mean([w.wcs.get_pv()[0][-1] for w in current_wcses])
+        global_cdelt1 = np.mean([w.wcs.cdelt[0] for w in current_wcses])
+        global_cdelt2 = np.mean([w.wcs.cdelt[1] for w in current_wcses])
 
-                bg = sep.Background(data[file_index], bw=background, bh=background)
-                data_sub = data[file_index] - bg
-                objects = sep.extract(data_sub, threshold, err=bg.globalrms)
-                observed_coords = np.stack([objects["x"], objects["y"]], axis=-1)
+        for file_index in range(len(current_wcses)):
+            updated_wcs = current_wcses[file_index]
+            updated_wcs.wcs.cdelt = (global_cdelt1, global_cdelt2)
+            updated_wcs.wcs.set_pv([(2, 1, global_pv)])
 
-                new_stars = find_catalog_in_image(
-                    filter_for_visible_stars(load_hipparcos_catalog(), dimmest_magnitude=8.0),
-                    updated_wcs, data.shape[1:], mode='wcs')
-                all_no_distortion.append(np.stack([new_stars['x_pix'], new_stars['y_pix']], axis=-1))
+            bg = sep.Background(data[file_index], bw=background, bh=background)
+            data_sub = data[file_index] - bg
+            objects = sep.extract(data_sub, threshold, err=bg.globalrms)
+            observed_coords = np.stack([objects["x"], objects["y"]], axis=-1)
 
-                all_found_positions.append(observed_coords)
-                # all_no_distortion.append(no_distortion)
-                pbar.update(1)
+            new_stars = find_catalog_in_image(
+                filter_for_visible_stars(load_hipparcos_catalog(), dimmest_magnitude=8.0),
+                updated_wcs, data.shape[1:], mode='wcs')
+            all_no_distortion.append(np.stack([new_stars['x_pix'], new_stars['y_pix']], axis=-1))
+
+            all_found_positions.append(observed_coords)
 
         # log.append((all_corrected_positions, all_found_positions))
         # TODO: move lower to fix counting of stars
@@ -149,7 +157,7 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
         for i in range(len(all_no_distortion)):
             observed_filtered, refined_filtered = remove_pairless_points(all_found_positions[i],
                                                                          all_no_distortion[i],
-                                                                         max_distance=15)
+                                                                         max_distance=150)
             if (observed_filtered.ndim == 2 and refined_filtered.ndim == 2
                     and len(observed_filtered) > 0 and len(refined_filtered) > 0):
                 final_observations.append(observed_filtered)
@@ -164,6 +172,12 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
                                                         final_observations,
                                                         final_refined,
                                                         num_bins=num_bins)
+            if iteration != iterations - 1:
+                center_x_val = cpdis1.data[num_bins//2, num_bins//2]
+                center_y_val = cpdis2.data[num_bins//2, num_bins//2]
+
+                cpdis1.data -= center_x_val
+                cpdis2.data -= center_y_val
 
             for wcs in current_wcses:
                 wcs.cpdis1 = cpdis1
@@ -177,4 +191,4 @@ def determine_pointing_and_distortion(directory, byte_swap=True,  num_stars=20,
         _, extension = os.path.splitext(fn)
         hdul = updated_wcs.to_fits()  # improve the writing mechanism
         hdul[0].data = img
-        hdul.writeto(str(fn).replace(extension, "_repoint.fits"), overwrite=True)  # todo make postfix and option
+        hdul.writeto(str(fn).replace(extension, "_repoint.fits"), overwrite=True)  # todo make postfix an option

{thuban-0.0.5 → thuban-0.0.6}/thuban/distortion.py

@@ -131,7 +131,7 @@ def compute_distortion(
     img_shape: (int, int),
         catalog_positions: np.ndarray,
         found_positions: np.ndarray,
-        distortion_limit: float =20, num_bins: int =75, blur_sigma: float =4, med_filter_size: int=3
+        distortion_limit: float =20, num_bins: int =75, blur_sigma: float = 1, med_filter_size: int = 1
 ) -> (DistortionLookupTable, DistortionLookupTable):
     """ Given the derived catalog and actual star positions, determines the distortion
 

{thuban-0.0.5 → thuban-0.0.6}/thuban/pointing.py

@@ -4,7 +4,7 @@ from typing import Callable
 import astropy.units as u
 import numpy as np
 import pandas as pd
-import sep_pjw as sep
+import sep
 from astropy.wcs import WCS, utils
 from lmfit import Parameters, minimize
 
@@ -84,18 +84,15 @@ def _residual(params: Parameters,
     np.ndarray
         residual
     """
-    refined_wcs = WCS(naxis=2)
-    refined_wcs.wcs.ctype = guess_wcs.wcs.ctype
-    refined_wcs.wcs.cunit = guess_wcs.wcs.cunit
-    refined_wcs.wcs.cdelt = guess_wcs.wcs.cdelt
-    refined_wcs.wcs.crpix = guess_wcs.wcs.crpix
+    refined_wcs = guess_wcs.deepcopy()
+    refined_wcs.wcs.cdelt = (params['cdelt1'].value, params['cdelt2'].value)
     refined_wcs.wcs.crval = (params["crval1"].value, params["crval2"].value)
-    refined_wcs.wcs.pc = calculate_pc_matrix(params["crota"], refined_wcs.wcs.cdelt)
+    refined_wcs.wcs.pc = calculate_pc_matrix(params["crota"], (params['cdelt1'], params['cdelt2']))
     refined_wcs.cpdis1 = guess_wcs.cpdis1
     refined_wcs.cpdis2 = guess_wcs.cpdis2
-    refined_wcs.wcs.set_pv(guess_wcs.wcs.get_pv())
+    refined_wcs.wcs.set_pv([(2, 1, params['pv'].value)])
 
-    reduced_catalog = find_catalog_in_image(catalog, refined_wcs, image_shape=image_shape, mask=mask)
+    reduced_catalog = find_catalog_in_image(catalog, refined_wcs, image_shape=image_shape, mask=mask, mode='wcs')
     refined_coords = np.stack([reduced_catalog['x_pix'], reduced_catalog['y_pix']], axis=-1)
 
     image_bounds = (image_shape[0] - edge, image_shape[1] - edge)
@@ -119,7 +116,8 @@ def _residual(params: Parameters,
 def refine_pointing_wrapper(image, guess_wcs, file_num, observed_coords=None, catalog=None,
                     background_width=16, background_height=16,
                     detection_threshold=5, num_stars=30, max_trials=15, chisqr_threshold=0.1,
-                    dimmest_magnitude=6.0, method='leastsq', ra_tolerance=10, dec_tolerance=5, max_error=15):
+                    dimmest_magnitude=6.0, method='least_squares', ra_tolerance=10, dec_tolerance=5, max_error=15,
+                            fix_crval=False, fix_cdelt=True, fix_crota=False, fix_pv=True):
     new_wcs, observed_coords, solution, trial_num = refine_pointing(image,
                                                                     guess_wcs,
                                                                     observed_coords=observed_coords, catalog=catalog,
@@ -128,7 +126,9 @@ def refine_pointing_wrapper(image, guess_wcs, file_num, observed_coords=None, ca
                             chisqr_threshold=chisqr_threshold,
                     dimmest_magnitude=dimmest_magnitude, method=method,
                                                                     ra_tolerance=ra_tolerance,
-                                                                    dec_tolerance=dec_tolerance, max_error=max_error)
+                                                                    dec_tolerance=dec_tolerance, max_error=max_error,
+                                                                    fix_crval=fix_crval, fix_cdelt=fix_cdelt,
+                                                                    fix_crota=fix_crota, fix_pv=fix_pv)
     return new_wcs, observed_coords, solution, trial_num, file_num
 
 
@@ -141,30 +141,9 @@ def extract_crota_from_wcs(wcs: WCS) -> tuple[float, float]:
 def refine_pointing(image, guess_wcs, observed_coords=None, catalog=None,
                     background_width=16, background_height=16,
                     detection_threshold=5, num_stars=30, max_trials=15, chisqr_threshold=0.1,
-                    dimmest_magnitude=6.0, method='leastsq', edge=100, sigma=3.0, mask=None,
-                    ra_tolerance=10, dec_tolerance=5, max_error=15):
-    """ Refine the pointing for an image
-
-    Parameters
-    ----------
-    image : np.ndarray
-        the brightnesses of the image, no preprocessing necessary
-    guess_wcs : WCS
-        initial guess for th world coordinate system, must overlap with the true WCS
-    file_index
-    observed_coords
-    catalog
-    background_width
-    background_height
-    detection_threshold
-    x_lim
-    y_lim
-    n
-
-    Returns
-    -------
-
-    """
+                    dimmest_magnitude=6.0, method='least_squares', edge=100, sigma=3.0, mask=None,
+                    ra_tolerance=10, dec_tolerance=5, max_error=15,
+                    fix_crval=False, fix_cdelt=True, fix_crota=False, fix_pv=True):
     if catalog is None:
         catalog = filter_for_visible_stars(load_hipparcos_catalog(), dimmest_magnitude=dimmest_magnitude)
 
@@ -194,13 +173,26 @@ def refine_pointing(image, guess_wcs, observed_coords=None, catalog=None,
     # set up the optimization
     params = Parameters()
     initial_crota = extract_crota_from_wcs(guess_wcs)
-    params.add("crota", value=initial_crota.to(u.rad).value, min=-np.pi, max=np.pi)
+    params.add("crota", value=initial_crota.to(u.rad).value,
+               min=-np.pi, max=np.pi, vary=not fix_crota)
     params.add("crval1", value=guess_wcs.wcs.crval[0],
                min=guess_wcs.wcs.crval[0]-ra_tolerance,
-               max=guess_wcs.wcs.crval[0]+ra_tolerance, vary=True)
+               max=guess_wcs.wcs.crval[0]+ra_tolerance, vary=not fix_crval)
     params.add("crval2", value=guess_wcs.wcs.crval[1],
                min=guess_wcs.wcs.crval[1]-dec_tolerance,
-               max=guess_wcs.wcs.crval[1]+dec_tolerance, vary=True)
+               max=guess_wcs.wcs.crval[1]+dec_tolerance, vary=not fix_crval)
+    params.add("cdelt1", value=guess_wcs.wcs.cdelt[0],
+               min=guess_wcs.wcs.cdelt[0]-1,
+               max=guess_wcs.wcs.cdelt[0]+1, vary=not fix_cdelt)
+    params.add("cdelt2", value=guess_wcs.wcs.cdelt[1],
+               min=max(guess_wcs.wcs.cdelt[1]-0.1, 0),
+               max=guess_wcs.wcs.cdelt[1]+0.1, vary=not fix_cdelt)
+    # if guess_wcs.wcs.get_pv():
+    #     pv = guess_wcs.wcs.get_pv()[0][-1]
+    #     print(pv)
+    # else:
+    #     pv = 0.0
+    # params.add("pv", value=pv, min=0.0, max=1.0, vary=not fix_pv)
 
     # return guess_wcs, observed_coords, None, None
     # optimize
@@ -210,7 +202,8 @@ def refine_pointing(image, guess_wcs, observed_coords=None, catalog=None,
         try:
             out = minimize(_residual, params, method=method,
                            args=(observed_coords, catalog, guess_wcs,
-                                 num_stars, image.shape, edge, sigma, max_error, mask))
+                                 num_stars, image.shape, edge, sigma, max_error, mask),
+                           max_nfev=500, calc_covar=False)
             chisqr = out.chisqr
             result_minimizations.append(out)
         except IndexError:
@@ -220,16 +213,13 @@ def refine_pointing(image, guess_wcs, observed_coords=None, catalog=None,
                           ConvergenceWarning)
         else:
             # construct the result
-            result_wcs = WCS(naxis=2)
-            result_wcs.wcs.ctype = guess_wcs.wcs.ctype
-            result_wcs.wcs.cunit = guess_wcs.wcs.cunit
-            result_wcs.wcs.cdelt = guess_wcs.wcs.cdelt
-            result_wcs.wcs.crpix = guess_wcs.wcs.crpix
+            result_wcs = guess_wcs.deepcopy()
+            result_wcs.wcs.cdelt = (out.params["cdelt1"].value, out.params["cdelt2"].value)
             result_wcs.wcs.crval = (out.params["crval1"].value, out.params["crval2"].value)
             result_wcs.wcs.pc = calculate_pc_matrix(out.params["crota"], result_wcs.wcs.cdelt)
             result_wcs.cpdis1 = guess_wcs.cpdis1  # TODO: what if there is no known distortion
             result_wcs.cpdis2 = guess_wcs.cpdis2
-            result_wcs.wcs.set_pv(guess_wcs.wcs.get_pv())
+            result_wcs.wcs.set_pv([(2, 1, out.params['pv'].value)])
         result_wcses.append(result_wcs)
         trial_num += 1
         if chisqr < chisqr_threshold:

{thuban-0.0.5 → thuban-0.0.6}/thuban.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: thuban
-Version: 0.0.5
+Version: 0.0.6
 Summary: High precision and accuracy astrometric image solving from a guess
 Author-email: "J. Marcus Hughes" <hughes.jmb@gmail.com>
 Maintainer-email: "J. Marcus Hughes" <hughes.jmb@gmail.com>
@@ -19,7 +19,7 @@ Requires-Dist: numpy
 Requires-Dist: astropy
 Requires-Dist: matplotlib
 Requires-Dist: pandas
-Requires-Dist: sep-pjw
+Requires-Dist: sep
 Requires-Dist: scipy
 Requires-Dist: scikit-learn
 Requires-Dist: lmfit
@@ -39,13 +39,14 @@ Requires-Dist: pydata-sphinx-theme; extra == "docs"
 Requires-Dist: sphinx-favicon; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: packaging; extra == "docs"
+Dynamic: license-file
 
 # thuban
 
 High precision astrometric image solving from a guess.
 
 > [!WARNING]
-> This package is not yet ready for production usage.
+> This package may still have significant changes until v1. 
 
 
 ## To-do

{thuban-0.0.5 → thuban-0.0.6}/thuban.egg-info/SOURCES.txt

@@ -1,12 +1,15 @@
 .gitignore
 .pre-commit-config.yaml
 .readthedocs.yaml
+CHANGELOG.md
 CITATION.cff
 LICENSE
 MANIFEST.in
 README.md
 codecov.yaml
 pyproject.toml
+.github/ISSUE_TEMPLATE/bug_report.md
+.github/ISSUE_TEMPLATE/feature_request.md
 .github/workflows/ci.yaml
 .github/workflows/ci_fixed.yaml
 .github/workflows/publish.yaml

{thuban-0.0.5 → thuban-0.0.6}/thuban.egg-info/requires.txt

@@ -2,7 +2,7 @@ numpy
 astropy
 matplotlib
 pandas
-sep-pjw
+sep
 scipy
 scikit-learn
 lmfit