hyper-py-photometry 0.1.0__tar.gz → 0.1.2__tar.gz

hyper_py_photometry-0.1.2/.github/workflows/Hyper-py_paper.yml

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+name: JOSS PDF
+
+on:
+  push:
+    paths:
+      - paper/**
+      - .github/workflows/Hyper-py_paper.yml
+  workflow_dispatch:  # allow manual trigger
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Hyper-py JOSS paper
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Build Hyper JOSS paper PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper/paper.md  # adjust only if your .md file is not renamed
+
+      - name: Upload compiled PDF
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          path: paper/*.pdf

hyper_py_photometry-0.1.2/.github/workflows/pypi-publish.yml

@@ -0,0 +1,80 @@
+name: Release to PyPI (on tag)
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout (with tags)
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Derive version from tag
+        run: echo "PKG_VERSION=${GITHUB_REF_NAME#v}" >> $GITHUB_ENV
+
+      - name: Build sdist + wheel (version from tag)
+        env:
+          SETUPTOOLS_SCM_PRETEND_VERSION: ${{ env.PKG_VERSION }}
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build
+          python -m twine check dist/*
+
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+      contents: read
+    if: startsWith(github.ref, 'refs/tags/v')  # publish only on tags
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI via OIDC
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+
+  release_assets:
+    needs: build
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    permissions:
+      contents: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: GitHub Release (attach artifacts)
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ github.ref_name }}
+          files: dist/*
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

hyper_py_photometry-0.1.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+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
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+.DS_Store
+
+/Git_Ignore
+test/test_2dmap.config.yaml
+test/output/

hyper_py_photometry-0.1.2/.vscode/launch.json

@@ -0,0 +1,18 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+
+        {
+            "name": "Python Debugger: Current File",
+            "type": "debugpy",
+            "request": "launch",
+            // "program": "${workspaceFolder}/src/hyper_py/run_hyper.py",
+            "program": "${workspaceFolder}/test/test_hyper.py", 
+            "console": "integratedTerminal",
+            "args": ["${workspaceFolder}/src/hyper_py/config.yaml"],
+            "env": {
+                "MPLBACKEND": "TkAgg"
+            }
+        }
+    ]
+}

hyper_py_photometry-0.1.2/IDL_comparison/Gaussian_comparison_Hyper_py_IDL_ALL.py

@@ -0,0 +1,276 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Comparison of Reference catalog vs Hyper-py and Hyper-IDL per map, 
+with direct IDL-vs-py scatter plots and combined percentage difference histograms.
+@author: alessio
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import font_manager
+from astropy.table import Table
+from astropy import coordinates as coords
+from astropy import units as u
+
+# ################## Parameters ##################
+num_sources = 500
+n_sigma = 4
+tot_maps = 2
+tolerance = 0.02 * u.arcsec
+legend_properties = font_manager.FontProperties(weight='bold', size=12)
+
+# Beam and pixel info for unit conversion (deg)
+bmaj = 1.335631849037E-05
+bmin = 1.069115267860E-05
+cdelt = 3.611111108576E-06
+
+beam_area_sr = 1.1331 * bmaj * bmin
+pix_area_deg2 = cdelt**2
+beam_area_pix = beam_area_sr / pix_area_deg2
+
+# Paths
+dir_in_ref = "/Users/alessio/Dropbox/Work/Python/Hyper/IDL_comparison/"
+dir_in_py  = "/Users/alessio/Dropbox/Work/Python/Hyper/IDL_comparison/"
+dir_in_idl = "/Users/alessio/Dropbox/Work/Python/Hyper/IDL_comparison/"
+dir_out    = "/Users/alessio/Dropbox/Work/Python/Hyper/IDL_comparison/output/"
+
+background = 'polynomial'
+table_combined_stats = dir_out + 'combined_source_counts_comparison.txt'
+
+# Summary table
+summary_table = Table(
+    names=['Catalog', 'Source_Type', 'Total', 'Matched', 'False', 'False_Percentage'],
+    dtype=['i4', 'S10', 'i4', 'i4', 'i4', 'f4']
+)
+
+# ================== Helper Functions ==================
+def match_catalogs(cat_coords, ref_coords):
+    sep = ref_coords[:, None].separation(cat_coords[None, :])
+    min_sep = sep.min(axis=1)
+    min_idx = sep.argmin(axis=1)
+    matched = min_sep < tolerance
+    _, unique_idx = np.unique(min_idx[matched], return_index=True)
+    filtered = np.zeros_like(matched, dtype=bool)
+    filtered[np.where(matched)[0][unique_idx]] = True
+    return filtered, min_idx
+
+def scatter_comparison(ref_vals, cat_vals, flux_type, ylabel, label, color, marker, suffix):
+    plt.figure(figsize=(8, 6))
+    plt.scatter(ref_vals, cat_vals, color=color, marker=marker, label=label)
+    minf = min(np.min(ref_vals), np.min(cat_vals))
+    maxf = max(np.max(ref_vals), np.max(cat_vals))
+    
+    # plt.xlim(0, 1800)
+    # plt.ylim(0, 1800)
+
+    plt.plot([minf, maxf], [minf, maxf], 'k--', label='1:1 Line')
+    plt.xlabel(f'{flux_type} ($\mu$Jy)', fontsize=14, fontweight='bold')
+    plt.ylabel(ylabel, fontsize=14, fontweight='bold')
+    plt.legend(prop=legend_properties)
+    plt.title(f'{flux_type} Comparison: {label}', fontsize=16, fontweight='bold')
+    plt.tick_params(axis='both', labelsize=12, width=2)
+    for tick in plt.gca().get_xticklabels() + plt.gca().get_yticklabels():
+        tick.set_fontweight('bold')
+    ax = plt.gca()
+    for side in ['top', 'bottom', 'left', 'right']:
+        ax.spines[side].set_linewidth(2)
+    plt.savefig(f'{dir_out}Flux_Comparison_{suffix}.png')
+    plt.close()
+
+def plot_flux_difference_histogram(ref_list, py_list, idl_list, flux_type, filename):
+    ref_all = np.concatenate(ref_list)
+    py_all = np.concatenate(py_list)
+    idl_all = np.concatenate(idl_list)
+
+    # Percentage differences
+    diff_py = 100. * (py_all - ref_all) / ref_all
+    diff_idl = 100. * (idl_all - ref_all) / ref_all
+
+    plt.figure(figsize=(8, 6))
+    bins = np.linspace(
+        min(diff_py.min(), diff_idl.min()),
+        max(diff_py.max(), diff_idl.max()),
+        50
+    )
+    
+    plt.hist(diff_py, bins=bins, alpha=0.6, label='Hyper-py - Ref', color='blue', edgecolor='black')
+    plt.hist(diff_idl, bins=bins, alpha=0.6, label='Hyper-IDL - Ref', color='green', edgecolor='black')
+
+    for diff, label, color in [(diff_py, 'py', 'blue'), (diff_idl, 'idl', 'green')]:
+        mean = np.mean(diff)
+        median = np.median(diff)
+        plt.axvline(mean, color=color, linestyle='--', linewidth=2, label=f'Mean {label}: {mean:.1f}%')
+        plt.axvline(median, color=color, linestyle=':', linewidth=2, label=f'Median {label}: {median:.1f}%')
+
+    plt.xlabel(f'{flux_type} Difference (% vs Reference)', fontsize=14, fontweight='bold')
+    plt.ylabel('Counts', fontsize=14, fontweight='bold')
+    plt.title(f'{flux_type} Difference: Hyper-py & Hyper-IDL vs Reference', fontsize=16, fontweight='bold')
+    plt.legend(prop=legend_properties)
+    plt.tick_params(axis='both', labelsize=12, width=2)
+    for tick in plt.gca().get_xticklabels() + plt.gca().get_yticklabels():
+        tick.set_fontweight('bold')
+    ax = plt.gca()
+    for side in ['top', 'bottom', 'left', 'right']:
+        ax.spines[side].set_linewidth(2)
+    plt.savefig(f'{dir_out}{filename}')
+    plt.close()
+
+# Containers for histograms
+py_all_hyper_py_id, py_all_hyper_idl_id, ref_all_peak, py_all_peak, idl_all_peak = [], [], [], [], []
+ref_all_int, py_all_int, idl_all_int = [], [], []
+
+# ================== Loop Over Maps ==================
+for i in range(1, tot_maps + 1):
+    ref = Table.read(f'{dir_in_ref}table_{num_sources}_Gaussians_{i}.txt', format='ipac')
+    ref['RA'] = ref['RA'] * u.deg
+    ref['DEC'] = ref['DEC'] * u.deg
+    coords_ref = coords.SkyCoord(ra=ref['RA'], dec=ref['DEC'])
+
+    hpy = Table.read(f'{dir_in_py}hyper_output_map_{num_sources}_Gaussians_{i}.txt', format='ipac')
+    coords_py = coords.SkyCoord(ra=hpy['RA'], dec=hpy['DEC'])
+
+    hidl = Table.read(f'{dir_in_idl}photometry_sources_1300_ellipses_1300_{background}_background_'+str(n_sigma)+f'sigma_ipac_{i}.txt', format='ipac')
+    coords_idl = coords.SkyCoord(ra=hidl['ra'], dec=hidl['dec'])
+
+    # Match each to reference
+    m_py, idx_py = match_catalogs(coords_py, coords_ref)
+    m_idl, idx_idl = match_catalogs(coords_idl, coords_ref)
+
+    matched_py = hpy[idx_py[m_py]]
+    ref_matched_py = ref[m_py]
+    false_py = len(hpy) - len(matched_py)
+    summary_table.add_row([i, 'Hyper-py', len(ref), len(matched_py), false_py, false_py / len(hpy) * 100.])
+
+    matched_idl = hidl[idx_idl[m_idl]]
+    ref_matched_idl = ref[m_idl]
+    false_idl = len(hidl) - len(matched_idl)
+    summary_table.add_row([i, 'Hyper-IDL', len(ref), len(matched_idl), false_idl, false_idl / len(hidl) * 100.])
+
+
+    # Save IDs #
+    hyper_py_id = matched_py['HYPER_ID']
+    hyper_idl_id = matched_idl['HYPER_ID']
+
+    # Peak Flux plots
+    flux_peak_py_mjy = matched_py['FLUX_PEAK'] * beam_area_pix
+    flux_peak_idl_mjy = matched_idl['FLUX_PEAK_JY']
+
+    scatter_comparison(ref_matched_py['Flux_Peak'] * 1e6, flux_peak_py_mjy * 1e3, 'Flux Peak', 'Measured Flux Peak ($\mu$Jy)', 'Hyper-py', 'blue', 'o', f'Hyper_py_Peak_{i}')
+    scatter_comparison(ref_matched_idl['Flux_Peak'] * 1e6, flux_peak_idl_mjy * 1e3, 'Flux Peak', 'Measured Flux Peak ($\mu$Jy)', 'Hyper-IDL', 'green', 's', f'Hyper_IDL_Peak_{i}')
+
+    # Integrated Flux plots
+    scatter_comparison(ref_matched_py['Flux_Integrated'] * 1e6, matched_py['FLUX'] * 1e3, 'Integrated Flux', 'Measured Integrated Flux ($\mu$Jy)', 'Hyper-py', 'blue', 'o', f'Hyper_py_Int_{i}')
+    scatter_comparison(ref_matched_idl['Flux_Integrated'] * 1e6, matched_idl['FLUX'] * 1e3, 'Integrated Flux', 'Measured Integrated Flux ($\mu$Jy)', 'Hyper-IDL', 'green', 's', f'Hyper_IDL_Int_{i}')
+
+    # Common matches across all three
+    common = m_py & m_idl
+    if np.any(common):
+        ref_common = ref[common]
+        py_common = hpy[idx_py[common]]
+        idl_common = hidl[idx_idl[common]]
+        
+        
+        id_hyper_py = py_common['HYPER_ID']
+        id_hyper_idl = idl_common['HYPER_ID']
+        
+        py_all_hyper_py_id.append(id_hyper_py)
+        py_all_hyper_idl_id.append(id_hyper_idl)
+
+
+        peak_py = py_common['FLUX_PEAK'] * beam_area_pix *1.e3
+        peak_idl = idl_common['FLUX_PEAK_JY'] *1.e3
+        int_py = py_common['FLUX'] *1.e3
+        int_idl = idl_common['FLUX'] *1.e3
+
+        ref_all_peak.append(ref_common['Flux_Peak'] * 1e6)  # mJy
+        py_all_peak.append(peak_py)
+        idl_all_peak.append(peak_idl)
+
+        ref_all_int.append(ref_common['Flux_Integrated'] * 1e6)  # mJy
+        py_all_int.append(int_py)
+        idl_all_int.append(int_idl)
+
+        # Direct IDL vs py scatter
+        scatter_comparison(peak_idl * 1e3, peak_py * 1e3, 'Flux Peak', 'Hyper-py Flux Peak ($\mu$Jy)', 'Hyper-IDL vs Hyper-py', 'purple', 'd', f'Hyper_IDL_vs_py_Peak_{i}')
+        scatter_comparison(int_idl * 1e3, int_py * 1e3, 'Integrated Flux', 'Hyper-py Integrated Flux ($\mu$Jy)', 'Hyper-IDL vs Hyper-py', 'purple', 'd', f'Hyper_IDL_vs_py_Int_{i}')
+
+
+
+
+
+
+from astropy.table import Table
+
+# ================== Save Matched Source Table ==================
+
+# Flatten all lists
+all_ref_hyper_py_id = np.concatenate(py_all_hyper_py_id)
+all_ref_hyper_idl_id = np.concatenate(py_all_hyper_idl_id)
+
+
+all_ref_peak = np.concatenate(ref_all_peak)
+all_py_peak = np.concatenate(py_all_peak)
+all_idl_peak = np.concatenate(idl_all_peak)
+
+all_ref_int = np.concatenate(ref_all_int)
+all_py_int = np.concatenate(py_all_int)
+all_idl_int = np.concatenate(idl_all_int)
+
+# Percentage differences
+diff_peak_py = 100. * (all_py_peak - all_ref_peak) / all_ref_peak
+diff_peak_idl = 100. * (all_idl_peak - all_ref_peak) / all_ref_peak
+diff_int_py = 100. * (all_py_int - all_ref_int) / all_ref_int
+diff_int_idl = 100. * (all_idl_int - all_ref_int) / all_ref_int
+
+# Build and write the output table
+matched_table = Table(
+    [
+        np.arange(1, len(all_ref_peak) + 1),  # INDEX
+        all_ref_hyper_py_id,
+        all_ref_hyper_idl_id,
+        all_ref_peak, all_py_peak, all_idl_peak,
+        all_ref_int,  all_py_int,  all_idl_int,
+        diff_peak_py, diff_peak_idl,
+        diff_int_py,  diff_int_idl
+    ],
+    names=[
+        'INDEX',
+        'HYPER_ID_PY', 'HYPER_ID_IDL',
+        'PEAK_REF_mJy', 'PEAK_PY_mJy', 'PEAK_IDL_mJy',
+        'INT_REF_mJy',  'INT_PY_mJy',  'INT_IDL_mJy',
+        'D_PEAK_PY_pct', 'D_PEAK_IDL_pct',
+        'D_INT_PY_pct',  'D_INT_IDL_pct'
+    ],
+    dtype=[
+        'int32', 'int32', 'int32',
+        'float64', 'float64', 'float64',
+        'float64', 'float64', 'float64',
+        'float32', 'float32', 'float32', 'float32'
+    ]
+)
+
+# Format columns
+for col in [
+    'PEAK_REF_mJy', 'PEAK_PY_mJy', 'PEAK_IDL_mJy',
+    'INT_REF_mJy', 'INT_PY_mJy', 'INT_IDL_mJy',
+    'D_PEAK_PY_pct', 'D_PEAK_IDL_pct',
+    'D_INT_PY_pct', 'D_INT_IDL_pct'
+]:
+    matched_table[col].format = '6.1f'
+
+# Save table
+matched_table.meta['COMMENT'] = 'Flux comparison for sources matched in all three catalogs'
+matched_table.write(dir_out + 'matched_flux_comparison_table.txt', format='ascii.ipac', overwrite=True)
+
+
+
+
+
+
+# Histogram plots over all maps
+plot_flux_difference_histogram(ref_all_peak, py_all_peak, idl_all_peak, 'Flux Peak', 'Flux_Diff_Histogram_Peak.png')
+plot_flux_difference_histogram(ref_all_int, py_all_int, idl_all_int, 'Integrated Flux', 'Flux_Diff_Histogram_Int.png')
+
+# Save summary stats
+summary_table.write(table_combined_stats, format='ascii.ipac', overwrite=True)