isgri 0.6.1__tar.gz → 0.7.0__tar.gz

{isgri-0.6.1 → isgri-0.7.0}/.gitignore

@@ -1,218 +1,218 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[codz]
-*$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
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-# Flask stuff:
-instance/
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-.scrapy
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-# PyBuilder
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-target/
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-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
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-# Pipfile.lock
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-# uv.lock
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-# poetry
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-#   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
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-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
-#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
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-.pdm-python
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-# pixi
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-# Redis
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-#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
-# .idea/
-
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-
-# Visual Studio Code
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-#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
-#   you could uncomment the following to ignore the entire vscode folder
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-
-# Streamlit
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-
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+.vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
 docs/**

{isgri-0.6.1 → isgri-0.7.0}/.python-version

@@ -1 +1 @@
-3.9
+3.9

{isgri-0.6.1 → isgri-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: isgri
-Version: 0.6.1
+Version: 0.7.0
 Summary: Python package for INTEGRAL IBIS/ISGRI lightcurve analysis
 Author: Dominik Patryk Pacholski
 License: MIT
@@ -8,6 +8,7 @@ License-File: LICENSE
 Requires-Python: >=3.9
 Requires-Dist: astropy
 Requires-Dist: click
+Requires-Dist: joblib
 Requires-Dist: numpy
 Requires-Dist: platformdirs
 Requires-Dist: tomli-w
@@ -22,19 +23,20 @@ Python toolkit for INTEGRAL/ISGRI data analysis.
 
 ### Command Line Interface
 Query catalogs directly from the terminal:
+- Interactive and direct query modes
 - Filter by time, position, quality, revolution
-- Export results to FITS/CSV
-- List SWIDs for batch processing
+- Export results to FITS/CSV or SWID lists
 
 ### SCW Catalog Query
 Query INTEGRAL Science Window catalogs with a fluent Python API:
 - Filter by time, position, quality, revolution
 - Calculate detector offsets
-- Export results to any auto detectable astropy table extension or in table aligned data for any other extension.
+- Export results to any auto detectable astropy table extension or in table aligned data for any other extension
 
 ### Light Curve Analysis
 Extract and analyze ISGRI light curves:
-- Event loading with PIF weighting
+- Load from file paths or SWID/source lookup
+- PIF weighting with adjustable thresholds
 - Custom time binning
 - Module-by-module analysis
 - Quality metrics (chi-squared tests)
@@ -53,18 +55,26 @@ pip install isgri
 
 ```bash
 # Configure default paths (once)
-isgri config-set --catalog ~/data/scw_catalog.fits
+isgri config-set --archive /path/to/archive --catalog ~/data/scw_catalog.fits --pif /path/to/pif
 
-# Interactive method
-isgri query
-
-# Query by time range
-isgri query --tstart 2010-01-01 --tstop 2010-12-31
-
-# Query Crab with quality cut
-isgri query --ra 83.63 --dec 22.01 --max-chi 2.0 --fov full
+# View current config
+isgri config
 
-# Get list of SWIDs for processing
+# Interactive catalog query
+isgri query
+# query> time
+# Start: 2010-01-01
+# Stop: 2010-12-31
+# → 1234 SCWs
+# query> pos
+# RA: 83.63
+# Dec: 22.01
+# ...
+
+# Direct catalog query
+isgri query --tstart 2010-01-01 --tstop 2010-12-31 --ra 83.63 --dec 22.01 --max-chi 2.0
+
+# Get SWID list for batch processing
 isgri query --tstart 3000 --tstop 3100 --list-swids > swids.txt
 
 # Export results
@@ -87,8 +97,14 @@ results = (cat
     .get()
 )
 
-# Save selected columns to the file
-cat.write('example_file.any_extension',columns=['SWID','TSTART','TSTOP'])
+# Filter by revolution(s)
+results = cat.revolution([1000, 1001, 1002]).get()
+
+# Save selected columns
+cat.write('results.fits', columns=['SWID', 'TSTART', 'TSTOP'])
+
+# Get SWID list
+swids = cat.get_swids()
 
 print(f"Found {len(results)} observations")
 ```
@@ -98,20 +114,49 @@ print(f"Found {len(results)} observations")
 ```python
 from isgri.utils import LightCurve, QualityMetrics
 
-# Load events with PIF weighting
+# Method 1: Load from file paths
 lc = LightCurve.load_data(
     events_path="isgri_events.fits",
     pif_path="source_model.fits",
+    use_pif=True,
     pif_threshold=0.5
 )
 
-# Create 1-second binned light curve
-time, counts = lc.rebin(binsize=1.0, emin=20, emax=100)
+# Method 2: Load by SWID (requires config)
+lc = LightCurve.load_data(swid="255900280010")
+
+# Method 3: Load by SWID + source (auto-finds PIF)
+lc = LightCurve.load_data(
+    swid="255900280010",
+    source="SGR1935",
+    use_pif=True,
+    pif_threshold=0.5
+)
 
-# Compute quality metrics
-qm = QualityMetrics(lc, binsize=1.0, emin=20, emax=100)
-chi = qm.raw_chi_squared()
-print(f"Chisq/dof = {chi:.2f}")
+# Create binned lightcurve
+time, counts = lc.rebin(binsize=1.0, emin=30, emax=100)
+
+# Override PIF settings temporarily
+time, counts = lc.rebin(binsize=1.0, emin=30, emax=100, use_pif=True, pif_threshold=0.8)
+
+# Or change instance settings
+lc.pif_threshold = 0.7
+lc.use_pif = True
+time, counts = lc.rebin(binsize=1.0, emin=30, emax=100)
+
+# Module-by-module analysis
+times, module_counts = lc.rebin_by_modules(binsize=1.0, emin=30, emax=300)
+
+# Quality metrics
+qm = QualityMetrics(lc, binsize=1.0, emin=30, emax=100)
+chi_raw = qm.raw_chi_squared()
+chi_clipped = qm.sigma_clip_chi_squared(sigma=1)
+chi_gti = qm.gti_chi_squared()
+print(f"Chisq/dof = {chi_raw:.2f}")
+
+# Time conversions
+from isgri.utils.time_conversion import ijd2utc, utc2ijd
+print(f"Start time: {ijd2utc(lc.t0)}")
 ```
 
 ## Configuration
@@ -123,17 +168,30 @@ ISGRI stores configuration in default config folder for each system (see: platfo
 isgri config
 
 # Set paths
-isgri config-set --archive /path/to/archive --catalog /path/to/catalog.fits
+isgri config-set --archive /path/to/archive
+isgri config-set --catalog /path/to/catalog.fits
+isgri config-set --pif /path/to/pif
+
+# Set all at once
+isgri config-set --archive /path/to/archive --catalog /path/to/catalog.fits --pif /path/to/pif
 ```
 
-Config can also be used in Python:
+Config in Python:
 
 ```python
-from isgri.config import get_config
+from isgri.config import Config
 
-cfg = get_config()
+cfg = Config()
 print(cfg.archive_path)
 print(cfg.catalog_path)
+print(cfg.pif_path)
+
+# Create new config programmatically
+cfg.create_new(
+    archive_path="/path/to/archive",
+    catalog_path="/path/to/catalog.fits",
+    pif_path="/path/to/pif"
+)
 ```
 
 Local config file `isgri_config.toml` in current directory overrides global config.
@@ -144,4 +202,9 @@ Local config file `isgri_config.toml` in current directory overrides global conf
 - **CLI Reference**: Run `isgri --help` or `isgri <command> --help`
 - **Catalog Tutorial**: [scwquery_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/scwquery_walkthrough.ipynb)
 - **Light Curve Tutorial**: [lightcurve_walkthrough.ipynb](https://github.com/dominp/isgri/blob/main/demo/lightcurve_walkthrough.ipynb)
-- **API Reference**: Use `help()` in Python or see docstrings
+- **API Reference**: Use `help()` in Python or see docstrings
+
+
+## License
+
+MIT