isgri 0.6.1__tar.gz → 0.7.1__tar.gz

{isgri-0.6.1 → isgri-0.7.1}/.gitignore

@@ -1,218 +1,218 @@
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+# Byte-compiled / optimized / DLL files
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+share/python-wheels/
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+.pytest_cache/
+cover/
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+
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+#   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:
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+
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+#   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
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+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
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+
 docs/**

{isgri-0.6.1 → isgri-0.7.1}/.python-version

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

isgri-0.7.1/PKG-INFO

@@ -0,0 +1,266 @@
+Metadata-Version: 2.4
+Name: isgri
+Version: 0.7.1
+Summary: Python package for INTEGRAL IBIS/ISGRI lightcurve analysis
+Author: Dominik Patryk Pacholski
+License: MIT
+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
+Requires-Dist: tomli>=2.0.0; python_version < '3.11'
+Description-Content-Type: text/markdown
+
+# ISGRI
+
+Python toolkit for INTEGRAL/ISGRI data analysis.
+
+## Features
+
+### 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 or SWID lists
+- Update catalogs with new science windows from archive
+
+### 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
+
+### Catalog Builder
+Build and update INTEGRAL/ISGRI science window catalogs:
+- Automatic discovery of new science windows in archive
+- Parallel processing of quality metrics
+- Optional light curve caching
+- Incremental catalog updates
+
+### Light Curve Analysis
+Extract and analyze ISGRI light curves:
+- 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)
+- Time conversions (IJD to/from UTC)
+
+
+## Installation
+
+```bash
+pip install isgri
+```
+
+## Quick Start
+
+### CLI Usage
+
+```bash
+# Configure default paths (once)
+isgri config-set --archive /path/to/archive --catalog ~/data/scw_catalog.fits --pif /path/to/pif
+
+# View current config
+isgri config
+
+# Update catalog from archive
+isgri update
+
+# 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
+isgri query --tstart 3000 --tstop 3100 --output results.fits
+```
+
+### Query SCW Catalog
+
+```python
+from isgri.catalog import ScwQuery
+
+# Load catalog
+cat = ScwQuery("path_to_catalog.fits")
+
+# Find Crab observations in 2010 with good quality
+results = (cat
+    .time(tstart="2010-01-01", tstop="2010-12-31")
+    .quality(max_chi=2.0)
+    .position(ra=83.63, dec=22.01, fov_mode="full")
+    .get()
+)
+
+# 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")
+```
+
+### Build/Update SCW Catalog
+
+#### Command Line
+
+```bash
+# Update catalog using configured paths
+isgri update
+
+# Update with custom paths
+isgri update --archive /anita/archivio/ --catalog ~/data/catalog.fits 
+
+# Enable light curve caching (15-1000 keV, 1s bins)
+isgri update --cache ~/data/lightcurves/
+
+# Limit CPU cores for parallel processing
+isgri update --cores 4
+```
+
+#### Python API
+
+```python
+from isgri.catalog import CatalogBuilder
+
+# Create builder instance
+builder = CatalogBuilder(
+    archive_path="/path/to/archive",
+    catalog_path="scw_catalog.fits",
+    lightcurve_cache="/path/to/cache",  # optional
+    n_cores=8
+)
+
+# Update catalog with new science windows
+builder.update_catalog()
+
+# Find all science windows in archive
+swids, paths = builder.find_scws()
+print(f"Found {len(swids)} science windows")
+```
+
+The builder:
+- Scans archive for new ScWs not in catalog
+- Computes quality metrics (raw, sigma-clipped, GTI-filtered chi-squared)
+- Processes in parallel by revolution
+- Optionally caches 1s light curves (15-1000 keV)
+
+### Analyze Light Curves
+
+```python
+from isgri.utils import LightCurve, QualityMetrics
+
+# 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
+)
+
+# 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
+)
+
+# 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
+
+ISGRI stores configuration in default config folder for each system (see: platformdirs package)
+
+```bash
+# View current config
+isgri config
+
+# Set paths
+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 in Python:
+
+```python
+from isgri.config import 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.
+
+
+## Documentation
+
+- **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
+
+
+## License
+
+MIT