isgri 0.7.0__py3-none-any.whl → 0.7.2__py3-none-any.whl

isgri/__version__.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.2"

isgri/catalog/builder.py

@@ -306,7 +306,14 @@ class CatalogBuilder:
         data = Parallel(n_jobs=self.n_cores, backend="multiprocessing")(
             delayed(self._process_scw)(path) for path in rev_paths
         )
-        table_data_list, array_data_dicts = zip(*[d for d in data if d[0] is not None])
+
+        # Filter out None results
+        valid_data = [d for d in data if d[0] is not None]
+
+        if not valid_data:
+            return None, None
+
+        table_data_list, array_data_dicts = zip(*valid_data)
 
         dtype = [("SWID", "U16"), ("TIME", "O"), ("COUNTS", "O"), ("MODULE_COUNTS", "O"), ("GTIS", "O")]
         array_data = np.empty(len(array_data_dicts), dtype=dtype)
@@ -426,6 +433,11 @@ class CatalogBuilder:
         for revolution, rev_paths in revolutions.items():
             print(f"Processing revolution {revolution} with {len(rev_paths)} ScWs...")
             table_data_rows, array_data_list = self._process_rev(rev_paths)
+
+            if table_data_rows is None:
+                print(f"No valid ScWs found in revolution {revolution}, skipping.")
+                continue
+
             print(f"Adding {len(table_data_rows)} ScWs from revolution {revolution} to catalog.")
             self._add_catalog_data(table_data_rows)
             if self.lightcurve_cache is not None:

isgri/cli/builder.py

@@ -0,0 +1,102 @@
+import click
+from pathlib import Path
+from ..catalog.builder import CatalogBuilder
+from ..config import Config
+
+
+@click.command()
+@click.option(
+    "--archive", type=click.Path(), help="Path to INTEGRAL archive directory. If not provided, uses config value."
+)
+@click.option("--catalog", type=click.Path(), help="Path to catalog FITS file. If not provided, uses config value.")
+@click.option("--cache", type=click.Path(), help="Path to light curve cache directory. Optional.")
+@click.option("--cores", type=int, help="Number of CPU cores for parallel processing. Defaults to all available.")
+def update(archive, catalog, cache, cores):
+    """
+    Update science window catalog from archive.
+
+    Scans the INTEGRAL archive for new science windows not present in the catalog,
+    processes them in parallel by revolution, and adds results to the catalog.
+
+    If archive or catalog paths are not provided, uses values from configuration.
+    Optionally caches light curve arrays to the specified directory.
+
+    Examples:
+
+        Update using configured paths:
+
+            isgri update
+
+        Update with custom paths:
+
+            isgri update --archive /anita/archivio/ --catalog ~/data/catalog.fits
+
+        Update with light curve caching:
+
+            isgri update --cache ~/data/lightcurves/
+
+        Update using 4 CPU cores:
+
+            isgri update --cores 4
+    """
+    if archive is None or catalog is None:
+        cfg = Config()
+
+        if archive is None:
+            archive = cfg.archive_path
+            if not archive:
+                click.echo("Error: No archive path configured", err=True)
+                raise click.Abort()
+
+        if catalog is None:
+            catalog = cfg.catalog_path
+            if not catalog:
+                click.echo("Error: No catalog path configured", err=True)
+                raise click.Abort()
+
+    archive_path = Path(archive).expanduser().resolve()
+    catalog_path = Path(catalog).expanduser().resolve()
+    cache_path = Path(cache).expanduser().resolve() if cache else None
+
+    if not archive_path.exists():
+        click.echo(f"Error: Archive directory does not exist: {archive_path}", err=True)
+        raise click.Abort()
+
+    if not catalog_path.parent.exists():
+        click.echo(f"Warning: Catalog directory does not exist: {catalog_path.parent}", err=True)
+        if not click.confirm("Create new catalog file?"):
+            raise click.Abort()
+
+    if cache_path and not cache_path.exists():
+        click.echo(f"Warning: Cache directory does not exist: {cache_path}", err=True)
+        if not click.confirm("Create directory?"):
+            raise click.Abort()
+        cache_path.mkdir(parents=True, exist_ok=True)
+        click.echo(f"✓ Created cache directory: {cache_path}")
+
+    click.echo(f"Archive: {archive_path}")
+    click.echo(f"Catalog: {catalog_path}")
+    if cache_path:
+        click.echo(f"Cache: {cache_path}")
+    else:
+        click.echo("Cache: (none)")
+    if cores:
+        click.echo(f"CPU cores: {cores}")
+    click.echo()
+
+    try:
+        builder = CatalogBuilder(
+            archive_path=str(archive_path),
+            catalog_path=str(catalog_path),
+            lightcurve_cache=str(cache_path) if cache_path else None,
+            n_cores=cores,
+        )
+
+        builder.update_catalog()
+
+        click.echo()
+        click.echo("Catalog update complete")
+
+    except Exception as e:
+        click.echo(f"Error during catalog update: {e}", err=True)
+        raise click.Abort()

isgri/cli/main.py

@@ -4,6 +4,7 @@ from ..catalog import ScwQuery
 from ..__version__ import __version__
 from ..config import Config
 from .query import query_direct, query_interactive
+from .builder import update
 
 
 @click.group()
@@ -29,7 +30,10 @@ def main():
 )
 @click.option("--list-swids", is_flag=True, help="Only output SWID list")
 @click.option("--count", is_flag=True, help="Only show count")
-def query(catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count):
+@click.option("--columns", help="Comma-separated list of columns to save (e.g., SWID,TSTART,TSTOP)")
+def query(
+    catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count, columns
+):
     """
     Query INTEGRAL science window catalog.
 
@@ -58,6 +62,10 @@ def query(catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revol
 
             isgri query --tstart 3000 --tstop 3100 --output results.fits
 
+        Save specific columns:
+
+            isgri query --tstart 3000 --tstop 3100 --output results.fits --columns SWID,TSTART,TSTOP,CHI
+
         Get only SWID list:
 
             isgri query --tstart 3000 --tstop 3100 --list-swids
@@ -69,14 +77,26 @@ def query(catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revol
     if catalog is None:
         cfg = Config()
         catalog = cfg.catalog_path
-
-        if not catalog:
-            click.echo("Error: No catalog configured", err=True)
+        if catalog is None:
+            click.echo("Error: No catalog path configured", err=True)
             raise click.Abort()
 
     if any(param is not None for param in [tstart, tstop, ra, dec, radius, max_chi, revolution]):
         query_direct(
-            catalog, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count
+            catalog,
+            tstart,
+            tstop,
+            ra,
+            dec,
+            radius,
+            fov,
+            max_chi,
+            chi_type,
+            revolution,
+            output,
+            list_swids,
+            count,
+            columns,
         )
     else:
         query_interactive(catalog)
@@ -181,5 +201,7 @@ def config_set(archive, catalog, pif):
     click.echo(f"Configuration saved to: {cfg.path}")
 
 
+main.add_command(update)
+
 if __name__ == "__main__":
     main()

isgri/cli/query.py

@@ -55,10 +55,10 @@ def match_command(user_input):
     commands = {
         "time": ["time", "t"],
         "pos": ["pos", "position", "p"],
-        "quality": ["quality", "qual", "q"],
-        "revolution": ["revolution", "rev", "r"],
+        "quality": ["quality", "qual"],
+        "revolution": ["revolution", "rev"],
         "show": ["show", "s", "display"],
-        "reset": ["reset", "clear"],
+        "reset": ["reset", "clear", "r"],
         "save": ["save", "write"],
         "help": ["help", "h", "?"],
         "exit": ["exit", "quit", "q"],
@@ -77,7 +77,20 @@ def match_command(user_input):
 
 
 def query_direct(
-    catalog_path, tstart, tstop, ra, dec, radius, fov, max_chi, chi_type, revolution, output, list_swids, count
+    catalog_path,
+    tstart,
+    tstop,
+    ra,
+    dec,
+    radius,
+    fov,
+    max_chi,
+    chi_type,
+    revolution,
+    output,
+    list_swids,
+    count,
+    columns,
 ):
     try:
         q = ScwQuery(catalog_path)
@@ -108,7 +121,17 @@ def query_direct(
             click.echo(q.count())
 
         elif output:
-            q.write(output, overwrite=True, swid_only=list_swids)
+            col_list = None
+            if columns and not list_swids:
+                col_list = [c.strip() for c in columns.split(",")]
+                available = q.catalog.colnames
+                invalid = [c for c in col_list if c not in available]
+                if invalid:
+                    click.echo(f"Error: Invalid columns: {invalid}", err=True)
+                    click.echo(f"Available: {', '.join(available)}", err=True)
+                    raise click.Abort()
+
+            q.write(output, overwrite=True, swid_only=list_swids, columns=col_list)
             click.echo(f"Saved {q.count()} SCWs to {output}")
 
         else:
@@ -196,9 +219,33 @@ def query_interactive(catalog_path):
                 click.echo(f"→ {len(q.catalog)} SCWs")
             elif cmd == "save":
                 swid_only = click.confirm("Save only SWID list?", default=False)
+
+                col_list = None
+                if not swid_only:
+                    if click.confirm("Select specific columns?", default=False):
+                        click.echo("\nAvailable columns:")
+                        available = q.catalog.colnames
+                        for i, col in enumerate(available, 1):
+                            click.echo(f"  {i:2d}. {col}")
+
+                        click.echo("\nEnter column names (comma-separated) or leave empty for all:")
+                        col_input = click.prompt("Columns", default="", show_default=False)
+
+                        if col_input:
+                            col_list = [c.strip() for c in col_input.split(",")]
+                            invalid = [c for c in col_list if c not in available]
+                            if invalid:
+                                click.echo(f"Warning: Invalid columns ignored: {invalid}")
+                                col_list = [c for c in col_list if c in available]
+
+                            if not col_list:
+                                click.echo("No valid columns selected, using all")
+                                col_list = None
+
                 path = click.prompt("File")
-                q.write(path, overwrite=True, swid_only=swid_only)
-                click.echo(f"✓ Saved")
+                q.write(path, overwrite=True, swid_only=swid_only, columns=col_list)
+                click.echo(f"Saved {q.count()} SCWs to {path}")
+
             elif cmd is None:
                 click.echo(f"Unknown command: {user_input}. Type 'help' for available commands.")
             else:

{isgri-0.7.0.dist-info → isgri-0.7.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: isgri
-Version: 0.7.0
+Version: 0.7.2
 Summary: Python package for INTEGRAL IBIS/ISGRI lightcurve analysis
 Author: Dominik Patryk Pacholski
 License: MIT
@@ -26,6 +26,7 @@ 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:
@@ -33,6 +34,13 @@ Query INTEGRAL Science Window catalogs with a fluent Python API:
 - 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
@@ -60,6 +68,9 @@ isgri config-set --archive /path/to/archive --catalog ~/data/scw_catalog.fits --
 # View current config
 isgri config
 
+# Update catalog from archive
+isgri update
+
 # Interactive catalog query
 isgri query
 # query> time
@@ -109,6 +120,51 @@ 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

{isgri-0.7.0.dist-info → isgri-0.7.2.dist-info}/RECORD

@@ -1,21 +1,22 @@
 isgri/__init__.py,sha256=V2hnOxXKcjMiusdGP8sOAR4QsBlWHQ0pZZMN2Cean6o,38
-isgri/__version__.py,sha256=P1kRuZW02tF-ekLuBqSjV_tIKKqcbfRPDdpp9C8ftUY,21
+isgri/__version__.py,sha256=ISWV9_SJtaCeILz1FAMYHSjVkHbV08KnnT23Ww0_w-o,21
 isgri/config.py,sha256=8hziHnQN_dnS3FkOtrPUUV1QLJ9HmGiPzDuAiq3GoXc,5044
 isgri/catalog/__init__.py,sha256=IGfzGcGx1F1zplj7YIUuzE5Cvvxg7XJi0zu0aBXI0-A,113
-isgri/catalog/builder.py,sha256=EDda0QIHBRwh1nPUndSYfw4nvJHxjXPmVgyPscksBrM,15490
+isgri/catalog/builder.py,sha256=J1Z_p699hoQtiQjYw5-jvf0aSIIOcpe8djbCjh-NOng,15779
 isgri/catalog/scwquery.py,sha256=v7nR6-6PmYaBunFeGtmDWPqDkUBUvwjv2jtM1RbGQx4,20397
 isgri/catalog/wcs.py,sha256=mD6bZxiBxKYpuYCl8f2tSCc8uuWFzMRL2jf5SuFAhfg,5562
 isgri/cli/__init__.py,sha256=SCIcTdOvfEkrZd1doOtOnvCj8PmdRuXu18YYJQxfFrs,24
-isgri/cli/main.py,sha256=EfBN4E9oUvhB0GfQldLU3eSvmRC4JjxM72qWFEc2_IA,6379
-isgri/cli/query.py,sha256=jIAJ8Ghr73OivSIqTjqYE-y-gn9hw4-QpEeH-z6Bny0,8012
+isgri/cli/builder.py,sha256=dCp9ECl9MoThTRXAkXXazafHYSMQF0FLHKDzlWwT7vE,3494
+isgri/cli/main.py,sha256=gOK8UDOviwb_o4YqhnZY_zsytNxNe7NZNWD7yu1rSrM,6883
+isgri/cli/query.py,sha256=o2AV8pwLNgRL2goAppVT0z_gZApLy5_5CjtzA4iqYs8,9830
 isgri/utils/__init__.py,sha256=H83Al7urc6LNW5KUzUBRdtRBUTahiZmkehKFiK90RrU,183
 isgri/utils/file_loaders.py,sha256=E4-0QA6r1QAX1gV1Dd5qhKPDXZIdSEk7AWdOQrovHGo,17423
 isgri/utils/lightcurve.py,sha256=v_JNLzf1SBvFLzrU7ZXpSj44eRKaZChiO4gvS2_O35Y,17408
 isgri/utils/pif.py,sha256=sAtzQhe3spLS41UkP1yZsqGPxe3IHLmIGA_d3bVg2v4,9121
 isgri/utils/quality.py,sha256=7CbYaNstoX60AYz2_ym-xjMkiDLpkYgQfaTStYuQZtk,13409
 isgri/utils/time_conversion.py,sha256=MNPVjrsrmwRDbCWmqdWN0xRs8PtHkFGli-H2cYwF9Ns,5204
-isgri-0.7.0.dist-info/METADATA,sha256=7MSVI7E4DdtSpm7GZXdYJ-SD1mTTddf0sewrJNkgYcE,5115
-isgri-0.7.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-isgri-0.7.0.dist-info/entry_points.txt,sha256=aM2K4RGihbwsj9crjPG-BvWhErcdtZt3tJqT6AaOojU,46
-isgri-0.7.0.dist-info/licenses/LICENSE,sha256=Q8oxmHR1cSnEXSHCjY3qeXMtupZI_1ZQZ1MBt4oeANE,1102
-isgri-0.7.0.dist-info/RECORD,,
+isgri-0.7.2.dist-info/METADATA,sha256=Z3bs7SF2VmrGBMBjBSZGcLorkqRj4ild1NFDOpY6B1c,6499
+isgri-0.7.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+isgri-0.7.2.dist-info/entry_points.txt,sha256=aM2K4RGihbwsj9crjPG-BvWhErcdtZt3tJqT6AaOojU,46
+isgri-0.7.2.dist-info/licenses/LICENSE,sha256=Q8oxmHR1cSnEXSHCjY3qeXMtupZI_1ZQZ1MBt4oeANE,1102
+isgri-0.7.2.dist-info/RECORD,,