pyreduce-astro 0.7a6__tar.gz → 0.7a7__tar.gz

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/CHANGELOG.md

@@ -1,6 +1,15 @@
 # Changelog
 
 
+## [0.7a7] - 2026-01-04
+
+### Added
+- `--settings` option for CLI to override reduction parameters from JSON file
+
+### Changed
+- Rename `extraction_width` to `extraction_height` in settings (clarifies coordinate system)
+- Rename `orders` to `traces` in extract.py internal API
+
 ## [0.7a6] - 2026-01-03
 
 ### Added

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/CLAUDE.md

@@ -54,6 +54,16 @@ pyreduce/
     └── slit_func_2d_xi_zeta_bd.c
 ```
 
+## Image Coordinate Convention
+
+PyReduce uses the convention that **dispersion runs horizontally (along x-axis)** and **cross-dispersion runs vertically (along y-axis)**. The `clipnflip()` function in `instruments/common.py` rotates and flips raw images to ensure this orientation.
+
+This means:
+- **Columns (x)** = wavelength/dispersion direction
+- **Rows (y)** = spatial/cross-dispersion direction
+- **Traces** are polynomial functions of x, giving y-position
+- **`extraction_height`** refers to pixels above/below each trace (in y)
+
 ## Pipeline Steps
 
 The reduction pipeline consists of these steps (in typical order):
@@ -145,7 +155,7 @@ Defines HOW to reduce - algorithm parameters per step:
     "filter_size": 120
   },
   "norm_flat": {
-    "extraction_width": 0.5,
+    "extraction_height": 0.5,
     "smooth_slitfunction": 1,
     "oversampling": 10
   },
@@ -156,7 +166,7 @@ Defines HOW to reduce - algorithm parameters per step:
   },
   "science": {
     "extraction_method": "optimal",
-    "extraction_width": 0.5,
+    "extraction_height": 0.5,
     "oversampling": 10
   }
 }
@@ -283,3 +293,43 @@ uv run ruff check --fix .            # Lint and fix
 | `pyreduce/instruments/models.py` | Pydantic config models |
 | `pyreduce/clib/*.c` | C code for slit function decomposition |
 | `hatch_build.py` | CFFI extension build hook |
+
+## Release Process
+
+To release a new version (e.g., `0.7a6`):
+
+1. **Update documentation** for any renamed steps, new CLI options, etc:
+   - `README.md` - Quick start examples
+   - `docs/cli.md` - CLI reference
+   - `docs/index.md`, `docs/howto.md`, `docs/examples.md` - Usage examples
+   - `docs/configuration_file.md` - Config key names
+
+2. **Update CHANGELOG.md** with release date and changes
+
+3. **Update version** in `pyproject.toml`
+
+3a. **sync** - run `uv sync` to get the new version into uv.lock
+
+4. **Update example headers** - all `examples/*.py` have PEP 723 metadata:
+   ```python
+   # /// script
+   # dependencies = ["pyreduce-astro>=0.7a6"]
+   # ///
+   ```
+
+5. **Commit, tag, and push**:
+   ```bash
+   git add -A && git commit -m "Release v0.7a6"
+   git tag v0.7a6
+   git push && git push --tags
+   ```
+
+6. **Monitor GitHub Actions** - the tag push triggers:
+   - Tests on Python 3.13
+   - Wheel builds (Linux, Windows, macOS)
+   - PyPI upload
+   - GitHub Release creation
+
+   ```bash
+   gh run watch  # watch the triggered workflow
+   ```

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a6
+Version: 0.7a7
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -101,4 +101,4 @@ Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
 
 ## Output
 
-PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/README.md

@@ -59,4 +59,4 @@ Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
 
 ## Output
 
-PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.
@@ -26,6 +26,7 @@ import os
 
 import numpy as np
 
+from pyreduce.extract import extract
 from pyreduce.instruments.instrument_info import load_instrument
 from pyreduce.trace import group_and_refit, merge_traces, trace
 
@@ -41,6 +42,7 @@ orders_file = os.path.join(raw_dir, "ANDES_75fibre_J_orders.npz")
 # Output
 output_dir = os.path.expanduser("~/REDUCE_DATA/AJ/reduced")
 output_file = os.path.join(output_dir, "fiber_traces.npz")
+output_blaze = os.path.join(output_dir, "fiber_blaze.npz")
 
 # Load order centers from npz file
 orders_data = np.load(orders_file)
@@ -65,7 +67,7 @@ trace_params = {
     "border_width": 0,
     "manual": False,
     "auto_merge_threshold": 1.0,
-    "merge_min_threshold": 0.1,
+    "merge_min_threshold": 1.0,  # 1.0 disables merging entirely
     "sigma": 0,
     "plot": 1,
 }
@@ -90,6 +92,10 @@ print(f"  Shape: {img_even.shape}, dtype: {img_even.dtype}")
 print(f"Loading {file_odd}...")
 img_odd, head_odd = instrument.load_fits(file_odd, channel=channel, extension=0)
 
+# Combine even and odd flats for extraction
+img_combined = img_even.astype(np.float64) + img_odd.astype(np.float64)
+print(f"Combined flat shape: {img_combined.shape}")
+
 # --- Step 2: Trace each flat independently ---
 print("\nTracing even-illuminated fibers...")
 traces_even, cr_even = trace(
@@ -166,4 +172,38 @@ else:
     save_dict["column_range"] = all_cr
 
 np.savez(output_file, **save_dict)
-print(f"\nSaved to: {output_file}")
+print(f"\nSaved traces to: {output_file}")
+
+# --- Step 6: Extract spectra from all fiber traces ---
+# Flatten all traces into a single orders array for extraction
+all_traces = np.vstack([traces_by_order[k] for k in sorted(traces_by_order.keys())])
+all_cr = np.vstack([cr_by_order[k] for k in sorted(cr_by_order.keys())])
+print(f"\nExtracting {len(all_traces)} fiber traces...")
+
+# Extraction parameters
+extract_params = {
+    "extraction_height": 0.5,
+    "lambda_sf": 0.1,  # smooth_slitfunction
+    "lambda_sp": 0,  # smooth_spectrum
+    "osample": 10,  # oversampling
+    "swath_width": 200,
+    "plot": 1,
+}
+
+norm, spec, blaze, unc = extract(
+    img_combined,
+    all_traces,
+    column_range=all_cr,
+    extraction_type="normalize",
+    gain=1.0,
+    readnoise=0.0,
+    dark=0.0,
+    **extract_params,
+)
+
+print(f"  Extracted blaze shape: {blaze.shape}")
+print(f"  Normalized flat shape: {norm.shape}")
+
+# Save extraction results
+np.savez(output_blaze, blaze=blaze, norm=norm, spec=spec, unc=unc)
+print(f"Saved blaze to: {output_blaze}")

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import os.path
 
@@ -71,7 +71,7 @@ kwargs_comb["nstep"] = 0
 kwargs["plot"] = False
 
 
-for key in ["extraction_method", "extraction_width", "extraction_cutoff"]:
+for key in ["extraction_method", "extraction_height", "extraction_cutoff"]:
     del kwargs_comb[key]
     del kwargs[key]
 

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/metis_lss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/micado_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -48,11 +48,11 @@ config = pyreduce.configuration.get_configuration_for_instrument(instrument)
 
 
 # config["trace"]["noise"] = 100
-# config["curvature"]["extraction_width"] = 350 # curvature can still be improved with this and the following parameters
+# config["curvature"]["extraction_height"] = 350 # curvature can still be improved with this and the following parameters
 # config["curvature"]["peak_threshold"] =10
 # config["curvature"]["peak_width"] =2 #CHECK 6 also works and detects one less line
 # config["curvature"]["window_width"] = 5
-# config["wavecal"]["extraction_width"] = 350
+# config["wavecal"]["extraction_height"] = 350
 
 # NOTE: micado.thar_master.fits (created and controlled by wavecal_master) is NOT overwritten if any parameter in the steps in or before it are changed. Thus it has to be deleted before running PyReduce again.
 

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/neid_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 NEID reduction example

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/nirspec_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/toes_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import numpy as np
 
@@ -90,7 +90,7 @@ config["trace"]["min_width"] = 200
 config["trace"]["manual"] = True
 config["norm_flat"]["oversampling"] = 8  # Subpixel scale for slit function modelling
 config["norm_flat"]["swath_width"] = 400  # Extraction swath width (columns)
-config["wavecal_master"]["extraction_width"] = 2
+config["wavecal_master"]["extraction_height"] = 2
 config["wavecal_master"]["collapse_function"] = "sum"
 config["wavecal_master"]["bias_scaling"] = "number_of_files"
 config["wavecal"]["medium"] = "vac"
@@ -102,7 +102,7 @@ config["science"]["oversampling"] = 8  # Subpixel scale for slit function modell
 config["science"]["swath_width"] = 400  # Extraction swath width (columns)
 config["science"]["smooth_slitfunction"] = 1.0  # Smoothing of the slit function
 config["science"]["smooth_spectrum"] = 1.0e-6  # Smoothing in spectral direction
-config["science"]["extraction_width"] = [5, 5]  # Extraction slit height (rows)
+config["science"]["extraction_height"] = [5, 5]  # Extraction slit height (rows)
 config["science"]["bias_scaling"] = "number_of_files"
 
 # Since we can't find the files ourselves (at least not without defining the criteria we are looking for)

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/uves_callfunc.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Example showing direct function calls for each step.

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/uves_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/examples/xshooter_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a6"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyreduce-astro"
-version = "0.7a6"
+version = "0.7a7"
 requires-python = ">=3.13"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/pyreduce/__main__.py

@@ -67,6 +67,12 @@ def cli():
     default=None,
     help="Order range to process (e.g., '1,21')",
 )
+@click.option(
+    "--settings",
+    default=None,
+    type=click.Path(exists=True),
+    help="JSON file with settings overrides",
+)
 def run(
     instrument,
     target,
@@ -78,13 +84,14 @@ def run(
     output_dir,
     plot,
     order_range,
+    settings,
 ):
     """Run the reduction pipeline.
 
     INSTRUMENT: Name of the instrument (e.g., UVES, HARPS, XSHOOTER)
     TARGET: Target star name or regex pattern
     """
-    from .configuration import get_configuration_for_instrument
+    from .configuration import get_configuration_for_instrument, load_settings_override
     from .reduce import main as reduce_main
 
     # Parse steps
@@ -100,6 +107,8 @@ def run(
 
     # Load configuration
     config = get_configuration_for_instrument(instrument)
+    if settings:
+        config = load_settings_override(config, settings)
 
     # Run reduction
     reduce_main(
@@ -292,10 +301,28 @@ def make_step_command(step_name):
         default=None,
         help="Specific input file (bypasses file discovery)",
     )
+    @click.option(
+        "--settings",
+        default=None,
+        type=click.Path(exists=True),
+        help="JSON file with settings overrides",
+    )
     def cmd(
-        instrument, target, night, channel, base_dir, input_dir, output_dir, plot, file
+        instrument,
+        target,
+        night,
+        channel,
+        base_dir,
+        input_dir,
+        output_dir,
+        plot,
+        file,
+        settings,
     ):
-        from .configuration import get_configuration_for_instrument
+        from .configuration import (
+            get_configuration_for_instrument,
+            load_settings_override,
+        )
         from .reduce import main as reduce_main
 
         if file:
@@ -305,7 +332,6 @@ def make_step_command(step_name):
             import numpy as np
 
             from . import reduce as reduce_module
-            from .configuration import get_configuration_for_instrument
             from .instruments.instrument_info import load_instrument
 
             inst = load_instrument(instrument)
@@ -317,6 +343,8 @@ def make_step_command(step_name):
 
             # Load configuration for this step
             config = get_configuration_for_instrument(instrument)
+            if settings:
+                config = load_settings_override(config, settings)
             step_config = config.get(step_name, {})
             step_config["plot"] = plot
 
@@ -355,6 +383,8 @@ def make_step_command(step_name):
             step.run(files=np.array([file]), mask=None, bias=None)
         else:
             config = get_configuration_for_instrument(instrument)
+            if settings:
+                config = load_settings_override(config, settings)
             reduce_main(
                 instrument=instrument,
                 target=target,

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/pyreduce/configuration.py

@@ -43,6 +43,26 @@ def get_configuration_for_instrument(instrument, **kwargs):
     return config
 
 
+def load_settings_override(config, settings_file):
+    """Apply settings overrides from a JSON file.
+
+    Parameters
+    ----------
+    config : dict
+        Base configuration to override
+    settings_file : str
+        Path to JSON file with override settings
+
+    Returns
+    -------
+    config : dict
+        Updated configuration
+    """
+    with open(settings_file) as f:
+        overrides = json.load(f)
+    return update(config, overrides, check=False)
+
+
 def load_config(configuration, instrument, j=0):
     if configuration is None:
         logger.info(

{pyreduce_astro-0.7a6 → pyreduce_astro-0.7a7}/pyreduce/estimate_background_scatter.py

@@ -18,7 +18,7 @@ def estimate_background_scatter(
     img,
     orders,
     column_range=None,
-    extraction_width=0.1,
+    extraction_height=0.1,
     scatter_degree=4,
     sigma_cutoff=2,
     border_width=10,
@@ -38,7 +38,7 @@ def estimate_background_scatter(
         order polynomial coefficients
     column_range : array[nord, 2], optional
         range of columns to use in each order (default: None == all columns)
-    extraction_width : float, array[nord, 2], optional
+    extraction_height : float, array[nord, 2], optional
         extraction width for each order, values below 1.5 are considered fractional, others as number of pixels (default: 0.1)
     scatter_degree : int, optional
         polynomial degree of the 2d fit for the background scatter (default: 4)
@@ -56,8 +56,8 @@ def estimate_background_scatter(
     nrow, ncol = img.shape
     nord, _ = orders.shape
 
-    extraction_width, column_range, orders = fix_parameters(
-        extraction_width,
+    extraction_height, column_range, orders = fix_parameters(
+        extraction_height,
         column_range,
         orders,
         nrow,
@@ -73,16 +73,16 @@ def estimate_background_scatter(
         mask[:bw] = mask[-bw:] = mask[:, :bw] = mask[:, -bw:] = False
     for i in range(nord):
         left, right = column_range[i]
-        left -= extraction_width[i, 1] * 2
-        right += extraction_width[i, 0] * 2
+        left -= extraction_height[i, 1] * 2
+        right += extraction_height[i, 0] * 2
         left = max(0, left)
         right = min(ncol, right)
 
         x_order = np.arange(left, right)
         y_order = np.polyval(orders[i], x_order)
 
-        y_above = y_order + extraction_width[i, 1]
-        y_below = y_order - extraction_width[i, 0]
+        y_above = y_order + extraction_height[i, 1]
+        y_below = y_order - extraction_height[i, 0]
 
         y_above = np.floor(y_above)
         y_below = np.ceil(y_below)