pyreduce-astro 0.7a6__cp314-cp314-win_amd64.whl → 0.7a7__cp314-cp314-win_amd64.whl

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/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/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)