pyreduce-astro 0.7a5__cp314-cp314-win_amd64.whl → 0.7a7__cp314-cp314-win_amd64.whl

pyreduce/__main__.py

@@ -4,8 +4,8 @@ PyReduce command-line interface.
 Usage:
     uv run reduce --help
     uv run reduce run UVES HD132205 --night 2010-04-01
-    uv run reduce run UVES HD132205 --steps bias,flat,orders
-    uv run reduce bias UVES HD132205
+    uv run reduce run UVES HD132205 --steps bias,flat,trace
+    uv run reduce trace UVES HD132205
     uv run reduce combine --output combined.fits *.final.fits
 """
 
@@ -14,7 +14,7 @@ import click
 ALL_STEPS = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",
@@ -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(
@@ -279,30 +288,115 @@ def make_step_command(step_name):
 
     @click.command(name=step_name)
     @click.argument("instrument")
-    @click.argument("target")
+    @click.argument("target", required=False, default="")
     @click.option("--night", "-n", default=None, help="Observation night")
     @click.option("--channel", "-c", default=None, help="Instrument channel")
     @click.option("--base-dir", "-b", default=None, help="Base directory")
     @click.option("--input-dir", "-i", default="raw", help="Input directory")
     @click.option("--output-dir", "-o", default="reduced", help="Output directory")
     @click.option("--plot", "-p", default=0, help="Plot level")
-    def cmd(instrument, target, night, channel, base_dir, input_dir, output_dir, plot):
-        from .configuration import get_configuration_for_instrument
+    @click.option(
+        "--file",
+        "-f",
+        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,
+        settings,
+    ):
+        from .configuration import (
+            get_configuration_for_instrument,
+            load_settings_override,
+        )
         from .reduce import main as reduce_main
 
-        config = get_configuration_for_instrument(instrument)
-        reduce_main(
-            instrument=instrument,
-            target=target,
-            night=night,
-            channels=channel,
-            steps=(step_name,),
-            base_dir=base_dir or "",
-            input_dir=input_dir,
-            output_dir=output_dir,
-            configuration=config,
-            plot=plot,
-        )
+        if file:
+            # Direct file mode: run step on specific file
+            import os
+
+            import numpy as np
+
+            from . import reduce as reduce_module
+            from .instruments.instrument_info import load_instrument
+
+            inst = load_instrument(instrument)
+            channel = channel or (inst.channels[0] if inst.channels else "")
+            output_dir_full = output_dir
+            if base_dir:
+                output_dir_full = os.path.join(base_dir, output_dir)
+            os.makedirs(output_dir_full, exist_ok=True)
+
+            # 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
+
+            # Get the step class
+            step_classes = {
+                "bias": reduce_module.Bias,
+                "flat": reduce_module.Flat,
+                "trace": reduce_module.OrderTracing,
+                "curvature": reduce_module.SlitCurvatureDetermination,
+                "scatter": reduce_module.BackgroundScatter,
+                "norm_flat": reduce_module.NormalizeFlatField,
+                "wavecal_master": reduce_module.WavelengthCalibrationMaster,
+                "wavecal_init": reduce_module.WavelengthCalibrationInitialize,
+                "wavecal": reduce_module.WavelengthCalibrationFinalize,
+                "freq_comb_master": reduce_module.LaserFrequencyCombMaster,
+                "freq_comb": reduce_module.LaserFrequencyCombFinalize,
+                "science": reduce_module.ScienceExtraction,
+                "continuum": reduce_module.ContinuumNormalization,
+            }
+
+            if step_name not in step_classes:
+                raise click.ClickException(
+                    f"Step '{step_name}' does not support --file option"
+                )
+
+            step_class = step_classes[step_name]
+            step = step_class(
+                inst,
+                channel,
+                target=target or "",
+                night=night,
+                output_dir=output_dir_full,
+                order_range=None,
+                **step_config,
+            )
+            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,
+                night=night,
+                channels=channel,
+                steps=(step_name,),
+                base_dir=base_dir or "",
+                input_dir=input_dir,
+                output_dir=output_dir,
+                configuration=config,
+                plot=plot,
+            )
 
     cmd.__doc__ = f"Run the '{step_name}' step."
     return cmd

pyreduce/cli.py

@@ -287,7 +287,7 @@ def run(config_file: str, steps: str, skip_existing: bool, plot: int):
         pipe = pipe.flat(_expand_globs(files["flat"]))
 
     if "trace" in config_steps:
-        trace_files = files.get("orders") or files.get("flat")
+        trace_files = files.get("trace") or files.get("flat")
         pipe = pipe.trace_orders(_expand_globs(trace_files) if trace_files else None)
 
     if "scatter" in config_steps:

pyreduce/combine_frames.py

@@ -305,6 +305,14 @@ def combine_frames(
     if instrument is None or isinstance(instrument, str):
         instrument = load_instrument(instrument)
 
+    # For multi-amplifier instruments, use simple combination since the
+    # row-by-row approach doesn't work with multi-extension assembly
+    if instrument.config.amplifiers is not None:
+        logger.debug("Multi-amplifier instrument detected, using simple combination")
+        return combine_frames_simple(
+            files, instrument, channel, extension=extension, dtype=dtype, **kwargs
+        )
+
     # summarize file info
     logger.debug("Files:")
     for i, fname in zip(range(len(files)), files, strict=False):

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)