pyreduce-astro 0.7a4__cp313-cp313-win_amd64.whl → 0.7a6__cp313-cp313-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",
@@ -40,7 +40,7 @@ def cli():
 @click.argument("instrument")
 @click.argument("target")
 @click.option("--night", "-n", default=None, help="Observation night (YYYY-MM-DD)")
-@click.option("--arm", "-a", default=None, help="Instrument arm/detector")
+@click.option("--channel", "-c", default=None, help="Instrument channel")
 @click.option(
     "--steps",
     "-s",
@@ -71,7 +71,7 @@ def run(
     instrument,
     target,
     night,
-    arm,
+    channel,
     steps,
     base_dir,
     input_dir,
@@ -106,7 +106,7 @@ def run(
         instrument=instrument,
         target=target,
         night=night,
-        arms=arm,
+        channels=channel,
         steps=steps,
         base_dir=base_dir or "",
         input_dir=input_dir,
@@ -279,30 +279,94 @@ 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("--arm", "-a", default=None, help="Instrument arm")
+    @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, arm, base_dir, input_dir, output_dir, plot):
+    @click.option(
+        "--file",
+        "-f",
+        default=None,
+        help="Specific input file (bypasses file discovery)",
+    )
+    def cmd(
+        instrument, target, night, channel, base_dir, input_dir, output_dir, plot, file
+    ):
         from .configuration import get_configuration_for_instrument
         from .reduce import main as reduce_main
 
-        config = get_configuration_for_instrument(instrument)
-        reduce_main(
-            instrument=instrument,
-            target=target,
-            night=night,
-            arms=arm,
-            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 .configuration import get_configuration_for_instrument
+            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)
+            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)
+            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

@@ -146,7 +146,7 @@ def fix_bad_pixels(probability, buffer, readnoise, gain, threshold):
 
 
 def combine_frames_simple(
-    files, instrument, arm, extension=None, dtype=np.float32, **kwargs
+    files, instrument, channel, extension=None, dtype=np.float32, **kwargs
 ):
     """
     Simple addition of similar images.
@@ -157,8 +157,8 @@ def combine_frames_simple(
         list of fits files to combine
     instrument : str
         instrument id for modinfo
-    arm : str
-        instrument arm
+    channel : str
+        instrument channel
     extension : int, optional
         fits extension to load (default: 1)
     dtype : np.dtype, optional
@@ -175,13 +175,13 @@ def combine_frames_simple(
 
     # Load the first file to get the shape and header
     result, head = instrument.load_fits(
-        files[0], arm, dtype=dtype, extension=extension, **kwargs
+        files[0], channel, dtype=dtype, extension=extension, **kwargs
     )
 
     # Sum the remaining files
     for fname in files[1:]:
         data, _ = instrument.load_fits(
-            fname, arm, dtype=dtype, extension=extension, **kwargs
+            fname, channel, dtype=dtype, extension=extension, **kwargs
         )
         result += data
 
@@ -208,7 +208,7 @@ def combine_frames_simple(
 def combine_frames(
     files,
     instrument,
-    arm,
+    channel,
     extension=None,
     threshold=3.5,
     window=50,
@@ -276,8 +276,8 @@ def combine_frames(
         list of fits files to combine
     instrument : str
         instrument id for arminfo
-    arm : str
-        instrument arm
+    channel : str
+        instrument channel
     extension : int, optional
         fits extension to load (default: 1)
     threshold : float, optional
@@ -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):
@@ -315,7 +323,7 @@ def combine_frames(
         raise ValueError("No files given for combine frames")
     elif len(files) == 1:
         result, head = instrument.load_fits(
-            files[0], arm, dtype=dtype, extension=extension, **kwargs
+            files[0], channel, dtype=dtype, extension=extension, **kwargs
         )
         readnoise = np.atleast_1d(head.get("e_readn", 0))
         total_exposure_time = head.get("exptime", 0)
@@ -325,12 +333,12 @@ def combine_frames(
     # Two images
     elif len(files) == 2:
         bias1, head1 = instrument.load_fits(
-            files[0], arm, dtype=dtype, extension=extension, **kwargs
+            files[0], channel, dtype=dtype, extension=extension, **kwargs
         )
         exp1 = head1.get("exptime", 0)
 
         bias2, head2 = instrument.load_fits(
-            files[1], arm, dtype=dtype, extension=extension, **kwargs
+            files[1], channel, dtype=dtype, extension=extension, **kwargs
         )
         exp2 = head2.get("exptime", 0)
         readnoise = head2.get("e_readn", 0)
@@ -349,7 +357,7 @@ def combine_frames(
 
         heads = [
             instrument.load_fits(
-                f, arm, header_only=True, dtype=dtype, extension=extension, **kwargs
+                f, channel, header_only=True, dtype=dtype, extension=extension, **kwargs
             )
             for f in files
         ]
@@ -398,7 +406,7 @@ def combine_frames(
         # Load all image hdus, but leave the data on the disk, using memmap
         # Need to scale data later
         if extension is None:
-            extension = [instrument.get_extension(h, arm) for h in heads]
+            extension = [instrument.get_extension(h, channel) for h in heads]
         else:
             extension = [extension] * len(heads)
 
@@ -524,7 +532,7 @@ def combine_frames(
 def combine_calibrate(
     files,
     instrument,
-    arm,
+    channel,
     mask=None,
     bias=None,
     bhead=None,
@@ -545,8 +553,8 @@ def combine_calibrate(
         list of file names to load
     instrument : Instrument
         PyReduce instrument object with load_fits method
-    arm : str
-        descriptor of the instrument arm
+    channel : str
+        descriptor of the instrument channel
     mask : array
         2D Bad Pixel Mask to apply to the master image
     bias : tuple(bias, bhead), optional
@@ -575,7 +583,7 @@ def combine_calibrate(
         Unrecognised bias_scaling option
     """
     # Combine the images and try to remove bad pixels
-    orig, thead = combine_frames(files, instrument, arm, mask=mask, **kwargs)
+    orig, thead = combine_frames(files, instrument, channel, mask=mask, **kwargs)
 
     # Subtract bias
     if bias is not None and bias_scaling is not None and bias_scaling != "none":
@@ -636,7 +644,7 @@ def combine_calibrate(
 
 
 def combine_polynomial(
-    files, instrument, arm, mask, degree=1, plot=False, plot_title=None
+    files, instrument, channel, mask, degree=1, plot=False, plot_title=None
 ):
     """
     Combine the input files by fitting a polynomial of the pixel value versus
@@ -648,8 +656,8 @@ def combine_polynomial(
         list of file names
     instrument : Instrument
         PyReduce instrument object with load_fits method
-    arm : str
-        arm identifier for this instrument
+    channel : str
+        channel identifier for this instrument
     mask : array
         bad pixel mask to apply to the coefficients
     degree : int, optional
@@ -666,7 +674,7 @@ def combine_polynomial(
     bhead : Header
         combined FITS header of the coefficients
     """
-    hdus = [instrument.load_fits(f, arm) for f in tqdm(files)]
+    hdus = [instrument.load_fits(f, channel) for f in tqdm(files)]
     data = np.array([h[0] for h in hdus])
     exptimes = np.array([h[1]["EXPTIME"] for h in hdus])
     # Numpy polyfit can fit all polynomials at the same time
@@ -708,7 +716,7 @@ def combine_polynomial(
 def combine_bias(
     files,
     instrument,
-    arm,
+    channel,
     extension=None,
     plot=False,
     plot_title=None,
@@ -724,7 +732,7 @@ def combine_bias(
     files : list(str)
         bias files to combine
     instrument : str
-        instrument arm for arminfo
+        instrument channel for arminfo
     extension : {int, str}, optional
         fits extension to use (default: 1)
     xr : 2-tuple(int), optional
@@ -756,10 +764,10 @@ def combine_bias(
     n2 = len(list2)
 
     # Separately images in two groups.
-    bias1, head1 = combine_frames(list1, instrument, arm, extension, **kwargs)
+    bias1, head1 = combine_frames(list1, instrument, channel, extension, **kwargs)
     bias1 /= n1
 
-    bias2, head = combine_frames(list2, instrument, arm, extension, **kwargs)
+    bias2, head = combine_frames(list2, instrument, channel, extension, **kwargs)
     bias2 /= n2
 
     # Make sure we know the gain.

pyreduce/instruments/aj.yaml

@@ -9,7 +9,7 @@ telescope: Simulated
 date: DATE-OBS
 date_format: fits
 
-arms: [ALL]
+channels: [ALL]
 extension: 0
 orientation: 0
 transpose: false

pyreduce/instruments/andes.py

@@ -25,30 +25,30 @@ class ANDES(Instrument):
         self.filters["decker"] = Filter(self.info["id_decker"])
         self.shared += ["band", "decker"]
 
-    def add_header_info(self, header, arm, **kwargs):
+    def add_header_info(self, header, channel, **kwargs):
         """read data from header and add it as REDUCE keyword back to the header"""
         # "Normal" stuff is handled by the general version, specific changes to values happen here
         # alternatively you can implement all of it here, whatever works
-        band, decker, detector = self.parse_arm(arm)
+        band, decker, detector = self.parse_channel(channel)
         header = super().add_header_info(header, band)
         self.load_info()
 
         return header
 
-    def get_supported_arms(self):
+    def get_supported_channels(self):
         settings = self.info["settings"]
         deckers = self.info["deckers"]
         detectors = self.info["chips"]
-        arms = [
+        channels = [
             "_".join([s, d, c]) for s, d, c in product(settings, deckers, detectors)
         ]
-        return arms
+        return channels
 
-    def parse_arm(self, arm):
+    def parse_channel(self, channel):
         pattern = r"([A-Z]+)(_(Open|pos1|pos2))?_det(\d)"
-        match = re.match(pattern, arm, flags=re.IGNORECASE)
+        match = re.match(pattern, channel, flags=re.IGNORECASE)
         if not match:
-            raise ValueError(f"Invalid arm format: {arm}")
+            raise ValueError(f"Invalid channel format: {channel}")
         band = match.group(1).upper()
         if match.group(3) is not None:
             decker = match.group(3).lower().capitalize()
@@ -57,9 +57,9 @@ class ANDES(Instrument):
         detector = match.group(4)
         return band, decker, detector
 
-    def get_expected_values(self, target, night, arm):
+    def get_expected_values(self, target, night, channel):
         expectations = super().get_expected_values(target, night)
-        band, decker, detector = self.parse_arm(arm)
+        band, decker, detector = self.parse_channel(channel)
 
         for key in expectations.keys():
             if key == "bias":
@@ -69,28 +69,28 @@ class ANDES(Instrument):
 
         return expectations
 
-    def get_extension(self, header, arm):
-        band, decker, detector = self.parse_arm(arm)
+    def get_extension(self, header, channel):
+        band, decker, detector = self.parse_channel(channel)
         extension = int(detector)
         return extension
 
-    def get_wavecal_filename(self, header, arm, **kwargs):
+    def get_wavecal_filename(self, header, channel, **kwargs):
         """Get the filename of the wavelength calibration config file"""
         cwd = os.path.dirname(__file__)
-        fname = f"{self.name}_{arm}.npz"
+        fname = f"{self.name}_{channel}.npz"
         fname = os.path.join(cwd, "..", "wavecal", fname)
         return fname
 
-    def get_mask_filename(self, arm, **kwargs):
+    def get_mask_filename(self, channel, **kwargs):
         i = self.name.lower()
-        band, decker, detector = self.parse_arm(arm)
+        band, decker, detector = self.parse_channel(channel)
 
         fname = f"mask_{i}_det{detector}.fits.gz"
         cwd = os.path.dirname(__file__)
         fname = os.path.join(cwd, "..", "masks", fname)
         return fname
 
-    def get_wavelength_range(self, header, arm, **kwargs):
+    def get_wavelength_range(self, header, channel, **kwargs):
         wmin = [header["ESO INS WLEN MIN%i" % i] for i in range(1, 11)]
         wmax = [header["ESO INS WLEN MAX%i" % i] for i in range(1, 11)]
 

pyreduce/instruments/andes.yaml

@@ -15,7 +15,7 @@ id_band: "ESO INS WLEN ID"
 id_decker: "ESO INS OPTI8 ID"
 id_lamp: "ESO INS1 LAMP? ID"
 
-arms: [SL, IFU]
+channels: [SL, IFU]
 deckers: [Open, pos1, pos2]
 bands: [UBV, RIZ, YJH, K]
 settings: [B, V, R, IZ, Y, J, H, K]