pyreduce-astro 0.7a3__cp313-cp313-win_amd64.whl → 0.7a5__cp313-cp313-win_amd64.whl

pyreduce/__main__.py

@@ -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,
@@ -161,20 +161,25 @@ def download(instrument):
     "--list", "-l", "list_examples", is_flag=True, help="List available examples"
 )
 @click.option("--all", "-a", "download_all", is_flag=True, help="Download all examples")
+@click.option("--run", "-r", is_flag=True, help="Run the example after downloading")
 @click.option("--output", "-o", default=".", help="Output directory")
-def examples(filename, list_examples, download_all, output):
-    """List or download example scripts from GitHub.
+def examples(filename, list_examples, download_all, run, output):
+    """List, download, or run example scripts from GitHub.
 
     Downloads examples matching your installed PyReduce version.
 
     \b
     Examples:
-        reduce examples              # List available examples
-        reduce examples uves_example.py    # Download to current dir
-        reduce examples --all -o ~/scripts # Download all to ~/scripts
+        reduce examples                     # List available examples
+        reduce examples uves_example.py     # Download to current dir
+        reduce examples -r uves_example.py  # Download and run
+        reduce examples --all -o ~/scripts  # Download all to ~/scripts
     """
     import json
     import os
+    import subprocess
+    import sys
+    import tempfile
     import urllib.request
     from urllib.error import HTTPError
 
@@ -212,6 +217,32 @@ def examples(filename, list_examples, download_all, output):
             click.echo(f"  {name}")
         return
 
+    if run and download_all:
+        raise click.ClickException("Cannot use --run with --all")
+
+    # Run mode: download to temp and execute
+    if run:
+        if filename not in example_files:
+            raise click.ClickException(
+                f"Unknown example '{filename}'. Use 'reduce examples --list' to see available."
+            )
+        url = f"{github_raw}/{filename}"
+        with tempfile.NamedTemporaryFile(mode="w", suffix=".py", delete=False) as f:
+            try:
+                with urllib.request.urlopen(url) as resp:
+                    f.write(resp.read().decode())
+                temp_path = f.name
+            except HTTPError as e:
+                raise click.ClickException(
+                    f"Failed to download {filename}: {e}"
+                ) from None
+        try:
+            click.echo(f"Running {filename}...")
+            result = subprocess.run([sys.executable, temp_path], check=False)
+            sys.exit(result.returncode)
+        finally:
+            os.unlink(temp_path)
+
     # Ensure output directory exists
     os.makedirs(output, exist_ok=True)
 
@@ -250,12 +281,12 @@ def make_step_command(step_name):
     @click.argument("instrument")
     @click.argument("target")
     @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):
+    def cmd(instrument, target, night, channel, base_dir, input_dir, output_dir, plot):
         from .configuration import get_configuration_for_instrument
         from .reduce import main as reduce_main
 
@@ -264,7 +295,7 @@ def make_step_command(step_name):
             instrument=instrument,
             target=target,
             night=night,
-            arms=arm,
+            channels=channel,
             steps=(step_name,),
             base_dir=base_dir or "",
             input_dir=input_dir,

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
@@ -315,7 +315,7 @@ 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 +325,12 @@ 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 +349,7 @@ 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 +398,7 @@ 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 +524,7 @@ def combine_frames(
 def combine_calibrate(
     files,
     instrument,
-    arm,
+    channel,
     mask=None,
     bias=None,
     bhead=None,
@@ -545,8 +545,8 @@ 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 +575,7 @@ 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 +636,7 @@ 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 +648,8 @@ 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 +666,7 @@ 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 +708,7 @@ def combine_polynomial(
 def combine_bias(
     files,
     instrument,
-    arm,
+    channel,
     extension=None,
     plot=False,
     plot_title=None,
@@ -724,7 +724,7 @@ 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 +756,10 @@ 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]