pyreduce-astro 0.7a4__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,
@@ -281,12 +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
 
@@ -295,7 +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]

pyreduce/instruments/common.py

@@ -18,7 +18,7 @@ from dateutil import parser
 from tqdm import tqdm
 
 from ..clipnflip import clipnflip
-from .filters import ArmFilter, Filter, InstrumentFilter, NightFilter, ObjectFilter
+from .filters import ChannelFilter, Filter, InstrumentFilter, NightFilter, ObjectFilter
 from .models import InstrumentConfig
 
 logger = logging.getLogger(__name__)
@@ -58,18 +58,18 @@ def observation_date_to_night(observation_date):
 
 
 class getter:
-    """Get data from a header/dict, based on the given arm, and applies replacements"""
+    """Get data from a header/dict, based on the given channel, and applies replacements"""
 
-    def __init__(self, header, info, arm):
+    def __init__(self, header, info, channel):
         self.header = header
         self.info = info.copy()
         try:
-            self.index = find_first_index(info["arms"], arm.upper())
+            self.index = find_first_index(info["channels"], channel.upper())
         except KeyError:
-            logger.warning("No instrument arms found in instrument info")
+            logger.warning("No instrument channels found in instrument info")
             self.index = 0
 
-        # Pick values for the given arm
+        # Pick values for the given channel
         for k, v in self.info.items():
             if isinstance(v, list):
                 self.info[k] = v[self.index]
@@ -133,10 +133,10 @@ class Instrument:
         self.science = "science"
         self.shared = ["instrument", "night"]
 
-        # Add arm filter if kw_arm is defined (for instruments with separate files per arm)
-        if self.config.kw_arm is not None:
-            self.filters["arm"] = ArmFilter(self.config.kw_arm)
-            self.shared.append("arm")
+        # Add channel filter if kw_channel is defined (for instruments with separate files per channel)
+        if self.config.kw_channel is not None:
+            self.filters["channel"] = ChannelFilter(self.config.kw_channel)
+            self.shared.append("channel")
         self.find_closest = [
             "bias",
             "flat",
@@ -151,9 +151,9 @@ class Instrument:
         return self.name
 
     @property
-    def arms(self) -> list[str] | None:
-        """Available instrument arms (detectors/channels)."""
-        return self.config.arms
+    def channels(self) -> list[str] | None:
+        """Available instrument channels."""
+        return self.config.channels
 
     @property
     def extension(self) -> int | str | list:
@@ -170,17 +170,17 @@ class Instrument:
         """Instrument identifier for header matching."""
         return self.config.id_instrument
 
-    def get(self, key, header, arm, alt=None):
-        get = getter(header, self.info, arm)
+    def get(self, key, header, channel, alt=None):
+        get = getter(header, self.info, channel)
         return get(key, alt=alt)
 
-    def get_extension(self, header, arm):
-        arm = arm.upper()
+    def get_extension(self, header, channel):
+        channel = channel.upper()
         ext = self.extension  # Use property
 
         if isinstance(ext, list):
-            iarm = find_first_index(self.arms, arm)
-            ext = ext[iarm]
+            ichannel = find_first_index(self.channels, channel)
+            ext = ext[ichannel]
 
         return ext
 
@@ -197,8 +197,8 @@ class Instrument:
             dictionary of REDUCE names for properties to Header keywords/static values
         """
         # Tips & Tricks:
-        # if several arms are supported, use a list for arms
-        # if a value changes depending on the arm, use a list with the same order as "arms"
+        # if several channels are supported, use a list for channels
+        # if a value changes depending on the channel, use a list with the same order as "channels"
         # you can also use values from this dictionary as placeholders using {name}, just like str.format
 
         this = os.path.dirname(__file__)
@@ -225,13 +225,13 @@ class Instrument:
         return config, info
 
     def load_fits(
-        self, fname, arm, extension=None, mask=None, header_only=False, dtype=None
+        self, fname, channel, extension=None, mask=None, header_only=False, dtype=None
     ):
         """
         load fits file, REDUCE style
 
         primary and extension header are combined
-        arm-specific info is applied to header
+        channel-specific info is applied to header
         data is clipnflipped
         mask is applied
 
@@ -241,8 +241,8 @@ class Instrument:
             filename
         instrument : str
             name of the instrument
-        arm : str
-            instrument arm (detector/channel)
+        channel : str
+            instrument channel
         extension : int
             data extension of the FITS file to load
         mask : array, optional
@@ -257,22 +257,22 @@ class Instrument:
         data : masked_array
             FITS data, clipped and flipped, and with mask
         header : fits.header
-            FITS header (Primary and Extension + arm info)
+            FITS header (Primary and Extension + channel info)
 
         ONLY the header is returned if header_only is True
         """
 
-        arm = arm.upper()
+        channel = channel.upper()
 
         hdu = fits.open(fname)
         h_prime = hdu[0].header
         if extension is None:
-            extension = self.get_extension(h_prime, arm)
+            extension = self.get_extension(h_prime, channel)
 
         header = hdu[extension].header
         if extension != 0:
             header.extend(h_prime, strip=False)
-        header = self.add_header_info(header, arm)
+        header = self.add_header_info(header, channel)
         header["e_input"] = (os.path.basename(fname), "Original input filename")
 
         if header_only:
@@ -289,15 +289,15 @@ class Instrument:
         hdu.close()
         return data, header
 
-    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
 
         Parameters
         ----------
         header : fits.header, dict
             header to read/write info from/to
-        arm : str
-            instrument arm (detector/channel)
+        channel : str
+            instrument channel
 
         Returns
         -------
@@ -306,7 +306,7 @@ class Instrument:
         """
 
         info = self.info
-        get = getter(header, info, arm)
+        get = getter(header, info, channel)
 
         # Use HIERARCH prefix only for FITS Header objects to avoid warnings
         # For dict objects, HIERARCH is not needed and would break key access
@@ -386,7 +386,7 @@ class Instrument:
         files = np.array(files)
         return files
 
-    def get_expected_values(self, target, night, arm=None, **kwargs):
+    def get_expected_values(self, target, night, channel=None, **kwargs):
         expectations = {
             "bias": {
                 "instrument": self.config.id_instrument,
@@ -431,13 +431,15 @@ class Instrument:
             },
         }
 
-        # Add arm filter if this instrument has separate files per arm
-        if arm is not None and self.config.kw_arm is not None:
-            id_arm = self.config.id_arm
-            arms = self.config.arms
-            arm_id = id_arm[arms.index(arm)] if arm in arms else arm
+        # Add channel filter if this instrument has separate files per channel
+        if channel is not None and self.config.kw_channel is not None:
+            id_channel = self.config.id_channel
+            channels = self.config.channels
+            channel_id = (
+                id_channel[channels.index(channel)] if channel in channels else channel
+            )
             for key in expectations:
-                expectations[key]["arm"] = arm_id
+                expectations[key]["channel"] = channel_id
 
         return expectations
 
@@ -618,8 +620,8 @@ class Instrument:
             name of the target as in the fits headers
         night : str
             observation night, possibly with wildcards
-        arm : str
-            instrument arm
+        channel : str
+            instrument channel
         Returns
         -------
         files_per_night : list[dict{str:dict{str:list[str]}}]
@@ -638,15 +640,15 @@ class Instrument:
         )
         return files
 
-    def get_wavecal_filename(self, header, arm, **kwargs):
+    def get_wavecal_filename(self, header, channel, **kwargs):
         """Get the filename of the pre-existing wavelength solution for the current setting
 
         Parameters
         ----------
         header : fits.header, dict
             header of the wavelength calibration file
-        arm : str
-            instrument arm
+        channel : str
+            instrument channel
 
         Returns
         -------
@@ -658,23 +660,23 @@ class Instrument:
         instrument = "wavecal"
 
         cwd = os.path.dirname(__file__)
-        fname = f"{instrument.lower()}_{arm}_{specifier}.npz"
+        fname = f"{instrument.lower()}_{channel}_{specifier}.npz"
         fname = os.path.join(cwd, "..", "wavecal", fname)
         return fname
 
-    def get_supported_arms(self):
-        return self.arms
+    def get_supported_channels(self):
+        return self.channels
 
-    def get_mask_filename(self, arm, **kwargs):
+    def get_mask_filename(self, channel, **kwargs):
         i = self.name.lower()
-        a = arm.lower()
-        fname = f"mask_{i}_{a}.fits.gz"
+        c = channel.lower()
+        fname = f"mask_{i}_{c}.fits.gz"
         cwd = os.path.dirname(__file__)
         fname = os.path.join(cwd, "..", "masks", fname)
         return fname
 
-    def get_wavelength_range(self, header, arm, **kwargs):
-        return self.get("wavelength_range", header, arm)
+    def get_wavelength_range(self, header, channel, **kwargs):
+        return self.get("wavelength_range", header, channel)
 
 
 class COMMON(Instrument):
@@ -699,13 +701,13 @@ def create_custom_instrument(
             except:
                 return None, info
 
-        def get_extension(self, header, arm):
+        def get_extension(self, header, channel):
             return extension
 
-        def get_mask_filename(self, arm, **kwargs):
+        def get_mask_filename(self, channel, **kwargs):
             return mask_file
 
-        def get_wavecal_filename(self, header, arm, **kwargs):
+        def get_wavecal_filename(self, header, channel, **kwargs):
             return wavecal_file
 
     return CUSTOM()