pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/extraction_width.py

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+import logging
+
+import numpy as np
+
+from .util import make_index
+
+logger = logging.getLogger(__name__)
+
+
+def estimate_extraction_width(
+    img, orders, column_range, plot=False
+):  # pragma: no cover
+    raise NotImplementedError
+    nrow, ncol = img.shape
+    nord, _ = orders.shape
+    extraction_width = np.zeros((nord, 2), dtype=int)
+
+    for i in range(nord):
+        # first guess, half way to the next order
+        # To order above
+        if i < nord - 1:
+            beg = max(column_range[[i, i + 1], 0])
+            end = min(column_range[[i, i + 1], 1])
+            x = np.arange(beg, end)
+            y = np.polyval(orders[i], x)
+            y_above = np.polyval(orders[i + 1], x)
+            width_above = int(np.mean(y_above - y) // 2)
+
+        # To order below
+        if i > 0:
+            beg = max(column_range[[i - 1, i], 0])
+            end = min(column_range[[i - 1, i], 1])
+            x = np.arange(beg, end)
+            y = np.polyval(orders[i], x)
+            y_below = np.polyval(orders[i - 1], x)
+            width_below = int(np.mean(y - y_below) // 2)
+        else:
+            width_below = width_above
+
+        if i == nord - 1:
+            width_above = width_below
+
+        beg, end = column_range[i]
+        x = np.arange(beg, end)
+        y = np.polyval(orders[i], x)
+
+        y_int = y.astype(int)
+        y_above = y_int + width_above
+        y_below = y_int - width_below
+
+        if np.ma.any(y_above >= nrow) or np.ma.any(y_below < 0):
+            beg, end = np.where((y_above < nrow) & (y_below >= 0))[0][[0, -1]]
+
+        index = make_index(y_int - width_below, y_int + width_above, beg, end, True)
+
+        np.ma.sum(img[index], axis=1)
+
+        # TODO fit rectangular profile
+
+        # width = int(4 * coef[2])
+
+        # plt.plot(p, slitf)
+        # plt.plot(p, gaussval(p, *coef))
+        # plt.vlines([coef[1] - width, coef[1] + width], slitf.min(), slitf.max())
+        # plt.show()
+
+        # width_below = min(width_below, width)
+        # width_above = min(width_above, width)
+
+        # index = make_index(y_int - width_below, y_int + width_above, beg, end, True)
+
+        # plt.imshow(np.log(img[index]), aspect="auto", origin="lower")
+        # plt.show()
+        width = 0.5
+        extraction_width[i] = [width, width]
+
+    return extraction_width

pyreduce/instruments/aj.py

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+"""
+AJ instrument - simulated echelle spectrograph with 75 fibers per order.
+"""
+
+from .common import Instrument
+
+
+class AJ(Instrument):
+    pass

pyreduce/instruments/aj.yaml

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+# AJ instrument configuration
+# Simulated echelle spectrograph with 75 fibers per order
+
+__instrument__: AJ
+instrument: PYE1
+id_instrument: ".*ZEMAX.*"
+telescope: Simulated
+
+date: DATE-OBS
+date_format: fits
+
+arms: [ALL]
+extension: 0
+orientation: 0
+transpose: false
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: 1
+readnoise: 0
+dark: 0
+sky: 0
+exposure_time: EXPTIME
+
+ra: null
+dec: null
+target: PYE1
+
+# File classification
+# For fiber bundle tracing, we need separate even/odd flat files
+# These are matched by filename pattern since header values aren't reliable
+kw_bias: PYE1
+kw_flat: PYE1
+kw_flat_even: FILENAME
+kw_flat_odd: FILENAME
+kw_orders: PYE1
+kw_wave: PYE1
+kw_spec: PYE1
+
+id_bias: ".*bias.*"
+id_flat: ".*"
+id_flat_even: ".*even.*"
+id_flat_odd: ".*odd.*"
+id_orders: ".*"
+id_wave: ".*"
+id_spec: ".*"

pyreduce/instruments/andes.py

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+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+import re
+from itertools import product
+
+import numpy as np
+
+from .common import Instrument
+from .filters import Filter
+
+logger = logging.getLogger(__name__)
+
+
+class ANDES(Instrument):
+    def __init__(self):
+        super().__init__()
+        self.filters["lamp"] = Filter(self.info["id_lamp"])
+        self.filters["band"] = Filter(self.info["id_band"])
+        self.filters["decker"] = Filter(self.info["id_decker"])
+        self.shared += ["band", "decker"]
+
+    def add_header_info(self, header, arm, **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)
+        header = super().add_header_info(header, band)
+        self.load_info()
+
+        return header
+
+    def get_supported_arms(self):
+        settings = self.info["settings"]
+        deckers = self.info["deckers"]
+        detectors = self.info["chips"]
+        arms = [
+            "_".join([s, d, c]) for s, d, c in product(settings, deckers, detectors)
+        ]
+        return arms
+
+    def parse_arm(self, arm):
+        pattern = r"([A-Z]+)(_(Open|pos1|pos2))?_det(\d)"
+        match = re.match(pattern, arm, flags=re.IGNORECASE)
+        if not match:
+            raise ValueError(f"Invalid arm format: {arm}")
+        band = match.group(1).upper()
+        if match.group(3) is not None:
+            decker = match.group(3).lower().capitalize()
+        else:
+            decker = "Open"
+        detector = match.group(4)
+        return band, decker, detector
+
+    def get_expected_values(self, target, night, arm):
+        expectations = super().get_expected_values(target, night)
+        band, decker, detector = self.parse_arm(arm)
+
+        for key in expectations.keys():
+            if key == "bias":
+                continue
+            expectations[key]["band"] = band
+            expectations[key]["decker"] = decker
+
+        return expectations
+
+    def get_extension(self, header, arm):
+        band, decker, detector = self.parse_arm(arm)
+        extension = int(detector)
+        return extension
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = f"{self.name}_{arm}.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_mask_filename(self, arm, **kwargs):
+        i = self.name.lower()
+        band, decker, detector = self.parse_arm(arm)
+
+        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):
+        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)]
+
+        wavelength_range = np.array([wmin, wmax]).T
+        # Invert the order numbering
+        wavelength_range = wavelength_range[::-1]
+        # Convert from nm to Angstrom
+        wavelength_range *= 10
+        return wavelength_range

pyreduce/instruments/andes.yaml

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+# ANDES instrument configuration
+# Note: red and middle are in the same fits file, with different extensions,
+# i.e. share the same mode identifier, but have different extensions
+
+__instrument__: ANDES
+instrument: INSTRUME
+id_instrument: ANDES
+telescope: VLT
+
+date: DATE-OBS
+date_format: fits
+
+id_mode: "ESO INS MODE"
+id_band: "ESO INS WLEN ID"
+id_decker: "ESO INS OPTI8 ID"
+id_lamp: "ESO INS1 LAMP? ID"
+
+arms: [SL, IFU]
+deckers: [Open, pos1, pos2]
+bands: [UBV, RIZ, YJH, K]
+settings: [B, V, R, IZ, Y, J, H, K]
+chips: [det1]
+
+extension: CHIP1.INT1
+orientation: 0
+transpose: false
+
+prescan_x: 5
+overscan_x: 5
+prescan_y: 5
+overscan_y: 5
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: "HIERARCH ESO DET CHIP GAIN"
+readnoise: "HIERARCH ESO DET CHIP RON"
+dark: "HIERARCH ESO DET DIT"
+sky: 0
+exposure_time: EXPTIME
+
+image_type: OBJECT
+category: "HIERARCH ESO DPR CATG"
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: "HIERARCH ESO TEL GEOLON"
+latitude: "HIERARCH ESO TEL GEOLAT"
+altitude: "HIERARCH ESO TEL GEOELEV"
+target: OBJECT
+observation_type: "ESO DPR TYPE"
+
+id_lamp_wavecal: UNe_HCL
+id_lamp_etalon: Etalon_Halogen
+
+# File classification keywords and patterns
+kw_bias: "ESO DPR TYPE"
+kw_flat: "ESO DPR TYPE"
+kw_curvature: "ESO DPR TYPE"
+kw_scatter: "ESO DPR TYPE"
+kw_orders: "ESO DPR TYPE"
+kw_wave: "ESO DPR TYPE"
+kw_comb: "ESO DPR TYPE"
+kw_spec: "ESO DPR TYPE"
+
+id_bias: DARK
+id_flat: FLAT
+id_orders: FLAT
+id_curvature: "WAVE,FPET"
+id_scatter: FLAT
+id_wave: "WAVE,UNE"
+id_comb: "WAVE,FPET"
+id_spec: "STAR,*,*"