pyreduce-astro 0.6.0b1__py3-none-any.whl

pyreduce/extraction_width.py

@@ -0,0 +1,77 @@
+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/andes.json

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+{
+    "__comment__": "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_lamp": "ESO INS1 LAMP? ID",
+    "modes": ["SL", "IFU"],
+    "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",
+
+    "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,*,*",
+    "id_lamp_wavecal" : "UNe_HCL",
+    "id_lamp_etalon": "Etalon_Halogen"
+}

pyreduce/instruments/andes.py

@@ -0,0 +1,100 @@
+"""
+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, mode, **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_mode(mode)
+        header = super().add_header_info(header, band)
+        self.load_info()
+
+        return header
+
+    def get_supported_modes(self):
+        settings = self.info["settings"]
+        deckers = self.info["deckers"]
+        detectors = self.info["chips"]
+        modes = [
+            "_".join([s, d, c]) for s, d, c in product(settings, deckers, detectors)
+        ]
+        return modes
+
+    def parse_mode(self, mode):
+        pattern = r"([YJHKLM]\d{4})(_(Open|pos1|pos2))?_det(\d)"
+        match = re.match(pattern, mode, flags=re.IGNORECASE)
+        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, mode):
+        expectations = super().get_expected_values(target, night)
+        band, decker, detector = self.parse_mode(mode)
+
+        for key in expectations.keys():
+            if key == "bias":
+                continue
+            expectations[key]["band"] = band
+            expectations[key]["decker"] = decker
+
+        return expectations
+
+    def get_extension(self, header, mode):
+        band, decker, detector = self.parse_mode(mode)
+        extension = int(detector)
+        return extension
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = f"{self.name}_{mode}.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_mask_filename(self, mode, **kwargs):
+        i = self.name.lower()
+        band, decker, detector = self.parse_mode(mode)
+
+        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, mode, **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/common.json

@@ -0,0 +1,46 @@
+{
+    "__instrument__": "COMMON",
+    "instrument": "INSTRUME",
+    "id_instrument": "COMMON",
+    "telescope": "TELESCOP",
+    "target": "OBJECT",
+    "date": "DATE-OBS",
+    "date_format": "fits",
+    "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": "RA",
+    "dec": "DEC",
+    "longitude": null,
+    "latitude": null,
+    "altitude": null,
+    "__comment__": "These define the keywords we look for, and the values they should have in the fits header, to be sorted into that category",
+    "kw_bias" : "",
+    "kw_flat" : "",
+    "kw_curvature": "",
+    "kw_scatter": "",
+    "kw_orders" : "",
+    "kw_wave": "",
+    "kw_comb": "",
+    "kw_spec": "",
+    "id_bias" : "BIAS",
+    "id_flat": "FLAT",
+    "id_orders": "ORDER",
+    "id_curvature": "CURV",
+    "id_scatter": "SCATTER",
+    "id_wave": "WAVE",
+    "id_comb": "COMB",
+    "id_spec": "SPEC",
+    "wavelength_range": null
+}