Merge dev_master in preparation for release

.github/workflows/badge_report.yml

@@ -27,10 +27,10 @@ jobs:
     name: Generate Badges
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.12
 

.github/workflows/notebooktests.yml

@@ -50,10 +50,10 @@ jobs:
     name: Run MICADO Notebooks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           # No matrix is used since this is a time-consuming task.
           python-version: 3.11
@@ -89,9 +89,9 @@ jobs:
     name: Run METIS Notebooks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           # No matrix is used since this is a time-consuming task.
           python-version: 3.11

.github/workflows/tests.yml

@@ -56,9 +56,9 @@ jobs:
         python-version: ['3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

HAWKI/test_hawki/test_full_package_hawki.py

@@ -80,8 +80,8 @@ def test_works_seamlessly_for_hawki_package(self, capsys):
 
         # test that we have a system throughput
         wave = np.linspace(0.7, 2.5, 181) * u.um
-        tc = opt.optics_manager.surfaces_table.throughput
-        ec = opt.optics_manager.surfaces_table.emission
+        tc = opt.optics_manager.system_transmission
+        # ec = opt.optics_manager.surfaces_table.emission
         # ..todo:: something super wierd is going on here when running pytest in the top directory
         # ..todo:: perhaps this is has to be relaxed due to different filter
         # assert 0.5 < np.max(tc(wave)).value < 0.55
@@ -91,9 +91,9 @@ def test_works_seamlessly_for_hawki_package(self, capsys):
             plt.plot(wave, tc(wave))
             plt.show()
 
-        if PLOTS:
-            plt.plot(wave, ec(wave))
-            plt.show()
+        # if PLOTS:
+        #     plt.plot(wave, ec(wave))
+        #     plt.show()
 
         # test that we have the correct number of FOVs for Ks band
         # assert len(opt.fov_manager.fovs) == 18

LFOA/tests/test_lfoa.py

@@ -38,7 +38,7 @@ def test_something_comes_out(self):
         if PLOTS:
             plt.subplot(121)
             wave = np.arange(3000, 11000)
-            plt.plot(wave, lfoa.optics_manager.surfaces_table.throughput(wave))
+            plt.plot(wave, lfoa.optics_manager.system_tranmission(wave))
 
             plt.subplot(122)
             im = hdus[0][1].data

METIS/code/LMS_Traces/README

@@ -0,0 +1,9 @@
+This directory contains a script `write_aperture_list.py`, which converts
+Alistair Glasse's LMS distortion files into FITS format as required by
+Scopesim. The required input files `lms_dist_poly.txt` and `lms_dist_wcal.txt`
+for the nominal distortion solution are provided (gunzip before use).
+
+The file `TRACE_LMS.fits` that is included in the METIS instrument package was
+originally created using the script (2021-09-08). The second extension was
+edited by hand on 2022-05-13 to reflect a change in the slice length (columns
+`xi_min` and `xi_max`). The script includes that change.

METIS/code/LMS_Traces/write_aperture_list.py

@@ -0,0 +1,101 @@
+"""
+Script to convert Alistair Glasse's LMS distortion files to FITS
+
+The file requires two input files defined as WCAL_FILE and POLY_FILE below.
+The output is a FITS file named TRACE_LMS.fits.
+"""
+import numpy as np
+from astropy.io import fits
+from astropy.io import ascii as ioascii
+
+NSLICE = 28
+SLITLENGTH = 109.4  # originally 122
+SLICEWIDTH = 0.0207
+PIXSCALE = 0.0082
+
+WCAL_FILE = "lms_dist_wcal.txt"
+POLY_FILE = "lms_dist_poly.txt"
+
+def aperture_list():
+    slice_id = np.arange(NSLICE) + 1
+    xi_max = np.array([SLITLENGTH * PIXSCALE / 2] * NSLICE)
+    xi_min = -xi_max
+    eta_min = (np.arange(NSLICE) - NSLICE / 2) * SLICEWIDTH
+    eta_max = eta_min + SLICEWIDTH
+    angle = np.array([0] * NSLICE)
+    conserve_image = [True] * NSLICE
+    shape = ["rect"] * NSLICE
+
+    hdu = fits.BinTableHDU.from_columns(
+        [fits.Column(name='id', format='I2', array=slice_id),
+         fits.Column(name='left', format='F.4', array=xi_min, unit="arcsec"),
+         fits.Column(name='right', format='F.4', array=xi_max, unit="arcsec"),
+         fits.Column(name='top', format='F.4', array=eta_max, unit="arcsec"),
+         fits.Column(name='bottom', format='F.4', array=eta_min, unit="arcsec"),
+         fits.Column(name='angle', format='F.1', array=angle, unit="deg"),
+         fits.Column(name='conserve_image', format='A4', array=conserve_image),
+         fits.Column(name='shape', format='A6', array=shape)
+         ])
+    hdu.header['EXTNAME'] = "Aperture List"
+    hdu.header['DESCRIPT'] = "Aperture List for METIS LMS, nominal mode"
+    hdu.header['X_UNIT'] = "arcsec"
+    hdu.header['Y_UNIT'] = "arcsec"
+    hdu.header['ANGLE_UNIT'] = "deg"
+    return hdu
+
+def wcal():
+    wcal = ioascii.read(WCAL_FILE, comment="^#", format="csv")
+    wcal['c0'].unit = "deg / um"
+    wcal['c1'].unit = "deg"
+    wcal['ic0'].unit = "um / deg"
+    wcal['ic1'].unit = "um"
+    hdu = fits.table_to_hdu(wcal)
+    hdu.header['EXTNAME'] = "WCAL"
+    return hdu
+
+
+def poly():
+    poly = ioascii.read(POLY_FILE, comment="^#", format="csv")
+    hdu = fits.table_to_hdu(poly)
+    hdu.header['EXTNAME'] = "Polynomial coefficients"
+    return hdu
+
+def catalogue():
+    desc = fits.Column(name="description", format="10A",
+                       array=["APERTURE", "WCAL", "POLY"])
+    ext_id = fits.Column(name="extension_id", format="I",
+                         array=[2, 3, 4])
+    aperture_id = fits.Column(name="aperture_id", format="I",
+                              array=[0, 0, 0])
+    image_plane_id = fits.Column(name="image_plane_id", format="I",
+                                 array=[0, 0, 0])
+    hdu = fits.BinTableHDU.from_columns([desc, ext_id, aperture_id, image_plane_id])
+    hdu.header['EXTNAME'] = "Catalogue"
+    return hdu
+
+if __name__ == "__main__":
+
+    pheader = fits.Header()
+    pheader['AUTHOR'] = "Oliver Czoske"
+    pheader['DATE'] = '2021-09-08'
+    pheader['ORIGDATE'] = '2021-09-08'
+    pheader['STATUS'] = 'Design'
+    pheader['SOURCE'] = "E-REP-ATC-MET-1003_2-0, E-REP-ATC-MET-1016_1-0"
+    pheader['DESCRIPT'] = "METIS LMS trace layout and slice definition"
+    pheader['DATE_CRE'] = "2021-09-08"
+    pheader['DATE_MOD'] = "2025-08-12"
+    pheader['FILETYPE'] = "Spectral Layout Definition"
+    pheader['ECAT'] = 1
+    pheader['EDATA'] = 2
+
+    primary_hdu = fits.PrimaryHDU(header=pheader)
+    catalogue_hdu = catalogue()
+    aperture_hdu = aperture_list()
+    wcal_hdu = wcal()
+    poly_hdu = poly()
+    hdul = fits.HDUList([primary_hdu,
+                         catalogue_hdu,
+                         aperture_hdu,
+                         wcal_hdu,
+                         poly_hdu])
+    hdul.writeto("TRACE_LMS.fits", overwrite=True)

METIS/wcu/fp_mask_grid_lms.dat

@@ -0,0 +1,38 @@
+# description : WCU focal plane mask, grid LMS
+# name : WCU FP mask
+# author : Oliver Czoske
+# source : LMS_astrometric_calibration_mask.pdf, RvB
+# date_created : 2025-08-02
+# date_modified : 2025-08-02
+# status : Design
+# type : aperture:aperture_mask
+# x_unit : arcsec
+# y_unit : arcsec
+# diam_unit : arcsec
+# changes :
+#
+ x         y          diam
+-0.320850    0.320850   0.007539
+-0.155250    0.320850   0.007539
+ 0.010350    0.320850   0.007539
+ 0.175950    0.320850   0.007539
+ 0.341550    0.320850   0.007539
+-0.320850    0.155250   0.007539
+-0.155250    0.155250   0.007539
+ 0.010350    0.155250   0.007539
+ 0.175950    0.155250   0.007539
+ 0.341550    0.155250   0.007539
+-0.320850   -0.010350   0.007539
+-0.155250   -0.010350   0.007539
+ 0.010350   -0.010350   0.007539
+ 0.175950   -0.010350   0.007539
+ 0.341550   -0.010350   0.007539
+-0.320850   -0.175950   0.007539
+ 0.010350   -0.175950   0.007539
+ 0.175950   -0.175950   0.007539
+ 0.341550   -0.175950   0.007539
+-0.320850   -0.341550   0.007539
+-0.155250   -0.341550   0.007539
+ 0.010350   -0.341550   0.007539
+ 0.175950   -0.341550   0.007539
+ 0.341550   -0.341550   0.007539

MICADO/MICADO_Standalone_RO.yaml

@@ -6,13 +6,14 @@ description : Simple stand-alone relay optics module
 
 properties :
     temperature : "!ATMO.temperature"
+    psf_file: "PSF_SCAO_ConstPSF_0_5off.fits"
 
 effects :
 -   name : relay_psf
     description : SCAO PSF
     class : FieldConstantPSF
     kwargs:
-        filename : PSF_SCAO_ConstPSF_0_5off.fits
+        filename : "!RO.psf_file"
         warning : "Default PSF is NOT field varying. See documentation."
 
 -   name: relay_surface_list

MICADO/code/make_scao_psf.py

@@ -0,0 +1,55 @@
+from astropy.io import fits
+import anisocado as aniso
+import argparse
+
+
+def make_standard_scao_constpsf(psf_size: int = 256, offset: float = 5.0):
+    waves = [1.2, 1.6, 2.15]
+    psfs = []
+    offset = 5
+
+    # override header to place PSF in the centre of the WCS
+    hdukeys = {
+        "CRPIX1" : int(psf_size/2) + 1,
+        "CRPIX2" : int(psf_size/2) + 1,
+        "CRVAL1" : 0,
+        "CRVAL2" : 0,
+    }
+
+    for wave in waves:
+        psf = aniso.AnalyticalScaoPsf(pixelSize=0.004, N=psf_size, wavelength=wave)
+        psf.shift_off_axis(0, offset)
+        hdr = psf.hdu.header
+        hdr.update(hdukeys)
+        psfs += [fits.ImageHDU(psf.hdu.data, header=hdr)]
+
+    keys = {"AUTHOR" : "Kieran Leschinski",
+            "DATE_CRE" : "2019-07-30",
+            "DATE_MOD" : "2019-07-30",
+            "SOURCE" : "AnisoCADO",
+            "STATUS" : "Best guess for a standard observations",
+            "ETYPE" : "CONSTPSF",
+            "ECAT" : (-1, "Field constant. No layer catalogue"),
+            "EDATA" : (1, "PSFs begin from EXT 1"),
+            "XOFFSET": (0, "[arcsec] offset from NGS"),
+            "YOFFSET": (offset, "[arcsec] offset from NGS"),
+            }
+
+    pri = fits.PrimaryHDU()
+    pri.header.update(keys)
+
+    hdus = fits.HDUList([pri] + psfs)
+    hdus.writeto(f"SCAO_ConstPSF_{offset}off_{psf_size}.fits", overwrite=True)
+    print(hdus.info())
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--psfsize', help='size of the PSF image in pixels',
+                        type=int, default=256)
+    parser.add_argument('--offset',
+                        help='psf offset from optical axis in arcseconds',
+                        type=float, default=5.0)
+    parser.print_usage()
+    args = parser.parse_args()
+
+    make_standard_scao_constpsf(args.psfsize, args.offset)