Merge pull request #45 from AstarVienna/dev_master

Merge dev_master into master for 0.4.3 release

MANIFEST.in

@@ -2,5 +2,7 @@ include README.md
 include LICENCE.txt
 include scopesim_templates/defaults.yaml
 include scopesim_templates/stellar/mamajek_alt.dat
+graft scopesim_templates/micado/data/
+graft scopesim_templates/micado/viking_fields/
 prune scopesim_templates/tests*
 prune *OLD_*

scopesim_templates/extragalactic/galaxy_utils.py

@@ -57,7 +57,7 @@ def sersic_profile(r_eff=100, n=4, ellipticity=0.5, angle=30,
     """
 
     # Silently cast to integer
-    os_factor = np.int(oversample)
+    os_factor = int(oversample)
 
     if os_factor <= 0:
         raise ValueError("Oversampling factor must be >=1.")

scopesim_templates/micado/__init__.py

@@ -1,5 +1,6 @@
 from .darkness import darkness as _darkness
 from .flatlamp import flatlamp as _flatlamp
+from .pinhole_masks import pinhole_mask as _pinhole_mask
 from .cluster import cluster as _cluster
 from .viking_fields import viking_fields
 from ..utils.general_utils import add_function_call_str
@@ -23,9 +24,14 @@ def flatlamp():
     return _flatlamp()
 
 
+@add_function_call_str
+def pinhole_mask():
+    return _pinhole_mask()
+
+
 @add_function_call_str
 def cluster():
     return _cluster()
 
 
-__all__ = [darkness, flatlamp, empty_sky, cluster]
+__all__ = [darkness, flatlamp, empty_sky, cluster, pinhole_mask]

scopesim_templates/micado/flatlamp.py

@@ -1,10 +1,10 @@
 """Flat lamp for MICADO."""
 import numpy
 import numpy as np
-import scopesim
 from astropy.io import fits
-from scopesim import Source
 import astropy.units as u
+from scopesim import Source
+import scopesim
 
 
 def flatlamp(
@@ -76,7 +76,8 @@ def flatlamp(
 
     sa = 1.0200000e+02
     se = 3.3502039e+05
-    lam = numpy.logspace(numpy.log(sa), numpy.log(se), base=numpy.e, num=number_of_points) * u.Angstrom
+    lam = numpy.logspace(numpy.log(sa), numpy.log(se), base=numpy.e,
+                         num=number_of_points) * u.Angstrom
 
     return Source(
             image_hdu=hdu,

scopesim_templates/micado/pinhole_masks.py

@@ -0,0 +1,60 @@
+import numpy as np
+from astropy import units as u
+from scopesim import Source
+from synphot import BlackBody1D, SourceSpectrum, Empirical1D
+
+
+def pinhole_mask(x, y, waves, temperature=1500*u.K, sum_factor=1):
+    """
+    Creates a Source object with point sources at coordinates (x, y) in the slit
+
+    Parameters
+    ----------
+    x, y : array-like
+        [arcsec] Coords relative to centre of FOV (i.e. optical axis)
+    waves : array-like, u.Quantity
+        [um] Array of wavelength values.
+    temperature : float, u.Quantity, optional
+        [deg K] Temperature of WCU blackbody spectrum.
+    sum_factor : float, optional
+        Rescale the spectrum to sum to this value
+
+
+    Returns
+    -------
+    src : scopesim.Source
+
+
+    Examples
+    --------
+    Pin-holes every 0.5 arcsec along the MICADO long-slit
+    ::
+        x = np.arange(-1.5, 13.51, 0.5)
+        y = np.zeros_like(x)
+        waves = np.arange(0.7, 2.5, 0.001) * u.um
+
+        src = pinhole_mask(x, y, waves, sum_factor=9001)
+
+    A grid of pin-holes every 5 arcsec for the MICADO 4mas IMG mode
+    ::
+        dr = np.arange(-25, 26, 5)      # [arcsec]
+        x, y = np.meshgrid(dr, dr)
+        x, y = x.flatten(), y.flatten()
+        waves = np.arange(0.7, 2.5, 0.001) * u.um
+
+        src = pinhole_mask(x, y, waves, sum_factor=9001)
+
+    """
+    if not isinstance(waves, u.Quantity):
+        waves *= u.um
+    if not isinstance(temperature, u.Quantity):
+        temperature *= u.K
+
+    blackbody_spectrum = BlackBody1D(temperature=temperature)
+    flux = blackbody_spectrum(waves.to(u.AA))
+    flux *= sum_factor / np.trapz(flux)
+    spec = SourceSpectrum(Empirical1D, points=waves, lookup_table=flux)
+    src = Source(x=x, y=y, ref=np.ones_like(x), weight=np.ones_like(x),
+                 spectra=[spec])
+
+    return src

scopesim_templates/stellar/mamajek_alt.dat

@@ -28,8 +28,8 @@ A4V     |  1.76 |  1.47 |  1.41 | 1.90
 A5V     |  1.84 |  1.51 |  1.44 | 1.85 
 A6V     |  1.89 |  1.54 |  1.46 | 1.83 
 A7V     |  2.07 |  1.64 |  1.54 | 1.76 
-A8V     |  2.29 |  1.78 |  1.66 | 1.67 
-A9V     |  2.30 |  1.78 |  1.66 | 1.67 
+A8V     |  2.29 |  1.78 |  1.66 | 1.68
+A9V     |  2.30 |  1.79 |  1.67 | 1.67
 F0V     |  2.51 |  1.90 |  1.76 | 1.59 
 F1V     |  2.79 |  2.13 |  1.96 | 1.50 
 F2V     |  2.99 |  2.26 |  2.07 | 1.44 
@@ -82,9 +82,9 @@ M5V     | 14.30 |  9.25 |  8.36 | 0.16
 M5.5V   | 15.51 |  9.93 |  9.01 | 0.12 
 M6V     | 16.62 | 10.28 |  9.32 | 0.10 
 M6.5V   | 17.07 | 10.47 |  9.47 | 0.097
-M7V     | 17.81 | 10.76 |  9.76 | 0.090
-M7.5V   | 18.42 | 10.68 |  9.97 | 0.089
+M7V     | 17.81 | 10.66 |  9.76 | 0.090
+M7.5V   | 18.42 | 10.78 |  9.97 | 0.089
 M8V     | 18.84 | 11.23 | 10.11 | 0.082
 M8.5V   | 19.14 | 11.45 | 10.22 | 0.081
 M9V     | 19.36 | 11.53 | 10.30 | 0.079
-M9V     | 30.00 | 20.00 | 20.00 | 0.01 
+M9.5V   | 30.00 | 20.00 | 20.00 | 0.01

scopesim_templates/stellar/stars.py

@@ -19,7 +19,8 @@
            ]
 
 
-def star_field(n, mmin, mmax, width, height=None, filter_name="V", ra=RA0, dec=DEC0, **kwargs):
+def star_field(n, mmin, mmax, width, height=None, filter_name="V",
+               ra=RA0, dec=DEC0, **kwargs):
     """
     Creates a super basic field of stars with random positions and brightnesses
 
@@ -145,7 +146,8 @@ def star_grid(n, mmin, mmax, filter_name="V", separation=1, ra=RA0, dec=DEC0):
 
 
 @deprecated_renamed_argument('mags', 'amplitudes', '0.1')
-def stars(filter_name, amplitudes, spec_types, x, y, library="pyckles", ra=RA0, dec=DEC0):
+def stars(filter_name, amplitudes, spec_types, x, y, library="pyckles",
+          ra=RA0, dec=DEC0):
     """
     Creates a scopesim.Source object for a list of stars with given amplitudes
     
@@ -166,9 +168,11 @@ def stars(filter_name, amplitudes, spec_types, x, y, library="pyckles", ra=RA0,
     ra, dec : float
         coordinates of the center of the field
     library: str
-        Library where the spectroscopic types are taken. By default are taken from the pickles library using
-        the `pyckles` package. Other libraries available are kurucz, bosz/lr, bosz/mr, bosz/hr, etc for MIR coverage
-        and different spectral resolutions. Please see the `spextra` package for more information
+        Library where the spectroscopic types are taken. By default are taken
+        from the pickles library using the `pyckles` package. Other libraries
+        available are kurucz, bosz/lr, bosz/mr, bosz/hr, etc for MIR coverage
+        and different spectral resolutions. Please see the `spextra` package
+        for more information
 
 
     Returns

scopesim_templates/tests/test_micado/test_flatlamp.py

@@ -1,6 +1,7 @@
 """Test for flatlamp."""
 from astropy.io.fits import ImageHDU
 from synphot import SourceSpectrum
+
 from scopesim_templates.micado import flatlamp
 from scopesim_templates.rc import Source
 

scopesim_templates/tests/test_micado/test_pinhole_mask.py

@@ -0,0 +1,46 @@
+"""Test for flatlamp."""
+import numpy as np
+from astropy.table import Table
+from astropy import units as u
+from matplotlib import pyplot as plt
+from synphot import SourceSpectrum
+
+from scopesim import load_example_optical_train
+
+from scopesim_templates.micado.pinhole_masks import pinhole_mask
+from scopesim_templates.rc import Source
+
+PLOTS = False
+
+
+class TestPinholeMask:
+    def test_pinhole_mask_returns_source_object(self):
+        """ Example from pinhole_mask docstring"""
+        dr = np.arange(-25, 26, 5)      # [arcsec]
+        x, y = np.meshgrid(dr, dr)
+        x, y = x.flatten(), y.flatten()
+        waves = np.arange(0.7, 2.5, 0.001) * u.um
+
+        ph_mask = pinhole_mask(x, y, waves, sum_factor=9001)
+
+        assert isinstance(ph_mask, Source)
+        assert isinstance(ph_mask.spectra[0], SourceSpectrum)
+        assert isinstance(ph_mask.fields[0], Table)
+
+    def test_pinhole_with_basic_instrument(self):
+        dr = np.arange(-25, 26, 5)      # [arcsec]
+        x, y = np.meshgrid(dr, dr)
+        x, y = x.flatten(), y.flatten()
+        waves = np.arange(0.7, 2.5, 0.001) * u.um
+
+        src = pinhole_mask(x, y, waves, sum_factor=9001)
+        opt = load_example_optical_train()
+        opt.observe(src)
+
+        im = opt.image_planes[0].data
+
+        if PLOTS:
+            plt.imshow(im)
+            plt.show()
+
+        assert np.max(im) > np.average(im)

scopesim_templates/tests/test_stellar/test_cluster_utils.py

@@ -36,8 +36,8 @@ def test_returns_a0v_for_2_3_msun(self):
     def test_returns_g2v_for_1_msun(self):
         assert cu.mass2spt(1.02) == "G2V"
 
-    def test_returns_m9v_for_0_01_msun(self):
-        assert cu.mass2spt(0.01) == "M9V"
+    def test_returns_m95v_for_0_01_msun(self):
+        assert cu.mass2spt(0.01) == "M9.5V"
 
     def test_multiple_masses_at_once(self):
         spts = cu.mass2spt([2.3, 1.02])

scopesim_templates/version.py

@@ -1,6 +1,10 @@
-version = '0.4.2'
-date    = '2022-07-12 17:00:00 GMT'
+version = '0.4.3'
+date    = '2023-02-15 17:00:00 GMT'
 yaml_descriptions = """
+- version : 0.4.3
+  date : 2023-02-15
+  comment : Add pinhole mask and minor bugfixes
+
 - version : 0.4.2
   date : 2022-07-12
   comment : Updated DLC server to point to scopesim.univie.ac.at