Additional hotfix for the removed currsys

pyproject.toml

@@ -85,10 +85,12 @@ filterwarnings = [
     # Should probably be fixed:
     "ignore::ResourceWarning",
     "ignore:The fit may be poorly conditioned:astropy.utils.exceptions.AstropyUserWarning",
+    "ignore::astropy.units.core.UnitsWarning",
     # Perhaps fix?
     "ignore:divide by zero encountered in scalar divide:RuntimeWarning",
     "ignore:divide by zero encountered in double_scalars:RuntimeWarning",
     "ignore:invalid value encountered in multiply:RuntimeWarning",
+    "ignore:invalid value encountered in divide:RuntimeWarning",
     "ignore:Cannot merge meta key.*:astropy.utils.metadata.MergeConflictWarning",
     "default:The fov_grid*:DeprecationWarning",
     # Raised when saving fits files, not so important to fix:
@@ -102,7 +104,7 @@ filterwarnings = [
     "ignore:datetime.datetime.utcfromtimestamp()*:DeprecationWarning",
     # Pytest Notebook stuff
     "ignore:The*:pytest.PytestRemovedIn8Warning",
-    "ignore:Proactor*:RuntimeWarning"
+    "ignore:Proactor*:RuntimeWarning",
 ]
 
 [tool.coverage.report]

scopesim/effects/data_container.py

@@ -128,6 +128,9 @@
         self.meta.update(hdr_dict)
         # self.table.meta.update(hdr_dict)
         self.table.meta.update(self.meta)
+        if self.table.meta.get("cmds"):
+            self.table.meta.pop("cmds")
+
         self.meta["history"] += ["ASCII table read from "
                                  f"{self.meta['filename']}"]
 

scopesim/effects/effects_utils.py

@@ -13,30 +13,6 @@
 logger = get_logger(__name__)
 
 
-def combine_surface_effects_OLD(surface_effects):
-    surflist_list = [eff for eff in surface_effects
-                     if isinstance(eff, efs.SurfaceList)]
-    surf_list = [eff for eff in surface_effects
-                 if isinstance(eff, efs.TERCurve)]
-
-    if len(surflist_list) == 0:
-        surf = empty_surface_list()
-        surf.meta["name"] = "Radiometry Table"
-        surflist_list += [surf]
-
-    new_surflist = deepcopy(surflist_list[0])
-    for surflist in surflist_list[1:]:
-        new_surflist.add_surface_list(surflist)
-
-    for surf in surf_list:
-        position = surf.meta["position"] if "position" in surf.meta else -1
-        new_surflist.add_surface(surf, surf.meta["name"], position=position)
-
-    new_surflist.table = new_surflist.radiometry_table.table
-
-    return new_surflist
-
-
 def combine_surface_effects(surface_effects):
     surflist_list = [eff for eff in surface_effects
                      if isinstance(eff, efs.SurfaceList)]

scopesim/effects/fits_headers.py

@@ -218,7 +218,7 @@ class ExtraFitsKeywords(Effect):
 
     """
 
-    def __init__(self, **kwargs):
+    def __init__(self, cmds=None, **kwargs):
         # don't pass kwargs, as DataContainer can't handle yaml files
         super().__init__()
         params = {"name": "extra_fits_keywords",
@@ -419,7 +419,7 @@ class EffectsMetaKeywords(ExtraFitsKeywords):
 
     """
 
-    def __init__(self, **kwargs):
+    def __init__(self, cmds=None, **kwargs):
         super(ExtraFitsKeywords, self).__init__()
         params = {"name": "effects_fits_keywords",
                   "description": "Effect Meta FITS headers",
@@ -453,7 +453,7 @@ def apply_to(self, hdul, **kwargs):
                 keys = list(eff_meta.keys())
                 for key in keys:
                     value = eff_meta[key]
-                    if key in ["history", "notes", "changes"]:
+                    if key in ["history", "notes", "changes", "cmds"]:
                         eff_meta.pop(key)
                     if isinstance(value, Table):
                         eff_meta[key] = f"Table object of length: {len(value)}"
@@ -506,7 +506,7 @@ class SourceDescriptionFitsKeywords(ExtraFitsKeywords):
 
     """
 
-    def __init__(self, **kwargs):
+    def __init__(self,  cmds=None, **kwargs):
         super(ExtraFitsKeywords, self).__init__()
         params = {"name": "source_fits_keywords",
                   "description": "Source description FITS headers",
@@ -590,7 +590,7 @@ class SimulationConfigFitsKeywords(ExtraFitsKeywords):
 
     """
 
-    def __init__(self, **kwargs):
+    def __init__(self, cmds=None, **kwargs):
         super(ExtraFitsKeywords, self).__init__()
         params = {"name": "simulation_fits_keywords",
                   "description": "Simulation Config FITS headers",

scopesim/effects/spectral_trace_list.py

@@ -489,9 +489,9 @@ def __init__(self, **kwargs):
         self.trace_lists = {}
         for name in from_currsys(self.meta["trace_list_names"], self.cmds):
             kwargs["name"] = name
+            kwargs["cmds"] = self.cmds
             fname = str(path).format(name)
             self.trace_lists[name] = SpectralTraceList(filename=fname,
-                                                       cmds=self.cmds,
                                                        **kwargs)
 
     def apply_to(self, obj, **kwargs):

scopesim/effects/surface_list.py

@@ -1,12 +1,14 @@
 """TBA."""
+from collections import OrderedDict
+from copy import deepcopy
 
 import warnings
 import numpy as np
 from astropy import units as u
 
 from .ter_curves import TERCurve, FilterWheelBase
 from ..optics import radiometry_utils as rad_utils
-from ..optics.surface import PoorMansSurface
+from ..optics.surface import PoorMansSurface, SpectralSurface
 from ..utils import quantify, from_currsys, figure_factory
 
 
@@ -21,11 +23,18 @@ def __init__(self, **kwargs):
         self.meta.update(params)
         self.meta.update(kwargs)
 
-        tbl = from_currsys(self.table, self.cmds)
-        self.surfaces = rad_utils.make_surface_dict_from_table(tbl)
         self._surface = None
         self._throughput = None
         self._emission = None
+        self.surfaces = OrderedDict({})
+
+        if self.table is not None:
+            for row in self.table:
+                surf_kwargs = deepcopy(self.table.meta)
+                surf_kwargs.update(dict(row))
+                surf_kwargs["cmds"] = self.cmds
+                surf_kwargs["filename"] = from_currsys(surf_kwargs["filename"], self.cmds)
+                self.surfaces[surf_kwargs["name"]] = SpectralSurface(**surf_kwargs)
 
     def fov_grid(self, which="waveset", **kwargs):
         warnings.warn("The fov_grid method is deprecated and will be removed "
@@ -137,8 +146,8 @@ def add_surface(self, surface, name=None, position=-1, add_to_table=True):
     def add_surface_list(self, surface_list, prepend=False):
         if isinstance(surface_list, SurfaceList):
             self.surfaces.update(surface_list.surfaces)
-            new_tbl = from_currsys(surface_list.table, self.cmds),
-            self.table = rad_utils.combine_tables(new_tbl, self.table, prepend)
+            # new_tbl = from_currsys(surface_list.table, self.cmds),
+            self.table = rad_utils.combine_tables(surface_list.table, self.table, prepend)
 
     def plot(self, which="x", wavelength=None, *, axes=None, **kwargs):
         """Plot TER curves.

scopesim/optics/__init__.py

@@ -9,7 +9,6 @@
 
 from .surface import SpectralSurface
 from . import surface_utils
-from .radiometry import RadiometryTable
 from . import radiometry_utils
 
 from .fov import FieldOfView

scopesim/optics/optics_manager.py

@@ -94,7 +94,7 @@ def load_effects(self, yaml_dicts, **kwargs):
         """
         if not isinstance(yaml_dicts, Sequence):
             yaml_dicts = [yaml_dicts]
-        self.optical_elements.extend(OpticalElement(dic, **kwargs)
+        self.optical_elements.extend(OpticalElement(dic, cmds=self.cmds, **kwargs)
                                      for dic in yaml_dicts if "effects" in dic)
 
     def add_effect(self, effect, ext=0):

scopesim/optics/radiometry_utils.py

@@ -144,28 +144,3 @@ def add_surface_to_table(tbl, surf, name, position, silent=True):
     new_tbl = change_table_entry(new_tbl, colname, name, position=position)
 
     return new_tbl
-
-
-def add_surface_to_dict(dic, surf, name, position=0):
-    new_entry = OrderedDict({name : surf})
-    dic = insert_into_ordereddict(dic, new_entry, position)
-
-    return dic
-
-
-def make_surface_dict_from_table(tbl):
-    surf_dict = OrderedDict({})
-    if tbl is not None and len(tbl) > 0:
-        names = tbl[real_colname("name", tbl.colnames)]
-        for ii, row in enumerate(tbl):
-            surf_dict[names[ii]] = make_surface_from_row(row, **tbl.meta)
-
-    return surf_dict
-
-
-def make_surface_from_row(row, **kwargs):
-    row_dict = {colname.lower(): row[colname] for colname in row.colnames}
-    kwargs.update(row_dict)
-    surface = SpectralSurface(**kwargs)
-
-    return surface