Do not set user commands as rc.__currsys__

scopesim/effects/data_container.py

@@ -60,33 +60,56 @@ class DataContainer:
 
     """
 
+    meta = None
+
     def __init__(self, filename=None, table=None, array_dict=None, cmds=None,
                  **kwargs):
 
         self.cmds = cmds
+        # Setting a default for cmds cannot be done here, because from_currsys
+        # checks whether cmds is None. TODO: make this possible.
+        # if self.cmds is None:
+        #     from scopesim import UserCommands
+        #     self.cmds = UserCommands()
+
         if filename is None and "file_name" in kwargs:
             warn("The 'file_name' kwarg is deprecated and will raise an error "
                  "in the future, please use 'filename' instead!",
                  DeprecationWarning, stacklevel=2)
             filename = kwargs["file_name"]
 
+        # A !-string filename is immediately resolved, but the file is not yet
+        # searched for. This makes sense, as the filename should end up in the
+        # FITS headers, and should therefor be independent of any particular
+        # system.
+        #
+        # It would perhaps be even better to not resolve a !-string filename
+        # here, but that currently does not make sense because the file is
+        # directly read in. That is, the file would not be read again if
+        # someone changes the value that the !-string points to. So changing
+        # the value a !-string points to would lead to an inconsistent state.
+        # Immediately resolving the !-string prevents such an inconsistency.
         if isinstance(filename, str) and filename.startswith("!"):
             filename = utils.from_currsys(filename, self.cmds)
 
-        filename = utils.find_file(filename)
-        self.meta = {
+        # A derived clas might have set .meta before calling super().__init__()
+        if self.meta is None:
+            self.meta = {}
+        self.meta.update({
             "filename": filename,
             "description": "",
             "history": [],
             "name": "<empty>",
-        }
+        })
         self.meta.update(kwargs)
 
         self.headers = []
         self.table = None
         self._file = None
 
-        if filename is not None:
+        # Need to check whether the file exists before trying to load it.
+        filename_full = utils.find_file(self.meta["filename"])
+        if filename_full is not None:
             if self.is_fits:
                 self._load_fits()
             else:
@@ -116,7 +139,8 @@ def _from_arrays(self, array_dict):
         self.table.meta.update(self.meta)
 
     def _load_ascii(self):
-        self.table = ioascii.read(self.meta["filename"],
+        filename_full = utils.find_file(self.meta["filename"])
+        self.table = ioascii.read(filename_full,
                                   format="basic", guess=False)
         hdr_dict = utils.convert_table_comments_to_dict(self.table)
         if isinstance(hdr_dict, dict):
@@ -135,7 +159,8 @@ def _load_ascii(self):
                                  f"{self.meta['filename']}"]
 
     def _load_fits(self):
-        self._file = fits.open(self.meta["filename"])
+        filename_full = utils.find_file(self.meta["filename"])
+        self._file = fits.open(filename_full)
         for ext in self._file:
             self.headers += [ext.header]
 
@@ -186,7 +211,8 @@ def is_fits(self):
         if isinstance(self._file, fits.HDUList):
             flag = True
         elif isinstance(self.meta["filename"], str):
-            flag = utils.is_fits(self.meta["filename"])
+            filename_full = utils.find_file(self.meta["filename"])
+            flag = utils.is_fits(filename_full)
 
         return flag
 

scopesim/effects/effects.py

@@ -34,8 +34,8 @@ class Effect(DataContainer):
 
     """
 
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
+    def __init__(self, filename=None, **kwargs):
+        super().__init__(filename=filename, **kwargs)
         self.meta["z_order"] = []
         self.meta["include"] = True
         self.meta.update(kwargs)

scopesim/effects/electronic.py

@@ -105,9 +105,9 @@
 
         self.meta["detector_readout_mode"] = mode_name
         props_dict = self.mode_properties[mode_name]
-        rc.__currsys__["!OBS.detector_readout_mode"] = mode_name
+        self.cmds["!OBS.detector_readout_mode"] = mode_name
         for key, value in props_dict.items():
-            rc.__currsys__[key] = value
+            self.cmds[key] = value
 
         return obj
 
@@ -185,6 +185,9 @@
         params = {"z_order": [902]}
         self.meta.update(params)
         self.meta.update(kwargs)
+        if self.cmds is None:
+            from scopesim import UserCommands
+            self.cmds = UserCommands()
 
         required_keys = ["fill_frac", "full_well", "mindit"]
         check_keys(self.meta, required_keys, action="error")
@@ -226,8 +229,8 @@
             logger.info("Exposure parameters: DIT=%.3f s  NDIT=%d", dit, ndit)
             logger.info("Total exposure time: %.3f s", dit * ndit)
 
-            rc.__currsys__["!OBS.dit"] = dit
-            rc.__currsys__["!OBS.ndit"] = ndit
+            self.cmds["!OBS.dit"] = dit
+            self.cmds["!OBS.ndit"] = ndit
 
         return obj
 

scopesim/effects/fits_headers.py

@@ -425,7 +425,7 @@ class EffectsMetaKeywords(ExtraFitsKeywords):
     """
 
     def __init__(self, cmds=None, **kwargs):
-        super(ExtraFitsKeywords, self).__init__()
+        super(ExtraFitsKeywords, self).__init__(cmds=cmds, **kwargs)
         params = {"name": "effects_fits_keywords",
                   "description": "Effect Meta FITS headers",
                   "z_order": [998],
@@ -512,7 +512,7 @@ class SourceDescriptionFitsKeywords(ExtraFitsKeywords):
     """
 
     def __init__(self,  cmds=None, **kwargs):
-        super(ExtraFitsKeywords, self).__init__()
+        super(ExtraFitsKeywords, self).__init__(cmds=cmds, **kwargs)
         params = {"name": "source_fits_keywords",
                   "description": "Source description FITS headers",
                   "z_order": [997],
@@ -596,7 +596,7 @@ class SimulationConfigFitsKeywords(ExtraFitsKeywords):
     """
 
     def __init__(self, cmds=None, **kwargs):
-        super(ExtraFitsKeywords, self).__init__()
+        super(ExtraFitsKeywords, self).__init__(cmds=cmds, **kwargs)
         params = {"name": "simulation_fits_keywords",
                   "description": "Simulation Config FITS headers",
                   "z_order": [996],

scopesim/effects/metis_lms_trace_list.py

@@ -1,5 +1,5 @@
 """SpectralTraceList and SpectralTrace for the METIS LM spectrograph."""
-
+import copy
 import warnings
 
 import numpy as np
@@ -307,7 +307,8 @@
         y_min = aperture["bottom"]
         y_max = aperture["top"]
 
-        layout = ioascii.read(find_file("!DET.layout.filename"))
+        filename_det_layout = from_currsys("!DET.layout.file_name", cmds=self.cmds)
+        layout = ioascii.read(find_file(filename_det_layout))
         det_lims = {}
         xhw = layout["pixel_size"] * layout["x_size"] / 2
         yhw = layout["pixel_size"] * layout["y_size"] / 2
@@ -561,8 +562,11 @@
     }
 
     def __init__(self, **kwargs):
-        self.meta = self._class_params
-        self.meta.update(kwargs)
+        # TODO: Refactor these _class_params?
+        self.meta = copy.copy(self._class_params)
+        assert "grat_spacing" in self.meta, "grat_spacing is missing from self.meta 1"
+        super().__init__(**kwargs)
+        assert "grat_spacing" in self.meta, "grat_spacing is missing from self.meta 2"
 
         filename = find_file(self.meta["filename"])
         wcal = fits.getdata(filename, extname="WCAL")

scopesim/effects/psf_utils.py

@@ -109,9 +109,9 @@ def make_strehl_map_from_table(tbl, pixel_scale=1*u.arcsec):
     return map_hdu
 
 
-def rescale_kernel(image, scale_factor, spline_order=None):
+def rescale_kernel(image, scale_factor, spline_order=None, cmds=None):
     if spline_order is None:
-        spline_order = utils.from_currsys("!SIM.computing.spline_order")
+        spline_order = utils.from_currsys("!SIM.computing.spline_order", cmds=cmds)
     sum_image = np.sum(image)
     image = zoom(image, scale_factor, order=spline_order)
     image = np.nan_to_num(image, copy=False)        # numpy version >=1.13

scopesim/effects/psfs.py

@@ -495,7 +495,7 @@ def remake_kernel(self, x):
     def wavelength(self):
         wave = from_currsys(self.meta["wavelength"], self.cmds)
         if isinstance(wave, str) and wave in tu.FILTER_DEFAULTS:
-            wave = tu.get_filter_effective_wavelength(wave)
+            wave = tu.get_filter_effective_wavelength(wave, cmds=self.cmds)
         wave = quantify(wave, u.um).value
 
         return wave

scopesim/effects/ter_curves.py

@@ -73,8 +73,8 @@ class TERCurve
 
     """
 
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
+    def __init__(self, filename=None, **kwargs):
+        super().__init__(filename=filename, **kwargs)
         params = {
             "z_order": [10, 110, 510],
             "ignore_wings": False,
@@ -89,7 +89,7 @@ def __init__(self, **kwargs):
         self.meta.update(params)
         self.meta.update(kwargs)
 
-        self.surface = SpectralSurface()
+        self.surface = SpectralSurface(cmds=self.cmds)
         self.surface.meta.update(self.meta)
         self._background_source = None
 
@@ -398,7 +398,7 @@ def __init__(self, cmds=None, **kwargs):
                                  "(`filename`, `array_dict`, `table`) or both "
                                  f"(`filter_name`, `filename_format`): {kwargs}")
 
-        super().__init__(**kwargs)
+        super().__init__(cmds=cmds, **kwargs)
         if self.table is None:
             raise ValueError("Could not initialise filter. Either filename "
                              "not found, or array are not compatible")
@@ -872,7 +872,7 @@ def __init__(self, transmission, cmds=None, **kwargs):
         self.cmds = cmds
         wave_min = from_currsys(self.params["wave_min"], self.cmds) * u.um
         wave_max = from_currsys(self.params["wave_max"], self.cmds) * u.um
-        transmission = from_currsys(transmission)
+        transmission = from_currsys(transmission, cmds=self.cmds)
 
         super().__init__(wavelength=[wave_min, wave_max],
                          transmission=[transmission, transmission],
@@ -901,8 +901,8 @@ class ADCWheel(Effect):
     required_keys = {"adc_names", "filename_format", "current_adc"}
     _current_str = "current_adc"
 
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
+    def __init__(self, cmds=None, **kwargs):
+        super().__init__(cmds=cmds, **kwargs)
         check_keys(kwargs, self.required_keys, action="error")
 
         params = {"z_order": [125, 225, 525],
@@ -915,9 +915,10 @@ def __init__(self, **kwargs):
 
         path = self._get_path()
         self.adcs = {}
-        for name in from_currsys(self.meta["adc_names"]):
+        for name in from_currsys(self.meta["adc_names"], cmds=self.cmds):
             kwargs["name"] = name
             self.adcs[name] = TERCurve(filename=str(path).format(name),
+                                       cmds=cmds,
                                        **kwargs)
 
         self.table = self.get_table()
@@ -937,7 +938,7 @@ def change_adc(self, adcname=None):
     @property
     def current_adc(self):
         """Return the currently used ADC."""
-        curradc = from_currsys(self.meta["current_adc"])
+        curradc = from_currsys(self.meta["current_adc"], cmds=self.cmds)
         if not curradc:
             return False
         return self.adcs[curradc]

scopesim/effects/ter_curves_utils.py

@@ -50,9 +50,9 @@
 PATH_SVO_DATA = PATH_HERE.parent / "data" / "svo"
 
 
-def get_filter_effective_wavelength(filter_name):
+def get_filter_effective_wavelength(filter_name, cmds=None):
     if isinstance(filter_name, str):
-        filter_name = from_currsys(filter_name)
+        filter_name = from_currsys(filter_name, cmds=cmds)
         wave, trans = download_svo_filter(FILTER_DEFAULTS[filter_name],
                                           return_style="quantity")
         eff_wave = np.sum(wave * trans) / np.sum(trans)      # convert from Angstrom

scopesim/optics/fov.py

@@ -563,10 +563,10 @@ def make_cube_hdu(self):
 
         # 1. Make waveset and canvas cube (area, bin_width are applied at end)
         # TODO: Why is this not self.waveset? What's different?
-        wave_unit = u.Unit(from_currsys("!SIM.spectral.wave_unit"), self.cmds)
+        wave_unit = u.Unit(from_currsys("!SIM.spectral.wave_unit", self.cmds))
         fov_waveset = np.arange(
             self.meta["wave_min"].value, self.meta["wave_max"].value,
-            from_currsys("!SIM.spectral.spectral_bin_width"), self.cmds) * wave_unit
+            from_currsys("!SIM.spectral.spectral_bin_width", self.cmds)) * wave_unit
         fov_waveset = fov_waveset.to(u.um)
 
         # TODO: what's with this code??

scopesim/optics/fov_manager.py

@@ -166,8 +166,13 @@ def generate_fovs_list(self):
                 det_eff = eu.get_all_effects(self.effects, DetectorList)[0]
                 dethdr = det_eff.image_plane_header
 
-            fovs.append(FieldOfView(skyhdr, waverange, detector_header=dethdr,
-                                    **vol["meta"]))
+            fovs.append(FieldOfView(
+                skyhdr,
+                waverange,
+                detector_header=dethdr,
+                cmds=self.cmds,
+                **vol["meta"],
+            ))
 
         return fovs
 

scopesim/optics/optical_train.py

@@ -139,7 +139,10 @@
         #        UserCommands via rc.__currsys__, but on the other hand some
         #        tests (now with proper patching) fail because of this type
         #        change. THIS IS A PROBLEM!
-        rc.__currsys__ = user_commands
+        # NOTE: All tests pass without setting rc.__currsys__ to user_commands.
+        #       Nevertheless, I'm a bit reluctant to removing this code just
+        #       yet. So it is commented out.
+        # rc.__currsys__ = user_commands
         self.yaml_dicts = self.cmds.yaml_dicts
         self.optics_manager = OpticsManager(self.yaml_dicts, self.cmds)
         self.update()
@@ -323,7 +326,7 @@
             # Put on fov wavegrid
             wave_min = min(fov.meta["wave_min"] for fov in self.fov_manager.fovs)
             wave_max = max(fov.meta["wave_max"] for fov in self.fov_manager.fovs)
-            wave_unit = u.Unit(from_currsys("!SIM.spectral.wave_unit"), self.cmds)
+            wave_unit = u.Unit(from_currsys("!SIM.spectral.wave_unit", self.cmds))
             dwave = from_currsys("!SIM.spectral.spectral_bin_width", self.cmds)  # Not a quantity
             fov_waveset = np.arange(wave_min.value, wave_max.value, dwave) * wave_unit
             fov_waveset = fov_waveset.to(u.um)