From 2f39b674b0269fcdc6583a88ef54933377cfefdd Mon Sep 17 00:00:00 2001
From: teutoburg <ghost@instruct.at>
Date: Fri, 4 Aug 2023 17:15:03 +0200
Subject: [PATCH 1/6] Improved plot methods using mpl OOP API and more configs

---
 scopesim/effects/detector_list.py             | 23 ++---
 scopesim/effects/spectral_trace_list.py       | 19 +++--
 scopesim/effects/spectral_trace_list_utils.py | 85 +++++++++++++------
 3 files changed, 83 insertions(+), 44 deletions(-)

diff --git a/scopesim/effects/detector_list.py b/scopesim/effects/detector_list.py
index 405e21e6..d093401c 100644
--- a/scopesim/effects/detector_list.py
+++ b/scopesim/effects/detector_list.py
@@ -4,6 +4,8 @@
 from astropy import units as u
 from astropy.table import Table
 
+from matplotlib import pyplot as plt
+
 from ..base_classes import FOVSetupBase
 from .effects import Effect
 from .apertures import ApertureMask
@@ -251,22 +253,21 @@ def detector_headers(self, ids=None):
 
         return hdrs
 
-    def plot(self):
-        import matplotlib.pyplot as plt
-        plt.gcf().clf()
+    def plot(self, axes=None):
+        if axes is None:
+            _, axes = plt.subplots()
 
         for hdr in self.detector_headers():
             x_mm, y_mm = calc_footprint(hdr, "D")
-            x_cen, y_cen = np.average(x_mm), np.average(y_mm)
-            x_mm = list(x_mm) + [x_mm[0]]
-            y_mm = list(y_mm) + [y_mm[0]]
-            plt.gca().plot(x_mm, y_mm)
-            plt.gca().text(x_cen, y_cen, hdr["ID"])
+            axes.plot(np.append(x_mm, x_mm[0]), np.append(y_mm, y_mm[0]))
+            axes.text(*np.mean((x_mm, y_mm), axis=1), hdr["ID"],
+                      ha="center", va="center")
 
-        plt.gca().set_aspect("equal")
-        plt.ylabel("Size [mm]")
+        axes.set_aspect("equal")
+        axes.set_xlabel("Size [mm]")
+        axes.set_ylabel("Size [mm]")
 
-        return plt.gcf()
+        return axes
 
 
 class DetectorWindow(DetectorList):
diff --git a/scopesim/effects/spectral_trace_list.py b/scopesim/effects/spectral_trace_list.py
index 553c7879..fa935d79 100644
--- a/scopesim/effects/spectral_trace_list.py
+++ b/scopesim/effects/spectral_trace_list.py
@@ -7,8 +7,10 @@
 
 from pathlib import Path
 import logging
+from itertools import cycle
 
 import numpy as np
+from matplotlib import pyplot as plt
 
 from astropy.io import fits
 from astropy.table import Table
@@ -318,23 +320,22 @@ def rectify_cube(self, hdulist):
         """Rectify traces and combine into a cube"""
         raise(NotImplementedError)
 
-    def plot(self, wave_min=None, wave_max=None, **kwargs):
+    def plot(self, wave_min=None, wave_max=None, axes=None, **kwargs):
         if wave_min is None:
             wave_min = from_currsys("!SIM.spectral.wave_min")
         if wave_max is None:
             wave_max = from_currsys("!SIM.spectral.wave_max")
 
-        from matplotlib import pyplot as plt
-        from matplotlib._pylab_helpers import Gcf
-        if len(Gcf.figs) == 0:
-            plt.figure(figsize=(12, 12))
+        if axes is None:
+            fig, axes = plt.subplots(figsize=(12, 12))
+        else:
+            fig = axes.figure
 
         if self.spectral_traces is not None:
-            clrs = "rgbcymk" * (1 + len(self.spectral_traces) // 7)
-            for spt, c in zip(self.spectral_traces.values(), clrs):
-                spt.plot(wave_min, wave_max, c=c)
+            for spt, c in zip(self.spectral_traces.values(), cycle("rgbcymk")):
+                spt.plot(wave_min, wave_max, c=c, axes=axes, **kwargs)
 
-        return plt.gcf()
+        return fig
 
     def __repr__(self):
         # "\n".join([spt.__repr__() for spt in self.spectral_traces])
diff --git a/scopesim/effects/spectral_trace_list_utils.py b/scopesim/effects/spectral_trace_list_utils.py
index d43df124..815b831e 100644
--- a/scopesim/effects/spectral_trace_list_utils.py
+++ b/scopesim/effects/spectral_trace_list_utils.py
@@ -17,7 +17,7 @@
 from scipy.interpolate import interp1d
 from matplotlib import pyplot as plt
 
-from astropy.table import Table
+from astropy.table import Table, vstack
 from astropy.modeling import fitting
 from astropy.io import fits
 from astropy import units as u
@@ -481,43 +481,80 @@ def footprint(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None):
         return ([x_edge.min(), x_edge.max(), x_edge.max(), x_edge.min()],
                 [y_edge.min(), y_edge.min(), y_edge.max(), y_edge.max()])
 
-    def plot(self, wave_min=None, wave_max=None, c="r"):
+    def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
+             c="r", axes=None, plot_footprint=True, plot_text=True,
+             plot_ctrlpnts=True, plot_outline=False, plot_trace_id=False):
         """Plot control points of the SpectralTrace"""
+        if axes is None:
+            _, axes = plt.subplots()
 
         # Footprint (rectangle enclosing the trace)
         xlim, ylim  = self.footprint(wave_min=wave_min, wave_max=wave_max)
         if xlim is None:
-            return
+            return axes
 
         xlim.append(xlim[0])
         ylim.append(ylim[0])
-        plt.plot(xlim, ylim)
+        if plot_footprint:
+            axes.plot(xlim, ylim)
+
+        # for convenience...
+        xname = self.meta["x_colname"]
+        yname = self.meta["y_colname"]
+        wname = self.meta["wave_colname"]
+        sname = self.meta["s_colname"]
 
         # Control points
-        waves = self.table[self.meta["wave_colname"]]
+        waves = self.table[wname]
         if wave_min is None:
             wave_min = waves.min()
         if wave_max is None:
             wave_max = waves.max()
-
-        mask = (waves >= wave_min) * (waves <= wave_max)
-        if sum(mask) > 2:
-            w = waves[mask]
-
-            x = self.table[self.meta["x_colname"]][mask]
-            y = self.table[self.meta["y_colname"]][mask]
-            plt.plot(x, y, "o", c=c)
-
-            for wave in np.unique(w):
-                xx = x[w==wave]
-                xx.sort()
-                dx = xx[-1] - xx[-2]
-
-                plt.text(x[w==wave].max() + 0.5 * dx,
-                         y[w==wave].mean(),
-                         str(wave), va='center', ha='left')
-
-            plt.gca().set_aspect("equal")
+        xis = self.table[sname]
+        if xi_min is None:
+            xi_min = xis.min()
+        if xi_max is None:
+            xi_max = xis.max()
+
+        mask = ((waves >= wave_min) & (waves <= wave_max)
+                & (xis >= xi_min)& (xis <= xi_max))
+        if sum(mask) <= 2:
+            return axes
+
+        w = waves[mask]
+
+        x = self.table[xname][mask]
+        y = self.table[yname][mask]
+        if plot_ctrlpnts:
+            axes.plot(x, y, "o", c=c)
+
+        if plot_outline:
+            blue_end = self.table[mask][w == w.min()]
+            red_end = self.table[mask][w == w.max()]
+            blue_end.sort(sname)
+            red_end.sort(sname)
+            corners = vstack([blue_end[[0, -1]][xname, yname],
+                              red_end[[-1, 0]][xname, yname],
+                              blue_end[0][xname, yname]])
+            axes.plot(corners[xname], corners[yname], c=c)
+
+        if plot_trace_id:
+            axes.text(corners[xname][:-1].mean(), corners[yname][:-1].mean(),
+                      self.meta["trace_id"], c=c, rotation="vertical",
+                      ha="center", va="center")
+
+        for wave in np.unique(w):
+            xx = x[w==wave]
+            xx.sort()
+            dx = xx[-1] - xx[-2]
+
+            if plot_text:
+                axes.text(x[w==wave].max() + 0.5 * dx,
+                          y[w==wave].mean(),
+                          str(wave), va="center", ha="left")
+
+        axes.set_aspect("equal")
+        return axes
 
     @property
     def trace_id(self):

From 50f92dec97be4c8ce050c06770914192b4c8aedc Mon Sep 17 00:00:00 2001
From: teutoburg <ghost@instruct.at>
Date: Fri, 4 Aug 2023 17:15:32 +0200
Subject: [PATCH 2/6] Define some _repr_pretty_ methods for IPython display

---
 scopesim/detector/detector_array.py | 15 +++++++++++++++
 scopesim/optics/optical_element.py  |  7 +++++++
 scopesim/optics/optical_train.py    | 30 +++++++++++++++++++++++++++++
 3 files changed, 52 insertions(+)

diff --git a/scopesim/detector/detector_array.py b/scopesim/detector/detector_array.py
index 10321eb9..c073b27b 100644
--- a/scopesim/detector/detector_array.py
+++ b/scopesim/detector/detector_array.py
@@ -101,6 +101,21 @@ def readout(self, image_planes, array_effects=[], dtcr_effects=[], **kwargs):
 
         return self.latest_exposure
 
+    def __repr__(self):
+        msg = (f"{self.__class__.__name__}"
+               f"({self.detector_list!r}, **{self.meta!r})")
+        return msg
+
+    def __str__(self):
+        return f"{self.__class__.__name__} with {self.detector_list!s}"
+
+    def _repr_pretty_(self, p, cycle):
+        """For ipython"""
+        if cycle:
+            p.text(f"{self.__class__.__name__}(...)")
+        else:
+            p.text(str(self))
+
 
 def make_primary_hdu(meta):
     """Create the primary header from meta data"""
diff --git a/scopesim/optics/optical_element.py b/scopesim/optics/optical_element.py
index f2b46545..7f630c49 100644
--- a/scopesim/optics/optical_element.py
+++ b/scopesim/optics/optical_element.py
@@ -215,6 +215,13 @@ def __repr__(self):
     def __str__(self):
         return f"{self.__class__.__name__}: \"{self.display_name}\""
 
+    def _repr_pretty_(self, p, cycle):
+        """For ipython"""
+        if cycle:
+            p.text(f"{self.__class__.__name__}(...)")
+        else:
+            p.text(str(self))
+
     @property
     def properties_str(self):
         prop_str = ""
diff --git a/scopesim/optics/optical_train.py b/scopesim/optics/optical_train.py
index d0ed34dc..65178279 100644
--- a/scopesim/optics/optical_train.py
+++ b/scopesim/optics/optical_train.py
@@ -497,6 +497,36 @@ def __repr__(self):
     def __str__(self):
         return self._description
 
+    def _repr_pretty_(self, p, cycle):
+        """For ipython"""
+        if cycle:
+            p.text(f"{self.__class__.__name__}(...)")
+        else:
+            p.text(f"{self.__class__.__name__} ")
+            p.text(f"for {self.cmds['!OBS.instrument']} ")
+            p.text(f"@ {self.cmds['!TEL.telescope']}:")
+            p.breakable()
+            p.text("UserCommands:")
+            p.breakable()
+            p.pretty(self.cmds)
+            p.breakable()
+            p.text("OpticalElements:")
+            with p.indent(2):
+                for item in self:
+                    p.breakable()
+                    p.pretty(item)
+            p.breakable()
+            p.text("DetectorArrays:")
+            with p.indent(2):
+                for item in self.detector_arrays:
+                    p.breakable()
+                    p.pretty(item)
+            p.breakable()
+            p.text("Effects:")
+            p.breakable()
+            with p.indent(2):
+                p.pretty(self.effects)
+
     def __getitem__(self, item):
         return self.optics_manager[item]
 

From 92de6b48bfd2fd0e03e41f7ee15f1587edf706f2 Mon Sep 17 00:00:00 2001
From: teutoburg <ghost@instruct.at>
Date: Fri, 4 Aug 2023 20:34:56 +0200
Subject: [PATCH 3/6] Fix failing report because of fig/ax change

---
 scopesim/effects/effects.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/scopesim/effects/effects.py b/scopesim/effects/effects.py
index 00dbe9e9..2581e87b 100644
--- a/scopesim/effects/effects.py
+++ b/scopesim/effects/effects.py
@@ -239,7 +239,12 @@ def report(self, filename=None, output="rst", rst_title_chars="*+",
 """
 
         if params["report_plot_include"] and hasattr(self, "plot"):
+            from matplotlib.figure import Figure
             fig = self.plot()
+            # HACK: plot methods should always return the same, while this is
+            #       not sorted out, deal with both fig and ax
+            if not isinstance(fig, Figure):
+                fig = fig.figure
 
             if fig is not None:
                 path = params["report_image_path"]

From f416dede524d155eb84fc12cd1ffc35e51a74000 Mon Sep 17 00:00:00 2001
From: teutoburg <ghost@instruct.at>
Date: Fri, 4 Aug 2023 23:31:21 +0200
Subject: [PATCH 4/6] Minor improvements along the way...

---
 scopesim/effects/effects.py                   | 35 ++++++++---------
 scopesim/effects/spectral_trace_list.py       | 17 ++++-----
 scopesim/effects/spectral_trace_list_utils.py | 38 +++++++++----------
 3 files changed, 42 insertions(+), 48 deletions(-)

diff --git a/scopesim/effects/effects.py b/scopesim/effects/effects.py
index 2581e87b..4f62ec3d 100644
--- a/scopesim/effects/effects.py
+++ b/scopesim/effects/effects.py
@@ -113,15 +113,12 @@ def display_name(self):
 
     @property
     def meta_string(self):
-        meta_str = ""
-        max_key_len = max(len(key) for key in self.meta.keys())
-        padlen = max_key_len + 4
-        for key in self.meta:
-            if key not in {"comments", "changes", "description", "history",
-                           "report_table_caption", "report_plot_caption",
-                           "table"}:
-                meta_str += f"{key:>{padlen}} : {self.meta[key]}\n"
-
+        padlen = 4 + len(max(self.meta, key=len))
+        exclude = {"comments", "changes", "description", "history",
+                   "report_table_caption", "report_plot_caption", "table"}
+        meta_str = "\n".join(f"{key:>{padlen}} : {value}"
+                             for key, value in self.meta.items()
+                             if key not in exclude)
         return meta_str
 
     def report(self, filename=None, output="rst", rst_title_chars="*+",
@@ -199,7 +196,7 @@ def report(self, filename=None, output="rst", rst_title_chars="*+",
 
         """
         changes = self.meta.get("changes", [])
-        changes_str = "- " + "\n- ".join([str(entry) for entry in changes])
+        changes_str = "- " + "\n- ".join(str(entry) for entry in changes)
         cls_doc = self.__doc__ if self.__doc__ is not None else "<no docstring>"
         cls_descr = cls_doc.lstrip().splitlines()[0]
 
@@ -262,6 +259,9 @@ def report(self, filename=None, output="rst", rst_title_chars="*+",
                 #                            params["report_rst_path"])
                 # rel_file_path = os.path.join(rel_path, fname)
 
+                # TODO: fname is set in a loop above, so using it here in the
+                #       fstring will only access the last value from the loop,
+                #       is that intended?
                 rst_str += f"""
 .. figure:: {fname}
     :name: {"fig:" + params.get("name", "<unknown Effect>")}
@@ -292,16 +292,11 @@ def report(self, filename=None, output="rst", rst_title_chars="*+",
         return rst_str
 
     def info(self):
-        """
-        Prints basic information on the effect, notably the description
-        """
-        text = str(self)
-
-        desc = self.meta.get("description")
-        if desc is not None:
-            text += f"\nDescription: {desc}"
-
-        print(text)
+        """Print basic information on the effect, notably the description."""
+        if (desc := self.meta.get("description")) is not None:
+            print(f"{self}\nDescription: {desc}")
+        else:
+            print(self)
 
     def __repr__(self):
         return f"{self.__class__.__name__}(**{self.meta!r})"
diff --git a/scopesim/effects/spectral_trace_list.py b/scopesim/effects/spectral_trace_list.py
index fa935d79..0ef92a1f 100644
--- a/scopesim/effects/spectral_trace_list.py
+++ b/scopesim/effects/spectral_trace_list.py
@@ -181,7 +181,7 @@ def apply_to(self, obj, **kwargs):
                     ex_vol["meta"].update(vol)
                     ex_vol["meta"].pop("wave_min")
                     ex_vol["meta"].pop("wave_max")
-                new_vols_list += extracted_vols
+                new_vols_list.extend(extracted_vols)
 
             obj.volumes = new_vols_list
 
@@ -197,8 +197,7 @@ def apply_to(self, obj, **kwargs):
                 logging.info("Making cube")
                 obj.cube = obj.make_cube_hdu()
 
-            trace_id = obj.meta["trace_id"]
-            spt = self.spectral_traces[trace_id]
+            spt = self.spectral_traces[obj.meta["trace_id"]]
             obj.hdu = spt.map_spectra_to_focal_plane(obj)
 
         return obj
@@ -210,11 +209,11 @@ def footprint(self):
         xfoot, yfoot = [], []
         for spt in self.spectral_traces.values():
             xtrace, ytrace = spt.footprint()
-            xfoot += xtrace
-            yfoot += ytrace
+            xfoot.extend(xtrace)
+            yfoot.extend(ytrace)
 
-        xfoot = [np.min(xfoot), np.max(xfoot), np.max(xfoot), np.min(xfoot)]
-        yfoot = [np.min(yfoot), np.min(yfoot), np.max(yfoot), np.max(yfoot)]
+        xfoot = [min(xfoot), max(xfoot), max(xfoot), min(xfoot)]
+        yfoot = [min(yfoot), min(yfoot), max(yfoot), max(yfoot)]
 
         return xfoot, yfoot
 
@@ -301,7 +300,7 @@ def rectify_traces(self, hdulist, xi_min=None, xi_max=None, interps=None,
         #pdu.header['FILTER'] = from_currsys("!OBS.filter_name_fw1")
         outhdul = fits.HDUList([pdu])
 
-        for i, trace_id in enumerate(self.spectral_traces):
+        for i, trace_id in enumerate(self.spectral_traces, start=1):
             hdu = self[trace_id].rectify(hdulist,
                                          interps=interps,
                                          bin_width=bin_width,
@@ -309,7 +308,7 @@ def rectify_traces(self, hdulist, xi_min=None, xi_max=None, interps=None,
                                          wave_min=wave_min, wave_max=wave_max)
             if hdu is not None:   # ..todo: rectify does not do that yet
                 outhdul.append(hdu)
-                outhdul[0].header[f"EXTNAME{i+1}"] = trace_id
+                outhdul[0].header[f"EXTNAME{i}"] = trace_id
 
         outhdul[0].header.update(inhdul[0].header)
 
diff --git a/scopesim/effects/spectral_trace_list_utils.py b/scopesim/effects/spectral_trace_list_utils.py
index 815b831e..e47d3ac3 100644
--- a/scopesim/effects/spectral_trace_list_utils.py
+++ b/scopesim/effects/spectral_trace_list_utils.py
@@ -86,7 +86,6 @@ def fov_grid(self):
         Spatial limits are determined by the `ApertureMask` effect
         and are not returned here.
         """
-        trace_id = self.meta["trace_id"]
         aperture_id = self.meta["aperture_id"]
         lam_arr = self.table[self.meta["wave_colname"]]
 
@@ -94,7 +93,7 @@ def fov_grid(self):
         wave_min = np.min(lam_arr)
 
         return {"wave_min": wave_min, "wave_max": wave_max,
-                "trace_id": trace_id, "aperture_id": aperture_id}
+                "trace_id": self.trace_id, "aperture_id": aperture_id}
 
     def compute_interpolation_functions(self):
         """
@@ -118,7 +117,7 @@ def compute_interpolation_functions(self):
         self._xiy2x = Transform2D.fit(xi_arr, y_arr, x_arr)
         self._xiy2lam = Transform2D.fit(xi_arr, y_arr, lam_arr)
 
-        if self.dispersion_axis == 'unknown':
+        if self.dispersion_axis == "unknown":
             dlam_dx, dlam_dy = self.xy2lam.gradient()
             wave_mid = 0.5 * (self.wave_min + self.wave_max)
             xi_mid = np.mean(xi_arr)
@@ -142,7 +141,7 @@ def map_spectra_to_focal_plane(self, fov):
         The method returns a section of the fov image along with info on
         where this image lies in the focal plane.
         """
-        logging.info("Mapping %s", fov.meta['trace_id'])
+        logging.info("Mapping %s", fov.meta["trace_id"])
         # Initialise the image based on the footprint of the spectral
         # trace and the focal plane WCS
         wave_min = fov.meta["wave_min"].value       # [um]
@@ -176,7 +175,7 @@ def map_spectra_to_focal_plane(self, fov):
         ## Check if spectral trace footprint is outside FoV
         if xmax < 0 or xmin > naxis1d or ymax < 0 or ymin > naxis2d:
             logging.info("Spectral trace %s: footprint is outside FoV",
-                         fov.meta['trace_id'])
+                         fov.meta["trace_id"])
             return None
 
         # Only work on parts within the FoV
@@ -207,7 +206,7 @@ def map_spectra_to_focal_plane(self, fov):
             xilam = XiLamImage(fov, self.dlam_per_pix)
             self._xilamimg = xilam   # ..todo: remove or make available with a debug flag?
         except ValueError:
-            print(f" ---> {self.meta['trace_id']} gave ValueError")
+            print(f" ---> {self.trace_id} gave ValueError")
 
         npix_xi, npix_lam = xilam.npix_xi, xilam.npix_lam
         xilam_wcs = xilam.wcs
@@ -321,7 +320,7 @@ def rectify(self, hdulist, interps=None, wcs=None, **kwargs):
             bin_width = np.abs(self.dlam_per_pix.y).min()
         logging.info("   Bin width %.02g um", bin_width)
 
-        pixscale = from_currsys(self.meta['pixel_scale'])
+        pixscale = from_currsys(self.meta["pixel_scale"])
 
         # Temporary solution to get slit length
         xi_min = kwargs.get("xi_min", None)
@@ -341,8 +340,8 @@ def rectify(self, hdulist, interps=None, wcs=None, **kwargs):
 
         if wcs is None:
             wcs = WCS(naxis=2)
-            wcs.wcs.ctype = ['WAVE', 'LINEAR']
-            wcs.wcs.cunit = ['um', 'arcsec']
+            wcs.wcs.ctype = ["WAVE", "LINEAR"]
+            wcs.wcs.cunit = ["um", "arcsec"]
             wcs.wcs.crpix = [1, 1]
             wcs.wcs.cdelt = [bin_width, pixscale] # PIXSCALE
 
@@ -372,13 +371,14 @@ def rectify(self, hdulist, interps=None, wcs=None, **kwargs):
         rect_spec = np.zeros_like(Xarr, dtype=np.float32)
 
         ihdu = 0
+        # TODO: make this more iteratory
         for hdu in hdulist:
             if not isinstance(hdu, fits.ImageHDU):
                 continue
 
             wcs_fp = WCS(hdu.header, key="D")
-            n_x = hdu.header['NAXIS1']
-            n_y = hdu.header['NAXIS2']
+            n_x = hdu.header["NAXIS1"]
+            n_y = hdu.header["NAXIS2"]
             iarr, jarr = wcs_fp.all_world2pix(Xarr, Yarr, 0)
             mask = (iarr > 0) * (iarr < n_x) * (jarr > 0) * (jarr < n_y)
             if np.any(mask):
@@ -388,7 +388,7 @@ def rectify(self, hdulist, interps=None, wcs=None, **kwargs):
             ihdu += 1
 
         header = wcs.to_header()
-        header['EXTNAME'] = self.trace_id
+        header["EXTNAME"] = self.trace_id
         return fits.ImageHDU(data=rect_spec, header=header)
 
 
@@ -540,7 +540,7 @@ def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
 
         if plot_trace_id:
             axes.text(corners[xname][:-1].mean(), corners[yname][:-1].mean(),
-                      self.meta["trace_id"], c=c, rotation="vertical",
+                      self.trace_id, c=c, rotation="vertical",
                       ha="center", va="center")
 
         for wave in np.unique(w):
@@ -559,7 +559,7 @@ def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
     @property
     def trace_id(self):
         """Return the name of the trace"""
-        return self.meta['trace_id']
+        return self.meta["trace_id"]
 
     def _set_dispersion(self, wave_min, wave_max, pixsize=None):
         """Computation of dispersion dlam_per_pix along xi=0
@@ -575,8 +575,8 @@ def _set_dispersion(self, wave_min, wave_max, pixsize=None):
             dlam_grad = self.xy2lam.gradient()[0]  # dlam_by_dx
         else:
             dlam_grad = self.xy2lam.gradient()[1]  # dlam_by_dy
-        pixsize = (from_currsys(self.meta['pixel_scale']) /
-                   from_currsys(self.meta['plate_scale']))
+        pixsize = (from_currsys(self.meta["pixel_scale"]) /
+                   from_currsys(self.meta["plate_scale"]))
         self.dlam_per_pix = interp1d(lam,
                                      dlam_grad(x_mm, y_mm) * pixsize,
                                      fill_value="extrapolate")
@@ -585,7 +585,7 @@ def __repr__(self):
         return f"{self.__class__.__name__}({self.table!r}, **{self.meta!r})"
 
     def __str__(self):
-        msg = (f"<SpectralTrace> \"{self.meta['trace_id']}\" : "
+        msg = (f"<SpectralTrace> \"{self.trace_id}\" : "
                f"[{self.wave_min:.4f}, {self.wave_max:.4f}]um : "
                f"Ext {self.meta['extension_id']} : "
                f"Aperture {self.meta['aperture_id']} : "
@@ -929,8 +929,8 @@ def make_image_interpolations(hdulist, **kwargs):
     for hdu in hdulist:
         if isinstance(hdu, fits.ImageHDU):
             interps.append(
-                RectBivariateSpline(np.arange(hdu.header['NAXIS1']),
-                                    np.arange(hdu.header['NAXIS2']),
+                RectBivariateSpline(np.arange(hdu.header["NAXIS1"]),
+                                    np.arange(hdu.header["NAXIS2"]),
                                     hdu.data, **kwargs)
             )
     return interps

From fd72a2ec248040e73a55d3ea08cce0407f96c10d Mon Sep 17 00:00:00 2001
From: teutoburg <ghost@instruct.at>
Date: Sat, 5 Aug 2023 00:16:46 +0200
Subject: [PATCH 5/6] Mostly docstrings

---
 scopesim/effects/spectral_trace_list.py       | 22 ++++++++-
 scopesim/effects/spectral_trace_list_utils.py | 45 +++++++++++++++++--
 2 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/scopesim/effects/spectral_trace_list.py b/scopesim/effects/spectral_trace_list.py
index 0ef92a1f..9c06037f 100644
--- a/scopesim/effects/spectral_trace_list.py
+++ b/scopesim/effects/spectral_trace_list.py
@@ -314,12 +314,32 @@ def rectify_traces(self, hdulist, xi_min=None, xi_max=None, interps=None,
 
         return outhdul
 
-
     def rectify_cube(self, hdulist):
         """Rectify traces and combine into a cube"""
         raise(NotImplementedError)
 
     def plot(self, wave_min=None, wave_max=None, axes=None, **kwargs):
+        """Plot every spectral trace in the spectral trace list.
+
+        Parameters
+        ----------
+        wave_min : float, optional
+            Minimum wavelength, if any. If None, value from_currsys is used.
+        wave_max : float, optional
+            Maximum wavelength, if any. If None, value from_currsys is used.
+        axes : matplotlib axes, optional
+            The axes object to use for the plot. If None (default), a new
+            figure with one axes will be created.
+        **kwargs : dict
+            Any other parameters passed along to the plot method of the
+            individual spectral traces.
+
+        Returns
+        -------
+        fig : matplotlib figure
+            DESCRIPTION.
+
+        """
         if wave_min is None:
             wave_min = from_currsys("!SIM.spectral.wave_min")
         if wave_max is None:
diff --git a/scopesim/effects/spectral_trace_list_utils.py b/scopesim/effects/spectral_trace_list_utils.py
index e47d3ac3..bb3bc1d3 100644
--- a/scopesim/effects/spectral_trace_list_utils.py
+++ b/scopesim/effects/spectral_trace_list_utils.py
@@ -482,9 +482,48 @@ def footprint(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None):
                 [y_edge.min(), y_edge.min(), y_edge.max(), y_edge.max()])
 
     def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
-             c="r", axes=None, plot_footprint=True, plot_text=True,
+             c="r", axes=None, plot_footprint=True, plot_wave=True,
              plot_ctrlpnts=True, plot_outline=False, plot_trace_id=False):
-        """Plot control points of the SpectralTrace"""
+        """Plot control points (and/or footprint) of the SpectralTrace.
+
+        Parameters
+        ----------
+        wave_min : float, optional
+            Minimum wavelength, if any.
+        wave_max : float, optional
+            Maximum wavelength, if any.
+        xi_min : float, optional
+            Minimum slit, if any.
+        xi_max : float, optional
+            Maximum slit, if any.
+        c : str, optional
+            Colour, any valid matplotlib colour string. The default is "r".
+        axes : matplotlib axes, optional
+            The axes object to use for the plot. If None (default), a new
+            figure with one axes will be created.
+
+        Returns
+        -------
+        axes : matplotlib axes
+            The axes object containing the plot.
+
+        Other Parameters
+        ----------------
+        plot_footprint : bool, optional
+            Plot a rectangle encompassing all control points, which may be
+            larger than the area actually covered by the trace, if the trace is
+            not exactly perpendicular to the detector. The default is True.
+        plot_wave : bool, optional
+            Annotate the wavelength points. The default is True.
+        plot_ctrlpnts : bool, optional
+            Plot the individual control points as makers. The default is True.
+        plot_outline : bool, optional
+            Plot the smallest tetragon encompassing all control points.
+            The default is False.
+        plot_trace_id : bool, optional
+            Write the trace ID in the middle of the trace.
+            The default is False.
+        """
         if axes is None:
             _, axes = plt.subplots()
 
@@ -548,7 +587,7 @@ def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
             xx.sort()
             dx = xx[-1] - xx[-2]
 
-            if plot_text:
+            if plot_wave:
                 axes.text(x[w==wave].max() + 0.5 * dx,
                           y[w==wave].mean(),
                           str(wave), va="center", ha="left")

From 331e12a654c5cf83d6712fbb8003477e58f88dab Mon Sep 17 00:00:00 2001
From: teutoburg <73600109+teutoburg@users.noreply.github.com>
Date: Wed, 9 Aug 2023 09:07:26 +0200
Subject: [PATCH 6/6] oczosked

---
 scopesim/effects/spectral_trace_list_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scopesim/effects/spectral_trace_list_utils.py b/scopesim/effects/spectral_trace_list_utils.py
index bb3bc1d3..47e0511a 100644
--- a/scopesim/effects/spectral_trace_list_utils.py
+++ b/scopesim/effects/spectral_trace_list_utils.py
@@ -556,7 +556,7 @@ def plot(self, wave_min=None, wave_max=None, xi_min=None, xi_max=None, *,
             xi_max = xis.max()
 
         mask = ((waves >= wave_min) & (waves <= wave_max)
-                & (xis >= xi_min)& (xis <= xi_max))
+                & (xis >= xi_min) & (xis <= xi_max))
         if sum(mask) <= 2:
             return axes