Docs fixes (#285)

* removed get_best_fit_spectrum: not robust enough and not needed if set_spectrum_to_match is called

* robust linear solver when components are degenerate (closes #282)

* refactored src and obs loops

* closes #254

* notebook fixes, closes #271

* it's 2024 now..

docs/0-quickstart.ipynb

@@ -237,10 +237,7 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "cell_type": "markdown",
    "source": [
     "sources = []\n",
     "for k,center in enumerate(centers):\n",
@@ -256,7 +253,10 @@
     "\n",
     "for k, src in enumerate(sources):\n",
     "    print (f\"{k}: {src.__class__.__name__}\")"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "markdown",

docs/conf.py

@@ -59,7 +59,7 @@
 
 # General information about the project.
 project = "scarlet"
-copyright = "2018-2021, Fred Moolekamp and Peter Melchior"
+copyright = "2018-2024, Fred Moolekamp and Peter Melchior"
 author = "Fred Moolekamp and Peter Melchior"
 
 # The version info for the project you're documenting, acts as replacement for

docs/tutorials/lite.ipynb

@@ -537,7 +537,6 @@
     "for k, blend in blends.items():\n",
     "    display.show_scene(\n",
     "        blend,\n",
-    "        observation,\n",
     "        show_model=False,\n",
     "        show_rendered=True,\n",
     "        show_observed=True,\n",
@@ -547,7 +546,6 @@
     "    # Show the scene again with the reweighted flux\n",
     "    display.show_scene(\n",
     "        blend,\n",
-    "        observation,\n",
     "        show_model=False,\n",
     "        show_rendered=True,\n",
     "        show_observed=True,\n",
@@ -593,13 +591,6 @@
    "source": [
     "display.compare_spectra(**sources)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

docs/tutorials/wavelet_model.ipynb

@@ -363,10 +363,10 @@
    "outputs": [],
    "source": [
     "# find all sources with very similar colors to the Starlet source of the diffuse emission\n",
-    "spectrum = sources[-1].spectrum\n",
+    "spectrum = sources[-1].spectrum.get_parameter(0)\n",
     "C = np.zeros(len(sources))\n",
     "for j, src in enumerate(sources):\n",
-    "    spectrum_ = src.spectrum\n",
+    "    spectrum_ = src.spectrum.get_parameter(0)\n",
     "    # cosine similarity\n",
     "    C[j] = spectrum @ spectrum_ / np.sqrt(spectrum @ spectrum) / np.sqrt(spectrum_ @ spectrum_)\n",
     "\n",

scarlet/initialization.py

@@ -306,7 +306,7 @@ def init_all_sources(
     model will be kept, otherwise one component is removed and the source reinitialized.
     If a source cannot be initialized, its index is returned in `skipped`.
 
-    See `~init_sources` for a description of the arguments
+    See `~init_source` for a description of the arguments
 
     Parameters
     ----------
@@ -404,8 +404,7 @@ def init_source(
         The `Observation` that contains the images, weights, and PSF
         used to generate the model.
     thresh : `float`
-        Fraction of the background to use as a threshold for
-        each pixel in the initialization
+        Multiple of the backround RMS used as a flux cutoff for morphology initialization
     max_components : int
         The maximum number of components in a source.
         If `fallback` is `True` then when
@@ -417,7 +416,9 @@ def init_source(
         The minimum number of components in a source.
         Only relevent for `fallback=True`.
     min_snr: float
-        Mininmum SNR per component to accept the source.
+        Mininmum SNR per component of a multi-component source.
+        If fallback=True, every component needs to have at least min_snr, otherwise the component number will be reduced
+        At last resort, the component is initialized with a PointSource morphology
     shifting : bool
         Whether or not to fit the position of a source.
         This is an expensive operation and is typically only used when