Add specviz pondering, update imviz

.gitignore

@@ -17,6 +17,7 @@ htmlcov
 MANIFEST
 .ipynb_checkpoints
 notebooks/*.fits
+notebooks/*.ecsv
 
 # Sphinx
 docs/api

notebooks/concepts/imviz_composite_subset_api.ipynb

@@ -81,7 +81,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plg_subset = imviz.plugins[\"Subsets\"]"
+    "plg_subset = imviz.plugins[\"Subset Tools\"]"
    ]
   },
   {

notebooks/concepts/specviz_composite_subset_api.ipynb

@@ -0,0 +1,258 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4f2841a4-9ba6-4238-9243-8f2a8873ceec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "from astropy import units as u\n",
+    "from specutils import Spectrum1D, SpectralRegion\n",
+    "\n",
+    "from jdaviz import Specviz"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "99f14f77-a6db-457d-8c27-e74d3a845059",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wave = np.linspace(1, 5, 100) * u.um\n",
+    "flux = np.random.random(wave.shape) * u.nJy\n",
+    "sp = Spectrum1D(flux=flux, spectral_axis=wave)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13f27c01-ab03-44ae-b386-f754d44a8148",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz = Specviz()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b548a4e-5c9e-4764-8426-e9e2bd6d40bd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz.load_data(sp, data_label=\"Spectrum\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bb8cee0d-6bd3-4b62-bf87-13a8727f21d3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "282eafc9-a148-44f4-832b-e0dab78df76b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_subset = specviz.plugins[\"Subset Tools\"]"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "4a26ecfb-ad98-4add-8cb2-98e9ff33763a",
+   "metadata": {},
+   "source": [
+    "# This works\n",
+    "spreg_1 = SpectralRegion(1.5 * u.um, 2 * u.um)\n",
+    "spreg_2 = SpectralRegion(3 * u.um, 3.5 * u.um)\n",
+    "plg_subset.import_region([spreg_1, spreg_2], combination_mode=\"or\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6b2092ae-4638-4bec-9e56-4c8109055fcc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# This kinda works because Export simplifies it to\n",
+    "#     lower_bound upper_bound\n",
+    "#     1.5 3.0\n",
+    "#     3.5 4.5\n",
+    "#\n",
+    "# Same output but original values lost.\n",
+    "spreg_1 = SpectralRegion(1.5 * u.um, 4.5 * u.um)\n",
+    "spreg_2 = SpectralRegion(3 * u.um, 3.5 * u.um)\n",
+    "plg_subset.import_region([spreg_1, spreg_2], combination_mode=\"xor\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e41755b2-fe38-4342-a279-eb728867928f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_export = specviz.plugins[\"Export\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "67b29aec-78b1-450f-9847-4303874a1cfa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_export.subset = \"Subset 1\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1d4dd45a-c6a0-4e19-bf62-44fe671e6302",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_export.subset_format = \"ecsv\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "482515ec-c87e-4460-a46e-205703809a2a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_export.export(overwrite=True)  # Subset_1.ecsv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "534d36ed-3a45-49fb-b005-4185d4e2d9e4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!cat Subset_1.ecsv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "07db40cd-ba74-4bf4-b343-48275be38f60",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz_2 = Specviz()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "014a7856-20f9-4670-a424-38c0c27b46fa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz_2.load_data(sp, data_label=\"Spectrum\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8a6e3c1e-8499-44ec-b5f2-01cd0d822571",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "specviz_2.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e5c556c-675c-49f7-a4d0-8e0903d3384c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plg_subset_2 = specviz_2.plugins[\"Subset Tools\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "83f54337-e98c-4e81-ae34-396448240d7e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Because ECSV output was simplified, the combination_mode can break\n",
+    "# things if you are not careful!\n",
+    "#plg_subset_2.import_region(\"Subset_1.ecsv\")  # BAD -- first subregion missing\n",
+    "plg_subset_2.import_region(\"Subset_1.ecsv\", combination_mode=\"or\")  # OK\n",
+    "#plg_subset_2.import_region(\"Subset_1.ecsv\", combination_mode=\"and\")  # BAD -- null subset\n",
+    "#plg_subset_2.import_region(\"Subset_1.ecsv\", combination_mode=\"new\")  # BAD -- two subsets"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "190c99e2-ee01-4f11-8d74-03d2c43c56c5",
+   "metadata": {},
+   "source": [
+    "### Additional work\n",
+    "\n",
+    "If we want perfect roundtrip, to do it properly, we need an equivalent of\n",
+    "[compound region](https://astropy-regions.readthedocs.io/en/latest/compound.html) for\n",
+    "[SpectralRegion](https://specutils.readthedocs.io/en/stable/spectral_regions.html) upstream.\n",
+    "This could take significant effort, so we might have to just acknowledge the limitations\n",
+    "and move on. Is keeping original inputs that important if simplified version still give\n",
+    "you the same thing?\n",
+    "\n",
+    "If you want support for arbitrary operators from the same ECSV file, this is not possible\n",
+    "without native operator support in `specutils` (see above).\n",
+    "\n",
+    "The `import_region` API can have \"wild\" behaviors depending on `combination_mode`\n",
+    "when a filename is given. This needs to be reined in.\n",
+    "\n",
+    "### Recommendations\n",
+    "\n",
+    "1. Acknowledge that original inputs might be lost upon saving it back out\n",
+    "   because we simplify the composite spectral regions.\n",
+    "2. Acknowledge that one file can only store one subset.\n",
+    "   (Needs extra pondering if you also want to support `\"new\"` to create one subset\n",
+    "   per file entry.)\n",
+    "4. Only allow `combination_mode=\"or\"` when a filename is given.\n",
+    "   Since default is actually `None` (which `glue` translated to `\"replace\"`,\n",
+    "   maybe have to recode `None` to mean `\"or\"` when input is filename.\n",
+    "   Raise exception for any other value."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}