update branch with main

.github/workflows/ci.yml

@@ -25,13 +25,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         # setuptools_scm requires a non-shallow clone of the repository
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -52,10 +52,10 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: "3.11"
 

.github/workflows/pypi.yml

@@ -14,15 +14,15 @@ jobs:
       id-token: write
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
           # setuptools_scm requires a non-shallow clone of the repository
           fetch-depth: 0
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       name: Install Python
 
     - name: Build SDist
       run: pipx run build --sdist
 
-    - uses: pypa/gh-action-pypi-publish@v1.12.4
+    - uses: pypa/gh-action-pypi-publish@v1.13.0

.gitignore

@@ -154,9 +154,11 @@ cython_debug/
 rubix/version.py
 notebooks/*.h5
 notebooks/output
+notebooks/frames
 
 rubix/**/*.ipynb
 
+rubix/spectra/ssp/templates/fsps.h5
 rubix/spectra/ssp/templates/*.gz
 rubix/spectra/ssp/templates/*fits.gz
 rubix/spectra/cue/cue/*
@@ -169,3 +171,8 @@ utils/*
 firebase.json
 .firebase/*
 
+rubix/spectra/ssp/templates/fsps.h5
+
+notebooks/frames
+notebooks/frames/*
+notebooks/data/*

.pre-commit-config.yaml

@@ -1,17 +1,22 @@
 
 repos:
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
     - id: nbstripout
       files: ".ipynb"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v6.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 24.2.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
     - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 7.0.0
+    hooks:
+      - id: isort
+        name: isort (python)

notebooks/compare_filtercurves.ipynb

@@ -0,0 +1,253 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "import os\n",
+    "#os.environ['SPS_HOME'] = '/Users/annalena/Documents/GitHub/fsps'\n",
+    "os.environ['SPS_HOME'] = '/home/annalena/sps_fsps'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "config = {\n",
+    "    \"pipeline\": {\"name\": \"calc_ifu\"},\n",
+    "    \n",
+    "    \"logger\": {\n",
+    "        \"log_level\": \"DEBUG\",\n",
+    "        \"log_file_path\": None,\n",
+    "        \"format\": \"%(asctime)s - %(name)s - %(levelname)s - %(message)s\",\n",
+    "    },\n",
+    "    \"data\": {\n",
+    "        \"name\": \"IllustrisAPI\",\n",
+    "        \"args\": {\n",
+    "            \"api_key\": os.environ.get(\"ILLUSTRIS_API_KEY\"),\n",
+    "            \"particle_type\": [\"stars\"],\n",
+    "            \"simulation\": \"TNG50-1\",\n",
+    "            \"snapshot\": 99,\n",
+    "            \"save_data_path\": \"data\",\n",
+    "        },\n",
+    "        \n",
+    "        \"load_galaxy_args\": {\n",
+    "        \"id\": 11,\n",
+    "        \"reuse\": True,\n",
+    "        },\n",
+    "\n",
+    "        \"subset\": {\n",
+    "            \"use_subset\": True,\n",
+    "            \"subset_size\": 100000,\n",
+    "        },\n",
+    "    },\n",
+    "    \"simulation\": {\n",
+    "        \"name\": \"IllustrisTNG\",\n",
+    "        \"args\": {\n",
+    "            \"path\": \"data/galaxy-id-11.hdf5\",\n",
+    "        },\n",
+    "    \n",
+    "    },\n",
+    "    \"output_path\": \"output\",\n",
+    "    \"output_modified\": False,\n",
+    "\n",
+    "    \"telescope\": {\n",
+    "        \"name\": \"MUSE\",\n",
+    "        \"psf\": {\"name\": \"gaussian\", \"size\": 5, \"sigma\": 0.5},\n",
+    "        \"lsf\": {\"sigma\": 0.5},\n",
+    "        \"noise\": {\"signal_to_noise\": 100, \"noise_distribution\": \"normal\"},\n",
+    "    },\n",
+    "    \"cosmology\": {\"name\": \"PLANCK15\"},\n",
+    "    \"galaxy\": {\n",
+    "        \"dist_z\": 0.1,\n",
+    "        \"rotation\": {\"type\": \"face-on\"},\n",
+    "    },\n",
+    "    \"ssp\": {\n",
+    "        \"template\": {\"name\": \"FSPS\"},\n",
+    "    },\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "import jax.numpy as jnp\n",
+    "from rubix.core.pipeline import RubixPipeline\n",
+    "pipe = RubixPipeline(config)\n",
+    "\n",
+    "rubixdata = pipe.run()\n",
+    "rubixdata_fsps = rubixdata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "from rubix.spectra.ifu import convert_luminoisty_to_flux\n",
+    "from rubix.cosmology import PLANCK15\n",
+    "\n",
+    "observation_lum_dist = PLANCK15.luminosity_distance_to_z(config[\"galaxy\"][\"dist_z\"])\n",
+    "observation_z = config[\"galaxy\"][\"dist_z\"]\n",
+    "pixel_size = 1.0\n",
+    "\n",
+    "spectra_fsps = convert_luminoisty_to_flux(rubixdata_fsps.stars.datacube, observation_lum_dist, observation_z, pixel_size)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "from rubix.telescope.filters import load_filter, print_filter_list, print_filter_list_info, print_filter_property\n",
+    "# NBVAL_SKIP\n",
+    "# load all fliter curves for SLOAN\n",
+    "curves = load_filter(\"SLOAN\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "curves.plot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "from rubix.telescope.filters import convolve_filter_with_spectra\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "wave = pipe.telescope.wave_seq\n",
+    "datacube = spectra_fsps\n",
+    "\n",
+    "for filter in curves:\n",
+    "    convolved = convolve_filter_with_spectra(filter, datacube, wave)\n",
+    "    plt.figure()\n",
+    "    plt.imshow(convolved)\n",
+    "    plt.colorbar()\n",
+    "    plt.title(filter.name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#NBVAL_SKIP\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "from matplotlib.cm import ScalarMappable\n",
+    "from matplotlib.colors import Normalize\n",
+    "\n",
+    "# Assuming curves, datacube, and wave are defined\n",
+    "num_filters = len(curves)\n",
+    "nrows = 2\n",
+    "ncols = 5\n",
+    "\n",
+    "fig, axes = plt.subplots(nrows, ncols, figsize=(15, 6))\n",
+    "\n",
+    "# Find the global min and max for the colorbars for each row\n",
+    "vmin_row1 = np.inf\n",
+    "vmax_row1 = -np.inf\n",
+    "vmin_row2 = np.inf\n",
+    "vmax_row2 = -np.inf\n",
+    "convolved_list = []\n",
+    "\n",
+    "for i, filter in enumerate(curves):\n",
+    "    convolved = convolve_filter_with_spectra(filter, datacube, wave)\n",
+    "    convolved_list.append(convolved)\n",
+    "    if i in [0, 3, 5, 7, 9]:  # First row\n",
+    "        vmin_row1 = min(vmin_row1, convolved.min())\n",
+    "        vmax_row1 = max(vmax_row1, convolved.max())\n",
+    "    else:  # Second row\n",
+    "        vmin_row2 = min(vmin_row2, convolved.min())\n",
+    "        vmax_row2 = max(vmax_row2, convolved.max())\n",
+    "\n",
+    "# Plot each convolved image in the grid\n",
+    "for i, ax in enumerate(axes.flat):\n",
+    "    if i < 5:  # First row\n",
+    "        filter_index = [0, 3, 5, 7, 9][i]\n",
+    "        im = ax.imshow(convolved_list[filter_index], vmin=vmin_row1, vmax=vmax_row1, cmap='viridis')\n",
+    "        ax.set_title(curves[filter_index].name)\n",
+    "    else:  # Second row\n",
+    "        filter_index = [1, 2, 4, 6, 8][i - 5]\n",
+    "        im = ax.imshow(convolved_list[filter_index], vmin=vmin_row2, vmax=vmax_row2, cmap='inferno')\n",
+    "        ax.set_title(curves[filter_index].name)\n",
+    "    ax.axis('off')\n",
+    "\n",
+    "# Adjust layout with tight_layout\n",
+    "plt.tight_layout()\n",
+    "\n",
+    "# Create smaller axes for the colorbars outside the grid\n",
+    "fig.subplots_adjust(right=0.85)\n",
+    "cbar_ax1 = fig.add_axes([0.87, 0.55, 0.02, 0.35])  # Position for the colorbar of the first row\n",
+    "cbar_ax2 = fig.add_axes([0.87, 0.07, 0.02, 0.35])  # Position for the colorbar of the second row\n",
+    "\n",
+    "# Create ScalarMappable objects for the colorbars\n",
+    "norm_row1 = Normalize(vmin=vmin_row1, vmax=vmax_row1)\n",
+    "norm_row2 = Normalize(vmin=vmin_row2, vmax=vmax_row2)\n",
+    "sm_row1 = ScalarMappable(norm=norm_row1, cmap='viridis')\n",
+    "sm_row2 = ScalarMappable(norm=norm_row2, cmap='inferno')\n",
+    "\n",
+    "# Add colorbars for each row with different colormaps\n",
+    "fig.colorbar(sm_row1, cax=cbar_ax1)\n",
+    "fig.colorbar(sm_row2, cax=cbar_ax2)\n",
+    "\n",
+    "plt.savefig(\"output/filters_fsps_galaxy.png\")\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "rubix",
+   "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}