diff --git a/_sources/tutorials/extragalactic_gcr_cluster_colors.ipynb b/_sources/tutorials/extragalactic_gcr_cluster_colors.ipynb
index db514940..a1d40541 100644
--- a/_sources/tutorials/extragalactic_gcr_cluster_colors.ipynb
+++ b/_sources/tutorials/extragalactic_gcr_cluster_colors.ipynb
@@ -8,7 +8,7 @@
     "\n",
     "Owners: **Dan Korytov [@dkorytov](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@dkorytov)**\n",
     "\n",
-    "Last verified run: Nov 30, 2018 (by @yymao)\n",
+    "Last verified run: Mar 8, 2024 (by @patricialarsen)\n",
     "\n",
     "This notebook demonstrates how to access the extra galactic catalog through the Generic Catalog Reader (GCR, https://github.com/yymao/generic-catalog-reader) as well as how filter on galaxy features and cluster membership.\n",
     "\n",
@@ -16,18 +16,20 @@
     "\n",
     "After working through and studying this Notebook you should be able to\n",
     "\n",
-    "1. Access extragalactic catalogs (protoDC2, cosmoDC2) through the GCR\n",
+    "1. Access extragalactic catalogs (cosmoDC2, skysim, roman_rubin) through the GCR\n",
     "2. Filter on galaxy properties\n",
     "3. Select and plot cluster members\n",
     "\n",
     "\n",
-    "__Logistics__: This notebook is intended to be run through the JupyterHub NERSC interface available here: https://jupyter-dev.nersc.gov. To setup your NERSC environment, please follow the instructions available here: https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC"
+    "__Logistics__: This notebook is intended to be run through the JupyterHub NERSC interface available here: https://jupyter.nersc.gov. To setup your NERSC environment, please follow the instructions available here: https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import GCRCatalogs\n",
@@ -40,16 +42,50 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Other catalog options:\n",
+    "Some alternate catalogs that you might want to look at include skysim, which is a 5000 square degree extragalactic catalog, and the Roman Rubin catalog which is a smaller extragalactic catalog and image simulation. To load these instead execute one of the two cells below.\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "gc = GCRCatalogs.load_catalog('skysim5000_v1.1.2_small')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "gc = GCRCatalogs.load_catalog('roman_rubin_2023_v1.1.3_elais')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data = gc.get_quantities(['halo_mass', 'redshift',\n",
@@ -65,7 +101,8 @@
     "We load in the catalog with the \"load_catalog\" command, and then the values with the \"get_quantities\" command using filters to select sub-samples of the catalog. For this case we only need the magnitudes in several filters and the redshift. Galaxies are filtered on host halo mass to be at least 3e13 h$^{-1}$M$_\\odot$.\n",
     "\n",
     "### Help for error messages:\n",
-    "If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: \"source /global/common/software/lsst/common/miniconda/setup_current_python.sh\"\n",
+    "If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: \"source \n",
+    "/global/common/software/lsst/common/miniconda/kernels/setup.sh\"\n",
     "\n",
     "We are loading in a smaller version of the full cosmoDC2 catalog - this contains the same information as the full catalog but with a smaller sky area."
    ]
@@ -73,7 +110,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "plt.figure()\n",
@@ -95,7 +134,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "plt.figure()\n",
@@ -122,7 +163,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "After load the catalog and data, we are able to plot the color distribution as a function of redshift for cluster galaxies with very little effort!"
+    "After loading the catalog and data, we are able to plot the color distribution as a function of redshift for cluster galaxies with very little effort!"
    ]
   }
  ],
@@ -142,9 +183,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/_sources/tutorials/extragalactic_gcr_cluster_members.ipynb b/_sources/tutorials/extragalactic_gcr_cluster_members.ipynb
index ddc97175..d3ce0ea5 100644
--- a/_sources/tutorials/extragalactic_gcr_cluster_members.ipynb
+++ b/_sources/tutorials/extragalactic_gcr_cluster_members.ipynb
@@ -10,7 +10,7 @@
     "\n",
     "Owners: **Dan Korytov [@dkorytov](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@dkorytov)**, **Patricia Larsen**\n",
     "\n",
-    "Last verified run: **Nov 30, 2018** by @yymao\n",
+    "Last verified run: **March 8, 2024** by @patricialarsen\n",
     "\n",
     "This notebook demonstrates how to access the extra galactic catalog through the Generic Catalog Reader (GCR, https://github.com/yymao/generic-catalog-reader) as well as how filter on galaxy features and cluster membership.\n",
     "\n",
@@ -18,19 +18,21 @@
     "\n",
     "After working through and studying this Notebook you should be able to\n",
     "\n",
-    "1. Access extragalactic catalogs (protoDC2, cosmoDC2) through the GCR.\n",
+    "1. Access extragalactic catalogs (cosmoDC2, skysim, roman_rubin) through the GCR.\n",
     "2. Select galaxy cluster centrals as a proxy for clusters.\n",
     "3. Select galaxies in individual clusters by using the host_id quantity.\n",
     "4. Plotting galaxy clustermembers positions on the sky as well as their comoving position in space.\n",
     "\n",
     "\n",
-    "__Logistics__: This notebook is intended to be run through the JupyterHub NERSC interface available here: https://jupyter-dev.nersc.gov. To setup your NERSC environment, please follow the instructions available here: https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC"
+    "__Logistics__: This notebook is intended to be run through the JupyterHub NERSC interface available here: https://jupyter.nersc.gov. To setup your NERSC environment, please follow the instructions available here: https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import GCRCatalogs\n",
@@ -49,7 +51,8 @@
     "We load in the catalog with the \"load_catalog\" command, and then the values with the \"get_quantities\" command using filters to select sub-samples of the catalog.  \n",
     "\n",
     "### Help for error messages:\n",
-    "If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: \"source /global/common/software/lsst/common/miniconda/setup_current_python.sh\"\n",
+    "If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: \"source \n",
+    "/global/common/software/lsst/common/miniconda/kernels/setup.sh\"\n",
     "\n",
     "We are loading in a smaller version of the full cosmoDC2 catalog - this contains the same information as the full catalog but with a smaller sky area."
    ]
@@ -63,10 +66,42 @@
     "gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Other catalog options:\n",
+    "Some alternate catalogs that you might want to look at include skysim, which is a 5000 square degree extragalactic catalog, and the Roman Rubin catalog which is a smaller extragalactic catalog and image simulation. To load these instead execute one of the two cells below.\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "gc = GCRCatalogs.load_catalog('skysim5000_v1.1.2_small')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "gc = GCRCatalogs.load_catalog('roman_rubin_2023_v1.1.3_elais')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "galaxy_data = gc.get_quantities(['ra', 'dec', 'mag_r', 'halo_id'], filters=['mag_r < 19'])\n",
@@ -79,7 +114,7 @@
    "metadata": {},
    "source": [
     "### Plot individual clusters\n",
-    "The cluster_data we loaded selects for central galaxies in clusters of mass higher than 10^14 solar masses/h below redshift 0.2. We will plot three such clusters in the proto-DC2 region. \n",
+    "The cluster_data we loaded selects for central galaxies in clusters of mass higher than 10^14 solar masses/h below redshift 0.2. We will plot three such clusters in the skysim region. \n",
     "\n",
     "For each of these clusters we can match the galaxies by selecting on 'halo_id' and make a scatter plot of the projected positions around the central galaxy. Note that the size of the circles corresponds to the r-band magnitude of the galaxies. \n",
     "\n",
@@ -89,7 +124,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "cluster_data = Table(cluster_data)\n",
@@ -126,7 +163,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "galaxy_data = gc.get_quantities(['ra', 'dec', 'mag_r', 'halo_id', 'position_x', 'position_y', 'velocity_x', 'velocity_y'], filters=['mag_r < 19'])\n",
@@ -137,7 +176,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "cluster_data = Table(cluster_data)\n",
@@ -161,6 +202,13 @@
     "    plt.colorbar(label='km/s')\n",
     "plt.show()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -179,9 +227,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/_sources/tutorials/extragalactic_gcr_hod.ipynb b/_sources/tutorials/extragalactic_gcr_hod.ipynb
index e18e1798..aa3b4553 100644
--- a/_sources/tutorials/extragalactic_gcr_hod.ipynb
+++ b/_sources/tutorials/extragalactic_gcr_hod.ipynb
@@ -6,12 +6,12 @@
    "source": [
     "# Halo Occupation Distribution from extragalactic catalogs\n",
     "\n",
-    "> Notebook owner: Yao-Yuan Mao [@yymao](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@yymao). Last run: Nov 30, 2018\n",
+    "> Notebook owner: Yao-Yuan Mao [@yymao](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@yymao). Last run: Mar 8, 2024 by @patricialarsen\n",
     "\n",
-    "In this notebook we demostrate how to plot the halo occupation distribution of the protoDC2/cosmoDC2 galaxy catalog.\n",
+    "In this notebook we demostrate how to plot the halo occupation distribution of the cosmoDC2/skysim/roman_rubin galaxy catalogs.\n",
     "\n",
     "## Learning objectives\n",
-    "- Use `GCRCatalogs` to access the protoDC2 or cosmoDC2 catalogs. \n",
+    "- Use `GCRCatalogs` to access the cosmoDC2, skysim or roman_rubin catalogs. \n",
     "- Access cosmology in the extragalactic catalogs.\n",
     "- Use `CCL` to predict Halo Mass Function."
    ]
@@ -19,7 +19,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import GCRCatalogs"
@@ -28,7 +30,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import pyccl as ccl"
@@ -37,7 +41,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -45,19 +51,33 @@
     "%matplotlib inline"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Catalog selection\n",
+    "Uncomment the line corresponding to the catalog you want to inspect"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')"
+    "#gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')\n",
+    "gc = GCRCatalogs.load_catalog('skysim5000_v1.1.2_small')\n",
+    "#gc = GCRCatalogs.load_catalog('roman_rubin_2023_v1.1.3_elais')\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "zmax = 0.25\n",
@@ -65,19 +85,41 @@
     "mass_center = np.sqrt(mass_bins[1:] * mass_bins[:-1])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Get the data\n",
+    "Retrieve the data given the maximum redshift value determined above\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "data = gc.get_quantities(['halo_mass', 'Mag_true_r_lsst_z0', 'redshift'], filters=['redshift < {}'.format(zmax)])"
+    "data = gc.get_quantities(['halo_mass', 'Mag_true_r_lsst_z0', 'redshift','halo_id'], filters=['redshift < {}'.format(zmax)])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "### Cosmology\n",
+    "Retrieve the cosmological parameters and use them to create a ccl cosmology object"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "cosmo = ccl.Cosmology(\n",
@@ -90,21 +132,45 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Get expected halo mass function from CCL\n",
+    "We approximate the hmf by using the mean redshift, create a mass definition and decide which mass function to use"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# approximate hmf using mean redshift\n",
     "mean_scale_factor = 1.0/(1.0+data['redshift'].mean())\n",
-    "hmf_dn_dlogm = ccl.massfunc(cosmo, mass_center, mean_scale_factor)"
+    "\n",
+    "hmd_fof = ccl.halos.MassDefFof\n",
+    "mf = ccl.halos.MassFuncSheth99(mass_def=hmd_fof)\n",
+    "hmf_dn_dlogm =  mf(cosmo, mass_center, mean_scale_factor)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Determine expected number of halos\n",
+    "\n",
+    "Use the halo mass function and the volume (given by 4/3 pi * fsky * r^3) to get the total number of halos expected in the volume. We also select on halo ids to get the true number of halos in the volume. "
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "d = gc.cosmology.comoving_distance(zmax).to('Mpc').value\n",
@@ -114,27 +180,50 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "dlogm = np.ediff1d(np.log10(mass_bins))\n",
-    "nhalo_expected = hmf_dn_dlogm * volume * dlogm"
+    "nhalo_expected = hmf_dn_dlogm * volume * dlogm\n",
+    "\n",
+    "hid,idx,count=np.unique(data['halo_id'],return_index=True,return_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "### Plot halo occupation distribution"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "for Mr_thres, color in zip((-21.5, -21, -20.5, -20), plt.cm.tab20c.colors):\n",
     "    plt.loglog(\n",
     "        mass_center, \n",
     "        np.histogram(data['halo_mass'][data['Mag_true_r_lsst_z0'] < Mr_thres], mass_bins)[0] / nhalo_expected,\n",
+    "        label=r'$CCL:\\ M_r < {}$'.format(Mr_thres),\n",
+    "        c=color,\n",
+    "    );\n",
+    "    plt.loglog(\n",
+    "        mass_center, \n",
+    "        np.histogram(data['halo_mass'][data['Mag_true_r_lsst_z0'] < Mr_thres], mass_bins)[0]/np.histogram(data['halo_mass'][idx], mass_bins)[0],\n",
     "        label=r'$M_r < {}$'.format(Mr_thres),\n",
     "        c=color,\n",
+    "        linestyle='--'\n",
     "    );\n",
     "\n",
+    "\n",
     "plt.xlabel(r'${\\rm M}_h \\,/\\, {\\rm M}_\\odot$');\n",
     "plt.ylabel(r'$\\langle N_{\\rm gal} \\,|\\, {\\rm M}_h \\rangle$');\n",
     "plt.title(r'HOD $(z < 0.25)$');\n",
@@ -142,6 +231,13 @@
     "plt.axhline(1, lw=0.5, c='k');\n",
     "plt.legend();"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -160,9 +256,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/_sources/tutorials/extragalactic_gcr_mass_relations.ipynb b/_sources/tutorials/extragalactic_gcr_mass_relations.ipynb
index d7cdbe25..5d463b29 100644
--- a/_sources/tutorials/extragalactic_gcr_mass_relations.ipynb
+++ b/_sources/tutorials/extragalactic_gcr_mass_relations.ipynb
@@ -6,12 +6,12 @@
    "source": [
     "# Extragalactic catalogs: mass relations\n",
     "\n",
-    "> Notebook owner: Yao-Yuan Mao [@yymao](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@yymao). Last run: Nov 30, 2018\n",
+    "> Notebook owner: Yao-Yuan Mao [@yymao](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@yymao). Last run: Mar 8, 2024 by @patricialarsen\n",
     "\n",
-    "In this notebook we demostrate how to plot the halo mass-stellar mass relation and also the BH mass-bulge mass relation for the protoDC2/cosmoDC2 galaxy catalog.\n",
+    "In this notebook we demostrate how to plot the halo mass-stellar mass relation and also the BH mass-bulge mass relation for the cosmoDC2/ skysim/ roman_rubin galaxy catalog.\n",
     "\n",
     "## Learning objectives\n",
-    "- Use `GCRCatalogs` to access the protoDC2 or cosmoDC2 catalogs. \n",
+    "- Use `GCRCatalogs` to access the cosmoDC2, roman_rubin or skysim catalogs. \n",
     "- Be able to explore useful quantities using `GCRCatalogs`.\n",
     "- Be able to use filters when accessing quantities."
    ]
@@ -19,7 +19,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import GCRCatalogs"
@@ -28,7 +30,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -36,19 +40,32 @@
     "%matplotlib inline"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Uncomment the line corresponding to the catalog you're inspecting"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')"
+    "gc = GCRCatalogs.load_catalog('cosmoDC2_v1.1.4_small')\n",
+    "#gc = GCRCatalogs.load_catalog('skysim5000_v1.1.2_small')\n",
+    "#gc = GCRCatalogs.load_catalog('roman_rubin_2023_v1.1.1_elais')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# let's see what masses are availble \n",
@@ -65,7 +82,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data = gc.get_quantities(['stellar_mass', 'halo_mass'], filters=['redshift < 0.2', 'is_central'])\n",
@@ -86,7 +105,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data = gc.get_quantities(['stellar_mass', 'halo_mass'], filters=['redshift > 0.9', 'redshift < 1', 'is_central'])\n",
@@ -107,7 +128,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data = gc.get_quantities(['stellar_mass_bulge', 'blackHoleMass'], filters=['redshift < 0.2', 'is_central'])\n",
@@ -116,6 +139,13 @@
     "plt.xlabel(r'$\\log \\, {\\rm M}_{\\rm bulge} \\, / \\, {\\rm M}_\\odot$');\n",
     "plt.ylabel(r'$\\log \\, {\\rm M}_{\\rm BH} \\, / \\, {\\rm M}_\\odot$');"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -134,9 +164,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/_sources/tutorials/extragalactic_gcr_photoz_catalogs.ipynb b/_sources/tutorials/extragalactic_gcr_photoz_catalogs.ipynb
index 376c3d8f..f527282c 100644
--- a/_sources/tutorials/extragalactic_gcr_photoz_catalogs.ipynb
+++ b/_sources/tutorials/extragalactic_gcr_photoz_catalogs.ipynb
@@ -7,7 +7,7 @@
     "# cosmoDC2 extragalactic catalog photometric redshifts\n",
     "Owner:**Sam Schmidt [@sschmidt23](https://github.com/LSSTDESC/DC2-analysis/issues/new?body=@sschmidt23)**\n",
     "\n",
-    "Last Verifed to Run: **2020-06-09** (by @sschmidt23)\n",
+    "Last Verifed to Run: **2024-03-08** (by @patricialarsen)\n",
     "\n",
     "This notebook will show you how to access the \"add-on\" columns that provide the photometric redshift (photo-z) information for the extragalactic catalog (cosmoDC2_v1.1.4_image). \n",
     "\n",
@@ -32,7 +32,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -44,7 +46,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import GCRCatalogs\n",
@@ -66,7 +70,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "%%time\n",
@@ -103,7 +109,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# uncomment the line below to see a list of *all* available quantities in the composite catalog\n",
@@ -115,7 +123,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data = cat.get_quantities(['photoz_mask','photoz_pdf','photoz_mean','photoz_mode','photoz_odds','photoz_mode_ml_red_chi2','mag_i_lsst','mag_i_photoz','redshift'],\n",
@@ -137,7 +147,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "redshift = data['redshift']\n",
@@ -151,7 +163,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "redshift = redshift[photoz_mask]\n",
@@ -169,7 +183,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "pzdict = {'specz':redshift,'zmode':photoz_mode,'zmean':data['photoz_mean'],'odds':data['photoz_odds'],'ml_chi2':data['photoz_mode_ml_red_chi2'],\n",
@@ -181,7 +197,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "df.info()"
@@ -190,7 +208,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "magcut = 23.6"
@@ -206,7 +226,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "brightmask = (df['mag_i_photoz']<magcut)\n",
@@ -245,7 +267,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "oddscut = (brightdf['odds']>0.99)\n",
@@ -285,7 +309,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# NOTE: Need to set `only_use_master_attr` to False to allow accessing add-on attributes.  \n",
@@ -297,7 +323,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(5, 2, figsize=(18,16))\n",
@@ -323,7 +351,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig = plt.figure(figsize=(12,8))\n",
@@ -346,7 +376,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "tomocut = ((brightdf['zmode']>0.4) & (brightdf['zmode']<=0.6))\n",
@@ -371,7 +403,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "tomocut = ((brightdf['zmode']>0.1) & (brightdf['zmode']<=0.3))\n",
@@ -397,7 +431,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "del df\n",
@@ -421,7 +457,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "%%time\n",
@@ -431,7 +469,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data2 = cat2.get_quantities(['photoz_mask','photoz_pdf','photoz_mean','photoz_mode','photoz_odds','photoz_mode_ml_red_chi2','mag_i_lsst','mag_i_photoz','redshift'],\n",
@@ -448,7 +488,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fz_redshift = data2['redshift']\n",
@@ -472,7 +514,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "pzdict = {'specz':fz_redshift,'zmode':fz_photoz_mode,'zmean':data2['photoz_mean'],'odds':data2['photoz_odds'],'ml_chi2':data2['photoz_mode_ml_red_chi2'],\n",
@@ -484,7 +528,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fz_df.info()"
@@ -493,7 +539,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "brightmask = (fz_df['mag_i_photoz']<magcut)\n",
@@ -531,7 +579,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# NOTE: Need to set `only_use_master_attr` to False to allow accessing add-on attributes.  \n",
@@ -543,7 +593,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(5, 2, figsize=(18,16))\n",
@@ -569,7 +621,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig = plt.figure(figsize=(12,8))\n",
@@ -593,7 +647,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fztomocut = ((fz_brightdf['zmode']>0.4) & (fz_brightdf['zmode']<=0.6))\n",
@@ -611,7 +667,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fztomocut = ((fz_brightdf['zmode']>0.1) & (fz_brightdf['zmode']<=0.3))\n",
@@ -664,7 +722,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
diff --git a/_sources/tutorials/matching_fof.ipynb b/_sources/tutorials/matching_fof.ipynb
index 5d73ba73..b521399e 100644
--- a/_sources/tutorials/matching_fof.ipynb
+++ b/_sources/tutorials/matching_fof.ipynb
@@ -6,8 +6,8 @@
    "source": [
     "# Match truth and object catalogs for DC2 Run 2.2i\n",
     "Owner: Yao-Yuan Mao, Scott Daniel (with help from Anže Slosar, Bhairav Valera, HyeYun Park) <br>\n",
-    "Updated by: Javier Sanchez, Yao-Yuan Mao <br>\n",
-    "Last Verified to Run: 2021-07-01 by Yao-Yuan Mao\n",
+    "Updated by: Javier Sanchez, Yao-Yuan Mao, Patricia Larsen <br>\n",
+    "Last Verified to Run: 2024-Mar-11 by Patricia Larsen\n",
     "\n",
     "**Notes:**\n",
     "- Follow this [step-by-step guide](https://confluence.slac.stanford.edu/x/Xgg4Dg) if you don't know how to run this notebook.\n",
@@ -26,7 +26,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -39,7 +41,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "from astropy.coordinates import SkyCoord\n",
@@ -54,7 +58,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# load object catalog (for a single tract)\n",
@@ -64,7 +70,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Let's first visually inspect the footprint of a few tracts of the object catalog.\n",
@@ -85,7 +93,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Let's also define a magnitude cut\n",
@@ -98,7 +108,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# let's add total ellipticity for later use (not needed for now)\n",
@@ -109,7 +121,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Load ra and dec from object, using both of the filters we just defined.\n",
@@ -124,7 +138,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Let's now turn to the truth catalog. Here we just append galaxies and stars; \n",
@@ -135,17 +151,21 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Load the stars\n",
-    "stars_cat = GCRCatalogs.load_catalog(\"dc2_truth_run2.2i_star_truth_summary\")"
+    "stars_cat = GCRCatalogs.load_catalog(\"dc2_run2.2i_truth_star_summary\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "max_ra = np.nanmax(object_data['ra'])\n",
@@ -163,7 +183,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# get ra and dec from truth catalog\n",
@@ -178,19 +200,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "if not stars_cat.has_quantity(\"mag_i\"):\n",
     "    stars_cat.add_derived_quantity(\"mag_i\", flux_to_mag, \"flux_i\")\n",
-    "quantities = ['id', 'ra', 'dec', 'mag_i', 'redshift']\n",
+    "quantities = ['id', 'ra', 'dec', 'mag_i']\n",
     "stars_data = stars_cat.get_quantities(quantities, filters=pos_filters)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Adjust the tables of galaxies and stars so that we can merge them into one table\n",
@@ -209,7 +235,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "plt.scatter(truth_data_all['ra'][::100], truth_data_all['dec'][::100], s=0.1)\n",
@@ -219,7 +247,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# now we can really do the matching!\n",
@@ -236,7 +266,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# now we want to count the number of truth and object objects *for each group*\n",
@@ -266,7 +298,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Let's further inspect the objects in the groups that have 1-to-1 truth/object match.\n",
@@ -282,7 +316,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "truth_sc = SkyCoord(truth_data_all['ra'][truth_idx], truth_data_all['dec'][truth_idx], unit=\"deg\")\n",
@@ -296,7 +332,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "plt.figure(figsize=(7.3, 6))  # Pick a figuresize that will result in a square equal-axis plus colorbar\n",
@@ -312,7 +350,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "#Plotting Delta angle for the outputs\n",
@@ -324,7 +364,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# merge the matched objects\n",
@@ -336,7 +378,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Select only those truth objects that are galaxies which were not sprinkled\n",
@@ -347,7 +391,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# load redshift and ellipticity from the extragalactic catalog, only for galaxies that are already in `matched_gals`\n",
@@ -361,7 +407,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# merge extragalactic_data to matched_gals\n",
@@ -371,7 +419,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# compare the magnitude\n",
@@ -388,7 +438,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# compare the ellipticity (naively -- see below for further discussion)\n",
@@ -424,7 +476,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# compare the ellipticity (smartly)\n",
@@ -456,7 +510,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "def calc_lensed_ellipticity(es1, es2, gamma1, gamma2, kappa):\n",
@@ -473,7 +529,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Now let's get the newly defined ellipticity and add to our merged pandas data frame:\n",
@@ -488,7 +546,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "# Now we compare the ellipticity again (and don't forget the definition conversion!)\n",
@@ -534,7 +594,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,
diff --git a/searchindex.js b/searchindex.js
index 9c8ce8b4..97f84d58 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["README", "tutorials/README", "tutorials/dia_sn_vs_truth", "tutorials/dia_source_object_stamp", "tutorials/dm_butler_lensing_cuts", "tutorials/dm_butler_postage_stamps", "tutorials/dm_butler_postage_stamps_for_object_catalogs", "tutorials/dm_butler_skymap", "tutorials/extragalactic_gcr_cluster_colors", "tutorials/extragalactic_gcr_cluster_members", "tutorials/extragalactic_gcr_hod", "tutorials/extragalactic_gcr_mass_relations", "tutorials/extragalactic_gcr_photoz_catalogs", "tutorials/extragalactic_gcr_redshift_dist", "tutorials/matching_fof", "tutorials/matching_stack", "tutorials/object_gcr_1_intro", "tutorials/object_gcr_2_lensing_cuts", "tutorials/object_gcr_3_challenges", "tutorials/object_gcr_4_photoz", "tutorials/object_pandas_stellar_locus", "tutorials/object_per_visit_postage_stamp", "tutorials/object_spark_1_intro", "tutorials/postgres_forcedsource", "tutorials/postgres_object_1_intro", "tutorials/postgres_object_2", "tutorials/postgres_truth", "tutorials/truth_gcr_intro", "tutorials/truth_gcr_variables", "validation/DC2_calexp_src_validation_1p2", "validation/README", "validation/Run_1.2p_PSF_tests", "validation/validate_dc2_object_table", "validation/validate_dc2_run2.1i_object_table", "validation/validate_dc2_run2.2i_object_table"], "filenames": ["README.md", "tutorials/README.rst", "tutorials/dia_sn_vs_truth.ipynb", "tutorials/dia_source_object_stamp.ipynb", "tutorials/dm_butler_lensing_cuts.ipynb", "tutorials/dm_butler_postage_stamps.ipynb", "tutorials/dm_butler_postage_stamps_for_object_catalogs.ipynb", "tutorials/dm_butler_skymap.ipynb", "tutorials/extragalactic_gcr_cluster_colors.ipynb", "tutorials/extragalactic_gcr_cluster_members.ipynb", "tutorials/extragalactic_gcr_hod.ipynb", "tutorials/extragalactic_gcr_mass_relations.ipynb", "tutorials/extragalactic_gcr_photoz_catalogs.ipynb", "tutorials/extragalactic_gcr_redshift_dist.ipynb", "tutorials/matching_fof.ipynb", "tutorials/matching_stack.ipynb", "tutorials/object_gcr_1_intro.ipynb", "tutorials/object_gcr_2_lensing_cuts.ipynb", "tutorials/object_gcr_3_challenges.ipynb", "tutorials/object_gcr_4_photoz.ipynb", "tutorials/object_pandas_stellar_locus.ipynb", "tutorials/object_per_visit_postage_stamp.ipynb", "tutorials/object_spark_1_intro.ipynb", "tutorials/postgres_forcedsource.ipynb", "tutorials/postgres_object_1_intro.ipynb", "tutorials/postgres_object_2.ipynb", "tutorials/postgres_truth.ipynb", "tutorials/truth_gcr_intro.ipynb", "tutorials/truth_gcr_variables.ipynb", "validation/DC2_calexp_src_validation_1p2.ipynb", "validation/README.md", "validation/Run_1.2p_PSF_tests.ipynb", "validation/validate_dc2_object_table.ipynb", "validation/validate_dc2_run2.1i_object_table.ipynb", "validation/validate_dc2_run2.2i_object_table.ipynb"], "titles": ["DC2-analysis", "DC2 Tutorials", "DIA Analysis: Supernovae from the Run 1.2p Test", "DIA Analysis: Source, Object, and Postage Stamps for Run 1.2p Test", "Accessing the Coadd data using the Data Butler", "DC2: Generate Postage Stamps for set of RA, Dec coordinates", "DC2: Generate Postage Stamps (Cutouts) for objects in the Object Catalog", "Plotting the DC2 Run2.1i skyMap", "Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs", "Plotting Positions of Galaxy Cluster Members in Extragalactic Catalogs", "Halo Occupation Distribution from extragalactic catalogs", "Extragalactic catalogs: mass relations", "cosmoDC2 extragalactic catalog photometric redshifts", "Plot N versus z Distributions in the extragalactic catalogs", "Match truth and object catalogs for DC2 Run 2.2i", "Using the LSST Stack tools to do positional matching on coadd and src catalogs", "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part I: GCR access", "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part II: Lensing Cuts", "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part III: Guided Challenges", "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part IV: accessing photo-z", "Looking at the \u201cObject Catalogs\u201d: merged tract-patch catalogs in DC2 Run 1.1p", "DC2 Retrieve Visit-Level Forced Src Photometry and Postage Stamps from Object Catalog.", "DC2 object Run1.1p Apache Spark tutorial \u2013 Part I: Apache Spark access", "Accessing DC2 forced source data in PostgreSQL at NERSC", "Accessing DC2 data in PostgreSQL at NERSC", "Accessing DC2 data in PostgreSQL at NERSC part 2", "Accessing DC2 truth and simulated observations data in PostgreSQL at NERSC", "Accessing Truth Catalog Information", "Accessing variable and transient objects in the truth catalog", "Validation tests for DC2 1.2i/p single visit catalogs", "Introduction", "Validation tests on DC2 <code class=\"docutils literal notranslate\"><span class=\"pre\">calexps</span></code> and <code class=\"docutils literal notranslate\"><span class=\"pre\">src</span></code> catalogs", "Inspection of DC2 Object Table", "Inspection of DC2 Run 2.1i Object Table", "Inspection of DC2 Run 2.2i DR6 Object Table"], "terms": 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"questions"]], "DC2 Tutorials": [[1, "dc2-tutorials"]], "Notes for Tutorial Users": [[1, "notes-for-tutorial-users"]], "Notes for Tutorial Contributors": [[1, "notes-for-tutorial-contributors"]], "Semi-continuous Integration": [[1, "semi-continuous-integration"]], "DIA Analysis: Supernovae from the Run 1.2p Test": [[2, "dia-analysis-supernovae-from-the-run-1-2p-test"]], "Select SNe from the truth catalog": [[2, "select-sne-from-the-truth-catalog"]], "Select SNe from the truth catalog in the DIA test region": [[2, "select-sne-from-the-truth-catalog-in-the-dia-test-region"]], "A Lightcurve": [[2, "a-lightcurve"], [3, "a-lightcurve"]], "Match to DIAObject Catalog": [[2, "match-to-diaobject-catalog"]], "DIA Analysis: Source, Object, and Postage Stamps for Run 1.2p Test": [[3, "dia-analysis-source-object-and-postage-stamps-for-run-1-2p-test"]], "Introduction and Key Concepts": [[3, "introduction-and-key-concepts"]], "DIAObject statistics": [[3, "diaobject-statistics"]], "Match to Truth 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"learning-objectives"], [13, "learning-objectives"], [20, "learning-objectives"]], "Logistics": [[5, "logistics"], [6, "logistics"], [20, "logistics"], [21, "logistics"]], "Interactive backends and NERSC Jupyter vs JupyterLab": [[5, "interactive-backends-and-nersc-jupyter-vs-jupyterlab"]], "How To Make a Cutout Image": [[5, "how-to-make-a-cutout-image"]], "Making Some Postage Stamps": [[5, "making-some-postage-stamps"]], "AFW Display": [[5, "afw-display"]], "Using mask planes": [[5, "using-mask-planes"]], "Comparing plt.imshow and afwDisplay:": [[5, "comparing-plt-imshow-and-afwdisplay"]], "Using the PSF Model": [[5, "using-the-psf-model"]], "DC2: Generate Postage Stamps (Cutouts) for objects in the Object Catalog": [[6, "dc2-generate-postage-stamps-cutouts-for-objects-in-the-object-catalog"]], "Set up": [[6, "set-up"]], "Get a list of interesting objects": [[6, "get-a-list-of-interesting-objects"]], "What are tracts and patches?": [[6, "what-are-tracts-and-patches"]], "How do I find tract/patch for given RA/Dec?": [[6, "how-do-i-find-tract-patch-for-given-ra-dec"]], "Load coadd images using butler": [[6, "load-coadd-images-using-butler"]], "Make a postage stamp!": [[6, "make-a-postage-stamp"]], "A different way to load cutout image by specifying a bbox": [[6, "a-different-way-to-load-cutout-image-by-specifying-a-bbox"]], "Make a false color RGB image": [[6, "make-a-false-color-rgb-image"]], "Yay! Let\u2019s put this all together now!": [[6, "yay-let-s-put-this-all-together-now"]], "Plotting the DC2 Run2.1i skyMap": [[7, "plotting-the-dc2-run2-1i-skymap"]], "Plotting Functions": [[7, "plotting-functions"]], "Making the Plot": [[7, "making-the-plot"]], "Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs": [[8, "plotting-galaxy-cluster-member-colors-in-extragalactic-catalogs"]], "Reading catalog": [[8, "reading-catalog"], [9, "reading-catalog"]], "Help for error messages:": [[8, "help-for-error-messages"], [9, "help-for-error-messages"]], "Plotting Positions of Galaxy Cluster Members in Extragalactic Catalogs": [[9, "plotting-positions-of-galaxy-cluster-members-in-extragalactic-catalogs"]], "Plot individual clusters": [[9, "plot-individual-clusters"]], "Extensions:": [[9, "extensions"]], "Halo Occupation Distribution from extragalactic catalogs": [[10, "halo-occupation-distribution-from-extragalactic-catalogs"]], "Learning objectives": [[10, "learning-objectives"], [11, "learning-objectives"], [14, "learning-objectives"]], "Extragalactic catalogs: mass relations": [[11, "extragalactic-catalogs-mass-relations"]], "stellar mass - halo mass relation for low-z central galaxies": [[11, "stellar-mass-halo-mass-relation-for-low-z-central-galaxies"]], "bulge mass - black hole mass relation for low-z central galaxies": [[11, "bulge-mass-black-hole-mass-relation-for-low-z-central-galaxies"]], "cosmoDC2 extragalactic catalog photometric redshifts": [[12, "cosmodc2-extragalactic-catalog-photometric-redshifts"]], "Load the catalog": [[12, "load-the-catalog"], [19, "load-the-catalog"]], "Photo-z access methods": [[12, "photo-z-access-methods"], [19, "photo-z-access-methods"]], "FlexZBoost: Machine Learning photo-z\u2019s": [[12, "flexzboost-machine-learning-photo-z-s"]], "Plot N versus z Distributions in the extragalactic catalogs": [[13, "plot-n-versus-z-distributions-in-the-extragalactic-catalogs"]], "Appendix: Using a development version of GCRCatalogs": [[13, "appendix-using-a-development-version-of-gcrcatalogs"]], "Match truth and object catalogs for DC2 Run 2.2i": [[14, "match-truth-and-object-catalogs-for-dc2-run-2-2i"]], "Using the LSST Stack tools to do positional matching on coadd and src catalogs": [[15, "using-the-lsst-stack-tools-to-do-positional-matching-on-coadd-and-src-catalogs"]], "How To Create a Source Catalog": [[15, "how-to-create-a-source-catalog"]], "Selecting Galaxies": [[15, "selecting-galaxies"]], "Matching Experiments": [[15, "matching-experiments"]], "Sources or Objects?": [[15, "sources-or-objects"]], "Focusing on Well-measured Galaxies": [[15, "focusing-on-well-measured-galaxies"]], "Extracting the Truth Info": [[15, "extracting-the-truth-info"]], "Doing the Matching": [[15, "doing-the-matching"]], "Going Further": [[15, "going-further"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part I: GCR access": [[16, "dc2-object-catalog-run2-2i-gcr-tutorial-part-i-gcr-access"]], "Accessing the object catalog with the GCR": [[16, "accessing-the-object-catalog-with-the-gcr"]], "DC2 object catalog Schema": [[16, "dc2-object-catalog-schema"]], "Accessing the data": [[16, "accessing-the-data"]], "Applying filters and cuts": [[16, "applying-filters-and-cuts"], [22, "applying-filters-and-cuts"]], "Example of filtering: Star/galaxy separation": [[16, "example-of-filtering-star-galaxy-separation"], [22, "example-of-filtering-star-galaxy-separation"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part II: Lensing Cuts": [[17, "dc2-object-catalog-run2-2i-gcr-tutorial-part-ii-lensing-cuts"]], "Selecting a useful sample of galaxies: lensing cuts from HSC DR1": [[17, "selecting-a-useful-sample-of-galaxies-lensing-cuts-from-hsc-dr1"]], "Sample selection": [[17, "sample-selection"]], "Looking at the depth of the survey": [[17, "looking-at-the-depth-of-the-survey"]], "Impact of blendedness": [[17, "impact-of-blendedness"]], "So, one thing may jump to eye, these objects are supposed to be large, extremely well resolved, yet they often look fairly small\u2026 but they have a lot of sometimes very bright neighbours. This is very suspicious and may indicate a problem with the DM deblender.": [[17, "so-one-thing-may-jump-to-eye-these-objects-are-supposed-to-be-large-extremely-well-resolved-yet-they-often-look-fairly-small-but-they-have-a-lot-of-sometimes-very-bright-neighbours-this-is-very-suspicious-and-may-indicate-a-problem-with-the-dm-deblender"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part III: Guided Challenges": [[18, "dc2-object-catalog-run2-2i-gcr-tutorial-part-iii-guided-challenges"]], "Challenge 1: Galaxy counts-in-cells": [[18, "challenge-1-galaxy-counts-in-cells"]], "Challenge 2: Check if PSF residuals are within requirements": [[18, "challenge-2-check-if-psf-residuals-are-within-requirements"]], "Step 1: Select a clean sample of point sources": [[18, "step-1-select-a-clean-sample-of-point-sources"]], "Step 2: Computes size and ellipticity from second moments": [[18, "step-2-computes-size-and-ellipticity-from-second-moments"]], "Step 3: Extract sample": [[18, "step-3-extract-sample"]], "Step 4: Size and ellipticity residuals as a function of magnitude and seeing": [[18, "step-4-size-and-ellipticity-residuals-as-a-function-of-magnitude-and-seeing"]], "Step 5: Compute \\rho-statistics in Stile": [[18, "step-5-compute-rho-statistics-in-stile"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part IV: accessing photo-z": [[19, "dc2-object-catalog-run2-2i-gcr-tutorial-part-iv-accessing-photo-z"]], "Example": [[19, "example"]], "Looking at the \u201cObject Catalogs\u201d: merged tract-patch catalogs in DC2 Run 1.1p": [[20, "looking-at-the-object-catalogs-merged-tract-patch-catalogs-in-dc2-run-1-1p"]], "Purpose:": [[20, "purpose"]], "Restrict to \u201cgood\u201d sources": [[20, "restrict-to-good-sources"]], "Color-Magnitude plot": [[20, "color-magnitude-plot"]], "Appendix": [[20, "appendix"]], "Generic Catalog Reader (GCR)": [[20, "generic-catalog-reader-gcr"]], "DC2 Retrieve Visit-Level Forced Src Photometry and Postage Stamps from Object Catalog.": [[21, "dc2-retrieve-visit-level-forced-src-photometry-and-postage-stamps-from-object-catalog"]], "See Also": [[21, "see-also"]], "Reading a Forced-Position Photometry Catalog": [[21, "reading-a-forced-position-photometry-catalog"]], "Finding the Visits that Contain a Given Position": [[21, "finding-the-visits-that-contain-a-given-position"]], "Find the Tract(s), Patch(es) for a given RA, Dec": [[21, "find-the-tract-s-patch-es-for-a-given-ra-dec"]], "Here\u2019s Some Code to Generate Postage Stamps": [[21, "here-s-some-code-to-generate-postage-stamps"]], "Finally, Let\u2019s Make Some Stamps": [[21, "finally-let-s-make-some-stamps"]], "For a Bit of Perspective, let\u2019s end by looking at the full image": [[21, "for-a-bit-of-perspective-let-s-end-by-looking-at-the-full-image"]], "DC2 object Run1.1p Apache Spark tutorial \u2013 Part I: Apache Spark access": [[22, "dc2-object-run1-1p-apache-spark-tutorial-part-i-apache-spark-access"]], "Accessing the object catalog with Apache Spark": [[22, "accessing-the-object-catalog-with-apache-spark"]], "DC2 Object catalog Schema": [[22, "dc2-object-catalog-schema"]], "Accessing the data (taken from the original GCR notebook)": [[22, "accessing-the-data-taken-from-the-original-gcr-notebook"]], "Accessing DC2 forced source data in PostgreSQL at NERSC": [[23, "accessing-dc2-forced-source-data-in-postgresql-at-nersc"]], "Prerequisites": [[23, "prerequisites"], [24, "prerequisites"], [25, "prerequisites"], [26, "prerequisites"]], "Where Forced Source data can be found": [[23, "where-forced-source-data-can-be-found"]], "Light curves": [[23, "light-curves"], [26, "light-curves"]], "Get the data": [[23, "get-the-data"], [26, "get-the-data"]], "Plotting": [[23, "plotting"], [24, "plotting"], [26, "plotting"]], "Accessing DC2 data in PostgreSQL at NERSC": [[24, "accessing-dc2-data-in-postgresql-at-nersc"]], "Tutorial organization": [[24, "tutorial-organization"]], "Color-color": [[24, "color-color"]], "Using cuts": [[24, "using-cuts"]], "SQL Primer": [[24, "sql-primer"]], "Connecting to the Database": [[24, "connecting-to-the-database"]], "Tables": [[24, "tables"]], "Table definitions": [[24, "table-definitions"]], "Table data": [[24, "table-data"]], "Views": [[24, "views"]], "Fetching data: SELECT": [[24, "fetching-data-select"]], "What to fetch": [[24, "what-to-fetch"]], "Table expressions": [[24, "table-expressions"]], "Technical details": [[24, "technical-details"]], "Selection conditions": [[24, "selection-conditions"]], "Other optional clauses": [[24, "other-optional-clauses"]], "GROUP BY": [[24, "group-by"]], "ORDER BY": [[24, "order-by"]], "LIMIT": [[24, "limit"]], "Still more": [[24, "still-more"]], "Using Python module psycopg2": [[24, "using-python-module-psycopg2"]], "Connect": [[24, "connect"]], "Issue a query": [[24, "issue-a-query"]], "Retrieve results": [[24, "retrieve-results"]], "References": [[24, "references"]], "PostgreSQL 9.6": [[24, "postgresql-9-6"]], "psycopg2": [[24, "psycopg2"]], "Accessing DC2 data in PostgreSQL at NERSC part 2": [[25, "accessing-dc2-data-in-postgresql-at-nersc-part-2"]], "Finding Data": [[25, "finding-data"]], "Finding Datasets": [[25, "finding-datasets"]], "Querying on Native Quantities": [[25, "querying-on-native-quantities"]], "Adjustments for Larger Datasets": [[25, "adjustments-for-larger-datasets"]], "User-defined Functions (UDFs)": [[25, "user-defined-functions-udfs"]], "Restricting by tract or patch": [[25, "restricting-by-tract-or-patch"]], "Area Searches": [[25, "area-searches"]], "Cone search": [[25, "cone-search"]], "Box search": [[25, "box-search"]], "Accessing DC2 truth and simulated observations data in PostgreSQL at NERSC": [[26, "accessing-dc2-truth-and-simulated-observations-data-in-postgresql-at-nersc"]], "Conventions": [[26, "conventions"]], "Sample Query": [[26, "sample-query"]], "Area searches": [[26, "area-searches"]], "Plot light curves for one star": [[26, "plot-light-curves-for-one-star"]], "Is it in the object table?": [[26, "is-it-in-the-object-table"]], "Accessing Truth Catalog Information": [[27, "accessing-truth-catalog-information"]], "Accessing variable and transient objects in the truth catalog": [[28, "accessing-variable-and-transient-objects-in-the-truth-catalog"]], "Summary catalog": [[28, "summary-catalog"]], "light curve catalog": [[28, "light-curve-catalog"]], "Example 1: getting RA and Dec of all SNe whose brightest magnitude is brighter than a certain value": [[28, "example-1-getting-ra-and-dec-of-all-sne-whose-brightest-magnitude-is-brighter-than-a-certain-value"]], "Example 2: a histogram of brighest mag for all SNe in a particular area": [[28, "example-2-a-histogram-of-brighest-mag-for-all-sne-in-a-particular-area"]], "Validation tests for DC2 1.2i/p single visit catalogs": [[29, "validation-tests-for-dc2-1-2i-p-single-visit-catalogs"]], "Introduction": [[30, "introduction"]], "Notebooks": [[30, "notebooks"]], "Scripts": [[30, "scripts"]], "Validation tests on DC2 calexps and src catalogs": [[31, "validation-tests-on-dc2-calexps-and-src-catalogs"]], "Inspection of DC2 Object Table": [[32, "inspection-of-dc2-object-table"]], "Michael Wood-Vasey (@wmwv)": [[32, "michael-wood-vasey-wmwv"], [33, "michael-wood-vasey-wmwv"], [34, "michael-wood-vasey-wmwv"]], "Last Verified to Run: 2019-05-08": [[32, "last-verified-to-run-2019-05-08"]], "Load Data": [[32, "load-data"], [33, "load-data"], [34, "load-data"]], "Object Density in RA, Dec": [[32, "object-density-in-ra-dec"], [33, "object-density-in-ra-dec"], [34, "object-density-in-ra-dec"]], "Color-Color Diagrams and the Stellar Locus": [[32, "color-color-diagrams-and-the-stellar-locus"], [33, "color-color-diagrams-and-the-stellar-locus"], [34, "color-color-diagrams-and-the-stellar-locus"]], "1D Density Plots": [[32, "d-density-plots"], [33, "d-density-plots"], [34, "d-density-plots"]], "Blendedness and Extendedness": [[32, "blendedness-and-extendedness"]], "Shape Parameters": [[32, "shape-parameters"], [33, "shape-parameters"], [34, "shape-parameters"]], "FWHM": [[32, "fwhm"]], "Inspection of DC2 Run 2.1i Object Table": [[33, "inspection-of-dc2-run-2-1i-object-table"]], "Last Verified to Run: 2019-08-09": [[33, "last-verified-to-run-2019-08-09"]], "Run 2.1i includes": [[33, "run-2-1i-includes"]], "Quick Data Size estimates": [[33, "quick-data-size-estimates"], [34, "quick-data-size-estimates"]], "Import Needed Modules": [[33, "import-needed-modules"], [34, "import-needed-modules"]], "Define Catalog and Subsampling": [[33, "define-catalog-and-subsampling"], [34, "define-catalog-and-subsampling"]], "CosmoDC2": [[33, "cosmodc2"]], "HSC XMM": [[33, "hsc-xmm"]], "Compare to HSC and CosmocDC galaxy densities": [[33, "compare-to-hsc-and-cosmocdc-galaxy-densities"]], "Blendedness": [[33, "blendedness"], [34, "blendedness"]], "Extendedness": [[33, "extendedness"], [34, "extendedness"]], "FWHM of the PSF": [[33, "fwhm-of-the-psf"], [34, "fwhm-of-the-psf"]], "Inspection of DC2 Run 2.2i DR6 Object Table": [[34, "inspection-of-dc2-run-2-2i-dr6-object-table"]], "Last Verified to Run: 2020-06-11 by MWV": [[34, "last-verified-to-run-2020-06-11-by-mwv"]], "Run 2.2i DR6 as of 2020-06-04 includes": [[34, "run-2-2i-dr6-as-of-2020-06-04-includes"]], "Fix PSF definition": [[34, "fix-psf-definition"]], "Magnitude Error vs. Magnitude": [[34, "magnitude-error-vs-magnitude"]]}, "indexentries": {}})
\ No newline at end of file
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"tutorials/object_gcr_1_intro.ipynb", "tutorials/object_gcr_2_lensing_cuts.ipynb", "tutorials/object_gcr_3_challenges.ipynb", "tutorials/object_gcr_4_photoz.ipynb", "tutorials/object_pandas_stellar_locus.ipynb", "tutorials/object_per_visit_postage_stamp.ipynb", "tutorials/object_spark_1_intro.ipynb", "tutorials/postgres_forcedsource.ipynb", "tutorials/postgres_object_1_intro.ipynb", "tutorials/postgres_object_2.ipynb", "tutorials/postgres_truth.ipynb", "tutorials/truth_gcr_intro.ipynb", "tutorials/truth_gcr_variables.ipynb", "validation/DC2_calexp_src_validation_1p2.ipynb", "validation/README.md", "validation/Run_1.2p_PSF_tests.ipynb", "validation/validate_dc2_object_table.ipynb", "validation/validate_dc2_run2.1i_object_table.ipynb", "validation/validate_dc2_run2.2i_object_table.ipynb"], "titles": ["DC2-analysis", "DC2 Tutorials", "DIA Analysis: Supernovae from the Run 1.2p Test", "DIA Analysis: Source, Object, and Postage Stamps for Run 1.2p Test", "Accessing the Coadd data using the 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"mwv": 34, "04": 34, "fix": 34}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx": 60}, "alltitles": {"DC2-analysis": [[0, "dc2-analysis"]], "Links": [[0, "links"]], "License, credit": [[0, "license-credit"]], "How to get involved": [[0, "how-to-get-involved"]], "Notebook review": [[0, "notebook-review"]], "Questions?": [[0, "questions"]], "DC2 Tutorials": [[1, "dc2-tutorials"]], "Notes for Tutorial Users": [[1, "notes-for-tutorial-users"]], "Notes for Tutorial Contributors": [[1, "notes-for-tutorial-contributors"]], "Semi-continuous Integration": [[1, "semi-continuous-integration"]], "DIA Analysis: Supernovae from the Run 1.2p Test": [[2, "dia-analysis-supernovae-from-the-run-1-2p-test"]], "Select SNe from the truth catalog": [[2, "select-sne-from-the-truth-catalog"]], "Select SNe from the truth catalog in the DIA test region": [[2, "select-sne-from-the-truth-catalog-in-the-dia-test-region"]], "A Lightcurve": [[2, "a-lightcurve"], [3, "a-lightcurve"]], "Match to DIAObject Catalog": [[2, "match-to-diaobject-catalog"]], "DIA Analysis: Source, Object, and Postage Stamps for Run 1.2p Test": [[3, "dia-analysis-source-object-and-postage-stamps-for-run-1-2p-test"]], "Introduction and Key Concepts": [[3, "introduction-and-key-concepts"]], "DIAObject statistics": [[3, "diaobject-statistics"]], "Match to Truth Catalog": [[3, "match-to-truth-catalog"]], "Postage Stamp for DIA Object": [[3, "postage-stamp-for-dia-object"]], "How these data products were generated": [[3, "how-these-data-products-were-generated"]], "Accessing the Coadd data using the Data Butler": [[4, "accessing-the-coadd-data-using-the-data-butler"]], "Learning Objectives": [[4, "learning-objectives"], [21, "learning-objectives"]], "Set Up": [[4, "set-up"], [5, "set-up"], [7, "set-up"], [15, "set-up"]], "How To Read DM Science Pipelines Coadd Catalogs into a Pandas Dataframe": [[4, "how-to-read-dm-science-pipelines-coadd-catalogs-into-a-pandas-dataframe"]], "Accessing the DM Science Pipeline processed data": [[4, "accessing-the-dm-science-pipeline-processed-data"]], "Making the Selection": [[4, "making-the-selection"]], "DC2: Generate Postage Stamps for set of RA, Dec coordinates": [[5, "dc2-generate-postage-stamps-for-set-of-ra-dec-coordinates"]], "Learning Objectives:": [[5, "learning-objectives"], [6, "learning-objectives"], [13, "learning-objectives"], [20, "learning-objectives"]], "Logistics": [[5, "logistics"], [6, "logistics"], [20, "logistics"], [21, "logistics"]], "Interactive backends and NERSC Jupyter vs JupyterLab": [[5, "interactive-backends-and-nersc-jupyter-vs-jupyterlab"]], "How To Make a Cutout Image": [[5, "how-to-make-a-cutout-image"]], "Making Some Postage Stamps": [[5, "making-some-postage-stamps"]], "AFW Display": [[5, "afw-display"]], "Using mask planes": [[5, "using-mask-planes"]], "Comparing plt.imshow and afwDisplay:": [[5, "comparing-plt-imshow-and-afwdisplay"]], "Using the PSF Model": [[5, "using-the-psf-model"]], "DC2: Generate Postage Stamps (Cutouts) for objects in the Object Catalog": [[6, "dc2-generate-postage-stamps-cutouts-for-objects-in-the-object-catalog"]], "Set up": [[6, "set-up"]], "Get a list of interesting objects": [[6, "get-a-list-of-interesting-objects"]], "What are tracts and patches?": [[6, "what-are-tracts-and-patches"]], "How do I find tract/patch for given RA/Dec?": [[6, "how-do-i-find-tract-patch-for-given-ra-dec"]], "Load coadd images using butler": [[6, "load-coadd-images-using-butler"]], "Make a postage stamp!": [[6, "make-a-postage-stamp"]], "A different way to load cutout image by specifying a bbox": [[6, "a-different-way-to-load-cutout-image-by-specifying-a-bbox"]], "Make a false color RGB image": [[6, "make-a-false-color-rgb-image"]], "Yay! Let\u2019s put this all together now!": [[6, "yay-let-s-put-this-all-together-now"]], "Plotting the DC2 Run2.1i skyMap": [[7, "plotting-the-dc2-run2-1i-skymap"]], "Plotting Functions": [[7, "plotting-functions"]], "Making the Plot": [[7, "making-the-plot"]], "Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs": [[8, "plotting-galaxy-cluster-member-colors-in-extragalactic-catalogs"]], "Other catalog options:": [[8, "other-catalog-options"], [9, "other-catalog-options"]], "Reading catalog": [[8, "reading-catalog"], [9, "reading-catalog"]], "Help for error messages:": [[8, "help-for-error-messages"], [9, "help-for-error-messages"]], "Plotting Positions of Galaxy Cluster Members in Extragalactic Catalogs": [[9, "plotting-positions-of-galaxy-cluster-members-in-extragalactic-catalogs"]], "Plot individual clusters": [[9, "plot-individual-clusters"]], "Extensions:": [[9, "extensions"]], "Halo Occupation Distribution from extragalactic catalogs": [[10, "halo-occupation-distribution-from-extragalactic-catalogs"]], "Learning objectives": [[10, "learning-objectives"], [11, "learning-objectives"], [14, "learning-objectives"]], "Catalog selection": [[10, "catalog-selection"]], "Get the data": [[10, "get-the-data"], [23, "get-the-data"], [26, "get-the-data"]], "Cosmology": [[10, "cosmology"]], "Get expected halo mass function from CCL": [[10, "get-expected-halo-mass-function-from-ccl"]], "Determine expected number of halos": [[10, "determine-expected-number-of-halos"]], "Plot halo occupation distribution": [[10, "plot-halo-occupation-distribution"]], "Extragalactic catalogs: mass relations": [[11, "extragalactic-catalogs-mass-relations"]], "Uncomment the line corresponding to the catalog you\u2019re inspecting": [[11, "uncomment-the-line-corresponding-to-the-catalog-you-re-inspecting"]], "stellar mass - halo mass relation for low-z central galaxies": [[11, "stellar-mass-halo-mass-relation-for-low-z-central-galaxies"]], "bulge mass - black hole mass relation for low-z central galaxies": [[11, "bulge-mass-black-hole-mass-relation-for-low-z-central-galaxies"]], "cosmoDC2 extragalactic catalog photometric redshifts": [[12, "cosmodc2-extragalactic-catalog-photometric-redshifts"]], "Load the catalog": [[12, "load-the-catalog"], [19, "load-the-catalog"]], "Photo-z access methods": [[12, "photo-z-access-methods"], [19, "photo-z-access-methods"]], "FlexZBoost: Machine Learning photo-z\u2019s": [[12, "flexzboost-machine-learning-photo-z-s"]], "Plot N versus z Distributions in the extragalactic catalogs": [[13, "plot-n-versus-z-distributions-in-the-extragalactic-catalogs"]], "Appendix: Using a development version of GCRCatalogs": [[13, "appendix-using-a-development-version-of-gcrcatalogs"]], "Match truth and object catalogs for DC2 Run 2.2i": [[14, "match-truth-and-object-catalogs-for-dc2-run-2-2i"]], "Using the LSST Stack tools to do positional matching on coadd and src catalogs": [[15, "using-the-lsst-stack-tools-to-do-positional-matching-on-coadd-and-src-catalogs"]], "How To Create a Source Catalog": [[15, "how-to-create-a-source-catalog"]], "Selecting Galaxies": [[15, "selecting-galaxies"]], "Matching Experiments": [[15, "matching-experiments"]], "Sources or Objects?": [[15, "sources-or-objects"]], "Focusing on Well-measured Galaxies": [[15, "focusing-on-well-measured-galaxies"]], "Extracting the Truth Info": [[15, "extracting-the-truth-info"]], "Doing the Matching": [[15, "doing-the-matching"]], "Going Further": [[15, "going-further"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part I: GCR access": [[16, "dc2-object-catalog-run2-2i-gcr-tutorial-part-i-gcr-access"]], "Accessing the object catalog with the GCR": [[16, "accessing-the-object-catalog-with-the-gcr"]], "DC2 object catalog Schema": [[16, "dc2-object-catalog-schema"]], "Accessing the data": [[16, "accessing-the-data"]], "Applying filters and cuts": [[16, "applying-filters-and-cuts"], [22, "applying-filters-and-cuts"]], "Example of filtering: Star/galaxy separation": [[16, "example-of-filtering-star-galaxy-separation"], [22, "example-of-filtering-star-galaxy-separation"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part II: Lensing Cuts": [[17, "dc2-object-catalog-run2-2i-gcr-tutorial-part-ii-lensing-cuts"]], "Selecting a useful sample of galaxies: lensing cuts from HSC DR1": [[17, "selecting-a-useful-sample-of-galaxies-lensing-cuts-from-hsc-dr1"]], "Sample selection": [[17, "sample-selection"]], "Looking at the depth of the survey": [[17, "looking-at-the-depth-of-the-survey"]], "Impact of blendedness": [[17, "impact-of-blendedness"]], "So, one thing may jump to eye, these objects are supposed to be large, extremely well resolved, yet they often look fairly small\u2026 but they have a lot of sometimes very bright neighbours. This is very suspicious and may indicate a problem with the DM deblender.": [[17, "so-one-thing-may-jump-to-eye-these-objects-are-supposed-to-be-large-extremely-well-resolved-yet-they-often-look-fairly-small-but-they-have-a-lot-of-sometimes-very-bright-neighbours-this-is-very-suspicious-and-may-indicate-a-problem-with-the-dm-deblender"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part III: Guided Challenges": [[18, "dc2-object-catalog-run2-2i-gcr-tutorial-part-iii-guided-challenges"]], "Challenge 1: Galaxy counts-in-cells": [[18, "challenge-1-galaxy-counts-in-cells"]], "Challenge 2: Check if PSF residuals are within requirements": [[18, "challenge-2-check-if-psf-residuals-are-within-requirements"]], "Step 1: Select a clean sample of point sources": [[18, "step-1-select-a-clean-sample-of-point-sources"]], "Step 2: Computes size and ellipticity from second moments": [[18, "step-2-computes-size-and-ellipticity-from-second-moments"]], "Step 3: Extract sample": [[18, "step-3-extract-sample"]], "Step 4: Size and ellipticity residuals as a function of magnitude and seeing": [[18, "step-4-size-and-ellipticity-residuals-as-a-function-of-magnitude-and-seeing"]], "Step 5: Compute \\rho-statistics in Stile": [[18, "step-5-compute-rho-statistics-in-stile"]], "DC2 Object Catalog Run2.2i GCR tutorial \u2013 Part IV: accessing photo-z": [[19, "dc2-object-catalog-run2-2i-gcr-tutorial-part-iv-accessing-photo-z"]], "Example": [[19, "example"]], "Looking at the \u201cObject Catalogs\u201d: merged tract-patch catalogs in DC2 Run 1.1p": [[20, "looking-at-the-object-catalogs-merged-tract-patch-catalogs-in-dc2-run-1-1p"]], "Purpose:": [[20, "purpose"]], "Restrict to \u201cgood\u201d sources": [[20, "restrict-to-good-sources"]], "Color-Magnitude plot": [[20, "color-magnitude-plot"]], "Appendix": [[20, "appendix"]], "Generic Catalog Reader (GCR)": [[20, "generic-catalog-reader-gcr"]], "DC2 Retrieve Visit-Level Forced Src Photometry and Postage Stamps from Object Catalog.": [[21, "dc2-retrieve-visit-level-forced-src-photometry-and-postage-stamps-from-object-catalog"]], "See Also": [[21, "see-also"]], "Reading a Forced-Position Photometry Catalog": [[21, "reading-a-forced-position-photometry-catalog"]], "Finding the Visits that Contain a Given Position": [[21, "finding-the-visits-that-contain-a-given-position"]], "Find the Tract(s), Patch(es) for a given RA, Dec": [[21, "find-the-tract-s-patch-es-for-a-given-ra-dec"]], "Here\u2019s Some Code to Generate Postage Stamps": [[21, "here-s-some-code-to-generate-postage-stamps"]], "Finally, Let\u2019s Make Some Stamps": [[21, "finally-let-s-make-some-stamps"]], "For a Bit of Perspective, let\u2019s end by looking at the full image": [[21, "for-a-bit-of-perspective-let-s-end-by-looking-at-the-full-image"]], "DC2 object Run1.1p Apache Spark tutorial \u2013 Part I: Apache Spark access": [[22, "dc2-object-run1-1p-apache-spark-tutorial-part-i-apache-spark-access"]], "Accessing the object catalog with Apache Spark": [[22, "accessing-the-object-catalog-with-apache-spark"]], "DC2 Object catalog Schema": [[22, "dc2-object-catalog-schema"]], "Accessing the data (taken from the original GCR notebook)": [[22, "accessing-the-data-taken-from-the-original-gcr-notebook"]], "Accessing DC2 forced source data in PostgreSQL at NERSC": [[23, "accessing-dc2-forced-source-data-in-postgresql-at-nersc"]], "Prerequisites": [[23, "prerequisites"], [24, "prerequisites"], [25, "prerequisites"], [26, "prerequisites"]], "Where Forced Source data can be found": [[23, "where-forced-source-data-can-be-found"]], "Light curves": [[23, "light-curves"], [26, "light-curves"]], "Plotting": [[23, "plotting"], [24, "plotting"], [26, "plotting"]], "Accessing DC2 data in PostgreSQL at NERSC": [[24, "accessing-dc2-data-in-postgresql-at-nersc"]], "Tutorial organization": [[24, "tutorial-organization"]], "Color-color": [[24, "color-color"]], "Using cuts": [[24, "using-cuts"]], "SQL Primer": [[24, "sql-primer"]], "Connecting to the Database": [[24, "connecting-to-the-database"]], "Tables": [[24, "tables"]], "Table definitions": [[24, "table-definitions"]], "Table data": [[24, "table-data"]], "Views": [[24, "views"]], "Fetching data: SELECT": [[24, "fetching-data-select"]], "What to fetch": [[24, "what-to-fetch"]], "Table expressions": [[24, "table-expressions"]], "Technical details": [[24, "technical-details"]], "Selection conditions": [[24, "selection-conditions"]], "Other optional clauses": [[24, "other-optional-clauses"]], "GROUP BY": [[24, "group-by"]], "ORDER BY": [[24, "order-by"]], "LIMIT": [[24, "limit"]], "Still more": [[24, "still-more"]], "Using Python module psycopg2": [[24, "using-python-module-psycopg2"]], "Connect": [[24, "connect"]], "Issue a query": [[24, "issue-a-query"]], "Retrieve results": [[24, "retrieve-results"]], "References": [[24, "references"]], "PostgreSQL 9.6": [[24, "postgresql-9-6"]], "psycopg2": [[24, "psycopg2"]], "Accessing DC2 data in PostgreSQL at NERSC part 2": [[25, "accessing-dc2-data-in-postgresql-at-nersc-part-2"]], "Finding Data": [[25, "finding-data"]], "Finding Datasets": [[25, "finding-datasets"]], "Querying on Native Quantities": [[25, "querying-on-native-quantities"]], "Adjustments for Larger Datasets": [[25, "adjustments-for-larger-datasets"]], "User-defined Functions (UDFs)": [[25, "user-defined-functions-udfs"]], "Restricting by tract or patch": [[25, "restricting-by-tract-or-patch"]], "Area Searches": [[25, "area-searches"]], "Cone search": [[25, "cone-search"]], "Box search": [[25, "box-search"]], "Accessing DC2 truth and simulated observations data in PostgreSQL at NERSC": [[26, "accessing-dc2-truth-and-simulated-observations-data-in-postgresql-at-nersc"]], "Conventions": [[26, "conventions"]], "Sample Query": [[26, "sample-query"]], "Area searches": [[26, "area-searches"]], "Plot light curves for one star": [[26, "plot-light-curves-for-one-star"]], "Is it in the object table?": [[26, "is-it-in-the-object-table"]], "Accessing Truth Catalog Information": [[27, "accessing-truth-catalog-information"]], "Accessing variable and transient objects in the truth catalog": [[28, "accessing-variable-and-transient-objects-in-the-truth-catalog"]], "Summary catalog": [[28, "summary-catalog"]], "light curve catalog": [[28, "light-curve-catalog"]], "Example 1: getting RA and Dec of all SNe whose brightest magnitude is brighter than a certain value": [[28, "example-1-getting-ra-and-dec-of-all-sne-whose-brightest-magnitude-is-brighter-than-a-certain-value"]], "Example 2: a histogram of brighest mag for all SNe in a particular area": [[28, "example-2-a-histogram-of-brighest-mag-for-all-sne-in-a-particular-area"]], "Validation tests for DC2 1.2i/p single visit catalogs": [[29, "validation-tests-for-dc2-1-2i-p-single-visit-catalogs"]], "Introduction": [[30, "introduction"]], "Notebooks": [[30, "notebooks"]], "Scripts": [[30, "scripts"]], "Validation tests on DC2 calexps and src catalogs": [[31, "validation-tests-on-dc2-calexps-and-src-catalogs"]], "Inspection of DC2 Object Table": [[32, "inspection-of-dc2-object-table"]], "Michael Wood-Vasey (@wmwv)": [[32, "michael-wood-vasey-wmwv"], [33, "michael-wood-vasey-wmwv"], [34, "michael-wood-vasey-wmwv"]], "Last Verified to Run: 2019-05-08": [[32, "last-verified-to-run-2019-05-08"]], "Load Data": [[32, "load-data"], [33, "load-data"], [34, "load-data"]], "Object Density in RA, Dec": [[32, "object-density-in-ra-dec"], [33, "object-density-in-ra-dec"], [34, "object-density-in-ra-dec"]], "Color-Color Diagrams and the Stellar Locus": [[32, "color-color-diagrams-and-the-stellar-locus"], [33, "color-color-diagrams-and-the-stellar-locus"], [34, "color-color-diagrams-and-the-stellar-locus"]], "1D Density Plots": [[32, "d-density-plots"], [33, "d-density-plots"], [34, "d-density-plots"]], "Blendedness and Extendedness": [[32, "blendedness-and-extendedness"]], "Shape Parameters": [[32, "shape-parameters"], [33, "shape-parameters"], [34, "shape-parameters"]], "FWHM": [[32, "fwhm"]], "Inspection of DC2 Run 2.1i Object Table": [[33, "inspection-of-dc2-run-2-1i-object-table"]], "Last Verified to Run: 2019-08-09": [[33, "last-verified-to-run-2019-08-09"]], "Run 2.1i includes": [[33, "run-2-1i-includes"]], "Quick Data Size estimates": [[33, "quick-data-size-estimates"], [34, "quick-data-size-estimates"]], "Import Needed Modules": [[33, "import-needed-modules"], [34, "import-needed-modules"]], "Define Catalog and Subsampling": [[33, "define-catalog-and-subsampling"], [34, "define-catalog-and-subsampling"]], "CosmoDC2": [[33, "cosmodc2"]], "HSC XMM": [[33, "hsc-xmm"]], "Compare to HSC and CosmocDC galaxy densities": [[33, "compare-to-hsc-and-cosmocdc-galaxy-densities"]], "Blendedness": [[33, "blendedness"], [34, "blendedness"]], "Extendedness": [[33, "extendedness"], [34, "extendedness"]], "FWHM of the PSF": [[33, "fwhm-of-the-psf"], [34, "fwhm-of-the-psf"]], "Inspection of DC2 Run 2.2i DR6 Object Table": [[34, "inspection-of-dc2-run-2-2i-dr6-object-table"]], "Last Verified to Run: 2020-06-11 by MWV": [[34, "last-verified-to-run-2020-06-11-by-mwv"]], "Run 2.2i DR6 as of 2020-06-04 includes": [[34, "run-2-2i-dr6-as-of-2020-06-04-includes"]], "Fix PSF definition": [[34, "fix-psf-definition"]], "Magnitude Error vs. Magnitude": [[34, "magnitude-error-vs-magnitude"]]}, "indexentries": {}})
\ No newline at end of file
diff --git a/tutorials/extragalactic_gcr_cluster_colors.html b/tutorials/extragalactic_gcr_cluster_colors.html
index 8a5c205d..3be874ec 100644
--- a/tutorials/extragalactic_gcr_cluster_colors.html
+++ b/tutorials/extragalactic_gcr_cluster_colors.html
@@ -383,6 +383,7 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#other-catalog-options">Other catalog options:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#reading-catalog">Reading catalog</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#help-for-error-messages">Help for error messages:</a></li>
 </ul>
@@ -399,16 +400,16 @@ <h2> Contents </h2>
   <section class="tex2jax_ignore mathjax_ignore" id="plotting-galaxy-cluster-member-colors-in-extragalactic-catalogs">
 <h1>Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs<a class="headerlink" href="#plotting-galaxy-cluster-member-colors-in-extragalactic-catalogs" title="Link to this heading">#</a></h1>
 <p>Owners: <strong>Dan Korytov <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;dkorytov">&#64;dkorytov</a></strong></p>
-<p>Last verified run: Nov 30, 2018 (by &#64;yymao)</p>
+<p>Last verified run: Mar 8, 2024 (by &#64;patricialarsen)</p>
 <p>This notebook demonstrates how to access the extra galactic catalog through the Generic Catalog Reader (GCR, <a class="github reference external" href="https://github.com/yymao/generic-catalog-reader">yymao/generic-catalog-reader</a>) as well as how filter on galaxy features and cluster membership.</p>
 <p><strong>Objectives</strong>:</p>
 <p>After working through and studying this Notebook you should be able to</p>
 <ol class="arabic simple">
-<li><p>Access extragalactic catalogs (protoDC2, cosmoDC2) through the GCR</p></li>
+<li><p>Access extragalactic catalogs (cosmoDC2, skysim, roman_rubin) through the GCR</p></li>
 <li><p>Filter on galaxy properties</p></li>
 <li><p>Select and plot cluster members</p></li>
 </ol>
-<p><strong>Logistics</strong>: This notebook is intended to be run through the JupyterHub NERSC interface available here: <a class="reference external" href="https://jupyter-dev.nersc.gov">https://jupyter-dev.nersc.gov</a>. To setup your NERSC environment, please follow the instructions available here: <a class="reference external" href="https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC">https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC</a></p>
+<p><strong>Logistics</strong>: This notebook is intended to be run through the JupyterHub NERSC interface available here: <a class="reference external" href="https://jupyter.nersc.gov">https://jupyter.nersc.gov</a>. To setup your NERSC environment, please follow the instructions available here: <a class="reference external" href="https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC">https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC</a></p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">GCRCatalogs</span>
@@ -427,6 +428,23 @@ <h1>Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs<a class="hea
 </div>
 </div>
 </div>
+<section id="other-catalog-options">
+<h2>Other catalog options:<a class="headerlink" href="#other-catalog-options" title="Link to this heading">#</a></h2>
+<p>Some alternate catalogs that you might want to look at include skysim, which is a 5000 square degree extragalactic catalog, and the Roman Rubin catalog which is a smaller extragalactic catalog and image simulation. To load these instead execute one of the two cells below.</p>
+<div class="cell docutils container">
+<div class="cell_input docutils container">
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;skysim5000_v1.1.2_small&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+<div class="cell docutils container">
+<div class="cell_input docutils container">
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;roman_rubin_2023_v1.1.3_elais&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="o">=</span> <span class="n">gc</span><span class="o">.</span><span class="n">get_quantities</span><span class="p">([</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">,</span> <span class="s1">&#39;redshift&#39;</span><span class="p">,</span>
@@ -436,13 +454,15 @@ <h1>Plotting Galaxy Cluster Member Colors in Extragalactic Catalogs<a class="hea
 </div>
 </div>
 </div>
+</section>
 <section id="reading-catalog">
 <h2>Reading catalog<a class="headerlink" href="#reading-catalog" title="Link to this heading">#</a></h2>
 <p>We load in the catalog with the “load_catalog” command, and then the values with the “get_quantities” command using filters to select sub-samples of the catalog. For this case we only need the magnitudes in several filters and the redshift. Galaxies are filtered on host halo mass to be at least 3e13 h<span class="math notranslate nohighlight">\(^{-1}\)</span>M<span class="math notranslate nohighlight">\(_\odot\)</span>.</p>
 </section>
 <section id="help-for-error-messages">
 <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages" title="Link to this heading">#</a></h2>
-<p>If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: “source /global/common/software/lsst/common/miniconda/setup_current_python.sh”</p>
+<p>If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: “source
+/global/common/software/lsst/common/miniconda/kernels/setup.sh”</p>
 <p>We are loading in a smaller version of the full cosmoDC2 catalog - this contains the same information as the full catalog but with a smaller sky area.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -482,7 +502,7 @@ <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages
 </div>
 </div>
 </div>
-<p>After load the catalog and data, we are able to plot the color distribution as a function of redshift for cluster galaxies with very little effort!</p>
+<p>After loading the catalog and data, we are able to plot the color distribution as a function of redshift for cluster galaxies with very little effort!</p>
 </section>
 </section>
 
@@ -550,6 +570,7 @@ <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#other-catalog-options">Other catalog options:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#reading-catalog">Reading catalog</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#help-for-error-messages">Help for error messages:</a></li>
 </ul>
diff --git a/tutorials/extragalactic_gcr_cluster_members.html b/tutorials/extragalactic_gcr_cluster_members.html
index 1616d4c2..34c78af1 100644
--- a/tutorials/extragalactic_gcr_cluster_members.html
+++ b/tutorials/extragalactic_gcr_cluster_members.html
@@ -383,6 +383,7 @@ <h2> Contents </h2>
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#reading-catalog">Reading catalog</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#help-for-error-messages">Help for error messages:</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#other-catalog-options">Other catalog options:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#plot-individual-clusters">Plot individual clusters</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#extensions">Extensions:</a></li>
 </ul>
@@ -400,17 +401,17 @@ <h2> Contents </h2>
 <h1>Plotting Positions of Galaxy Cluster Members in Extragalactic Catalogs<a class="headerlink" href="#plotting-positions-of-galaxy-cluster-members-in-extragalactic-catalogs" title="Link to this heading">#</a></h1>
 <p>In this example script we show how to select for and look at members of individual clusters.</p>
 <p>Owners: <strong>Dan Korytov <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;dkorytov">&#64;dkorytov</a></strong>, <strong>Patricia Larsen</strong></p>
-<p>Last verified run: <strong>Nov 30, 2018</strong> by &#64;yymao</p>
+<p>Last verified run: <strong>March 8, 2024</strong> by &#64;patricialarsen</p>
 <p>This notebook demonstrates how to access the extra galactic catalog through the Generic Catalog Reader (GCR, <a class="github reference external" href="https://github.com/yymao/generic-catalog-reader">yymao/generic-catalog-reader</a>) as well as how filter on galaxy features and cluster membership.</p>
 <p><strong>Objectives</strong>:</p>
 <p>After working through and studying this Notebook you should be able to</p>
 <ol class="arabic simple">
-<li><p>Access extragalactic catalogs (protoDC2, cosmoDC2) through the GCR.</p></li>
+<li><p>Access extragalactic catalogs (cosmoDC2, skysim, roman_rubin) through the GCR.</p></li>
 <li><p>Select galaxy cluster centrals as a proxy for clusters.</p></li>
 <li><p>Select galaxies in individual clusters by using the host_id quantity.</p></li>
 <li><p>Plotting galaxy clustermembers positions on the sky as well as their comoving position in space.</p></li>
 </ol>
-<p><strong>Logistics</strong>: This notebook is intended to be run through the JupyterHub NERSC interface available here: <a class="reference external" href="https://jupyter-dev.nersc.gov">https://jupyter-dev.nersc.gov</a>. To setup your NERSC environment, please follow the instructions available here: <a class="reference external" href="https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC">https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter-dev+at+NERSC</a></p>
+<p><strong>Logistics</strong>: This notebook is intended to be run through the JupyterHub NERSC interface available here: <a class="reference external" href="https://jupyter.nersc.gov">https://jupyter.nersc.gov</a>. To setup your NERSC environment, please follow the instructions available here: <a class="reference external" href="https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC">https://confluence.slac.stanford.edu/display/LSSTDESC/Using+Jupyter+at+NERSC</a></p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">GCRCatalogs</span>
@@ -429,7 +430,8 @@ <h2>Reading catalog<a class="headerlink" href="#reading-catalog" title="Link to
 </section>
 <section id="help-for-error-messages">
 <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages" title="Link to this heading">#</a></h2>
-<p>If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: “source /global/common/software/lsst/common/miniconda/setup_current_python.sh”</p>
+<p>If this fails to find the appropriate quantities, check that the desc-python kernel is being used and if this is not available source the kernels by running the following command on a terminal at nersc: “source
+/global/common/software/lsst/common/miniconda/kernels/setup.sh”</p>
 <p>We are loading in a smaller version of the full cosmoDC2 catalog - this contains the same information as the full catalog but with a smaller sky area.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -438,6 +440,24 @@ <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages
 </div>
 </div>
 </div>
+</section>
+<section id="other-catalog-options">
+<h2>Other catalog options:<a class="headerlink" href="#other-catalog-options" title="Link to this heading">#</a></h2>
+<p>Some alternate catalogs that you might want to look at include skysim, which is a 5000 square degree extragalactic catalog, and the Roman Rubin catalog which is a smaller extragalactic catalog and image simulation. To load these instead execute one of the two cells below.</p>
+<div class="cell docutils container">
+<div class="cell_input docutils container">
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;skysim5000_v1.1.2_small&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
+<div class="cell docutils container">
+<div class="cell_input docutils container">
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;roman_rubin_2023_v1.1.3_elais&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+</div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">galaxy_data</span> <span class="o">=</span> <span class="n">gc</span><span class="o">.</span><span class="n">get_quantities</span><span class="p">([</span><span class="s1">&#39;ra&#39;</span><span class="p">,</span> <span class="s1">&#39;dec&#39;</span><span class="p">,</span> <span class="s1">&#39;mag_r&#39;</span><span class="p">,</span> <span class="s1">&#39;halo_id&#39;</span><span class="p">],</span> <span class="n">filters</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;mag_r &lt; 19&#39;</span><span class="p">])</span>
@@ -450,7 +470,7 @@ <h2>Help for error messages:<a class="headerlink" href="#help-for-error-messages
 </section>
 <section id="plot-individual-clusters">
 <h2>Plot individual clusters<a class="headerlink" href="#plot-individual-clusters" title="Link to this heading">#</a></h2>
-<p>The cluster_data we loaded selects for central galaxies in clusters of mass higher than 10^14 solar masses/h below redshift 0.2. We will plot three such clusters in the proto-DC2 region.</p>
+<p>The cluster_data we loaded selects for central galaxies in clusters of mass higher than 10^14 solar masses/h below redshift 0.2. We will plot three such clusters in the skysim region.</p>
 <p>For each of these clusters we can match the galaxies by selecting on ‘halo_id’ and make a scatter plot of the projected positions around the central galaxy. Note that the size of the circles corresponds to the r-band magnitude of the galaxies.</p>
 <p>The cluster data is cast into a familiar astropy table.</p>
 <div class="cell docutils container">
@@ -587,6 +607,7 @@ <h2>Extensions:<a class="headerlink" href="#extensions" title="Link to this head
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#reading-catalog">Reading catalog</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#help-for-error-messages">Help for error messages:</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#other-catalog-options">Other catalog options:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#plot-individual-clusters">Plot individual clusters</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#extensions">Extensions:</a></li>
 </ul>
diff --git a/tutorials/extragalactic_gcr_hod.html b/tutorials/extragalactic_gcr_hod.html
index f7c075a9..5e4e7063 100644
--- a/tutorials/extragalactic_gcr_hod.html
+++ b/tutorials/extragalactic_gcr_hod.html
@@ -381,7 +381,15 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#catalog-selection">Catalog selection</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#get-the-data">Get the data</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cosmology">Cosmology</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#get-expected-halo-mass-function-from-ccl">Get expected halo mass function from CCL</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#determine-expected-number-of-halos">Determine expected number of halos</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#plot-halo-occupation-distribution">Plot halo occupation distribution</a></li>
+</ul>
+</li>
 </ul>
             </nav>
         </div>
@@ -396,13 +404,13 @@ <h2> Contents </h2>
   <section class="tex2jax_ignore mathjax_ignore" id="halo-occupation-distribution-from-extragalactic-catalogs">
 <h1>Halo Occupation Distribution from extragalactic catalogs<a class="headerlink" href="#halo-occupation-distribution-from-extragalactic-catalogs" title="Link to this heading">#</a></h1>
 <blockquote>
-<div><p>Notebook owner: Yao-Yuan Mao <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;yymao">&#64;yymao</a>. Last run: Nov 30, 2018</p>
+<div><p>Notebook owner: Yao-Yuan Mao <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;yymao">&#64;yymao</a>. Last run: Mar 8, 2024 by &#64;patricialarsen</p>
 </div></blockquote>
-<p>In this notebook we demostrate how to plot the halo occupation distribution of the protoDC2/cosmoDC2 galaxy catalog.</p>
+<p>In this notebook we demostrate how to plot the halo occupation distribution of the cosmoDC2/skysim/roman_rubin galaxy catalogs.</p>
 <section id="learning-objectives">
 <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="Link to this heading">#</a></h2>
 <ul class="simple">
-<li><p>Use <code class="docutils literal notranslate"><span class="pre">GCRCatalogs</span></code> to access the protoDC2 or cosmoDC2 catalogs.</p></li>
+<li><p>Use <code class="docutils literal notranslate"><span class="pre">GCRCatalogs</span></code> to access the cosmoDC2, skysim or roman_rubin catalogs.</p></li>
 <li><p>Access cosmology in the extragalactic catalogs.</p></li>
 <li><p>Use <code class="docutils literal notranslate"><span class="pre">CCL</span></code> to predict Halo Mass Function.</p></li>
 </ul>
@@ -429,9 +437,14 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </div>
+<section id="catalog-selection">
+<h3>Catalog selection<a class="headerlink" href="#catalog-selection" title="Link to this heading">#</a></h3>
+<p>Uncomment the line corresponding to the catalog you want to inspect</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;cosmoDC2_v1.1.4_small&#39;</span><span class="p">)</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1">#gc = GCRCatalogs.load_catalog(&#39;cosmoDC2_v1.1.4_small&#39;)</span>
+<span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;skysim5000_v1.1.2_small&#39;</span><span class="p">)</span>
+<span class="c1">#gc = GCRCatalogs.load_catalog(&#39;roman_rubin_2023_v1.1.3_elais&#39;)</span>
 </pre></div>
 </div>
 </div>
@@ -445,13 +458,21 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </div>
+</section>
+<section id="get-the-data">
+<h3>Get the data<a class="headerlink" href="#get-the-data" title="Link to this heading">#</a></h3>
+<p>Retrieve the data given the maximum redshift value determined above</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="o">=</span> <span class="n">gc</span><span class="o">.</span><span class="n">get_quantities</span><span class="p">([</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">,</span> <span class="s1">&#39;Mag_true_r_lsst_z0&#39;</span><span class="p">,</span> <span class="s1">&#39;redshift&#39;</span><span class="p">],</span> <span class="n">filters</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;redshift &lt; </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">zmax</span><span class="p">)])</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="o">=</span> <span class="n">gc</span><span class="o">.</span><span class="n">get_quantities</span><span class="p">([</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">,</span> <span class="s1">&#39;Mag_true_r_lsst_z0&#39;</span><span class="p">,</span> <span class="s1">&#39;redshift&#39;</span><span class="p">,</span><span class="s1">&#39;halo_id&#39;</span><span class="p">],</span> <span class="n">filters</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;redshift &lt; </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">zmax</span><span class="p">)])</span>
 </pre></div>
 </div>
 </div>
 </div>
+</section>
+<section id="cosmology">
+<h3>Cosmology<a class="headerlink" href="#cosmology" title="Link to this heading">#</a></h3>
+<p>Retrieve the cosmological parameters and use them to create a ccl cosmology object</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">cosmo</span> <span class="o">=</span> <span class="n">ccl</span><span class="o">.</span><span class="n">Cosmology</span><span class="p">(</span>
@@ -466,15 +487,26 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </div>
+</section>
+<section id="get-expected-halo-mass-function-from-ccl">
+<h3>Get expected halo mass function from CCL<a class="headerlink" href="#get-expected-halo-mass-function-from-ccl" title="Link to this heading">#</a></h3>
+<p>We approximate the hmf by using the mean redshift, create a mass definition and decide which mass function to use</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># approximate hmf using mean redshift</span>
 <span class="n">mean_scale_factor</span> <span class="o">=</span> <span class="mf">1.0</span><span class="o">/</span><span class="p">(</span><span class="mf">1.0</span><span class="o">+</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;redshift&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">())</span>
-<span class="n">hmf_dn_dlogm</span> <span class="o">=</span> <span class="n">ccl</span><span class="o">.</span><span class="n">massfunc</span><span class="p">(</span><span class="n">cosmo</span><span class="p">,</span> <span class="n">mass_center</span><span class="p">,</span> <span class="n">mean_scale_factor</span><span class="p">)</span>
+
+<span class="n">hmd_fof</span> <span class="o">=</span> <span class="n">ccl</span><span class="o">.</span><span class="n">halos</span><span class="o">.</span><span class="n">MassDefFof</span>
+<span class="n">mf</span> <span class="o">=</span> <span class="n">ccl</span><span class="o">.</span><span class="n">halos</span><span class="o">.</span><span class="n">MassFuncSheth99</span><span class="p">(</span><span class="n">mass_def</span><span class="o">=</span><span class="n">hmd_fof</span><span class="p">)</span>
+<span class="n">hmf_dn_dlogm</span> <span class="o">=</span>  <span class="n">mf</span><span class="p">(</span><span class="n">cosmo</span><span class="p">,</span> <span class="n">mass_center</span><span class="p">,</span> <span class="n">mean_scale_factor</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 </div>
+</section>
+<section id="determine-expected-number-of-halos">
+<h3>Determine expected number of halos<a class="headerlink" href="#determine-expected-number-of-halos" title="Link to this heading">#</a></h3>
+<p>Use the halo mass function and the volume (given by 4/3 pi * fsky * r^3) to get the total number of halos expected in the volume. We also select on halo ids to get the true number of halos in the volume.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">d</span> <span class="o">=</span> <span class="n">gc</span><span class="o">.</span><span class="n">cosmology</span><span class="o">.</span><span class="n">comoving_distance</span><span class="p">(</span><span class="n">zmax</span><span class="p">)</span><span class="o">.</span><span class="n">to</span><span class="p">(</span><span class="s1">&#39;Mpc&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">value</span>
@@ -487,20 +519,33 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">dlogm</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ediff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">mass_bins</span><span class="p">))</span>
 <span class="n">nhalo_expected</span> <span class="o">=</span> <span class="n">hmf_dn_dlogm</span> <span class="o">*</span> <span class="n">volume</span> <span class="o">*</span> <span class="n">dlogm</span>
+
+<span class="n">hid</span><span class="p">,</span><span class="n">idx</span><span class="p">,</span><span class="n">count</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;halo_id&#39;</span><span class="p">],</span><span class="n">return_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span><span class="n">return_counts</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
 </div>
+</section>
+<section id="plot-halo-occupation-distribution">
+<h3>Plot halo occupation distribution<a class="headerlink" href="#plot-halo-occupation-distribution" title="Link to this heading">#</a></h3>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">Mr_thres</span><span class="p">,</span> <span class="n">color</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">((</span><span class="o">-</span><span class="mf">21.5</span><span class="p">,</span> <span class="o">-</span><span class="mi">21</span><span class="p">,</span> <span class="o">-</span><span class="mf">20.5</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">),</span> <span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">tab20c</span><span class="o">.</span><span class="n">colors</span><span class="p">):</span>
     <span class="n">plt</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span>
         <span class="n">mass_center</span><span class="p">,</span> 
         <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">][</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;Mag_true_r_lsst_z0&#39;</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">Mr_thres</span><span class="p">],</span> <span class="n">mass_bins</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">nhalo_expected</span><span class="p">,</span>
+        <span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;$CCL:\ M_r &lt; </span><span class="si">{}</span><span class="s1">$&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">Mr_thres</span><span class="p">),</span>
+        <span class="n">c</span><span class="o">=</span><span class="n">color</span><span class="p">,</span>
+    <span class="p">);</span>
+    <span class="n">plt</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span>
+        <span class="n">mass_center</span><span class="p">,</span> 
+        <span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">][</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;Mag_true_r_lsst_z0&#39;</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">Mr_thres</span><span class="p">],</span> <span class="n">mass_bins</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">histogram</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;halo_mass&#39;</span><span class="p">][</span><span class="n">idx</span><span class="p">],</span> <span class="n">mass_bins</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
         <span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;$M_r &lt; </span><span class="si">{}</span><span class="s1">$&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">Mr_thres</span><span class="p">),</span>
         <span class="n">c</span><span class="o">=</span><span class="n">color</span><span class="p">,</span>
+        <span class="n">linestyle</span><span class="o">=</span><span class="s1">&#39;--&#39;</span>
     <span class="p">);</span>
 
+
 <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;${\rm M}_h \,/\, {\rm M}_\odot$&#39;</span><span class="p">);</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$\langle N_{\rm gal} \,|\, {\rm M}_h \rangle$&#39;</span><span class="p">);</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;HOD $(z &lt; 0.25)$&#39;</span><span class="p">);</span>
@@ -512,6 +557,7 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </section>
+</section>
 </section>
 
     <script type="text/x-thebe-config">
@@ -578,7 +624,15 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#catalog-selection">Catalog selection</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#get-the-data">Get the data</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cosmology">Cosmology</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#get-expected-halo-mass-function-from-ccl">Get expected halo mass function from CCL</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#determine-expected-number-of-halos">Determine expected number of halos</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#plot-halo-occupation-distribution">Plot halo occupation distribution</a></li>
+</ul>
+</li>
 </ul>
   </nav></div>
 
diff --git a/tutorials/extragalactic_gcr_mass_relations.html b/tutorials/extragalactic_gcr_mass_relations.html
index 90638b9a..4f3e9dea 100644
--- a/tutorials/extragalactic_gcr_mass_relations.html
+++ b/tutorials/extragalactic_gcr_mass_relations.html
@@ -381,7 +381,10 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#uncomment-the-line-corresponding-to-the-catalog-you-re-inspecting">Uncomment the line corresponding to the catalog you’re inspecting</a></li>
+</ul>
+</li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#stellar-mass-halo-mass-relation-for-low-z-central-galaxies">stellar mass - halo mass relation for low-z central galaxies</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#bulge-mass-black-hole-mass-relation-for-low-z-central-galaxies">bulge mass - black hole mass relation for low-z central galaxies</a></li>
 </ul>
@@ -398,13 +401,13 @@ <h2> Contents </h2>
   <section class="tex2jax_ignore mathjax_ignore" id="extragalactic-catalogs-mass-relations">
 <h1>Extragalactic catalogs: mass relations<a class="headerlink" href="#extragalactic-catalogs-mass-relations" title="Link to this heading">#</a></h1>
 <blockquote>
-<div><p>Notebook owner: Yao-Yuan Mao <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;yymao">&#64;yymao</a>. Last run: Nov 30, 2018</p>
+<div><p>Notebook owner: Yao-Yuan Mao <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;yymao">&#64;yymao</a>. Last run: Mar 8, 2024 by &#64;patricialarsen</p>
 </div></blockquote>
-<p>In this notebook we demostrate how to plot the halo mass-stellar mass relation and also the BH mass-bulge mass relation for the protoDC2/cosmoDC2 galaxy catalog.</p>
+<p>In this notebook we demostrate how to plot the halo mass-stellar mass relation and also the BH mass-bulge mass relation for the cosmoDC2/ skysim/ roman_rubin galaxy catalog.</p>
 <section id="learning-objectives">
 <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="Link to this heading">#</a></h2>
 <ul class="simple">
-<li><p>Use <code class="docutils literal notranslate"><span class="pre">GCRCatalogs</span></code> to access the protoDC2 or cosmoDC2 catalogs.</p></li>
+<li><p>Use <code class="docutils literal notranslate"><span class="pre">GCRCatalogs</span></code> to access the cosmoDC2, roman_rubin or skysim catalogs.</p></li>
 <li><p>Be able to explore useful quantities using <code class="docutils literal notranslate"><span class="pre">GCRCatalogs</span></code>.</p></li>
 <li><p>Be able to use filters when accessing quantities.</p></li>
 </ul>
@@ -424,9 +427,13 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </div>
+<section id="uncomment-the-line-corresponding-to-the-catalog-you-re-inspecting">
+<h3>Uncomment the line corresponding to the catalog you’re inspecting<a class="headerlink" href="#uncomment-the-line-corresponding-to-the-catalog-you-re-inspecting" title="Link to this heading">#</a></h3>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gc</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s1">&#39;cosmoDC2_v1.1.4_small&#39;</span><span class="p">)</span>
+<span class="c1">#gc = GCRCatalogs.load_catalog(&#39;skysim5000_v1.1.2_small&#39;)</span>
+<span class="c1">#gc = GCRCatalogs.load_catalog(&#39;roman_rubin_2023_v1.1.1_elais&#39;)</span>
 </pre></div>
 </div>
 </div>
@@ -440,6 +447,7 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 </div>
 </div>
 </section>
+</section>
 <section id="stellar-mass-halo-mass-relation-for-low-z-central-galaxies">
 <h2>stellar mass - halo mass relation for low-z central galaxies<a class="headerlink" href="#stellar-mass-halo-mass-relation-for-low-z-central-galaxies" title="Link to this heading">#</a></h2>
 <div class="cell docutils container">
@@ -548,7 +556,10 @@ <h2>bulge mass - black hole mass relation for low-z central galaxies<a class="he
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#learning-objectives">Learning objectives</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#uncomment-the-line-corresponding-to-the-catalog-you-re-inspecting">Uncomment the line corresponding to the catalog you’re inspecting</a></li>
+</ul>
+</li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#stellar-mass-halo-mass-relation-for-low-z-central-galaxies">stellar mass - halo mass relation for low-z central galaxies</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#bulge-mass-black-hole-mass-relation-for-low-z-central-galaxies">bulge mass - black hole mass relation for low-z central galaxies</a></li>
 </ul>
diff --git a/tutorials/extragalactic_gcr_photoz_catalogs.html b/tutorials/extragalactic_gcr_photoz_catalogs.html
index 32b5ea8e..05c1274b 100644
--- a/tutorials/extragalactic_gcr_photoz_catalogs.html
+++ b/tutorials/extragalactic_gcr_photoz_catalogs.html
@@ -402,7 +402,7 @@ <h2> Contents </h2>
   <section class="tex2jax_ignore mathjax_ignore" id="cosmodc2-extragalactic-catalog-photometric-redshifts">
 <h1>cosmoDC2 extragalactic catalog photometric redshifts<a class="headerlink" href="#cosmodc2-extragalactic-catalog-photometric-redshifts" title="Link to this heading">#</a></h1>
 <p>Owner:<strong>Sam Schmidt <a class="reference external" href="https://github.com/LSSTDESC/DC2-analysis/issues/new?body=&#64;sschmidt23">&#64;sschmidt23</a></strong></p>
-<p>Last Verifed to Run: <strong>2020-06-09</strong> (by &#64;sschmidt23)</p>
+<p>Last Verifed to Run: <strong>2024-03-08</strong> (by &#64;patricialarsen)</p>
 <p>This notebook will show you how to access the “add-on” columns that provide the photometric redshift (photo-z) information for the extragalactic catalog (cosmoDC2_v1.1.4_image).</p>
 <p><strong>Learning objectives</strong>: After going through this notebook, you should be able to:</p>
 <ol class="arabic simple">
diff --git a/tutorials/matching_fof.html b/tutorials/matching_fof.html
index 344d6eee..12008604 100644
--- a/tutorials/matching_fof.html
+++ b/tutorials/matching_fof.html
@@ -398,8 +398,8 @@ <h2> Contents </h2>
   <section class="tex2jax_ignore mathjax_ignore" id="match-truth-and-object-catalogs-for-dc2-run-2-2i">
 <h1>Match truth and object catalogs for DC2 Run 2.2i<a class="headerlink" href="#match-truth-and-object-catalogs-for-dc2-run-2-2i" title="Link to this heading">#</a></h1>
 <p>Owner: Yao-Yuan Mao, Scott Daniel (with help from Anže Slosar, Bhairav Valera, HyeYun Park) <br>
-Updated by: Javier Sanchez, Yao-Yuan Mao <br>
-Last Verified to Run: 2021-07-01 by Yao-Yuan Mao</p>
+Updated by: Javier Sanchez, Yao-Yuan Mao, Patricia Larsen <br>
+Last Verified to Run: 2024-Mar-11 by Patricia Larsen</p>
 <p><strong>Notes:</strong></p>
 <ul class="simple">
 <li><p>Follow this <a class="reference external" href="https://confluence.slac.stanford.edu/x/Xgg4Dg">step-by-step guide</a> if you don’t know how to run this notebook.</p></li>
@@ -512,7 +512,7 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Load the stars</span>
-<span class="n">stars_cat</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s2">&quot;dc2_truth_run2.2i_star_truth_summary&quot;</span><span class="p">)</span>
+<span class="n">stars_cat</span> <span class="o">=</span> <span class="n">GCRCatalogs</span><span class="o">.</span><span class="n">load_catalog</span><span class="p">(</span><span class="s2">&quot;dc2_run2.2i_truth_star_summary&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
@@ -550,7 +550,7 @@ <h2>Learning objectives<a class="headerlink" href="#learning-objectives" title="
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="ow">not</span> <span class="n">stars_cat</span><span class="o">.</span><span class="n">has_quantity</span><span class="p">(</span><span class="s2">&quot;mag_i&quot;</span><span class="p">):</span>
     <span class="n">stars_cat</span><span class="o">.</span><span class="n">add_derived_quantity</span><span class="p">(</span><span class="s2">&quot;mag_i&quot;</span><span class="p">,</span> <span class="n">flux_to_mag</span><span class="p">,</span> <span class="s2">&quot;flux_i&quot;</span><span class="p">)</span>
-<span class="n">quantities</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;ra&#39;</span><span class="p">,</span> <span class="s1">&#39;dec&#39;</span><span class="p">,</span> <span class="s1">&#39;mag_i&#39;</span><span class="p">,</span> <span class="s1">&#39;redshift&#39;</span><span class="p">]</span>
+<span class="n">quantities</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;ra&#39;</span><span class="p">,</span> <span class="s1">&#39;dec&#39;</span><span class="p">,</span> <span class="s1">&#39;mag_i&#39;</span><span class="p">]</span>
 <span class="n">stars_data</span> <span class="o">=</span> <span class="n">stars_cat</span><span class="o">.</span><span class="n">get_quantities</span><span class="p">(</span><span class="n">quantities</span><span class="p">,</span> <span class="n">filters</span><span class="o">=</span><span class="n">pos_filters</span><span class="p">)</span>
 </pre></div>
 </div>