issue/627/testskypixelcoords: New notebook to test coordinate system …

…effects with instructions to use example data (#629) * new notebook to test coordinate systems and shear measurements * editing README for the data availability * Added option to choose coordinate system for generated mock catalog * Added ellipticity coordinate system conversion tests to test_galaxycluster.py and test_mockdata.py * Added documentation to other test cases in Tomomi's notebook. Still need to incorporate Caio's added functionality for sky vs. pixel coordinates in CLMM * starting to work through and document example of lensing signal calculation of HSCY3 cluster without CLMM, but need to change colossus dependency because it is not easy to install on NERSC * added kwargs to GalaxyCluster instance definition in preparation for re-installing latest CLMM with Caio's added coordinate_system kwargs * test_coordinate.ipynb now runs from top to bottom using Caio's coordinate system implementation! * modified the Oguri example to also show incorrect coordinate assumption as noted by Caio * added a note for the CosmoDC2 clusters so the user is aware to not necessarily expect a strong signal in center regions * clarified why there might be less signal in the TXPipe outputted CosmoDC2 thing --------- Co-authored-by: Caio Lima de Oliveira <[email protected]> Co-authored-by: Camille Avestruz <[email protected]> Co-authored-by: Marina Ricci <[email protected]>
LSSTDESC · Aug 5, 2024 · 4068b53 · 4068b53
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diff --git a/README.md b/README.md
@@ -1,4 +1,3 @@
-
 # CLMM
 [![Build and Check](https://github.com/LSSTDESC/CLMM/workflows/Build%20and%20Check/badge.svg)](https://github.com/LSSTDESC/CLMM/actions?query=workflow%3A%22Build+and+Check%22)
 [![Coverage Status](https://coveralls.io/repos/github/LSSTDESC/CLMM/badge.svg?branch=main)](https://coveralls.io/github/LSSTDESC/CLMM?branch=main)
@@ -110,6 +109,7 @@ the `CCL` publication be cited.  See details
 The `Cluster Toolkit` documentation can be found
 [here](https://cluster-toolkit.readthedocs.io/en/latest/#).
 
+The data for the notebook test_coordinate.ipynb is available at https://www.dropbox.com/scl/fo/dwsccslr5iwb7lnkf8jvx/AJkjgFeemUEHpHaZaHHqpAg?rlkey=efbtsr15mdrs3y6xsm7l48o0r&st=xb58ap0g&dl=0
 
 # Contributing to CLMM <a name="contributing"></a>
 

diff --git a/docs/doc-config.ini b/docs/doc-config.ini
@@ -33,5 +33,6 @@ OTHER
 ../examples/demo_compute_deltasigma_weights.ipynb
 ../examples/demo_mass_conversion.ipynb
 ../examples/demo_mock_ensemble_realistic.ipynb
+../examples/demo_coordinate_system_datasets.ipynb
 #../examples/other_compare_NFW_critical_massdef.ipynb
 #../examples/other_flat_sky_limitations.ipynb
diff --git a/examples/DC2/DC2_gt_profiles.ipynb b/examples/DC2/DC2_gt_profiles.ipynb
@@ -600,7 +600,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -614,7 +614,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,

diff --git a/examples/DC2/data_and_model_demo_DC2.ipynb b/examples/DC2/data_and_model_demo_DC2.ipynb
@@ -340,7 +340,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,

diff --git a/examples/demo_boost_factors.ipynb b/examples/demo_boost_factors.ipynb
@@ -2,7 +2,6 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "b803f8e6",
    "metadata": {},
    "source": [
     "# Boost factors"
@@ -11,7 +10,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7180b199",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,7 +24,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11e76008",
    "metadata": {},
    "source": [
     "Make sure we know which version we're using"
@@ -35,7 +32,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "389d5ab7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +40,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d86fa53c",
    "metadata": {},
    "source": [
     "### Define cosmology object"
@@ -53,7 +48,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "74bcb35c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,15 +56,13 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6b458081",
    "metadata": {},
    "source": [
     "First, we want to generate a $\\Delta\\Sigma$ (excess surface density) profile from mock data, to which we can apply boost factors. The mock data is generated in the following cells."
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "de5340ee",
    "metadata": {},
    "source": [
     "Generate cluster object from mock data"
@@ -79,7 +71,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6cec7b64",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -107,7 +98,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "50045a1f",
    "metadata": {},
    "source": [
     "Loading this into a CLMM cluster object centered on (0,0)"
@@ -116,7 +106,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a564b1c9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +116,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "eb9c2218",
    "metadata": {},
    "source": [
     "Compute cross and tangential excess surface density for each source galaxy"
@@ -136,7 +124,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc5b051d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +141,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "26081451",
    "metadata": {},
    "source": [
     "Calculate the binned profile"
@@ -163,7 +149,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eaadac01",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -190,7 +175,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7e88afc4",
    "metadata": {},
    "source": [
     "Plot the $\\Delta\\Sigma$ profile"
@@ -199,7 +183,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0aeb2f52",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -219,15 +202,13 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e28ec4c5",
    "metadata": {},
    "source": [
     "## Boost Factors"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "19912d42",
    "metadata": {},
    "source": [
     "CLMM offers two boost models, the NFW boost model, and a powerlaw boost model. \n",
@@ -242,7 +223,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e6b6ee3d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -255,7 +235,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "58cbc299",
    "metadata": {},
    "source": [
     "Plot the two boost factors, $B(R)$"
@@ -264,7 +243,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1c1de291",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -278,7 +256,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "30e8e6a0",
    "metadata": {},
    "source": [
     "The $\\Delta\\Sigma$ profiles can be corrected with the boost factor using `correct_sigma_with_boost_values` or `correct_sigma_with_boost_model`. \n",
@@ -289,7 +266,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6c4daf84",
    "metadata": {},
    "source": [
     "\n",
@@ -309,7 +285,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "48e0f2ef",
    "metadata": {},
    "source": [
     "First we will apply the boost factor with `correct_sigma_with_boost_values`"
@@ -318,7 +293,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d7b5f71d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,7 +306,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15252880",
    "metadata": {},
    "source": [
     "Plot the result"
@@ -341,7 +314,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e2d90e0c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -380,7 +352,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "caf00c95",
    "metadata": {},
    "source": [
     "Now the same again but with `correct_sigma_with_boost_model`"
@@ -389,7 +360,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b4b3f953",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -440,7 +410,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -454,7 +424,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.6.9"
   }
  },
  "nbformat": 4,