Merge pull request #4 from bsipocz/CONT_cosmosim

Adding cosmoDC2 tutorial to the page

Author: bsipocz

conf.py

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-
-
 # Configuration file for the Sphinx documentation builder.
 #
 # -- Path setup --------------------------------------------------------------
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 # MyST-NB configuration
 nb_execution_timeout = 900
-nb_execution_excludepatterns = ['CosmoDC2_Parquet.md', 'Parallelize_Convolution.md']
+nb_execution_excludepatterns = ['Parallelize_Convolution.md']
 
 
 # -- Options for HTML output -------------------------------------------------

ignore_testing

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-tutorials/cosmosims
 tutorials/parallelize

index.md

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 ```
 
-<!---
 ### Catalogs
 
 ```{toctree}
 ---
 maxdepth: 1
 ---
 
+tutorials/cosmodc2/cosmoDC2_TAP_access.md
 
 ```
 
+
+<!---
+
 ## Visualizations
 ```{toctree}
 ---
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 tutorials/openuniversesims/openuniverse2024_roman_simulated_timedomainsurvey
 tutorials/openuniversesims/openuniverse2024_roman_simulated_wideareasurvey
+
 ```
 
 ## Generally useful techniques

tutorials/cosmodc2/cosmoDC2_TAP_access.md

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+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.16.2
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+---
+
+
+
+# CosmoDC2 Mock v1 catalogs with IRSA TAP
+
+This tutorial demonstrates how to access the CosmoDC2 Mock V1 catalogs. More information about these catalogs can be found here: https://irsa.ipac.caltech.edu/Missions/cosmodc2.html
+
+These catalogs can be accessed through IRSA's Virtual Ovservatory Table Access Protocol (TAP) service. See https://www.ivoa.net/documents/TAP/ for details on the protocol. This service can be accessed through Python using the PyVO library.
+
+```{code-cell} ipython3
+import pyvo as vo
+```
+
+```{code-cell} ipython3
+service = vo.dal.TAPService("https://irsa.ipac.caltech.edu/TAP")
+```
+
+## List the available DC2 tables
+
+```{code-cell} ipython3
+tables = service.tables
+for tablename in tables.keys():
+    if not "tap_schema" in tablename:
+        if "dc2" in tablename:
+            tables[tablename].describe()
+```
+
+## Choose the DC2 catalog you want to work with.
+
+IRSA currently offers 3 versions of the DC2 catalog.
+
+* ``cosmodc2mockv1_new`` has been optimized to make searches with constraints on stellar mass and redshift fast.
+
+* ``cosmodc2mockv1`` has been optimized to make searches with spatial constraints fast.
+
+* ``cosmodc2mockv1_heavy`` is the same as ``cosmodc2mockv1_new``, except that it does not contain galaxies with stellar masses <= 10^7 solar masses.
+
+If you are new to the DC2 catalog, we recommend that you start with ``cosmodc2mockv1_heavy``
+
+```{code-cell} ipython3
+# Choose the abridged table to start with.
+# Queries should be faster on smaller tables.
+
+tablename = 'cosmodc2mockv1_heavy'
+```
+
+## How many rows are in the chosen table?
+
+With TAP, you can query catalogs with constraints specified in IVOA Astronomical Data Query Language (ADQL; https://www.ivoa.net/documents/latest/ADQL.html), which is based on SQL.
+
+```{code-cell} ipython3
+# For example, this snippet of ADQL counts the number of elements in
+# the redshift column of the table we chose.
+adql = f"SELECT count(redshift) FROM {tablename}"
+adql
+```
+
+```{code-cell} ipython3
+# In order to use TAP with this ADQL string using pyvo, you can do the following:
+result = service.search(adql)
+result
+```
+
+The above query shows that there are 597,488,849 redshifts in this table.
+
++++
+
+## What is the default maximum number of rows returned by the service?
+
+This service will return a maximum of 2 billion rows by default.
+
+```{code-cell} ipython3
+service.maxrec
+```
+
+This default maximum can be changed, and there is no hard upper limit to what it can be changed to.
+
+```{code-cell} ipython3
+print(service.hardlimit)
+```
+
+## List the columns in the chosen table
+
+This table contains 301 columns.
+
+```{code-cell} ipython3
+columns = tables[tablename].columns
+print(len(columns))
+```
+
+Let's learn a bit more about them.
+
+```{code-cell} ipython3
+for col in columns:
+    print(f'{f"{col.name}":30s}  {col.description}')
+```
+
+## Create a histogram of redshifts
+
+Let's figure out what redshift range these galaxies cover. Since we found out above that it's a large catalog, we can start with a spatial search over a small area of 0.1 deg. The ADQL that is needed for the spatial constraint is:
+
+```{code-cell} ipython3
+adql = f"SELECT redshift FROM {tablename} WHERE CONTAINS(POINT('ICRS', RAMean, DecMean), CIRCLE('ICRS',54.218205903,-37.497959343,.1))=1"
+adql
+```
+
+Now we can use the previously-defined service to execute the query with the spatial contraint.
+
+```{code-cell} ipython3
+cone_results = service.search(adql)
+```
+
+```{code-cell} ipython3
+# Plot a histogram
+import numpy as np
+import matplotlib.mlab as mlab
+import matplotlib.pyplot as plt
+
+num_bins = 20
+# the histogram of the data
+n, bins, patches = plt.hist(cone_results['redshift'], num_bins,
+                            facecolor='blue', alpha = 0.5)
+plt.xlabel('Redshift')
+plt.ylabel('Number')
+plt.title('Redshift Histogram CosmoDC2 Mock Catalog V1 abridged')
+```
+
+We can easily see form this plot that the simulated galaxies go out to z = 3.
+
++++
+
+## Visualize galaxy colors at z ~ 0.5
+
+Now let's visualize the galaxy main sequence at z = 2.0. First, we'll do a narrow redshift cut with no spatial constraint.
+
+Let's do it as an asynchronous search since this might take awhile.
+
+```{code-cell} ipython3
+service = vo.dal.TAPService("https://irsa.ipac.caltech.edu/TAP")
+adql = f"SELECT Mag_true_r_sdss_z0, Mag_true_g_sdss_z0, redshift FROM {tablename} WHERE redshift > 0.5 and redshift < 0.54"
+results = service.run_async(adql)
+```
+
+```{code-cell} ipython3
+len(results['mag_true_r_sdss_z0'])
+```
+
+```{code-cell} ipython3
+# Since this results in almost 4 million galaxies,
+# we will construct a 2D histogram rather than a scatter plot.
+plt.hist2d(results['mag_true_r_sdss_z0'], results['mag_true_g_sdss_z0']-results['mag_true_r_sdss_z0'],
+           bins=200, cmap='plasma', cmax=500)
+
+# Plot a colorbar with label.
+cb = plt.colorbar()
+cb.set_label('Number')
+
+# Add title and labels to plot.
+plt.xlabel('SDSS Mag r')
+plt.ylabel('SDSS rest-frame g-r color')
+
+# Show the plot.
+plt.show()
+```
+
+## About this notebook
+
+ * Author: Vandana Desai (IRSA Science Lead)
+ * Updated: 2024-07-24
+ * Contact: https://irsa.ipac.caltech.edu/docs/help_desk.html