source commit: 73d69a3

CODE_OF_CONDUCT.md

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+---
+title: "Contributor Code of Conduct"
+---
+
+As contributors and maintainers of this project,
+we pledge to follow the [The Carpentries Code of Conduct][coc].
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+
+
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html

LICENSE.md

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+---
+title: "Licenses"
+---
+
+## Instructional Material
+
+All Carpentries (Software Carpentry, Data Carpentry, and Library Carpentry)
+instructional material is made available under the [Creative Commons
+Attribution license][cc-by-human]. The following is a human-readable summary of
+(and not a substitute for) the [full legal text of the CC BY 4.0
+license][cc-by-legal].
+
+You are free:
+
+- to **Share**---copy and redistribute the material in any medium or format
+- to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the license
+terms.
+
+Under the following terms:
+
+- **Attribution**---You must give appropriate credit (mentioning that your work
+  is derived from work that is Copyright (c) The Carpentries and, where
+  practical, linking to <https://carpentries.org/>), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do so in
+  any reasonable manner, but not in any way that suggests the licensor endorses
+  you or your use.
+
+- **No additional restrictions**---You may not apply legal terms or
+  technological measures that legally restrict others from doing anything the
+  license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the material in
+  the public domain or where your use is permitted by an applicable exception
+  or limitation.
+* No warranties are given. The license may not give you all of the permissions
+  necessary for your intended use. For example, other rights such as publicity,
+  privacy, or moral rights may limit how you use the material.
+
+## Software
+
+Except where otherwise noted, the example programs and other software provided
+by The Carpentries are made available under the [OSI][osi]-approved [MIT
+license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+## Trademark
+
+"The Carpentries", "Software Carpentry", "Data Carpentry", and "Library
+Carpentry" and their respective logos are registered trademarks of [Community
+Initiatives][ci].
+
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[ci]: https://communityin.org/
+[osi]: https://opensource.org

build.sh

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+# copy notebooks from jb
+
+cp ~/AstronomicalData/01_query.ipynb 01-query.ipynb
+cp ~/AstronomicalData/02_coords.ipynb 02-coords.ipynb
+
+# convert tags to comments
+python convert.py
+
+# convert ipynb to md
+jupyter nbconvert --to markdown 01-query.ipynb
+jupyter nbconvert --to markdown 02-coords.ipynb
+
+
+# push it to GutHub
+#git add 01-query.md
+#git add 02-coords.md
+#git commit -m "Automated push from AstronomicalData"
+#git push

calculating_MIST_isochrone.md

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+---
+title: Making the Isochrone DataFrame
+---
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Calculating Isochrone
+
+In fact, we can use [MESA Isochrones \& Stellar Tracks](https://waps.cfa.harvard.edu/MIST/) (MIST)
+to compute it for us.
+Using the [MIST Version 1.2 web interface](https://waps.cfa.harvard.edu/MIST/interp_isos.html),
+we computed an isochrone with the following parameters:
+
+- Rotation initial v/v\_crit = 0.4
+- Single age, linear scale = 12e9
+- Composition [Fe/H] = -1.35
+- Synthetic Photometry, PanStarrs
+- Extinction av = 0
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+The following cell downloads the results:
+
+```python
+download('https://github.com/AllenDowney/AstronomicalData/raw/main/' +
+         'data/MIST_iso_5fd2532653c27.iso.cmd')
+```
+
+To read this file we will download a Python module [from this
+repository](https://github.com/jieunchoi/MIST_codes).
+
+```python
+download('https://github.com/jieunchoi/MIST_codes/raw/master/scripts/' +
+         'read_mist_models.py')
+```
+
+Now we can read the file:
+
+```python
+import read_mist_models
+
+filename = 'MIST_iso_5fd2532653c27.iso.cmd'
+iso = read_mist_models.ISOCMD(filename)
+```
+
+```output
+Reading in: MIST_iso_5fd2532653c27.iso.cmd
+```
+
+The result is an `ISOCMD` object.
+
+```python
+type(iso)
+```
+
+```output
+read_mist_models.ISOCMD
+```
+
+It contains a list of arrays, one for each isochrone.
+
+```python
+type(iso.isocmds)
+```
+
+```output
+list
+```
+
+We only got one isochrone.
+
+```python
+len(iso.isocmds)
+```
+
+```output
+1
+```
+
+So we can select it like this:
+
+```python
+iso_array = iso.isocmds[0]
+```
+
+It is a NumPy array:
+
+```python
+type(iso_array)
+```
+
+```output
+numpy.ndarray
+```
+
+But it is an unusual NumPy array, because it contains names for the columns.
+
+```python
+iso_array.dtype
+```
+
+```output
+dtype([('EEP', '<i4'), ('isochrone_age_yr', '<f8'), ('initial_mass', '<f8'), ('star_mass', '<f8'), ('log_Teff', '<f8'), ('log_g', '<f8'), ('log_L', '<f8'), ('[Fe/H]_init', '<f8'), ('[Fe/H]', '<f8'), ('PS_g', '<f8'), ('PS_r', '<f8'), ('PS_i', '<f8'), ('PS_z', '<f8'), ('PS_y', '<f8'), ('PS_w', '<f8'), ('PS_open', '<f8'), ('phase', '<f8')])
+```
+
+Which means we can select columns using the bracket operator:
+
+```python
+iso_array['phase']
+```
+
+```output
+array([0., 0., 0., ..., 6., 6., 6.])
+```
+
+We can use `phase` to select the part of the isochrone for stars in
+the main sequence and red giant phases.
+
+```python
+phase_mask = (iso_array['phase'] >= 0) & (iso_array['phase'] < 3)
+phase_mask.sum()
+```
+
+```output
+354
+```
+
+```python
+main_sequence = iso_array[phase_mask]
+len(main_sequence)
+```
+
+```output
+354
+```
+
+The other two columns we will use are `PS_g` and `PS_i`, which contain
+simulated photometry data for stars with the given age and
+metallicity, based on a model of the Pan-STARRS sensors.
+
+We will use these columns to superimpose the isochrone on the
+color-magnitude diagram, but first we have to use a [distance
+modulus](https://en.wikipedia.org/wiki/Distance_modulus) to scale the
+isochrone based on the estimated distance of GD-1.
+
+We can use the `Distance` object from Astropy to compute the distance modulus.
+
+```python
+import astropy.coordinates as coord
+import astropy.units as u
+
+distance = 7.8 * u.kpc
+distmod = coord.Distance(distance).distmod.value
+distmod
+```
+
+```output
+14.4604730134524
+```
+
+Now we can compute the scaled magnitude and color of the isochrone.
+
+```python
+mag_g = main_sequence['PS_g'] + distmod
+color_g_i = main_sequence['PS_g'] - main_sequence['PS_i']
+```
+
+Now we can plot it on the color-magnitude diagram like this.
+
+```python
+plot_cmd(candidate_df)
+plt.plot(color_g_i, mag_g);
+```
+
+```output
+<Figure size 432x288 with 1 Axes>
+```
+
+![](fig/07-photo_files/07-photo_42_0.png){alt='Color magnitude diagram of our selected stars with theoretical isochrone overlaid as blue curve.'}
+
+The theoretical isochrone passes through the overdense region where we
+expect to find stars in GD-1.
+
+We will save this result so we can reload it later without repeating the
+steps in this section.
+
+So we can save the data in an HDF5 file, we will put it in a Pandas
+`DataFrame` first:
+
+```python
+import pandas as pd
+
+iso_df = pd.DataFrame()
+iso_df['mag_g'] = mag_g
+iso_df['color_g_i'] = color_g_i
+
+iso_df.head()
+```
+
+```output
+       mag_g  color_g_i
+0  28.294743   2.195021
+1  28.189718   2.166076
+2  28.051761   2.129312
+3  27.916194   2.093721
+4  27.780024   2.058585
+```
+
+And then save it.
+
+```python
+filename = 'gd1_isochrone.hdf5'
+iso_df.to_hdf(filename, 'iso_df')
+```
+
+