Add the base folder for Serialization

PythonSerialize/README.md

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+# Python Serialization (and other script fun)
+
+## Binder
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OZAstroComputingResources/MQCoffee-CodeResources/python-serialize?urlpath=lab)

PythonSerialize/Use-Planet-Config.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import yaml\n",
+    "import json\n",
+    "import numpy as np\n",
+    "from matplotlib import pyplot as plt\n",
+    "%matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "planet_config = 'planet_config.yaml'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Our convenience function (could be loaded rather than copied):\n",
+    "def load_config(filename):\n",
+    "    with open(filename, 'r') as f:\n",
+    "        my_config = yaml.safe_load(f.read())\n",
+    "        \n",
+    "    return my_config"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "planets = load_config(planet_config)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "planets"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## What about Bob?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "name = 'Bob'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "planets[name]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for lc_json_file in planets[name]:\n",
+    "    # Load the json data\n",
+    "    with open(lc_json_file, 'r') as f:\n",
+    "        lc0 = json.loads(f.read())\n",
+    "        \n",
+    "    plt.plot(np.array(lc0))\n",
+    "    plt.title(name)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### All planets"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig, ax = plt.subplots(1)\n",
+    "fig.set_size_inches(12, 9)\n",
+    "\n",
+    "\n",
+    "for name, files in planets.items():\n",
+    "    for lc_json_file in files:\n",
+    "        # Load the json data\n",
+    "        with open(lc_json_file, 'r') as f:\n",
+    "            lc0 = json.loads(f.read())\n",
+    "\n",
+    "        ax.plot(np.array(lc0), label=f'{name} - {lc_json_file}')\n",
+    "        ax.set_title(name)\n",
+    "        ax.legend()\n",
+    "        "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

PythonSerialize/config.yaml

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+---
+######################### PANOPTES UNIT ########################################
+# name:   Can be anything you want it to be. This name is displayed in several
+#         places and should be a "personal" name for the unit.
+#
+# pan_id: This is an identification number assigned by the PANOPTES team and is
+#         the official designator for your unit. This id is used to store image
+#         files and communicate with the Google Cloud network.
+#
+#         Leave the pan_id at `PAN000` for testing until you have been assigned
+#         an official id. Update pocs_local.yaml with offical name once received.
+################################################################################
+name: Generic PANOPTES Unit
+pan_id: PAN000   
+
+location:
+    name: Mauna Loa Observatory
+    latitude: 19.54 # Degrees
+    longitude: -155.58 # Degrees
+    elevation: 3400.0 # Meters
+    horizon: 30 # Degrees; targets must be above this to be considered valid.
+    flat_horizon: -6 # Degrees - Flats when sun between this and focus horizon.
+    focus_horizon: -12 # Degrees - Dark enough to focus on stars.
+    observe_horizon: -18 # Degrees - Sun below this limit to observe.
+    timezone: US/Hawaii
+    gmt_offset: -600 # Offset in minutes from GMT during.
+                     # standard time (not daylight saving).
+directories:
+    base: /var/panoptes
+    images: images
+    data: data
+    resources: POCS/resources/
+    targets: POCS/resources/targets
+    mounts: POCS/resources/mounts
+db: 
+    name: panoptes
+    type: file
+scheduler:
+    type: dispatch
+    fields_file: simple.yaml
+    check_file: False
+mount:
+    brand: ioptron
+    model: 30
+    driver: ioptron
+    serial:
+        port: /dev/ttyUSB0
+        timeout: 0.
+        baudrate: 9600
+    non_sidereal_available: True
+pointing:
+    auto_correct: False
+    threshold: 500 # arcseconds ~ 50 pixels
+    exptime: 30 # seconds
+    max_iterations: 3
+cameras:
+    auto_detect: True
+    primary: 14d3bd
+    devices:
+    -
+        model: canon_gphoto2
+    -
+        model: canon_gphoto2
+messaging:
+    # Must match ports in peas.yaml.
+    cmd_port: 6500
+    msg_port: 6510
+
+########################## Observations ########################################
+# An observation folder contains a contiguous sequence of images of a target/field
+# recorded by a single camera, with no slewing of the mount during the sequence; 
+# there may be tracking adjustments during the observation.
+#
+# An example folder structure would be:
+#
+#   $PANDIR/images/fields/Hd189733/14d3bd/20180901T120001/
+#
+# In this folder will be stored JPG and FITS images. A timelapse of the
+# observation can be made (one per camera) and the JPGs optionally removed
+# afterward.
+#
+# TODO: Add options for cleaning up old data (e.g. >30 days)
+################################################################################
+observations:
+    make_timelapse: True
+    keep_jpgs: True
+
+######################## Google Network ########################################
+# By default all images are stored on googlecloud servers and we also
+# use a few google services to store metadata, communicate with servers, etc.
+#
+# See $POCS/pocs/utils/google/README.md for details about authentication.
+#
+# Options to change:
+#   image_storage: If images should be uploaded to Google Cloud Storage.
+#   service_account_key: Location of the JSON service account key.
+################################################################################
+panoptes_network:
+    image_storage: True
+    service_account_key: # Location of JSON account key
+    project_id: panoptes-survey
+    buckets:
+        images: panoptes-survey
+
+#Enable to output POCS messages to social accounts
+# social_accounts:
+#     twitter:
+#         consumer_key: [your_consumer_key]
+#         consumer_secret: [your_consumer_secret]
+#         access_token: [your_access_token]
+#         access_token_secret: [your_access_token_secret] 
+#     slack:
+#         webhook_url: [your_webhook_url]
+#         output_timestamp: False
+
+state_machine: simple_state_table
+

PythonSerialize/scripts/argparse-lc-plotter.py

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+#!/usr/bin/env python
+
+import os
+import yaml
+import json
+import numpy as np
+from matplotlib import pyplot as plt
+
+def main(filename, planet_name, overwrite=False, verbose=False):
+    if verbose:
+        print(f'Making plot for {planet_name}')
+
+    # Our convenience function (could be loaded rather than copied):
+    def load_config(filename):
+        if verbose:
+            print(f'Loading {filename}')
+
+        with open(filename, 'r') as f:
+            my_config = yaml.safe_load(f.read())
+
+        return my_config
+
+    # Load our planet info
+    planets = load_config(filename)
+
+    fig, ax = plt.subplots(1)
+    fig.set_size_inches(12, 9)
+
+    for lc_json_file in planets[planet_name]:
+        # Load the json data
+        with open(lc_json_file, 'r') as f:
+            lc0 = json.loads(f.read())
+
+        ax.plot(np.array(lc0))
+        ax.set_title(planet_name)
+
+    plot_filename = f'plots/{planet_name.lower()}-light-curve.png'
+
+    if os.path.exists(plot_filename) is False or overwrite is True:
+        fig.savefig(plot_filename)
+        if verbose:
+            print(f'Plot created for {planet_name} at {plot_filename}')
+    else:
+        print(f'Plot already exists for {planet_name}, use --overwrite')
+
+    plt.close(fig)
+
+if __name__ == '__main__':
+
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Make a plot for a planet")
+    parser.add_argument('--config', default='planet_config.yaml',
+                        help='Config file to use')
+    parser.add_argument('--planet-name', required=True,
+                        help='Planet to plot')
+    parser.add_argument('--overwrite', action='store_true', default=False,
+                        help='Overwrite any existing files, default False.')
+    parser.add_argument('--verbose', action='store_true', default=False, help='Verbose.')
+
+    # Load the arguments
+    args = parser.parse_args()
+
+    if not os.path.exists(args.config):
+        print("Config file does not exist:", args.config)
+
+    clean_dir = main(
+            filename=args.config,
+            planet_name=args.planet_name,
+            overwrite=args.overwrite,
+            verbose=args.verbose
+            )
+    if args.verbose:
+        print("Done making plot for", args.planet_name)

PythonSerialize/scripts/lc-plotter.py

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+#!/usr/bin/env python
+
+import yaml
+import json
+import numpy as np
+from matplotlib import pyplot as plt
+
+planet_config = 'planet_config.yaml'
+planet_name = 'Bob'
+
+# Our convenience function (could be loaded rather than copied):
+def load_config(filename):
+    with open(filename, 'r') as f:
+        my_config = yaml.safe_load(f.read())
+
+    return my_config
+
+# Load our planet info
+planets = load_config(planet_config)
+
+fig, ax = plt.subplots(1)
+fig.set_size_inches(12, 9)
+
+for lc_json_file in planets[planet_name]:
+    # Load the json data
+    with open(lc_json_file, 'r') as f:
+        lc0 = json.loads(f.read())
+
+    ax.plot(np.array(lc0))
+    ax.set_title(planet_name)
+
+fig.savefig(f'plots/{planet_name.lower()}-light-curve.png')
+plt.close(fig)