Reorganisation & visualisation

.coveragerc

@@ -3,6 +3,8 @@ branch = false
 parallel = true
 data_file = ${FINK_CLIENT_HOME}/.coverage
 omit=
+    *visualisation.py
+    app.py
     *setup.py
     *dist/*
     */lib/*

README.md

@@ -11,7 +11,7 @@
 Clone the GitHub repository
 ```bash
 git clone https://github.com/astrolabsoftware/fink-client.git
-cd fink-client && export FINK_CLIENT_HOME=$(PWD) >> ~/.bash_profile
+cd fink-client && echo 'export FINK_CLIENT_HOME=${PWD}' >> ~/.bash_profile
 ```
 The above expression will place the environment variable for `$FINK_CLIENT_HOME`
 into your `~/.bash_profile` such that this variable should not be required to be set again.

bin/fink_alert_viewer

@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+# Copyright 2019-2020 AstroLab Software
+# Author: Julien Peloton
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Display cutouts and lightcurve from a ZTF alert """
+import argparse
+
+import matplotlib
+import matplotlib.pyplot as plt
+
+import numpy as np
+
+from fink_client.avroUtils import AlertReader
+from fink_client.visualisation import show_stamps
+from fink_client.visualisation import extract_field
+
+# For plots
+font = {
+    'weight': 'bold',
+    'size': 22
+}
+
+matplotlib.rc('font', **font)
+
+# Bands
+filter_color = {1: '#1f77b4', 2: '#ff7f0e', 3: '#2ca02c'}
+# [
+#     '#1f77b4',  # muted blue
+#     '#ff7f0e',  # safety orange
+#     '#2ca02c',  # cooked asparagus green
+#     '#d62728',  # brick red
+#     '#9467bd',  # muted purple
+#     '#8c564b',  # chestnut brown
+#     '#e377c2',  # raspberry yogurt pink
+#     '#7f7f7f',  # middle gray
+#     '#bcbd22',  # curry yellow-green
+#     '#17becf'   # blue-teal
+# ]
+filter_name = {1: 'g band', 2: 'r band', 3: 'i band'}
+
+def main():
+    """ """
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        '-filename', type=str, default='',
+        help="Path to an alert data file (avro format)")
+    args = parser.parse_args(None)
+
+    r = AlertReader(args.filename)
+
+    # Display the cutouts contained in the alert
+    alert = r.to_list(size=1)[0]
+    print(alert['objectId'])
+    fig = plt.figure(num=0, figsize=(12, 4))
+    show_stamps(alert, fig)
+
+    # extract current and historical data as one vector
+    mag = extract_field(alert, 'magpsf')
+    error = extract_field(alert, 'sigmapsf')
+    upper = extract_field(alert, "diffmaglim")
+
+    # filter bands
+    fid = extract_field(alert, "fid")
+
+    # Rescale dates to end at 0
+    jd = extract_field(alert, "jd")
+    dates = np.array([i - jd[0] for i in jd])
+
+    # Title of the plot (alert ID)
+    title = alert["objectId"]
+
+    # loop over filters
+    fig = plt.figure(num=1, figsize=(12,4))
+
+    # Loop over each filter
+    for filt in filter_color.keys():
+        mask = np.where(fid == filt)[0]
+
+        # Skip if no data
+        if len(mask) == 0:
+            continue
+
+        # y data
+        maskNotNone = mag[mask] != None
+        plt.errorbar(
+            dates[mask][maskNotNone], mag[mask][maskNotNone],
+            yerr=error[mask][maskNotNone],
+            color=filter_color[filt], marker='o', ls='',
+            label=filter_name[filt], mew=4)
+        # Upper limits
+        plt.plot(
+            dates[mask][~maskNotNone], upper[mask][~maskNotNone],
+            color=filter_color[filt], marker='v', ls='', mew=4, alpha=0.5)
+        plt.title(title)
+    plt.legend()
+    plt.gca().invert_yaxis()
+    plt.xlabel('Days to candidate')
+    plt.ylabel('Difference magnitude')
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()

bin/fink_client_test.sh

@@ -15,6 +15,15 @@
 # limitations under the License.
 set -e
 
+
+# Run the test suite on the modules
+for i in ${FINK_CLIENT_HOME}/fink_client/*.py
+do
+  coverage run \
+    --source=${FINK_CLIENT_HOME} \
+    --rcfile ${FINK_CLIENT_HOME}/.coveragerc $i
+done
+
 TEST_DIR=${FINK_CLIENT_HOME}/tests
 
 # start Kafka in docker container

bin/fink_consumer

@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+# Copyright 2019-2020 AstroLab Software
+# Author: Julien Peloton
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Kafka consumer to listen and archive Fink streams """
+import argparse
+import time
+
+import matplotlib
+import matplotlib.pyplot as plt
+
+import numpy as np
+
+from fink_client.consumer import AlertConsumer
+import fink_client.fink_client_conf_cloud as fcc
+
+def main():
+    """ """
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        '-config', type=str, default='fink_client/fink_client_conf.py',
+        help="Path to your Fink configuration file.")
+    parser.add_argument(
+        '--display', action='store_true',
+        help="If specified, print on screen information about incoming alert.")
+    parser.add_argument(
+        '--save', action='store_true',
+        help="If specified, save alert data on disk (Avro). See also -outdir.")
+    parser.add_argument(
+        '-outdir', type=str, default='.',
+        help="Folder to store incoming alerts if --save is set. It must exist.")
+    args = parser.parse_args(None)
+
+    myconfig = {
+        "username": fcc.username,
+        'bootstrap.servers': fcc.servers,
+        'group_id': fcc.group_id}
+
+    if fcc.password is not None:
+        myconfig['password'] = fcc.password
+
+    # Instantiate a consumer
+    consumer = AlertConsumer(fcc.mytopics, myconfig, schema=fcc.schema)
+
+    # Time to wait before polling again if no alerts
+    maxtimeout = fcc.maxtimeout
+
+    # infinite loop
+    while True:
+        if args.save:
+            # Save alerts on disk
+            topic, alert = consumer.poll_and_write(
+                outdir=args.outdir,
+                timeout=maxtimeout,
+                overwrite=fcc.testmode)
+        else:
+            # TODO: this is useless to get it and done nothing
+            # why not thinking about handler like Comet?
+            topic, alert = consumer.poll(timeout=maxtimeout)
+
+        if args.display and topic is not None:
+            print("-" * 65)
+            row = [
+                time.ctime(), alert['timestamp'], topic, alert['objectId'],
+                alert['cdsxmatch'], alert['rfscore']
+            ]
+            print("{}|{:<25}|{:<10}|{:<15}|{:<10}|{:<5}|".format(*row))
+        elif args.display:
+            print('No alerts the last {} seconds'.format(maxtimeout))
+
+
+if __name__ == "__main__":
+    main()