From b22deb9783de362997975ff7f778a443cba48d34 Mon Sep 17 00:00:00 2001
From: Aaron LI <aly@aaronly.me>
Date: Tue, 11 Jul 2017 20:20:27 +0800
Subject: Add two CASA scripts: addnoise.py & uvaddsub.py

Signed-off-by: Aaron LI <aly@aaronly.me>
---
 astro/casa/addnoise.py | 60 +++++++++++++++++++++++++++++++++
 astro/casa/uvaddsub.py | 91 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 151 insertions(+)
 create mode 100755 astro/casa/addnoise.py
 create mode 100755 astro/casa/uvaddsub.py

diff --git a/astro/casa/addnoise.py b/astro/casa/addnoise.py
new file mode 100755
index 0000000..84d3428
--- /dev/null
+++ b/astro/casa/addnoise.py
@@ -0,0 +1,60 @@
+#!casa-script
+# -*- mode: python -*-
+#
+# Copyright (c) 2017 Aaron LI <aly@aaronly.me>
+# MIT License
+#
+
+"""
+Add random Gaussian noises to the MeasurementSet DATA.
+
+NOTE: the input MS is modified in place.
+"""
+
+import sys
+import argparse
+
+import numpy as np
+
+# from casac.ms import ms
+
+
+def add_noise(msname, sigma):
+    print("Opening MS: %s ..." % msname)
+    ms.open(msname, nomodify=False)
+    ms.selectinit(datadescid=0)
+    print("Geting MS data column ...")
+    rec = ms.getdata(["data"])
+    data = rec["data"]
+    print("data mean: (%g, %g)" % (data.real.mean(), data.imag.mean()))
+    print("data std: (%g, %g)" % (data.real.std(), data.imag.std()))
+    print("Add Gaussian noises sigma=%g ..." % sigma)
+    nreal = np.random.normal(scale=sigma, size=data.shape)
+    nimag = np.random.normal(scale=sigma, size=data.shape)
+    noise = nreal + 1j*nimag
+    data += noise
+    rec = {"data": data}
+    ms.putdata(rec)
+    ms.writehistory("Add Gaussian noises: sigma=%g" % sigma)
+    ms.close()
+    print("Closed MS: %s" % msname)
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(
+        description="Add random noise to MS visibilities")
+    parser.add_argument("-s", "--sigma", dest="sigma",
+                        required=True, type=float,
+                        help="sigma of the random Gaussian noises")
+    parser.add_argument("-m", "--ms", dest="ms", required=True,
+                        help="input MeasurementSet to be modified")
+    args = parser.parse_args(argv)
+
+    add_noise(args.ms, sigma=args.sigma)
+
+
+if __name__ == "__main__":
+    argi = sys.argv.index("--") + 1
+    argv = sys.argv[argi:]
+    print("argv:", argv)
+    main(argv)
diff --git a/astro/casa/uvaddsub.py b/astro/casa/uvaddsub.py
new file mode 100755
index 0000000..20b0473
--- /dev/null
+++ b/astro/casa/uvaddsub.py
@@ -0,0 +1,91 @@
+#!casa-script
+# -*- mode: python -*-
+#
+# Copyright (c) 2017 Aaron LI <aly@aaronly.me>
+# MIT License
+#
+
+"""
+Copy the first MeasurementSet as the output MeasurementSet, and
+subtract/add the DATA from the second MeasurementSet.
+
+NOTE: The output MeasurementSet DATA column is altered directly.
+"""
+
+import sys
+import argparse
+import shutil
+
+# from casac.ms import ms
+
+
+def get_data(msname):
+    print("Opening MS: %s ..." % msname)
+    ms.open(msname, nomodify=True)
+    ms.selectinit(datadescid=0)
+    print("Geting MS data column ...")
+    rec = ms.getdata(["data"])
+    data = rec["data"]
+    print("data mean:", data.mean())
+    ms.close()
+    print("Closed MS: %s" % msname)
+    return data
+
+
+def calc_ms(msname, data2, operation="sub"):
+    print("Opening MS: %s ..." % msname)
+    ms.open(msname, nomodify=False)
+    ms.selectinit(datadescid=0)
+    print("Geting MS data column ...")
+    rec = ms.getdata(["data"])
+    data1 = rec["data"]
+    print("data1 mean:", data1.mean())
+    print("data2 mean:", data2.mean())
+    if operation == "sub":
+        data_out = data1 - data2
+    elif operation == "add":
+        data_out = data1 + data2
+    else:
+        raise ValueError("invalid operation: %s" % operation)
+    print("data_out mean:", data_out.mean())
+    rec = {"data": data_out}
+    print("Putting new data ...")
+    ms.putdata(rec)
+    ms.close()
+    print("Closed MS: %s" % msname)
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description="MS addition/subtraction")
+    parser.add_argument("--operation", dest="operation", required=True,
+                        choices=["add", "sub"],
+                        help="operation (add/sub) to be performed")
+    parser.add_argument("--ms1", dest="ms1", required=True,
+                        help="the first MeasurementSet")
+    parser.add_argument("--ms2", dest="ms2", required=True,
+                        help="the second MeasurementSet")
+    exgrp = parser.add_mutually_exclusive_group(required=True)
+    exgrp.add_argument("--inplace", dest="inplace", action="store_true",
+                       help="modify the first MS in place")
+    exgrp.add_argument("--ms-out", dest="msout",
+                       help="output MeasurementSet name (copied from " +
+                       "the first MS)")
+    args = parser.parse_args(argv)
+
+    if args.inplace:
+        print("Modify MS1 in place!")
+        msout = args.ms1
+    else:
+        print("Copying MS1 to be output MS ...")
+        msout = args.msout
+        shutil.copytree(args.ms1, msout)
+
+    data2 = get_data(args.ms2)
+    calc_ms(msout, data2, operation=args.operation)
+
+
+if __name__ == "__main__":
+    argi = sys.argv.index("--") + 1
+    argv = sys.argv[argi:]
+    print("argv:", argv)
+    main(argv)
-- 
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