From f9d444cbaad3da876d2c1b47316fc984aec6a75b Mon Sep 17 00:00:00 2001
From: jurjen93 <jurjendejong93@gmail.com>
Date: Thu, 17 Oct 2024 21:01:23 +0200
Subject: [PATCH 1/2] refactor

---
 .gitignore                            |  3 +++
 README.md                             | 12 +++++++++--
 ds9_helpers/split_polygon_facets.py   |  2 +-
 h5_helpers/overwrite_table.py         | 31 ---------------------------
 ms_helpers/applycal.py                |  2 +-
 ms_helpers/remove_flagged_stations.py |  2 +-
 pyproject.toml                        |  3 +--
 subtract/subtract_with_wsclean.py     |  2 +-
 8 files changed, 18 insertions(+), 39 deletions(-)
 delete mode 100644 h5_helpers/overwrite_table.py

diff --git a/.gitignore b/.gitignore
index 3aad4aac..b063d14f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+#package
+build
+lofar_helpers.egg-info
 # csv files
 *.csv
 #text files
diff --git a/README.md b/README.md
index 9043d186..29c39e1f 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,16 @@ Some of these scripts have been integrated in data reduction pipelines as well.
 You are free to use the scripts for your own work.
 
 Clone the repo with: ```git clone https://github.com/jurjen93/lofar_helpers.git``` \
-If you are only interested in ```h5_merger.py```, use:\
-```wget "https://raw.githubusercontent.com/jurjen93/lofar_helpers/master/h5_merger.py"```
+Or install with: ```pip install -v git+https://github.com/jurjen93/lofar_helpers.git``` \
+Installing gives you the following command line functionalities:
+- split_polygon_facets
+- crop_nan_boundaries
+- cut_fits_with_region
+- close_h5
+- concat_with_dummies
+- remove_flagged_stations
+- applycal
+- subtract_with_wsclean
 
 #### Contact
 Let me know if you have any issues or suggestions for improvements.
diff --git a/ds9_helpers/split_polygon_facets.py b/ds9_helpers/split_polygon_facets.py
index 34f5435f..089dfe05 100644
--- a/ds9_helpers/split_polygon_facets.py
+++ b/ds9_helpers/split_polygon_facets.py
@@ -120,7 +120,7 @@ def point_in_polygon(point, poly_reg):
 def parse_args():
     """Argument parser"""
 
-    parser = ArgumentParser(description='Split facet file with multiple polygons into multiple files per facet (Values standard in degrees)')
+    parser = ArgumentParser(description='Split multi-facet region file with polygon regions out into multiple region files')
     parser.add_argument('--reg', help='region file', type=str, required=True)
     parser.add_argument('--h5', help='h5 file to write directions from', type=str, required=True)
     parser.add_argument('--extra_boundary', help='make polygons with extra boundaries', type=float, default=0.)
diff --git a/h5_helpers/overwrite_table.py b/h5_helpers/overwrite_table.py
deleted file mode 100644
index 9b7c9250..00000000
--- a/h5_helpers/overwrite_table.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import numpy as np
-import tables
-import sys
-
-def overwrite_table(h5, table, new_arr):
-    """
-    Overwrite h5 source or antenna table
-
-    :param h5: h5parm table
-    :param table: table name (antenna or source)
-    :param new_arr: new values
-    """
-
-    T = tables.open_file(h5, 'r+')
-
-    ss = T.root._f_get_child('sol000')
-    ss._f_get_child(table)._f_remove()
-    if table == 'source':
-        values = np.array(new_arr, dtype=[('name', 'S128'), ('dir', '<f4', (2,))])
-        title = 'Source names and directions'
-    elif table == 'antenna':
-        title = 'Antenna names and positions'
-        values = np.array(new_arr, dtype=[('name', 'S16'), ('position', '<f4', (3,))])
-    else:
-        sys.exit('ERROR: table needs to be source or antenna')
-
-    T.create_table(ss, table, values, title=title)
-
-    T.close()
-
-    return
\ No newline at end of file
diff --git a/ms_helpers/applycal.py b/ms_helpers/applycal.py
index 7af3f371..70e0b95c 100644
--- a/ms_helpers/applycal.py
+++ b/ms_helpers/applycal.py
@@ -100,7 +100,7 @@ def run(self):
 def parse_args():
     """Argument parser"""
 
-    parser = ArgumentParser(description='Applycal on MS with H5')
+    parser = ArgumentParser(description='Apply h5parm on MeasurementSet')
     parser.add_argument('msin', nargs='+', type=str, help='input measurement set')
     parser.add_argument('--msout', type=str, default='.', help='output measurement set')
     parser.add_argument('--h5', type=str, help='h5 calibration', required=True)
diff --git a/ms_helpers/remove_flagged_stations.py b/ms_helpers/remove_flagged_stations.py
index 8ddf79ba..d5c2e172 100644
--- a/ms_helpers/remove_flagged_stations.py
+++ b/ms_helpers/remove_flagged_stations.py
@@ -72,7 +72,7 @@ def parse_args():
     Parse input arguments
     """
 
-    parser = ArgumentParser(description='MS stacking')
+    parser = ArgumentParser(description='Remove stations from the MS that are fully flagged')
     parser.add_argument('msin', type=str, help='Input Measurement Set')
     parser.add_argument('--msout', type=str, default=None, help='Output Measurement Set')
     parser.add_argument('--overwrite', action='store_true', help='Overwrite input Measurement Set')
diff --git a/pyproject.toml b/pyproject.toml
index 73fb3ff4..f845e15d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "lofar_helpers"
 version = "1.0.0"
 description = "LOFAR helper scripts and tools"
-dependencies = []
+dependencies = ["numpy","tables","losoto","shapely","python-casacore","pyregion","astropy","pandas"]
 
 [project.scripts]
 split_polygon_facets = "ds9_helpers.split_polygon_facets:main"
@@ -17,7 +17,6 @@ concat_with_dummies = "ms_helpers.concat_with_dummies:main"
 remove_flagged_stations = "ms_helpers.remove_flagged_stations:main"
 applycal = "ms_helpers.applycal:main"
 subtract_with_wsclean = "subtract.subtract_with_wsclean:main"
-h5_merger = "h5_merger:main"
 
 [tool.setuptools]
 packages = ["ds9_helpers", "fits_helpers", "h5_helpers", "ms_helpers", "subtract"]
diff --git a/subtract/subtract_with_wsclean.py b/subtract/subtract_with_wsclean.py
index 13512bad..8a5ba5d0 100644
--- a/subtract/subtract_with_wsclean.py
+++ b/subtract/subtract_with_wsclean.py
@@ -749,7 +749,7 @@ def parse_args():
     """
     Command line argument parser
     """
-    parser = ArgumentParser(description='Subtract region with WSClean')
+    parser = ArgumentParser(description='Subtract or predict region with WSClean')
     parser.add_argument('--mslist', nargs='+', help='measurement sets', required=True)
     parser.add_argument('--region', type=str, help='region file')
     parser.add_argument('--output_name', type=str, help='name of output files (default is model image name)')

From d17396fe022e09dd1727ab37d0c6b05a7c8d73a5 Mon Sep 17 00:00:00 2001
From: jurjen93 <jurjendejong93@gmail.com>
Date: Thu, 17 Oct 2024 21:02:12 +0200
Subject: [PATCH 2/2] refactor

---
 README.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 29c39e1f..81e414d1 100644
--- a/README.md
+++ b/README.md
@@ -9,9 +9,10 @@ I have tried to write them such they can be used for more general use-cases as w
 Some of these scripts have been integrated in data reduction pipelines as well.
 You are free to use the scripts for your own work.
 
-Clone the repo with: ```git clone https://github.com/jurjen93/lofar_helpers.git``` \
-Or install with: ```pip install -v git+https://github.com/jurjen93/lofar_helpers.git``` \
-Installing gives you the following command line functionalities:
+Clone the repo with: ```git clone https://github.com/jurjen93/lofar_helpers.git```
+
+Or install with: ```pip install -v git+https://github.com/jurjen93/lofar_helpers.git```
+This gives you the following command line functionalities:
 - split_polygon_facets
 - crop_nan_boundaries
 - cut_fits_with_region