Merge pull request #30 from jurjen93/refactor

Refactor

.gitignore

@@ -1,3 +1,6 @@
+#package
+build
+lofar_helpers.egg-info
 # csv files
 *.csv
 #text files

README.md

@@ -9,9 +9,18 @@ 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``` \
-If you are only interested in ```h5_merger.py```, use:\
-```wget "https://raw.githubusercontent.com/jurjen93/lofar_helpers/master/h5_merger.py"```
+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
+- 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.

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.)

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)

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')

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"]

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)')