Issue 10

.gitignore

@@ -3,6 +3,13 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Radio Astro
+*.fits
+*.zarr
+*.ms
+*.ipynb
+
+
 # C extensions
 *.so
 

contsub/parser/imcontsub.py

@@ -55,8 +55,8 @@ def runit(**kwargs):
 
     chunks = dict(ra = opts.ra_chunks or 64, dec=None, spectral=None)
 
-
-    zds = zds_from_fits(infits, chunks=chunks)
+    rest_freq = opts.rest_freq
+    zds = zds_from_fits(infits, chunks=chunks, rest_freq=rest_freq)
     base_dims = ["ra", "dec", "spectral", "stokes"]
     if not hasattr(zds, "stokes"):
         base_dims.remove("stokes")
@@ -75,13 +75,13 @@ def runit(**kwargs):
 
     if len(opts.order) != len(opts.segments):
         raise ValueError("If setting multiple --order and --segments, they must be of equal length. "
-                         f"Got {len(opts.order)} orders and {len(opts.segments)} segments.")
+                    f"Got {len(opts.order)} orders and {len(opts.segments)} segments.")
     niter = len(opts.order)
 
     nomask = True
     automask = False 
     if getattr(opts, "mask_image", None):
-        mask = zds_from_fits(opts.mask_image, chunks=chunks).DATA
+        mask = zds_from_fits(opts.mask_image, chunks=chunks, rest_freq=rest_freq).DATA
         nomask = False
 
     if getattr(opts, "sigma_clip", None):

contsub/parser/imcontsub.yaml

@@ -24,6 +24,14 @@ inputs:
     dtype: List[float]
     policies:
       repeat: "[]"
+    default:
+    - 5
+    - 4
+    - 3
+  automask-per-iter:
+    info: Generate a new mask per iteration.
+    dtype: bool
+    default: False
   fit-model:
     info: "### NOT IMPLEMENTED ### Fit function to model the continuum."
     dtype: str
@@ -45,6 +53,9 @@ inputs:
     dtype: int
     default: 0
     choices: [0,1,2,3]
+  rest-freq:
+    info: Cube rest frequency in MHz. Will ignore the one in the FITS header if it exists.
+    dtype: float
   stokes-axis:
     info: "### DEPRECATED #### Set this flag if the input image has a stokes dimension. (Default is True)."
     default: yes

contsub/utils.py

@@ -43,7 +43,7 @@ def get_automask(xspec, cube, sigma_clip=5, order=3, segments=400):
     return mask
 
 
-def zds_from_fits(fname, chunks=None):
+def zds_from_fits(fname, chunks=None, rest_freq=None):
     """ Creates Zarr store from a FITS file. The resulting array has 
     dimensions = RA, DEC, SPECTRAL[, STOKES]
 
@@ -62,6 +62,8 @@ def zds_from_fits(fname, chunks=None):
     fds = xds_from_fits(fname)[0]
 
     header = fds.hdu.header
+    if rest_freq:
+        header["RESTFRQ"] = rest_freq * 1e6 # set it to Hz
     wcs = WCS(header, naxis="spectral stokes".split())
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "contsub"
-version = "1.0.2"
+version = "1.0.3"
 description = "Radio astronomy data continuum subtraction tools"
 authors = ["Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo"]
 license = "MIT"