From f13d63739fc1f7850000f4a9f5fe89cc0d990b0d Mon Sep 17 00:00:00 2001
From: sphemakh <sphemakh@gmail.com>
Date: Sat, 30 Aug 2025 12:57:52 +0200
Subject: [PATCH 1/2] Fixes #25

---
 contsub/parser/imcontsub.py   | 2 +-
 contsub/parser/imcontsub.yaml | 5 +++++
 contsub/utils.py              | 4 ++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/contsub/parser/imcontsub.py b/contsub/parser/imcontsub.py
index 3c9d375..ad69b31 100644
--- a/contsub/parser/imcontsub.py
+++ b/contsub/parser/imcontsub.py
@@ -56,7 +56,7 @@ def runit(**kwargs):
     chunks = dict(ra = opts.ra_chunks or 64, dec=None, spectral=None)
     
     rest_freq = opts.rest_freq
-    zds = zds_from_fits(infits, chunks=chunks, rest_freq=rest_freq)
+    zds = zds_from_fits(infits, chunks=chunks, rest_freq=rest_freq, hdu_idx=opts.hdu_index)
     base_dims = ["ra", "dec", "spectral", "stokes"]
     if not hasattr(zds, "stokes"):
         base_dims.remove("stokes")
diff --git a/contsub/parser/imcontsub.yaml b/contsub/parser/imcontsub.yaml
index e79df72..94d2b26 100644
--- a/contsub/parser/imcontsub.yaml
+++ b/contsub/parser/imcontsub.yaml
@@ -60,6 +60,11 @@ inputs:
     info: "### DEPRECATED #### Set this flag if the input image has a stokes dimension. (Default is True)."
     default: yes
     dtype: bool
+  hdu-index:
+    info: FITS primary HDU index
+    dtype: int
+    default: 0
+    abbreviation: hi
   ra-chunks:
     info: Chunking along RA-axis. If set to zero, no Chunking is perfomed.
     dtype: int 
diff --git a/contsub/utils.py b/contsub/utils.py
index c5c518b..d588d9a 100644
--- a/contsub/utils.py
+++ b/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, rest_freq=None):
+def zds_from_fits(fname, chunks=None, rest_freq=None, hdu_idx=0):
     """ Creates Zarr store from a FITS file. The resulting array has 
     dimensions = RA, DEC, SPECTRAL[, STOKES]
 
@@ -59,7 +59,7 @@ def zds_from_fits(fname, chunks=None, rest_freq=None):
         Zarr: Zarr array (persistant store, mode=w)
     """
     chunks = chunks or dict(ra=64,dec=None, spectral=None)
-    fds = xds_from_fits(fname)[0]
+    fds = xds_from_fits(fname, hdus=hdu_idx)[0]
     
     header = fds.hdu.header
     if rest_freq:

From 55c56b87c4eb0f2bd31d0d464f64f7957eb74713 Mon Sep 17 00:00:00 2001
From: sphemakh <sphemakh@gmail.com>
Date: Sat, 30 Aug 2025 12:59:45 +0200
Subject: [PATCH 2/2] Fixes #25

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7abd4b3..56196bc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "contsub"
-version = "1.0.3"
+version = "1.0.4"
 description = "Radio astronomy data continuum subtraction tools"
 authors = ["Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo"]
 license = "MIT"