From 4408974b5bb6e20476473c2ef97c0e670eccd408 Mon Sep 17 00:00:00 2001
From: afrendeiro <afrendeiro@gmail.com>
Date: Wed, 8 Dec 2021 12:12:44 -0500
Subject: [PATCH] remove unused domain labeling

---
 src/analysis.py | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/src/analysis.py b/src/analysis.py
index 2720d27..56e48ab 100644
--- a/src/analysis.py
+++ b/src/analysis.py
@@ -131,29 +131,6 @@ def main(cli=None) -> int:
     # Illustrate tumor and immune phenotype differences between primary and metastasis
     illustrate_change_with_metastasis()
 
-    # Label topological domains
-    from imc.operations import (
-        label_domains,
-        collect_domains,
-        illustrate_domains,
-        get_domains_per_cell,
-    )
-
-    output_dir = results_dir / "domains"
-    label_domains(
-        [prj.rois[0]],
-        output_dir,
-        channels=["Keratin", "CD", "DNA"],
-        overwrite=True,
-    )
-    topo_annots = collect_domains(output_dir)
-    with open(metadata_dir / "domain_annotations.json", "w") as handle:
-        json.dump(topo_annots, handle, indent=4)
-    illustrate_domains(
-        topo_annots, prj.rois, output_dir, channels=["Keratin", "Coltype", "DNA"]
-    )
-    get_domains_per_cell(topo_annots, prj.rois)
-
     return 0