From 759862a223e28d89d64d0cf68b1f4927486df1b8 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Mon, 24 Mar 2025 16:09:19 +0100
Subject: [PATCH] remove zone id file

---
 PyNutil/main.py                                               | 1 -
 PyNutil/processing/data_analysis.py                           | 4 ++--
 README.md                                                     | 2 ++
 .../pynutil_settings.json:Zone.Identifier                     | 0
 4 files changed, 4 insertions(+), 3 deletions(-)
 delete mode 100644 tests/expected_outputs/brainglobe_atlas_damage/pynutil_settings.json:Zone.Identifier

diff --git a/PyNutil/main.py b/PyNutil/main.py
index 7de7282..0c1fc8e 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -227,7 +227,6 @@ class PyNutil:
                 for i in self.per_section_df:
                     c, i = apply_custom_regions(i, self.custom_regions_dict)
                     self.custom_per_section_df.append(c)
-                self.custom_label_df
         except Exception as e:
             raise ValueError(f"Error quantifying coordinates: {e}")
 
diff --git a/PyNutil/processing/data_analysis.py b/PyNutil/processing/data_analysis.py
index b695e52..a18bdb7 100644
--- a/PyNutil/processing/data_analysis.py
+++ b/PyNutil/processing/data_analysis.py
@@ -55,11 +55,11 @@ def apply_custom_regions(df, custom_regions_dict):
         "region_area", "undamaged_region_area", "damaged_region_area",
         "object_count", "undamaged_object_count", "damaged_object_count",
         "left_hemi_pixel_count", "left_hemi_undamaged_pixel_count",
-        "left_hemi_damaged_pixel_counts", "left_hemi_region_area",
+        "left_hemi_damaged_pixel_count", "left_hemi_region_area",
         "left_hemi_undamaged_region_area", "left_hemi_damaged_region_area",
         "left_hemi_object_count", "left_hemi_undamaged_object_count",
         "left_hemi_damaged_object_count", "right_hemi_pixel_count",
-        "right_hemi_undamaged_pixel_count", "right_hemi_damaged_pixel_counts",
+        "right_hemi_undamaged_pixel_count", "right_hemi_damaged_pixel_count",
         "right_hemi_region_area", "right_hemi_undamaged_region_area",
         "right_hemi_damaged_region_area", "right_hemi_object_count",
         "right_hemi_undamaged_object_count", "right_hemi_damaged_object_count"
diff --git a/README.md b/README.md
index 6e7179c..aef431c 100644
--- a/README.md
+++ b/README.md
@@ -62,6 +62,8 @@ PyNutil generates a series of reports in the folder which you specify.
 If you use an atlas which has a hemisphere map (All brainglobe atlases have this, it is a volume in the shape of the atlas with 1 in the lft hemisphere and 2 in the right) PyNutil will generate per-hemisphere quantifications in addition to total numbers. In addition, PyNutil will also genearte additional per-hemisphere point cloud files for viewing in meshview.
 ## Damage Quantification
 The QCAlign tool allows you to mark damaged areas on your section. This means that these damaged areas are excluded from your point clouds. In addition, PyNutil will seperately quantify damaged and undamaged areas. Note the undamaged, and damaged column names. 
+# Meshview json files
+PyNutil will produce meshview json files
 # Interpreting the Results
 Each column name has the following definition
 | Column        | Definition                                                                          |
diff --git a/tests/expected_outputs/brainglobe_atlas_damage/pynutil_settings.json:Zone.Identifier b/tests/expected_outputs/brainglobe_atlas_damage/pynutil_settings.json:Zone.Identifier
deleted file mode 100644
index e69de29..0000000
-- 
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