From 26fa142e54259eedb8ff8f72b47c8d38b11cf933 Mon Sep 17 00:00:00 2001
From: Cody Crewson <crcrewso@localhost.localdomain>
Date: Sun, 24 May 2020 09:45:20 -0600
Subject: [PATCH] Created offset calculations for Catphan604 HU linearity
 module differences

---
 .gitignore    | 2 ++
 pylinac/ct.py | 5 +++++
 2 files changed, 7 insertions(+)

diff --git a/.gitignore b/.gitignore
index 1e8b660e8..5271920e4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 # Folders to ignore
+.vscode
 env/*
 **/pylinac.egg-info
 #**/demo_files
@@ -7,3 +8,4 @@ env/*
 #Files to ignore
 *.old
 .directory
+
diff --git a/pylinac/ct.py b/pylinac/ct.py
index e9a4fd6e2..f8396a737 100644
--- a/pylinac/ct.py
+++ b/pylinac/ct.py
@@ -19,6 +19,7 @@
 import webbrowser
 import zipfile
 from typing import Optional
+from math import ceil, floor
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -1023,6 +1024,10 @@ def find_origin_slice(self):
 
         if not hu_slices:
             raise ValueError("No slices were found that resembled the HU linearity module")
+        if isinstance(self, CatPhan604):
+            _604_hu_offset_index_front = int(ceil(5 / self.dicom_stack.metadata.SliceThickness))
+            _604_hu_offset_index_back = int(ceil(2 / self.dicom_stack.metadata.SliceThickness))
+            hu_slices = hu_slices[_604_hu_offset_index_front:-_604_hu_offset_index_back]
         hu_slices = np.array(hu_slices)
         c = int(round(np.median(hu_slices)))
         ln = len(hu_slices)