From cc4c5cbefd8764f24373ee3662570fbca6e1852d Mon Sep 17 00:00:00 2001
From: JeanBilheux <bilheuxjm@ornl.gov>
Date: Thu, 10 Mar 2022 11:02:24 -0500
Subject: [PATCH 1/2] Fixed work. this refs #4

---
 .gitignore                            |  3 +++
 neutronimaging/detector_correction.py | 13 ++++++++++---
 scripts/mcp_detector_correction.py    | 10 +++++++++-
 setup.py                              |  2 +-
 4 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 250f520..58d3567 100644
--- a/.gitignore
+++ b/.gitignore
@@ -356,3 +356,6 @@ $RECYCLE.BIN/
 
 # End of https://www.toptal.com/developers/gitignore/api/macos,linux,windows,pycharm,vscode,vim,python,jupyternotebooks
 .vscode/settings.json
+
+# pycharm
+.idea
\ No newline at end of file
diff --git a/neutronimaging/detector_correction.py b/neutronimaging/detector_correction.py
index a295db6..c842818 100644
--- a/neutronimaging/detector_correction.py
+++ b/neutronimaging/detector_correction.py
@@ -68,8 +68,12 @@ def skipping_meta_data(meta: pd.DataFrame) -> pd.DataFrame:
     return pd.concat(_with_skips)
 
 
-def load_images(raw_imamge_dir: str) -> Type[Normalization]:
-    """Loading all Images into memory"""
+def load_images(raw_imamge_dir: str, nbr_of_duplicated_runs: int = 1) -> Type[Normalization]:
+    """Loading all Images into memory
+
+    if the nbr_of_duplicated_runs is higher than 1 (default value) that means the MCP produced by
+    mistake other sets of the same data, those must be removed and not used in the reconstruction
+    """
     import glob
     from neutronimaging.util import in_jupyter
 
@@ -81,6 +85,9 @@ def load_images(raw_imamge_dir: str) -> Type[Normalization]:
     ]
     _img_names.sort()
 
+    final_index = int(len(_img_names) / nbr_of_duplicated_runs)
+    _img_names = _img_names[0: final_index]
+
     o_norm.load(file=_img_names, notebook=in_jupyter())
     return o_norm
 
@@ -131,7 +138,7 @@ def correct_images(
     import os
 
     _file_root = os.path.dirname(os.path.abspath(__file__))
-    test_data_dir = os.path.join(_file_root, "../data")
+    test_data_dir = os.path.join(_file_root, "../../../../NeutronImagingScripts/data")
     #
     shutter_counts_file = os.path.join(test_data_dir, "OB_1_005_ShutterCount.txt")
     df_shutter_count = read_shutter_count(shutter_counts_file)
diff --git a/scripts/mcp_detector_correction.py b/scripts/mcp_detector_correction.py
index 64a6419..cf1dcdb 100755
--- a/scripts/mcp_detector_correction.py
+++ b/scripts/mcp_detector_correction.py
@@ -40,6 +40,14 @@
     output_dir = args["<output_dir>"]
     skip_first_last_img = args["--skipimg"]
     verbose = args["--verbose"]
+
+    # in some rare instances, the MCP creates a duplicate set of the run in the same folder
+    # we need to only consider the first set in the autoreduction
+    shutter_count_files = glob.glob(input_dir + "/*_ShutterCount.txt")
+    nbr_of_duplicated_runs = len(shutter_count_files)
+    if nbr_of_duplicated_runs > 1:
+        print(f"The folder contains {nbr_of_duplicated_runs} sets of the same data!")
+
     shutter_count_file = glob.glob(input_dir + "/*_ShutterCount.txt")[0]
     shutter_time_file = glob.glob(input_dir + "/*_ShutterTimes.txt")[0]
     spectra_file = glob.glob(input_dir + "/*_Spectra.txt")[0]
@@ -64,7 +72,7 @@
 
     # load images
     print("Loading images into memory")
-    o_norm = load_images(input_dir)
+    o_norm = load_images(input_dir, nbr_of_duplicated_runs)
 
     # perform image correction
     print("Perform correction")
diff --git a/setup.py b/setup.py
index e201af4..632c221 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 from setuptools import setup, find_packages
 
 NAME = "NeutronImaging"
-META_PATH = os.path.join("neutronimaging", "__init__.py")
+META_PATH = os.path.join("../ToFImaging/jupyter_notebooks/code/neutronimaging", "__init__.py")
 KEYWORDS = "neutron imaging mcp"
 CLASSIFIERS = [
     "Development Status :: 5 - Production/Stable",

From 80456d3314bb3a444e261d8e626657c322e36891 Mon Sep 17 00:00:00 2001
From: JeanBilheux <bilheuxjm@ornl.gov>
Date: Thu, 10 Mar 2022 11:56:46 -0500
Subject: [PATCH 2/2] reverted setup.py change. this refs #4

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 632c221..e201af4 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 from setuptools import setup, find_packages
 
 NAME = "NeutronImaging"
-META_PATH = os.path.join("../ToFImaging/jupyter_notebooks/code/neutronimaging", "__init__.py")
+META_PATH = os.path.join("neutronimaging", "__init__.py")
 KEYWORDS = "neutron imaging mcp"
 CLASSIFIERS = [
     "Development Status :: 5 - Production/Stable",