From 9fe79f8762e30bb127c396fdbc91bfbf4ce81bd6 Mon Sep 17 00:00:00 2001
From: Arman <arman.avesta@yale.edu>
Date: Wed, 25 Sep 2024 11:09:21 -0400
Subject: [PATCH] Updated project files

---
 README.md          | 14 +++++++-------
 images_register.py |  2 +-
 setup.py           |  5 ++++-
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 25574ac..6509e7f 100644
--- a/README.md
+++ b/README.md
@@ -34,19 +34,19 @@ apptainer exec docker://fnndsc/pl-images-register images_register --help
 
 ## Examples
 
-`images_register` requires two positional arguments: a directory containing
-input data, and a directory where to create output data.
-First, create the input directory and move input data into it.
+`images_register` requires two positional arguments: a directory containing input images, i.e.
+a fixed_image and a moving_image, and a directory where to create output data, i.e. registered_image and 
+transform_matrix. First, create the input directory and move input data into it.
 
 ```shell
-mkdir incoming/ outgoing/
-mv some.dat other.dat incoming/
-apptainer exec docker://fnndsc/pl-images-register:latest images_register [--args] incoming/ outgoing/
+mkdir incoming outgoing
+mv fixed_image.nii.gz moving_image.nii.gz incoming
+apptainer exec docker://fnndsc/pl-images-register:latest images_register [--args] incoming outgoing
 ```
 
 ## Development
 
-Instructions for developers.
+The registration algorithms are found in images_register.py module.
 
 ### Building
 
diff --git a/images_register.py b/images_register.py
index 9edf1a9..b438dd4 100644
--- a/images_register.py
+++ b/images_register.py
@@ -16,7 +16,7 @@
 from chris_plugin import chris_plugin
 
 # Version:
-__version__ = '1.0.1'
+# __version__ = '1.0.1'
 
 # ---------------------------------------------- ARGUMENT PARSING -----------------------------------------------------
 
diff --git a/setup.py b/setup.py
index 69461b3..24dd756 100644
--- a/setup.py
+++ b/setup.py
@@ -6,6 +6,9 @@
 """
 
 # ----------------------------------------------- ENVIRONMENT SETUP ---------------------------------------------------
+# Global variables:
+VERSION='1.0.0'     # <-------------------------- SET VERSION HERE
+
 # Project imports:
 
 
@@ -60,7 +63,7 @@ def parse_requirements(file_path):
 setup(
     name='images-register',
     # version=get_version('images_register.py'),
-    version='1.0.0',
+    version=VERSION,
     description='A ChRIS plugin to do multiple image registration',
     author='FNNDSC',
     author_email='arman.avasta@childrens.harvard.edu',