further clarified README

Author: stavis1

README.md

@@ -30,9 +30,10 @@ To use the tool with either method:
 
 ## The Docker version
 The docker container has trained models provided under /models/. To use these get the default options.toml from step 1 below:
-1. Run `docker run --rm -v /path/to/your/data/:/data/ stavisvols/msdpostprocess python -m MSDpostprocess --print /data/options.toml`
-2. Edit the options file for your experiment.
-3. Run `docker run --rm -v /path/to/your/data/:/data/ stavisvols/msdpostprocess python -m MSDpostprocess --options /data/options.toml`
+1. Run `docker pull stavisvols/msdpostprocess`
+2. Run `docker run --rm -v /path/to/your/data/:/data/ stavisvols/msdpostprocess python -m MSDpostprocess --print /data/options.toml`
+3. Edit the options file for your experiment.
+4. Run `docker run --rm -v /path/to/your/data/:/data/ stavisvols/msdpostprocess python -m MSDpostprocess --options /data/options.toml`
 The working directory will be within the docker container's filesystem.
 
 ## Example analysis

src/MSDpostprocess/options.py

@@ -76,12 +76,10 @@ def print_options(self, path):
             resolved_path = os.path.abspath(sys._MEIPASS)
         else:
             resolved_path = os.path.abspath(os.path.dirname(__file__))
-
         if os.environ.get('AM_I_IN_A_DOCKER_CONTAINER', False):
             example_options = os.path.join(resolved_path, 'docker_example_options.toml')
         else:
             example_options = os.path.join(resolved_path, 'example_options.toml')
- 
         shutil.copy2(example_options, path)
 
 def validate_inputs(args):