diff --git a/src/aslm/log_files/log_functions.py b/src/aslm/log_files/log_functions.py
index d6e9e323d..6f24e1eaa 100644
--- a/src/aslm/log_files/log_functions.py
+++ b/src/aslm/log_files/log_functions.py
@@ -1,24 +1,80 @@
+from email.mime import base
 import logging.config
 import logging.handlers
 import yaml
 from pathlib import Path
 
+def update_nested_dict(d, find_func, apply_func):
+    """
+    Loops through a nested dictionary and if find_func() conditions are met,
+    run apply_func on that key.
+
+    TODO: This is highly general and doesn't belong here.
+    TODO: It might be nice to make this non-recursive.
+    
+    Parameters
+    ----------
+    find_func : func
+        Accepts key, value pair and matches a condition based on these. Returns bool.
+    apply_func : func
+        Accepts a value returns the new value.
+
+    Returns
+    -------
+    d2 : dict
+        An version of d, updated according to the passed functions.
+    """
+    d2 = {}
+    for k, v in d.items():
+        if find_func(k, v):
+            d2[k] = apply_func(v)
+        else:
+            d2[k] = v
+        if isinstance(v, dict):
+            d2[k] = update_nested_dict(v, find_func, apply_func)
+    return d2
+
+def find_filename(k, v):
+    """
+    Check that we've met the condition dictionary key == 'filename'
+    """
+    if k == 'filename':
+        return True
+    return False
 
 def log_setup(fname):
+    """
+    Initialize a logger from a YAML file containing information in the Python logging
+    dictionary format
+    (see https://docs.python.org/3/library/logging.config.html#logging-config-dictschema).
+
+    Parameters
+    ----------
+    fname : str
+        Path to file to be loaded. Relative to the location of the folder containing this file.
+    """
+
+    # the path to fname is set relative to the location of the folder containing this file (log_functions.py)
     base_directory = Path(__file__).resolve().parent
     logging_path = Path.joinpath(base_directory, fname)
+
+    # Function to map filename to base_directory/filename in the dictionary
+    def update_filename(v):
+        return Path.joinpath(base_directory, v)
+
     with open(logging_path, 'r') as f:
         try:
             config_data = yaml.load(f.read(), Loader=yaml.FullLoader)
-            logging.config.dictConfig(config_data)  # Configures our loggers from logging.yml
+            # Force all log files to be created relative to base_directory
+            config_data2 = update_nested_dict(config_data, find_filename, update_filename)
+            logging.config.dictConfig(config_data2)  # Configures our loggers from updated logging.yml
         except yaml.YAMLError as yaml_error:
             print(yaml_error)
 
-
 def main_process_listener(queue):
-    '''
+    """
     This function will listen for new logs put in queue from sub processes, it will then log via the main process.
-    '''
+    """
     while True:
         try:
             record = queue.get()
diff --git a/src/aslm/log_files/logging.yml b/src/aslm/log_files/logging.yml
index f35d770fa..957324c27 100644
--- a/src/aslm/log_files/logging.yml
+++ b/src/aslm/log_files/logging.yml
@@ -20,21 +20,21 @@ handlers:
     class: logging.FileHandler
     level: INFO
     formatter: base
-    filename: log_files/view_controller_info.log
+    filename: view_controller_info.log
     filters: [not_performance]
     mode: w
   vc_debug:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/view_controller_debug.log
+    filename: view_controller_debug.log
     filters: [not_performance]
     mode: w
   performance:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/performance.log
+    filename: performance.log
     filters: [performance_specs]
     mode: w
 loggers:
diff --git a/src/aslm/log_files/model_logging.yml b/src/aslm/log_files/model_logging.yml
index 61496b55b..5e43c2986 100644
--- a/src/aslm/log_files/model_logging.yml
+++ b/src/aslm/log_files/model_logging.yml
@@ -20,21 +20,21 @@ handlers:
     class: logging.FileHandler
     level: INFO
     formatter: base
-    filename: log_files/model_info.log
+    filename: model_info.log
     filters: [not_performance]
     mode: w
   model_debug:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/model_debug.log
+    filename: model_debug.log
     filters: [not_performance]
     mode: w
   model_performance:
     class: logging.FileHandler
     level: DEBUG
     formatter: base
-    filename: log_files/model_performance.log
+    filename: model_performance.log
     filters: [performance_specs]
     mode: w
 loggers:
diff --git a/src/aslm/main.py b/src/aslm/main.py
index 1e8cfd2f1..400cc6d7d 100644
--- a/src/aslm/main.py
+++ b/src/aslm/main.py
@@ -79,27 +79,20 @@ def main():
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='Multiscale Microscope Command Line Arguments')
     input_args = parser.add_argument_group('Input Arguments')
-    input_args.add_argument('--verbose',
+    input_args.add_argument('-v', '--verbose',
                             required=False,
                             default=False,
                             action='store_true',
                             help='Enables the software to operate in a verbose mode.  Warning: Excessively verbose.')
 
-    input_args.add_argument('--synthetic_hardware',
+    input_args.add_argument('-sh', '--synthetic_hardware',
                             required=False,
                             default=False,
                             action='store_true',
                             help='Synthetic Hardware - '
                                  'Allows launching of the software without the physical devices attached.')
 
-    input_args.add_argument('--sh',
-                            required=False,
-                            default=False,
-                            action='store_true',
-                            help='Synthetic Hardware - '
-                                 'Allows launching of the software without the physical devices attached.')
-
-    input_args.add_argument('--debug',
+    input_args.add_argument('-d', '--debug',
                             required=False,
                             default=False,
                             action='store_true',