diff --git a/bwscanner/configutil.py b/bwscanner/configutil.py
index aef3500..60f2c02 100644
--- a/bwscanner/configutil.py
+++ b/bwscanner/configutil.py
@@ -6,15 +6,28 @@
 
 
 def read_config(cfg_path):
-    log.debug('reading config %s' % cfg_path)
+    log.debug('Reading config %s' % cfg_path)
     if not config_exists(cfg_path):
         copy_config(cfg_path)
     parser = SafeConfigParser()
     parser.read([cfg_path])
-    # FIXME: handle section names
-    section = 'default'
-    return dict(parser.items(section))
-
+    cfg_dict = dict(parser.items('default'))
+    int_keys = cfg_dict['int_keys'].split(' ')
+    bool_keys = cfg_dict['bool_keys'].split(' ')
+    for k in int_keys:
+        cfg_dict[k] = int(cfg_dict[k])
+    for i in bool_keys:
+        cfg_dict[k] = bool(cfg_dict[k])
+    bw_files = dict(parser.items('bw_files'))
+    cfg_bw_files = {}
+    for k, v in bw_files.items():
+        print(k, v)
+        if 'm' in k:
+            number = k.rstrip('m')
+            size = 1024 * int(number)
+            cfg_bw_files[size] = (k.upper(), v)
+    cfg_dict['bw_files'] = cfg_bw_files
+    return cfg_dict
 
 def config_exists(cfg_path):
     return os.path.isfile(cfg_path)
diff --git a/bwscanner/scanner.py b/bwscanner/scanner.py
index 39d16dd..fe1f4ec 100755
--- a/bwscanner/scanner.py
+++ b/bwscanner/scanner.py
@@ -18,19 +18,18 @@
 CONFIG_FILE = 'config.ini'
 LOG_FILE = 'bwscanner.log'
 
-CTX = dict(
-    default_map=read_config(os.path.join(DATA_DIR, CONFIG_FILE))
-)
-
 
 class ScanInstance(object):
     """
     Store the configuration and state for the CLI tool.
     """
-    def __init__(self, data_dir):
+    def __init__(self, data_dir, measurement_dir=None):
         self.data_dir = data_dir
-        self.measurement_dir = os.path.join(data_dir, 'measurements')
-        self.tor_dir = os.path.join(data_dir, 'tor_data')
+        if measurement_dir is None:
+            self.measurement_dir = os.path.join(data_dir, 'measurements')
+        else:
+            self.measurement_dir = measurement_dir
+        self.tor_state = None
 
     def __repr__(self):
         return '<BWScan %r>' % self.data_dir
@@ -40,26 +39,19 @@ def __repr__(self):
 
 
 # FIXME: change all options to take defaults from CTX, ie config file?
-@click.group(context_settings=CTX)
+@click.group()
 @click.option('--data-dir', type=click.Path(),
-              default=os.environ.get("BWSCANNER_DATADIR",
-                                     CTX.get('data_dir',
-                                             click.get_app_dir(APP_NAME))),
               help='Directory where bwscan should stores its measurements and '
               'other data.')
 @click.option('-l', '--loglevel',
               help='The logging level the scanner will use (default: info)',
-              default=CTX.get('loglevel', 'info'),
-              type=click.Choice(['debug', 'info', 'warn', 'error', 'critical']))
+              type=click.Choice(
+                      ['debug', 'info', 'warn', 'error', 'critical']))
 @click.option('-f', '--logfile', type=click.Path(),
-              help='The file the log will be written to',
-              default=os.environ.get("BWSCANNER_LOGFILE",
-                                     CTX.get('logfile', LOG_FILE)))
+              help='The file the log will be written to')
 @click.option('--launch-tor/--no-launch-tor',
-              default=CTX.get('launch_tor', False),
               help='Launch Tor or try to connect to an existing Tor instance.')
 @click.option('--circuit-build-timeout',
-              default=CTX.get('circuit_build_timeout', 20),
               help='Option passed when launching Tor.')
 @click.version_option(BWSCAN_VERSION)
 @click.pass_context
@@ -69,9 +61,12 @@ def cli(ctx, data_dir, loglevel, logfile, launch_tor, circuit_build_timeout):
     bandwidth measurements can then be aggregate to create the bandwidth
     values used by the Tor bandwidth authorities when creating the Tor consensus.
     """
+    for k,v in ctx.default_map.items():
+        if ctx.params.get(k) is None:
+            ctx.params[k] = v
+
     # Create the data directory if it doesn't exist
-    data_dir = os.path.abspath(data_dir)
-    ctx.obj = ScanInstance(data_dir)
+    ctx.obj = ScanInstance(ctx.params.get('data_dir'))
 
     if not os.path.isdir(ctx.obj.measurement_dir):
         os.makedirs(ctx.obj.measurement_dir)
@@ -81,7 +76,8 @@ def cli(ctx, data_dir, loglevel, logfile, launch_tor, circuit_build_timeout):
                                        ctx.obj.tor_dir)
 
     # Set up the logger to only output log lines of level `loglevel` and above.
-    setup_logging(log_level=loglevel, log_name=logfile)
+    setup_logging(log_level=ctx.params.get('loglevel'),
+                  log_name=ctx.params.get('logfile'))
 
 
 @cli.command(short_help="Measure the Tor relays.")
@@ -103,7 +99,8 @@ def scan(scan, partitions, current_partition, timeout, request_limit):
 
     # XXX: check that each run is producing the same input set!
     scan_time = str(int(time.time()))
-    scan_data_dir = os.path.join(scan.measurement_dir, '{}.running'.format(scan_time))
+    scan_data_dir = os.path.join(scan.measurement_dir,
+                                 '{}.running'.format(scan_time))
     if not os.path.isdir(scan_data_dir):
         os.makedirs(scan_data_dir)
 
@@ -178,3 +175,8 @@ def aggregate(scan, scan_name, previous):
     scan.tor_state.addErrback(lambda failure: log.failure("Unexpected error"))
     scan.tor_state.addCallback(lambda _: reactor.stop())
     reactor.run()
+
+
+def start():
+    config = read_config(os.path.join(DATA_DIR, CONFIG_FILE))
+    return cli(default_map=config)
diff --git a/setup.py b/setup.py
index cf89041..df235e4 100644
--- a/setup.py
+++ b/setup.py
@@ -42,6 +42,6 @@
       include_package_data=True,
       entry_points={
         "console_scripts": [
-            'bwscan = bwscanner.scanner:cli',
+            'bwscan = bwscanner.scanner:start',
         ]},
      )