Update readme and version

Author: MaxvandenBoom

README.md

@@ -1,41 +1,76 @@
 # Evoked Response Detection
-A python package and docker application for the automatic detection of evoked responses in CCEP data
+A python package and docker application for the automatic detection of evoked responses in SPES/CCEP data
 
 ## Usage
 
+### Docker
+
 To launch an instance of the container and analyse data in BIDS format, type:
 
 ```
-$ docker run multimodalneuro/n1detect bids_dir output_dir [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
+$ docker run multimodalneuro/n1detect <bids_dir> <output_dir> [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
 ```
 For example, to run an analysis, type:
 
 ```
 $ docker run -ti --rm \
-  -v /path/to/local/bids/input/dataset/:/data \
+  -v /path/to/local/bids_input/dataset/:/data \
   -v /path/to/local/output/:/output \
   multimodalneuro/n1detect /data /output --participant_label 01 --skip_bids_validator
 ```
 
+
+### Python
+
+1. First install ERdetect, in the command-line run:
+```
+pip install erdetect
+```
+
+2a. Run directly in a python script:
+```
+import erdetect
+erdetect.process('/path/to/bids_input/dataset/', '/path/to/output/')
+```
+
+2b. Run from a windows/mac/unix commandline:
+```
+python -m erdetect <bids_dir> <output_dir>/ [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
+```
+
+
 ## Configure detection
 To adjust the preprocessing, evoked response detection and visualization settings, a JSON file can be passed using the ```--config_filepath [JSON_FILEPATH]``` parameter.
 An example JSON of the standard settings has the following content:
 ```
 {
+    "preprocess": {
+        "high_pass":                        false,
+        "line_noise_removal":               "off",
+        "early_re_referencing": {
+            "enabled":                      false,
+            "method":                       "CAR",
+            "stim_excl_epoch":              [-1.0,        2.0]
+        }
+    },
+	
     "trials": {
-        "trial_epoch":                      [-1.0,        3.0],
+        "trial_epoch":                      [-1.0,        2.0],
         "out_of_bounds_handling":           "first_last_only",
-        "baseline_epoch":                   [-1.0,       -0.1],
+        "baseline_epoch":                   [-0.5,      -0.02],
         "baseline_norm":                    "median",
         "concat_bidirectional_pairs":       true,
         "minimum_stimpair_trials":          5
     },
 
     "channels": {
-        "types":                            ["ECOG", "SEEG", "DBS"]
+        "measured_types":                   ["ECOG", "SEEG", "DBS"],
+        "stim_types":                       ["ECOG", "SEEG", "DBS"]
     },
 
     "detection": {
+        "negative":                         true,
+        "positive":                         false,
         "peak_search_epoch":                [ 0,          0.5],
         "response_search_epoch":            [ 0.009,     0.09],
         "method":                           "std_base",
@@ -46,15 +81,17 @@ An example JSON of the standard settings has the following content:
     },
 
     "visualization": {
+        "negative":                         true,
+        "positive":                         false,
         "x_axis_epoch":                     [-0.2,          1],
         "blank_stim_epoch":                 [-0.015,   0.0025],
-        "generate_electrode_images":        false,
-        "generate_stimpair_images":         false,
+        "generate_electrode_images":        true,
+        "generate_stimpair_images":         true,
         "generate_matrix_images":           true
     }
 }
 ```
-For more information the settings...
+
 
 ## Acknowledgements
 

erdetect/version.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"