Merge pull request #348 from VisLab/develop

Reorganized the code under src rather than hedcode

README.md

@@ -18,7 +18,7 @@ The [**hedcode**](https://github.com/hed-standard/hed-examples/tree/main/hedcode
 subdirectory contains MATLAB scripts, Python Jupyter Notebooks,
 and Python scripts with direct calls to HedTools.
 The repository also contains example code in python and matlab. 
-See [**hedcode/README.md**](./hedcode/README.md) for details.
+See [**hedcode/README.md**](src/README.md) for details.
 The Python scripts and notebooks require the installation of
 `hedtools` whose [**installation**](./README.md#installation-of-hedtools)
 is described below.

docs/_static/data/AOMIC_splitevents_rmdl.json

@@ -0,0 +1,22 @@
+[
+    {
+        "operation": "split_rows",
+        "description": "Split response event from trial event based on response_time column.",
+        "parameters": {
+            "anchor_column": "trial_type",
+            "new_events": {
+                "response": {
+                    "onset_source": ["response_time"],
+                    "duration": [0],
+                    "copy_columns": ["response_accuracy", "response_hand"]
+                },
+                "stop_signal": {
+                    "onset_source": ["stop_signal_delay"],
+                    "duration": [0.5],
+                    "copy_columns": []
+                }
+            },
+            "remove_parent_row": false
+        }
+    }
+]

docs/_static/data/AOMIC_summary_rmdl.json

@@ -0,0 +1,10 @@
+[
+    {
+        "operation": "summarize_column_names",
+        "description": "Summarize existing column header across entire AOMIC dataset.",
+        "parameters": {
+            "summary_name": "AOMIC_column_headers",
+            "summary_filename": "AOMIC_column_headers"
+            }    
+    }
+]

docs/_static/data/eeglab-tutorial_events.json

@@ -0,0 +1,14 @@
+{
+  "position": {
+    "HED": {
+      "1": "(Square, (To-left-of, Cross, Angle/0.096))",
+      "2": "(Square, (To-left-of, Cross, Angle/0.047))"
+    }
+  },
+  "type": {
+    "HED": {
+      "square": "Description/Appearance of a filled disk in a green colored square in on a black background. Subjects were supposed to respond with a button press, Sensory-event, Visual-presentation, (Foreground-view, ((Circle, Black), Within, (Square, Width/1.6 cm, Green))),(Background-view, Black)",
+      "rt": "Description/Subject presses a button; supposedly in response to seeing the filled disk appeaing in the attended square, Agent-action, (Participant-response, Intended-effect), (Press, Push-button)"
+    }
+  }
+}

docs/_static/data/empty_flattened_merged.json

@@ -0,0 +1,64 @@
+{
+    "event_type": {
+        "Levels": {
+            "setup_right_sym": "Description for setup_right_sym",
+            "show_face_initial": "Description for show_face_initial",
+            "double_press": "Description for double_press",
+            "left_press": "Description for left_press",
+            "right_press": "Description for right_press",
+            "show_face": "Description for show_face",
+            "show_circle": "Description for show_circle",
+            "show_cross": "Description for show_cross"
+        },
+        "HED": {
+            "setup_right_sym": "Label/setup_right_sym",
+            "show_face_initial": "Label/show_face_initial",
+            "double_press": "Label/double_press",
+            "left_press": "Label/left_press",
+            "right_press": "Label/right_press",
+            "show_face": "Label/show_face",
+            "show_circle": "Label/show_circle",
+            "show_cross": "Label/show_cross"
+        }
+    },
+    "face_type": {
+        "Levels": {
+            "unfamiliar_face": "Description for unfamiliar_face",
+            "famous_face": "Description for famous_face",
+            "scrambled_face": "Description for scrambled_face"
+        },
+        "HED": {
+            "unfamiliar_face": "Label/unfamiliar_face",
+            "famous_face": "Label/famous_face",
+            "scrambled_face": "Label/scrambled_face"
+        }
+    },
+    "rep_status": {
+        "Levels": {
+            "delayed_repeat": "Description for delayed_repeat",
+            "immediate_repeat": "Description for immediate_repeat",
+            "first_show": "Description for first_show"
+        },
+        "HED": {
+            "delayed_repeat": "Label/delayed_repeat",
+            "immediate_repeat": "Label/immediate_repeat",
+            "first_show": "Label/first_show"
+        }
+    },
+    "trial": {
+        "Description": "Description for trial",
+        "HED": "Label/#"
+    },
+    "rep_lag": {
+        "Description": "Description for rep_lag",
+        "HED": "Label/#"
+    },
+    "value": {
+        "Description": "Description for value",
+        "HED": "Label/#"
+    },
+    "stim_file": {
+        "Description": "Description for stim_file",
+        "HED": "Label/#"
+    }
+}

docs/_static/data/empty_flattened_mergeddesc.json

@@ -0,0 +1,64 @@
+{
+    "event_type": {
+        "Levels": {
+            "setup_right_sym": "Description for setup_right_sym",
+            "show_face_initial": "Description for show_face_initial",
+            "double_press": "Description for double_press",
+            "left_press": "Description for left_press",
+            "right_press": "Description for right_press",
+            "show_face": "Description for show_face",
+            "show_circle": "Description for show_circle",
+            "show_cross": "Description for show_cross"
+        },
+        "HED": {
+            "setup_right_sym": "Label/setup_right_sym, Description/Description for setup_right_sym",
+            "show_face_initial": "Label/show_face_initial, Description/Description for show_face_initial",
+            "double_press": "Label/double_press, Description/Description for double_press",
+            "left_press": "Label/left_press, Description/Description for left_press",
+            "right_press": "Label/right_press, Description/Description for right_press",
+            "show_face": "Label/show_face, Description/Description for show_face",
+            "show_circle": "Label/show_circle, Description/Description for show_circle",
+            "show_cross": "Label/show_cross, Description/Description for show_cross"
+        }
+    },
+    "face_type": {
+        "Levels": {
+            "unfamiliar_face": "Description for unfamiliar_face",
+            "famous_face": "Description for famous_face",
+            "scrambled_face": "Description for scrambled_face"
+        },
+        "HED": {
+            "unfamiliar_face": "Label/unfamiliar_face, Description/Description for unfamiliar_face",
+            "famous_face": "Label/famous_face, Description/Description for famous_face",
+            "scrambled_face": "Label/scrambled_face, Description/Description for scrambled_face"
+        }
+    },
+    "rep_status": {
+        "Levels": {
+            "delayed_repeat": "Description for delayed_repeat",
+            "immediate_repeat": "Description for immediate_repeat",
+            "first_show": "Description for first_show"
+        },
+        "HED": {
+            "delayed_repeat": "Label/delayed_repeat, Description/Description for delayed_repeat",
+            "immediate_repeat": "Label/immediate_repeat, Description/Description for immediate_repeat",
+            "first_show": "Label/first_show, Description/Description for first_show"
+        }
+    },
+    "trial": {
+        "Description": "Description for trial",
+        "HED": "Label/#, Description/Description for trial"
+    },
+    "rep_lag": {
+        "Description": "Description for rep_lag",
+        "HED": "Label/#, Description/Description for rep_lag"
+    },
+    "value": {
+        "Description": "Description for value",
+        "HED": "Label/#, Description/Description for value"
+    },
+    "stim_file": {
+        "Description": "Description for stim_file",
+        "HED": "Label/#, Description/Description for stim_file"
+    }
+}

docs/_static/data/sub-0013_task-stopsignal_acq-seq_events.tsv

@@ -0,0 +1,101 @@
+onset	duration	trial_type	stop_signal_delay	response_time	response_accuracy	response_hand	sex
+0.0776	0.5083	go	n/a	0.565	correct	right	female
+5.5774	0.5083	unsuccesful_stop	0.2	0.49	correct	right	female
+9.5856	0.5084	go	n/a	0.45	correct	right	female
+13.5939	0.5083	succesful_stop	0.2	n/a	n/a	right	female
+17.1021	0.5083	unsuccesful_stop	0.25	0.633	correct	left	male
+21.6103	0.5083	go	n/a	0.443	correct	left	male
+24.6186	0.5083	go	n/a	0.439	correct	left	male
+28.6268	0.5083	go	n/a	0.667	correct	left	male
+32.1434	0.5083	go	n/a	0.55	correct	right	female
+36.1516	0.5083	succesful_stop	0.25	n/a	n/a	right	female
+41.6514	0.5084	go	n/a	0.59	correct	right	female
+44.6597	0.5083	unsuccesful_stop	0.3	0.511	correct	right	female
+49.6679	0.5083	go	n/a	0.604	correct	right	female
+52.1845	0.5083	go	n/a	0.743	correct	left	male
+56.1927	0.5084	succesful_stop	0.3	n/a	n/a	right	female
+60.6926	0.5083	unsuccesful_stop	0.35	0.555	correct	left	male
+65.7008	0.5083	go	n/a	0.584	correct	right	female
+73.7173	0.5083	succesful_stop	0.35	n/a	n/a	right	female
+76.7255	0.5083	succesful_stop	0.4	n/a	n/a	right	male
+81.2337	0.5084	go	n/a	0.615	correct	left	male
+84.742	0.5083	go	n/a	0.754	correct	left	male
+89.2502	0.5083	go	n/a	0.777	correct	right	female
+92.2668	0.5083	go	n/a	0.644	correct	right	female
+97.2666	0.5084	unsuccesful_stop	0.45	0.629	correct	right	female
+100.2832	0.5083	go	n/a	0.714	correct	right	female
+104.7831	0.5083	go	n/a	0.627	correct	left	male
+108.2997	0.5083	go	n/a	0.668	correct	left	male
+113.2995	0.5084	go	n/a	0.558	correct	left	male
+117.3078	0.5083	go	n/a	1.038	incorrect	left	female
+120.816	0.5083	go	n/a	0.764	correct	left	male
+125.8242	0.5083	go	n/a	0.782	correct	right	female
+129.3325	0.5083	unsuccesful_stop	0.5	0.722	correct	left	male
+132.8407	0.5083	go	n/a	0.716	correct	right	female
+137.8489	0.5083	go	n/a	0.741	correct	right	female
+141.3571	0.5084	succesful_stop	0.5	n/a	n/a	right	male
+145.8653	0.5084	go	n/a	1.027	correct	right	female
+149.3736	0.5083	go	n/a	0.881	correct	left	male
+153.3818	0.5083	go	n/a	0.801	correct	right	female
+157.89	0.5084	go	n/a	0.803	correct	left	male
+160.8983	0.5083	go	n/a	0.771	correct	right	female
+164.4149	0.5083	succesful_stop	0.55	n/a	n/a	right	female
+169.4147	0.5083	go	n/a	0.899	correct	left	male
+172.923	0.5083	unsuccesful_stop	0.6	0.754	correct	left	male
+176.9312	0.5083	go	n/a	1.11	correct	left	male
+180.4478	0.5083	succesful_stop	0.65	n/a	n/a	right	male
+188.9559	0.5083	unsuccesful_stop	0.7	0.867	correct	right	female
+193.4641	0.5083	unsuccesful_stop	0.75	0.814	correct	left	male
+197.4723	0.5083	go	n/a	1.21	correct	right	female
+201.4805	0.5084	go	n/a	0.859	correct	left	male
+204.9888	0.5083	unsuccesful_stop	0.75	0.973	correct	right	female
+212.5136	0.5083	go	n/a	1.02	correct	left	male
+221.5217	0.5083	go	n/a	0.817	correct	left	male
+225.5299	0.5083	go	n/a	1.038	correct	right	female
+228.5465	0.5083	go	n/a	1.049	correct	right	female
+234.0463	0.5084	go	n/a	0.92	correct	left	male
+237.0546	0.5083	succesful_stop	0.7	n/a	n/a	right	female
+241.0628	0.5083	go	n/a	1.266	correct	right	female
+245.071	0.5084	unsuccesful_stop	0.7	0.854	correct	right	female
+248.5876	0.5083	go	n/a	0.985	correct	left	male
+254.0875	0.5083	go	n/a	0.789	correct	right	female
+260.6123	0.5083	go	n/a	0.928	correct	right	female
+266.1122	0.5083	go	n/a	0.807	correct	left	male
+269.6204	0.5083	go	n/a	0.735	correct	left	male
+273.6286	0.5083	succesful_stop	0.65	n/a	n/a	right	male
+277.6368	0.5084	go	n/a	0.896	correct	right	female
+281.6451	0.5083	succesful_stop	0.65	n/a	n/a	right	female
+289.6615	0.5083	unsuccesful_stop	0.7	0.831	correct	right	female
+293.1698	0.5083	go	n/a	0.876	correct	left	male
+296.6863	0.5084	go	n/a	1.021	correct	right	female
+302.1862	0.5083	unsuccesful_stop	0.7	1.085	correct	left	male
+306.1944	0.5083	succesful_stop	0.65	n/a	n/a	right	female
+309.2027	0.5083	go	n/a	0.814	correct	right	female
+313.2109	0.5083	go	n/a	1.053	correct	left	male
+318.2191	0.5083	go	n/a	1.002	correct	left	male
+322.2273	0.5083	go	n/a	1.057	correct	right	female
+326.2355	0.5084	succesful_stop	0.65	n/a	n/a	right	male
+330.2438	0.5083	succesful_stop	0.7	n/a	n/a	right	male
+334.252	0.5083	go	n/a	0.962	correct	left	male
+341.2685	0.5083	go	n/a	0.817	correct	right	female
+346.2767	0.5083	unsuccesful_stop	0.75	0.822	correct	left	male
+350.2849	0.5083	go	n/a	0.889	correct	left	male
+353.2932	0.5083	go	n/a	0.946	correct	right	female
+358.3014	0.5083	go	n/a	0.911	correct	right	female
+360.818	0.5083	unsuccesful_stop	0.8	1.054	correct	left	male
+364.8262	0.5083	go	n/a	0.966	correct	right	female
+368.8344	0.5083	unsuccesful_stop	0.8	0.99	correct	right	female
+373.8343	0.5083	go	n/a	1.004	correct	right	female
+377.8425	0.5083	unsuccesful_stop	0.75	0.909	correct	left	male
+381.8507	0.5084	go	n/a	0.859	correct	left	male
+385.859	0.5083	go	n/a	1.186	correct	right	female
+389.3672	0.5083	go	n/a	1.288	correct	right	female
+393.3754	0.5083	go	n/a	0.979	correct	left	male
+398.3836	0.5084	go	n/a	1.067	correct	left	male
+400.9002	0.5083	succesful_stop	0.7	n/a	n/a	right	male
+409.4083	0.5084	go	n/a	0.901	correct	left	male
+414.4165	0.5084	unsuccesful_stop	0.65	0.879	correct	left	male
+418.4248	0.5083	go	n/a	1.003	correct	left	male
+422.433	0.5083	succesful_stop	0.6	n/a	n/a	right	female
+429.9495	0.5083	succesful_stop	0.55	n/a	n/a	right	female
+437.9659	0.5083	go	n/a	0.866	correct	left	male