Merge pull request #228 from VisLab/develop

Minor adjustments in remodeling file format
hed-standard · Feb 11, 2023 · 39d7240 · 39d7240
2 parents 40c3b06 + f8e6db4
commit 39d7240
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diff --git a/docs/source/FileRemodelingTools.md b/docs/source/FileRemodelingTools.md
@@ -1664,7 +1664,8 @@ Dataset: Number of files=1
 
 Individual files:
 
-   sub-0013_task-stopsignal_acq-seq_events.tsv: ['onset', 'duration', 'trial_type', 'stop_signal_delay', 'response_time', 'response_accuracy', 'response_hand', 'sex']
+sub-0013_task-stopsignal_acq-seq_events.tsv: 
+   ['onset', 'duration', 'trial_type', 'stop_signal_delay', 'response_time', 'response_accuracy', 'response_hand', 'sex']
 		
 ```
 ````
@@ -1771,7 +1772,8 @@ Dataset: Total events=6 Total files=1
 
 Individual files:
 
-   sub-0013_task-stopsignal_acq-seq_events.tsv:
+sub-0013_task-stopsignal_acq-seq_events.tsv:
+Total events=200
       Categorical column values[Events, Files]:
          response_accuracy:
             correct[5, 1] n/a[1, 1]
@@ -1801,7 +1803,7 @@ For a more extensive example see the
 and [**JSON**](./_static/data/summaries/FacePerception_column_values_summary.json) 
 format summaries of the sample dataset 
 [**ds003645s_hed**](https://github.com/hed-standard/hed-examples/tree/main/datasets/eeg_ds003645s_hed) 
-using the [**summarize_columns_rmdl.json**](./static/data/summarize_columns_rmdl.json)
+using the [**summarize_columns_rmdl.json**](./static/data/summaries/summarize_columns_rmdl.json)
 remodeling file.
 
 
@@ -2022,9 +2024,8 @@ Context name: summarize_hed_tags
 Context type: hed_tag_summary
 Context filename: summarize_hed_tags
 
-Summary details:
-
-Dataset: Total events=6 Total files=1
+Overall summary:
+Dataset: Total events=1200 Total1 file=6
 	Main tags[events,files]:
 		Sensory events:
 			Sensory-presentation[6,1] Visual-presentation[6,1] Auditory-presentation[3,1]
@@ -2036,17 +2037,18 @@ Dataset: Total events=6 Total files=1
 		Label[6,1] Def[6,1] Delay[3,1]
 
 Individual files:
-    
-    aomic_sub-0013_excerpt_events.tsv: Type=condition-variable Total events=6 
-        Main tags[events,files]:
-            Sensory events:
-                Sensory-presentation[6,1] Visual-presentation[6,1] Auditory-presentation[3,1]
-            Agent actions:
-                Incorrect-action[2,1] Correct-action[1,1]
-            Objects:
-                Image[6,1]
-        Other tags[events,files]:
-            Label[6,1] Def[6,1] Delay[3,1]
+
+aomic_sub-0013_excerpt_events.tsv:    
+Total events=6 
+   Main tags[events,files]:
+       Sensory events:
+          Sensory-presentation[6,1] Visual-presentation[6,1] Auditory-presentation[3,1]
+       Agent actions:
+          Incorrect-action[2,1] Correct-action[1,1]
+       Objects:
+          Image[6,1]
+   Other tags[events,files]:
+       Label[6,1] Def[6,1] Delay[3,1]
 
 ```
 ````
@@ -2065,7 +2067,7 @@ For a more extensive example, see the
 and [**JSON**](./_static/data/summaries/FacePerception_hed_tag_summary.json) 
 format summaries of the sample dataset 
 [**ds003645s_hed**](https://github.com/hed-standard/hed-examples/tree/main/datasets/eeg_ds003645s_hed) 
-using the [**summarize_hed_tags_rmdl.json**](./static/data/summarize_hed_tags_rmdl.json)
+using the [**summarize_hed_tags_rmdl.json**](./static/data/summaries/summarize_hed_tags_rmdl.json)
 remodeling file.
 
 (summarize-hed-type-anchor)=
@@ -2128,24 +2130,22 @@ Context name: AOMIC_condition_variables
 Context type: hed_type_summary
 Context filename: AOMIC_condition_variables
 
-Summary details:
+Overall summary:
 
-Dataset: Type=condition-variable Total events=6 Total files=1
-   image-sex:
-      Files:['aomic_sub-0013_excerpt_events.tsv']
-      Events: 6 out of 6 total events in 1 files
-         Levels[Events,Files]: [Tags]
-            female-image-cond [4,1]: ['Female', 'Image', 'Face']
-            male-image-cond [2,1]: ['Male', 'Image', 'Face']
+Dataset: Type=condition-variable Type values=1 Total events=6 Total files=1
+   image-sex: 2 levels in 6 event(s)s out of 6 total events in 1 file(s)
+       female-image-cond [4,1]: ['Female', 'Image', 'Face']
+       male-image-cond [2,1]: ['Male', 'Image', 'Face']
 
 Individual files:
 
-   aomic_sub-0013_excerpt_events.tsv: Type=condition-variable Total events=6 
-      image-sex:
-         Levels:2  Events:6
-         Levels[Events,Files]: [Tags]
-            female-image-cond [4,1]: ['Female', 'Image', 'Face']
-            male-image-cond [2,1]: ['Male', 'Image', 'Face']
+aomic_sub-0013_excerpt_events.tsv:
+Type=condition-variable Total events=6 
+      image-sex: 2 levels in 6 events
+         female-image-cond [4 events, 1 files]: 
+            Tags: ['Female', 'Image', 'Face']
+         male-image-cond [2 events, 1 files]: 
+            Tags: ['Male', 'Image', 'Face']
 ```
 ````
 
@@ -2160,7 +2160,7 @@ For a more extensive example, see the
 and [**JSON**](./_static/data/summaries/FacePerception_hed_type_summary.json) 
 format summaries of the sample dataset 
 [**ds003645s_hed**](https://github.com/hed-standard/hed-examples/tree/main/datasets/eeg_ds003645s_hed) 
-using the [**summarize_hed_types_rmdl.json**](./static/data/summarize_hed_types_rmdl.json)
+using the [**summarize_hed_types_rmdl.json**](./static/data/summaries/summarize_hed_types_rmdl.json)
 remodeling file.
 
 (summarize-hed-validation-anchor)=

diff --git a/docs/source/_static/data/summaries/FacePerception_column_values_summary.txt b/docs/source/_static/data/summaries/FacePerception_column_values_summary.txt
@@ -20,7 +20,7 @@ Dataset: Total events=1200 Total files=6
 Individual files:
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             double_press[1, 1] left_press[20, 1] right_press[23, 1] setup_right_sym[1, 1] show_circle[52, 1] show_cross[51, 1] show_face[51, 1] show_face_initial[1, 1]
@@ -36,7 +36,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             right_press[29, 1] setup_right_sym[1, 1] show_circle[57, 1] show_cross[56, 1] show_face[56, 1] show_face_initial[1, 1]
@@ -52,7 +52,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             right_press[29, 1] setup_right_sym[1, 1] show_circle[57, 1] show_cross[56, 1] show_face[56, 1] show_face_initial[1, 1]
@@ -68,7 +68,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             left_press[22, 1] right_press[28, 1] setup_right_sym[1, 1] show_circle[50, 1] show_cross[49, 1] show_face[49, 1] show_face_initial[1, 1]
@@ -84,7 +84,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             left_press[17, 1] right_press[33, 1] setup_right_sym[1, 1] show_circle[50, 1] show_cross[49, 1] show_face[49, 1] show_face_initial[1, 1]
@@ -100,7 +100,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv: 200 events
+Total events=200
       Categorical column values[Events, Files]:
          event_type:
             left_press[24, 1] right_press[26, 1] setup_right_sym[1, 1] show_circle[50, 1] show_cross[49, 1] show_face[49, 1] show_face_initial[1, 1]

diff --git a/docs/source/_static/data/summaries/FacePerception_hed_tag_summary.txt b/docs/source/_static/data/summaries/FacePerception_hed_tag_summary.txt
@@ -3,7 +3,7 @@ Context type: hed_tag_summary
 Context filename: hed_tag_summary
 
 Overall summary:
-Dataset: 6 files with a total of 1200 events
+Dataset: Total events=1200 Total files=6
 
    Main tags[events,files]:
       Sensory events:
@@ -22,7 +22,7 @@ Dataset: 6 files with a total of 1200 events
 Individual files:
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:
@@ -40,7 +40,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:
@@ -58,7 +58,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv:
-g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:
@@ -76,7 +76,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:
@@ -94,7 +94,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:
@@ -112,7 +112,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv: 200 e
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv:
-g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv: 200 events
+Total events=200
 
    Main tags[events,files]:
       Sensory events:

diff --git a/docs/source/_static/data/summaries/FacePerception_hed_type_summary.txt b/docs/source/_static/data/summaries/FacePerception_hed_type_summary.txt
@@ -3,12 +3,12 @@ Context type: hed_type_summary
 Context filename: hed_type_summary
 
 Overall summary:
-Dataset: 3 condition-variable types in 6 files with a total of 1200
-   key-assignment: 1 levels in 1200 events out of 1200 total events in 6 files
+Dataset: Type=condition-variable Type values=3 Total events=1200 Total files=6
+   key-assignment: 1 levels in 1200 event(s) out of 1200 total events in 6 file(s)
       right-sym-cond [1200 events, 6 files]:
          Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
          Description: Right index finger key press indicates a face with above average symmetry.
-   face-type: 3 levels in 316 events out of 1200 total events in 6 files
+   face-type: 3 levels in 316 event(s) out of 1200 total events in 6 file(s)
       unfamiliar-face-cond [105 events, 6 files]:
          Tags: ['Image', 'Face', 'Unfamiliar']
          Description: A face that should not be recognized by the participants.
@@ -18,7 +18,7 @@ Dataset: 3 condition-variable types in 6 files with a total of 1200
       scrambled-face-cond [103 events, 6 files]:
          Tags: ['Image', 'Face', 'Disordered']
          Description: A scrambled face image generated by taking face 2D FFT.
-   repetition-type: 3 levels in 316 events out of 1200 total events in 6 files
+   repetition-type: 3 levels in 316 event(s) out of 1200 total events in 6 file(s)
       first-show-cond [168 events, 6 files]:
          Tags: ['Item-count', 'Face', 'Item-interval']
          Description: Factor level indicating the first display of this face.
@@ -32,7 +32,7 @@ Dataset: 3 condition-variable types in 6 files with a total of 1200
 Individual files:
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv:
-   g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
@@ -60,7 +60,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-1_events.tsv:
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv:
-   g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
@@ -88,7 +88,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-2_events.tsv:
 
 
 g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv:
-   g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
@@ -116,7 +116,7 @@ g:\eeg_ds003645s\sub-002\eeg\sub-002_task-FacePerception_run-3_events.tsv:
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv:
-   g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
@@ -144,7 +144,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-1_events.tsv:
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv:
-   g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']
@@ -172,7 +172,7 @@ g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-2_events.tsv:
 
 
 g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv:
-   g:\eeg_ds003645s\sub-003\eeg\sub-003_task-FacePerception_run-3_events.tsv: Type=condition-variable Total events=200 
+Type=condition-variable Type values=3 Total events=200
       key-assignment: 1 levels in 200 events
          right-sym-cond [200 events, 1 files]:
             Tags: ['Index-finger', 'Right-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Symmetrical', 'Index-finger', 'Left-side-of', 'Experiment-participant', 'Behavioral-evidence', 'Asymmetrical']

diff --git a/docs/source/_static/data/summaries/summarize_columns_rmdl.json b/docs/source/_static/data/summaries/summarize_columns_rmdl.json
@@ -0,0 +1,20 @@
+[
+   {
+        "operation": "summarize_column_names",
+        "description": "Summarize the unique orders of column names.",
+        "parameters": {
+            "summary_name": "column name summary",
+            "summary_filename": "column_name_summary"
+        }
+    },
+    {
+        "operation": "summarize_column_values",
+        "description": "Summarize column values.",
+        "parameters": {
+            "summary_name": "column values summary",
+            "summary_filename": "column_values_summary",
+            "skip_columns": ["onset", "duration", "sample", "value"],
+            "value_columns": ["stim_file", "trial"]
+        }
+    }
+]
diff --git a/docs/source/_static/data/summaries/summarize_hed_tags_rmdl.json b/docs/source/_static/data/summaries/summarize_hed_tags_rmdl.json
@@ -0,0 +1,36 @@
+ [
+     {
+         "operation": "summarize_hed_tags",
+         "description": "Produce a summary of HED tags.",
+         "parameters": {
+             "summary_name": "hed_tag_summary",
+             "summary_filename": "hed_tag_summary",
+             "tags": {
+                 "Sensory events": [
+                     "Sensory-event",
+                     "Sensory-presentation",
+                     "Task-stimulus-role",
+                     "Experimental-stimulus"
+                 ],
+                 "Agent actions": [
+                     "Agent-action",
+                     "Agent",
+                     "Action",
+                     "Agent-task-role",
+                     "Task-action-type",
+                     "Participant-response"
+                 ],
+                 "Task properties": [
+                     "Task-property"
+                 ],
+                 "Objects": [
+                     "Item"
+                 ],
+                 "Properties": [
+                     "Property"
+                 ]
+             },
+             "expand_context": false
+         }
+     }
+]
diff --git a/docs/source/_static/data/summaries/summarize_hed_types_rmdl.json b/docs/source/_static/data/summaries/summarize_hed_types_rmdl.json
@@ -0,0 +1,11 @@
+[
+    {
+        "operation": "summarize_hed_type",
+        "description": "Summarize a hed type tag such as condition-variable",
+        "parameters": {
+            "summary_name": "hed type summary",
+            "summary_filename": "hed_type_summary",
+            "type_tag": "condition-variable"
+        }
+    }
+]