Merge pull request #218 from hed-standard/develop

Updated documentation on remap

datasets/eeg_ds003654s_hed_library/dataset_description.json

@@ -1,7 +1,7 @@
 {
     "Name": "Face processing MEEG dataset with HED annotation",
     "BIDSVersion": "1.8.4",
-    "HEDVersion": ["8.0.0", "sc:score_0.0.1",  "test:testlib_1.0.2"],
+    "HEDVersion": ["8.0.0", "sc:score_1.0.0",  "test:testlib_1.0.2"],
     "License": "CC0",
     "Authors": [
         "Daniel G. Wakeman",

datasets/eeg_ds003654s_hed_library/task-FacePerception_events.json

@@ -25,7 +25,7 @@
       "show_face": "Sensory-event, test:Experimental-stimulus, (Def/Face-image, Onset), (Def/Blink-inhibition-task,Onset),(Def/Cross-only, Offset)",
       "show_face_initial": "Sensory-event, Experimental-stimulus, (Def/Face-image, Onset), (Def/Blink-inhibition-task,Onset), (Def/Fixation-task, Onset)",
       "show_circle": "Sensory-event, (Intended-effect, Cue), (Def/Circle-only, Onset), (Def/Face-image, Offset), (Def/Blink-inhibition-task, Offset), (Def/Fixation-task, Offset)",
-      "show_cross": "Sensory-event, (Intended-effect, Cue), (Def/Cross-only, Onset), (Def/Fixation-task, Onset),  (Def/Circle-only, Offset), sc:Quality-of-hyperventilation",
+      "show_cross": "Sensory-event, (Intended-effect, Cue), (Def/Cross-only, Onset), (Def/Fixation-task, Onset),  (Def/Circle-only, Offset), sc:Hyperventilation-refused-procedure/Could not comply",
       "left_press": "Agent-action, Participant-response, Def/Press-left-finger",
       "right_press": "Agent-action, Participant-response, Def/Press-right-finger",
       "setup_left_sym": "Experiment-structure, (Def/Left-sym-cond, Onset), (Def/Initialize-recording, Onset)",

docs/requirements.txt

@@ -1,31 +1,3 @@
-attrs>=21.4.0
-click>=8.1.3
-coverage>=6.3.2
-defusedxml>=0.7.1
-et-xmlfile>=1.1.0
-Flask>=2.1.2
-Flask-WTF>=1.0.1
-hedtools >= 0.1.0
-inflect>=5.5.2
-itsdangerous>=2.1.2
-jdcal>=1.4.1
-Jinja2>=3.0.0
-jupyter>=1.0.0
-MarkupSafe>=2.1.1
-myst-parser>=0.18.1
-numpy>=1.20.3
-numpydoc>=1.3.1
-openpyxl>=3.0.9
-pandas>=1.3.5
-portalocker>=2.4.0
-Pygments>=2.12.0
-python-dateutil==2.8.2
-pytz>=2022.1
-semantic_version>=2.9.0
-six>=1.16.0
 Sphinx>=5.2.2
-SphinxExtensions>=0.2.0
+myst-parser>=0.18.1
 sphinx_rtd_theme>=1.0.0
-Werkzeug>=2.1.2
-WTForms>=3.0.1
-xlrd>=2.0.1

docs/source/DocumentationSummary.md

@@ -36,21 +36,21 @@ and tagging hints.
 * - Expandable HTML	
   - [https://www.hedtags.org/display_hed.html](https://www.hedtags.org/display_hed.html)
 * - Expandable prerelease HTML	
-  - [https://www.hedtags.org/display_hed_prelease.html](https://www.hedtags.org/display_hed_prelease.html)
+  - [https://www.hedtags.org/display_hed_prerelease.html](https://www.hedtags.org/display_hed_prerelease.html)
 * - Mediawiki	
-  - [https://github.com/hed-standard/hed-specification/blob/master/hedwiki/HED8.0.0.mediawiki](https://github.com/hed-standard/hed-specification/blob/master/hedwiki/HED8.0.0.mediawiki)
+  - [https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedwiki/HED8.1.0.mediawiki](https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedwiki/HED8.1.0.mediawiki)
 * - XML	
-  - [https://github.com/hed-standard/hed-specification/blob/master/hedxml/HED8.0.0.xml](https://github.com/hed-standard/hed-specification/blob/master/hedxml/HED8.0.0.xml)
+  - [https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedxml/HED8.1.0.xml](https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedxml/HED8.1.0.xml)
 * - **Score library schemas**
   - 
 * - Expandable HTML
   - [https://www.hedtags.org/display_hed_score.html](https://www.hedtags.org/display_hed_score.html)
-* - Expandable prelease HTML
+* - Expandable prerelease HTML
   - [https://www.hedtags.org/display_hed_score_prerelease.html](https://www.hedtags.org/display_hed_score_prerelease.html)
 * - Mediawiki	
-  - [https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/score/hedwiki/HED_score_0.0.1.mediawiki](https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/score/hedwiki/HED_score_0.0.1.mediawiki)
+  - [https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki)
 * - XML	
-  - [https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/score/hedxml/HED_score_0.0.1.xml](https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/score/hedxml/HED_score_0.0.1.xml)
+  - [https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_1.0.0.xml](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_1.0.0.xml)
 `````  
 
 ## 3. HED Websites

docs/source/FileRemodelingQuickstart.md

@@ -119,7 +119,7 @@ stored in the `derivatives/remodel/backups` subdirectory of the dataset.
 Restructuring applies a sequence of remodeling operations given in a JSON remodeling
 file to produce a final result.
 By convention, we name these remodeling instruction files `_rmdl.json` 
-and try to store them in the `derivatives/remodel/models` directory relative
+and try to store them in the `derivatives/remodel/remodeling_files` directory relative
 to the dataset root directory.
 
 The restructuring always proceeds by looking up each data file in the backup
@@ -349,7 +349,7 @@ The remodeling tools expect the full path for the JSON remodeling operation file
 when the remodeling is executed.
 However, it is a good practice to include all remodeling files used with the dataset.
 The JSON remodeling operation files are usually located in the
-`derivatives/remodel/models` subdirectory below the dataset root,
+`derivatives/remodel/remodeling_files` subdirectory below the dataset root,
 and have file names ending in `_rmdl.json`.
 
 The backups are always in the `derivatives/remodel/backups` subdirectory under the dataset root.
@@ -415,7 +415,7 @@ An example command line call for `run_remodel` is shown in the following example
 :class: tip
 
 ```bash
-python run_remodel.py /data/ds002790  /data/ds002790/derivatives/remodel/models/AOMIC_summarize_rmdl.json \
+python run_remodel.py /data/ds002790  /data/ds002790/derivatives/remodel/remodeling_files/AOMIC_summarize_rmdl.json \
 -s .txt -x derivatives -b 
 
 ```
@@ -473,7 +473,7 @@ The exact paths will look different on your computer but the full command-line c
 :class: tip
 
 ```bash
-python run_remodel.py /data/ds002790  /data/ds002790/derivatives/remodel/models/AOMIC_summarize_rmdl.json \
+python run_remodel.py /data/ds002790  /data/ds002790/derivatives/remodel/remodeling_files/AOMIC_summarize_rmdl.json \
 -s .txt -x derivatives -b 
 
 ```

docs/source/FileRemodelingTools.md

@@ -116,7 +116,7 @@ Within its context information, most summarization operations keep a separate
 summary for each individual file and have methods to create an overall summary
 of the information for all the files that have been processed by the summarization..
 
-Summarization results are available in JSON (`.json`) and text (`.txt) formats.
+Summarization results are available in JSON (`.json`) and text (`.txt`) formats.
 
 (available-operations-anchor)=
 ### Available operations
@@ -228,7 +228,7 @@ Example notebooks can be found in the
 ### Calling remodel tools
 
 The remodeling tools provide three Python programs for backup (`run_remodel_backup`),
-remodeling (`run_remodel`) and restoring (`run_remodel_restor`) event files.
+remodeling (`run_remodel`) and restoring (`run_remodel_restore`) event files.
 These programs can be called from the command line or from another Python program.
 
 The programs use a standard command-line argument list for specifying input as summarized in the following table.
@@ -238,7 +238,7 @@ The programs use a standard command-line argument list for specifying input as s
 | Script name | Arguments | Purpose | 
 | ----------- | -------- | ------- |
 |*run_remodel_backup* | *data_dir*<br/>*-e -\\-extensions*<br/>*-f -\\-file-suffix*<br/>*-n -\\-backup-name*<br/>*-t -\\-task-names*<br/>*-v -\\-verbose*<br/>*-x -\\-exclude-dirs*| Create a backup event files. |
-|*run_remodel* | *data_dir*<br/>*model_path*<br/>*-b -\\-bids-format*<br/>*-e -\\-extensions*<br/>*-f -\\-file-suffix*<br/>*-i -\\-include-individual*<br/>*-n -\\-backup-name*<br/>*-j -\\-json-sidecar*<br/>*-r -\\-hed-version*<br/>*-s -\\-save-formats*<br/>*-t -\\-task-names*<br/>*-v -\\-verbose*<br/>*-x -\\-exclude-dirs* | Restructure or summarize the event files.<br/> <br/>If the backup name (*-n*) argument is omitted,<br>the backup called *default_back* is used.<br/>If you want to skip the backup, use *''*. |
+|*run_remodel* | *data_dir*<br/>*model_path*<br/>*-b -\\-bids-format*<br/>*-e -\\-extensions*<br/>*-f -\\-file-suffix*<br/>*-i -\\-individual-summaries*<br/>*-n -\\-backup-name*<br/>*-j -\\-json-sidecar*<br/>*-r -\\-hed-version*<br/>*-s -\\-save-formats*<br/>*-t -\\-task-names*<br/>*-v -\\-verbose*<br/>*-x -\\-exclude-dirs* | Restructure or summarize the event files.<br/> <br/>If the backup name (*-n*) argument is omitted,<br>the backup called *default_back* is used.<br/>If you want to skip the backup, use *''*. |
 |*run_remodel_restore* | *data_dir*<br/>*-n -\\-backup-name*<br/>*-t -\\-task-names**-v -\\-verbose* | Restore a backup of event files. |
 
 ````
@@ -289,9 +289,11 @@ Users are free to use either form.
 > The filename without the extension must end in one of the specified suffixes in order to be
 > backed up or transformed.
 
-`-i`, `--include-individual`
-> If this flag is present, summary information for individual files as well as an overall dataset summary
-> is reported for all summarization operations.
+`-i`, `--individual-summaries`
+> This option offers a choice among three options:
+>    - `separate`: Individual summaries for each file in separate files in addition the overall summary.
+>    - `consolidated`: Individual summaries written in the same file as the overall summary.
+>    - `none`: Only an overall summary.
 
 `-j`, `--json-sidecar`
 > This option is followed by the full path of the JSON sidecar with HED annotations to be
@@ -457,7 +459,7 @@ python run_remodel.py /datasets/eeg_ds003654s_hed_remodel /datasets/remove_extra
 
 The script has two required arguments the dataset root and the path to the JSON remodel file.
 Usually, the JSON remodel files are stored with the dataset itself in the 
-`derivatives/remodel/models` subdirectory, but common scripts can be stored in a central place elsewhere.
+`derivatives/remodel/remodeling_files` subdirectory, but common scripts can be stored in a central place elsewhere.
 
 The additional keyword option, `-x` in the example indicates that directory paths containing the component `derivatives` or the component `stimuli` should be excluded.
 Excluded directories need not have their excluded path component at the top level of the dataset.
@@ -582,7 +584,7 @@ using the `-r` option.
 The `-r` option supports a list of HED versions if multiple HED schemas are used.
 For example: `-r 8.1.0 sc:score_1.0.0` specifies that vocabulary will be drawn
 from standard HED Version [**8.1.0**](https://www.hedtags.org/display_hed.html) and from
-HED SCORE library version [**0.0.1**](https://www.hedtags.org/display_hed_score.html).
+HED SCORE library version [**1.0.0**](https://www.hedtags.org/display_hed_score.html).
 Annotations containing tags from SCORE should be prefixed with `sc:`.
 
 Usually, annotators will consolidate HED annotations in a single JSON sidecar file

docs/source/HedSchemaDevelopmentGuide.md

@@ -215,8 +215,8 @@ As changes are accepted, they are incorporated into the
 **prerelease CHANGES.md**. 
 These files are located in the **prerelease** subdirectory for the respective schema.
 Examples of these files for the standard schema can be found in the standard schema
-[**prelease directory**](https://github.com/hed-standard/hed-schemas/tree/main/standard_schema/prerelease).
-[**Expandable html view of the prerelease HED schema**](https://www.hedtags.org/display_hed_prelease.html) 
+[**prerelease directory**](https://github.com/hed-standard/hed-schemas/tree/main/standard_schema/prerelease).
+[**Expandable html view of the prerelease HED schema**](https://www.hedtags.org/display_hed_prerelease.html) 
 
 Upon final review, the new HED schema is released, the XML file is copied to the
 [**hedxml directory**](https://github.com/hed-standard/hed-schemas/tree/main/standard_schema/hedxml),

docs/source/HedSchemaViewers.md

@@ -22,7 +22,7 @@ if they come from the standard schema.
 
 | Viewer | Link | Use |
 | ------ | ---- | --- |
-|Expandable<br/>HTML | [**Latest**](http://www.hedtags.org/display_hed.html) or<br/> [**Prerelease**](https://www.hedtags.org/display_hed_prelease.html) | Look up or search for tags.<br/>View during vocabulary development. |
+|Expandable<br/>HTML | [**Latest**](http://www.hedtags.org/display_hed.html) or<br/> [**Prerelease**](https://www.hedtags.org/display_hed_prerelease.html) | Look up or search for tags.<br/>View during vocabulary development. |
 | XML | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/standard_schema/hedxml/HED8.1.0.xml) or</br>[**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedxml/HED8.1.0.xml) | Accessed by tools for validation and analysis. |
 | Mediawiki | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/standard_schema/hedwiki/HED8.1.0.mediawiki) or<br/> [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/standard_schema/hedwiki/HED8.1.0.mediawiki) |  Edit to create a new schema. |
 
@@ -32,5 +32,5 @@ if they come from the standard schema.
 | Viewer | Link | Use |
 | ------ | ---- |  --- |
 |Expandable<br/>HTML | [**Latest**](https://www.hedtags.org/display_hed_score.html) or<br/> [**Prerelease**](https://www.hedtags.org/display_hed_score_prerelease.html) | Look up or search for tags.<br/>View during vocabulary development. |
-| XML | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedxml/HED_score_0.0.1.xml) or<br/>[**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_0.0.1.xml) | Accessed by tools for validation and analysis. |
-| Mediawiki | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedwiki/HED_score_0.0.1.mediawiki) or<br/> [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_0.0.1.mediawiki) |  Edit to create a new schema.  |
+| XML | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedxml/HED_score_1.0.0.xml) or<br/>[**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedxml/HED_score_1.0.0.xml) | Accessed by tools for validation and analysis. |
+| Mediawiki | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki) or<br/> [**Formatted**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/hedwiki/HED_score_1.0.0.mediawiki) |  Edit to create a new schema.  |

docs/source/HedTestDatasets.md

@@ -49,7 +49,7 @@ This is eeg_ds003654s_hed_inheritance
 
 This dataset is designed to test the HED library schema facility.
 It uses HED 8.0.0 as a base schema and as the "test" library schema.
-In addition, this dataset uses the SCORE library version 0.0.1 as a library schema.
+In addition, this dataset uses the SCORE library version 1.0.0 as a library schema.
 
 The schema used are specified in the `dataset_description.json` file using the 
 proposed format.

docs/source/WhatsNew.md

@@ -1,21 +1,29 @@
 (whats-new-anchor)=
 # What's new?
 
+**January 28, 2023**: **HED SCORE Library v1.0.0 released**<br/>
+
+> The HED score library schema v1.0.0 has been officially released.
+> This library is based on the Standardized Computer-based Organized Reporting of EEG
+> ([**SCORE**](https://pubmed.ncbi.nlm.nih.gov/28838815/)) standard and adapted for
+> annotation using the HED infrastructure and requirements. 
+> For more information see the [**SCORE schema library**](https://hed-schemas.readthedocs.io/en/latest/hed_score_library.html) guide.
+
 **January 20, 2023**: **New preprint available**<br/>
 
 > **Actionable event annotation and analysis in fMRI** [**preprint**](https://osf.io/h7puk)<br/>
-> *Monique Denissen*, *Fabio Richlan*, *Jürgen Birkibauer*, *Mateusz Pawlik*, *Anna Ravenschlag*, *Nicole Himmelstoß*, *Florian Hutzler*, *Kay Robbins*</br>
-> Supporting materials and data are available at [** https://osf.io/93km8/**]( https://osf.io/93km8/)
-> to appear in the book *Methods for analyzing large neuroimaging datasets*
-edited by Robert Whelan and Herve Lemaitre
+> *Monique Denissen*, *Fabio Richlan*, *Jürgen Birkibauer*, *Mateusz Pawlik*, *Anna Ravenschlag*, *Nicole Himmelstoß*, *Florian Hutzler*, *Kay Robbins*<br/>
+> Supporting materials and data are available at [**https://osf.io/93km8/**](https://osf.io/93km8/).<br/>
+> Chapter to appear in the book *Methods for analyzing large neuroimaging datasets*
+edited by Robert Whelan and Herve Lemaitre.
 
 **January 4, 2023**: **New preprint available**<br/>
 
 > **End-to-end processing of M/EEG data with BIDS, HED, and EEGLAB** [**preprint**](https://osf.io/h7puk)<br/>
 > *Dung Truong*, *Kay Robbins*, *Arnaud Delorme*, and *Scott Makeig*</br>
-> Supporting materials and data are available at [**https://osf.io/8brgv/**](https://osf.io/8brgv/)
-> to appear in the book *Methods for analyzing large neuroimaging datasets*
-edited by Robert Whelan and Herve Lemaitre
+> Supporting materials and data are available at [**https://osf.io/8brgv/**](https://osf.io/8brgv/).<br/>
+> Chapter to appear in the book *Methods for analyzing large neuroimaging datasets*
+edited by Robert Whelan and Herve Lemaitre.
 
 **January 3, 2023**: **Project page live**<br/>
 

hedcode/jupyter_notebooks/bids/README.md

@@ -31,6 +31,3 @@ To install directly from the
 
 HEDTools require python 3.7 or greater.
 
-A related GitHub repository
-[**hed-curation**](https://github.com/hed-standard/hed-curation)
-is holds code related to curation.

hedcode/jupyter_notebooks/bids/bids_validate_dataset_with_libraries.ipynb

@@ -84,9 +84,9 @@
     "## Now validate using prerelease schema\n",
     "print(\"\\nNow validating with the prerelease schema.\")\n",
     "base_version = '8.0.0'\n",
-    "library1_url = \"https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/\" + \\\n",
-    "               \"library_schemas/score/hedxml/HED_score_0.0.1.xml\"\n",
-    "library2_url = \"https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/\" + \\\n",
+    "library1_url = \"https://raw.githubusercontent.com/hed-standard/hed-schemas/main/\" + \\\n",
+    "               \"library_schemas/score/hedxml/HED_score_1.0.0.xml\"\n",
+    "library2_url = \"https://raw.githubusercontent.com/hed-standard/hed-schemas/main/\" + \\\n",
     "               \"library_schemas/testlib/hedxml/HED_testlib_1.0.2.xml\"\n",
     "schema_list = [load_schema_version(xml_version=base_version),\n",
     "               load_schema(library1_url, schema_prefix=\"sc\"),\n",

hedcode/matlab_scripts/web_services/testLibraryServices.m

@@ -18,7 +18,7 @@
                   'events_string', data.eventsText, ...
                   'check_for_warnings', 'off');
 request1.schema_version = ...
-    {'8.0.0', 'sc:score_0.0.1', 'test:testlib_1.0.2'};
+    {'8.0.0', 'sc:score_1.0.0', 'test:testlib_1.0.2'};
 response1 = webwrite(servicesUrl, request1, options);
 response1 = jsondecode(response1);
 outputReport(response1, 'Example 1 validating a valid event file.');
@@ -34,7 +34,7 @@
                   'events_string', data.eventsText, ...
                   'check_for_warnings', 'off');
 request2.schema_version = ...
-    {'8.0.0', 'sc:score_0.0.1', 'test:testlib_1.0.2'};
+    {'8.0.0', 'sc:score_1.0.0', 'test:testlib_1.0.2'};
 response2 = webwrite(servicesUrl, request2, options);
 response2 = jsondecode(response2);
 outputReport(response2, 'Example 2 validating a valid event file with libraries.');