From 5cb08f117f94d7f506dbeb80d65b9282ecfe9e30 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Mon, 23 Jan 2023 08:14:28 -0600 Subject: [PATCH 1/6] Corrected the what's new --- docs/source/WhatsNew.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/source/WhatsNew.md b/docs/source/WhatsNew.md index 5debecc..e208a0e 100644 --- a/docs/source/WhatsNew.md +++ b/docs/source/WhatsNew.md @@ -4,18 +4,18 @@ **January 20, 2023**: **New preprint available**
> **Actionable event annotation and analysis in fMRI** [**preprint**](https://osf.io/h7puk)
-> *Monique Denissen*, *Fabio Richlan*, *Jürgen Birkibauer*, *Mateusz Pawlik*, *Anna Ravenschlag*, *Nicole Himmelstoß*, *Florian Hutzler*, *Kay Robbins*
-> 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*
+> Supporting materials and data are available at [** https://osf.io/93km8/**](https://osf.io/93km8/).
+> 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**
> **End-to-end processing of M/EEG data with BIDS, HED, and EEGLAB** [**preprint**](https://osf.io/h7puk)
> *Dung Truong*, *Kay Robbins*, *Arnaud Delorme*, and *Scott Makeig*
-> 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/).
+> 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**
From e0d8c4df78da2f3e97c502620edf250d56e6701f Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Mon, 23 Jan 2023 08:27:56 -0600 Subject: [PATCH 2/6] Fixed additional typos in whats new --- docs/source/WhatsNew.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/WhatsNew.md b/docs/source/WhatsNew.md index e208a0e..829a139 100644 --- a/docs/source/WhatsNew.md +++ b/docs/source/WhatsNew.md @@ -5,7 +5,7 @@ > **Actionable event annotation and analysis in fMRI** [**preprint**](https://osf.io/h7puk)
> *Monique Denissen*, *Fabio Richlan*, *Jürgen Birkibauer*, *Mateusz Pawlik*, *Anna Ravenschlag*, *Nicole Himmelstoß*, *Florian Hutzler*, *Kay Robbins*
-> Supporting materials and data are available at [** https://osf.io/93km8/**](https://osf.io/93km8/).
+> Supporting materials and data are available at [**https://osf.io/93km8/**](https://osf.io/93km8/).
> Chapter to appear in the book *Methods for analyzing large neuroimaging datasets* edited by Robert Whelan and Herve Lemaitre. From f8e7fde44b43498cc2ca996159a7c911ce5e8f7d Mon Sep 17 00:00:00 2001 From: IanCa Date: Fri, 27 Jan 2023 17:51:53 -0600 Subject: [PATCH 3/6] Remove extraneous requirements --- docs/requirements.txt | 30 +----------------------------- 1 file changed, 1 insertion(+), 29 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index c8a5b03..f6d0317 100644 --- a/docs/requirements.txt +++ b/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 From ccd89cc987880b5a4d3f60a0da157d7ab497a01e Mon Sep 17 00:00:00 2001 From: IanCa Date: Fri, 27 Jan 2023 17:58:46 -0600 Subject: [PATCH 4/6] delete base requirements file --- requirements.txt | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index a266f30..0000000 --- a/requirements.txt +++ /dev/null @@ -1,15 +0,0 @@ -coverage>=6.3.2 -defusedxml>=0.7.1 -inflect>=5.5.2 -jupyter>=1.0.0 -numpy>=1.21.5 -openpyxl>=3.0.9 -pandas>=1.3.5 -portalocker>=2.4.0 -semantic_version>=2.9.0 -Werkzeug>=2.1.2 -flake8>=4.0.1 -importlib-metadata>=3.8.0 -sphinx>=4.5.0 -SphinxExtensions>=0.2.0 -attrs>=21.4.0 From da81064080db8d64b73a6e6889c9dae3d801eed1 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Mon, 30 Jan 2023 10:11:27 -0600 Subject: [PATCH 5/6] Updated various links and versions --- .../dataset_description.json | 2 +- .../task-FacePerception_events.json | 2 +- docs/source/DocumentationSummary.md | 12 ++++++------ docs/source/FileRemodelingQuickstart.md | 8 ++++---- docs/source/FileRemodelingTools.md | 18 ++++++++++-------- docs/source/HedSchemaDevelopmentGuide.md | 4 ++-- docs/source/HedSchemaViewers.md | 6 +++--- docs/source/HedTestDatasets.md | 2 +- docs/source/WhatsNew.md | 8 ++++++++ hedcode/jupyter_notebooks/bids/README.md | 3 --- .../bids_validate_dataset_with_libraries.ipynb | 6 +++--- .../web_services/testLibraryServices.m | 4 ++-- .../run_bids_style_file_validate.py | 4 ++-- 13 files changed, 43 insertions(+), 36 deletions(-) diff --git a/datasets/eeg_ds003654s_hed_library/dataset_description.json b/datasets/eeg_ds003654s_hed_library/dataset_description.json index d6a763a..fbd1f5e 100644 --- a/datasets/eeg_ds003654s_hed_library/dataset_description.json +++ b/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", diff --git a/datasets/eeg_ds003654s_hed_library/task-FacePerception_events.json b/datasets/eeg_ds003654s_hed_library/task-FacePerception_events.json index 3a718d8..f542dc1 100644 --- a/datasets/eeg_ds003654s_hed_library/task-FacePerception_events.json +++ b/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)", diff --git a/docs/source/DocumentationSummary.md b/docs/source/DocumentationSummary.md index 83f03b7..53ce12c 100644 --- a/docs/source/DocumentationSummary.md +++ b/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 diff --git a/docs/source/FileRemodelingQuickstart.md b/docs/source/FileRemodelingQuickstart.md index ef3cdf0..1ebdac9 100644 --- a/docs/source/FileRemodelingQuickstart.md +++ b/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 ``` diff --git a/docs/source/FileRemodelingTools.md b/docs/source/FileRemodelingTools.md index b294e50..da49ce9 100644 --- a/docs/source/FileRemodelingTools.md +++ 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*
*-e -\\-extensions*
*-f -\\-file-suffix*
*-n -\\-backup-name*
*-t -\\-task-names*
*-v -\\-verbose*
*-x -\\-exclude-dirs*| Create a backup event files. | -|*run_remodel* | *data_dir*
*model_path*
*-b -\\-bids-format*
*-e -\\-extensions*
*-f -\\-file-suffix*
*-i -\\-include-individual*
*-n -\\-backup-name*
*-j -\\-json-sidecar*
*-r -\\-hed-version*
*-s -\\-save-formats*
*-t -\\-task-names*
*-v -\\-verbose*
*-x -\\-exclude-dirs* | Restructure or summarize the event files.

If the backup name (*-n*) argument is omitted,
the backup called *default_back* is used.
If you want to skip the backup, use *''*. | +|*run_remodel* | *data_dir*
*model_path*
*-b -\\-bids-format*
*-e -\\-extensions*
*-f -\\-file-suffix*
*-i -\\-individual-summaries*
*-n -\\-backup-name*
*-j -\\-json-sidecar*
*-r -\\-hed-version*
*-s -\\-save-formats*
*-t -\\-task-names*
*-v -\\-verbose*
*-x -\\-exclude-dirs* | Restructure or summarize the event files.

If the backup name (*-n*) argument is omitted,
the backup called *default_back* is used.
If you want to skip the backup, use *''*. | |*run_remodel_restore* | *data_dir*
*-n -\\-backup-name*
*-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 diff --git a/docs/source/HedSchemaDevelopmentGuide.md b/docs/source/HedSchemaDevelopmentGuide.md index b221a51..1f33bb1 100644 --- a/docs/source/HedSchemaDevelopmentGuide.md +++ b/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), diff --git a/docs/source/HedSchemaViewers.md b/docs/source/HedSchemaViewers.md index b8dd552..37370a0 100644 --- a/docs/source/HedSchemaViewers.md +++ b/docs/source/HedSchemaViewers.md @@ -22,7 +22,7 @@ if they come from the standard schema. | Viewer | Link | Use | | ------ | ---- | --- | -|Expandable
HTML | [**Latest**](http://www.hedtags.org/display_hed.html) or
[**Prerelease**](https://www.hedtags.org/display_hed_prelease.html) | Look up or search for tags.
View during vocabulary development. | +|Expandable
HTML | [**Latest**](http://www.hedtags.org/display_hed.html) or
[**Prerelease**](https://www.hedtags.org/display_hed_prerelease.html) | Look up or search for tags.
View during vocabulary development. | | XML | [**Raw**](https://raw.githubusercontent.com/hed-standard/hed-schemas/main/standard_schema/hedxml/HED8.1.0.xml) or
[**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
[**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
HTML | [**Latest**](https://www.hedtags.org/display_hed_score.html) or
[**Prerelease**](https://www.hedtags.org/display_hed_score_prerelease.html) | Look up or search for tags.
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
[**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
[**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
[**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
[**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. | diff --git a/docs/source/HedTestDatasets.md b/docs/source/HedTestDatasets.md index 974f031..b020a5e 100644 --- a/docs/source/HedTestDatasets.md +++ b/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. diff --git a/docs/source/WhatsNew.md b/docs/source/WhatsNew.md index 829a139..19e6bef 100644 --- a/docs/source/WhatsNew.md +++ b/docs/source/WhatsNew.md @@ -1,6 +1,14 @@ (whats-new-anchor)= # What's new? +**January 28, 2023**: **HED SCORE Library v1.0.0 released**
+ +The HED score library schema v1.0.0 has been officially released. +This library is based on the on 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**
> **Actionable event annotation and analysis in fMRI** [**preprint**](https://osf.io/h7puk)
diff --git a/hedcode/jupyter_notebooks/bids/README.md b/hedcode/jupyter_notebooks/bids/README.md index 6d250d0..82dfc46 100644 --- a/hedcode/jupyter_notebooks/bids/README.md +++ b/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. \ No newline at end of file diff --git a/hedcode/jupyter_notebooks/bids/bids_validate_dataset_with_libraries.ipynb b/hedcode/jupyter_notebooks/bids/bids_validate_dataset_with_libraries.ipynb index bbb118f..80a1449 100644 --- a/hedcode/jupyter_notebooks/bids/bids_validate_dataset_with_libraries.ipynb +++ b/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", diff --git a/hedcode/matlab_scripts/web_services/testLibraryServices.m b/hedcode/matlab_scripts/web_services/testLibraryServices.m index 219ae64..830e943 100644 --- a/hedcode/matlab_scripts/web_services/testLibraryServices.m +++ b/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.'); diff --git a/hedcode/python_scripts/needs_refactoring/run_bids_style_file_validate.py b/hedcode/python_scripts/needs_refactoring/run_bids_style_file_validate.py index 1a35001..4a17d5e 100644 --- a/hedcode/python_scripts/needs_refactoring/run_bids_style_file_validate.py +++ b/hedcode/python_scripts/needs_refactoring/run_bids_style_file_validate.py @@ -11,9 +11,9 @@ if __name__ == '__main__': hed_xml_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master/hedxml/HED8.0.0.xml' hed_library_url1 = \ - 'https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/hedxml/HED_score_0.0.1.xml' + 'https://raw.githubusercontent.com/hed-standard/hed-schemas/main/hedxml/HED_score_1.0.0.xml' hed_library_url2 = \ - 'https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/hedxml/HED_test_1.0.2.xml' + 'https://raw.githubusercontent.com/hed-standard/hed-schemas/main/hedxml/HED_test_1.0.2.xml' hed_schema = load_schema(hed_xml_url) hed_schema_lib1 = load_schema(hed_library_url1) hed_schema_lib1.set_library_prefix("sc") From dc60f8a600001a13f41945b7d73224acf27db741 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Tue, 31 Jan 2023 08:44:09 -0600 Subject: [PATCH 6/6] Updated what's new and other links --- docs/source/WhatsNew.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/WhatsNew.md b/docs/source/WhatsNew.md index 19e6bef..20dc5b0 100644 --- a/docs/source/WhatsNew.md +++ b/docs/source/WhatsNew.md @@ -3,11 +3,11 @@ **January 28, 2023**: **HED SCORE Library v1.0.0 released**
-The HED score library schema v1.0.0 has been officially released. -This library is based on the on 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. +> 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**