From 77a0f9e34602993f4769f4d5cf8ca8b3c6431814 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Mon, 24 Jun 2024 15:33:55 -0500 Subject: [PATCH] Corrected additional links --- .lycheeignore | 1 + docs/source/BidsAnnotationQuickstart.md | 3 ++- docs/source/HedMatlabTools.md | 28 +++++++++++-------------- docs/source/HedOnlineTools.md | 2 +- docs/source/HedPythonTools.md | 2 +- docs/source/HedSchemas.md | 2 +- docs/source/HowCanYouUseHed.md | 2 +- docs/source/index.rst | 3 ++- src/jupyter_notebooks/bids/README.md | 20 +++++++++--------- 9 files changed, 31 insertions(+), 32 deletions(-) diff --git a/.lycheeignore b/.lycheeignore index 0b18600..b889dde 100644 --- a/.lycheeignore +++ b/.lycheeignore @@ -1,5 +1,6 @@ https://www.sciencedirect.com/science/article/pii/S1053811921010387 https://www.sciencedirect.com/science/article/pii/S0010945221001106 +https://www.sciencedirect.com/science/article/pii/S1388245717309069 (_anchor|-anchor) diff --git a/docs/source/BidsAnnotationQuickstart.md b/docs/source/BidsAnnotationQuickstart.md index c1a5345..3303f7b 100644 --- a/docs/source/BidsAnnotationQuickstart.md +++ b/docs/source/BidsAnnotationQuickstart.md @@ -363,6 +363,7 @@ Once you have a JSON sidecar template, you should edit in your event annotations The following is an edited version of the JSON template from the previous step containing a minimal set of HED annotations. +(excerpted-json-file-with-tags-anchor)= `````{admonition} JSON sidecar with completed annotation. :class: tip ```json @@ -496,7 +497,7 @@ or in a tool such as Excel. You may save the edited spreadsheet in either `.tsv` or `.xslx` format. The following is the extracted spreadsheet corresponding to the -[**edited JSON sidecar above**](excerpted-json-file-with-tags). +[**edited JSON sidecar above**](excerpted-json-file-with-tags-anchor). ````{admonition} HED annotation table extracted from JSON sidecar template. | **column_name** | **column_value** | **description** | **HED** | diff --git a/docs/source/HedMatlabTools.md b/docs/source/HedMatlabTools.md index e7e2d69..da8f934 100644 --- a/docs/source/HedMatlabTools.md +++ b/docs/source/HedMatlabTools.md @@ -454,9 +454,8 @@ See [**MathWorks Python Compatibility Docs**](https://www.mathworks.com/support/ The greatest difficulty for users who are unfamiliar with Python is getting Python connected to MATLAB. -Once that is done, many of the standard `hedtools` functions have -[**MATLAB HED tool wrapper functions**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/hedtools_wrappers) -that take MATLAB variables as arguments and return either MATLAB variables or opaque objects that +Once that is done, many of the standard `hedtools` functions can be accessed through +method call that take MATLAB variables and return either MATLAB variables or opaque objects that can be passed to other MATLAB functions. Thus, once the setup is done, you don't have to learn any Python syntax to use the tools. @@ -669,7 +668,6 @@ Using HEDTOOLS version: {'date': '2022-06-20T14:40:24-0500', 'dirty': False, 'er ``` ```` - ### MATLAB functions for Python The following table lists the relevant MATLAB functions that are available. @@ -727,8 +725,6 @@ The remodeling file used in this example can be found at See [**File remodeling quickstart**](FileRemodelingQuickstart.md) and [**File remodeling tools**](FileRemodelingTools.md) for additional information. -The wrapper functions are available on GitHub in -the [**hedtools_wrappers**](https://github.com/hed-standard/hed-examples/tree/develop/src/matlab_scripts/hedtools_wrappers) directory. (web-service-matlab-demos-anchor)= ### Web service MATLAB demos @@ -745,16 +741,16 @@ directory of the [**hed-matlab**](https://github.com/hed-standard/hed-matlab) Gi The following MATLAB code demos are available to show how to access HED web services. -| Target | MATLAB source | Purpose | -| ------ |-----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------| -| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) | Harness for running all demos. | -| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m) | List available services. | -| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-examples/main/hedcode/matlab_scripts/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. | -| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m) | Search, assembly. | -| Schema | *in progress* | For schema library developers. | -| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m) | Validation, conversion, extraction, merging. | -| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m) | Validation, conversion. | -| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m) | Validation, conversion. | +| Target | MATLAB source | Purpose | +| ------ |----------------------------------------------------------------------------------------------------------------------------------------------------------|-----------| +| Overall | [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) | Harness for running all demos. | +| Overall | [**demoGetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoGetServices.m) | List available services. | +| Events | [**demoEventServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventServices.m) | Validation, conversion, sidecar generation. | +| Events | [**demoEventSearchServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoEventSearchServices.m) | Search, assembly. | +| Schema | *in progress* | For schema library developers. | +| Sidecars | [**demoSidecarServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSidecarServices.m) | Validation, conversion, extraction, merging. | +| Spreadsheets | [**demoSpreadsheetServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoSpreadsheetServices.m) | Validation, conversion. | +| Strings | [**demoStringServices.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/demoStringServices.m) | Validation, conversion. | The [**runAllDemos.m**](https://raw.githubusercontent.com/hed-standard/hed-matlab/main/hedmat/web_services_demos/runAllDemos.m) diff --git a/docs/source/HedOnlineTools.md b/docs/source/HedOnlineTools.md index 6ae89aa..4c70e5f 100644 --- a/docs/source/HedOnlineTools.md +++ b/docs/source/HedOnlineTools.md @@ -560,7 +560,7 @@ JSON sidecars, BIDS-style events files, and spreadsheets in `.tsv` or `.xlsx` fo Support is also included for assembling the annotations for a BIDS-style events file with a JSON sidecar and for generating a template of a JSON sidecar from a BIDS events file. -The [**web_services**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services) +The [**web_services_demos**](https://github.com/hed-standard/hed-matlab/tree/main/hedmat/web_services_demos) directory in the `hed-examples` GitHub repository provides MATLAB examples of how to call these services in MATLAB. diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index 4e557a8..02b3f57 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -43,7 +43,7 @@ and an online version of the tools. The [**Create a JSON template**](https://hed-examples.readthedocs.io/en/latest/BidsAnnotationQuickstart.html#create-a-json-template) tutorial provides a step-by-step tutorial for using the online tool that creates a template based on the information in a single `events.tsv` file. For most datasets, this is sufficient. -In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/hedcode/jupyter_notebooks/bids/extract_json_template.ipynb) +In contrast, the [**extract_json_template.ipynb**](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) Jupyter notebook bases the extracted template on the entire dataset. To use this notebook, substitute the specifics of your BIDS diff --git a/docs/source/HedSchemas.md b/docs/source/HedSchemas.md index 665b5fa..e0cc837 100644 --- a/docs/source/HedSchemas.md +++ b/docs/source/HedSchemas.md @@ -92,7 +92,7 @@ directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas) ### The SCORE library -The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069?via%3Dihub) standard for clinical annotation of EEG by neurologists. +The HED SCORE library is an implementation of the [**SCORE**](https://www.sciencedirect.com/science/article/pii/S1388245717309069) standard for clinical annotation of EEG by neurologists. For more information and the latest references see [**HED SCORE schema**](https://github.com/hed-standard/hed-schemas/blob/main/library_schemas/score/README.md). diff --git a/docs/source/HowCanYouUseHed.md b/docs/source/HowCanYouUseHed.md index 4f18b6e..f23e680 100644 --- a/docs/source/HowCanYouUseHed.md +++ b/docs/source/HowCanYouUseHed.md @@ -616,7 +616,7 @@ for more information on installation and use. The project source code is located in the [**CTagger**](https://github.com/hed-standard/ctagger) GitHub repository.

-[*MATLAB HedTools**](https://www.hed-resources.org/en/latest/MatlabHedTools.md) explains how the +[*HED MATLAB Tools**](https://www.hed-resources.org/en/latest/HedMatlab.md) explains how the users can use the HEDTools in MATLAB using one of three approaches: using MATLAB wrappers for the HED Python tools, using MATLAB wrappers for the HED web services, or by calling HED tools through EEGLAB. diff --git a/docs/source/index.rst b/docs/source/index.rst index 4f4d5d3..1359dd6 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -86,7 +86,8 @@ San Diego (UCSD) under funding by The Swartz Foundation and by U.S. National Ins Further **HED (Gen 2, 4.0.0 <= version < 8.0.0)** development led by Kay Robbins of the University of Texas San Antonio was -funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022. +funded by The Cognition and Neuroergonomics Collaborative Technology Alliance (CaN CTA) program +of U.S Army Research Laboratory (ARL) under Cooperative Agreement Number W911NF-10-2-0022. **HED (Gen 3, version >= 8.0.0)** is now maintained and further developed by the HED Working Group led by Kay Robbins and Scott Makeig with Dung Truong, Monique Denissen, diff --git a/src/jupyter_notebooks/bids/README.md b/src/jupyter_notebooks/bids/README.md index a6c07c7..54c5fd9 100644 --- a/src/jupyter_notebooks/bids/README.md +++ b/src/jupyter_notebooks/bids/README.md @@ -5,16 +5,16 @@ validating, summarizing, and analyzing your BIDS datasets. **Table 1:** Useful Jupyter notebooks for processing BIDS datasets. -| Notebooks | Purpose | -|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------| -| [`extract_json_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_sidecar.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. | -| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. | -| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/bids_merge_sidecarmerge_spreadsheet_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. | -| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. | -| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. | -| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. | -| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. | -| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. | +| Notebooks | Purpose | +|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------| +| [`extract_json_template`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. | +| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. | +| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheedt_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. | +| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. | +| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. | +| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. | +| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. | +| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. | These notebooks require HEDTools, which can be installed using `pip` or directly.