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| @@ -1,83 +1,96 @@ | ||
| [](https://www.hed-matlab.org/en/latest/?badge=latest) | ||
| [](https://doi.org/10.5281/zenodo.13201056) | ||
|
|
||
| # HED-MATLAB | ||
| This repository contains the MATLAB supporting code infrastructure | ||
| for Hierarchical Event Descriptors (HED). | ||
| HED is an ecosystem that includes standardized vocabularies and | ||
| tools for annotating what happened during an experiment. | ||
| HED is used for human behaviorial and neuroimaging experiments. | ||
| See the [**HED Homepage**](https://www.hedtags.org) for more information. | ||
|
|
||
| The documentation for `hed-matlab` can be found at | ||
| [**HED MATLAB Tools**](https://www.hed-resources.org/en/latest/HedMatlabTools.html). | ||
|
|
||
| ## Two ways of using HED | ||
|
|
||
| The `hed-matlab` MATLAB library provides two approaches for | ||
| using the HED toolbase: 1) through webservices and 2) through | ||
| MATLAB calls to the HED Python tools. | ||
| These approaches provide identical interfaces and are accessed | ||
| through MATLAB using the same method calls. | ||
|
|
||
| ### Approach 1: HED web services | ||
|
|
||
| In this approach, the HEDTools are accessed through MATLAB | ||
| wrapper functions that package the function parameters, | ||
| call the HED web services, retrieve the result, and transform | ||
| back to suitable MATLAB values. | ||
|
|
||
| **Advantages:** No extra installation. | ||
|
|
||
| **Disadvantages:** Requires access to Internet. | ||
|
|
||
| ### Approach 2: HEDTools Python calls | ||
|
|
||
| In this approach, the HEDTools are accessed through MATLAB | ||
| wrapper functions that package function parameters and | ||
| call the Python `HedTools` directly from MATLAB lab. | ||
|
|
||
| **Advantages:** No Internet access needed. Some additional | ||
| functionality not in the `hed-matlab` interface is provided. | ||
|
|
||
| **Disadvantages:** Installation of Python in MATLAB can be | ||
| tricky and requires MATLAB version >= 2022b. | ||
|
|
||
|
|
||
| ## Basic installation | ||
|
|
||
| To use the HED tools for MATLAB you need to download the tools | ||
| either by downloading from GitHub or from MATHWorks File Exchange. | ||
|
|
||
| Go to the directory that you want to download the library into. | ||
| If you are using Git, clone the | ||
| [**hed-matlab**](https://github.com/hed-standard/hed-matlab) repository. | ||
|
|
||
| ```shell | ||
| git clone https://github.com/hed-standard/hed-matlab.git | ||
| ``` | ||
|
|
||
| You can also download the latest release as a zip file | ||
| from the [**hed-matlab releases**](https://github.com/hed-standard/hed-matlab/releases) | ||
| tab on GitHub. | ||
|
|
||
|
|
||
| Once you have download and unzipped if necessary, you have | ||
| to add the path of the `hedmat` subdirectory of `hed-matlab` to your workspace: | ||
|
|
||
| ```matlab | ||
| > myPath = 'xxx'; # This should be the full path to hedmat | ||
| > addpath(addpath(genpath(myPath)); | ||
| ``` | ||
|
|
||
| ### Additional steps for Python | ||
|
|
||
| The Python approach requires you to install Python, install the | ||
| Python HedTools, and link to MATLAB. | ||
| See [**Matlab Python Install**](https://www.hed-resources.org/en/latest/HedMatlabTools.html#matlab-python-install) | ||
| for detailed instructions. | ||
|
|
||
| ## Funding | ||
|
|
||
| Partial support for this project was provided by | ||
| [**NIH 1R01MH126700-01A1**](https://reporter.nih.gov/project-details/10480619). | ||
| [](https://www.hed-matlab.org/en/latest/?badge=latest) | ||
| [](https://doi.org/10.5281/zenodo.13201056) | ||
|
|
||
| # HED-MATLAB | ||
| This repository contains the MATLAB supporting code infrastructure | ||
| for Hierarchical Event Descriptors (HED). | ||
| HED is an ecosystem that includes standardized vocabularies and | ||
| tools for annotating what happened during an experiment. | ||
| HED is used for human behaviorial and neuroimaging experiments. | ||
| See the [**HED Homepage**](https://www.hedtags.org) for more information. | ||
|
|
||
| The documentation for `hed-matlab` can be found at | ||
| [**HED MATLAB Tools**](https://www.hed-resources.org/en/latest/HedMatlabTools.html). | ||
|
|
||
| ## Two ways of using HED | ||
|
|
||
| The `hed-matlab` MATLAB library provides two approaches for | ||
| using the HED toolbase: 1) through webservices and 2) through | ||
| MATLAB calls to the HED Python tools. | ||
| These approaches provide identical interfaces and are accessed | ||
| through MATLAB using the same method calls. | ||
|
|
||
| ### Approach 1: HED web services | ||
|
|
||
| In this approach, the HEDTools are accessed through MATLAB | ||
| wrapper functions that package the function parameters, | ||
| call the HED web services, retrieve the result, and transform | ||
| back to suitable MATLAB values. | ||
|
|
||
| **Advantages:** No extra installation. | ||
|
|
||
| **Disadvantages:** Requires access to Internet. | ||
|
|
||
| ### Approach 2: HEDTools Python calls | ||
|
|
||
| In this approach, the HEDTools are accessed through MATLAB | ||
| wrapper functions that package function parameters and | ||
| call the Python `HedTools` directly from MATLAB lab. | ||
|
|
||
| **Advantages:** No Internet access needed. Some additional | ||
| functionality not in the `hed-matlab` interface is provided. | ||
|
|
||
| **Disadvantages:** Installation of Python in MATLAB can be | ||
| tricky and requires MATLAB version >= 2022b. | ||
|
|
||
| ## Usage | ||
|
|
||
| To use HED tools, you first create a HED object by calling `getHedTools`. | ||
| If you provide the optional host argument, the HED tools use services, otherwise | ||
| direct calls to Python. Once created, you simply call the available methods | ||
| using that reference. The process is summarized in the following diagram. | ||
|
|
||
|
|
||
|  | ||
|
|
||
| The MATLAB HedTools accept a variety of different types of MATLAB variables | ||
| as input and convert as appropriate for the underlying calls. | ||
| On return, the tools convert back to MATLAB types. | ||
|
|
||
| ## Basic installation | ||
|
|
||
| To use the HED tools for MATLAB you need to download the tools | ||
| either by downloading from GitHub or from MATHWorks File Exchange. | ||
|
|
||
| Go to the directory that you want to download the library into. | ||
| If you are using Git, clone the | ||
| [**hed-matlab**](https://github.com/hed-standard/hed-matlab) repository. | ||
|
|
||
| ```shell | ||
| git clone https://github.com/hed-standard/hed-matlab.git | ||
| ``` | ||
|
|
||
| You can also download the latest release as a zip file | ||
| from the [**hed-matlab releases**](https://github.com/hed-standard/hed-matlab/releases) | ||
| tab on GitHub. | ||
|
|
||
|
|
||
| Once you have download and unzipped if necessary, you have | ||
| to add the path of the `hedmat` subdirectory of `hed-matlab` to your workspace: | ||
|
|
||
| ```matlab | ||
| > myPath = 'xxx'; # This should be the full path to hedmat | ||
| > addpath(addpath(genpath(myPath)); | ||
| ``` | ||
|
|
||
| ### Additional steps for Python | ||
|
|
||
| The Python approach requires you to install Python, install the | ||
| Python HedTools, and link to MATLAB. | ||
| See [**Matlab Python Install**](https://www.hed-resources.org/en/latest/HedMatlabTools.html#matlab-python-install) | ||
| for detailed instructions. | ||
|
|
||
| ## Funding | ||
|
|
||
| Partial support for this project was provided by | ||
| [**NIH 1R01MH126700-01A1**](https://reporter.nih.gov/project-details/10480619). |