From 601f23f8a4376ababc5ffde35731f92871387178 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Fri, 26 Jul 2024 12:51:27 -0500 Subject: [PATCH] Fixed broken links because of omitted .md extension --- docs/source/HedMatlabTools.md | 4 ++-- docs/source/HedPythonTools.md | 2 +- docs/source/HedRemodelingQuickstart.md | 18 ++++++++-------- docs/source/HedRemodelingTools.md | 2 +- docs/source/HedValidationGuide.md | 6 +++--- docs/source/HowCanYouUseHed.md | 30 +++++++++++++------------- 6 files changed, 31 insertions(+), 31 deletions(-) diff --git a/docs/source/HedMatlabTools.md b/docs/source/HedMatlabTools.md index 4720b2b..ba4a1fa 100644 --- a/docs/source/HedMatlabTools.md +++ b/docs/source/HedMatlabTools.md @@ -722,8 +722,8 @@ For the remodeling operations, first and second operation must be the dataset ro directory and the remodeling file name, respectively. In this example, dataset `ds003645` has been downloaded from [**openNeuro**](https://openneuro.org) to the `G:\` drive. The remodeling file used in this example can be found at -See [**HED remodeling quickstart**](HedRemodelingQuickstart) -and [**HED remodeling tools**](HedRemodelingTools) for +See [**HED remodeling quickstart**](HedRemodelingQuickstart.md) +and [**HED remodeling tools**](HedRemodelingTools.md) for additional information. (web-service-matlab-demos-anchor)= diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index 5a60524..83b6d5b 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -2,7 +2,7 @@ The primary codebase for HED support is in Python. Source code for the HED Python tools is available in the -[**hed-python**](https://github.com/hed-standard/hed-pythong) GitHub repository +[**hed-python**](https://github.com/hed-standard/hed-python) GitHub repository See the [**HED tools API documentation**](https://hed-python.readthedocs.io/en/latest/) for detailed information about the HED Tools API. diff --git a/docs/source/HedRemodelingQuickstart.md b/docs/source/HedRemodelingQuickstart.md index 357212e..527c5e0 100644 --- a/docs/source/HedRemodelingQuickstart.md +++ b/docs/source/HedRemodelingQuickstart.md @@ -16,7 +16,7 @@ for example, during the conversion from the experimental control software format The tools can be run using a command-line script, called from a Jupyter notebook, or run using online tools. This quickstart covers the basic concepts of remodeling and develops some basic examples of how remodeling is used. See the -[**HED remodeling tools**](./HedRemodelingTools) +[**HED remodeling tools**](./HedRemodelingTools.md) guide for detailed descriptions of the available operations. * [**What is remodeling?**](what-is-remodeling-anchor) @@ -170,7 +170,7 @@ the *trial_type* column to *event_type*. ```` Each remodel operation has its own specific set of required parameters -that can be found under [**HED remodeling tools**](./HedRemodelingTools). +that can be found under [**HED remodeling tools**](./HedRemodelingTools.md). For *rename_columns*, the required operations are *column_mapping* and *ignore_missing*. Some operations also have optional parameters. @@ -295,8 +295,8 @@ Event markers such as the participant's response key-press are encoded implicitl as an offset from the stimulus presentation. while event encoding includes event markers for each individual event within the trial. -The [**Split rows**](./HedRemodelingTools#split-rows) -explanation under [**HED remodeling tools**](./HedRemodelingTools) +The [**Split rows**](./HedRemodelingTools.md#split-rows) +explanation under [**HED remodeling tools**](./HedRemodelingTools.md) shows the required parameters for the *split_rows* operation. The required parameters are *anchor_column*, *new_events*, and *remove_parent_row*. @@ -396,12 +396,12 @@ if you turn the *Include summaries* option on. (the-command-line-interface-anchor)= ### The command-line interface -After [**installing the remodeler**](./HedRemodelingTools#installing-the-remodel-tools), +After [**installing the remodeler**](./HedRemodelingTools.md#installing-the-remodel-tools), you can run the tools on a full BIDS dataset, or on any directory using the command-line interface using `run_remodel_backup`, `run_remodel`, and `run_remodel_restore`. A full overview of all arguments is available at -[**HED remodeling tools**](./HedRemodelingTools#remodel-command-line-arguments). +[**HED remodeling tools**](./HedRemodelingTools.md#remodel-command-line-arguments). The `run_remodel_backup` is usually run only once for a dataset. It makes the baseline backup of the event files to assure that nothing will be lost. @@ -432,9 +432,9 @@ The parameters are as follows: There are three types of command line arguments: -[**Positional arguments**](./HedRemodelingTools#positional-arguments), -[**Named arguments**](./HedRemodelingTools#named-arguments), -and [**Named arguments with values**](./HedRemodelingTools#named-arguments). +[**Positional arguments**](./HedRemodelingTools.md#positional-arguments), +[**Named arguments**](./HedRemodelingTools.md#named-arguments), +and [**Named arguments with values**](./HedRemodelingTools.md#named-arguments). The positional arguments, `data_dir` and `model_path` are not optional and must be the first and second arguments to `run_remodel`, respectively. diff --git a/docs/source/HedRemodelingTools.md b/docs/source/HedRemodelingTools.md index ce3decb..f3a8aab 100644 --- a/docs/source/HedRemodelingTools.md +++ b/docs/source/HedRemodelingTools.md @@ -14,7 +14,7 @@ the tabular files unchanged. The file remodeling tools can be applied to any tab-separated value (`.tsv`) file but are particularly useful for restructuring files representing experimental events. -Please read the [**HED remodeling quickstart**](./HedRemodelingQuickstart) +Please read the [**HED remodeling quickstart**](./HedRemodelingQuickstart.md) tutorials for an introduction and basic use of the tools. The file remodeling tools can be applied to individual files using the diff --git a/docs/source/HedValidationGuide.md b/docs/source/HedValidationGuide.md index 757d3f8..9fdc5a7 100644 --- a/docs/source/HedValidationGuide.md +++ b/docs/source/HedValidationGuide.md @@ -250,7 +250,7 @@ Errors, if any are printed to the command line. #### Remodeling validation summaries Validation is also available through HED remodeling tool interface. -As explained in [**HED remodeling quickstart**](./HedRemodelingQuickstart), +As explained in [**HED remodeling quickstart**](./HedRemodelingQuickstart.md), the HED remodeling tools allow users to restructure their event files and/or summarize their contents in various ways. Users specify a list of operations in a JSON remodeling file, @@ -318,7 +318,7 @@ For example, the text file is: `/root_path/derivatives/remodel/summaries/validate_initial_xxx.txt` where xxx is the time of generation. -For more information see [**HED remodeling quickstart**](./HedRemodelingQuickstart) +For more information see [**HED remodeling quickstart**](./HedRemodelingQuickstart.md) for an overview of the remodeling process and -[**HED remodeling tools**](./HedRemodelingTools) for detailed descriptions of +[**HED remodeling tools**](./HedRemodelingTools.md) for detailed descriptions of the operations that are currently supported. \ No newline at end of file diff --git a/docs/source/HowCanYouUseHed.md b/docs/source/HowCanYouUseHed.md index 46d9595..b55ea01 100644 --- a/docs/source/HowCanYouUseHed.md +++ b/docs/source/HowCanYouUseHed.md @@ -92,7 +92,7 @@ in post-processing and assure that the conditions are correctly marked. #### Logs to event files Although the HED tools do not yet directly support any particular experimental presentation/control -software packages, the HED [**HED remodeling tools**](./HedRemodelingTools) can +software packages, the HED [**HED remodeling tools**](./HedRemodelingTools.md) can be useful in working with logged data. Assuming that you can put the information from your experimental log into a tabular form such as: @@ -108,8 +108,8 @@ Assuming that you can put the information from your experimental log into a tabu ```` -The [**summarize column values**](./HedRemodelingTools#summarize-column-values) -operation in the HED [**file remodeling tools**](./HedRemodelingTools) +The [**summarize column values**](./HedRemodelingTools.md#summarize-column-values) +operation in the HED [**file remodeling tools**](./HedRemodelingTools.md) compiles detailed summaries of the contents of tabular files. Use the following remodeling file and your tabular log file as input to the HED online [**event remodeling**](https://hedtools.ucsd.edu/hed_dev/events) tools @@ -135,10 +135,10 @@ to quickly get an overview of its contents. ### Post-processing the event data The information that first comes off the experimental logs is usually not directly usable for -sharing and analysis. A number of HED [**HED remodeling tools**](./HedRemodelingTools) +sharing and analysis. A number of HED [**HED remodeling tools**](./HedRemodelingTools.md) might be helpful for restructuring your first pass at the event files. -The [**remap columns**](./HedRemodelingTools#remap-columns) transformation is +The [**remap columns**](./HedRemodelingTools.md#remap-columns) transformation is particularly useful during the initial processing of tabular log information as exemplified by the following example @@ -395,7 +395,7 @@ to improperly handle these situations, reducing the accuracy of analysis. At this time, your only option is to do manual checks or write custom code to detect these types of experiment-specific inconsistencies. However, work is underway to include some standard types of checks in the -HED [**HED remodeling tools**](./HedRemodelingTools) in future releases. +HED [**HED remodeling tools**](./HedRemodelingTools.md) in future releases. You may also want to reorganize the event files using the remodeling tools. See the [**Remap columns**](remap-columns-anchor) @@ -431,7 +431,7 @@ work and possibly contact with the data authors for correct use and interpretati You can get a preliminary sense about what is actually in the data by downloading a single event file (e.g., a BIDS `_events.tsv`) and its associated JSON sidecar (e.g., a BIDS `_events.json`) and creating HED remodeling tool summaries using the -[**HED online tools for debugging**](./HedRemodelingQuickstart#online-tools-for-debugging). +[**HED online tools for debugging**](./HedRemodelingQuickstart.md#online-tools-for-debugging). Summaries of particular use for analysts include: - The [**column value summary**](./HedSummaryGuide.md#column-value-summary) compiles a summary of @@ -449,11 +449,11 @@ or temporal layout of the experiment. While HED tag summary and the experimental design summaries require that the dataset have HED annotations, these summaries do not rely on the experiment-specific event-coding used in each experiment and can be used to compare information for different datasets. -The [**HED remodeling quickstart**](./HedRemodelingQuickstart) tutorial +The [**HED remodeling quickstart**](./HedRemodelingQuickstart.md) tutorial gives an overview of the remodeling tools and how to use them. -More detailed information can be found in [**HED remodeling tools**](./HedRemodelingTools). +More detailed information can be found in [**HED remodeling tools**](./HedRemodelingTools.md). -The [**Online tools for debugging**](./HedRemodelingQuickstart#online-tools-for-debugging) +The [**Online tools for debugging**](./HedRemodelingQuickstart.md#online-tools-for-debugging) shows how to use remodeling tools to obtain these summaries without writing any code. The [**HED conditions and design matrices**](HedConditionsAndDesignMatrices.md) guide explains how @@ -474,8 +474,8 @@ additional code, while generality allows comparison of criteria across different experiments. The factor generation as described in the next section relies on the HED -[**HED remodeling tools**](HedRemodelingTools). -See [**HED remodeling tools**](HedRemodelingTools). +[**HED remodeling tools**](HedRemodelingTools.md). +See [**HED remodeling tools**](HedRemodelingTools.md). (factor-vectors-and-selection-anchor)= #### Factor vectors and selection @@ -490,18 +490,18 @@ rows as the event file (each row corresponding to an event marker). Factor vectors contain 1's for rows in which a specified criterion is satisfied and 0's otherwise. -- The [**factor column operation**](./HedRemodelingTools#factor-column) +- The [**factor column operation**](./HedRemodelingTools.md#factor-column) creates factor vectors based on the unique values in specified columns. This factor operation does not require any HED information.

-- The [**factor HED tags**](./HedRemodelingTools#factor-hed-tags) +- The [**factor HED tags**](./HedRemodelingTools.md#factor-hed-tags) creates factor vectors based on a HED tag query. The [**HED search guide**](./HedSearchGuide.md) explains the HED query structure and available search options.

-- The [**factor HED type**](./HedRemodelingTools#factor-hed-type) +- The [**factor HED type**](./HedRemodelingTools.md#factor-hed-type) creates factors based on a HED tag representing structural information about the data such as *Condition-variable* (for experimental design and experimental conditions) or *Task*.