Merge pull request #390 from hed-standard/develop

Updated what's new and added info on HED NWB extension

Author: VisLab

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)=

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.
 
@@ -29,7 +29,7 @@ The HedTools package is available on PyPi and can be installed using:
  pip install hedtools
 ```
 Prerelease versions of HedTools are available on the `develop` branch of the
-[**hed-python**](https://github.com/hed-standard/hed-pythong) GitHub repository
+[**hed-python**](https://github.com/hed-standard/hed-python) GitHub repository
 and can be installed using:
 
 ```shell

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.

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 

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.

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.
 <p></p>
 
-- 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.
 <p></p>
 
-- 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*.