further improvement

docs/getting_started/folders_and_files/metadata/json.md

@@ -18,6 +18,8 @@ JSON files are text files that take the following structure:
 Note that they can be nested (curly brackets within curly brackets).
 Here are some common ways to read / write these files.
 
+- [Official documentation about JSON](https://www.json.org/json-en.html)
+
 ## Editing JSON file
 
 ### Online
@@ -57,24 +59,28 @@ to that of Python dictionaries (assuming you are only storing text / numbers in
 
 ### MATLAB / Octave
 
-There are many toolboxes in MATLAB or [Octave](https://octave.org/) (an open-source drop-in compatible with many Matlab scripts)
-for reading / writing JSON files.
+Since MATLAB R2016b
+and [Octave](https://octave.org/) >= 7.1 (an open-source drop-in compatible with many Matlab scripts),
+you can use the built-in functions
+[`jsonencode`](https://www.mathworks.com/help/matlab/ref/jsonencode.html)
+and [`jsondecode`](https://www.mathworks.com/help/matlab/ref/jsondecode.html)
+to help your read and write JSON files.
 
-<!-- TODO check is more recent Octave have JSON support. -->
-Since MATLAB R2016b, you can use the built-in functions `jsonencode` (to write) and `jsondecode` (to read) JSON files.
-They should be available in Octave 6.1.
+!!! note -- "bids-matlab and other libraries"
 
-The [JSONio library](https://github.com/gllmflndn/JSONio) will allow you to read
-and write JSON files with MATLAB and octave (see examples below to use `jsonwrite` and `jsonread`).
+    There are also several toolboxes in MATLAB or Octave
+    for reading / writing JSON files.
 
-SPM12 uses the JSONio library by calling `spm_jsonwrite` and `spm_jsonread` and
-it has [other interesting functions to help you with BIDS](https://en.wikibooks.org/wiki/SPM/BIDS).
+    [bids-matlab](https://github.com/bids-standard/bids-matlab) has functions
+    ([`bids.util.jsonencode`](https://bids-matlab.readthedocs.io/en/main/utility_functions.html#bids.util.jsonencode)
+    and [`bids.util.jsondecode`](https://bids-matlab.readthedocs.io/en/main/utility_functions.html#bids.util.jsonencode))
+    that act as wrappers and will use whatever implementation (MATLAB, Octave...) is available.
 
-!!! note -- "bids-matlab"
+    The [JSONio library](https://github.com/gllmflndn/JSONio) will allow you to read
+    and write JSON files with MATLAB and Octave with the `jsonread` and `jsonwrite` functions.
 
-    [bids-matlab](https://github.com/bids-standard/bids-matlab) has 2 functions
-    (`bids.util.jsonencode` and `bids.util.jsondecode`) that act as wrappers and
-    will use whatever implementation (SPM, JSONio, MATLAB) is available.
+    SPM12 uses the JSONio library by calling `spm_jsonwrite` and `spm_jsonread` and
+    it has [other interesting functions to help you with BIDS](https://en.wikibooks.org/wiki/SPM/BIDS).
 
 ### R
 
@@ -84,10 +90,6 @@ Remember to install and call a package before using it.
 
 <!-- There is a new package to help intract with BIDS datasets: [bidser](https://github.com/bbuchsbaum/bidser) -->
 
-```R
-install.packages('jsonlite')
-```
-
 ## Reading a `.json` file
 
 === "python"
@@ -103,7 +105,10 @@ install.packages('jsonlite')
     For MATLAB >= R2016b
 
     ```matlab
-    metadata = jsonencode('myfile.json')
+    % Read JSON data from a file
+    jsonStr = fileread('myfile.json');
+    % Convert JSON string to MATLAB variables
+    jsonData = jsondecode(jsonStr);
     ```
 
 === "octave"
@@ -116,10 +121,13 @@ install.packages('jsonlite')
 
 === "R"
 
+    The example below uses the [jsonlite](https://github.com/jeroen/jsonlite) library.
+
     ```R
-    install.packages('jsonlite')
+    # install jsonlite in case you did not already do it
+    # install.packages('jsonlite')
     library(jsonlite)
-    metadata = fromJSON('myfile.json', pretty=TRUE)
+    metadata = fromJSON('myfile.json')
     ```
 
 ## Writing a `.json` file
@@ -145,16 +153,21 @@ install.packages('jsonlite')
     The example below uses the [JSONio library](https://github.com/gllmflndn/JSONio).
 
     ```matlab
+    metadata = struct('field1', 'value1', 'field2', 3, 'field3', 'field3')
     jsonwrite('my_output_file.json', metadata)
     ```
 
 === "R"
 
+    The example below uses the [jsonlite](https://github.com/jeroen/jsonlite) library.
+
     ```R
-    install.packages('jsonlite')
+    # install jsonlite in case you did not already do it
+    # install.packages('jsonlite')
     library(jsonlite)
-    metadata = '{"field1": "value1", "field2": 3, "field3": "field3"}'
-    writeLines(metadata, file="my_output_file.json")
+    metadata <- list(field1 = "value1", field2 = 3, field3 = "field3")
+    metadata = toJSON(metadata, pretty=TRUE)
+    write(metadata, "my_output_file.json")
     ```
 
 ## Interoperability issues
@@ -191,7 +204,7 @@ json_content =
     key: 'value'
 ```
 
-There are however some strict rules for what makes a valid fieldname in MATLAB and octave.
+There are however some strict rules for what makes a valid fieldname in MATLAB and Octave.
 
 Fieldnames must:
 

docs/getting_started/folders_and_files/metadata/tsv.md

@@ -4,29 +4,47 @@ A Tab-Separate Values (TSV) file is a text file where tab characters (`\t`) sepa
 It is structured as a table, with each column representing a field of interest,
 and each row representing a single datapoint.
 
+## Python
+
+In Python, the easiest way to work with TSV files is to use the [Pandas library](https://pandas.pydata.org/).
+This provides a high-level structure to organize, manipulate, clean, and visualize tabular data.
+You can install `pandas` with the following command:
+
+```bash
+pip install pandas
+```
+
+## MATLAB / Octave
+
+Since MATLAB R2013b,
+there is a [`readtable`](https://www.mathworks.com/help/matlab/ref/readtable.html) function that can load TSV files,
+and a [`writetable`](https://www.mathworks.com/help/matlab/ref/writetable.html) function to write them.
+
+For Octave, the `writetable` function is not implemented in older version of Octave
+(e.g 4.2.2) and the `table` function differs from its MATLAB counterpart,
+so it may be easier to rely on [bids-matlab](https://github.com/bids-standard/bids-matlab) functions
+([`bids.util.tsvwrite`](https://bids-matlab.readthedocs.io/en/main/utility_functions.html#bids.util.tsvwrite) and
+[`bids.util.tsvread`](https://bids-matlab.readthedocs.io/en/main/utility_functions.html#bids.util.tsvread))
+to help you work with those files.
+
+## R
+
+Reading and writing tab separated files comes natively in R, no need for extra packages.
+
 ## Reading a `.tsv` file
 
 === "python"
 
-    In Python, the easiest way to work with TSV files is to use the Pandas library.
-    This provides a high-level structure to organize, manipulate, clean, and
-    visualize tabular data.
-    You can install `pandas` with the following command:
-
-    ```bash
-    pip install pandas
-    ```
+    In this example, we assume the .tsv includes column names (headers),
+    and explicitly set column separator (delimiter) to tab (`'\t'`).
 
     ```python
     import pandas as pd
-    data = pd.pd.read_csv("file.tsv", sep="\t", headers=True)
+    data = pd.read_csv("file.tsv", sep="\t", headers=True)
     ```
 
 === "MATLAB"
 
-    Since MATLAB R2013b, there is a [`readtable`](https://www.mathworks.com/help/matlab/ref/readtable.html) function
-    that can load TSV files.
-
     ```matlab
     table_content = readtable('file.tsv', ...
                               'FileType', 'text', ...
@@ -36,75 +54,84 @@ and each row representing a single datapoint.
 
 === "octave"
 
+    The example below uses the [bids-matlab](https://github.com/bids-standard/bids-matlab) library.
+
     ```matlab
+    table_content = bids.util.tsvread('file.tsv');
     ```
 
 === "R"
 
-    Reading and writing tab separated files comes natively in R, no need for extra packages.
-
     In this example, we assume the .tsv includes column names (headers),
     and explicitly set column separator (delimiter) to tab (`'\t'`)
 
     ```R
-    data = read.table('myFile.tsv', header=TRUE, sep='\t')
+    data = read.table('file.tsv', header=TRUE, sep='\t')
     ```
 
-=== "Excel / [LibreOffice Calc](https://www.libreoffice.org/)"
-
-## Writing a `.tsv` file
+=== "Excel / LibreOffice Calc"
 
-## Matlab
+    Excel, [LibreOffice Calc](https://www.libreoffice.org/) and similar software to work with tables
+    should have no problem opening TSV files.
 
-```matlab
-root_dir = pwd;
-bidsProject = 'temp';
-mkdir(fullfile(root_dir, bidsProject));
-bids_participants_name = 'participants.tsv';
+## Writing a `.tsv` file
 
-participant_id = ['sub-01'; 'sub-02'];
-age = [20 30]';
-sex = ['m';'f'];
+=== "python"
 
-t = table(participant_id,age,sex);
-writetable(t, fullfile(root_dir, bidsProject, bids_participants_name), ...
-              'FileType', 'text', ...
-              'Delimiter', '\t');
-```
+    ```python
+    import pandas as pd
 
-## Octave
+    participants = pd.DataFrame(
+        {
+            "participant_id": ["sub-01", "sub-02"],
+            "age": [20, 30],
+            "sex": ["m", "f"],
+        }
+    )
+    participants.to_csv("participants.tsv")
+    ```
 
-The `writetable` function is not implemented in older version of Octave
-(e.g 4.2.2) and the `table` function differs from its matlab counterpart.
-These are still in development for future
-[releases](https://github.com/apjanke/octave-tablicious) so some of the scripts
-provided in the BIDS starter-kit repository in the matlab code folder
-to create .tsv might not work with octave because of that reason.
+=== "MATLAB"
 
-## Excel
+    ```matlab
+    participant_id = ['sub-01'; 'sub-02'];
+    age = [20; 30]';
+    sex = ['m'; 'f'];
+    participants = table(participant_id, age, sex);
+
+    writetable(participants, ...
+               'participants.tsv', ...
+               'FileType', 'text', ...
+               'Delimiter', '\t');
+    ```
 
--   Create a file with the following columns
-    (at least, for other values see paragraph the
-    [BIDS specification](https://bids-specification.readthedocs.io/en/latest/03-modality-agnostic-files.html#participants-file))
-    -   participant_id
-    -   age
-    -   sex
+=== "Octave"
 
--   Save as tab separated `.txt` and change extension to `.tsv`
+    The example below uses the [bids-matlab](https://github.com/bids-standard/bids-matlab) library.
 
-## R
+    ```matlab
+    participants = struct(...
+        'participant_id', ['sub-01', 'sub-02'];
+        'age', [20, 30]';
+        'sex', ['m', 'f']
+        );
 
-### Writing a `.tsv` file
+    bids.util.tsvwrite('participants.tsv', participants);
+    ```
 
-When writing files, column and row names are always saved, we remove row names,
-and quotes from the outpur explicitly by setting them to FALSE.
+=== "R"
 
-```R
-data = cbind.data.frame(
-  participant_id = c('sub-01', 'sub-02'),
-  age = c(20,30),
-  sex = c('m','f'))
+    When writing files, column and row names are always saved,
+    we remove row names and quotes from the output explicitly by setting them to `FALSE`.
 
-write.table(data, file='myData.tsv',sep='\t',
-  row.names = FALSE, quote = FALSE)
-```
+    ```R
+    participant_id <- c('sub-01', 'sub-02');
+    age <- c(20, 30);
+    sex <- c('m', 'f');
+    participants <- data.frame(participant_id, age, sex)
+    write.table(participants,
+                file='participants.tsv',
+                sep='\t',
+                row.names = FALSE,
+                quote = FALSE)
+    ```

docs/getting_started/resources/dependencies.md

@@ -20,8 +20,6 @@ It'll work for all the languages below!
 
 [**_Octave Information_**](https://www.gnu.org/software/octave/)
 
-Required JSON package [**JSONio**](https://github.com/gllmflndn/JSONio)
-
 ## Python
 
 [**_Information_**](https://www.python.org/) (Both Python 2 and 3 will work for BIDS)

temp/participants.tsv

@@ -0,0 +1,3 @@
+participant_id	age	sex
+sub-01	20	m
+sub-02	30	f

tmp.py

@@ -0,0 +1,10 @@
+import pandas as pd
+
+participants = pd.DataFrame(
+    {
+        "participant_id": ["sub-01", "sub-02"],
+        "age": [20, 30],
+        "sex": ["m", "f"],
+    }
+)
+participants.to_csv("participants.tsv")