From b7e52cbee0cf4434120868700b44325ad2fa4153 Mon Sep 17 00:00:00 2001 From: Peter Van Dyken Date: Wed, 18 Oct 2023 10:20:56 -0400 Subject: [PATCH] Remove mention of regex_search from documentation --- docs/bids_app/config.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/docs/bids_app/config.md b/docs/bids_app/config.md index de387717..db9e890e 100644 --- a/docs/bids_app/config.md +++ b/docs/bids_app/config.md @@ -9,11 +9,11 @@ Config Variables ### `pybids_inputs` -A dictionary that describes each type of input you want to grab from an input BIDS dataset. Snakebids will parse your dataset with {func}`generate_inputs() `, converting each input type into a {class}`BidsComponent `. The value of each item should be a dictionary with keys ``filters`` and ``wildcards``. +A dictionary that describes each type of input you want to grab from an input BIDS dataset. Snakebids will parse your dataset with {func}`generate_inputs() `, converting each input type into a {class}`BidsComponent `. The value of each item should be a dictionary with keys `filters` and `wildcards`. -The value of ``filters`` should be a dictionary where each key corresponds to a BIDS entity, and the value specifies which values of that entity should be grabbed. The dictionary for each input is sent to the [PyBIDS' get() function ](#bids.layout.BIDSLayout). `filters` can be set according to a few different formats: +The value of `filters` should be a dictionary where each key corresponds to a BIDS entity, and the value specifies which values of that entity should be grabbed. The dictionary for each input is sent to the [PyBIDS' `get()` function ](#bids.layout.BIDSLayout). `filters` can be set according to a few different formats: -* [string](#str): specifies an exact value for the entity. In the following example: +* `[string](#str)``: specifies an exact value for the entity. In the following example: ```yaml pybids_inputs: bold: @@ -29,19 +29,17 @@ The value of ``filters`` should be a dictionary where each key corresponds to a sub-xxx/.../func/ent1-xxx_ent2-xxx_..._bold.nii.gz ``` -* [boolean](#bool): constrains presence or absence of the entity without restricting its value. `False` requires that the entity be **absent**, while `True` requires that the entity be **present**, regardless of value. +* `[boolean](#bool)``: constrains presence or absence of the entity without restricting its value. `False` requires that the entity be **absent**, while `True` requires that the entity be **present**, regardless of value. ```yaml pybids_inputs: derivs: filters: datatype: 'func' - desc: True # or true, or yes - acquisition: False # or false, or no + desc: True + acquisition: False ``` The above example maps all paths in the `func/` datatype folder that have a `_desc-` entity but do not have the `_acq-` entity. -In addition, the special filter `regex_search` can be set to `true`, which causes all other filters in the component to use regex matching instead of exact matching. - The value of ``wildcards`` should be a list of BIDS entities. Snakebids collects the values of any entities specified and saves them in the {attr}`entities ` and {attr}`~snakebids.BidsComponent.zip_lists` entries of the corresponding {class}`BidsComponent `. In other words, these are the entities to be preserved in output paths derived from the input being described. Placing an entity in `wildcards` does not require the entity be present. If an entity is not found, it will be left out of {attr}`entities `. To require the presence of an entity, place it under `filters` set to `true`. In the following (YAML-formatted) example, the ``bold`` input type is specified. BIDS files with the datatype ``func``, suffix ``bold``, and extension ``.nii.gz`` will be grabbed, and the ``subject``, ``session``, ``acquisition``, ``task``, and ``run`` entities of those files will be left as wildcards. The `task` entity must be present, but there must not be any `desc`.