bids.reports.utils¶
Generate publication-quality data acquisition methods section from BIDS dataset.
Utilities to generate the MRI data acquisition portion of a methods section from a BIDS dataset.
Functions
get_seqstr (config, metadata) |
Extract and reformat imaging sequence(s) and variant(s) into pretty strings. |
get_sizestr (img) |
Extract and reformat voxel size, matrix size, field of view, and number of slices into pretty strings. |
get_slice_info (slice_times) |
Extract slice order from slice timing info. |
list_to_str (lst) |
Turn a list into a comma- and/or and-separated string. |
num_to_str (num) |
Convert an int or float to a nice string. |
reminder () |
Remind users about things they need to do after generating the report. |
remove_duplicates (seq) |
Return unique elements from list while preserving order. |
-
get_seqstr
(config, metadata)[source]¶ Extract and reformat imaging sequence(s) and variant(s) into pretty strings.
Parameters: - config (
dict
) – A dictionary with relevant information regarding sequences, sequence variants, phase encoding directions, and task names. - metadata (
dict
) – The metadata for the scan.
Returns: - seqs (
str
) – Sequence names. - variants (
str
) – Sequence variant names.
- config (
-
get_sizestr
(img)[source]¶ Extract and reformat voxel size, matrix size, field of view, and number of slices into pretty strings.
Parameters: img ( nibabel.Nifti1Image
) – Image from scan from which to derive parameters.Returns: - n_slices (
int
) – Number of slices. - voxel_size (
str
) – Voxel size string (e.g., ‘2x2x2’) - matrix_size (
str
) – Matrix size string (e.g., ‘128x128’) - fov (
str
) – Field of view string (e.g., ‘256x256’)
- n_slices (
-
get_slice_info
(slice_times)[source]¶ Extract slice order from slice timing info.
TODO: Be more specific with slice orders. Currently anything where there’s some kind of skipping is interpreted as interleaved of some kind.
Parameters: slice_times (array-like) – A list of slice times in seconds or milliseconds or whatever. Returns: slice_order_name – The name of the slice order sequence. Return type: str
-
list_to_str
(lst)[source]¶ Turn a list into a comma- and/or and-separated string.
Parameters: lst ( list
) – A list of strings to join into a single string.Returns: str_ – A string with commas and/or ands separating th elements from lst
.Return type: str
-
num_to_str
(num)[source]¶ Convert an int or float to a nice string. E.g.,
21 -> ‘21’ 2.500 -> ‘2.5’ 3. -> ‘3’
-
remove_duplicates
(seq)[source]¶ Return unique elements from list while preserving order. From https://stackoverflow.com/a/480227/2589328