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
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Extract and reformat imaging sequence(s) and variant(s) into pretty strings. |
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Extract and reformat voxel size, matrix size, field of view, and number of slices into pretty strings. |
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Extract slice order from slice timing info. |
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Turn a list into a comma- and/or and-separated string. |
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Convert an int or float to a nice string. |
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Remind users about things they need to do after generating the report. |
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Return unique elements from list while preserving order. |
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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.
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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’)
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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
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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
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num_to_str
(num)[source]¶ Convert an int or float to a nice string. E.g.,
21 -> ‘21’ 2.500 -> ‘2.5’ 3. -> ‘3’
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remove_duplicates
(seq)[source]¶ Return unique elements from list while preserving order. From https://stackoverflow.com/a/480227/2589328