Bases: object
This is a class to represent multiple ROI objects, where the reference to a given domain is explicit.
A mutliple ROI object is a set of ROI defined on a given domain, each having its own ‘region-level’ characteristics (ROI features).
Every voxel of the domain can have its own characteristics yet, defined at the ‘voxel-level’, but those features can only be accessed familywise (i.e. the values are grouped by ROI).
Parameters : | `k`: int, :
`label`: array of shape (domain.size), dtype=np.int, :
`features`: dict{str: list of object, length=self.k} :
`roi_features`: dict{str: array-like, shape=(self.k, roi_feature_dim) :
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Methods
copy() | Returns a copy of self. |
feature_to_voxel_map(fid[, roi, method]) | Convert a feature to a flat voxel-mapping array. |
get_coord([id]) | Get coordinates of ROI’s voxels |
get_feature(fid[, id]) | Return a voxel-wise feature, grouped by ROI. |
get_id() | Return ROI’s id list. |
get_local_volume([id]) | Get volume of ROI’s voxels |
get_roi_feature(fid[, id]) | |
get_size([id]) | Get ROI size (counted in terms of voxels) |
get_volume([id]) | Get ROI volume |
integrate([fid, id]) | Integrate certain feature on each ROI and return the k results |
plot_feature(fid[, ax]) | Boxplot the distribution of features within ROIs. |
recompute_labels() | Redefine labels so that they are consecutive integers. |
remove_feature(fid) | Remove a certain feature |
remove_roi_feature(fid) | Remove a certain ROI feature. |
representative_feature(fid[, method, id, ...]) | Compute a ROI representative of a given feature. |
select_id(id[, roi]) | Convert a ROI id into an index to be used to index features safely. |
select_roi(id_list) | Returns an instance of MROI with only the subset of chosen ROIs. |
set_feature(fid, data[, id, override]) | Append or modify a feature |
set_roi_feature(fid, data[, id, override]) | Append or modify a ROI feature |
to_image([fid, roi, method, descrip]) | Generates a label image that represents self. |
Initialize subdomains instance
Parameters : | domain: ROI instance :
label: array of shape (domain.size), dtype=np.int, :
id: array of shape (n_roi) :
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Returns a copy of self.
Note that self.domain is not copied.
Convert a feature to a flat voxel-mapping array.
Get coordinates of ROI’s voxels
Parameters : | id: any hashable type :
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Return a voxel-wise feature, grouped by ROI.
Parameters : | fid: str, :
id: any hashable type :
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Return ROI’s id list.
Users must access ROIs with the use of the identifiers of this list and the methods that give access to their properties/features.
Get volume of ROI’s voxels
Parameters : | id: any hashable type :
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Get ROI size (counted in terms of voxels)
Parameters : | id: any hashable type :
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Get ROI volume
Parameters : | id: any hashable type :
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Integrate certain feature on each ROI and return the k results
Parameters : | fid : str
id: any hashable type :
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Returns : | lsum = array of shape (self.k, self.feature[fid].shape[1]), :
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Boxplot the distribution of features within ROIs. Note that this assumes 1-d features.
Parameters : | fid: string :
ax: axis handle, optional : |
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Redefine labels so that they are consecutive integers.
Labels are used as a map to associate voxels to a given ROI. It is an inner object that should not be accessed outside this class. The number of nodes is updated appropriately.
Remove a certain feature
Parameters : | fid: str, :
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Remove a certain ROI feature.
The id ROI feature cannot be removed.
Compute a ROI representative of a given feature.
Parameters : | fid: str, :
method: str, :
id: any hashable type :
assess_quality: bool :
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Convert a ROI id into an index to be used to index features safely.
Returns an instance of MROI with only the subset of chosen ROIs.
Parameters : | id_list: list of id (any hashable type) :
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Append or modify a feature
Parameters : | fid: str, :
data: list of self.k arrays of shape(self.size[k], p) or :
id: any hashable type :
override: bool, optional, :
Note that we cannot create a feature having the same name than : a ROI feature. : |
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Append or modify a ROI feature
Parameters : | fid: str, :
data: list of self.k features or a single feature :
id: any hashable type :
override: bool, optional, :
Note that we cannot create a ROI feature having the same name than : a feature. : Note that the `id` feature cannot be modified as an internal : component. : |
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Generates a label image that represents self.
Parameters : | fid: str, :
roi: bool, :
method: str, :
descrip: str, :
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Return a SubDomain from an n-d int array
Parameters : | label: np.array instance :
affine: np.array, optional :
nn: int, :
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Create discrete ROIs as a set of balls within a certain coordinate systems.
Parameters : | domain: StructuredDomain instance, :
positions: array of shape(k, dim): :
radii: array of shape(k): :
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Return a SubDomain instance from the input mask image.
Parameters : | mim: NiftiIImage instance, or string path toward such an image :
nn: int, optional :
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Returns : | The MultipleROI instance : |
Keep the set of labels of the image corresponding to a certain index so that their position is closest to the prescribed one.
Parameters : | mim: NiftiIImage instance, or string path toward such an image :
pos: array of shape(3) or list of length 3, :
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