shamo.core.problems.single.components.grid_sampler.CompGridSampler¶

class shamo.core.problems.single.components.grid_sampler.CompGridSampler(**kwargs)[source]¶

Bases: shamo.core.problems.single.components.abc.CompABC

Store information about a space grid sampler.

A grid sampler is used to convert outputs from GetDP into a NII file more suitable for neuroimaging studies.

Other Parameters

affinenumpy.ndarray: The affine matrix of the grid.
shapetuple [int]: The shape of the grid.
masknumpy.ndarray: The mask of the grid.

Methods

`check`	Check is the grid is properly set.
`clear`
`copy`
`fromkeys`	Create a new dictionary with keys from iterable and values set to value.
`get`	Return the value for key if key is in the dictionary, else default.
`items`
`keys`
`nii_from_pos`	Convert a POS file into a NII file.
`pop`	If key is not found, d is returned if given, otherwise KeyError is raised
`popitem`	Remove and return a (key, value) pair as a 2-tuple.
`set`	Set the grid component.
`setdefault`	Insert key with a value of default if key is not in the dictionary.
`to_pro_param`	Return if the grid can be used.
`to_py_param`	Return the parameters required to render python template.
`update`	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
`values`

Attributes

`affine`	Return the affine matrix of the grid.
`mask`	Return the mask of the grid.
`shape`	Return the shape of the grid.
`use_grid`	Return wether or not the grid can be used.

property affine¶

Return the affine matrix of the grid.

Returns

numpy.ndarray: The affine matrix of the grid.

check(name, **kwargs)[source]¶

Check is the grid is properly set.

Parameters

namestr: The name of the grid.

Raises

TypeError: If argument affine is not a numpy.ndarray.
ValueError: If argument affine is not (3, 4) or (4, 4) numpy.ndarray. If argument shape is not a 3D shape.

clear() → None. Remove all items from D.¶

copy() → a shallow copy of D¶

fromkeys(iterable, value=None, /)¶: Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /)¶: Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D’s items¶

keys() → a set-like object providing a view on D’s keys¶

property mask¶

Return the mask of the grid.

Returns

numpy.ndarray: The mask of the grid.

nii_from_pos(src, dst)[source]¶

Convert a POS file into a NII file.

Parameters

srcstr, byte or os.PathLike: The path to the POS file to convert.
dststr, byte or os.PathLike: The path where the generated NII image must be saved.
Returns
——-
nibabel.Nifti1Image: The generated NII image.

pop(k[, d]) → v, remove specified key and return the corresponding value.¶: If key is not found, d is returned if given, otherwise KeyError is raised

popitem(/)¶

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

set(affine, shape, mask=None, resize=False)[source]¶

Set the grid component.

Parameters

affinenumpy.ndarray: The affine matrix of the grid.
shametuple [int]: The shape of the grid.
masknumpy.ndarray, optional: The mask of the grid. If set to None, no mask is applied to the resulting data. (The default is None)
resizebool, optional: If set to True, the affine matrix is rescaled from meters to millimeters. (the default is False)

setdefault(key, default=None, /)¶

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

property shape¶

Return the shape of the grid.

Returns

tuple [int]: The shape of the grid.

to_pro_param(**kwargs)[source]¶

Return if the grid can be used.

Returns

bool: Return True if the grid is set.

to_py_param(**kwargs)[source]¶

Return the parameters required to render python template.

Returns

dict [str, str]: The parameters required to render python template.

update([E, ]**F) → None. Update D from dict/iterable E and F.¶: If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

property use_grid¶

Return wether or not the grid can be used.

Returns

bool: Return True if the grid can be used, False otherwise.

values() → an object providing a view on D’s values¶