Skip to content

Commit

Permalink
fix a bunch of numpydoc violations
Browse files Browse the repository at this point in the history
  • Loading branch information
@mscheltienne
mscheltienne committed Jul 22, 2024
1 parent 7124da3 commit 4614c3f
Show file tree
Hide file tree
Showing 3 changed files with 76 additions and 98 deletions.
21 changes: 9 additions & 12 deletions nigsp/blocks.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,13 @@


def nifti_to_timeseries(fname, atlasname):
"""
Read a nifti file and returns a normalised timeseries from an atlas.
"""Read a nifti file and returns a normalised timeseries from an atlas.
Parameters
----------
fname : string or os.PathLike
fname : str | os.PathLike
Filename (and path) of a functional timeseries nifti dataset.
atlasname : string or os.PathLike
atlasname : str | os.PathLike
Filename (and path) of an atlas nifti dataset.
Returns
Expand All @@ -49,8 +48,7 @@ def nifti_to_timeseries(fname, atlasname):


def export_metric(scgraph, outext, outprefix):
"""
Export the metrics computed within the library.
"""Export the metrics computed within the library.
Parameters
----------
Expand All @@ -64,7 +62,7 @@ def export_metric(scgraph, outext, outprefix):
Returns
-------
0
If everything goes well
If everything goes well.
"""
if outext in io.EXT_NIFTI:
try:
Expand Down Expand Up @@ -100,17 +98,16 @@ def export_metric(scgraph, outext, outprefix):


def plot_metric(scgraph, outprefix, atlas=None, thr=None):
"""
If possible, plot metrics as markerplot.
"""If possible, plot metrics as markerplot.
Parameters
----------
scgraph : SCGraph object
The internal object containing all data.
outprefix : str
The prefix of the png file to export
img : 3DNiftiImage or None, optional
The nifti image of the atlas
The prefix of the png file to export.
img : 3DNiftiImage | None
The nifti image of the atlas.
atlas : 3D Nifti1Image, numpy.ndarray, or None, optional
Either a nifti image containing a valid atlas or a set of parcel coordinates.
thr : float or None, optional
Expand Down
147 changes: 64 additions & 83 deletions nigsp/io.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,31 +40,30 @@


def check_ext(all_ext, fname, scan=False, remove=False):
"""
Check which extension a file has, and possibly remove it.
"""Check which extension a file has, and possibly remove it.
Parameters
----------
all_ext : list
All possible extensions to check within
All possible extensions to check within.
fname : str or os.PathLike
The filename to check
The filename to check.
scan : bool, optional
Scan the given path to see if there is a file with that extension
If True and no path declared, check if fname has a path, if not scan '.'
If False, don't scan any folder
If False, don't scan any folder.
remove : bool, optional
Remove the extension from fname if it has one
Remove the extension from fname if it has one.
Returns
-------
obj_return : Uses a list to return variable amount of options.
has_ext : boolean
True if the extension is found, false otherwise
True if the extension is found, false otherwise.
fname : str or os.PathLike
If `remove` is True, return (extensionless) fname
If ``remove`` is True, return (extensionless) fname.
ext : str
If both `remove` and `has_ext` are True, returns also found extension
If both ``remove`` and ``has_ext`` are True, returns also found extension.
"""
has_ext = False
all_ext = change_var_type(all_ext, list, stop=False, silent=True)
Expand Down Expand Up @@ -96,67 +95,65 @@ def check_ext(all_ext, fname, scan=False, remove=False):


def check_nifti_dim(fname, data, dim=4):
"""
Check number of dimensions in nifti file.
"""Check number of dimensions in nifti file.
Parameters
----------
fname : str
The name of the file representing `data`
The name of the file representing ``data``.
data : numpy.ndarray
The data which dimensionality needs to be checked
The data which dimensionality needs to be checked.
dim : int, optional
The amount of dimensions expected/desired in the data.
Returns
-------
numpy.ndarray
If `data.ndim` = `dim`, returns data.
If ``data.ndim = dim``, returns data.
Raises
------
ValueError
If `data` has different dimensions than `dim`
If ``data`` has different dimensions than ``dim``.
"""
data = data.squeeze()

if data.ndim != dim:
raise ValueError(
f"A {dim}D nifti file is required, but {fname} is "
f"{data.ndim}D. Please check the input file."
f"A {dim}D nifti file is required, but {fname} is {data.ndim}D. Please "
"check the input file."
)

return data


def check_mtx_dim(fname, data, shape=None):
"""
Check dimensions of a matrix.
"""Check dimensions of a matrix.
Parameters
----------
fname : str
The name of the file representing `data`
The name of the file representing ``data``.
data : np.ndarray
The data which dimensionality needs to be checked
shape : None, 'square', or 'rectangle'}, str, optional
Shape of matrix, if empty, skip shape check
The data which dimensionality needs to be checked.
shape : None | ``'square'`` | ``'rectangle'``
Shape of matrix, if empty, skip shape check.
Returns
-------
np.ndarray
If `data.ndim` = 2, returns data.
If `data.ndim` = 1 and `shape` == 'rectangle',
Returns data with added empty axis.
If ``data.ndim = 2``, returns data.
If ``data.ndim = 1`` and ``shape == 'rectangle'``, returns data with added empty
axis.
Raises
------
NotImplementedError
If `data` has more than 3 dimensions.
If `shape` is not None but `data` is 3D.
If ``data`` has more than 3 dimensions.
If ``shape`` is not None but `data` is 3D.
ValueError
If `data` is empty
If `shape` == 'square' and `data` dimensions have different lengths.
If ``data`` is empty
If ``shape == 'square'`` and ``data`` dimensions have different lengths.
"""
data = data.squeeze()
LGR.info("Checking data shape.")
Expand Down Expand Up @@ -187,30 +184,28 @@ def check_mtx_dim(fname, data, shape=None):


def load_nifti_get_mask(fname, is_mask=False, ndim=4):
"""
Load a nifti file and returns its data, its image, and a 3d mask.
"""Load a nifti file and returns its data, its image, and a 3D mask.
Parameters
----------
fname : str
The filename to read in
The filename to read in.
is_mask : bool, optional
If the file contains a mask.
Default: False
If the file contains a mask. Default to ``False``.
ndim : int or None, optional
The number of dimensions expected in the data.
If None (default), 4 dimensions are expected, unless is_mask=True.
If None (default), 4 dimensions are expected, unless ``is_mask=True``.
In the latter case, 3 dimensions will be checked.
Returns
-------
data : numpy.ndarray
Data from nifti file.
mask : numpy.ndarray
If `is_mask` is False, numpy.ndarray of one dimension less than data,
If ``is_mask`` is ``False``, numpy.ndarray of one dimension less than data,
in which any element that has at least a value different from zero
in the last dimension of `data` is True.
If `is_mask` is True, mask is a boolean representation of data.
in the last dimension of ``data`` is True.
If ``is_mask`` is ``True``, mask is a boolean representation of data.
img : nib.img
Image object from nibabel.
Expand All @@ -219,8 +214,8 @@ def load_nifti_get_mask(fname, is_mask=False, ndim=4):
import nibabel as nib
except ImportError:
raise ImportError(
"nibabel is required to import nifti files. "
"Please see install instructions."
"nibabel is required to import nifti files. Please see install "
"instructions."
)

LGR.info(f"Loading {fname}.")
Expand All @@ -243,20 +238,19 @@ def load_nifti_get_mask(fname, is_mask=False, ndim=4):


def load_txt(fname, shape=None):
"""
Read files in textual format.
"""Read files in textual format.
Parameters
----------
fname : str or os.PathLike
Path to the txt file
shape : None, 'square', or 'rectangle', optional
Shape of matrix, if empty, skip check
fname : str | os.PathLike
Path to the txt file.
shape : None | ``'square'`` | ``'rectangle'``
Shape of matrix, if empty, skip check.
Returns
-------
mtx : numpy.ndarray
Data matrix
Data matrix.
See also
--------
Expand All @@ -283,28 +277,27 @@ def load_txt(fname, shape=None):


def load_mat(fname, shape=None):
"""
Read files in matlab format.
"""Read files in MATLAB format.
Assumes the existence of a matrix/vector in the mat file, rendered as
a numpy.ndarray. If there is more than a matrix, the one with the largest
size will be selected.
Parameters
----------
fname : str or os.PathLike
Path to the mat file
shape : None, 'square', or 'rectangle'}, str, optional
Shape of matrix, if empty, skip check
fname : str | os.PathLike
Path to the ``.mat`` file.
shape : None | ``'square'`` | ``'rectangle'``
Shape of matrix, if empty, skip check.
Returns
-------
mtx : numpy.ndarray
Data matrix
Data matrix.
Notes
-----
Requires module pymatreader to work
Requires module ``pymatreader`` to work.
See also
--------
Expand Down Expand Up @@ -361,19 +354,14 @@ def load_mat(fname, shape=None):


def load_xls(fname, shape=""):
"""
Read files in xls format.
"""Read files in xls format.
Parameters
----------
fname : str or os.PathLike
Path to the mat file
shape : None, 'square', or 'rectangle'}, str, optional
Shape of matrix, if empty, skip check
Notes
-----
Requires module _ to work
fname : str | os.PathLike
Path to the xls file.
shape : None | ``'square'`` | ``'rectangle'``
Shape of matrix, if empty, skip check.
See also
--------
Expand All @@ -388,41 +376,35 @@ def load_xls(fname, shape=""):


def export_nifti(data, img, fname):
"""
Export a nifti file.
"""Export a nifti file.
Parameters
----------
data : numpy.ndarray
Data to be exported
Data to be exported.
img : nib.img
Nibabel image object
fname : str or os.PathLike
Name of the output file
Nibabel image object.
fname : str | os.PathLike
Name of the output file.
"""
try:
import nibabel as nib
except ImportError:
raise ImportError(
"nibabel is required to export nifti files. "
"Please see install instructions."
"nibabel is required to export nifti files. Please see install "
"instructions."
)

has_ext, fname, ext = check_ext(EXT_NIFTI, fname, remove=True)

if ext is None:
ext = ".nii.gz"

LGR.info(f"Exporting nifti data into {fname}{ext}.")
out_img = nib.Nifti1Image(data, img.affine, img.header)
out_img.to_filename(f"{fname}{ext}")

return 0


def export_txt(data, fname, ext=None):
"""
Export data into a text-like or mat file.
"""Export data into a text-like or mat file.
Parameters
----------
Expand Down Expand Up @@ -478,14 +460,13 @@ def export_txt(data, fname, ext=None):


def export_mtx(data, fname, ext=None):
"""
Export data into a text-like or mat file.
"""Export data into a text-like or mat file.
Parameters
----------
data : np.ndarray
Data to be exported.
fname : str or os.PathLike
fname : str | os.PathLike
Name of the output file.
ext : str or None, optional
Selected extension for export.
Expand Down
Loading

0 comments on commit 4614c3f

Please sign in to comment.