id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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237,200 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.to_file | def to_file(self, filename):
"""
Write the ANTsImage to file
Args
----
filename : string
filepath to which the image will be written
"""
filename = os.path.expanduser(filename)
libfn = utils.get_lib_fn('toFile%s'%self._libsuffix)
libfn... | python | def to_file(self, filename):
"""
Write the ANTsImage to file
Args
----
filename : string
filepath to which the image will be written
"""
filename = os.path.expanduser(filename)
libfn = utils.get_lib_fn('toFile%s'%self._libsuffix)
libfn... | [
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237,201 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.apply | def apply(self, fn):
"""
Apply an arbitrary function to ANTsImage.
Args
----
fn : python function or lambda
function to apply to ENTIRE image at once
Returns
-------
ANTsImage
image with function applied to it
"""
... | python | def apply(self, fn):
"""
Apply an arbitrary function to ANTsImage.
Args
----
fn : python function or lambda
function to apply to ENTIRE image at once
Returns
-------
ANTsImage
image with function applied to it
"""
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237,202 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.sum | def sum(self, axis=None, keepdims=False):
""" Return sum along specified axis """
return self.numpy().sum(axis=axis, keepdims=keepdims) | python | def sum(self, axis=None, keepdims=False):
""" Return sum along specified axis """
return self.numpy().sum(axis=axis, keepdims=keepdims) | [
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237,203 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.range | def range(self, axis=None):
""" Return range tuple along specified axis """
return (self.min(axis=axis), self.max(axis=axis)) | python | def range(self, axis=None):
""" Return range tuple along specified axis """
return (self.min(axis=axis), self.max(axis=axis)) | [
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237,204 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.argrange | def argrange(self, axis=None):
""" Return argrange along specified axis """
amin = self.argmin(axis=axis)
amax = self.argmax(axis=axis)
if axis is None:
return (amin, amax)
else:
return np.stack([amin, amax]).T | python | def argrange(self, axis=None):
""" Return argrange along specified axis """
amin = self.argmin(axis=axis)
amax = self.argmax(axis=axis)
if axis is None:
return (amin, amax)
else:
return np.stack([amin, amax]).T | [
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237,205 | ANTsX/ANTsPy | ants/core/ants_image.py | ANTsImage.unique | def unique(self, sort=False):
""" Return unique set of values in image """
unique_vals = np.unique(self.numpy())
if sort:
unique_vals = np.sort(unique_vals)
return unique_vals | python | def unique(self, sort=False):
""" Return unique set of values in image """
unique_vals = np.unique(self.numpy())
if sort:
unique_vals = np.sort(unique_vals)
return unique_vals | [
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237,206 | ANTsX/ANTsPy | ants/core/ants_image.py | LabelImage.uniquekeys | def uniquekeys(self, metakey=None):
"""
Get keys for a given metakey
"""
if metakey is None:
return self._uniquekeys
else:
if metakey not in self.metakeys():
raise ValueError('metakey %s does not exist' % metakey)
return self._u... | python | def uniquekeys(self, metakey=None):
"""
Get keys for a given metakey
"""
if metakey is None:
return self._uniquekeys
else:
if metakey not in self.metakeys():
raise ValueError('metakey %s does not exist' % metakey)
return self._u... | [
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237,207 | ANTsX/ANTsPy | ants/utils/label_clusters.py | label_clusters | def label_clusters(image, min_cluster_size=50, min_thresh=1e-6, max_thresh=1, fully_connected=False):
"""
This will give a unique ID to each connected
component 1 through N of size > min_cluster_size
ANTsR function: `labelClusters`
Arguments
---------
image : ANTsImage
input imag... | python | def label_clusters(image, min_cluster_size=50, min_thresh=1e-6, max_thresh=1, fully_connected=False):
"""
This will give a unique ID to each connected
component 1 through N of size > min_cluster_size
ANTsR function: `labelClusters`
Arguments
---------
image : ANTsImage
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ANTsR function: `labelClusters`
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237,208 | ANTsX/ANTsPy | ants/registration/make_points_image.py | make_points_image | def make_points_image(pts, mask, radius=5):
"""
Create label image from physical space points
Creates spherical points in the coordinate space of the target image based
on the n-dimensional matrix of points that the user supplies. The image
defines the dimensionality of the data so if the input ima... | python | def make_points_image(pts, mask, radius=5):
"""
Create label image from physical space points
Creates spherical points in the coordinate space of the target image based
on the n-dimensional matrix of points that the user supplies. The image
defines the dimensionality of the data so if the input ima... | [
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237,209 | ANTsX/ANTsPy | ants/utils/weingarten_image_curvature.py | weingarten_image_curvature | def weingarten_image_curvature(image, sigma=1.0, opt='mean'):
"""
Uses the weingarten map to estimate image mean or gaussian curvature
ANTsR function: `weingartenImageCurvature`
Arguments
---------
image : ANTsImage
image from which curvature is calculated
sigma : scalar
... | python | def weingarten_image_curvature(image, sigma=1.0, opt='mean'):
"""
Uses the weingarten map to estimate image mean or gaussian curvature
ANTsR function: `weingartenImageCurvature`
Arguments
---------
image : ANTsImage
image from which curvature is calculated
sigma : scalar
... | [
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ANTsR function: `weingartenImageCurvature`
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image : ANTsImage
image from which curvature is calculated
sigma : scalar
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opt : string
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237,210 | ANTsX/ANTsPy | ants/core/ants_image_io.py | from_numpy | def from_numpy(data, origin=None, spacing=None, direction=None, has_components=False, is_rgb=False):
"""
Create an ANTsImage object from a numpy array
ANTsR function: `as.antsImage`
Arguments
---------
data : ndarray
image data array
origin : tuple/list
image origin
s... | python | def from_numpy(data, origin=None, spacing=None, direction=None, has_components=False, is_rgb=False):
"""
Create an ANTsImage object from a numpy array
ANTsR function: `as.antsImage`
Arguments
---------
data : ndarray
image data array
origin : tuple/list
image origin
s... | [
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237,211 | ANTsX/ANTsPy | ants/core/ants_image_io.py | _from_numpy | def _from_numpy(data, origin=None, spacing=None, direction=None, has_components=False, is_rgb=False):
"""
Internal function for creating an ANTsImage
"""
if is_rgb: has_components = True
ndim = data.ndim
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ndim -= 1
dtype = data.dtype.name
ptype = _npy_to_itk_map... | python | def _from_numpy(data, origin=None, spacing=None, direction=None, has_components=False, is_rgb=False):
"""
Internal function for creating an ANTsImage
"""
if is_rgb: has_components = True
ndim = data.ndim
if has_components:
ndim -= 1
dtype = data.dtype.name
ptype = _npy_to_itk_map... | [
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237,212 | ANTsX/ANTsPy | ants/core/ants_image_io.py | make_image | def make_image(imagesize, voxval=0, spacing=None, origin=None, direction=None, has_components=False, pixeltype='float'):
"""
Make an image with given size and voxel value or given a mask and vector
ANTsR function: `makeImage`
Arguments
---------
shape : tuple/ANTsImage
input image size... | python | def make_image(imagesize, voxval=0, spacing=None, origin=None, direction=None, has_components=False, pixeltype='float'):
"""
Make an image with given size and voxel value or given a mask and vector
ANTsR function: `makeImage`
Arguments
---------
shape : tuple/ANTsImage
input image size... | [
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237,213 | ANTsX/ANTsPy | ants/core/ants_image_io.py | matrix_to_images | def matrix_to_images(data_matrix, mask):
"""
Unmasks rows of a matrix and writes as images
ANTsR function: `matrixToImages`
Arguments
---------
data_matrix : numpy.ndarray
each row corresponds to an image
array should have number of columns equal to non-zero voxels in the mask
... | python | def matrix_to_images(data_matrix, mask):
"""
Unmasks rows of a matrix and writes as images
ANTsR function: `matrixToImages`
Arguments
---------
data_matrix : numpy.ndarray
each row corresponds to an image
array should have number of columns equal to non-zero voxels in the mask
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237,214 | ANTsX/ANTsPy | ants/core/ants_image_io.py | images_to_matrix | def images_to_matrix(image_list, mask=None, sigma=None, epsilon=0.5 ):
"""
Read images into rows of a matrix, given a mask - much faster for
large datasets as it is based on C++ implementations.
ANTsR function: `imagesToMatrix`
Arguments
---------
image_list : list of ANTsImage types
... | python | def images_to_matrix(image_list, mask=None, sigma=None, epsilon=0.5 ):
"""
Read images into rows of a matrix, given a mask - much faster for
large datasets as it is based on C++ implementations.
ANTsR function: `imagesToMatrix`
Arguments
---------
image_list : list of ANTsImage types
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237,215 | ANTsX/ANTsPy | ants/core/ants_image_io.py | timeseries_to_matrix | def timeseries_to_matrix( image, mask=None ):
"""
Convert a timeseries image into a matrix.
ANTsR function: `timeseries2matrix`
Arguments
---------
image : image whose slices we convert to a matrix. E.g. a 3D image of size
x by y by z will convert to a z by x*y sized matrix
mas... | python | def timeseries_to_matrix( image, mask=None ):
"""
Convert a timeseries image into a matrix.
ANTsR function: `timeseries2matrix`
Arguments
---------
image : image whose slices we convert to a matrix. E.g. a 3D image of size
x by y by z will convert to a z by x*y sized matrix
mas... | [
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237,216 | ANTsX/ANTsPy | ants/core/ants_image_io.py | matrix_to_timeseries | def matrix_to_timeseries( image, matrix, mask=None ):
"""
converts a matrix to a ND image.
ANTsR function: `matrix2timeseries`
Arguments
---------
image: reference ND image
matrix: matrix to convert to image
mask: mask image defining voxels of interest
Returns
-------
... | python | def matrix_to_timeseries( image, matrix, mask=None ):
"""
converts a matrix to a ND image.
ANTsR function: `matrix2timeseries`
Arguments
---------
image: reference ND image
matrix: matrix to convert to image
mask: mask image defining voxels of interest
Returns
-------
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237,217 | ANTsX/ANTsPy | ants/core/ants_image_io.py | image_header_info | def image_header_info(filename):
"""
Read file info from image header
ANTsR function: `antsImageHeaderInfo`
Arguments
---------
filename : string
name of image file from which info will be read
Returns
-------
dict
"""
if not os.path.exists(filename):
raise... | python | def image_header_info(filename):
"""
Read file info from image header
ANTsR function: `antsImageHeaderInfo`
Arguments
---------
filename : string
name of image file from which info will be read
Returns
-------
dict
"""
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237,218 | ANTsX/ANTsPy | ants/core/ants_image_io.py | image_read | def image_read(filename, dimension=None, pixeltype='float', reorient=False):
"""
Read an ANTsImage from file
ANTsR function: `antsImageRead`
Arguments
---------
filename : string
Name of the file to read the image from.
dimension : int
Number of dimensions of the image rea... | python | def image_read(filename, dimension=None, pixeltype='float', reorient=False):
"""
Read an ANTsImage from file
ANTsR function: `antsImageRead`
Arguments
---------
filename : string
Name of the file to read the image from.
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237,219 | ANTsX/ANTsPy | ants/core/ants_image_io.py | dicom_read | def dicom_read(directory, pixeltype='float'):
"""
Read a set of dicom files in a directory into a single ANTsImage.
The origin of the resulting 3D image will be the origin of the
first dicom image read.
Arguments
---------
directory : string
folder in which all the dicom images exis... | python | def dicom_read(directory, pixeltype='float'):
"""
Read a set of dicom files in a directory into a single ANTsImage.
The origin of the resulting 3D image will be the origin of the
first dicom image read.
Arguments
---------
directory : string
folder in which all the dicom images exis... | [
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237,220 | ANTsX/ANTsPy | ants/core/ants_image_io.py | image_write | def image_write(image, filename, ri=False):
"""
Write an ANTsImage to file
ANTsR function: `antsImageWrite`
Arguments
---------
image : ANTsImage
image to save to file
filename : string
name of file to which image will be saved
ri : boolean
if True, return ima... | python | def image_write(image, filename, ri=False):
"""
Write an ANTsImage to file
ANTsR function: `antsImageWrite`
Arguments
---------
image : ANTsImage
image to save to file
filename : string
name of file to which image will be saved
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237,221 | ANTsX/ANTsPy | ants/segmentation/otsu.py | otsu_segmentation | def otsu_segmentation(image, k, mask=None):
"""
Otsu image segmentation
This is a very fast segmentation algorithm good for quick explortation,
but does not return probability maps.
ANTsR function: `thresholdImage(image, 'Otsu', k)`
Arguments
---------
image : ANTsImage
... | python | def otsu_segmentation(image, k, mask=None):
"""
Otsu image segmentation
This is a very fast segmentation algorithm good for quick explortation,
but does not return probability maps.
ANTsR function: `thresholdImage(image, 'Otsu', k)`
Arguments
---------
image : ANTsImage
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ANTsR function: `thresholdImage(image, 'Otsu', k)`
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237,222 | ANTsX/ANTsPy | ants/utils/crop_image.py | crop_image | def crop_image(image, label_image=None, label=1):
"""
Use a label image to crop a smaller ANTsImage from within a larger ANTsImage
ANTsR function: `cropImage`
Arguments
---------
image : ANTsImage
image to crop
label_image : ANTsImage
image with label values. If ... | python | def crop_image(image, label_image=None, label=1):
"""
Use a label image to crop a smaller ANTsImage from within a larger ANTsImage
ANTsR function: `cropImage`
Arguments
---------
image : ANTsImage
image to crop
label_image : ANTsImage
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ANTsR function: `cropImage`
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237,223 | ANTsX/ANTsPy | ants/utils/crop_image.py | decrop_image | def decrop_image(cropped_image, full_image):
"""
The inverse function for `ants.crop_image`
ANTsR function: `decropImage`
Arguments
---------
cropped_image : ANTsImage
cropped image
full_image : ANTsImage
image in which the cropped image will be put back
Returns
... | python | def decrop_image(cropped_image, full_image):
"""
The inverse function for `ants.crop_image`
ANTsR function: `decropImage`
Arguments
---------
cropped_image : ANTsImage
cropped image
full_image : ANTsImage
image in which the cropped image will be put back
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237,224 | ANTsX/ANTsPy | ants/segmentation/kmeans.py | kmeans_segmentation | def kmeans_segmentation(image, k, kmask=None, mrf=0.1):
"""
K-means image segmentation that is a wrapper around `ants.atropos`
ANTsR function: `kmeansSegmentation`
Arguments
---------
image : ANTsImage
input image
k : integer
integer number of classes
kmask : ANTsImag... | python | def kmeans_segmentation(image, k, kmask=None, mrf=0.1):
"""
K-means image segmentation that is a wrapper around `ants.atropos`
ANTsR function: `kmeansSegmentation`
Arguments
---------
image : ANTsImage
input image
k : integer
integer number of classes
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237,225 | ANTsX/ANTsPy | ants/registration/reorient_image.py | reorient_image2 | def reorient_image2(image, orientation='RAS'):
"""
Reorient an image.
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni2 = mni.reorient_image2()
"""
if image.dimension != 3:
raise ValueError('image must have 3 dimensions')
inpixelt... | python | def reorient_image2(image, orientation='RAS'):
"""
Reorient an image.
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni2 = mni.reorient_image2()
"""
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237,226 | ANTsX/ANTsPy | ants/registration/reorient_image.py | reorient_image | def reorient_image(image, axis1, axis2=None, doreflection=False, doscale=0, txfn=None):
"""
Align image along a specified axis
ANTsR function: `reorientImage`
Arguments
---------
image : ANTsImage
image to reorient
axis1 : list/tuple of integers
vector of size dim,... | python | def reorient_image(image, axis1, axis2=None, doreflection=False, doscale=0, txfn=None):
"""
Align image along a specified axis
ANTsR function: `reorientImage`
Arguments
---------
image : ANTsImage
image to reorient
axis1 : list/tuple of integers
vector of size dim,... | [
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237,227 | ANTsX/ANTsPy | ants/registration/reorient_image.py | get_center_of_mass | def get_center_of_mass(image):
"""
Compute an image center of mass in physical space which is defined
as the mean of the intensity weighted voxel coordinate system.
ANTsR function: `getCenterOfMass`
Arguments
---------
image : ANTsImage
image from which center of mass will be ... | python | def get_center_of_mass(image):
"""
Compute an image center of mass in physical space which is defined
as the mean of the intensity weighted voxel coordinate system.
ANTsR function: `getCenterOfMass`
Arguments
---------
image : ANTsImage
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237,228 | ANTsX/ANTsPy | ants/utils/convert_nibabel.py | to_nibabel | def to_nibabel(image):
"""
Convert an ANTsImage to a Nibabel image
"""
if image.dimension != 3:
raise ValueError('Only 3D images currently supported')
import nibabel as nib
array_data = image.numpy()
affine = np.hstack([image.direction*np.diag(image.spacing),np.array(image.origin).r... | python | def to_nibabel(image):
"""
Convert an ANTsImage to a Nibabel image
"""
if image.dimension != 3:
raise ValueError('Only 3D images currently supported')
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237,229 | ANTsX/ANTsPy | ants/utils/convert_nibabel.py | from_nibabel | def from_nibabel(nib_image):
"""
Convert a nibabel image to an ANTsImage
"""
tmpfile = mktemp(suffix='.nii.gz')
nib_image.to_filename(tmpfile)
new_img = iio2.image_read(tmpfile)
os.remove(tmpfile)
return new_img | python | def from_nibabel(nib_image):
"""
Convert a nibabel image to an ANTsImage
"""
tmpfile = mktemp(suffix='.nii.gz')
nib_image.to_filename(tmpfile)
new_img = iio2.image_read(tmpfile)
os.remove(tmpfile)
return new_img | [
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237,230 | ANTsX/ANTsPy | ants/contrib/sampling/affine3d.py | RandomShear3D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with
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range. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
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237,231 | ANTsX/ANTsPy | ants/contrib/sampling/affine3d.py | RandomZoom3D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with
zoom parameters randomly generated from the user-specified
range. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
... | python | def transform(self, X=None, y=None):
"""
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237,232 | ANTsX/ANTsPy | ants/contrib/sampling/affine2d.py | Translate2D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with the given
translation parameters. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
y : ANTsImage (optional)
An... | python | def transform(self, X=None, y=None):
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237,233 | ANTsX/ANTsPy | ants/contrib/sampling/affine2d.py | RandomTranslate2D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with
translation parameters randomly generated from the user-specified
range. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
... | python | def transform(self, X=None, y=None):
"""
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Arguments
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237,234 | ANTsX/ANTsPy | ants/contrib/sampling/affine2d.py | Shear2D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with the given
shear parameters. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
y : ANTsImage (optional)
Another... | python | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with the given
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Arguments
---------
X : ANTsImage
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237,235 | ANTsX/ANTsPy | ants/contrib/sampling/affine2d.py | Zoom2D.transform | def transform(self, X=None, y=None):
"""
Transform an image using an Affine transform with the given
zoom parameters. Return the transform if X=None.
Arguments
---------
X : ANTsImage
Image to transform
y : ANTsImage (optional)
Another ... | python | def transform(self, X=None, y=None):
"""
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Arguments
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237,236 | ANTsX/ANTsPy | ants/segmentation/kelly_kapowski.py | kelly_kapowski | def kelly_kapowski(s, g, w, its=50, r=0.025, m=1.5, **kwargs):
"""
Compute cortical thickness using the DiReCT algorithm.
Diffeomorphic registration-based cortical thickness based on probabilistic
segmentation of an image. This is an optimization algorithm.
Arguments
---------
s : AN... | python | def kelly_kapowski(s, g, w, its=50, r=0.025, m=1.5, **kwargs):
"""
Compute cortical thickness using the DiReCT algorithm.
Diffeomorphic registration-based cortical thickness based on probabilistic
segmentation of an image. This is an optimization algorithm.
Arguments
---------
s : AN... | [
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237,237 | ANTsX/ANTsPy | ants/core/ants_transform_io.py | new_ants_transform | def new_ants_transform(precision='float', dimension=3, transform_type='AffineTransform', parameters=None):
"""
Create a new ANTsTransform
ANTsR function: None
Example
-------
>>> import ants
>>> tx = ants.new_ants_transform()
"""
libfn = utils.get_lib_fn('newAntsTransform%s%i' % (u... | python | def new_ants_transform(precision='float', dimension=3, transform_type='AffineTransform', parameters=None):
"""
Create a new ANTsTransform
ANTsR function: None
Example
-------
>>> import ants
>>> tx = ants.new_ants_transform()
"""
libfn = utils.get_lib_fn('newAntsTransform%s%i' % (u... | [
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237,238 | ANTsX/ANTsPy | ants/core/ants_transform_io.py | create_ants_transform | def create_ants_transform(transform_type='AffineTransform',
precision='float',
dimension=3,
matrix=None,
offset=None,
center=None,
translation=None,
... | python | def create_ants_transform(transform_type='AffineTransform',
precision='float',
dimension=3,
matrix=None,
offset=None,
center=None,
translation=None,
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237,239 | ANTsX/ANTsPy | ants/core/ants_transform_io.py | read_transform | def read_transform(filename, dimension=2, precision='float'):
"""
Read a transform from file
ANTsR function: `readAntsrTransform`
Arguments
---------
filename : string
filename of transform
dimension : integer
spatial dimension of transform
precision : string
... | python | def read_transform(filename, dimension=2, precision='float'):
"""
Read a transform from file
ANTsR function: `readAntsrTransform`
Arguments
---------
filename : string
filename of transform
dimension : integer
spatial dimension of transform
precision : string
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237,240 | ANTsX/ANTsPy | ants/core/ants_transform_io.py | write_transform | def write_transform(transform, filename):
"""
Write ANTsTransform to file
ANTsR function: `writeAntsrTransform`
Arguments
---------
transform : ANTsTransform
transform to save
filename : string
filename of transform (file extension is ".mat" for affine transforms)
... | python | def write_transform(transform, filename):
"""
Write ANTsTransform to file
ANTsR function: `writeAntsrTransform`
Arguments
---------
transform : ANTsTransform
transform to save
filename : string
filename of transform (file extension is ".mat" for affine transforms)
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237,241 | ANTsX/ANTsPy | ants/registration/reflect_image.py | reflect_image | def reflect_image(image, axis=None, tx=None, metric='mattes'):
"""
Reflect an image along an axis
ANTsR function: `reflectImage`
Arguments
---------
image : ANTsImage
image to reflect
axis : integer (optional)
which dimension to reflect across, numbered from 0 to image... | python | def reflect_image(image, axis=None, tx=None, metric='mattes'):
"""
Reflect an image along an axis
ANTsR function: `reflectImage`
Arguments
---------
image : ANTsImage
image to reflect
axis : integer (optional)
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237,242 | ANTsX/ANTsPy | ants/contrib/bids/cohort.py | BIDSCohort.create_sampler | def create_sampler(self, inputs, targets, input_reader=None, target_reader=None,
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input_return_processor=None, target_return_processor=None, co_return_processor=None):
"""
Create a BIDSSampler that can be used to generate in... | python | def create_sampler(self, inputs, targets, input_reader=None, target_reader=None,
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] | 638020af2cdfc5ff4bdb9809ffe67aa505727a3b | https://github.com/ANTsX/ANTsPy/blob/638020af2cdfc5ff4bdb9809ffe67aa505727a3b/ants/contrib/bids/cohort.py#L88-L94 |
237,243 | ANTsX/ANTsPy | ants/utils/slice_image.py | slice_image | def slice_image(image, axis=None, idx=None):
"""
Slice an image.
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni2 = ants.slice_image(mni, axis=1, idx=100)
"""
if image.dimension < 3:
raise ValueError('image must have at least 3 dimensi... | python | def slice_image(image, axis=None, idx=None):
"""
Slice an image.
Example
-------
>>> import ants
>>> mni = ants.image_read(ants.get_data('mni'))
>>> mni2 = ants.slice_image(mni, axis=1, idx=100)
"""
if image.dimension < 3:
raise ValueError('image must have at least 3 dimensi... | [
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237,244 | ANTsX/ANTsPy | ants/utils/pad_image.py | pad_image | def pad_image(image, shape=None, pad_width=None, value=0.0, return_padvals=False):
"""
Pad an image to have the given shape or to be isotropic.
Arguments
---------
image : ANTsImage
image to pad
shape : tuple
- if shape is given, the image will be padded in each dimension
... | python | def pad_image(image, shape=None, pad_width=None, value=0.0, return_padvals=False):
"""
Pad an image to have the given shape or to be isotropic.
Arguments
---------
image : ANTsImage
image to pad
shape : tuple
- if shape is given, the image will be padded in each dimension
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237,245 | ANTsX/ANTsPy | ants/core/ants_metric.py | ANTsImageToImageMetric.set_fixed_image | def set_fixed_image(self, image):
"""
Set Fixed ANTsImage for metric
"""
if not isinstance(image, iio.ANTsImage):
raise ValueError('image must be ANTsImage type')
if image.dimension != self.dimension:
raise ValueError('image dim (%i) does not match metric... | python | def set_fixed_image(self, image):
"""
Set Fixed ANTsImage for metric
"""
if not isinstance(image, iio.ANTsImage):
raise ValueError('image must be ANTsImage type')
if image.dimension != self.dimension:
raise ValueError('image dim (%i) does not match metric... | [
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237,246 | ANTsX/ANTsPy | ants/core/ants_metric.py | ANTsImageToImageMetric.set_moving_image | def set_moving_image(self, image):
"""
Set Moving ANTsImage for metric
"""
if not isinstance(image, iio.ANTsImage):
raise ValueError('image must be ANTsImage type')
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"""
Set Moving ANTsImage for metric
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raise ValueError('image must be ANTsImage type')
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237,247 | ANTsX/ANTsPy | ants/utils/image_to_cluster_images.py | image_to_cluster_images | def image_to_cluster_images(image, min_cluster_size=50, min_thresh=1e-06, max_thresh=1):
"""
Converts an image to several independent images.
Produces a unique image for each connected
component 1 through N of size > min_cluster_size
ANTsR function: `image2ClusterImages`
Arguments
------... | python | def image_to_cluster_images(image, min_cluster_size=50, min_thresh=1e-06, max_thresh=1):
"""
Converts an image to several independent images.
Produces a unique image for each connected
component 1 through N of size > min_cluster_size
ANTsR function: `image2ClusterImages`
Arguments
------... | [
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237,248 | ANTsX/ANTsPy | ants/utils/threshold_image.py | threshold_image | def threshold_image(image, low_thresh=None, high_thresh=None, inval=1, outval=0, binary=True):
"""
Converts a scalar image into a binary image by thresholding operations
ANTsR function: `thresholdImage`
Arguments
---------
image : ANTsImage
Input image to operate on
low_thresh... | python | def threshold_image(image, low_thresh=None, high_thresh=None, inval=1, outval=0, binary=True):
"""
Converts a scalar image into a binary image by thresholding operations
ANTsR function: `thresholdImage`
Arguments
---------
image : ANTsImage
Input image to operate on
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237,249 | ANTsX/ANTsPy | ants/registration/symmetrize_image.py | symmetrize_image | def symmetrize_image(image):
"""
Use registration and reflection to make an image symmetric
ANTsR function: N/A
Arguments
---------
image : ANTsImage
image to make symmetric
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> image = ants.image_r... | python | def symmetrize_image(image):
"""
Use registration and reflection to make an image symmetric
ANTsR function: N/A
Arguments
---------
image : ANTsImage
image to make symmetric
Returns
-------
ANTsImage
Example
-------
>>> import ants
>>> image = ants.image_r... | [
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237,250 | freakboy3742/pyxero | xero/basemanager.py | BaseManager._get_attachments | def _get_attachments(self, id):
"""Retrieve a list of attachments associated with this Xero object."""
uri = '/'.join([self.base_url, self.name, id, 'Attachments']) + '/'
return uri, {}, 'get', None, None, False | python | def _get_attachments(self, id):
"""Retrieve a list of attachments associated with this Xero object."""
uri = '/'.join([self.base_url, self.name, id, 'Attachments']) + '/'
return uri, {}, 'get', None, None, False | [
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237,251 | freakboy3742/pyxero | xero/basemanager.py | BaseManager._put_attachment_data | def _put_attachment_data(self, id, filename, data, content_type, include_online=False):
"""Upload an attachment to the Xero object."""
uri = '/'.join([self.base_url, self.name, id, 'Attachments', filename])
params = {'IncludeOnline': 'true'} if include_online else {}
headers = {'Content-... | python | def _put_attachment_data(self, id, filename, data, content_type, include_online=False):
"""Upload an attachment to the Xero object."""
uri = '/'.join([self.base_url, self.name, id, 'Attachments', filename])
params = {'IncludeOnline': 'true'} if include_online else {}
headers = {'Content-... | [
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237,252 | freakboy3742/pyxero | examples/partner_oauth_flow/runserver.py | PartnerCredentialsHandler.page_response | def page_response(self, title='', body=''):
"""
Helper to render an html page with dynamic content
"""
f = StringIO()
f.write('<!DOCTYPE html>\n')
f.write('<html>\n')
f.write('<head><title>{}</title><head>\n'.format(title))
f.write('<body>\n<h2>{}</h2>\n'.... | python | def page_response(self, title='', body=''):
"""
Helper to render an html page with dynamic content
"""
f = StringIO()
f.write('<!DOCTYPE html>\n')
f.write('<html>\n')
f.write('<head><title>{}</title><head>\n'.format(title))
f.write('<body>\n<h2>{}</h2>\n'.... | [
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237,253 | freakboy3742/pyxero | examples/partner_oauth_flow/runserver.py | PartnerCredentialsHandler.redirect_response | def redirect_response(self, url, permanent=False):
"""
Generate redirect response
"""
if permanent:
self.send_response(301)
else:
self.send_response(302)
self.send_header("Location", url)
self.end_headers() | python | def redirect_response(self, url, permanent=False):
"""
Generate redirect response
"""
if permanent:
self.send_response(301)
else:
self.send_response(302)
self.send_header("Location", url)
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237,254 | freakboy3742/pyxero | xero/auth.py | PublicCredentials._init_credentials | def _init_credentials(self, oauth_token, oauth_token_secret):
"Depending on the state passed in, get self._oauth up and running"
if oauth_token and oauth_token_secret:
if self.verified:
# If provided, this is a fully verified set of
# credentials. Store the oa... | python | def _init_credentials(self, oauth_token, oauth_token_secret):
"Depending on the state passed in, get self._oauth up and running"
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237,255 | freakboy3742/pyxero | xero/auth.py | PublicCredentials._init_oauth | def _init_oauth(self, oauth_token, oauth_token_secret):
"Store and initialize a verified set of OAuth credentials"
self.oauth_token = oauth_token
self.oauth_token_secret = oauth_token_secret
self._oauth = OAuth1(
self.consumer_key,
client_secret=self.consumer_sec... | python | def _init_oauth(self, oauth_token, oauth_token_secret):
"Store and initialize a verified set of OAuth credentials"
self.oauth_token = oauth_token
self.oauth_token_secret = oauth_token_secret
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237,256 | freakboy3742/pyxero | xero/auth.py | PublicCredentials._process_oauth_response | def _process_oauth_response(self, response):
"Extracts the fields from an oauth response"
if response.status_code == 200:
credentials = parse_qs(response.text)
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"Extracts the fields from an oauth response"
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self._init_oauth(
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237,257 | freakboy3742/pyxero | xero/auth.py | PublicCredentials.state | def state(self):
"""Obtain the useful state of this credentials object so that
we can reconstruct it independently.
"""
return dict(
(attr, getattr(self, attr))
for attr in (
'consumer_key', 'consumer_secret', 'callback_uri',
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] | 5566f17fa06ed1f2fb9426c112951a72276b0f9a | https://github.com/freakboy3742/pyxero/blob/5566f17fa06ed1f2fb9426c112951a72276b0f9a/xero/auth.py#L245-L258 |
237,258 | freakboy3742/pyxero | xero/auth.py | PublicCredentials.verify | def verify(self, verifier):
"Verify an OAuth token"
# Construct the credentials for the verification request
oauth = OAuth1(
self.consumer_key,
client_secret=self.consumer_secret,
resource_owner_key=self.oauth_token,
resource_owner_secret=self.oau... | python | def verify(self, verifier):
"Verify an OAuth token"
# Construct the credentials for the verification request
oauth = OAuth1(
self.consumer_key,
client_secret=self.consumer_secret,
resource_owner_key=self.oauth_token,
resource_owner_secret=self.oau... | [
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237,259 | freakboy3742/pyxero | xero/auth.py | PublicCredentials.url | def url(self):
"Returns the URL that can be visited to obtain a verifier code"
# The authorize url is always api.xero.com
query_string = {'oauth_token': self.oauth_token}
if self.scope:
query_string['scope'] = self.scope
url = XERO_BASE_URL + AUTHORIZE_URL + '?' + \... | python | def url(self):
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# The authorize url is always api.xero.com
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237,260 | freakboy3742/pyxero | xero/auth.py | PartnerCredentials.refresh | def refresh(self):
"Refresh an expired token"
# Construct the credentials for the verification request
oauth = OAuth1(
self.consumer_key,
client_secret=self.consumer_secret,
resource_owner_key=self.oauth_token,
resource_owner_secret=self.oauth_tok... | python | def refresh(self):
"Refresh an expired token"
# Construct the credentials for the verification request
oauth = OAuth1(
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237,261 | freakboy3742/pyxero | xero/filesmanager.py | FilesManager._get_files | def _get_files(self, folderId):
"""Retrieve the list of files contained in a folder"""
uri = '/'.join([self.base_url, self.name, folderId, 'Files'])
return uri, {}, 'get', None, None, False, None | python | def _get_files(self, folderId):
"""Retrieve the list of files contained in a folder"""
uri = '/'.join([self.base_url, self.name, folderId, 'Files'])
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237,262 | dmulcahey/zha-device-handlers | zhaquirks/hivehome/__init__.py | MotionCluster.handle_cluster_request | def handle_cluster_request(self, tsn, command_id, args):
"""Handle the cluster command."""
if command_id == 0:
if self._timer_handle:
self._timer_handle.cancel()
loop = asyncio.get_event_loop()
self._timer_handle = loop.call_later(30, self._turn_off) | python | def handle_cluster_request(self, tsn, command_id, args):
"""Handle the cluster command."""
if command_id == 0:
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self._timer_handle.cancel()
loop = asyncio.get_event_loop()
self._timer_handle = loop.call_later(30, self._turn_off) | [
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237,263 | dmulcahey/zha-device-handlers | zhaquirks/xiaomi/__init__.py | BasicCluster._parse_attributes | def _parse_attributes(self, value):
"""Parse non standard atrributes."""
from zigpy.zcl import foundation as f
attributes = {}
attribute_names = {
1: BATTERY_VOLTAGE_MV,
3: TEMPERATURE,
4: XIAOMI_ATTR_4,
5: XIAOMI_ATTR_5,
6: XIA... | python | def _parse_attributes(self, value):
"""Parse non standard atrributes."""
from zigpy.zcl import foundation as f
attributes = {}
attribute_names = {
1: BATTERY_VOLTAGE_MV,
3: TEMPERATURE,
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237,264 | dmulcahey/zha-device-handlers | zhaquirks/xiaomi/__init__.py | BasicCluster._calculate_remaining_battery_percentage | def _calculate_remaining_battery_percentage(self, voltage):
"""Calculate percentage."""
min_voltage = 2500
max_voltage = 3000
percent = (voltage - min_voltage) / (max_voltage - min_voltage) * 200
return min(200, percent) | python | def _calculate_remaining_battery_percentage(self, voltage):
"""Calculate percentage."""
min_voltage = 2500
max_voltage = 3000
percent = (voltage - min_voltage) / (max_voltage - min_voltage) * 200
return min(200, percent) | [
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237,265 | dmulcahey/zha-device-handlers | zhaquirks/xiaomi/__init__.py | PowerConfigurationCluster.battery_reported | def battery_reported(self, voltage, rawVoltage):
"""Battery reported."""
self._update_attribute(BATTERY_PERCENTAGE_REMAINING, voltage)
self._update_attribute(self.BATTERY_VOLTAGE_ATTR,
int(rawVoltage / 100)) | python | def battery_reported(self, voltage, rawVoltage):
"""Battery reported."""
self._update_attribute(BATTERY_PERCENTAGE_REMAINING, voltage)
self._update_attribute(self.BATTERY_VOLTAGE_ATTR,
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237,266 | dmulcahey/zha-device-handlers | zhaquirks/smartthings/tag_v4.py | FastPollingPowerConfigurationCluster.configure_reporting | async def configure_reporting(self, attribute, min_interval,
max_interval, reportable_change):
"""Configure reporting."""
result = await super().configure_reporting(
PowerConfigurationCluster.BATTERY_VOLTAGE_ATTR,
self.FREQUENCY,
self... | python | async def configure_reporting(self, attribute, min_interval,
max_interval, reportable_change):
"""Configure reporting."""
result = await super().configure_reporting(
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237,267 | F5Networks/f5-common-python | f5/bigip/tm/sys/folder.py | Folder.update | def update(self, **kwargs):
'''Update the object, removing device group if inherited
If inheritedDevicegroup is the string "true" we need to remove
deviceGroup from the args before we update or we get the
following error:
The floating traffic-group: /Common/traffic-group-1 can ... | python | def update(self, **kwargs):
'''Update the object, removing device group if inherited
If inheritedDevicegroup is the string "true" we need to remove
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The floating traffic-group: /Common/traffic-group-1 can ... | [
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237,268 | F5Networks/f5-common-python | f5/bigip/tm/cm/device_group.py | Device_Group.sync_to | def sync_to(self):
"""Wrapper method that synchronizes configuration to DG.
Executes the containing object's cm :meth:`~f5.bigip.cm.Cm.exec_cmd`
method to sync the configuration TO the device-group.
:note:: Both sync_to, and sync_from methods are convenience
methods wh... | python | def sync_to(self):
"""Wrapper method that synchronizes configuration to DG.
Executes the containing object's cm :meth:`~f5.bigip.cm.Cm.exec_cmd`
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237,269 | F5Networks/f5-common-python | f5/bigip/tm/sys/application.py | Service._create | def _create(self, **kwargs):
'''Create service on device and create accompanying Python object.
:params kwargs: keyword arguments passed in from create call
:raises: HTTPError
:returns: Python Service object
'''
try:
return super(Service, self)._create(**kwa... | python | def _create(self, **kwargs):
'''Create service on device and create accompanying Python object.
:params kwargs: keyword arguments passed in from create call
:raises: HTTPError
:returns: Python Service object
'''
try:
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237,270 | F5Networks/f5-common-python | f5/bigip/tm/sys/application.py | Service._build_service_uri | def _build_service_uri(self, base_uri, partition, name):
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This follows the scheme:
<base_uri>/~<partition>~<<name>.app>~<name>
:param base_uri: str -- base uri for container
:param partition: str -- partition for this service
... | python | def _build_service_uri(self, base_uri, partition, name):
'''Build the proper uri for a service resource.
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237,271 | F5Networks/f5-common-python | f5/bigiq/cm/device/licensing/pool/utility.py | Members.delete | def delete(self, **kwargs):
"""Deletes a member from a license pool
You need to be careful with this method. When you use it, and it
succeeds on the remote BIG-IP, the configuration of the BIG-IP
will be reloaded. During this process, you will not be able to
access the REST inte... | python | def delete(self, **kwargs):
"""Deletes a member from a license pool
You need to be careful with this method. When you use it, and it
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237,272 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._set_attributes | def _set_attributes(self, **kwargs):
'''Set attributes for instance in one place
:param kwargs: dict -- dictionary of keyword arguments
'''
self.devices = kwargs['devices'][:]
self.partition = kwargs['partition']
self.device_group_name = 'device_trust_group'
sel... | python | def _set_attributes(self, **kwargs):
'''Set attributes for instance in one place
:param kwargs: dict -- dictionary of keyword arguments
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237,273 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain.validate | def validate(self):
'''Validate that devices are each trusted by one another
:param kwargs: dict -- keyword args for devices and partition
:raises: DeviceNotTrusted
'''
self._populate_domain()
missing = []
for domain_device in self.domain:
for truste... | python | def validate(self):
'''Validate that devices are each trusted by one another
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237,274 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._populate_domain | def _populate_domain(self):
'''Populate TrustDomain's domain attribute.
This entails an inspection of each device's certificate-authority
devices in its trust domain and recording them. After which, we
get a dictionary of who trusts who in the domain.
'''
self.domain = ... | python | def _populate_domain(self):
'''Populate TrustDomain's domain attribute.
This entails an inspection of each device's certificate-authority
devices in its trust domain and recording them. After which, we
get a dictionary of who trusts who in the domain.
'''
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237,275 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain.create | def create(self, **kwargs):
'''Add trusted peers to the root bigip device.
When adding a trusted device to a device, the trust is reflexive. That
is, the truster trusts the trustee and the trustee trusts the truster.
So we only need to add the trusted devices to one device.
:pa... | python | def create(self, **kwargs):
'''Add trusted peers to the root bigip device.
When adding a trusted device to a device, the trust is reflexive. That
is, the truster trusts the trustee and the trustee trusts the truster.
So we only need to add the trusted devices to one device.
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237,276 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain.teardown | def teardown(self):
'''Teardown trust domain by removing trusted devices.'''
for device in self.devices:
self._remove_trustee(device)
self._populate_domain()
self.domain = {} | python | def teardown(self):
'''Teardown trust domain by removing trusted devices.'''
for device in self.devices:
self._remove_trustee(device)
self._populate_domain()
self.domain = {} | [
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237,277 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._add_trustee | def _add_trustee(self, device):
'''Add a single trusted device to the trust domain.
:param device: ManagementRoot object -- device to add to trust domain
'''
device_name = get_device_info(device).name
if device_name in self.domain:
msg = 'Device: %r is already in th... | python | def _add_trustee(self, device):
'''Add a single trusted device to the trust domain.
:param device: ManagementRoot object -- device to add to trust domain
'''
device_name = get_device_info(device).name
if device_name in self.domain:
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237,278 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._remove_trustee | def _remove_trustee(self, device):
'''Remove a trustee from the trust domain.
:param device: MangementRoot object -- device to remove
'''
trustee_name = get_device_info(device).name
name_object_map = get_device_names_to_objects(self.devices)
delete_func = self._get_dele... | python | def _remove_trustee(self, device):
'''Remove a trustee from the trust domain.
:param device: MangementRoot object -- device to remove
'''
trustee_name = get_device_info(device).name
name_object_map = get_device_names_to_objects(self.devices)
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237,279 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._modify_trust | def _modify_trust(self, truster, mod_peer_func, trustee):
'''Modify a trusted peer device by deploying an iapp.
:param truster: ManagementRoot object -- device on which to perform
commands
:param mod_peer_func: function -- function to call to modify peer
:param ... | python | def _modify_trust(self, truster, mod_peer_func, trustee):
'''Modify a trusted peer device by deploying an iapp.
:param truster: ManagementRoot object -- device on which to perform
commands
:param mod_peer_func: function -- function to call to modify peer
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237,280 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._delete_iapp | def _delete_iapp(self, iapp_name, deploying_device):
'''Delete an iapp service and template on the root device.
:param iapp_name: str -- name of iapp
:param deploying_device: ManagementRoot object -- device where the
iapp will be deleted
'''
iap... | python | def _delete_iapp(self, iapp_name, deploying_device):
'''Delete an iapp service and template on the root device.
:param iapp_name: str -- name of iapp
:param deploying_device: ManagementRoot object -- device where the
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237,281 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._deploy_iapp | def _deploy_iapp(self, iapp_name, actions, deploying_device):
'''Deploy iapp to add trusted device
:param iapp_name: str -- name of iapp
:param actions: dict -- actions definition of iapp sections
:param deploying_device: ManagementRoot object -- device where the
... | python | def _deploy_iapp(self, iapp_name, actions, deploying_device):
'''Deploy iapp to add trusted device
:param iapp_name: str -- name of iapp
:param actions: dict -- actions definition of iapp sections
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237,282 | F5Networks/f5-common-python | f5/multi_device/trust_domain.py | TrustDomain._get_add_trustee_cmd | def _get_add_trustee_cmd(self, trustee):
'''Get tmsh command to add a trusted device.
:param trustee: ManagementRoot object -- device to add as trusted
:returns: str -- tmsh command to add trustee
'''
trustee_info = pollster(get_device_info)(trustee)
username = trustee.... | python | def _get_add_trustee_cmd(self, trustee):
'''Get tmsh command to add a trusted device.
:param trustee: ManagementRoot object -- device to add as trusted
:returns: str -- tmsh command to add trustee
'''
trustee_info = pollster(get_device_info)(trustee)
username = trustee.... | [
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237,283 | F5Networks/f5-common-python | f5/bigip/tm/vcmp/virtual_disk.py | Virtual_Disk.load | def load(self, **kwargs):
"""Loads a given resource
Loads a given resource provided a 'name' and an optional 'slot'
parameter. The 'slot' parameter is not a required load parameter
because it is provided as an optional way of constructing the
correct 'name' of the vCMP resource.... | python | def load(self, **kwargs):
"""Loads a given resource
Loads a given resource provided a 'name' and an optional 'slot'
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237,284 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._get_section_end_index | def _get_section_end_index(self, section, section_start):
'''Get end of section's content.
In the loop to match braces, we must not count curly braces that are
within a doubly quoted string.
:param section: string name of section
:param section_start: integer index of section's... | python | def _get_section_end_index(self, section, section_start):
'''Get end of section's content.
In the loop to match braces, we must not count curly braces that are
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:param section: string name of section
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237,285 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._get_section_start_index | def _get_section_start_index(self, section):
'''Get start of a section's content.
:param section: string name of section
:return: integer index of section's beginning
:raises: NonextantSectionException
'''
sec_start_re = r'%s\s*\{' % section
found = re.search(s... | python | def _get_section_start_index(self, section):
'''Get start of a section's content.
:param section: string name of section
:return: integer index of section's beginning
:raises: NonextantSectionException
'''
sec_start_re = r'%s\s*\{' % section
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237,286 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._get_template_name | def _get_template_name(self):
'''Find template name.
:returns: string of template name
:raises: NonextantTemplateNameException
'''
start_pattern = r"sys application template\s+" \
r"(\/[\w\.\-]+\/)?" \
r"(?P<name>[\w\.\-]+)\s*\{"
... | python | def _get_template_name(self):
'''Find template name.
:returns: string of template name
:raises: NonextantTemplateNameException
'''
start_pattern = r"sys application template\s+" \
r"(\/[\w\.\-]+\/)?" \
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237,287 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._get_template_attr | def _get_template_attr(self, attr):
'''Find the attribute value for a specific attribute.
:param attr: string of attribute name
:returns: string of attribute value
'''
attr_re = r'{0}\s+.*'.format(attr)
attr_found = re.search(attr_re, self.template_str)
if attr... | python | def _get_template_attr(self, attr):
'''Find the attribute value for a specific attribute.
:param attr: string of attribute name
:returns: string of attribute value
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237,288 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._add_sections | def _add_sections(self):
'''Add the found and required sections to the templ_dict.'''
for section in self.template_sections:
try:
sec_start = self._get_section_start_index(section)
except NonextantSectionException:
if section in self.sections_not_r... | python | def _add_sections(self):
'''Add the found and required sections to the templ_dict.'''
for section in self.template_sections:
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237,289 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._add_cli_scripts | def _add_cli_scripts(self):
'''Add the found external sections to the templ_dict.'''
pattern = r"cli script\s+" \
r"(\/[\w\.\-]+\/)?" \
r"(?P<name>[\w\.\-]+)\s*\{"
sections = re.finditer(pattern, self.template_str)
for section in sections:
... | python | def _add_cli_scripts(self):
'''Add the found external sections to the templ_dict.'''
pattern = r"cli script\s+" \
r"(\/[\w\.\-]+\/)?" \
r"(?P<name>[\w\.\-]+)\s*\{"
sections = re.finditer(pattern, self.template_str)
for section in sections:
... | [
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237,290 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._add_attrs | def _add_attrs(self):
'''Add the found and required attrs to the templ_dict.'''
for attr in self.template_attrs:
attr_value = self._get_template_attr(attr)
if not attr_value:
continue
attr, attr_value = self._transform_key_value(
attr... | python | def _add_attrs(self):
'''Add the found and required attrs to the templ_dict.'''
for attr in self.template_attrs:
attr_value = self._get_template_attr(attr)
if not attr_value:
continue
attr, attr_value = self._transform_key_value(
attr... | [
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237,291 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._parse_tcl_list | def _parse_tcl_list(self, attr, list_str):
'''Turns a string representation of a TCL list into a Python list.
:param attr: string name of attribute
:param list_str: string representation of a list
:returns: Python list
'''
list_str = list_str.strip()
if not lis... | python | def _parse_tcl_list(self, attr, list_str):
'''Turns a string representation of a TCL list into a Python list.
:param attr: string name of attribute
:param list_str: string representation of a list
:returns: Python list
'''
list_str = list_str.strip()
if not lis... | [
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237,292 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser._transform_key_value | def _transform_key_value(self, key, value, map_dict):
'''Massage keys and values for iapp dict to look like JSON.
:param key: string dictionary key
:param value: string dictionary value
:param map_dict: dictionary to map key names
'''
if key in self.tcl_list_patterns:
... | python | def _transform_key_value(self, key, value, map_dict):
'''Massage keys and values for iapp dict to look like JSON.
:param key: string dictionary key
:param value: string dictionary value
:param map_dict: dictionary to map key names
'''
if key in self.tcl_list_patterns:
... | [
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237,293 | F5Networks/f5-common-python | f5/utils/iapp_parser.py | IappParser.parse_template | def parse_template(self):
'''Parse the template string into a dict.
Find the (large) inner sections first, save them, and remove them from
a modified string. Then find the template attributes in the modified
string.
:returns: dictionary of parsed template
'''
s... | python | def parse_template(self):
'''Parse the template string into a dict.
Find the (large) inner sections first, save them, and remove them from
a modified string. Then find the template attributes in the modified
string.
:returns: dictionary of parsed template
'''
s... | [
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237,294 | F5Networks/f5-common-python | f5/bigip/shared/authn.py | Root._create | def _create(self, **kwargs):
"""wrapped by `create` override that in subclasses to customize"""
if 'uri' in self._meta_data:
error = "There was an attempt to assign a new uri to this "\
"resource, the _meta_data['uri'] is %s and it should"\
" not be ch... | python | def _create(self, **kwargs):
"""wrapped by `create` override that in subclasses to customize"""
if 'uri' in self._meta_data:
error = "There was an attempt to assign a new uri to this "\
"resource, the _meta_data['uri'] is %s and it should"\
" not be ch... | [
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237,295 | F5Networks/f5-common-python | f5sdk_plugins/fixtures.py | peer | def peer(opt_peer, opt_username, opt_password, scope="module"):
'''peer bigip fixture'''
p = BigIP(opt_peer, opt_username, opt_password)
return p | python | def peer(opt_peer, opt_username, opt_password, scope="module"):
'''peer bigip fixture'''
p = BigIP(opt_peer, opt_username, opt_password)
return p | [
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237,296 | F5Networks/f5-common-python | f5/bigip/tm/gtm/topology.py | Topology.exists | def exists(self, **kwargs):
"""Providing a partition is not necessary on topology; causes errors"""
kwargs.pop('partition', None)
kwargs['transform_name'] = True
return self._exists(**kwargs) | python | def exists(self, **kwargs):
"""Providing a partition is not necessary on topology; causes errors"""
kwargs.pop('partition', None)
kwargs['transform_name'] = True
return self._exists(**kwargs) | [
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237,297 | F5Networks/f5-common-python | f5/utils/responses/handlers.py | Stats._key_dot_replace | def _key_dot_replace(self, rdict):
"""Replace fullstops in returned keynames"""
temp_dict = {}
for key, value in iteritems(rdict):
if isinstance(value, dict):
value = self._key_dot_replace(value)
temp_dict[key.replace('.', '_')] = value
return temp... | python | def _key_dot_replace(self, rdict):
"""Replace fullstops in returned keynames"""
temp_dict = {}
for key, value in iteritems(rdict):
if isinstance(value, dict):
value = self._key_dot_replace(value)
temp_dict[key.replace('.', '_')] = value
return temp... | [
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237,298 | F5Networks/f5-common-python | f5/utils/responses/handlers.py | Stats._get_nest_stats | def _get_nest_stats(self):
"""Helper method to deal with nestedStats
as json format changed in v12.x
"""
for x in self.rdict:
check = urlparse(x)
if check.scheme:
nested_dict = self.rdict[x]['nestedStats']
tmp_dict = nested_dict['e... | python | def _get_nest_stats(self):
"""Helper method to deal with nestedStats
as json format changed in v12.x
"""
for x in self.rdict:
check = urlparse(x)
if check.scheme:
nested_dict = self.rdict[x]['nestedStats']
tmp_dict = nested_dict['e... | [
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237,299 | F5Networks/f5-common-python | f5/utils/responses/handlers.py | Stats.refresh | def refresh(self, **kwargs):
"""Refreshes stats attached to an object"""
self.resource.refresh(**kwargs)
self.rdict = self.resource.entries
self._update_stats() | python | def refresh(self, **kwargs):
"""Refreshes stats attached to an object"""
self.resource.refresh(**kwargs)
self.rdict = self.resource.entries
self._update_stats() | [
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