idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
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43,200 | def _from_numpy ( data , origin = None , spacing = None , direction = None , has_components = False , is_rgb = False ) : if is_rgb : has_components = True ndim = data . ndim if has_components : ndim -= 1 dtype = data . dtype . name ptype = _npy_to_itk_map [ dtype ] data = np . array ( data ) if origin is None : origin = tuple ( [ 0. ] * ndim ) if spacing is None : spacing = tuple ( [ 1. ] * ndim ) if direction is None : direction = np . eye ( ndim ) libfn = utils . get_lib_fn ( 'fromNumpy%s%i' % ( _ntype_type_map [ dtype ] , ndim ) ) if not has_components : itk_image = libfn ( data , data . shape [ : : - 1 ] ) ants_image = iio . ANTsImage ( pixeltype = ptype , dimension = ndim , components = 1 , pointer = itk_image ) ants_image . set_origin ( origin ) ants_image . set_spacing ( spacing ) ants_image . set_direction ( direction ) ants_image . _ndarr = data else : arrays = [ data [ i , ... ] . copy ( ) for i in range ( data . shape [ 0 ] ) ] data_shape = arrays [ 0 ] . shape ants_images = [ ] for i in range ( len ( arrays ) ) : tmp_ptr = libfn ( arrays [ i ] , data_shape [ : : - 1 ] ) tmp_img = iio . ANTsImage ( pixeltype = ptype , dimension = ndim , components = 1 , pointer = tmp_ptr ) tmp_img . set_origin ( origin ) tmp_img . set_spacing ( spacing ) tmp_img . set_direction ( direction ) tmp_img . _ndarr = arrays [ i ] ants_images . append ( tmp_img ) ants_image = utils . merge_channels ( ants_images ) if is_rgb : ants_image = ants_image . vector_to_rgb ( ) return ants_image | Internal function for creating an ANTsImage |
43,201 | def make_image ( imagesize , voxval = 0 , spacing = None , origin = None , direction = None , has_components = False , pixeltype = 'float' ) : if isinstance ( imagesize , iio . ANTsImage ) : img = imagesize . clone ( ) sel = imagesize > 0 if voxval . ndim > 1 : voxval = voxval . flatten ( ) if ( len ( voxval ) == int ( ( sel > 0 ) . sum ( ) ) ) or ( len ( voxval ) == 0 ) : img [ sel ] = voxval else : raise ValueError ( 'Num given voxels %i not same as num positive values %i in `imagesize`' % ( len ( voxval ) , int ( ( sel > 0 ) . sum ( ) ) ) ) return img else : if isinstance ( voxval , ( tuple , list , np . ndarray ) ) : array = np . asarray ( voxval ) . astype ( 'float32' ) . reshape ( imagesize ) else : array = np . full ( imagesize , voxval , dtype = 'float32' ) image = from_numpy ( array , origin = origin , spacing = spacing , direction = direction , has_components = has_components ) return image . clone ( pixeltype ) | Make an image with given size and voxel value or given a mask and vector |
43,202 | def matrix_to_images ( data_matrix , mask ) : if data_matrix . ndim > 2 : data_matrix = data_matrix . reshape ( data_matrix . shape [ 0 ] , - 1 ) numimages = len ( data_matrix ) numVoxelsInMatrix = data_matrix . shape [ 1 ] numVoxelsInMask = ( mask >= 0.5 ) . sum ( ) if numVoxelsInMask != numVoxelsInMatrix : raise ValueError ( 'Num masked voxels %i must match data matrix %i' % ( numVoxelsInMask , numVoxelsInMatrix ) ) imagelist = [ ] for i in range ( numimages ) : img = mask . clone ( ) img [ mask >= 0.5 ] = data_matrix [ i , : ] imagelist . append ( img ) return imagelist | Unmasks rows of a matrix and writes as images |
43,203 | def images_to_matrix ( image_list , mask = None , sigma = None , epsilon = 0.5 ) : def listfunc ( x ) : if np . sum ( np . array ( x . shape ) - np . array ( mask . shape ) ) != 0 : x = reg . resample_image_to_target ( x , mask , 2 ) return x [ mask ] if mask is None : mask = utils . get_mask ( image_list [ 0 ] ) num_images = len ( image_list ) mask_arr = mask . numpy ( ) >= epsilon num_voxels = np . sum ( mask_arr ) data_matrix = np . empty ( ( num_images , num_voxels ) ) do_smooth = sigma is not None for i , img in enumerate ( image_list ) : if do_smooth : data_matrix [ i , : ] = listfunc ( utils . smooth_image ( img , sigma , sigma_in_physical_coordinates = True ) ) else : data_matrix [ i , : ] = listfunc ( img ) return data_matrix | Read images into rows of a matrix given a mask - much faster for large datasets as it is based on C ++ implementations . |
43,204 | def timeseries_to_matrix ( image , mask = None ) : temp = utils . ndimage_to_list ( image ) if mask is None : mask = temp [ 0 ] * 0 + 1 return image_list_to_matrix ( temp , mask ) | Convert a timeseries image into a matrix . |
43,205 | def matrix_to_timeseries ( image , matrix , mask = None ) : if mask is None : mask = temp [ 0 ] * 0 + 1 temp = matrix_to_images ( matrix , mask ) newImage = utils . list_to_ndimage ( image , temp ) iio . copy_image_info ( image , newImage ) return ( newImage ) | converts a matrix to a ND image . |
43,206 | def image_header_info ( filename ) : if not os . path . exists ( filename ) : raise Exception ( 'filename does not exist' ) libfn = utils . get_lib_fn ( 'antsImageHeaderInfo' ) retval = libfn ( filename ) retval [ 'dimensions' ] = tuple ( retval [ 'dimensions' ] ) retval [ 'origin' ] = tuple ( [ round ( o , 4 ) for o in retval [ 'origin' ] ] ) retval [ 'spacing' ] = tuple ( [ round ( s , 4 ) for s in retval [ 'spacing' ] ] ) retval [ 'direction' ] = np . round ( retval [ 'direction' ] , 4 ) return retval | Read file info from image header |
43,207 | def image_read ( filename , dimension = None , pixeltype = 'float' , reorient = False ) : if filename . endswith ( '.npy' ) : filename = os . path . expanduser ( filename ) img_array = np . load ( filename ) if os . path . exists ( filename . replace ( '.npy' , '.json' ) ) : with open ( filename . replace ( '.npy' , '.json' ) ) as json_data : img_header = json . load ( json_data ) ants_image = from_numpy ( img_array , origin = img_header . get ( 'origin' , None ) , spacing = img_header . get ( 'spacing' , None ) , direction = np . asarray ( img_header . get ( 'direction' , None ) ) , has_components = img_header . get ( 'components' , 1 ) > 1 ) else : img_header = { } ants_image = from_numpy ( img_array ) else : filename = os . path . expanduser ( filename ) if not os . path . exists ( filename ) : raise ValueError ( 'File %s does not exist!' % filename ) hinfo = image_header_info ( filename ) ptype = hinfo [ 'pixeltype' ] pclass = hinfo [ 'pixelclass' ] ndim = hinfo [ 'nDimensions' ] ncomp = hinfo [ 'nComponents' ] is_rgb = True if pclass == 'rgb' else False if dimension is not None : ndim = dimension if pclass not in _supported_pclasses : raise ValueError ( 'Pixel class %s not supported!' % pclass ) if ptype in _unsupported_ptypes : ptype = _unsupported_ptype_map . get ( ptype , 'unsupported' ) if ptype == 'unsupported' : raise ValueError ( 'Pixeltype %s not supported' % ptype ) if ( ndim < 2 ) or ( ndim > 4 ) : raise ValueError ( 'Found %i-dimensional image - not supported!' % ndim ) libfn = utils . get_lib_fn ( _image_read_dict [ pclass ] [ ptype ] [ ndim ] ) itk_pointer = libfn ( filename ) ants_image = iio . ANTsImage ( pixeltype = ptype , dimension = ndim , components = ncomp , pointer = itk_pointer , is_rgb = is_rgb ) if pixeltype is not None : ants_image = ants_image . clone ( pixeltype ) if ( reorient != False ) and ( ants_image . dimension == 3 ) : if reorient == True : ants_image = ants_image . reorient_image2 ( 'RPI' ) elif isinstance ( reorient , str ) : ants_image = ants_image . reorient_image2 ( reorient ) return ants_image | Read an ANTsImage from file |
43,208 | def dicom_read ( directory , pixeltype = 'float' ) : slices = [ ] imgidx = 0 for imgpath in os . listdir ( directory ) : if imgpath . endswith ( '.dcm' ) : if imgidx == 0 : tmp = image_read ( os . path . join ( directory , imgpath ) , dimension = 3 , pixeltype = pixeltype ) origin = tmp . origin spacing = tmp . spacing direction = tmp . direction tmp = tmp . numpy ( ) [ : , : , 0 ] else : tmp = image_read ( os . path . join ( directory , imgpath ) , dimension = 2 , pixeltype = pixeltype ) . numpy ( ) slices . append ( tmp ) imgidx += 1 slices = np . stack ( slices , axis = - 1 ) return from_numpy ( slices , origin = origin , spacing = spacing , direction = direction ) | 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 . |
43,209 | def image_write ( image , filename , ri = False ) : if filename . endswith ( '.npy' ) : img_array = image . numpy ( ) img_header = { 'origin' : image . origin , 'spacing' : image . spacing , 'direction' : image . direction . tolist ( ) , 'components' : image . components } np . save ( filename , img_array ) with open ( filename . replace ( '.npy' , '.json' ) , 'w' ) as outfile : json . dump ( img_header , outfile ) else : image . to_file ( filename ) if ri : return image | Write an ANTsImage to file |
43,210 | def otsu_segmentation ( image , k , mask = None ) : if mask is not None : image = image . mask_image ( mask ) seg = image . threshold_image ( 'Otsu' , k ) return seg | Otsu image segmentation |
43,211 | def crop_image ( image , label_image = None , label = 1 ) : inpixeltype = image . pixeltype ndim = image . dimension if image . pixeltype != 'float' : image = image . clone ( 'float' ) if label_image is None : label_image = get_mask ( image ) if label_image . pixeltype != 'float' : label_image = label_image . clone ( 'float' ) libfn = utils . get_lib_fn ( 'cropImageF%i' % ndim ) itkimage = libfn ( image . pointer , label_image . pointer , label , 0 , [ ] , [ ] ) return iio . ANTsImage ( pixeltype = 'float' , dimension = ndim , components = image . components , pointer = itkimage ) . clone ( inpixeltype ) | Use a label image to crop a smaller ANTsImage from within a larger ANTsImage |
43,212 | def decrop_image ( cropped_image , full_image ) : inpixeltype = 'float' if cropped_image . pixeltype != 'float' : inpixeltype = cropped_image . pixeltype cropped_image = cropped_image . clone ( 'float' ) if full_image . pixeltype != 'float' : full_image = full_image . clone ( 'float' ) libfn = utils . get_lib_fn ( 'cropImageF%i' % cropped_image . dimension ) itkimage = libfn ( cropped_image . pointer , full_image . pointer , 1 , 1 , [ ] , [ ] ) ants_image = iio . ANTsImage ( pixeltype = 'float' , dimension = cropped_image . dimension , components = cropped_image . components , pointer = itkimage ) if inpixeltype != 'float' : ants_image = ants_image . clone ( inpixeltype ) return ants_image | The inverse function for ants . crop_image |
43,213 | def kmeans_segmentation ( image , k , kmask = None , mrf = 0.1 ) : dim = image . dimension kmimage = utils . iMath ( image , 'Normalize' ) if kmask is None : kmask = utils . get_mask ( kmimage , 0.01 , 1 , cleanup = 2 ) kmask = utils . iMath ( kmask , 'FillHoles' ) . threshold_image ( 1 , 2 ) nhood = 'x' . join ( [ '1' ] * dim ) mrf = '[%s,%s]' % ( str ( mrf ) , nhood ) kmimage = atropos ( a = kmimage , m = mrf , c = '[5,0]' , i = 'kmeans[%s]' % ( str ( k ) ) , x = kmask ) kmimage [ 'segmentation' ] = kmimage [ 'segmentation' ] . clone ( image . pixeltype ) return kmimage | K - means image segmentation that is a wrapper around ants . atropos |
43,214 | def reorient_image2 ( image , orientation = 'RAS' ) : if image . dimension != 3 : raise ValueError ( 'image must have 3 dimensions' ) inpixeltype = image . pixeltype ndim = image . dimension if image . pixeltype != 'float' : image = image . clone ( 'float' ) libfn = utils . get_lib_fn ( 'reorientImage2' ) itkimage = libfn ( image . pointer , orientation ) new_img = iio . ANTsImage ( pixeltype = 'float' , dimension = ndim , components = image . components , pointer = itkimage ) if inpixeltype != 'float' : new_img = new_img . clone ( inpixeltype ) return new_img | Reorient an image . |
43,215 | def reorient_image ( image , axis1 , axis2 = None , doreflection = False , doscale = 0 , txfn = None ) : inpixeltype = image . pixeltype if image . pixeltype != 'float' : image = image . clone ( 'float' ) axis_was_none = False if axis2 is None : axis_was_none = True axis2 = [ 0 ] * image . dimension axis1 = np . array ( axis1 ) axis2 = np . array ( axis2 ) axis1 = axis1 / np . sqrt ( np . sum ( axis1 * axis1 ) ) * ( - 1 ) axis1 = axis1 . astype ( 'int' ) if not axis_was_none : axis2 = axis2 / np . sqrt ( np . sum ( axis2 * axis2 ) ) * ( - 1 ) axis2 = axis2 . astype ( 'int' ) else : axis2 = np . array ( [ 0 ] * image . dimension ) . astype ( 'int' ) if txfn is None : txfn = mktemp ( suffix = '.mat' ) if isinstance ( doreflection , tuple ) : doreflection = list ( doreflection ) if not isinstance ( doreflection , list ) : doreflection = [ doreflection ] if isinstance ( doscale , tuple ) : doscale = list ( doscale ) if not isinstance ( doscale , list ) : doscale = [ doscale ] if len ( doreflection ) == 1 : doreflection = [ doreflection [ 0 ] ] * image . dimension if len ( doscale ) == 1 : doscale = [ doscale [ 0 ] ] * image . dimension libfn = utils . get_lib_fn ( 'reorientImage%s' % image . _libsuffix ) libfn ( image . pointer , txfn , axis1 . tolist ( ) , axis2 . tolist ( ) , doreflection , doscale ) image2 = apply_transforms ( image , image , transformlist = [ txfn ] ) if image . pixeltype != inpixeltype : image2 = image2 . clone ( inpixeltype ) return { 'reoimage' : image2 , 'txfn' : txfn } | Align image along a specified axis |
43,216 | def get_center_of_mass ( image ) : if image . pixeltype != 'float' : image = image . clone ( 'float' ) libfn = utils . get_lib_fn ( 'centerOfMass%s' % image . _libsuffix ) com = libfn ( image . pointer ) return tuple ( com ) | Compute an image center of mass in physical space which is defined as the mean of the intensity weighted voxel coordinate system . |
43,217 | def to_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 ) . reshape ( 3 , 1 ) ] ) affine = np . vstack ( [ affine , np . array ( [ 0 , 0 , 0 , 1. ] ) ] ) affine [ : 2 , : ] *= - 1 new_img = nib . Nifti1Image ( array_data , affine ) return new_img | Convert an ANTsImage to a Nibabel image |
43,218 | def from_nibabel ( nib_image ) : tmpfile = mktemp ( suffix = '.nii.gz' ) nib_image . to_filename ( tmpfile ) new_img = iio2 . image_read ( tmpfile ) os . remove ( tmpfile ) return new_img | Convert a nibabel image to an ANTsImage |
43,219 | def transform ( self , X = None , y = None ) : shear_x = random . gauss ( self . shear_range [ 0 ] , self . shear_range [ 1 ] ) shear_y = random . gauss ( self . shear_range [ 0 ] , self . shear_range [ 1 ] ) shear_z = random . gauss ( self . shear_range [ 0 ] , self . shear_range [ 1 ] ) self . params = ( shear_x , shear_y , shear_z ) tx = Shear3D ( ( shear_x , shear_y , shear_z ) , reference = self . reference , lazy = self . lazy ) return tx . transform ( X , y ) | Transform an image using an Affine transform with shear parameters randomly generated from the user - specified range . Return the transform if X = None . |
43,220 | def transform ( self , X = None , y = None ) : zoom_x = np . exp ( random . gauss ( np . log ( self . zoom_range [ 0 ] ) , np . log ( self . zoom_range [ 1 ] ) ) ) zoom_y = np . exp ( random . gauss ( np . log ( self . zoom_range [ 0 ] ) , np . log ( self . zoom_range [ 1 ] ) ) ) zoom_z = np . exp ( random . gauss ( np . log ( self . zoom_range [ 0 ] ) , np . log ( self . zoom_range [ 1 ] ) ) ) self . params = ( zoom_x , zoom_y , zoom_z ) tx = Zoom3D ( ( zoom_x , zoom_y , zoom_z ) , reference = self . reference , lazy = self . lazy ) return tx . transform ( X , y ) | Transform an image using an Affine transform with zoom parameters randomly generated from the user - specified range . Return the transform if X = None . |
43,221 | def transform ( self , X = None , y = None ) : translation_x , translation_y = self . translation translation_matrix = np . array ( [ [ 1 , 0 , translation_x ] , [ 0 , 1 , translation_y ] ] ) self . tx . set_parameters ( translation_matrix ) if self . lazy or X is None : return self . tx else : return self . tx . apply_to_image ( X , reference = self . reference ) | Transform an image using an Affine transform with the given translation parameters . Return the transform if X = None . |
43,222 | def transform ( self , X = None , y = None ) : translation_x = random . gauss ( self . translation_range [ 0 ] , self . translation_range [ 1 ] ) translation_y = random . gauss ( self . translation_range [ 0 ] , self . translation_range [ 1 ] ) self . params = ( translation_x , translation_y ) tx = Translate2D ( ( translation_x , translation_y ) , reference = self . reference , lazy = self . lazy ) return tx . transform ( X , y ) | Transform an image using an Affine transform with translation parameters randomly generated from the user - specified range . Return the transform if X = None . |
43,223 | def transform ( self , X = None , y = None ) : shear = [ math . pi / 180 * s for s in self . shear ] shear_x , shear_y = shear shear_matrix = np . array ( [ [ 1 , shear_x , 0 ] , [ shear_y , 1 , 0 ] ] ) self . tx . set_parameters ( shear_matrix ) if self . lazy or X is None : return self . tx else : return self . tx . apply_to_image ( X , reference = self . reference ) | Transform an image using an Affine transform with the given shear parameters . Return the transform if X = None . |
43,224 | def transform ( self , X = None , y = None ) : zoom_x , zoom_y = self . zoom self . params = ( zoom_x , zoom_y ) zoom_matrix = np . array ( [ [ zoom_x , 0 , 0 ] , [ 0 , zoom_y , 0 ] ] ) self . tx . set_parameters ( zoom_matrix ) if self . lazy or X is None : return self . tx else : return self . tx . apply_to_image ( X , reference = self . reference ) | Transform an image using an Affine transform with the given zoom parameters . Return the transform if X = None . |
43,225 | def kelly_kapowski ( s , g , w , its = 50 , r = 0.025 , m = 1.5 , ** kwargs ) : if isinstance ( s , iio . ANTsImage ) : s = s . clone ( 'unsigned int' ) d = s . dimension outimg = g . clone ( ) kellargs = { 'd' : d , 's' : s , 'g' : g , 'w' : w , 'c' : its , 'r' : r , 'm' : m , 'o' : outimg } for k , v in kwargs . items ( ) : kellargs [ k ] = v processed_kellargs = utils . _int_antsProcessArguments ( kellargs ) libfn = utils . get_lib_fn ( 'KellyKapowski' ) libfn ( processed_kellargs ) return outimg | Compute cortical thickness using the DiReCT algorithm . |
43,226 | def new_ants_transform ( precision = 'float' , dimension = 3 , transform_type = 'AffineTransform' , parameters = None ) : libfn = utils . get_lib_fn ( 'newAntsTransform%s%i' % ( utils . short_ptype ( precision ) , dimension ) ) itk_tx = libfn ( precision , dimension , transform_type ) ants_tx = tio . ANTsTransform ( precision = precision , dimension = dimension , transform_type = transform_type , pointer = itk_tx ) if parameters is not None : ants_tx . set_parameters ( parameters ) return ants_tx | Create a new ANTsTransform |
43,227 | def create_ants_transform ( transform_type = 'AffineTransform' , precision = 'float' , dimension = 3 , matrix = None , offset = None , center = None , translation = None , parameters = None , fixed_parameters = None , displacement_field = None , supported_types = False ) : def _check_arg ( arg , dim = 1 ) : if arg is None : if dim == 1 : return [ ] elif dim == 2 : return [ [ ] ] elif isinstance ( arg , np . ndarray ) : return arg . tolist ( ) elif isinstance ( arg , ( tuple , list ) ) : return list ( arg ) else : raise ValueError ( 'Incompatible input argument' ) matrix = _check_arg ( matrix , dim = 2 ) offset = _check_arg ( offset ) center = _check_arg ( center ) translation = _check_arg ( translation ) parameters = _check_arg ( parameters ) fixed_parameters = _check_arg ( fixed_parameters ) matrix_offset_types = { 'AffineTransform' , 'CenteredAffineTransform' , 'Euler2DTransform' , 'Euler3DTransform' , 'Rigid3DTransform' , 'Rigid2DTransform' , 'QuaternionRigidTransform' , 'Similarity2DTransform' , 'CenteredSimilarity2DTransform' , 'Similarity3DTransform' , 'CenteredRigid2DTransform' , 'CenteredEuler3DTransform' } if supported_types : return set ( list ( matrix_offset_types ) + [ 'DisplacementFieldTransform' ] ) if ( dimension < 2 ) or ( dimension > 4 ) : raise ValueError ( 'Unsupported dimension: %i' % dimension ) precision_types = ( 'float' , 'double' ) if precision not in precision_types : raise ValueError ( 'Unsupported Precision %s' % str ( precision ) ) if ( transform_type not in matrix_offset_types ) and ( transform_type != 'DisplacementFieldTransform' ) : raise ValueError ( 'Unsupported type %s' % str ( transform_type ) ) if ( transform_type == 'Euler3DTransform' ) : dimension = 3 elif ( transform_type == 'Euler2DTransform' ) : dimension = 2 elif ( transform_type == 'Rigid3DTransform' ) : dimension = 3 elif ( transform_type == 'QuaternionRigidTransform' ) : dimension = 3 elif ( transform_type == 'Rigid2DTransform' ) : dimension = 2 elif ( transform_type == 'CenteredRigid2DTransform' ) : dimension = 2 elif ( transform_type == 'CenteredEuler3DTransform' ) : dimension = 3 elif ( transform_type == 'Similarity3DTransform' ) : dimension = 3 elif ( transform_type == 'Similarity2DTransform' ) : dimension = 2 elif ( transform_type == 'CenteredSimilarity2DTransform' ) : dimension = 2 if displacement_field is not None : raise ValueError ( 'Displacement field transform not currently supported' ) libfn = utils . get_lib_fn ( 'matrixOffset%s%i' % ( utils . short_ptype ( precision ) , dimension ) ) itk_tx = libfn ( transform_type , precision , dimension , matrix , offset , center , translation , parameters , fixed_parameters ) return tio . ANTsTransform ( precision = precision , dimension = dimension , transform_type = transform_type , pointer = itk_tx ) | Create and initialize an ANTsTransform |
43,228 | def read_transform ( filename , dimension = 2 , precision = 'float' ) : filename = os . path . expanduser ( filename ) if not os . path . exists ( filename ) : raise ValueError ( 'filename does not exist!' ) libfn1 = utils . get_lib_fn ( 'getTransformDimensionFromFile' ) dimension = libfn1 ( filename ) libfn2 = utils . get_lib_fn ( 'getTransformNameFromFile' ) transform_type = libfn2 ( filename ) libfn3 = utils . get_lib_fn ( 'readTransform%s%i' % ( utils . short_ptype ( precision ) , dimension ) ) itk_tx = libfn3 ( filename , dimension , precision ) return tio . ANTsTransform ( precision = precision , dimension = dimension , transform_type = transform_type , pointer = itk_tx ) | Read a transform from file |
43,229 | def write_transform ( transform , filename ) : filename = os . path . expanduser ( filename ) libfn = utils . get_lib_fn ( 'writeTransform%s' % ( transform . _libsuffix ) ) libfn ( transform . pointer , filename ) | Write ANTsTransform to file |
43,230 | def reflect_image ( image , axis = None , tx = None , metric = 'mattes' ) : if axis is None : axis = image . dimension - 1 if ( axis > image . dimension ) or ( axis < 0 ) : axis = image . dimension - 1 rflct = mktemp ( suffix = '.mat' ) libfn = utils . get_lib_fn ( 'reflectionMatrix%s' % image . _libsuffix ) libfn ( image . pointer , axis , rflct ) if tx is not None : rfi = registration ( image , image , type_of_transform = tx , syn_metric = metric , outprefix = mktemp ( ) , initial_transform = rflct ) return rfi else : return apply_transforms ( image , image , rflct ) | Reflect an image along an axis |
43,231 | def create_sampler ( self , inputs , targets , input_reader = None , target_reader = None , input_transform = None , target_transform = None , co_transform = None , input_return_processor = None , target_return_processor = None , co_return_processor = None ) : pass | Create a BIDSSampler that can be used to generate infinite augmented samples |
43,232 | def slice_image ( image , axis = None , idx = None ) : if image . dimension < 3 : raise ValueError ( 'image must have at least 3 dimensions' ) inpixeltype = image . pixeltype ndim = image . dimension if image . pixeltype != 'float' : image = image . clone ( 'float' ) libfn = utils . get_lib_fn ( 'sliceImageF%i' % ndim ) itkimage = libfn ( image . pointer , axis , idx ) return iio . ANTsImage ( pixeltype = 'float' , dimension = ndim - 1 , components = image . components , pointer = itkimage ) . clone ( inpixeltype ) | Slice an image . |
43,233 | def pad_image ( image , shape = None , pad_width = None , value = 0.0 , return_padvals = False ) : inpixeltype = image . pixeltype ndim = image . dimension if image . pixeltype != 'float' : image = image . clone ( 'float' ) if pad_width is None : if shape is None : shape = [ max ( image . shape ) ] * image . dimension lower_pad_vals = [ math . floor ( max ( ns - os , 0 ) / 2 ) for os , ns in zip ( image . shape , shape ) ] upper_pad_vals = [ math . ceil ( max ( ns - os , 0 ) / 2 ) for os , ns in zip ( image . shape , shape ) ] else : if shape is not None : raise ValueError ( 'Cannot give both `shape` and `pad_width`. Pick one!' ) if len ( pad_width ) != image . dimension : raise ValueError ( 'Must give pad width for each image dimension' ) lower_pad_vals = [ ] upper_pad_vals = [ ] for p in pad_width : if isinstance ( p , ( list , tuple ) ) : lower_pad_vals . append ( p [ 0 ] ) upper_pad_vals . append ( p [ 1 ] ) else : lower_pad_vals . append ( math . floor ( p / 2 ) ) upper_pad_vals . append ( math . ceil ( p / 2 ) ) libfn = utils . get_lib_fn ( 'padImageF%i' % ndim ) itkimage = libfn ( image . pointer , lower_pad_vals , upper_pad_vals , value ) new_image = iio . ANTsImage ( pixeltype = 'float' , dimension = ndim , components = image . components , pointer = itkimage ) . clone ( inpixeltype ) if return_padvals : return new_image , lower_pad_vals , upper_pad_vals else : return new_image | Pad an image to have the given shape or to be isotropic . |
43,234 | def set_fixed_image ( self , image ) : 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 dim (%i)' % ( image . dimension , self . dimension ) ) self . _metric . setFixedImage ( image . pointer , False ) self . fixed_image = image | Set Fixed ANTsImage for metric |
43,235 | def set_moving_image ( self , image ) : 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 dim (%i)' % ( image . dimension , self . dimension ) ) self . _metric . setMovingImage ( image . pointer , False ) self . moving_image = image | Set Moving ANTsImage for metric |
43,236 | def image_to_cluster_images ( image , min_cluster_size = 50 , min_thresh = 1e-06 , max_thresh = 1 ) : if not isinstance ( image , iio . ANTsImage ) : raise ValueError ( 'image must be ANTsImage type' ) clust = label_clusters ( image , min_cluster_size , min_thresh , max_thresh ) labs = np . unique ( clust [ clust > 0 ] ) clustlist = [ ] for i in range ( len ( labs ) ) : labimage = image . clone ( ) labimage [ clust != labs [ i ] ] = 0 clustlist . append ( labimage ) return clustlist | Converts an image to several independent images . |
43,237 | def threshold_image ( image , low_thresh = None , high_thresh = None , inval = 1 , outval = 0 , binary = True ) : if high_thresh is None : high_thresh = image . max ( ) + 0.01 if low_thresh is None : low_thresh = image . min ( ) - 0.01 dim = image . dimension outimage = image . clone ( ) args = [ dim , image , outimage , low_thresh , high_thresh , inval , outval ] processed_args = _int_antsProcessArguments ( args ) libfn = utils . get_lib_fn ( 'ThresholdImage' ) libfn ( processed_args ) if binary : return outimage else : return outimage * image | Converts a scalar image into a binary image by thresholding operations |
43,238 | def symmetrize_image ( image ) : imager = reflect_image ( image , axis = 0 ) imageavg = imager * 0.5 + image for i in range ( 5 ) : w1 = registration ( imageavg , image , type_of_transform = 'SyN' ) w2 = registration ( imageavg , imager , type_of_transform = 'SyN' ) xavg = w1 [ 'warpedmovout' ] * 0.5 + w2 [ 'warpedmovout' ] * 0.5 nada1 = apply_transforms ( image , image , w1 [ 'fwdtransforms' ] , compose = w1 [ 'fwdtransforms' ] [ 0 ] ) nada2 = apply_transforms ( image , image , w2 [ 'fwdtransforms' ] , compose = w2 [ 'fwdtransforms' ] [ 0 ] ) wavg = ( iio . image_read ( nada1 ) + iio . image_read ( nada2 ) ) * ( - 0.5 ) wavgfn = mktemp ( suffix = '.nii.gz' ) iio . image_write ( wavg , wavgfn ) xavg = apply_transforms ( image , imageavg , wavgfn ) return xavg | Use registration and reflection to make an image symmetric |
43,239 | def _get_attachments ( self , id ) : uri = '/' . join ( [ self . base_url , self . name , id , 'Attachments' ] ) + '/' return uri , { } , 'get' , None , None , False | Retrieve a list of attachments associated with this Xero object . |
43,240 | def _put_attachment_data ( self , id , filename , data , content_type , include_online = False ) : uri = '/' . join ( [ self . base_url , self . name , id , 'Attachments' , filename ] ) params = { 'IncludeOnline' : 'true' } if include_online else { } headers = { 'Content-Type' : content_type , 'Content-Length' : str ( len ( data ) ) } return uri , params , 'put' , data , headers , False | Upload an attachment to the Xero object . |
43,241 | def page_response ( self , title = '' , body = '' ) : 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' . format ( title ) ) f . write ( '<div class="content">{}</div>\n' . format ( body ) ) f . write ( '</body>\n</html>\n' ) length = f . tell ( ) f . seek ( 0 ) self . send_response ( 200 ) encoding = sys . getfilesystemencoding ( ) self . send_header ( "Content-type" , "text/html; charset=%s" % encoding ) self . send_header ( "Content-Length" , str ( length ) ) self . end_headers ( ) self . copyfile ( f , self . wfile ) f . close ( ) | Helper to render an html page with dynamic content |
43,242 | def redirect_response ( self , url , permanent = False ) : if permanent : self . send_response ( 301 ) else : self . send_response ( 302 ) self . send_header ( "Location" , url ) self . end_headers ( ) | Generate redirect response |
43,243 | 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 : self . _init_oauth ( oauth_token , oauth_token_secret ) else : self . oauth_token = oauth_token self . oauth_token_secret = oauth_token_secret else : oauth = OAuth1 ( self . consumer_key , client_secret = self . consumer_secret , callback_uri = self . callback_uri , rsa_key = self . rsa_key , signature_method = self . _signature_method ) url = self . base_url + REQUEST_TOKEN_URL headers = { 'User-Agent' : self . user_agent } response = requests . post ( url = url , headers = headers , auth = oauth ) self . _process_oauth_response ( response ) | Depending on the state passed in get self . _oauth up and running |
43,244 | 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_secret , resource_owner_key = self . oauth_token , resource_owner_secret = self . oauth_token_secret , rsa_key = self . rsa_key , signature_method = self . _signature_method ) | Store and initialize a verified set of OAuth credentials |
43,245 | def _process_oauth_response ( self , response ) : "Extracts the fields from an oauth response" if response . status_code == 200 : credentials = parse_qs ( response . text ) self . _init_oauth ( credentials . get ( 'oauth_token' ) [ 0 ] , credentials . get ( 'oauth_token_secret' ) [ 0 ] ) self . oauth_session_handle = credentials . get ( 'oauth_session_handle' , [ None ] ) [ 0 ] oauth_expires_in = credentials . get ( 'oauth_expires_in' , [ OAUTH_EXPIRY_SECONDS ] ) [ 0 ] oauth_authorisation_expires_in = credentials . get ( 'oauth_authorization_expires_in' , [ OAUTH_EXPIRY_SECONDS ] ) [ 0 ] self . oauth_expires_at = datetime . datetime . now ( ) + datetime . timedelta ( seconds = int ( oauth_expires_in ) ) self . oauth_authorization_expires_at = datetime . datetime . now ( ) + datetime . timedelta ( seconds = int ( oauth_authorisation_expires_in ) ) else : self . _handle_error_response ( response ) | Extracts the fields from an oauth response |
43,246 | def state ( self ) : return dict ( ( attr , getattr ( self , attr ) ) for attr in ( 'consumer_key' , 'consumer_secret' , 'callback_uri' , 'verified' , 'oauth_token' , 'oauth_token_secret' , 'oauth_session_handle' , 'oauth_expires_at' , 'oauth_authorization_expires_at' , 'scope' ) if getattr ( self , attr ) is not None ) | Obtain the useful state of this credentials object so that we can reconstruct it independently . |
43,247 | def verify ( self , verifier ) : "Verify an OAuth token" oauth = OAuth1 ( self . consumer_key , client_secret = self . consumer_secret , resource_owner_key = self . oauth_token , resource_owner_secret = self . oauth_token_secret , verifier = verifier , rsa_key = self . rsa_key , signature_method = self . _signature_method ) url = self . base_url + ACCESS_TOKEN_URL headers = { 'User-Agent' : self . user_agent } response = requests . post ( url = url , headers = headers , auth = oauth ) self . _process_oauth_response ( response ) self . verified = True | Verify an OAuth token |
43,248 | def url ( self ) : "Returns the URL that can be visited to obtain a verifier code" query_string = { 'oauth_token' : self . oauth_token } if self . scope : query_string [ 'scope' ] = self . scope url = XERO_BASE_URL + AUTHORIZE_URL + '?' + urlencode ( query_string ) return url | Returns the URL that can be visited to obtain a verifier code |
43,249 | def refresh ( self ) : "Refresh an expired token" oauth = OAuth1 ( self . consumer_key , client_secret = self . consumer_secret , resource_owner_key = self . oauth_token , resource_owner_secret = self . oauth_token_secret , rsa_key = self . rsa_key , signature_method = self . _signature_method ) headers = { 'User-Agent' : self . user_agent } params = { 'oauth_session_handle' : self . oauth_session_handle } response = requests . post ( url = self . base_url + ACCESS_TOKEN_URL , params = params , headers = headers , auth = oauth ) self . _process_oauth_response ( response ) | Refresh an expired token |
43,250 | def _get_files ( self , folderId ) : uri = '/' . join ( [ self . base_url , self . name , folderId , 'Files' ] ) return uri , { } , 'get' , None , None , False , None | Retrieve the list of files contained in a folder |
43,251 | def handle_cluster_request ( self , tsn , command_id , args ) : 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 ) | Handle the cluster command . |
43,252 | def _parse_attributes ( self , value ) : 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 : XIAOMI_ATTR_6 , 10 : PATH } result = { } while value : skey = int ( value [ 0 ] ) svalue , value = f . TypeValue . deserialize ( value [ 1 : ] ) result [ skey ] = svalue . value for item , value in result . items ( ) : key = attribute_names [ item ] if item in attribute_names else "0xff01-" + str ( item ) attributes [ key ] = value if BATTERY_VOLTAGE_MV in attributes : attributes [ BATTERY_LEVEL ] = int ( self . _calculate_remaining_battery_percentage ( attributes [ BATTERY_VOLTAGE_MV ] ) ) return attributes | Parse non standard atrributes . |
43,253 | def _calculate_remaining_battery_percentage ( self , voltage ) : min_voltage = 2500 max_voltage = 3000 percent = ( voltage - min_voltage ) / ( max_voltage - min_voltage ) * 200 return min ( 200 , percent ) | Calculate percentage . |
43,254 | def battery_reported ( self , voltage , rawVoltage ) : self . _update_attribute ( BATTERY_PERCENTAGE_REMAINING , voltage ) self . _update_attribute ( self . BATTERY_VOLTAGE_ATTR , int ( rawVoltage / 100 ) ) | Battery reported . |
43,255 | async def configure_reporting ( self , attribute , min_interval , max_interval , reportable_change ) : result = await super ( ) . configure_reporting ( PowerConfigurationCluster . BATTERY_VOLTAGE_ATTR , self . FREQUENCY , self . FREQUENCY , self . MINIMUM_CHANGE ) return result | Configure reporting . |
43,256 | def update ( self , ** kwargs ) : inherit_device_group = self . __dict__ . get ( 'inheritedDevicegroup' , False ) if inherit_device_group == 'true' : self . __dict__ . pop ( 'deviceGroup' ) return self . _update ( ** kwargs ) | Update the object removing device group if inherited |
43,257 | def sync_to ( self ) : device_group_collection = self . _meta_data [ 'container' ] cm = device_group_collection . _meta_data [ 'container' ] sync_cmd = 'config-sync to-group %s' % self . name cm . exec_cmd ( 'run' , utilCmdArgs = sync_cmd ) | Wrapper method that synchronizes configuration to DG . |
43,258 | def _create ( self , ** kwargs ) : try : return super ( Service , self ) . _create ( ** kwargs ) except HTTPError as ex : if "The configuration was updated successfully but could not be " "retrieved" not in ex . response . text : raise if 'partition' not in kwargs : kwargs [ 'partition' ] = 'Common' kwargs_copy = kwargs . copy ( ) for key in kwargs_copy : if key not in self . _meta_data [ 'required_load_parameters' ] : kwargs . pop ( key ) return self . load ( ** kwargs ) | Create service on device and create accompanying Python object . |
43,259 | def _build_service_uri ( self , base_uri , partition , name ) : name = name . replace ( '/' , '~' ) return '%s~%s~%s.app~%s' % ( base_uri , partition , name , name ) | Build the proper uri for a service resource . |
43,260 | def delete ( self , ** kwargs ) : if 'id' not in kwargs : delete_uri = self . _meta_data [ 'uri' ] if delete_uri . endswith ( '/' ) : delete_uri = delete_uri [ 0 : - 1 ] kwargs [ 'id' ] = os . path . basename ( delete_uri ) uid = uuid . UUID ( kwargs [ 'id' ] , version = 4 ) if uid . hex != kwargs [ 'id' ] . replace ( '-' , '' ) : raise F5SDKError ( "The specified ID is invalid" ) requests_params = self . _handle_requests_params ( kwargs ) kwargs = self . _check_for_python_keywords ( kwargs ) kwargs = self . _prepare_request_json ( kwargs ) delete_uri = self . _meta_data [ 'uri' ] session = self . _meta_data [ 'bigip' ] . _meta_data [ 'icr_session' ] force = self . _check_force_arg ( kwargs . pop ( 'force' , True ) ) if not force : self . _check_generation ( ) response = session . delete ( delete_uri , json = kwargs , ** requests_params ) if response . status_code == 200 : self . __dict__ = { 'deleted' : True } time . sleep ( 1 ) | Deletes a member from a license pool |
43,261 | def _set_attributes ( self , ** kwargs ) : self . devices = kwargs [ 'devices' ] [ : ] self . partition = kwargs [ 'partition' ] self . device_group_name = 'device_trust_group' self . device_group_type = 'sync-only' | Set attributes for instance in one place |
43,262 | def validate ( self ) : self . _populate_domain ( ) missing = [ ] for domain_device in self . domain : for truster , trustees in iteritems ( self . domain ) : if domain_device not in trustees : missing . append ( ( domain_device , truster , trustees ) ) if missing : msg = '' for item in missing : msg += '\n%r is not trusted by %r, which trusts: %r' % ( item [ 0 ] , item [ 1 ] , item [ 2 ] ) raise DeviceNotTrusted ( msg ) self . device_group = DeviceGroup ( devices = self . devices , device_group_name = self . device_group_name , device_group_type = self . device_group_type , device_group_partition = self . partition ) | Validate that devices are each trusted by one another |
43,263 | def _populate_domain ( self ) : self . domain = { } for device in self . devices : device_name = get_device_info ( device ) . name ca_devices = device . tm . cm . trust_domains . trust_domain . load ( name = 'Root' ) . caDevices self . domain [ device_name ] = [ d . replace ( '/%s/' % self . partition , '' ) for d in ca_devices ] | Populate TrustDomain s domain attribute . |
43,264 | def create ( self , ** kwargs ) : self . _set_attributes ( ** kwargs ) for device in self . devices [ 1 : ] : self . _add_trustee ( device ) pollster ( self . validate ) ( ) | Add trusted peers to the root bigip device . |
43,265 | def teardown ( self ) : for device in self . devices : self . _remove_trustee ( device ) self . _populate_domain ( ) self . domain = { } | Teardown trust domain by removing trusted devices . |
43,266 | def _add_trustee ( self , device ) : device_name = get_device_info ( device ) . name if device_name in self . domain : msg = 'Device: %r is already in this trust domain.' % device_name raise DeviceAlreadyInTrustDomain ( msg ) self . _modify_trust ( self . devices [ 0 ] , self . _get_add_trustee_cmd , device ) | Add a single trusted device to the trust domain . |
43,267 | def _remove_trustee ( self , device ) : trustee_name = get_device_info ( device ) . name name_object_map = get_device_names_to_objects ( self . devices ) delete_func = self . _get_delete_trustee_cmd for truster in self . domain : if trustee_name in self . domain [ truster ] and truster != trustee_name : truster_obj = name_object_map [ truster ] self . _modify_trust ( truster_obj , delete_func , trustee_name ) self . _populate_domain ( ) for trustee in self . domain [ trustee_name ] : if trustee_name != trustee : self . _modify_trust ( device , delete_func , trustee ) self . devices . remove ( name_object_map [ trustee_name ] ) | Remove a trustee from the trust domain . |
43,268 | def _modify_trust ( self , truster , mod_peer_func , trustee ) : iapp_name = 'trusted_device' mod_peer_cmd = mod_peer_func ( trustee ) iapp_actions = self . iapp_actions . copy ( ) iapp_actions [ 'definition' ] [ 'implementation' ] = mod_peer_cmd self . _deploy_iapp ( iapp_name , iapp_actions , truster ) self . _delete_iapp ( iapp_name , truster ) | Modify a trusted peer device by deploying an iapp . |
43,269 | def _delete_iapp ( self , iapp_name , deploying_device ) : iapp = deploying_device . tm . sys . application iapp_serv = iapp . services . service . load ( name = iapp_name , partition = self . partition ) iapp_serv . delete ( ) iapp_tmpl = iapp . templates . template . load ( name = iapp_name , partition = self . partition ) iapp_tmpl . delete ( ) | Delete an iapp service and template on the root device . |
43,270 | def _deploy_iapp ( self , iapp_name , actions , deploying_device ) : tmpl = deploying_device . tm . sys . application . templates . template serv = deploying_device . tm . sys . application . services . service tmpl . create ( name = iapp_name , partition = self . partition , actions = actions ) pollster ( deploying_device . tm . sys . application . templates . template . load ) ( name = iapp_name , partition = self . partition ) serv . create ( name = iapp_name , partition = self . partition , template = '/%s/%s' % ( self . partition , iapp_name ) ) | Deploy iapp to add trusted device |
43,271 | def _get_add_trustee_cmd ( self , trustee ) : trustee_info = pollster ( get_device_info ) ( trustee ) username = trustee . _meta_data [ 'username' ] password = trustee . _meta_data [ 'password' ] return 'tmsh::modify cm trust-domain Root ca-devices add ' '\\{ %s \\} name %s username %s password %s' % ( trustee_info . managementIp , trustee_info . name , username , password ) | Get tmsh command to add a trusted device . |
43,272 | def load ( self , ** kwargs ) : kwargs [ 'transform_name' ] = True kwargs = self . _mutate_name ( kwargs ) return self . _load ( ** kwargs ) | Loads a given resource |
43,273 | def _get_section_end_index ( self , section , section_start ) : brace_count = 0 in_quote = False in_escape = False for index , char in enumerate ( self . template_str [ section_start : ] ) : if char == '\\' and not in_escape : in_escape = True elif char == '\\' and in_escape : in_escape = False if not in_escape : if char == '"' and not in_quote : in_quote = True elif char == '"' and in_quote : in_quote = False if char == '{' and not in_quote : brace_count += 1 elif char == '}' and not in_quote : brace_count -= 1 if brace_count is 0 : return index + section_start if brace_count is not 0 : raise CurlyBraceMismatchException ( 'Curly braces mismatch in section %s.' % section ) | Get end of section s content . |
43,274 | def _get_section_start_index ( self , section ) : sec_start_re = r'%s\s*\{' % section found = re . search ( sec_start_re , self . template_str ) if found : return found . end ( ) - 1 raise NonextantSectionException ( 'Section %s not found in template' % section ) | Get start of a section s content . |
43,275 | def _get_template_name ( self ) : start_pattern = r"sys application template\s+" r"(\/[\w\.\-]+\/)?" r"(?P<name>[\w\.\-]+)\s*\{" template_start = re . search ( start_pattern , self . template_str ) if template_start : return template_start . group ( 'name' ) raise NonextantTemplateNameException ( 'Template name not found.' ) | Find template name . |
43,276 | def _get_template_attr ( self , attr ) : attr_re = r'{0}\s+.*' . format ( attr ) attr_found = re . search ( attr_re , self . template_str ) if attr_found : attr_value = attr_found . group ( 0 ) . replace ( attr , '' , 1 ) return attr_value . strip ( ) | Find the attribute value for a specific attribute . |
43,277 | def _add_sections ( self ) : for section in self . template_sections : try : sec_start = self . _get_section_start_index ( section ) except NonextantSectionException : if section in self . sections_not_required : continue raise sec_end = self . _get_section_end_index ( section , sec_start ) section_value = self . template_str [ sec_start + 1 : sec_end ] . strip ( ) section , section_value = self . _transform_key_value ( section , section_value , self . section_map ) self . templ_dict [ 'actions' ] [ 'definition' ] [ section ] = section_value self . template_str = self . template_str [ : sec_start + 1 ] + self . template_str [ sec_end : ] | Add the found and required sections to the templ_dict . |
43,278 | def _add_cli_scripts ( self ) : pattern = r"cli script\s+" r"(\/[\w\.\-]+\/)?" r"(?P<name>[\w\.\-]+)\s*\{" sections = re . finditer ( pattern , self . template_str ) for section in sections : if 'scripts' not in self . templ_dict : self . templ_dict [ 'scripts' ] = [ ] try : sec_start = self . _get_section_start_index ( section . group ( 'name' ) ) except NonextantSectionException : continue sec_end = self . _get_section_end_index ( section . group ( 'name' ) , sec_start ) section_value = self . template_str [ sec_start + 1 : sec_end ] . strip ( ) self . templ_dict [ 'scripts' ] . append ( dict ( name = section . group ( 'name' ) , script = section_value ) ) self . template_str = self . template_str [ : sec_start + 1 ] + self . template_str [ sec_end : ] | Add the found external sections to the templ_dict . |
43,279 | def _add_attrs ( self ) : 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 , attr_value , self . attr_map ) self . templ_dict [ attr ] = attr_value | Add the found and required attrs to the templ_dict . |
43,280 | def _parse_tcl_list ( self , attr , list_str ) : list_str = list_str . strip ( ) if not list_str : return [ ] if list_str [ 0 ] != '{' and list_str [ - 1 ] != '}' : if list_str . find ( 'none' ) >= 0 : return list_str if not re . search ( self . tcl_list_patterns [ attr ] , list_str ) : raise MalformedTCLListException ( 'TCL list for "%s" is malformed. ' % attr ) list_str = list_str . strip ( '{' ) . strip ( '}' ) list_str = list_str . strip ( ) return list_str . split ( ) | Turns a string representation of a TCL list into a Python list . |
43,281 | def _transform_key_value ( self , key , value , map_dict ) : if key in self . tcl_list_patterns : value = self . _parse_tcl_list ( key , value ) if key in map_dict : key = map_dict [ key ] return key , value | Massage keys and values for iapp dict to look like JSON . |
43,282 | def parse_template ( self ) : self . templ_dict = { 'actions' : { 'definition' : { } } } self . templ_dict [ 'name' ] = self . _get_template_name ( ) self . _add_cli_scripts ( ) self . _add_sections ( ) self . _add_attrs ( ) return self . templ_dict | Parse the template string into a dict . |
43,283 | def _create ( self , ** kwargs ) : 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 changed." % ( self . _meta_data [ 'uri' ] ) raise URICreationCollision ( error ) self . _check_exclusive_parameters ( ** kwargs ) requests_params = self . _handle_requests_params ( kwargs ) self . _minimum_one_is_missing ( ** kwargs ) self . _check_create_parameters ( ** kwargs ) kwargs = self . _check_for_python_keywords ( kwargs ) for key1 , key2 in self . _meta_data [ 'reduction_forcing_pairs' ] : kwargs = self . _reduce_boolean_pair ( kwargs , key1 , key2 ) _create_uri = self . _meta_data [ 'container' ] . _meta_data [ 'uri' ] session = self . _meta_data [ 'bigip' ] . _meta_data [ 'icr_session' ] kwargs = self . _prepare_request_json ( kwargs ) response = session . post ( _create_uri , json = kwargs , ** requests_params ) result = self . _produce_instance ( response ) return result | wrapped by create override that in subclasses to customize |
43,284 | def peer ( opt_peer , opt_username , opt_password , scope = "module" ) : p = BigIP ( opt_peer , opt_username , opt_password ) return p | peer bigip fixture |
43,285 | def exists ( self , ** kwargs ) : kwargs . pop ( 'partition' , None ) kwargs [ 'transform_name' ] = True return self . _exists ( ** kwargs ) | Providing a partition is not necessary on topology ; causes errors |
43,286 | def _key_dot_replace ( self , rdict ) : 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_dict | Replace fullstops in returned keynames |
43,287 | def _get_nest_stats ( self ) : for x in self . rdict : check = urlparse ( x ) if check . scheme : nested_dict = self . rdict [ x ] [ 'nestedStats' ] tmp_dict = nested_dict [ 'entries' ] return self . _key_dot_replace ( tmp_dict ) return self . _key_dot_replace ( self . rdict ) | Helper method to deal with nestedStats |
43,288 | def refresh ( self , ** kwargs ) : self . resource . refresh ( ** kwargs ) self . rdict = self . resource . entries self . _update_stats ( ) | Refreshes stats attached to an object |
43,289 | def load ( self , ** kwargs ) : if LooseVersion ( self . tmos_ver ) == LooseVersion ( '11.6.0' ) : return self . _load_11_6 ( ** kwargs ) else : return super ( Rule , self ) . _load ( ** kwargs ) | Custom load method to address issue in 11 . 6 . 0 Final |
43,290 | def poll_for_exceptionless_callable ( callable , attempts , interval ) : @ wraps ( callable ) def poll ( * args , ** kwargs ) : for attempt in range ( attempts ) : try : return callable ( * args , ** kwargs ) except Exception as ex : if attempt == attempts - 1 : raise MaximumAttemptsReached ( ex ) time . sleep ( interval ) continue return poll | Poll with a given callable for a specified number of times . |
43,291 | def exists ( self , ** kwargs ) : if LooseVersion ( self . tmos_ver ) == LooseVersion ( '11.6.0' ) : return self . _exists_11_6 ( ** kwargs ) else : return super ( Network , self ) . _exists ( ** kwargs ) | Some objects when deleted still return when called by their |
43,292 | def _is_allowed_command ( self , command ) : cmds = self . _meta_data [ 'allowed_commands' ] if command not in self . _meta_data [ 'allowed_commands' ] : error_message = "The command value {0} does not exist. " "Valid commands are {1}" . format ( command , cmds ) raise InvalidCommand ( error_message ) | Checking if the given command is allowed on a given endpoint . |
43,293 | def _check_command_result ( self ) : if self . commandResult . startswith ( '/bin/bash' ) : raise UtilError ( '%s' % self . commandResult . split ( ' ' , 1 ) [ 1 ] ) if self . commandResult . startswith ( '/bin/mv' ) : raise UtilError ( '%s' % self . commandResult . split ( ' ' , 1 ) [ 1 ] ) if self . commandResult . startswith ( '/bin/ls' ) : raise UtilError ( '%s' % self . commandResult . split ( ' ' , 1 ) [ 1 ] ) if self . commandResult . startswith ( '/bin/rm' ) : raise UtilError ( '%s' % self . commandResult . split ( ' ' , 1 ) [ 1 ] ) if 'invalid option' in self . commandResult : raise UtilError ( '%s' % self . commandResult ) if 'Invalid option' in self . commandResult : raise UtilError ( '%s' % self . commandResult ) if 'usage: /usr/bin/get_dossier' in self . commandResult : raise UtilError ( '%s' % self . commandResult ) | If command result exists run these checks . |
43,294 | def exec_cmd ( self , command , ** kwargs ) : self . _is_allowed_command ( command ) self . _check_command_parameters ( ** kwargs ) return self . _exec_cmd ( command , ** kwargs ) | Wrapper method that can be changed in the inheriting classes . |
43,295 | def _exec_cmd ( self , command , ** kwargs ) : kwargs [ 'command' ] = command self . _check_exclusive_parameters ( ** kwargs ) requests_params = self . _handle_requests_params ( kwargs ) session = self . _meta_data [ 'bigip' ] . _meta_data [ 'icr_session' ] response = session . post ( self . _meta_data [ 'uri' ] , json = kwargs , ** requests_params ) new_instance = self . _stamp_out_core ( ) new_instance . _local_update ( response . json ( ) ) if 'commandResult' in new_instance . __dict__ : new_instance . _check_command_result ( ) return new_instance | Create a new method as command has specific requirements . |
43,296 | def get_device_info ( self , bigip ) : coll = bigip . tm . cm . devices . get_collection ( ) device = [ device for device in coll if device . selfDevice == 'true' ] assert len ( device ) == 1 return device [ 0 ] | Get device information about a specific BigIP device . |
43,297 | def _check_existence_by_collection ( self , container , item_name ) : coll = container . get_collection ( ) for item in coll : if item . name == item_name : return True return False | Check existnce of item based on get collection call . |
43,298 | def _return_object ( self , container , item_name ) : coll = container . get_collection ( ) for item in coll : if item . name == item_name : return item | Helper method to retrieve the object |
43,299 | def exec_cmd ( self , command , ** kwargs ) : if command == 'load' : if kwargs : kwargs = dict ( options = [ kwargs ] ) return self . _exec_cmd ( command , ** kwargs ) | Normal save and load only need the command . |
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