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from ..api import Api
[docs]class SynchronizationApi(Api):
'''HTTP client for image synchronization services uses the image alignment results from
the Informatics Data Processing Pipeline.
Note: all locations on SectionImages are reported in pixel coordinates
and all locations in 3-D ReferenceSpaces are reported in microns.
See `Image to Image Synchronization <http://help.brain-map.org/display/api/Image-to-Image+Synchronization>`_
for additional documentation.
'''
def __init__(self, base_uri=None):
super(SynchronizationApi, self).__init__(base_uri)
[docs] def get_image_to_atlas(self,
section_image_id,
x, y,
atlas_id):
'''For a specified Atlas, find the closest annotated SectionImage
and (x,y) location as defined by a seed SectionImage and seed (x,y) location.
Parameters
----------
section_image_id : integer
Seed for spatial sync.
x : float
Pixel coordinate of the seed location in the seed SectionImage.
y : float
Pixel coordinate of the seed location in the seed SectionImage.
atlas_id : int
Target Atlas for image sync.
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.image_to_atlas_endpoint,
'/',
str(section_image_id),
'.json',
'?x=%f&y=%f' % (x, y),
'&atlas_id=',
str(atlas_id)])
return self.json_msg_query(url)
[docs] def get_image_to_image(self,
section_image_id,
x, y,
section_data_set_ids):
'''For a list of target SectionDataSets, find the closest SectionImage
and (x,y) location as defined by a seed SectionImage and seed (x,y) pixel location.
Parameters
----------
section_image_id : integer
Seed for spatial sync.
x : float
Pixel coordinate of the seed location in the seed SectionImage.
y : float
Pixel coordinate of the seed location in the seed SectionImage.
section_data_set_ids : list of integers
Target SectionDataSet IDs for image sync.
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.image_to_image_endpoint,
'/',
str(section_image_id),
'.json',
'?x=%f&y=%f' % (x, y),
'§ion_data_set_ids=',
','.join(str(i) for i in section_data_set_ids)])
return self.json_msg_query(url)
[docs] def get_image_to_image_2d(self,
section_image_id,
x, y,
section_image_ids):
'''For a list of target SectionImages, find the closest (x,y) location
as defined by a seed SectionImage and seed (x,y) location.
Parameters
----------
section_image_id : integer
Seed for image sync.
x : float
Pixel coordinate of the seed location in the seed SectionImage.
y : float
Pixel coordinate of the seed location in the seed SectionImage.
section_image_ids : list of ints
Target SectionImage IDs for image sync.
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.image_to_image_2d_endpoint,
'/',
str(section_image_id),
'.json',
'?x=%f&y=%f' % (x, y),
'§ion_image_ids=',
','.join(str(i) for i in section_image_ids)])
return self.json_msg_query(url)
[docs] def get_reference_to_image(self,
reference_space_id,
x, y, z,
section_data_set_ids):
'''For a list of target SectionDataSets, find the closest SectionImage
and (x,y) location as defined by a (x,y,z) location in a specified ReferenceSpace.
Parameters
----------
reference_space_id : integer
Seed for spatial sync.
x : float
Coordinate (in microns) of the seed location in the seed ReferenceSpace.
y : float
Coordinate (in microns) of the seed location in the seed ReferenceSpace.
z : float
Coordinate (in microns) of the seed location in the seed ReferenceSpace.
section_data_set_ids : list of ints
Target SectionDataSets IDs for image sync.
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.reference_to_image_endpoint,
'/',
str(reference_space_id),
'.json',
'?x=%f&y=%f&z=%f' % (x, y, z),
'§ion_data_set_ids=',
','.join(str(i) for i in section_data_set_ids)])
return self.json_msg_query(url)
[docs] def get_image_to_reference(self,
section_image_id,
x, y):
'''For a specified SectionImage and (x,y) location,
return the (x,y,z) location in the ReferenceSpace of the associated SectionDataSet.
Parameters
----------
section_image_id : integer
Seed for image sync.
x : float
Pixel coordinate on the specified SectionImage.
y : float
Pixel coordinate on the specified SectionImage.
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.image_to_reference_endpoint,
'/',
str(section_image_id),
'.json',
'?x=%f&y=%f' % (x, y)])
return self.json_msg_query(url)
[docs] def get_structure_to_image(self,
section_data_set_id,
structure_ids):
'''For a list of target structures, find the closest SectionImage
and (x,y) location as defined by the centroid of each Structure.
Parameters
----------
section_data_set_id : integer
primary key
structure_ids : list of integers
primary key
Returns
-------
dict
The parsed json response
'''
url = ''.join([self.structure_to_image_endpoint,
'/',
str(section_data_set_id),
'.json',
'?structure_ids=',
','.join([str(i) for i in structure_ids])])
return self.json_msg_query(url)