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# Allen Institute Software License - This software license is the 2-clause BSD
# license plus a third clause that prohibits redistribution for commercial
# purposes without further permission.
#
# Copyright 2015-2017. Allen Institute. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Redistributions for commercial purposes are not permitted without the
# Allen Institute's written permission.
# For purposes of this license, commercial purposes is the incorporation of the
# Allen Institute's software into anything for which you will charge fees or
# other compensation. Contact terms@alleninstitute.org for commercial licensing
# opportunities.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
from .rma_api import RmaApi
from allensdk.api.cache import cacheable, Cache
from allensdk.core.obj_utilities import read_obj
import allensdk.core.sitk_utilities as sitk_utilities
import numpy as np
import nrrd
import six
class ReferenceSpaceApi(RmaApi):
AVERAGE_TEMPLATE = 'average_template'
ARA_NISSL = 'ara_nissl'
MOUSE_2011 = 'annotation/mouse_2011'
DEVMOUSE_2012 = 'annotation/devmouse_2012'
CCF_2015 = 'annotation/ccf_2015'
CCF_2016 = 'annotation/ccf_2016'
CCF_2017 = 'annotation/ccf_2017'
CCF_VERSION_DEFAULT = CCF_2017
VOXEL_RESOLUTION_10_MICRONS = 10
VOXEL_RESOLUTION_25_MICRONS = 25
VOXEL_RESOLUTION_50_MICRONS = 50
VOXEL_RESOLUTION_100_MICRONS = 100
def __init__(self, base_uri=None):
super(ReferenceSpaceApi, self).__init__(base_uri=base_uri)
@cacheable(strategy='create',
reader=nrrd.read,
pathfinder=Cache.pathfinder(file_name_position=3,
path_keyword='file_name'))
def download_annotation_volume(self,
ccf_version,
resolution,
file_name):
'''
Download the annotation volume at a particular resolution.
Parameters
----------
ccf_version: string
Which reference space version to download. Defaults to "annotation/ccf_2017"
resolution: int
Desired resolution to download in microns.
Must be 10, 25, 50, or 100.
file_name: string
Where to save the annotation volume.
Note: the parameters must be used as positional parameters, not keywords
'''
if ccf_version is None:
ccf_version = ReferenceSpaceApi.CCF_VERSION_DEFAULT
self.download_volumetric_data(ccf_version,
'annotation_%d.nrrd' % resolution,
save_file_path=file_name)
@cacheable(strategy='create', reader=sitk_utilities.read_ndarray_with_sitk,
pathfinder=Cache.pathfinder(file_name_position=3,
path_keyword='file_name'))
def download_mouse_atlas_volume(self, age, volume_type, file_name):
'''Download a reference volume (annotation, grid annotation, atlas volume)
from the mouse brain atlas project
Parameters
----------
age : str
Specify a mouse age for which to download the reference volume
volume_type : str
Specify the type of volume to download
file_name : str
Specify the path to the downloaded volume
'''
remote_file_name = '{}_{}.zip'.format(age, volume_type)
url = '/'.join([ self.informatics_archive_endpoint,
'current-release', 'mouse_annotation',
remote_file_name ])
self.retrieve_file_over_http(url, file_name, zipped=True)
@cacheable(strategy='create',
reader=nrrd.read,
pathfinder=Cache.pathfinder(file_name_position=2,
path_keyword='file_name'))
def download_template_volume(self, resolution, file_name):
'''
Download the registration template volume at a particular resolution.
Parameters
----------
resolution: int
Desired resolution to download in microns. Must be 10, 25, 50, or 100.
file_name: string
Where to save the registration template volume.
'''
self.download_volumetric_data(ReferenceSpaceApi.AVERAGE_TEMPLATE,
'average_template_%d.nrrd' % resolution,
save_file_path=file_name)
@cacheable(strategy='create',
reader=nrrd.read,
pathfinder=Cache.pathfinder(file_name_position=4,
path_keyword='file_name'))
def download_structure_mask(self, structure_id, ccf_version, resolution, file_name):
'''Download an indicator mask for a specific structure.
Parameters
----------
structure_id : int
Unique identifier for the annotated structure
ccf_version : string
Which reference space version to download. Defaults to "annotation/ccf_2017"
resolution : int
Desired resolution to download in microns. Must be 10, 25, 50, or 100.
file_name : string
Where to save the downloaded mask.
'''
if ccf_version is None:
ccf_version = ReferenceSpaceApi.CCF_VERSION_DEFAULT
structure_mask_dir = 'structure_masks_{0}'.format(resolution)
data_path = '{0}/{1}/{2}'.format(ccf_version, 'structure_masks', structure_mask_dir)
remote_file_name = 'structure_{0}.nrrd'.format(structure_id)
try:
self.download_volumetric_data(data_path, remote_file_name, save_file_path=file_name)
except Exception as e:
self._file_download_log.error('''We weren't able to download a structure mask for structure {0}.
You can instead build the mask locally using
ReferenceSpace.many_structure_masks''')
raise
@cacheable(strategy='create',
reader=read_obj,
pathfinder=Cache.pathfinder(file_name_position=3,
path_keyword='file_name'))
def download_structure_mesh(self, structure_id, ccf_version, file_name):
'''Download a Wavefront obj file containing a triangulated 3d mesh built
from an annotated structure.
Parameters
----------
structure_id : int
Unique identifier for the annotated structure
ccf_version : string
Which reference space version to download. Defaults to "annotation/ccf_2017"
file_name : string
Where to save the downloaded mask.
'''
if ccf_version is None:
ccf_version = ReferenceSpaceApi.CCF_VERSION_DEFAULT
data_path = '{0}/{1}'.format(ccf_version, 'structure_meshes')
remote_file_name = '{0}.obj'.format(structure_id)
try:
self.download_volumetric_data(data_path, remote_file_name, save_file_path=file_name)
except Exception as e:
self._file_download_log.error('unable to download a structure mesh for structure {0}.'.format(structure_id))
raise
def build_volumetric_data_download_url(self,
data_path,
file_name,
voxel_resolution=None,
release=None,
coordinate_framework=None):
'''Construct url to download 3D reference model in NRRD format.
Parameters
----------
data_path : string
'average_template', 'ara_nissl', 'annotation/ccf_{year}',
'annotation/mouse_2011', or 'annotation/devmouse_2012'
voxel_resolution : int
10, 25, 50 or 100
coordinate_framework : string
'mouse_ccf' (default) or 'mouse_annotation'
Notes
-----
See: `3-D Reference Models <http://help.brain-map.org/display/mouseconnectivity/API#API-3DReferenceModels>`_
for additional documentation.
'''
if voxel_resolution is None:
voxel_resolution = ReferenceSpaceApi.VOXEL_RESOLUTION_10_MICRONS
if release is None:
release = 'current-release'
if coordinate_framework is None:
coordinate_framework = 'mouse_ccf'
url = ''.join([self.informatics_archive_endpoint,
'/%s/%s/' % (release, coordinate_framework),
data_path,
'/',
file_name])
return url
def download_volumetric_data(self,
data_path,
file_name,
voxel_resolution=None,
save_file_path=None,
release=None,
coordinate_framework=None):
'''Download 3D reference model in NRRD format.
Parameters
----------
data_path : string
'average_template', 'ara_nissl', 'annotation/ccf_{year}',
'annotation/mouse_2011', or 'annotation/devmouse_2012'
file_name : string
server-side file name. 'annotation_10.nrrd' for example.
voxel_resolution : int
10, 25, 50 or 100
coordinate_framework : string
'mouse_ccf' (default) or 'mouse_annotation'
Notes
-----
See: `3-D Reference Models <http://help.brain-map.org/display/mouseconnectivity/API#API-3DReferenceModels>`_
for additional documentation.
'''
url = self.build_volumetric_data_download_url(data_path,
file_name,
voxel_resolution,
release,
coordinate_framework)
if save_file_path is None:
save_file_path = file_name
if save_file_path is None:
save_file_path = 'volumetric_data.nrrd'
self.retrieve_file_over_http(url, save_file_path)
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