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download_specimen.m

Download a specimen’s meta information (including the MNI transform).

 
function specimen = download_specimen(specimen_name)

Copyright 2013 Allen Institute for Brain Science Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

 
service = get_api_path();
requestFmt = '%s/Specimen/query.json?criteria=[name$eq''%s'']&include=alignment3d';
request = sprintf(requestFmt,service,specimen_name);
disp(request);

str = urlread(request);
json = parse_json(str);

specimen = json.msg{1};

Modify the transform so that it’s a proper matrix, rather than a struct array. Notice that the first nine elements of the transform are the 3x3 rotation matrix and the last three are the translation vector.

 
x = specimen.alignment3d;
specimen.alignment3d = [ x.tvr_00 x.tvr_01 x.tvr_02 x.tvr_09;
                         x.tvr_03 x.tvr_04 x.tvr_05 x.tvr_10;
                         x.tvr_06 x.tvr_07 x.tvr_08 x.tvr_11;
                         0        0        0        1];