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Search
The scitran.search method is useful when you are looking to find data of a particular type. For example, you may be interested to know how many examples of a T1 anatomical measurement are present in the database for men between 20 and 30 years of age. Or, how many diffusion weighted scans are there for women older than 50?
The search command returns a cell array, and each cell has the type flywheel.model.SearchResponse. This is a type of Matlab struct that contains great deal of information about the found objects. An example of one of the SearchResponse objects is
Illustrate here
Notice that the object describes the object that was sought in the 'returnType' field. The SearchResponse does not contain all of the information about the object, which can be found by using scitran.lookup or scitran.list. It does contain some additional information, however, say about the 'parent' fields of the returned object.
If you know what you want and where it is, use scitran.list or scitran.lookup. If you are exploring, say to create a Collection for data reuse, or to prepare a summary of the data available for machine-learning experiments, then usescitran.search.
The arguments to the search method specify (a) the type of object to return and (b) parameters that define the search. For example, to search for all the projects in the database you would use
projects = st.search('project');
The first argument (required) specifies the type of object you would like returned. The permissible strings are
'project','session','acquisition','file','collection', 'analysis','subject','note'
The additional search parameters are in parameter/val format and specify properties of the object. For example, to find a project with a particular label (case sensitive) use
vwfaProject = st.search('project',...
'project label exact','VWFA');
or to find all the sessions in a specific project
vwfaSessions = st.search('session',...
'project label exact','VWFA');
To find partial label matches (case insensitive) use
project = st.search('project',...
'project label contains','vwfa');
There are a great many possible key/value parameters for the search method. See the search examples page.
Run the search across the entire database ('all_data',true);
By default, you search only the projects you have access to. To search the entire database use argument
projects = st.search('project','allData',true);
N.B. Even if 'all_data' is true, you cannot query or download objects unless you have permission
A logical that indicates whether to print the number of found objects ('summary',true)
projects = st.search('project','summary',true);
You only have permission to view or download a subset of these, but you can learn about what is in the database from an 'allData' search. The Stanford Labs site will soon have more than 100 projects.
A logical to return a cell array of Flywheel containers rather than searchResponses
The SearchResponse and the Flywheel database object contain different information. If you are searching for only a few files, you may want the return to be in the format of the Flywheel object rather than the search response. The scitran method stSearch2Container uses the information in the SearchResponse to list the container. If that is what you really want, then you can use the 'fw' option to return a cell array of Containers rather than a cell array of SearchResponses.
projectContainers = st.search('project','group label','wandell','fw',true);
Limit the number of search responses. The default is 10,000, a very large number.
projectContainers = st.search('project','group label','wandell','limit',2);
The search method uses elastic search, an advanced method for searching large databases. Elastic search is constantly indexing the data base, and the search is based on this index. For this reason, there may be some delay between the time when you modify the MongoDB itself, and when you can find the modification using elastic search. Typically, the time is fairly short - a few seconds or so.
Flywheel is about to provide a means for querying whether the indexing is done, or perhaps the system has received a lot of new data or been rebooted and is currently very active. This information will be shown in the browser interface and perhaps be made available through the Flywheel-SDK.