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'''[[Slicer3:Developers#Slicer_3_Projects | Back to Slicer3 Projects List ]]'''
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<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Remote_Data_Handling  here]</font></big>
 
 
 
 
 
 
= ITK-based mechanism handling remote data (for command line modules, batch processing, and grid processing) --Nicole =
 
 
 
= vtkMRMLStorageNode methods for handling remote data (for loading and saving data for interactive use) --Wendy =
 
 
 
The first goal is to figure out what workflows to support, and a good implementation approach.
 
 
 
Currently, '''Load Scene''', '''Import Scene''', and '''Add Data''' options in Slicer all encapsulate two steps:
 
* locating a dataset, usually accomplished through a file browser, and
 
* selecting a dataset to initiate loading.
 
Then MRML files, Xcede catalog files, or individual datasets are loaded from local disk. Does this sketch look right?:
 
 
 
[[image:DataLoadingCurrent.png]]
 
 
 
For loading remote datasets, the following options are available:
 
* break these two steps apart explicitly (easiest option),
 
* bind them together under the hood,
 
* or support both of these paradigms.
 
 
 
==Breaking apart "find data" and "load data":==
 
 
 
'''Possible workflow A'''
 
* User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
 
* From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file listed in the archive is downloaded to /tmp directory (always locally cached) by the Download Manager, and then loaded into Slicer via a vtkMRMLStorageNode method when download is complete.
 
 
 
'''Possible workflow B'''
 
* User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
 
* From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file in the archive is downloaded to /tmp (only if a flag is set) by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete. (How does load work if we don't save to disk first?)
 
 
 
'''Possible workflow C'''
 
* User locates a MRML file, .xcat archive, or individual dataset on the HID or an XNAT web interface
 
* User types the uri into the ''Load Scene'', ''Import Scene'', or ''Add Data'' interfaces.
 
* If no locally cached versions exist, each remote file in the archive is cached to /tmp by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete.
 
 
 
In each workflow, the data gets saved to disk first and then loaded into Slicer. Here's a first pass at how things might work -- we can discuss at meeting:
 
 
 
[[image:DataLoadingSketch.png]]
 
 
 
==Or, bundling together "find data" and "load data":==
 
 
 
'''Possible workflow D'''
 
 
 
In this workflow, Slicer would make calls to HID or XNAT webservices to determine what data of interest is available... Questions:
 
* How might this work?
 
* Do we really want to re-implement functionality in the HID web interface?
 
* Maybe Slicer can implement a workflow (A-C) but also offer a simplified BIRN query interface that has functionality like:
 
** Request BIRNIDs for all subjects who have a complete FIPS/FreeSurfer analysis
 
** Request an xcat for one of these BIRNIDs
 
 
 
== Saving Data back to remote site ==
 
* Since we have no plan for where to save MRML files on HID, can we have a webservices function we can call from Slicer that writes a file to /dev/null on HID in the meanwhile?
 
 
 
== What data do we need in an .xcat file? ==
 
For the fBIRN QueryAtlas use case, we need a combination of '''FreeSurfer morphology analysis''' and a '''FIPS analysis''' of the same subject. With the combined data in Slicer, we can view activation overlays co-registered to and overlayed onto the high resolution structural MRI using the FIPS analysis, and determine the names of brain regions where activations occur using the co-registered morphology analysis.
 
 
 
The required analyses including all derived data are in two standard directory structures on local disk, and *hopefully* somewhere on the HID within a standard structure (check with Burak). These directory trees contain a LOT of files we don't need... Below are the files we *do* need for fBIRN QueryAtlas use case.
 
 
 
===FIPS analysis (.feat) directory and required data===
 
For instance, the FIPS output directory in our example dataset from Doug Greve at MGH is called sirp-hp65-stc-to7-gam.feat. Under this directory, QueryAtlas needs the following datasets:
 
* sirp-hp65-stc-to7-gam.feat/reg/example_func.nii
 
* sirp-hp65-stc-to7-gam.feat/reg/freesurfer/anat2exf.register.dat
 
* sirp-hp65-stc-to7-gam.feat/stats/(all statistics files of interest)
 
* sirp-hp65-stc-to7-gam.feat/design.gif (this image relates statistics files to experimental conditions)
 
 
 
===FreeSurfer analysis directory, and required data ===
 
For instance, the FreeSurfer morphology analysis directory in our example dataset from Doug Greve at MGH is called fbph2-000670986943. Under this directory, QueryAtlas needs the following datasets:
 
 
 
* fbph2-000670986943/mri/brain.mgz
 
* fbph2-000670986943/mri/aparc+aseg.mgz
 
* fbph2-000670986943/surf/lh.pial
 
* fbph2-000670986943/surf/rh.pial
 
* fbph2-000670986943/label/lh.aparc.annot
 
* fbph2-000670986943/label/rh.aparc.annot
 
 
 
== What do we want HID webservices to provide? ==
 
 
 
 
 
 
 
* The BIRN HID webservices shouldn't really need to know the subset of data that QueryAtlas needs... maybe the web interface can take a BIRN ID and create a FIPS/FreeSurfer xcede catalog with all uris in the FIPS and FreeSurfer directories, and package these into an Xcede catalog.
 
 
 
* The catalog could be requested and downloaded from the HID web GUI, with a name like .xcat or .xcat.gzip or whatever. QueryAtlas could then open this file (or unzip and open) and find only the relevant uris for an fBIRN QueryAtlas session.  
 
 
 
* Maybe this catalog could be requested programmatically from a Slicer webservices client, that gives a particular BIRN ID. (I'm not sure this capability buys us much value just now).
 
 
 
* Then, for each uri in a catalog (or .xml MRML file), we need to be able to download programmatically using http:// or ftp:// etc. '''We are assuming all datasets are publicly readable.'''
 
 
 
[[ Slicer3:XCEDE_use_cases | See this page for more discussion of QueryAtlas's current use of Xcede catalogs, and assumptions... ]]
 
 
 
= Asynchronous I/O Manager --Wendy =
 
 
 
vtkMRMLStorageNode superclass needs to have methods which handle remote or local data loading, whether the uris are contained in an xcat or mrml file. Kind of like this:
 
 
 
* Each subclass of vtkMRMLStorageNode will call the superclass method first.
 
* Superclass method will look at uri, and decide if dataset is local or remote.
 
* If local, the subclass will load the data and return.
 
* If remote, the superclass will check to see if the data is cached on disk (in /tmp or wherever).
 
* If data is cached, subclass method will load that dataset from disk and return.
 
* If data is not cached, subclass method will spawn an independent thread of control that will interact with the Asynchronous I/O Manager, passing it the type of storage node required for the dataset:
 
** Thread will create a new download entry and observe the cancel button
 
** it will make whatever call it needs to download (http)
 
** it will display progress on a progress meter.
 
** and when complete, it will call a method on the vtkMRMLStorageNode subclass to load dataset from local cache.
 
 
 
[[image:DataIOManager.png]]
 

Latest revision as of 18:07, 10 July 2017

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