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| − | '''[[Slicer3:Developers#Slicer_3_Projects | Back to Slicer3 Projects List ]]''' | + | <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> |
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| − | = ITK-based mechanism handling remote data (for command line modules, batch processing, and grid processing) --Nicole =
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| − | = vtkMRMLStorageNode methods for handling remote data (for loading and saving data for interactive use) --Wendy =
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| − | The first goal is to figure out what workflows to support, and a good implementation approach.
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| − | Currently, '''Load Scene''', '''Import Scene''', and '''Add Data''' options in Slicer all encapsulate two steps:
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| − | * locating a dataset, usually accomplished through a file browser, and
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| − | * selecting a dataset to initiate loading.
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| − | Then MRML files, Xcede catalog files, or individual datasets are loaded from local disk. Does this sketch look right?:
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| − | [[image:DataLoadingCurrent.png]]
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| − | For loading remote datasets, the following options are available:
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| − | * break these two steps apart explicitly (easiest option),
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| − | * bind them together under the hood,
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| − | * or support both of these paradigms.
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| − | ==Breaking apart "find data" and "load data":==
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| − | '''Possible workflow A'''
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| − | * User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
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| − | * 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.
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| − | '''Possible workflow B'''
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| − | * User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
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| − | * 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?)
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| − | '''Possible workflow C'''
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| − | * User locates a MRML file, .xcat archive, or individual dataset on the HID or an XNAT web interface
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| − | * User types the uri into the ''Load Scene'', ''Import Scene'', or ''Add Data'' interfaces.
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| − | * 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.
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| − | 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:
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| − | [[image:DataLoadingSketch.png]]
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| − | ==Or, bundling together "find data" and "load data":== | |
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| − | '''Possible workflow D'''
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| − | In this workflow, Slicer would make calls to HID or XNAT webservices to determine what data of interest is available... Questions:
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| − | * How might this work?
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| − | * Do we really want to re-implement functionality in the HID web interface?
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| − | * Maybe Slicer can implement a workflow (A-C) but also offer a simplified BIRN query interface that has functionality like:
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| − | ** Request BIRNIDs for all subjects who have a complete FIPS/FreeSurfer analysis
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| − | ** Request an xcat for one of these BIRNIDs
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| − | == Saving Data back to remote site ==
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| − | * 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?
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| − | == What data do we need in an .xcat file? ==
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| − | 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.
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| − | 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. | |
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| − | ===FIPS analysis (.feat) directory and required data===
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| − | 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:
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| − | * sirp-hp65-stc-to7-gam.feat/reg/example_func.nii
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| − | * sirp-hp65-stc-to7-gam.feat/reg/freesurfer/anat2exf.register.dat
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| − | * sirp-hp65-stc-to7-gam.feat/stats/(all statistics files of interest)
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| − | * sirp-hp65-stc-to7-gam.feat/design.gif (this image relates statistics files to experimental conditions)
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| − | ===FreeSurfer analysis directory, and required data ===
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| − | 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:
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| − | * fbph2-000670986943/mri/brain.mgz
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| − | * fbph2-000670986943/mri/aparc+aseg.mgz
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| − | * fbph2-000670986943/surf/lh.pial
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| − | * fbph2-000670986943/surf/rh.pial
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| − | * fbph2-000670986943/label/lh.aparc.annot
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| − | * fbph2-000670986943/label/rh.aparc.annot
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| − | == What do we want HID webservices to provide? ==
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| − | * 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.
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| − | * 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.
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| − | * 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).
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| − | * 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.'''
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| − | [[ Slicer3:XCEDE_use_cases | See this page for more discussion of QueryAtlas's current use of Xcede catalogs, and assumptions... ]]
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| − | = Asynchronous I/O Manager --Wendy =
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| − | 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:
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| − | * Each subclass of vtkMRMLStorageNode will call the superclass method first.
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| − | * Superclass method will look at uri, and decide if dataset is local or remote.
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| − | * If local, the subclass will load the data and return.
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| − | * If remote, the superclass will check to see if the data is cached on disk (in /tmp or wherever).
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| − | * If data is cached, subclass method will load that dataset from disk and return.
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| − | * 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:
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| − | ** Thread will create a new download entry and observe the cancel button
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| − | ** it will make whatever call it needs to download (http)
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| − | ** it will display progress on a progress meter.
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| − | ** and when complete, it will call a method on the vtkMRMLStorageNode subclass to load dataset from local cache.
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| − | [[image:DataIOManager.png]]
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