ITK/Git/Develop/Data
 | This section is currently out-of-date and may contain errors but is retained for historical reference. For peer-reviewed, authoritative guidance on ITK, see The ITK Software Guide. Additional guidance can be found via the ITK Discourse. |
This page documents how to add test data while developing ITK. See our table of contents for more information.
Contents
Setup
The workflow below depends on local hooks to function properly.
Follow the main developer setup instructions before proceeding.
In particular, run
SetupForDevelopment.sh:
$ ./Utilities/SetupForDevelopment.sh
Workflow
Our workflow for adding data integrates with our standard Git development process. Start by creating a topic. Return here when you reach the "edit files" step.
These instructions follow a typical use case of adding a new test with a baseline image.
Add Data
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Copy the data file into your local source tree. | |
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Add Test
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Edit the test CMakeLists.txt file and reference the data file in an
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Run CMake
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CMake will move the original file. Keep your own copy if necessary. Run cmake on the build tree:
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During configuration CMake will display a message such as:
This means that CMake converted the file into a data object referenced by a "content link". |
Commit
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Continue to create the topic and edit other files as necessary. Add the content link and commit it along with the other changes:
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The local
This means that the pre-commit hook recognized that the content link references a new data object and prepared it for upload. |
Push
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Follow the instructions to share the topic. When you push it to Gerrit for review using
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part of the output will be of the form
This means that the git-gerrit-push script pushed the topic and uploaded the data it references. Options for
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Building
Download
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For the test data to be downloaded and made available to the tests in your build tree the
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The downloaded files appear in |
Local Store
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It is possible to configure one or more local ExternalData object stores shared among multiple builds.
Configure for each build the advanced cache entry
The ExternalData module will store downloaded objects in the local store instead of the build tree. Once an object has been downloaded by one build it will persist in the local store for re-use by other builds without downloading again. |
Discussion
An ITK test data file is not stored in the main source tree under version control.
Instead the source tree contains a "content link" that refers to a data object by a hash of its content.
At build time the the
ExternalData.cmake
module fetches data needed by enabled tests.
This allows arbitrarily large data to be added and removed without bloating the version control history.
The above workflow allows developers to add a new data file almost as if committing it to the source tree. The following subsections discuss details of the workflow implementation.
ExternalData
While CMake runs the
ExternalData
module evaluates DATA{} references.
ITK sets
the ExternalData_LINK_CONTENT option to MD5 to enable automatic conversion of raw data files into content links.
When the module detects a real data file in the source tree it performs the following transformation as specified in the module documentation:
- Compute the MD5 hash of the file
- Store the
${hash}in a file with the original name plus.md5 - Rename the original file to
.ExternalData_MD5_${hash}
The real data now sit in a file that we tell Git to ignore. For example:
$ cat Modules/.../test/Baseline/.ExternalData_MD5_477e602800c18624d9bc7a32fa706b97 |md5sum 477e602800c18624d9bc7a32fa706b97 - $ cat Modules/.../test/Baseline/MyTest.png.md5 477e602800c18624d9bc7a32fa706b97
Recover Data File
To recover the original file after running CMake but before committing, undo the operation:
$ cd Modules/.../test/Baseline $ mv .ExternalData_MD5_$(cat MyTest.png.md5) MyTest.png
pre-commit
While committing a new or modified content link the
pre-commit
hook moves the real data object from the .ExternalData_MD5_${hash} file left by the ExternalData module
to a local object repository stored in a .ExternalData directory at the top of the source tree.
The hook also uses Git plumbing commands to store the data object as a blob in the local Git repository.
The blob is not referenced by the new commit but instead by refs/data/MD5/${hash}.
This keeps the blob alive in the local repository but does not add it to the project history.
For example:
$ git for-each-ref --format="%(refname)" refs/data refs/data/MD5/477e602800c18624d9bc7a32fa706b97 $ git cat-file blob refs/data/MD5/477e602800c18624d9bc7a32fa706b97 | md5sum 477e602800c18624d9bc7a32fa706b97 -
git gerrit-push
The "git gerrit-push" command is actually an
alias
for the
Utilities/Git/git-gerrit-push
script.
In addition to pushing the topic branch to Gerrit the script also detects content links added or modified by the commits in the topic.
It reads the data object hashes from the content links and looks for matching refs/data/ entries in the local Git repository.
The script pushes the matching data objects to Gerrit inside a temporary commit object disjoint from the rest of history. For example:
$ git gerrit-push --dry-run --no-topic * f59717cfb68a7093010d18b84e8a9a90b6b42c11:refs/data/commits/f59717cfb68a7093010d18b84e8a9a90b6b42c11 [new branch] Pushed refs/data and removed local copy: MD5/477e602800c18624d9bc7a32fa706b97 $ git ls-tree -r --name-only f59717cf MD5/477e602800c18624d9bc7a32fa706b97 $ git log --oneline f59717cf f59717c data
A robot runs every few minutes to fetch the objects from Gerrit and upload them to a location that we tell ExternalData to search at build time.
