Difference between revisions of "ITK/Git/Develop/Data"

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This page documents how to add test data while developing ITK.
+
Up to date information can be found on GitHub:
See our [[ITK/Git|table of contents]] for more information.
+
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/Data.md
__TOC__
 
= Setup =
 
 
 
The workflow below depends on local hooks to function properly.
 
Follow the main [[ITK/Git/Develop#Setup|developer setup instructions]] before proceeding.
 
In particular, run
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/SetupForDevelopment.sh;hb=HEAD <code>SetupForDevelopment.sh</code>]:
 
 
 
$ ./Utilities/SetupForDevelopment.sh
 
 
 
= Workflow =
 
 
 
Our workflow for adding data integrates with our standard Git [[ITK/Git/Develop|development process]].
 
Start by [[ITK/Git/Develop#Create_a_Topic|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 ==
 
 
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
Copy the data file into your local source tree.
 
|-
 
|
 
:<code>$ mkdir -p Modules/.../test/Baseline</code>
 
:<code>$ cp ~/''MyTest.png'' Modules/.../test/Baseline/''MyTest.png''</code>
 
|
 
|}
 
 
 
== Add Test ==
 
 
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
Edit the test CMakeLists.txt file and reference the data file in an <code>itk_add_test</code> call.
 
Specify the file inside <code>DATA{...}</code> using a path relative to the test directory:
 
:<code>$ edit Modules/.../test/CMakeLists.txt</code>
 
:{|
 
|
 
itk_add_test(NAME MyTest COMMAND ... --compare DATA{Baseline/''MyTest.png'',:} ...)
 
|}
 
* Files in <code>Testing/Data</code> may be referenced as <code>DATA{${ITK_DATA_ROOT}/Input/''MyInput.png''}</code>.
 
* If the data file references other data files, e.g. <code>.mhd -> .raw</code>, follow the link to the ExternalData module on the right and read the documentation on "associated" files.
 
* Multiple baseline images and other series are handled automatically when the reference ends in the ",:" option; follow the link to the ExternalData module on the right for details.
 
|align="center"|
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ExternalData.cmake;hb=HEAD <code>ExternalData.cmake</code>]
 
|}
 
 
 
== Run CMake ==
 
 
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
''CMake will [[#ExternalData|move the original file]].  Keep your own copy if necessary.''
 
 
 
Run cmake on the build tree:
 
:<code>$ cd ../ITK-build</code>
 
:<code>$ cmake .</code>
 
:''(Or just run "make" to do a full configuration and build.)''
 
:<code>$ cd ../ITK</code>
 
|align="center"|
 
[[#Recover_Data_File|Need to recover the original file]]?
 
|-
 
|
 
During configuration CMake will display a message such as:
 
:{|
 
|
 
Linked Modules/.../test/Baseline/''MyTest.png''.md5 to ExternalData MD5/...
 
|}
 
This means that CMake converted the file into a data object referenced by a "content link".
 
|align="center"|
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ExternalData.cmake;hb=HEAD <code>ExternalData.cmake</code>]
 
|}
 
 
 
== Commit ==
 
 
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
Continue to [[ITK/Git/Develop#Create_a_Topic|create the topic]] and edit other files as necessary.
 
Add the content link and commit it along with the other changes:
 
:<code>$ git add Modules/.../test/Baseline/''MyTest.png''.md5</code>
 
:<code>$ git add Modules/.../test/CMakeLists.txt</code>
 
:<code>$ git commit</code>
 
|align="center"|
 
[http://www.kernel.org/pub/software/scm/git/docs/git-add.html <code>git help add</code>]
 
<br/>
 
[http://www.kernel.org/pub/software/scm/git/docs/git-commit.html <code>git help commit</code>]
 
|-
 
|
 
The local <code>pre-commit</code> hook will display a message such as:
 
:{|
 
|
 
Modules/.../test/Baseline/''MyTest.png''.md5: Added content to Git at refs/data/MD5/...
 
Modules/.../test/Baseline/''MyTest.png''.md5: Added content to local store at .ExternalData/MD5/...
 
Content link Modules/.../test/Baseline/''MyTest.png''.md5 -> .ExternalData/MD5/...
 
|}
 
This means that the pre-commit hook recognized that the content link references a new data object and [[#pre-commit|prepared it for upload]].
 
|align="center"|
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/Hooks/pre-commit;hb=HEAD <code>pre-commit</code>]
 
|}
 
 
 
== Push ==
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
Follow the instructions to [[ITK/Git/Develop#Share_a_Topic|share the topic]].
 
When you push it to Gerrit for review using
 
:<code>$ git gerrit-push</code>
 
|align="center"|
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/Git/git-gerrit-push;hb=HEAD <code>git-gerrit-push</code>]
 
|-
 
|
 
part of the output will be of the form
 
:{|
 
|
 
*      ...:refs/data/commits/...      [new branch]
 
*      HEAD:refs/for/master/''my-topic''  [new branch]
 
Pushed refs/data and removed local copy:
 
  MD5/...
 
|}
 
This means that the git-gerrit-push script pushed the topic and [[#git-gerrit-push|uploaded the data]] it references.
 
 
 
Options for <code>gerrit-push</code>:
 
* <code>--dry-run</code>: Report push that would occur without actually doing it
 
* <code>--no-topic</code>: Push the data referenced by the topic but not the topic itself
 
|}
 
 
 
= Building =
 
 
 
== Download ==
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
For the test data to be downloaded and made available to the tests in your build tree the <code>ITKData</code> target must be built.
 
One may build the target directly, e.g. <code>make ITKData</code>, to obtain the data without a complete build.
 
The output will be something like
 
:{|
 
|
 
-- Fetching ".../ExternalData/MD5/..."
 
-- [download 100% complete]
 
-- Downloaded object: "''ITK-build''/ExternalData/Objects/MD5/..."
 
|}
 
|-
 
|
 
The downloaded files appear in <code>''ITK-build''/ExternalData</code> by default.
 
|
 
|}
 
 
 
== Local Store ==
 
{| style="width: 100%"
 
|-
 
|width=60%|
 
It is possible to configure one or more local ExternalData object stores shared among multiple builds.
 
Configure for each build the advanced cache entry <code>ExternalData_OBJECT_STORES</code> to a directory on your local disk outside all build trees, e.g. "<code>/home/user/.ExternalData</code>":
 
:<code>$ cmake -DExternalData_OBJECT_STORES=/home/user/.ExternalData ../ITK</code>
 
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.
 
|align="center"|
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ExternalData.cmake;hb=HEAD <code>ExternalData.cmake</code>]
 
|}
 
 
 
= 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
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ExternalData.cmake;hb=HEAD <code>ExternalData.cmake</code>]
 
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|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 [[#Run_CMake|CMake runs]] the
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ExternalData.cmake;hb=HEAD ExternalData]
 
module evaluates [[#Add_Test|DATA{} references]].
 
ITK [http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ITKExternalData.cmake;hb=HEAD sets]
 
the <code>ExternalData_LINK_CONTENT</code> option to <code>MD5</code> 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 <code>${hash}</code> in a file with the original name plus <code>.md5</code>
 
* Rename the original file to <code>.ExternalData_MD5_${hash}</code>
 
The real data now sit in a file that we [http://itk.org/gitweb?p=ITK.git;a=blob;f=.gitignore;hb=HEAD 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 [[#Commit|committing]] a new or modified content link the
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/Hooks/pre-commit;hb=HEAD <code>pre-commit</code>]
 
hook moves the real data object from the <code>.ExternalData_MD5_${hash}</code> file left by the ExternalData module
 
to a local object repository stored in a <code>.ExternalData</code> 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 <code>refs/data/MD5/${hash}</code>.
 
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 "<code>git gerrit-push</code>" command is actually an
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/DevelopmentSetupScripts/SetupGitAliases.sh;hb=HEAD alias]
 
for the
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=Utilities/Git/git-gerrit-push;hb=HEAD <code>Utilities/Git/git-gerrit-push</code>]
 
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 <code>refs/data/</code> 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
 
[http://www.itk.org/files/ExternalData location] that we
 
[http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ITKExternalData.cmake;hb=HEAD tell ExternalData to search]
 
at build time.
 

Latest revision as of 12:54, 13 August 2019

Up to date information can be found on GitHub: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/Data.md