Please remember this is a docker container, I can’t start slicer there. Also the slicer-base image is supposed to have a prebuilt image of Slicer, I just need to add the elastix extension by default. I can trigger the instalation in Slicer by:
but in the docker environment this fails with the error:
Traceback (most recent call last):
File "installElastix.py", line 2, in <module>
emm = slicer.app.extensionsManagerModel()
AttributeError: module 'slicer' has no attribute 'app'
vtkDebugLeaks has found no leaks.
E15TY:~ alexvergaragil$ docker run -it slicer/buildenv /bin/bash
Unable to find image 'slicer/buildenv:latest' locally
docker: Error response from daemon: pull access denied for slicer/buildenv, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.
I have tried this approach and in the test it will fail with
CMake Error at CMakeLists.txt:17 (find_package):
By not providing "FindSlicer.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Slicer", but
CMake did not find one.
Could not find a package configuration file provided by "Slicer" with any
of the following names:
SlicerConfig.cmake
slicer-config.cmake
Add the installation prefix of "Slicer" to CMAKE_PREFIX_PATH or set
"Slicer_DIR" to a directory containing one of the above files. If "Slicer"
provides a separate development package or SDK, be sure it has been
installed.
The CMakeList.txt in my extension is:
cmake_minimum_required(VERSION 3.5)
project(Dosimetry4D)
#-----------------------------------------------------------------------------
# Extension meta-information
set(EXTENSION_HOMEPAGE "http://gitlab.com/opendose/opendose4d")
set(EXTENSION_CATEGORY "Dosimetry")
set(EXTENSION_CONTRIBUTORS "Alex Vergara Gil (INSERM) and Janick Rueegger (KSA)")
set(EXTENSION_DESCRIPTION "This extension contains the entire dosimetry workflow for a multipoint study")
set(EXTENSION_ICONURL "https://opendose.org/themes/default/images/opendose_favicon.png")
set(EXTENSION_SCREENSHOTURLS "http://www.example.com/Slicer/Extensions/Dosimetry/Screenshots/1.png")
set(EXTENSION_DEPENDS SlicerElastix) # Specified as a space separated string, a list or 'NA' if any
#-----------------------------------------------------------------------------
# Extension dependencies
find_package(Slicer REQUIRED)
include(${Slicer_USE_FILE})
#-----------------------------------------------------------------------------
# Extension modules
add_subdirectory(Dosimetry4D)
## NEXT_MODULE
#-----------------------------------------------------------------------------
include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})
#-----------------------------------------------------------------------------
option(ENABLE_TESTS "Enable tests" OFF)
if (${ENABLE_TESTS})
enable_testing()
endif()
but my extension is just a python module, Is there a way to avoid the find_package(Slicer REQUIRED) line??
I have done that, but that path does not contain any cmake file in the nightly build. You can use docker run -it unnmdnwb3/slicer3d-nightly:0.8.0 /bin/bash to test this approach. It contains a slicer-base image with a preinstalled slicer-nightly. the Slicer_DIR is /usr/src/Slicer
I see. An install tree is not sufficient for build&test. As a workaround, you could create a script that runs Pytjon selftests manually. You can find the full command-line of each test on CDash.
Actually I only require the slicerMacroBuildScriptedModule macro definition to run the tests. This file does not depend on any slicer header, but is the one who builds the python module.
Are the command lines like this one?
It would be nice to properly build and test your extension. It would increase the test coverage (it would test building) and you never know when you’ll need to add a loadable or CLI module to your extension.
I can perform normal test without elastix, but that will truncate half the functionality of my extension. Is it possible to have a build sequence that leaves me with a built Slicer+Elastix by default?
jcfr
(Jean Christophe Fillion Robin (Kitware))
#17
Are you still trying to do the following:
want a docker image of slicer with elastix extension preinstalled
If yes, there is no need to base your image of slicer/slicer-base. Using a centos7 base should be sufficient.
Also, what would you like to do with this docker image ?
I have tried to run manually the tests and this happens
$ /usr/src/Slicer/bin/PythonSlicer -c "import slicer.testing; slicer.testing.runUnitTest(['$CI_BUILDS_DIR/dosimetry4d-build/Dosimetry4D/Logic', '$CI_BUILDS_DIR/opendose/opendose4d/Dosimetry4D/Logic'], 'Dosimetry4DTest')"
Dosimetry4DTest (unittest.loader._FailedTest) ... ERROR
======================================================================
ERROR: Dosimetry4DTest (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: Dosimetry4DTest
Traceback (most recent call last):
File "/usr/src/Slicer/lib/Python/lib/python3.6/unittest/loader.py", line 153, in loadTestsFromName
module = __import__(module_name)
File "/builds/dosimetry4d-build/Dosimetry4D/Logic/Dosimetry4DTest.py", line 3, in <module>
from slicer.ScriptedLoadableModule import ScriptedLoadableModuleTest
File "/usr/src/Slicer/bin/Python/slicer/ScriptedLoadableModule.py", line 4, in <module>
import qt, ctk, slicer
File "/usr/src/Slicer/bin/Python/qt/__init__.py", line 19, in <module>
from PythonQt.private import QObject
ModuleNotFoundError: No module named 'PythonQt'
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/src/Slicer/bin/Python/slicer/testing.py", line 26, in runUnitTest
exitFailure()
File "/usr/src/Slicer/bin/Python/slicer/testing.py", line 11, in exitFailure
raise Exception(message)
Exception
No module named 'logic'
-------------------------------------------
path: ['/builds/dosimetry4d-build/Dosimetry4D/Logic', '/builds/opendose/opendose4d/Dosimetry4D/Logic']
testname: Dosimetry4DTest
-------------------------------------------
vtkDebugLeaks has found no leaks.
I think preinstalled slicer leads to even more errors than building it
I have succeeded to make a Full Test using BrainsFit, not optimal but good enough solution. The Full Test in graphical mode (Reload and test) will use elastix if it is installed.
The module is complete, I am just waiting for testers answers. Next steps will be:
Write the article (shall be presented in ECMP2020 or EANM2020)
Open the source (as soon as the abstract is accepted)
integrating in Slicer as scripted module (I will need your help in this point). The module shall be accesible by the time the article is published.