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Mirrors
SuperElastix
Commits
1eaf3de6
Commit
1eaf3de6
authored
Nov 24, 2016
by
Kasper Marstal
Browse files
COMP: Move data directory to Testing/Data, create Testing/Integration directory
parent
399a4c39
Changes
59
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Applications/CMakeLists.txt
View file @
1eaf3de6
...
...
@@ -39,7 +39,7 @@ if( NOT CMAKE_PROJECT_NAME STREQUAL "SuperElastix" )
#TODO SuperElastix Application should not link against elastix libraries
# If OpenMP is supported by this machine, elastix will be compiled with
# OpenMP flags, and we need to add them here as well
find_package
(
OpenMP
)
find_package
(
OpenMP
QUIET
)
if
(
OPENMP_FOUND
)
set
(
CMAKE_CXX_FLAGS
"
${
CMAKE_CXX_FLAGS
}
${
OpenMP_CXX_FLAGS
}
"
)
set
(
CMAKE_C_FLAGS
"
${
CMAKE_C_FLAGS
}
${
OpenMP_C_FLAGS
}
"
)
...
...
CMakeLists.txt
View file @
1eaf3de6
...
...
@@ -104,6 +104,21 @@ selxmodule_enable( ModuleController )
# ---------------------------------------------------------------------
# Testing
set
(
SUPERELASTIX_INPUT_DATA_DIR
${
CMAKE_CURRENT_BINARY_DIR
}
/Testing/Data/Input
)
set
(
SUPERELASTIX_OUTPUT_DATA_DIR
${
CMAKE_CURRENT_BINARY_DIR
}
/Testing/Data/Output
)
set
(
SUPERELASTIX_BASELINE_DATA_DIR
${
CMAKE_CURRENT_BINARY_DIR
}
/Testing/Data/Baseline
)
set
(
SUPERELASTIX_CONFIGURATION_DATA_DIR
${
CMAKE_CURRENT_SOURCE_DIR
}
/Testing/Data/Configuration
)
if
(
NOT EXISTS
${
SUPERELASTIX_OUTPUT_DATA_DIR
}
)
file
(
MAKE_DIRECTORY
${
SUPERELASTIX_OUTPUT_DATA_DIR
}
)
endif
()
if
(
NOT EXISTS
${
SUPERELASTIX_OUTPUT_DATA_DIR
}
)
message
(
FATAL_ERROR
"Could not create directory for output data. Make sure CMake has write permissions."
)
endif
()
option
(
SUPERELASTIX_BUILD_TESTING
"Enable building tests."
ON
)
if
(
${
SUPERELASTIX_BUILD_TESTING
}
)
mark_as_advanced
(
SUPERELASTIX_BUILD_LONG_TESTS
)
...
...
Modules/Components/Elastix/ModuleElastix.cmake
View file @
1eaf3de6
...
...
@@ -21,7 +21,7 @@ set( MODULE ModuleElastix )
# If OpenMP is supported by this machine, elastix will be compiled with
# OpenMP flags, and we need to add them here as well
find_package
(
OpenMP
)
find_package
(
OpenMP
QUIET
)
if
(
OPENMP_FOUND
)
set
(
CMAKE_CXX_FLAGS
"
${
CMAKE_CXX_FLAGS
}
${
OpenMP_CXX_FLAGS
}
"
)
set
(
CMAKE_C_FLAGS
"
${
CMAKE_C_FLAGS
}
${
OpenMP_C_FLAGS
}
"
)
...
...
Testing/Benchmark/CMakeLists.txt
deleted
100644 → 0
View file @
399a4c39
#=========================================================================
#
# Copyright Leiden University Medical Center, Erasmus University Medical
# Center and contributors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#=========================================================================
Testing/CMakeLists.txt
View file @
1eaf3de6
...
...
@@ -54,28 +54,28 @@ ExternalData_Add_Target( SuperElastixData )
find_package
(
GTest REQUIRED
)
include_directories
(
${
GTEST_INCLUDE_DIRS
}
)
set
(
TEST_LIBRARIES
${
GTEST_BOTH_LIBRARIES
}
set
(
TEST_LIBRARIES
${
GTEST_BOTH_LIBRARIES
}
)
# ---------------------------------------------------------------------
# Build data manager
configure_file
(
${
CMAKE_CURRENT_SOURCE_DIR
}
/selxDataDirectories.h.in
${
CMAKE_CURRENT_BINARY_DIR
}
/selxDataDirectories.h
ESCAPE_QUOTES
)
include_directories
(
${
CMAKE_CURRENT_SOURCE_DIR
}
)
# selxDataManager.h
include_directories
(
${
CMAKE_CURRENT_BINARY_DIR
}
)
# selxDataDirectories.h
add_library
(
DataManager selxDataManager.cxx
)
list
(
APPEND TEST_LIBRARIES DataManager
)
# ---------------------------------------------------------------------
# Build test suite
set
(
CTEST_CONFIGURATION_TYPE Debug
)
# Unit tests
add_subdirectory
(
Unit
)
add_subdirectory
(
Integration
)
# Make data directories available parent cmake for installation of SuperElastix
set
(
SUPERELASTIX_UNITTEST_INPUT_DATA_DIR
${
SUPERELASTIX_UNITTEST_INPUT_DATA_DIR
}
PARENT_SCOPE
)
set
(
SUPERELASTIX_UNITTEST_BASELINE_DATA_DIR
${
SUPERELASTIX_UNITTEST_BASELINE_DATA_DIR
}
PARENT_SCOPE
)
set
(
SUPERELASTIX_UNITTEST_CONFIGURATION_DATA_DIR
${
SUPERELASTIX_UNITTEST_CONFIGURATION_DATA_DIR
}
PARENT_SCOPE
)
# ---------------------------------------------------------------------
# Configure dashboard
mark_as_advanced
(
SUPERELASTIX_BUILD_DASHBOARD
)
option
(
SUPERELASTIX_BUILD_DASHBOARD
"Enable SuperElastix dashboard."
OFF
)
if
(
${
SUPERELASTIX_BUILD_DASHBOARD
}
)
add_subdirectory
(
Dashboard
)
endif
()
Testing/Dashboard/CMakeLists.txt
deleted
100644 → 0
View file @
399a4c39
#=========================================================================
#
# Copyright Leiden University Medical Center, Erasmus University Medical
# Center and contributors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#=========================================================================
# ---------------------------------------------------------------------
# Dashboard configuration
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_SOURCE_DIR
)
set
(
SUPERELASTIX_DASHBOARD_SOURCE_DIR
"
${
CMAKE_SOURCE_DIR
}
/Testing/Dashboard"
)
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_BINARY_DIR
)
set
(
SUPERELASTIX_DASHBOARD_BINARY_DIR
"
${
CMAKE_BINARY_DIR
}
/Testing/Dashboard"
)
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE
)
set
(
SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE
"selxLogstash.crt"
)
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY
)
set
(
SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY
"selxLogstash.key"
)
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_VOLUME
)
if
(
NOT EXISTS
"
${
SUPERELASTIX_DASHBOARD_VOLUME
}
"
)
set
(
ELASTIX_DASHBOARD_VOLUME
"
${
SUPERELASTIX_DASHBOARD_BINARY_DIR
}
/Data"
)
file
(
MAKE_DIRECTORY
"
${
SUPERELASTIX_DASHBOARD_VOLUME
}
"
)
endif
()
# Test/Benchmark results will be forwarded to this IP. You will probably
# have change this in order to match docker settings on your own machine.
mark_as_advanced
(
SUPERELASTIX_DASHBOARD_IP
)
set
(
SUPERELASTIX_DASHBOARD_IP
"192.168.59.103"
)
configure_file
(
${
SUPERELASTIX_DASHBOARD_SOURCE_DIR
}
/selxDashboard.yml.in
${
SUPERELASTIX_DASHBOARD_BINARY_DIR
}
/selxDashboard.yml
)
configure_file
(
${
SUPERELASTIX_DASHBOARD_SOURCE_DIR
}
/selxLogstashForwarder.yml.in
${
SUPERELASTIX_DASHBOARD_BINARY_DIR
}
/selxLogstashForwarder.yml
)
configure_file
(
${
SUPERELASTIX_DASHBOARD_SOURCE_DIR
}
/selxLogstash.conf.in
${
SUPERELASTIX_DASHBOARD_BINARY_DIR
}
/Logstash/selxLogstash.conf
)
configure_file
(
${
SUPERELASTIX_DASHBOARD_SOURCE_DIR
}
/selxLogstashForwarder.json.in
${
SUPERELASTIX_DASHBOARD_BINARY_DIR
}
/selxLogstashForwarder.json
)
# ---------------------------------------------------------------------
# SSL certificates
# Use the following OpenSSL command to generate a test certificate and key if needed
# openssl req -subj '/CN=*/' -x509 -batch -nodes -days 9999 -newkey rsa:2048 -keyout selxLogstash.key -out selxLogstash.crt
Testing/Dashboard/selxDashboard.yml.in
deleted
100644 → 0
View file @
399a4c39
SuperElastix:
image: willdurand/elk
ports:
- "80:80"
- "5043:5043"
volumes_from:
- data
data:
image: busybox
volumes:
- @SUPERELASTIX_DASHBOARD_SOURCE_DIR@:/etc/ssl
- @SUPERELASTIX_DASHBOARD_VOLUME@:/data
- @SUPERELASTIX_DASHBOARD_BINARY_DIR@/Logstash:/etc/logstash
Testing/Dashboard/selxLogstash.conf.in
deleted
100644 → 0
View file @
399a4c39
input {
lumberjack {
port => 5043
ssl_certificate => "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@"
ssl_key => "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY@"
}
}
filter {
xml {
source => message
target => result
}
}
output {
elasticsearch {
protocol => http
}
}
\ No newline at end of file
Testing/Dashboard/selxLogstash.crt
deleted
100644 → 0
View file @
399a4c39
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
Testing/Dashboard/selxLogstash.key
deleted
100644 → 0
View file @
399a4c39
-----BEGIN RSA PRIVATE KEY-----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-----END RSA PRIVATE KEY-----
Testing/Dashboard/selxLogstashForwarder.json.in
deleted
100644 → 0
View file @
399a4c39
{
"network": {
"servers": [ "SuperElastix:5043" ],
"timeout": 15,
"ssl certificate": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@",
"ssl key": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY@",
"ssl ca": "/etc/ssl/@SUPERELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE@"
},
"files": [
{
"paths": [
"/var/unit/*.xml"
],
"fields": {
"type": "unittest",
"lib": "SuperElastix"
}
},
{
"paths": [
"/var/benchmark/*.xml"
],
"fields": {
"type": "benchmark",
"lib": "SuperElastix"
}
}
]
}
Testing/Dashboard/selxLogstashForwarder.yml.in
deleted
100644 → 0
View file @
399a4c39
forwarder:
image: willdurand/logstash-forwarder
extra_hosts:
- "SuperElastix:@SUPERELASTIX_DASHBOARD_IP@"
volumes_from:
- data
data:
image: busybox
volumes:
- @SUPERELASTIX_DASHBOARD_BINARY_DIR@/selxLogstashForwarder.json:/etc/logstash-forwarder/config.json
- @SUPERELASTIX_DASHBOARD_SOURCE_DIR@:/etc/ssl
- @CMAKE_BINARY_DIR@/Testing/Unit:/var/unit
- @CMAKE_BINARY_DIR@/Testing/Benchmark:/var/benchmark
Testing/
Unit/
Data/Baseline/elastix_BS_MSD_Displacement.mhd.md5
→
Testing/Data/Baseline/elastix_BS_MSD_Displacement.mhd.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_MSD_Displacement.raw.md5
→
Testing/Data/Baseline/elastix_BS_MSD_Displacement.raw.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_MSD_Image.mhd.md5
→
Testing/Data/Baseline/elastix_BS_MSD_Image.mhd.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_MSD_Image.raw.md5
→
Testing/Data/Baseline/elastix_BS_MSD_Image.raw.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_NCC_Displacement.mhd.md5
→
Testing/Data/Baseline/elastix_BS_NCC_Displacement.mhd.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_NCC_Displacement.raw.md5
→
Testing/Data/Baseline/elastix_BS_NCC_Displacement.raw.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_NCC_Image.mhd.md5
→
Testing/Data/Baseline/elastix_BS_NCC_Image.mhd.md5
View file @
1eaf3de6
File moved
Testing/
Unit/
Data/Baseline/elastix_BS_NCC_Image.raw.md5
→
Testing/Data/Baseline/elastix_BS_NCC_Image.raw.md5
View file @
1eaf3de6
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