diff --git a/CMakeExternals/Vigra.cmake b/CMakeExternals/Vigra.cmake
index 80e0fd99ee..f79b5ff82c 100644
--- a/CMakeExternals/Vigra.cmake
+++ b/CMakeExternals/Vigra.cmake
@@ -1,65 +1,72 @@
#-----------------------------------------------------------------------------
# VIGRA
#-----------------------------------------------------------------------------
if(MITK_USE_Vigra)
# Sanity checks
if(DEFINED Vigra_DIR AND NOT EXISTS ${Vigra_DIR})
message(FATAL_ERROR "Vigra_DIR variable is defined but corresponds to non-existing directory")
endif()
if(NOT ${MITK_USE_HDF5})
message(FATAL_ERROR "HDF5 is required for Vigra. Please enable it.")
endif()
set(proj Vigra)
set(proj_DEPENDENCIES HDF5)
set(Vigra_DEPENDS ${proj})
# If a mac ports installation is present some imaging-io-libraries may interfere with the vigra build.
# Hence, we exclude them here.
set(mac_additional_cmake_args)
if(APPLE)
- set(mac_additional_cmake_args -DJPEG_INCLUDE_DIR= -DJPEG_LIBRARY= -DTIFF_INCLUDE_DIR= -DTIFF_LIBRARY= -DPNG_LIBRARY_RELEASE= -DPNG_PNG_INCLUDE_DIR= )
+ set(mac_additional_cmake_args
+ -DJPEG_INCLUDE_DIR=
+ -DJPEG_LIBRARY=
+ -DTIFF_INCLUDE_DIR=
+ -DTIFF_LIBRARY=
+ -DPNG_LIBRARY_RELEASE=
+ -DPNG_PNG_INCLUDE_DIR=
+ )
endif()
if(NOT DEFINED Vigra_DIR)
set(additional_cmake_args )
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
ExternalProject_Add(${proj}
URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/vigra-1.10.0-src.tar.gz
URL_MD5 4f963f0be4fcb8b06271c2aa40baa9be
PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Vigra.patch
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_cmake_args}
${mac_additional_cmake_args}
-DAUTOEXEC_TESTS:BOOL=OFF
-DWITH_VIGRANUMPY:BOOL=OFF
-DHDF5_DIR:PATH=${HDF5_DIR}
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=TRUE
-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
CMAKE_CACHE_ARGS
${ep_common_cache_args}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
DEPENDS ${proj_DEPENDENCIES}
)
set(Vigra_DIR ${ep_prefix})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif(MITK_USE_Vigra)
diff --git a/CMakeExternals/Vigra.patch b/CMakeExternals/Vigra.patch
index bac3758ab4..8002ed96bb 100644
--- a/CMakeExternals/Vigra.patch
+++ b/CMakeExternals/Vigra.patch
@@ -1,479 +1,519 @@
diff -urNb vigra-Version-1-10-0/CMakeLists.txt Vigra/CMakeLists.txt
--- vigra-Version-1-10-0/CMakeLists.txt 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/CMakeLists.txt 2015-03-03 10:13:57.693725000 +0100
@@ -70,7 +70,12 @@ IF(WITH_OPENEXR)
ENDIF()
IF(WITH_HDF5)
+ FIND_PACKAGE(HDF5 PATHS ${HDF5_DIR} PATH_SUFFIXES hdf5 NO_DEFAULT_PATH NO_MODULE)
+ IF(NOT HDF5_FOUND)
VIGRA_FIND_PACKAGE(HDF5)
+ ENDIF()
+ # HDF5 changed their config, this ports the new style to the old style
+ set(HDF5_LIBRARIES ${HDF5_EXPORT_LIBRARIES})
ENDIF()
IF(WITH_BOOST_GRAPH)
@@ -395,3 +398,4 @@
ENDIF()
MESSAGE( STATUS "---------------------------------------------------------" )
+
diff -urNb vigra-Version-1-10-0/config/VigraConfig.cmake.in Vigra/config/VigraConfig.cmake.in
--- vigra-Version-1-10-0/config/VigraConfig.cmake.in 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/config/VigraConfig.cmake.in 2015-03-03 10:13:57.693725000 +0100
@@ -1,7 +1,9 @@
get_filename_component(SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
get_filename_component(Vigra_TOP_DIR "${SELF_DIR}/../../" ABSOLUTE)
-include(${SELF_DIR}/vigra-targets.cmake)
+if(NOT TARGET vigraimpex)
+ include(${SELF_DIR}/vigra-targets.cmake)
+endif()
get_target_property(VIGRA_TYPE vigraimpex TYPE)
if(${VIGRA_TYPE} STREQUAL "STATIC_LIBRARY")
SET(VIGRA_STATIC_LIB True)
@@ -12,3 +14,4 @@
IF(EXISTS ${SELF_DIR}/../vigranumpy/VigranumpyConfig.cmake)
INCLUDE(${SELF_DIR}/../vigranumpy/VigranumpyConfig.cmake)
ENDIF()
+
diff -urNb vigra-Version-1-10-0/include/vigra/random_forest/rf_common.hxx Vigra/include/vigra/random_forest/rf_common.hxx
--- vigra-Version-1-10-0/include/vigra/random_forest/rf_common.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/random_forest/rf_common.hxx 2015-07-08 18:55:16.000000000 +0200
@@ -558,6 +558,7 @@
int is_weighted_; // class_weights_ are used
double precision_; // termination criterion for regression loss
int response_size_;
+ int max_tree_depth;
template<class T>
void to_classlabel(int index, T & out) const
@@ -583,7 +584,8 @@
EQUALS(class_weights_),
EQUALS(is_weighted_),
EQUALS(precision_),
- EQUALS(response_size_)
+ EQUALS(response_size_),
+ EQUALS(max_tree_depth)
{
std::back_insert_iterator<ArrayVector<Label_t> >
iter(classes);
@@ -604,7 +606,8 @@
EQUALS(class_weights_),
EQUALS(is_weighted_),
EQUALS(precision_),
- EQUALS(response_size_)
+ EQUALS(response_size_),
+ EQUALS(max_tree_depth)
{
std::back_insert_iterator<ArrayVector<Label_t> >
iter(classes);
@@ -624,7 +627,8 @@
EQUALS(used_);
EQUALS(is_weighted_);
EQUALS(precision_);
- EQUALS(response_size_)
+ EQUALS(response_size_);
+ EQUALS(max_tree_depth)
class_weights_.clear();
std::back_insert_iterator<ArrayVector<double> >
iter2(class_weights_);
@@ -648,7 +652,8 @@
EQUALS(used_);
EQUALS(is_weighted_);
EQUALS(precision_);
- EQUALS(response_size_)
+ EQUALS(response_size_);
+ EQUALS(max_tree_depth)
class_weights_.clear();
std::back_insert_iterator<ArrayVector<double> >
iter2(class_weights_);
@@ -677,7 +682,8 @@
COMPARE(used_);
COMPARE(class_weights_);
COMPARE(classes);
- COMPARE(response_size_)
+ COMPARE(response_size_);
+ COMPARE(max_tree_depth)
#undef COMPARE
return result;
}
@@ -715,6 +721,7 @@
PULL(used_, int);
PULL(precision_, double);
PULL(response_size_, int);
+ PULL(max_tree_depth, int);
if(is_weighted_)
{
vigra_precondition(end - begin == 10 + 2*class_count_,
@@ -747,6 +754,7 @@
PUSH(used_);
PUSH(precision_);
PUSH(response_size_);
+ PUSH(max_tree_depth);
if(is_weighted_)
{
std::copy(class_weights_.begin(),
@@ -773,6 +781,7 @@
PULL(used_, int);
PULL(precision_, double);
PULL(response_size_, int);
+ PULL(max_tree_depth, int);
class_weights_ = in["class_weights_"];
#undef PUSH
}
@@ -789,6 +798,7 @@
PUSH(used_);
PUSH(precision_);
PUSH(response_size_);
+ PUSH(max_tree_depth);
in["class_weights_"] = class_weights_;
#undef PUSH
}
@@ -805,7 +815,8 @@
used_(false),
is_weighted_(false),
precision_(0.0),
- response_size_(1)
+ response_size_(1),
+ max_tree_depth(50)
{}
@@ -857,7 +868,7 @@
is_weighted_ = false;
precision_ = 0.0;
response_size_ = 0;
-
+ max_tree_depth = 50;
}
bool used() const
diff -urNb vigra-Version-1-10-0/include/vigra/random_forest/rf_decisionTree.hxx Vigra/include/vigra/random_forest/rf_decisionTree.hxx
--- vigra-Version-1-10-0/include/vigra/random_forest/rf_decisionTree.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/random_forest/rf_decisionTree.hxx 2015-07-08 18:55:16.000000000 +0200
@@ -90,6 +90,8 @@
ProblemSpec<> ext_param_;
unsigned int classCount_;
+ std::map<int, int> m_Parents;
+
public:
/* \brief Create tree with parameters */
@@ -350,6 +352,22 @@
continueLearn(features,labels,stack_entry,split,stop,visitor,randint);
}
+template < class TRandomForest>
+int GetTreeDepthForNode(int nodeIndex, TRandomForest* rf)
+{
+ int depth = 0;
+ while (true)
+ {
+ if (nodeIndex < 1)
+ {
+ break;
+ }
+ ++depth;
+ nodeIndex = rf->m_Parents[nodeIndex];
+ }
+ return depth;
+}
+
template < class U, class C,
class U2, class C2,
class StackEntry_t,
@@ -374,6 +392,11 @@
size_t last_node_pos = 0;
StackEntry_t top=stack.back();
+ Split_t* splitPointer = &split;
+ bool isDepthSplitter = true;
+
+ int maximumTreeDepth = splitPointer->GetMaximumTreeDepth();
+
while(!stack.empty())
{
@@ -392,7 +415,20 @@
//kind of node to make
TreeInt NodeID;
- if(stop(top))
+ bool depthStop = false;
+ if (isDepthSplitter)
+ {
+ int currentDepthLevel;
+ if (top.leftParent != StackEntry_t::DecisionTreeNoParent)
+ currentDepthLevel = GetTreeDepthForNode(top.leftParent, this);
+ else
+ currentDepthLevel = GetTreeDepthForNode(top.rightParent, this);
+
+ depthStop = (currentDepthLevel >= maximumTreeDepth);
+ }
+ if(stop(top) || (depthStop))
+
+ //if (stop(top) || currentDepthLevel >= MaximumSplitDepth(split))
NodeID = split.makeTerminalNode(features,
labels,
top,
@@ -421,17 +457,20 @@
// Using InteriorNodeBase because exact parameter form not needed.
// look at the Node base before getting scared.
last_node_pos = topology_.size();
+ m_Parents[last_node_pos] = StackEntry_t::DecisionTreeNoParent;
if(top.leftParent != StackEntry_t::DecisionTreeNoParent)
{
NodeBase(topology_,
parameters_,
top.leftParent).child(0) = last_node_pos;
+ m_Parents[last_node_pos] = top.leftParent;
}
else if(top.rightParent != StackEntry_t::DecisionTreeNoParent)
{
NodeBase(topology_,
parameters_,
top.rightParent).child(1) = last_node_pos;
+ m_Parents[last_node_pos] = top.rightParent;
}
diff -urNb vigra-Version-1-10-0/include/vigra/random_forest/rf_nodeproxy.hxx Vigra/include/vigra/random_forest/rf_nodeproxy.hxx
--- vigra-Version-1-10-0/include/vigra/random_forest/rf_nodeproxy.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/random_forest/rf_nodeproxy.hxx 2015-07-08 18:55:16.000000000 +0200
@@ -50,7 +50,11 @@
namespace vigra
{
-
+class DepthSplitterBase
+{
+public:
+ virtual int GetMaximumTreeDepth() const = 0;
+};
enum NodeTags
{
diff -urNb vigra-Version-1-10-0/include/vigra/random_forest/rf_split.hxx Vigra/include/vigra/random_forest/rf_split.hxx
--- vigra-Version-1-10-0/include/vigra/random_forest/rf_split.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/random_forest/rf_split.hxx 2015-07-08 18:55:16.000000000 +0200
@@ -108,6 +108,11 @@
\ref SplitBase::findBestSplit() or \ref SplitBase::makeTerminalNode().
**/
+ virtual int GetMaximumTreeDepth() const
+ {
+ return ext_param_.max_tree_depth;
+ }
+
template<class T>
void set_external_parameters(ProblemSpec<T> const & in)
{
diff -urNb vigra-Version-1-10-0/include/vigra/random_forest.hxx Vigra/include/vigra/random_forest.hxx
--- vigra-Version-1-10-0/include/vigra/random_forest.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/random_forest.hxx 2015-07-15 14:08:18.548277915 +0200
@@ -165,6 +165,7 @@
ProblemSpec_t ext_param_;
/*mutable ArrayVector<int> tree_indices_;*/
rf::visitors::OnlineLearnVisitor online_visitor_;
+ bool multithreadPrediction; // enable/disable multithreaded predictProbabilities and predictLabels
void reset()
@@ -584,6 +585,18 @@
{
vigra_precondition(features.shape(0) == labels.shape(0),
"RandomForest::predictLabels(): Label array has wrong size.");
+ if (multithreadPrediction)
+ {
+#pragma omp parallel for
+ for(int k=0; k<features.shape(0); ++k)
+ {
+ vigra_precondition(!detail::contains_nan(rowVector(features, k)),
+ "RandomForest::predictLabels(): NaN in feature matrix.");
+ labels(k,0) = detail::RequiresExplicitCast<T>::cast(predictLabel(rowVector(features, k), rf_default()));
+ }
+ }
+ else
+ {
for(int k=0; k<features.shape(0); ++k)
{
vigra_precondition(!detail::contains_nan(rowVector(features, k)),
@@ -591,6 +604,7 @@
labels(k,0) = detail::RequiresExplicitCast<T>::cast(predictLabel(rowVector(features, k), rf_default()));
}
}
+ }
/** \brief predict multiple labels with given features
*
@@ -1261,6 +1275,60 @@
}
*/
//Classify for each row.
+ if (multithreadPrediction)
+ {
+#pragma omp parallel for
+ for(int row=0; row < rowCount(features); ++row)
+ {
+ MultiArrayView<2, U, StridedArrayTag> currentRow(rowVector(features, row));
+
+ // when the features contain an NaN, the instance doesn't belong to any class
+ // => indicate this by returning a zero probability array.
+ if(detail::contains_nan(currentRow))
+ {
+ rowVector(prob, row).init(0.0);
+ continue;
+ }
+
+ ArrayVector<double>::const_iterator weights;
+
+ //totalWeight == totalVoteCount!
+ double totalWeight = 0.0;
+
+ //Let each tree classify...
+ for(int k=0; k<options_.tree_count_; ++k)
+ {
+ //get weights predicted by single tree
+ weights = trees_[k /*tree_indices_[k]*/].predict(currentRow);
+
+ //update votecount.
+ int weighted = options_.predict_weighted_;
+ for(int l=0; l<ext_param_.class_count_; ++l)
+ {
+ double cur_w = weights[l] * (weighted * (*(weights-1))
+ + (1-weighted));
+ prob(row, l) += (T)cur_w;
+ //every weight in totalWeight.
+ totalWeight += cur_w;
+ }
+ if(stop.after_prediction(weights,
+ k,
+ rowVector(prob, row),
+ totalWeight))
+ {
+ break;
+ }
+ }
+
+ //Normalise votes in each row by total VoteCount (totalWeight
+ for(int l=0; l< ext_param_.class_count_; ++l)
+ {
+ prob(row, l) /= detail::RequiresExplicitCast<T>::cast(totalWeight);
+ }
+ }
+ }
+ else
+ {
for(int row=0; row < rowCount(features); ++row)
{
MultiArrayView<2, U, StridedArrayTag> currentRow(rowVector(features, row));
@@ -1309,6 +1377,7 @@
prob(row, l) /= detail::RequiresExplicitCast<T>::cast(totalWeight);
}
}
+ }
}
diff -u -r Vigra.orig/include/vigra/imagecontainer.hxx Vigra/include/vigra/imagecontainer.hxx
--- Vigra.orig/include/vigra/imagecontainer.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/imagecontainer.hxx 2017-08-26 11:02:40.079669325 +0200
@@ -760,7 +760,7 @@
/** swap contents of this array with the contents of other
(STL-Container interface)
*/
- void swap(const ImagePyramid<ImageType, Alloc> &other)
+ void swap(ImagePyramid<ImageType, Alloc> &other)
{
images_.swap(other.images_);
std::swap(lowestLevel_, other.lowestLevel_);
diff -urNb vigra-Version-1-10-0/include/vigra/functortraits.hxx Vigra/include/vigra/functortraits.hxx
--- vigra-Version-1-10-0/include/vigra/functortraits.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/functortraits.hxx 2022-03-17 15:15:01.637026200 +0100
@@ -195,8 +195,6 @@
VIGRA_DEFINE_STL_FUNCTOR(std::negate, VigraTrueType, VigraFalseType)
VIGRA_DEFINE_STL_FUNCTOR(std::logical_not, VigraTrueType, VigraFalseType)
VIGRA_DEFINE_STL_FUNCTOR(std::unary_negate, VigraTrueType, VigraFalseType)
-VIGRA_DEFINE_STL_FUNCTOR(std::binder1st, VigraTrueType, VigraFalseType)
-VIGRA_DEFINE_STL_FUNCTOR(std::binder2nd, VigraTrueType, VigraFalseType)
#undef VIGRA_DEFINE_STL_FUNCTOR
template <class R>
diff -urNb vigra-Version-1-10-0/src/impex/imageinfo.cxx Vigra/src/impex/imageinfo.cxx
--- vigra-Version-1-10-0/src/impex/imageinfo.cxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/src/impex/imageinfo.cxx 2022-03-17 15:22:20.975223000 +0100
@@ -1016,7 +1016,7 @@
do
{
numEndIt = std::find_if(numBeginIt, filename.rend(),(int (*)(int)) &isdigit);
- numBeginIt = std::find_if(numEndIt, filename.rend(), not1(std::ptr_fun((int (*)(int))&isdigit)));
+ numBeginIt = std::find_if(numEndIt, filename.rend(), std::not_fn((int (*)(int))&isdigit));
if(numEndIt != filename.rend())
{
diff -urNb vigra-1.10.0-src/include/vigra/separableconvolution.hxx Vigra/include/vigra/separableconvolution.hxx
--- vigra-1.10.0-src/include/vigra/separableconvolution.hxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/include/vigra/separableconvolution.hxx 2022-03-17 23:08:05.690694437 +0100
@@ -1409,9 +1409,6 @@
{}
~InitProxy()
-#ifndef _MSC_VER
- throw(PreconditionViolation)
-#endif
{
vigra_precondition(count_ == 1 || count_ == sum_,
"Kernel1D::initExplicitly(): "
diff -urNb vigra-1.10.0-src/src/impex/gif.cxx Vigra/src/impex/gif.cxx
--- vigra-1.10.0-src/src/impex/gif.cxx 2013-11-18 17:48:16.000000000 +0100
+++ Vigra/src/impex/gif.cxx 2022-03-17 23:17:05.896364451 +0100
@@ -482,12 +482,12 @@
in_code,
old_code;
- register int
+ int
bits,
code,
count;
- register unsigned long
+ unsigned long
datum;
void_vector<Int16> prefix(MaxStackSize);
@@ -496,8 +496,8 @@
void_vector<UInt8> packet(256);
void_vector<UInt16> indices(header.width*header.height);
- register UInt8 *c;
- register UInt16 *p = indices.begin();
+ UInt8 *c;
+ UInt16 *p = indices.begin();
UInt8
data_size,
@@ -624,7 +624,7 @@
int pass, x, y;
- register UInt16 *q;
+ UInt16 *q;
static int
interlace_rate[4] = { 8, 8, 4, 2 },
@@ -891,9 +891,9 @@
long
datum;
- register int k;
+ int k;
- register UInt8 *p;
+ UInt8 *p;
void_vector<Int16> hash_code(MaxHashTable);
void_vector<Int16> hash_prefix(MaxHashTable);
+diff -urNb vigra-1.10.0-src/include/vigra/random_forest/rf_algorithm.hxx Vigra/include/vigra/random_forest/rf_algorithm.hxx
+--- vigra-1.10.0-src/include/vigra/random_forest/rf_algorithm.hxx 2013-11-18 17:48:16.000000000 +0100
++++ Vigra/include/vigra/random_forest/rf_algorithm.hxx 2022-03-18 08:52:17.519102162 +0100
+@@ -34,6 +34,7 @@
+ /************************************************************************/
+ #define VIGRA_RF_ALGORITHM_HXX
+
++#include <random>
+ #include <vector>
+ #include "splices.hxx"
+ #include <queue>
+@@ -1151,7 +1152,7 @@
+ ArrayVector<Int32> indices(pr.features().shape(0));
+ for(int ii = 0; ii < pr.features().shape(0); ++ii)
+ indices.push_back(ii);
+- std::random_shuffle(indices.begin(), indices.end());
++ std::shuffle(indices.begin(), indices.end(), std::mt19937(std::random_device()()));
+ for(int ii = 0; ii < rf.ext_param_.row_count_; ++ii)
+ {
+ if(!sm.is_used()[indices[ii]] && cts[pr.response()(indices[ii], 0)] < 3000)
+diff -urNb vigra-1.10.0-src/include/vigra/random_forest/rf_visitors.hxx Vigra/include/vigra/random_forest/rf_visitors.hxx
+--- vigra-1.10.0-src/include/vigra/random_forest/rf_visitors.hxx 2013-11-18 17:48:16.000000000 +0100
++++ Vigra/include/vigra/random_forest/rf_visitors.hxx 2022-03-18 08:54:14.449776895 +0100
+@@ -41,6 +41,7 @@
+ #include <vigra/windows.h>
+ #include <iostream>
+ #include <iomanip>
++#include <random>
+
+ #include <vigra/multi_pointoperators.hxx>
+ #include <vigra/timing.hxx>
+@@ -909,7 +910,7 @@
+ {
+ ArrayVector<int> oob_indices;
+ ArrayVector<int> cts(class_count, 0);
+- std::random_shuffle(indices.begin(), indices.end());
++ std::shuffle(indices.begin(), indices.end(), std::mt19937(std::random_device()()));
+ for(int ii = 0; ii < rf.ext_param_.row_count_; ++ii)
+ {
+ if(!sm.is_used()[indices[ii]] && cts[pr.response()(indices[ii], 0)] < 40000)