diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.cpp
new file mode 100644
index 0000000000..d1b50b09df
--- /dev/null
+++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.cpp
@@ -0,0 +1,96 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.s
+
+============================================================================*/
+
+#include "QmitknnUNetFolderParser.h"
+
+QmitknnUNetFolderParser::QmitknnUNetFolderParser(const QString parentFolder)
+{
+ m_RootNode = std::make_shared<FolderNode>();
+ m_RootNode->path = parentFolder;
+ m_RootNode->name = QString("nnUNet");
+ m_RootNode->subFolders.clear();
+ InitDirs(m_RootNode, 0);
+}
+
+QString QmitknnUNetFolderParser::getResultsFolder()
+{
+ return m_RootNode->path;
+}
+
+std::function<bool(QString)> QmitknnUNetFolderParser::RuleEngine(int level)
+{
+ if (level == m_LEVEL - 1)
+ {
+ return [](QString path)
+ {
+ return (QFile::exists(path + QDir::separator() + QString("model_final_checkpoint.model")) &&
+ QFile::exists(path + QDir::separator() + QString("model_final_checkpoint.model.pkl")) &&
+ QFile::exists(path + QDir::separator() + QString("debug.json")));
+ };
+ }
+ if (level == m_LEVEL - 2)
+ {
+ return [](QString path) { return QFile::exists(path + QDir::separator() + QString("plans.pkl")); };
+ }
+ else
+ {
+ return [](QString /*path*/) { return true; };
+ }
+}
+
+std::shared_ptr<FolderNode> QmitknnUNetFolderParser::GetSubNodeMatchingNameCrietria(
+ const QString &queryName, std::shared_ptr<FolderNode> parentNode)
+{
+ std::shared_ptr<FolderNode> retNode;
+ std::vector<std::shared_ptr<FolderNode>> subNodes = parentNode->subFolders;
+ for (std::shared_ptr<FolderNode> node : subNodes)
+ {
+ if (node->name == queryName)
+ {
+ retNode = node;
+ break;
+ }
+ }
+ return retNode;
+}
+
+void QmitknnUNetFolderParser::InitDirs(std::shared_ptr<FolderNode> parent, int level)
+{
+ QString searchFolder = parent->path + QDir::separator() + parent->name;
+ auto rules = RuleEngine(level);
+ auto subFolders = FetchFoldersFromDir<QStringList>(searchFolder, rules);
+ level++;
+ foreach (QString folder, subFolders)
+ {
+ std::shared_ptr<FolderNode> fp = std::make_shared<FolderNode>();
+ fp->path = searchFolder;
+ fp->name = folder;
+ if (level < this->m_LEVEL)
+ {
+ InitDirs(fp, level);
+ }
+ parent->subFolders.push_back(fp);
+ }
+}
+
+void QmitknnUNetFolderParser::DeleteDirs(std::shared_ptr<FolderNode> parent, int level)
+{
+ level++;
+ for (std::shared_ptr<FolderNode> subFolder : parent->subFolders)
+ {
+ if (level < m_LEVEL)
+ {
+ DeleteDirs(subFolder, level);
+ }
+ parent->subFolders.clear();
+ }
+}
diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h
index 7edf2882fe..d37acf666a 100644
--- a/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h
+++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h
@@ -1,328 +1,257 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.s
============================================================================*/
#ifndef QmitknnUNetFolderParser_h_Included
#define QmitknnUNetFolderParser_h_Included
-#include "QmitknnUNetToolGUI.h"
#include <QDirIterator>
#include <QString>
#include <vector>
/**
* @brief Struct to store each (Folder) Node of the hierarchy tree structure.
*
*/
struct FolderNode
{
QString name;
QString path; // parent
std::vector<std::shared_ptr<FolderNode>> subFolders;
};
/**
* @brief Class to store and retreive folder hierarchy information
* of RESULTS_FOLDER. Only Root node is explicitly stored in m_RootNode.
* No. of sub levels in the hierachry is defined in the LEVEL constant.
*
*/
-class MITKSEGMENTATIONUI_EXPORT QmitknnUNetFolderParser
+class QmitknnUNetFolderParser
{
public:
/**
* @brief Construct a new QmitknnUNetFolderParser object
* Initializes root folder node object pointer calls
* @param parentFolder
*/
- QmitknnUNetFolderParser(const QString parentFolder)
- {
- m_RootNode = std::make_shared<FolderNode>();
- m_RootNode->path = parentFolder;
- m_RootNode->name = QString("nnUNet");
- m_RootNode->subFolders.clear();
- InitDirs(m_RootNode, 0);
- }
-
+ QmitknnUNetFolderParser(const QString parentFolder);
/**
* @brief Destroy the QmitknnUNetFolderParser object
*
*/
- ~QmitknnUNetFolderParser() = default; /*{ DeleteDirs(m_RootNode, LEVEL); }*/
-
+ ~QmitknnUNetFolderParser() = default;
/**
* @brief Returns the "Results Folder" string which is parent path of the root node.
*
* @return QString
*/
- QString getResultsFolder() { return m_RootNode->path; }
+ QString getResultsFolder();
/**
* @brief Returns the Model Names from root node. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getModelNames()
{
auto models = GetSubFolderNamesFromNode<T>(m_RootNode);
return models;
}
/**
* @brief Returns the task names for a given model. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param modelName
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getTasksForModel(const QString &modelName)
{
std::shared_ptr<FolderNode> modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode);
auto tasks = GetSubFolderNamesFromNode<T>(modelNode);
return tasks;
}
/**
* @brief Returns the models names for a given task. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param taskName
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getModelsForTask(const QString &taskName)
{
T modelsForTask;
auto models = GetSubFolderNamesFromNode<T>(m_RootNode);
foreach (QString model, models)
{
QStringList taskList = getTasksForModel<QStringList>(model);
if (taskList.contains(taskName, Qt::CaseInsensitive))
{
modelsForTask << model;
}
}
return modelsForTask;
}
/**
* @brief Returns all the task names present in the root node with possible duplicates.
* Template function, type can be any of stl or Qt containers which supports push_back call.
*
* @param T
* @param taskName
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getAllTasks()
{
T allTasks;
auto models = GetSubFolderNamesFromNode<T>(m_RootNode);
foreach (QString model, models)
{
allTasks << getTasksForModel<QStringList>(model);
}
return allTasks;
}
/**
* @brief Returns the trainer / planner names for a given task & model. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param taskName
* @param modelName
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getTrainerPlannersForTask(const QString &taskName, const QString &modelName)
{
std::shared_ptr<FolderNode> modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode);
std::shared_ptr<FolderNode> taskNode = GetSubNodeMatchingNameCrietria(taskName, modelNode);
auto tps = GetSubFolderNamesFromNode<T>(taskNode);
return tps;
}
/**
* @brief Returns the Folds names for a given trainer,planner,task & model name. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param trainer
* @param planner
* @param taskName
* @param modelName
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T getFoldsForTrainerPlanner(const QString &trainer,
const QString &planner,
const QString &taskName,
const QString &modelName)
{
std::shared_ptr<FolderNode> modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode);
std::shared_ptr<FolderNode> taskNode = GetSubNodeMatchingNameCrietria(taskName, modelNode);
QString trainerPlanner = trainer + QString("__") + planner;
std::shared_ptr<FolderNode> tpNode = GetSubNodeMatchingNameCrietria(trainerPlanner, taskNode);
auto folds = GetSubFolderNamesFromNode<T>(tpNode);
return folds;
}
private:
const int m_LEVEL = 4;
std::shared_ptr<FolderNode> m_RootNode;
/**
* @brief Returns rule function wrapper to check for specific files at given Result_Folder hierarchy level.
*
* @param level
* @return std::function<bool(QString)>
*/
- std::function<bool(QString)> RuleEngine(int level)
- {
- if (level == m_LEVEL - 1)
- {
- return [](QString path)
- {
- return (QFile::exists(path + QDir::separator() + QString("model_final_checkpoint.model")) &&
- QFile::exists(path + QDir::separator() + QString("model_final_checkpoint.model.pkl")) &&
- QFile::exists(path + QDir::separator() + QString("debug.json")));
- };
- }
- if (level == m_LEVEL - 2)
- {
- return [](QString path) { return QFile::exists(path + QDir::separator() + QString("plans.pkl")); };
- }
- else
- {
- return [](QString /*path*/) { return true; };
- }
- }
+ std::function<bool(QString)> RuleEngine(int level);
/**
* @brief Iterates through the root node and returns the sub FolderNode object Matching Name Crietria
*
* @param queryName
* @param parentNode
* @return std::shared_ptr<FolderNode>
*/
- std::shared_ptr<FolderNode> GetSubNodeMatchingNameCrietria(const QString &queryName,
- std::shared_ptr<FolderNode> parentNode)
- {
- std::shared_ptr<FolderNode> retNode;
- std::vector<std::shared_ptr<FolderNode>> subNodes = parentNode->subFolders;
- for (std::shared_ptr<FolderNode> node : subNodes)
- {
- if (node->name == queryName)
- {
- retNode = node;
- break;
- }
- }
- return retNode;
- }
+ std::shared_ptr<FolderNode> GetSubNodeMatchingNameCrietria(const QString &queryName, std::shared_ptr<FolderNode> parentNode);
/**
* @brief Returns the sub folder names for a folder node object. Template function,
* type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param std::shared_ptr<FolderNode>
* @return T (any of stl or Qt containers which supports push_back call)
*/
template <typename T>
T GetSubFolderNamesFromNode(const std::shared_ptr<FolderNode> parent)
{
T folders;
std::vector<std::shared_ptr<FolderNode>> subNodes = parent->subFolders;
for (std::shared_ptr<FolderNode> folder : subNodes)
{
folders.push_back(folder->name);
}
return folders;
}
/**
* @brief Iterates through the sub folder hierarchy upto a level provided
* and create a tree structure.
*
* @param parent
* @param level
*/
- void InitDirs(std::shared_ptr<FolderNode> parent, int level)
- {
- QString searchFolder = parent->path + QDir::separator() + parent->name;
- auto rules = RuleEngine(level);
- auto subFolders = FetchFoldersFromDir<QStringList>(searchFolder, rules);
- level++;
- foreach (QString folder, subFolders)
- {
- std::shared_ptr<FolderNode> fp = std::make_shared<FolderNode>();
- fp->path = searchFolder;
- fp->name = folder;
- if (level < this->m_LEVEL)
- {
- InitDirs(fp, level);
- }
- parent->subFolders.push_back(fp);
- }
- }
+ void InitDirs(std::shared_ptr<FolderNode> parent, int level);
/**
* @brief Iterates through the sub folder hierarchy upto a level provided
* and clears the sub folder std::vector from each node.
*
* @param parent
* @param level
*/
- void DeleteDirs(std::shared_ptr<FolderNode> parent, int level)
- {
- level++;
- for (std::shared_ptr<FolderNode> subFolder : parent->subFolders)
- {
- if (level < m_LEVEL)
- {
- DeleteDirs(subFolder, level);
- }
- parent->subFolders.clear();
- }
- }
+ void DeleteDirs(std::shared_ptr<FolderNode> parent, int level);
/**
* @brief Template function to fetch all folders inside a given path.
* The type can be any of stl or Qt containers which supports push_back call.
*
* @tparam T
* @param path
* @return T
*/
template <typename T>
T FetchFoldersFromDir(const QString &path, std::function<bool(QString)> callback)
{
T folders;
for (QDirIterator it(path, QDir::AllDirs, QDirIterator::NoIteratorFlags); it.hasNext();)
{
it.next();
if (!it.fileName().startsWith('.') && callback(it.filePath()))
{
folders.push_back(it.fileName());
}
}
return folders;
}
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp
new file mode 100644
index 0000000000..d0478d1332
--- /dev/null
+++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp
@@ -0,0 +1,52 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.s
+
+============================================================================*/
+
+#include "QmitknnUNetGPU.h"
+#include <QProcess>
+
+QmitkGPULoader::QmitkGPULoader()
+{
+ QProcess process;
+ process.start("nvidia-smi --query-gpu=name,memory.total --format=csv");
+ process.waitForFinished(-1);
+ QStringList infoStringList;
+ while (process.canReadLine())
+ {
+ QString line = process.readLine();
+ if (!line.startsWith("name"))
+ {
+ infoStringList << line;
+ }
+ }
+ unsigned int count = 0;
+ foreach (QString infoString, infoStringList)
+ {
+ QmitkGPUSpec spec;
+ QStringList gpuDetails;
+ gpuDetails = infoString.split(",");
+ spec.name = gpuDetails.at(0);
+ spec.id = count;
+ spec.memory = gpuDetails.at(1);
+ this->m_Gpus.push_back(spec);
+ ++count;
+ }
+}
+
+int QmitkGPULoader::GetGPUCount()
+{
+ return static_cast<int>(m_Gpus.size());
+}
+
+std::vector<QmitkGPUSpec> QmitkGPULoader::GetAllGPUSpecs()
+{
+ return m_Gpus;
+}
diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.h b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.h
index cf92c9e028..b7f0ccbf7d 100644
--- a/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.h
+++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.h
@@ -1,92 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.s
============================================================================*/
#ifndef QmitknnUNetToolGPU_h_Included
#define QmitknnUNetToolGPU_h_Included
-#include <QObject>
-#include <QProcess>
-#include <QString>
#include <vector>
+#include <QString>
+#include <MitkSegmentationUIExports.h>
/**
* @brief Struct to store GPU info.
*
*/
struct QmitkGPUSpec
{
QString name;
QString memory;
unsigned int id;
};
/**
* @brief Class to load and save GPU information
* for further validation
*/
-class QmitkGPULoader : public QObject
+class MITKSEGMENTATIONUI_EXPORT QmitkGPULoader
{
- Q_OBJECT
-
private:
std::vector<QmitkGPUSpec> m_Gpus;
public:
/**
* @brief Construct a new Qmitk GPU Loader object.
* Parses GPU info using `nvidia-smi` command and saves it as QmitkGPUSpec objects.
*/
- QmitkGPULoader()
- {
- QProcess process;
- process.start("nvidia-smi --query-gpu=name,memory.total --format=csv");
- process.waitForFinished(-1);
- QStringList infoStringList;
- while (process.canReadLine())
- {
- QString line = process.readLine();
- if (!line.startsWith("name"))
- {
- infoStringList << line;
- }
- }
- unsigned int count = 0;
- foreach (QString infoString, infoStringList)
- {
- QmitkGPUSpec spec;
- QStringList gpuDetails;
- gpuDetails = infoString.split(",");
- spec.name = gpuDetails.at(0);
- spec.id = count;
- spec.memory = gpuDetails.at(1);
- this->m_Gpus.push_back(spec);
- ++count;
- }
- }
+ QmitkGPULoader();
~QmitkGPULoader() = default;
/**
* @brief Returns the number of GPUs parsed and saved as QmitkGPUSpec objects.
*
* @return int
*/
- int GetGPUCount() { return static_cast<int>(m_Gpus.size()); }
+ int GetGPUCount();
/**
* @brief Returns all the parsed GPU information
*
* @return std::vector<QmitkGPUSpec>
*/
- std::vector<QmitkGPUSpec> GetAllGPUSpecs() { return m_Gpus; }
+ std::vector<QmitkGPUSpec> GetAllGPUSpecs();
};
#endif
diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake
index 818830625e..e1bf1397ec 100644
--- a/Modules/SegmentationUI/files.cmake
+++ b/Modules/SegmentationUI/files.cmake
@@ -1,77 +1,79 @@
set( CPP_FILES
Qmitk/QmitkSegWithPreviewToolGUIBase.cpp
Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp
Qmitk/QmitkBinaryThresholdToolGUIBase.cpp
Qmitk/QmitkBinaryThresholdToolGUI.cpp
Qmitk/QmitkBinaryThresholdULToolGUI.cpp
Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.cpp
Qmitk/QmitkConfirmSegmentationDialog.cpp
Qmitk/QmitkCopyToClipBoardDialog.cpp
Qmitk/QmitkDrawPaintbrushToolGUI.cpp
Qmitk/QmitkErasePaintbrushToolGUI.cpp
Qmitk/QmitkLiveWireTool2DGUI.cpp
Qmitk/QmitkOtsuTool3DGUI.cpp
Qmitk/QmitkPaintbrushToolGUI.cpp
Qmitk/QmitkPickingToolGUI.cpp
Qmitk/QmitkPixelManipulationToolGUI.cpp
Qmitk/QmitkSlicesInterpolator.cpp
Qmitk/QmitkToolGUI.cpp
Qmitk/QmitkToolGUIArea.cpp
Qmitk/QmitkToolSelectionBox.cpp
+Qmitk/QmitknnUNetFolderParser.cpp
Qmitk/QmitknnUNetToolGUI.cpp
Qmitk/QmitknnUNetWorker.cpp
+Qmitk/QmitknnUNetGPU.cpp
Qmitk/QmitkSurfaceStampWidget.cpp
Qmitk/QmitkMaskStampWidget.cpp
Qmitk/QmitkSliceBasedInterpolatorWidget.cpp
Qmitk/QmitkStaticDynamicSegmentationDialog.cpp
Qmitk/QmitkSurfaceBasedInterpolatorWidget.cpp
Qmitk/QmitkSimpleLabelSetListWidget.cpp
)
set(MOC_H_FILES
Qmitk/QmitkSegWithPreviewToolGUIBase.h
Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.h
Qmitk/QmitkBinaryThresholdToolGUIBase.h
Qmitk/QmitkBinaryThresholdToolGUI.h
Qmitk/QmitkBinaryThresholdULToolGUI.h
Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.h
Qmitk/QmitkConfirmSegmentationDialog.h
Qmitk/QmitkCopyToClipBoardDialog.h
Qmitk/QmitkDrawPaintbrushToolGUI.h
Qmitk/QmitkErasePaintbrushToolGUI.h
Qmitk/QmitkLiveWireTool2DGUI.h
Qmitk/QmitkOtsuTool3DGUI.h
Qmitk/QmitkPaintbrushToolGUI.h
Qmitk/QmitkPickingToolGUI.h
Qmitk/QmitkPixelManipulationToolGUI.h
Qmitk/QmitkSlicesInterpolator.h
Qmitk/QmitkToolGUI.h
Qmitk/QmitkToolGUIArea.h
Qmitk/QmitkToolSelectionBox.h
+Qmitk/QmitknnUNetFolderParser.h
Qmitk/QmitknnUNetToolGUI.h
Qmitk/QmitknnUNetGPU.h
Qmitk/QmitknnUNetWorker.h
Qmitk/QmitknnUNetEnsembleLayout.h
-Qmitk/QmitknnUNetFolderParser.h
Qmitk/QmitkSurfaceStampWidget.h
Qmitk/QmitkMaskStampWidget.h
Qmitk/QmitkSliceBasedInterpolatorWidget.h
Qmitk/QmitkStaticDynamicSegmentationDialog.h
Qmitk/QmitkSurfaceBasedInterpolatorWidget.h
Qmitk/QmitkSimpleLabelSetListWidget.h
)
set(UI_FILES
Qmitk/QmitkConfirmSegmentationDialog.ui
Qmitk/QmitkOtsuToolWidgetControls.ui
Qmitk/QmitkLiveWireTool2DGUIControls.ui
Qmitk/QmitkSurfaceStampWidgetGUIControls.ui
Qmitk/QmitkMaskStampWidgetGUIControls.ui
Qmitk/QmitkSliceBasedInterpolatorWidgetGUIControls.ui
Qmitk/QmitkSurfaceBasedInterpolatorWidgetGUIControls.ui
Qmitk/QmitknnUNetToolGUIControls.ui
)
set(QRC_FILES
resources/SegmentationUI.qrc
)