Cleanup, added model selection, improved version

CURTLab · Mar 26, 2024 · dd721d4 · dd721d4
1 parent f4f9306
commit dd721d4
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Showing 12 changed files with 180 additions and 95 deletions.
diff --git a/NanoMito3D/AnalyzeMitochondria.cpp b/NanoMito3D/AnalyzeMitochondria.cpp
@@ -60,7 +60,7 @@ void AnalyzeMitochondria::load(const QString &fileName, bool threaded)
 			m_fileName = fileName;
 			emit localizationsLoaded();
 			// increase axial range by 100 nm at each side to avoid clipping
-			m_locs.setAxialRange(m_locs.minZ() - 100.f, m_locs.maxZ() + 100.f);
+			//m_locs.setAxialRange(m_locs.minZ() - 100.f, m_locs.maxZ() + 100.f);
 		} catch(std::exception &e) {
 			qCritical().nospace() << tr("AnalyzeMitochondria::load Error: ") + e.what();
 			emit error(tr("Load localizations error"), e.what());
@@ -370,7 +370,7 @@ void AnalyzeMitochondria::classify(bool threaded)
 
 			emit progressRangeChanged(0, static_cast<int>(m_segments.size())-1);
 			for (size_t i = 0; i < m_segments.size(); ++i) {
-				cv::Mat dataSet(1, 14, CV_32FC1, &m_segments[i]->data);
+				cv::Mat dataSet(1, 14, CV_32FC1, m_segments[i]->data.values);
 				m_dtree->predict(dataSet, result, 0);
 
 				const int prediction = qRound(result.at<float>(0, 0));
@@ -405,8 +405,11 @@ void AnalyzeMitochondria::classify(bool threaded)
 		func();
 }
 
-void AnalyzeMitochondria::loadModel(const QString &fileName)
+bool AnalyzeMitochondria::loadModel(const QString &fileName)
 {
+	// clear model
+	m_dtree = {};
+
 	const auto fi = QFileInfo(fileName);
 	if (fi.completeSuffix().toLower() == "csv") {
 		// load header names from csv
@@ -418,7 +421,7 @@ void AnalyzeMitochondria::loadModel(const QString &fileName)
 			file.close();
 		} else {
 			emit error(tr("Load model"), tr("Could not load dataset! (%1)").arg(fileName));
-			return;
+			return false;
 		}
 
 		// generate training data from csv
@@ -438,7 +441,7 @@ void AnalyzeMitochondria::loadModel(const QString &fileName)
 		m_dtree->setMaxCategories(m_numClasses+1);
 		if (!m_dtree->train(trainData, cv::ml::ROW_SAMPLE, targetData)) {
 			emit error(tr("Load model"), tr("Could not train loaded dataset! (%1)").arg(fileName));
-			return;
+			return false;
 		}
 
 		// print variable importance
@@ -458,17 +461,19 @@ void AnalyzeMitochondria::loadModel(const QString &fileName)
 			m_numClasses = class_labels.size();
 		} else {
 			emit error(tr("Load model"), tr("Could not load dataset! (%1)").arg(fileName));
-			return;
+			return false;
 		}
 		// load model
 		m_dtree = cv::ml::StatModel::load<cv::ml::RTrees>(fileName.toStdString());
 	}
 
 	if (m_dtree.empty()) {
 		emit error(tr("Load model"), tr("Could not load model %1").arg(fileName));
-		return;
+		return false;
 	}
 
 	qDebug() << "Samples:" << m_dtree->getVarCount();
 	qDebug() << "Num classes:" << m_numClasses;
+
+	return true;
 }
diff --git a/NanoMito3D/AnalyzeMitochondria.h b/NanoMito3D/AnalyzeMitochondria.h
@@ -30,7 +30,6 @@
 #include "Volume.h"
 #include "Localizations.h"
 #include "Segments.h"
-#include "AnalyzeSkeleton.h"
 
 enum class ThresholdMethods {
 	LocalISOData,
@@ -61,7 +60,7 @@ class AnalyzeMitochondria : public QObject
 	void classify(bool threaded = true);
 
 	// load model eighter from csv training dataset or pretrained json model file
-	void loadModel(const QString &fileName);
+	bool loadModel(const QString &fileName);
 
 	inline constexpr const QString &fileName() const { return m_fileName; }
 	inline constexpr const Localizations &localizations() const { return m_locs; }

diff --git a/NanoMito3D/CMakeLists.txt b/NanoMito3D/CMakeLists.txt
@@ -4,15 +4,10 @@ project(NanoMito3D VERSION 0.1 LANGUAGES CXX)
 
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
-set(CMAKE_AUTOUIC ON)
-set(CMAKE_AUTOMOC ON)
-set(CMAKE_AUTORCC ON)
-
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set(CUDA_SUPPORT ON CACHE BOOL "Use CUDA support")
-set(RELEASE_VERSION OFF CACHE BOOL "Build as release version (No test paths)")
 
 if (CUDA_SUPPORT)
 	enable_language(CUDA)
@@ -25,6 +20,10 @@ endif()
 
 set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/../cmake ${CMAKE_MODULE_PATH})
 
+set(CMAKE_AUTOUIC ON)
+set(CMAKE_AUTOMOC ON)
+set(CMAKE_AUTORCC ON)
+
 find_package(QT NAMES Qt6 Qt5 REQUIRED COMPONENTS Widgets)
 find_package(Qt${QT_VERSION_MAJOR} REQUIRED COMPONENTS Widgets)
 find_package(VTK 8.0 REQUIRED COMPONENTS
@@ -105,7 +104,6 @@ if (CUDA_SUPPORT)
 	target_include_directories(${CMAKE_PROJECT_NAME} PRIVATE ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
 endif()
 
-
 if (RELEASE_VERSION)
 	target_compile_definitions(${CMAKE_PROJECT_NAME} PRIVATE -DRELEASE_VERSION)
 else()
@@ -118,7 +116,7 @@ vtk_module_autoinit(
 	MODULES ${VTK_LIBRARIES}
 )
 
-target_compile_definitions(${CMAKE_PROJECT_NAME} PRIVATE -D_USE_MATH_DEFINES -DNOMINMAX)
+target_compile_definitions(${CMAKE_PROJECT_NAME} PRIVATE -D_USE_MATH_DEFINES -DNOMINMAX -DUSE_OPENCV)
 
 set_target_properties(${CMAKE_PROJECT_NAME} PROPERTIES
 	MACOSX_BUNDLE_GUI_IDENTIFIER my.example.com

diff --git a/NanoMito3D/LocalThreshold.h b/NanoMito3D/LocalThreshold.h
@@ -40,7 +40,7 @@ enum Method {
 HOST_DEV uint8_t otsuThreshold(const uint16_t hist[256], int numPixels);
 HOST_DEV uint8_t isoDataThreshold(const uint16_t hist[256], int numPixels);
 
-void localThrehsold_gpu(Method method, const Volume &input, Volume &output, int windowSize);
+void localThrehsold_gpu(Method method, const Volume &input, Volume &output, int windowSize, bool original = false);
 void localThrehsold_cpu(Method method, const Volume &input, Volume &output, int windowSize, std::function<void(uint32_t, uint32_t)> cb = {});
 
 }

diff --git a/NanoMito3D/MainWindow.cpp b/NanoMito3D/MainWindow.cpp
@@ -66,13 +66,20 @@ MainWindow::MainWindow(QWidget *parent)
 	m_ui->actionExportSkeleton->setEnabled(false);
 	m_ui->actionExportSegmentation->setEnabled(false);
 
+	m_ui->comboThreshold->addItem("Local IsoData", QVariant::fromValue(ThresholdMethods::LocalISOData));
+	m_ui->comboThreshold->addItem("Local Otsu", QVariant::fromValue(ThresholdMethods::LocalOtsu));
+
 #ifndef CUDA_SUPPORT
 	m_ui->checkUseGPU->setVisible(false);
 #endif // CUDA_SUPPORT
 
-	setWindowTitle(tr("NanoMito3D r%1").arg(GIT_REVISION));
+	setWindowTitle("NanoMito3D " APP_VERSION);
 
-	m_analyis.loadModel("mitoTrainDataSet.csv");
+	const QString modelFile = "mitoTrainDataSet.csv";
+	if (QFile(modelFile).exists()) {
+		if (m_analyis.loadModel(modelFile))
+			m_ui->editModel->setText(QFileInfo(modelFile).absoluteFilePath());
+	}
 
 	connect(m_ui->actionExportVolume, &QAction::triggered,
 			this, [this]() {
@@ -129,7 +136,7 @@ MainWindow::MainWindow(QWidget *parent)
 	connect(m_ui->buttonSelectFile, &QAbstractButton::released,
 			this, [this]() {
 		m_bar->setVisible(false);
-		QString fileName = QFileDialog::getOpenFileName(this, "Open localization file", m_currentFile, "TSF File (*.tsf)");
+		QString fileName = QFileDialog::getOpenFileName(this, "Open localization file", m_currentFile, "TSF file (*.tsf)");
 		if (!fileName.isEmpty()) {
 			m_ui->statusbar->showMessage(tr("Load %1").arg(QFileInfo(fileName).fileName()));
 			m_ui->frame->setEnabled(false);
@@ -148,6 +155,16 @@ MainWindow::MainWindow(QWidget *parent)
 		}
 	});
 
+	// model selection
+	connect(m_ui->buttonSelectModel, &QAbstractButton::released,
+			this, [this]() {
+		QString fileName = QFileDialog::getOpenFileName(this, "Open model file", m_ui->editModel->text(), "Model file (*.json *.csv)");
+		if (fileName.isEmpty())
+			return;
+		if (m_analyis.loadModel(fileName))
+			m_ui->editModel->setText(QFileInfo(fileName).absoluteFilePath());
+	});
+
 	connect(&m_analyis, &AnalyzeMitochondria::localizationsLoaded, this, [this]() {
 		// reset UI
 		m_bar->setVisible(false);
@@ -218,7 +235,7 @@ MainWindow::MainWindow(QWidget *parent)
 		m_ui->frame->setEnabled(false);
 		m_bar->setVisible(true);
 		m_ui->statusbar->showMessage(tr("Analyzing volume ..."));
-		m_analyis.analyze(m_ui->spinGaussianSigma->value(), (ThresholdMethods)m_ui->comboThreshold->currentIndex(), m_ui->checkUseGPU->isChecked());
+		m_analyis.analyze(m_ui->spinGaussianSigma->value(),  m_ui->comboThreshold->currentData().value<ThresholdMethods>(), m_ui->checkUseGPU->isChecked());
 	});
 
 	connect(&m_analyis, &AnalyzeMitochondria::volumeAnalyzed, this, [this]() {

diff --git a/NanoMito3D/MainWindow.ui b/NanoMito3D/MainWindow.ui
@@ -317,33 +317,43 @@
             </widget>
            </item>
            <item row="1" column="1">
-            <widget class="QComboBox" name="comboThreshold">
-             <item>
-              <property name="text">
-               <string>Local IsoData</string>
-              </property>
-             </item>
-             <item>
-              <property name="text">
-               <string>Local Otsu</string>
-              </property>
-             </item>
-            </widget>
+            <widget class="QComboBox" name="comboThreshold"/>
            </item>
-           <item row="2" column="1">
+           <item row="3" column="1">
             <widget class="QPushButton" name="buttonAnalyse">
              <property name="text">
               <string>Analyze</string>
              </property>
             </widget>
            </item>
-           <item row="3" column="1">
+           <item row="4" column="1">
             <widget class="QPushButton" name="buttonClassify">
              <property name="text">
               <string>Classify</string>
              </property>
             </widget>
            </item>
+           <item row="2" column="1">
+            <layout class="QHBoxLayout" name="horizontalLayout_5">
+             <item>
+              <widget class="QLineEdit" name="editModel"/>
+             </item>
+             <item>
+              <widget class="QToolButton" name="buttonSelectModel">
+               <property name="text">
+                <string>...</string>
+               </property>
+              </widget>
+             </item>
+            </layout>
+           </item>
+           <item row="2" column="0">
+            <widget class="QLabel" name="label_14">
+             <property name="text">
+              <string>Model:</string>
+             </property>
+            </widget>
+           </item>
           </layout>
          </widget>
         </item>

diff --git a/NanoMito3D/Segments.h b/NanoMito3D/Segments.h
@@ -24,29 +24,31 @@
 
 #include <vector>
 #include <string>
-#include <opencv2/opencv.hpp>
 
 #include "Volume.h"
 #include "SkeletonGraph.h"
 #include "Bounds.h"
 
-struct SegmentData
+union SegmentData
 {
-	float numBranches;
-	float numEndPoints;
-	float numJunctionVoxels;
-	float numJunctions;
-	float numSlabs;
-	float numTriples;
-	float numQuadruples;
-	float averageBranchLength;
-	float maximumBranchLength;
-	float shortestPath;
-	float voxels;
-	float width;
-	float height;
-	float depth;
-	float signalCount;
+	struct {
+		float numBranches;
+		float numEndPoints;
+		float numJunctionVoxels;
+		float numJunctions;
+		float numSlabs;
+		float numTriples;
+		float numQuadruples;
+		float averageBranchLength;
+		float maximumBranchLength;
+		float shortestPath;
+		float voxels;
+		float width;
+		float height;
+		float depth;
+		float signalCount;
+	};
+	float values[15];
 };
 
 struct Segment

diff --git a/NanoMito3D/Volume.cpp b/NanoMito3D/Volume.cpp
@@ -26,9 +26,12 @@
 #include <hdf5.h>
 #endif // USE_H5
 
+#ifdef USE_OPENCV
+#include <opencv2/opencv.hpp>
+#endif
+
 #include <stdexcept>
 #include <assert.h>
-#include <opencv2/opencv.hpp>
 #include <filesystem>
 
 class VolumeData
@@ -114,6 +117,7 @@ void Volume::fill(uint8_t value)
 	std::fill_n(d->data, d->voxels, value);
 }
 
+#ifdef USE_OPENCV
 Volume Volume::loadTif(const std::string &fileName, std::array<float, 3> voxelSize, std::array<float, 3> origin)
 {
 	std::vector<cv::Mat> stack;
@@ -161,6 +165,7 @@ void Volume::saveTif(const std::string &fileName) const
 	if (!cv::imwritemulti(fileName, stack))
 		throw std::runtime_error("Could not save tif stack at " + fileName);
 }
+#endif // USE_OPENCV
 
 #ifdef USE_H5
 Volume Volume::loadH5(const std::string &fileName, std::string name)

diff --git a/NanoMito3D/Volume.h b/NanoMito3D/Volume.h
@@ -44,9 +44,11 @@ class Volume final
 	// fill the volume with value
 	void fill(uint8_t value);
 
+#ifdef USE_OPENCV
 	// load a tiff stack as volume
 	static Volume loadTif(const std::string &fileName, std::array<float,3> voxelSize = {1.f,1.f,1.f}, std::array<float,3> origin = {0.f});
 	void saveTif(const std::string &fileName) const;
+#endif // USE_OPENCV
 
 #ifdef USE_H5
 	// load and save volume as h5 file