Batch mode finally working. Also, fixed such that pipelines are now properly running in background threads, with and without projects, which means that the GUI is no longer freezing. Also, did some refactoring of the pipeline solution, and finalized the wrapper, which makes the final a lot cleaner and easier to read. Also, tested signal/slots for catching when inference is done, which works well. Also fixed a bug related to initial size of the RunForProject text boxes; they are now the same size.

Author: andreped

source/MainWindow.cpp

@@ -452,10 +452,10 @@ void MainWindow::loadPipelines() {
     foreach(QString currentFpl, pipelines) {
         //runPipelineMenu->addAction(QString::fromStdString(splitCustom(currentFpl.toStdString(), ".")[0]), this, &MainWindow::lowresSegmenter);
         auto currentAction = runPipelineMenu->addAction(currentFpl); //QString::fromStdString(splitCustom(splitCustom(currentFpl.toStdString(), "/")[-1], ".")[0]));
-        QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline, this, cwd + "data/Pipelines/" + currentFpl.toStdString()));
+        QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline_wrapper, this, cwd + "data/Pipelines/" + currentFpl.toStdString()));
 
         //auto currentAction = runPipelineMenu->addAction(QString::fromStdString(splitCustom(someFile, ".")[0]));
-        //QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline, this, someFile));
+        //QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline_wrapper, this, someFile));
     }
 }
 
@@ -2394,7 +2394,7 @@ void MainWindow::runForProject() {
 	for (const auto& item : m_runForProjectWsis) {
 		selectedFilesWidget->addItem(QString::fromStdString(item));
 	}
-	selectedFilesWidget->setMinimumWidth(selectedFilesWidget->sizeHintForColumn(0));
+	selectedFilesWidget->setMinimumWidth(allFilesWidget->sizeHintForColumn(0));  // set to use allFilesWidget size such that width always match
 
 	wsiDialogLayout->addWidget(allFilesWidget);
 	wsiDialogLayout->addWidget(buttonsWidget);
@@ -2502,13 +2502,13 @@ void MainWindow::addPipelines() {
             }
         }
         // should update runPipelineMenu as new pipelines are being added
-        //runPipelineMenu->addAction(QString::fromStdString(splitCustom(someFile, ".")[0]), this, &MainWindow::runPipeline);
+        //runPipelineMenu->addAction(QString::fromStdString(splitCustom(someFile, ".")[0]), this, &MainWindow::runPipeline_wrapper);
         //auto currentAction = new QAction(QString::fromStdString(splitCustom(someFile, ".")[0]));
         auto currentAction = runPipelineMenu->addAction(QString::fromStdString(splitCustom(someFile, ".")[0]));
-        QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline, this, someFile));
+        QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline_wrapper, this, someFile));
 
         //auto currentAction = runPipelineMenu->addAction(currentFpl); //QString::fromStdString(splitCustom(splitCustom(currentFpl.toStdString(), "/")[-1], ".")[0]));
-        //QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline, this, cwd + "data/Pipelines/" + currentFpl.toStdString()));
+        //QObject::connect(currentAction, &QAction::triggered, std::bind(&MainWindow::runPipeline_wrapper, this, cwd + "data/Pipelines/" + currentFpl.toStdString()));
     }
 }
 
@@ -3097,127 +3097,121 @@ void MainWindow::runPipeline_wrapper(std::string path) {
         currentWSIs = m_runForProjectWsis;
     }
     else {
-        currentWSIs.push_back(wsiList[curr_pos]);
+        currentWSIs.push_back(filename);
     }
 
     auto progDialog = QProgressDialog(mWidget);
     progDialog.setRange(0, (int)currentWSIs.size() - 1);
-    //progDialog.setContentsMargins(0, 0, 0, 0);
     progDialog.setVisible(true);
     progDialog.setModal(false);
     progDialog.setLabelText("Running pipeline across WSIs in project...");
-    //QRect screenrect = mWidget->screen()[0].geometry();
     progDialog.move(mWidget->width() - progDialog.width() * 1.1, progDialog.height() * 0.1);
     progDialog.show();
 
     QCoreApplication::processEvents(QEventLoop::AllEvents, 0);
 
-    auto counter = 0;
-    for (const auto& currWSI : currentWSIs) {
-
-        // if run for project is enabled, run the inference-export pipeline in a background thread, else don't
-        if (m_runForProject) {
-            std::atomic_bool stopped(false);
-            std::thread inferenceThread([&, path]() {
-                runPipeline(path);
-            });
-            inferenceThread.detach();
+    // always run pipeline in background thread
+    std::atomic_bool stopped(false);
+    std::thread inferenceThread([&, path, currentWSIs]() {
+        auto counter = 0;
+        for (const auto& currWSI : currentWSIs) {
+            runPipeline(path, currWSI, counter);
         }
-        else {
-            runPipeline(path);
+    });
+    inferenceThread.detach();
 
-            // now make it possible to edit prediction in the View Widget
-            // createDynamicViewWidget(modelMetadata["name"], someModelName);
-        }
-    }
+    // now make it possible to edit prediction in the View Widget
+    // createDynamicViewWidget(modelMetadata["name"], someModelName);
 }
 
-void MainWindow::runPipeline(std::string path) {
+void MainWindow::runPipeline(std::string path, std::string currWSI, int counter) {
 
-	std::vector<std::string> currentWSIs;
-	if (m_runForProject) {
-		currentWSIs = m_runForProjectWsis;
-	}
-	else {
-        currentWSIs.push_back(filename);
-	}
+    // setup paths for saving results
+    QString wsiResultPath = (projectFolderName.toStdString() + "/results/" + splitCustom(splitCustom(currWSI, "/").back(), ".")[0]).c_str();
+    wsiResultPath = wsiResultPath.replace("//", "/");
 
-	auto progDialog = QProgressDialog(mWidget);
-	progDialog.setRange(0, (int)currentWSIs.size() - 1);
-	progDialog.setVisible(true);
-	progDialog.setModal(false);
-	progDialog.setLabelText("Running pipeline across WSIs in project...");
-	progDialog.move(mWidget->width() - progDialog.width() * 1.1, progDialog.height() * 0.1);
-	progDialog.show();
+    // if folder does not exist, create one
+    if (!QDir(wsiResultPath).exists()) {
+        QDir().mkdir(wsiResultPath);
+    }
 
-	QCoreApplication::processEvents(QEventLoop::AllEvents, 0);
+    // TODO: This now always saves result as TIFF, which is not correct. Need generic way of knowing which results that are exported and how to save these
+    auto currPath = wsiResultPath.toStdString() + "/" + splitCustom(wsiResultPath.toStdString(), "/").back() + ".tiff";
 
-    auto counter = 0;
-    for (const auto& currWSI : currentWSIs) {
+    // TODO: Perhaps use corresponding .txt-file to feed arguments in the pipeline
+    // pipeline requires some user-defined inputs, e.g. which WSI to use (and which model?)
+    std::map<std::string, std::string> arguments;
+    arguments["filename"] = currWSI;
+    arguments["exportPath"] = currPath;
+    //arguments["modelPath"] = path;
 
-        // setup paths for saving results
-        std::cout << "Current save location: " << projectFolderName.toStdString() << std::endl;
-        QString wsiResultPath = (projectFolderName.toStdString() + "/results/" + splitCustom(splitCustom(currWSI, "/").back(), ".")[0]).c_str();
-        wsiResultPath = wsiResultPath.replace("//", "/");
+    // parse fpl-file, and run pipeline with corresponding input arguments
+    auto pipeline = Pipeline(path, arguments);
+    if (m_runForProject) {
+        pipeline.parse({}, false);
+    }
+    else {
+        pipeline.parse();
+    }
 
-        // if folder does not exist, create one
-        if (!QDir(wsiResultPath).exists()) {
-            QDir().mkdir(wsiResultPath);
+    // get and start running POs
+    for (auto&& po : pipeline.getProcessObjects()) {
+        if (po.second->getNrOfOutputPorts() == 0 && std::dynamic_pointer_cast<Renderer>(po.second) == nullptr) {
+            // Process object has no output ports, must add to window to make sure it is updated.
+            reportInfo() << "Process object " << po.first << " had no output ports defined in pipeline, therefore adding to window so it is updated." << reportEnd();
+            addProcessObject(po.second);
         }
+    }
 
-        // TODO: This now always saves result as TIFF, which is not correct. Need generic way of knowing which results that are exported and how to save these
-        auto currPath = wsiResultPath.toStdString() + "/" + splitCustom(wsiResultPath.toStdString(), "/").back() + ".tiff";
+    if (!m_runForProject) {
+        // load renderers, if any
+        for (const auto& renderer : pipeline.getRenderers()) {
+            auto currId = createRandomNumbers_(8);
+            insertRenderer("result_" + currId, renderer);
+            createDynamicViewWidget("result_" + currId, "result_" + currId);
+        }
+    }
 
-        // TODO: Perhaps use corresponding .txt-file to feed arguments in the pipeline
-        // pipeline requires some user-defined inputs, e.g. which WSI to use (and which model?)
-        std::map<std::string, std::string> arguments;
-        arguments["filename"] = filename;
-        arguments["exportPath"] = currPath;
-        //arguments["modelPath"] = path;
+    if (m_runForProject) {
+        // connect signal to update flag
+        connect(this, &MainWindow::currentPipelineFinished, this, &MainWindow::_nextPipeline);
+
+        auto data = pipeline.getAllPipelineOutputData([&, this](float progress) {
+            // this never runs? Why?
+            std::cout << "Progress: " << 100 * progress << "%" << std::endl;
+            if (int(progress) == 1) {  // run until finished
+                std::cout << "PIPELINE IS DONE --- STOP SIGNAL WAS EMITTED!" << std::endl;
+                emit currentPipelineFinished();
+            }
+        });
+        std::cout << "Done" << std::endl;
 
-        // parse fpl-file, and run pipeline with corresponding input arguments
-        auto pipeline = Pipeline(path, arguments);
-        if (m_runForProject) {
-            pipeline.parse({}, false);
-        }
-        else {
-            pipeline.parse();
-        }
+        // test if signal/slot stuff works -> WORKS!
+        /*
+        std::cout << "Current stop flag value: " << m_pipelineStopped << std::endl;
+        emit currentPipelineFinished();
+        std::cout << "After emit: " << m_pipelineStopped << std::endl;
+            */
 
-        if (m_runForProject) {
-            auto data = pipeline.getAllPipelineOutputData([](float progress) {
-                std::cout << "Progress: " << 100 * progress << "%" << std::endl;
-            });
-            std::cout << "Done" << std::endl;
-        }
+            //while (!m_pipelineStopped) { QCoreApplication::processEvents(QEventLoop::AllEvents, 0); };  // perhaps need to force update if I do this? Why doesn't it update with this? Does it interact with the mainthread somehow?
 
-        // get and start running POs
-        for (auto&& po : pipeline.getProcessObjects()) {
-            if (po.second->getNrOfOutputPorts() == 0 && std::dynamic_pointer_cast<Renderer>(po.second) == nullptr) {
-                // Process object has no output ports, must add to window to make sure it is updated.
-                reportInfo() << "Process object " << po.first << " had no output ports defined in pipeline, therefore adding to window so it is updated." << reportEnd();
-                addProcessObject(po.second);
-            }
-        }
+        m_pipelineStopped = false;  // reset when done
+    }
 
-        if (!m_runForProject) {
-            // load renderers, if any
-            for (const auto& renderer : pipeline.getRenderers()) {
-                auto currId = createRandomNumbers_(8);
-                insertRenderer("result_" + currId, renderer);
-                createDynamicViewWidget("result_" + currId, "result_" + currId);
-            }
-        }
+    // update progress bar
+    //progDialog.setValue(counter);  // cannot update this in another thread -> should add some signal/slot stuff for this
+    counter++;
 
-        // update progress bar
-        progDialog.setValue(counter);
-        counter++;
+    // to render straight away (avoid waiting on all WSIs to be handled before rendering)
+    QCoreApplication::processEvents(QEventLoop::AllEvents, 0);
+}
 
-        // to render straight away (avoid waiting on all WSIs to be handled before rendering)
-        QCoreApplication::processEvents(QEventLoop::AllEvents, 0);
-	}
+void MainWindow::_nextPipeline() {
+    std::cout << "---FINALLY Done" << std::endl;
+    m_pipelineStopped = true;
 }
 
+
 // Setting parameters for different methods
 std::map<std::string, std::string> MainWindow::setParameterDialog(std::map<std::string, std::string> modelMetadata, int *successFlag) {
     QDialog paramDialog;

source/MainWindow.hpp

@@ -55,6 +55,7 @@ class MainWindow : public Window {
         bool advancedMode = false;
         bool m_wsiSharpening = false;
         bool m_doneFirstWSI = false;
+        bool m_pipelineStopped = false;
 
         int curr_pos = 0;
         float magn_lvl;
@@ -342,9 +343,12 @@ class MainWindow : public Window {
         bool segmentTissue();
         /**
          * Deploys a selected pipeline, through parsing the text pipeline script and creating FAST POs before execution.
+         * Inputs the path of the FPL file, the path of the current WSIs, and the current pipeline in a list
          * @param path
+         * @param currWSI
+         * @param counter
          */
-        void runPipeline(std::string path);
+        void runPipeline(std::string path, std::string currWSI, int counter);
         /**
          * Simple wrapper of the alternative inference method, runPipeline. If ran with Projects enabled, it will be ran in a
          * non-blocking background thread and will not render any results. Otherwise the rendered results will be
@@ -532,11 +536,10 @@ class MainWindow : public Window {
         std::shared_ptr<Image> m_tumorMap;
 
     signals:
-        void inferenceFinished(std::string name);
+        void currentPipelineFinished();
 
     private slots:
         void updateChannelValue(int index);
-
+        void _nextPipeline();
     };
-
 }