diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui
index 46bf777f20..1cd3dcd9f0 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui
+++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui
@@ -1,293 +1,293 @@
QmitkTotalSegmentatorToolGUIControls
0
0
699
352
0
0
100
0
100000
100000
QmitkTotalSegmentatorToolWidget
0
0
0
0
-
-
0
0
<html><head/><body><p>Welcome to Total Segmentator tool in MITK. [Experimental]</p><p>Please note that this is only an interface to Total Segmentator. MITK does not ship with Total Segmentator. Make sure to have a working Python environment with TotalSegmentator set up beforehand. Choose that environment in the Python Path before inferencing. </p><p>Refer to <a href="https://github.com/wasserth/TotalSegmentator"><span style=" text-decoration: underline; color:#0000ff;">https://github.com/wasserth/TotalSegmentator</span></a> to learn everything about the Total Segmentator.</p><p><br/></p></body></html>
Qt::RichText
true
-
0
0
100000
16777215
Install Total Segmentator
-
0
0
Task:
-
-
0
0
Advanced
true
5
true
-
0
0
0
0
6
-
0
0
Fast
-
true
-
0
0
- Override install
+ Use Custom Installation
-
false
-
0
0
GPU Id:
-
-
0
0
- Override Python:
+ Custom Env. Path:
-
-
0
0
System Python:
-
-
0
0
100000
16777215
Run Total Segmentator
-
0
0
true
ctkComboBox
QComboBox
1
ctkCollapsibleGroupBox
QWidget
ctkCheckBox
QWidget
diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp
index 7e4fcf7b78..47c31e4702 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp
@@ -1,395 +1,391 @@
#include "QmitkTotalSegmentatorToolGUI.h"
#include "mitkProcessExecutor.h"
#include "mitkTotalSegmentatorTool.h"
#include
#include
#include
#include
#include
#include
#include
#include
#include
MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkTotalSegmentatorToolGUI, "")
QmitkTotalSegmentatorToolGUI::QmitkTotalSegmentatorToolGUI()
: QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc)
{
// Nvidia-smi command returning zero doesn't always imply lack of GPUs.
// Pytorch uses its own libraries to communicate to the GPUs. Hence, only a warning can be given.
if (m_GpuLoader.GetGPUCount() == 0)
{
std::string warning = "WARNING: No GPUs were detected on your machine. The TotalSegmentator tool can be very slow.";
this->ShowErrorMessage(warning);
}
m_EnableConfirmSegBtnFnc = [this](bool enabled)
{ return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; };
}
void QmitkTotalSegmentatorToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool)
{
Superclass::ConnectNewTool(newTool);
newTool->IsTimePointChangeAwareOff();
m_FirstPreviewComputation = true;
}
void QmitkTotalSegmentatorToolGUI::InitializeUI(QBoxLayout *mainLayout)
{
m_Controls.setupUi(this);
#ifndef _WIN32
m_Controls.sysPythonComboBox->addItem("/usr/bin");
#endif
m_Controls.sysPythonComboBox->addItem("Select");
this->AutoParsePythonPaths();
- m_Controls.pythonEnvComboBox->addItem("Default");
m_Controls.pythonEnvComboBox->addItem("Select");
m_Controls.pythonEnvComboBox->setDuplicatesEnabled(false);
m_Controls.pythonEnvComboBox->setDisabled(true);
m_Controls.previewButton->setDisabled(true);
m_Controls.statusLabel->setTextFormat(Qt::RichText);
m_Controls.subtaskComboBox->addItems(m_VALID_TASKS);
QString welcomeText;
this->SetGPUInfo();
if (m_GpuLoader.GetGPUCount() != 0)
{
welcomeText = "STATUS: Welcome to Total Segmentator tool. You're in luck: " +
QString::number(m_GpuLoader.GetGPUCount()) + " GPU(s) were detected.";
}
else
{
welcomeText = "STATUS: Welcome to Total Segmentator tool. Sorry, " +
QString::number(m_GpuLoader.GetGPUCount()) + " GPUs were detected.";
}
mainLayout->addLayout(m_Controls.verticalLayout);
connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewBtnClicked()));
connect(m_Controls.installButton, SIGNAL(clicked()), this, SLOT(OnInstallBtnClicked()));
connect(m_Controls.overrideBox, SIGNAL(stateChanged(int)), this, SLOT(OnOverrideChecked(int)));
+ connect(m_Controls.pythonEnvComboBox,
+ QOverload::of(&QComboBox::activated),
+ [=](int index) { OnPythonPathChanged(m_Controls.pythonEnvComboBox->itemText(index)); });
Superclass::InitializeUI(mainLayout);
//QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString();
//m_Controls.pythonEnvComboBox->insertItem(0, lastSelectedPyEnv);
const QString storageDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() +
qApp->organizationName() + QDir::separator() + m_VENV_NAME;
m_IsInstalled = this->IsTotalSegmentatorInstalled(storageDir);
if (m_IsInstalled)
{
m_PythonPath = GetPythonPathFromUI(storageDir);
m_Installer.SetVirtualEnvPath(m_PythonPath);
this->EnableAll(m_IsInstalled);
welcomeText += " Totalsegmentator is already found installed";
}
else
{
welcomeText += " Totalsegmentator not installed. Please click on \"Install Totalsegmentator\" above.";
}
this->WriteStatusMessage(welcomeText);
}
void QmitkTotalSegmentatorToolGUI::EnableWidgets(bool enabled)
{
Superclass::EnableWidgets(enabled);
}
void QmitkTotalSegmentatorToolGUI::SetGPUInfo()
{
std::vector specs = m_GpuLoader.GetAllGPUSpecs();
for (const QmitkGPUSpec &gpuSpec : specs)
{
m_Controls.gpuComboBox->addItem(QString::number(gpuSpec.id) + ": " + gpuSpec.name + " (" + gpuSpec.memory + ")");
}
if (specs.empty())
{
m_Controls.gpuComboBox->setEditable(true);
m_Controls.gpuComboBox->addItem(QString::number(0));
m_Controls.gpuComboBox->setValidator(new QIntValidator(0, 999, this));
}
}
unsigned int QmitkTotalSegmentatorToolGUI::FetchSelectedGPUFromUI()
{
QString gpuInfo = m_Controls.gpuComboBox->currentText();
if (m_GpuLoader.GetGPUCount() == 0)
{
return static_cast(gpuInfo.toInt());
}
else
{
QString gpuId = gpuInfo.split(":", QString::SplitBehavior::SkipEmptyParts).first();
return static_cast(gpuId.toInt());
}
}
void QmitkTotalSegmentatorToolGUI::EnableAll(bool isEnable)
{
m_Controls.previewButton->setEnabled(isEnable);
m_Controls.subtaskComboBox->setEnabled(isEnable);
m_Controls.installButton->setEnabled((!isEnable));
}
void QmitkTotalSegmentatorToolGUI::OnInstallBtnClicked()
{
bool isInstalled = false;
MITK_INFO << m_Controls.sysPythonComboBox->currentText().toStdString();
QString systemPython = GetPythonPathFromUI(m_Controls.sysPythonComboBox->currentText());
MITK_INFO << systemPython.toStdString();
if (systemPython.isEmpty())
{
this->WriteErrorMessage("Couldn't find Python");
return;
}
else
{
m_Installer.SetSystemPythonPath(systemPython);
}
isInstalled = m_Installer.SetupVirtualEnv();
if (isInstalled)
{
const QString pythonPath = m_Installer.GetVirtualEnvPath();
m_PythonPath = GetPythonPathFromUI(m_Installer.GetVirtualEnvPath());
this->WriteStatusMessage("Successfully installed TotalSegmentator");
}
else
{
this->WriteErrorMessage("Couldn't find TotalSegmentator");
}
this->EnableAll(isInstalled);
}
void QmitkTotalSegmentatorToolGUI::OnPreviewBtnClicked()
{
auto tool = this->GetConnectedToolAs();
if (nullptr == tool)
{
return;
}
// QString pythonPathTextItem = "";
try
{
m_Controls.previewButton->setEnabled(false);
qApp->processEvents();
if (!this->IsTotalSegmentatorInstalled(m_PythonPath))
{
throw std::runtime_error(m_WARNING_TOTALSEG_NOT_FOUND);
}
bool isFast = m_Controls.fastBox->isChecked();
QString subTask = m_Controls.subtaskComboBox->currentText();
if (subTask != m_VALID_TASKS[0])
{
isFast = true;
}
tool->SetPythonPath(m_PythonPath.toStdString());
tool->SetGpuId(FetchSelectedGPUFromUI());
tool->SetFast(isFast);
tool->SetSubTask(subTask.toStdString());
this->WriteStatusMessage(QString("STATUS: Starting Segmentation task... This might take a while."));
tool->UpdatePreview();
m_Controls.previewButton->setEnabled(true);
}
catch (const std::exception &e)
{
std::stringstream errorMsg;
errorMsg << "STATUS: Error while processing parameters for TotalSegmentator segmentation. Reason: "
<< e.what();
this->ShowErrorMessage(errorMsg.str());
this->WriteErrorMessage(QString::fromStdString(errorMsg.str()));
m_Controls.previewButton->setEnabled(true);
return;
}
catch (...)
{
std::string errorMsg = "Unkown error occured while generation TotalSegmentator segmentation.";
this->ShowErrorMessage(errorMsg);
m_Controls.previewButton->setEnabled(true);
return;
}
this->SetLabelSetPreview(tool->GetPreviewSegmentation());
tool->IsTimePointChangeAwareOn();
this->ActualizePreviewLabelVisibility();
this->WriteStatusMessage("STATUS: Segmentation task finished successfully.");
/* if (!pythonPathTextItem.isEmpty()) // only cache if the prediction ended without errors.
{
QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString();
if (lastSelectedPyEnv != pythonPathTextItem)
{
m_Settings.setValue("TotalSeg/LastPythonPath", pythonPathTextItem);
}
}*/
}
void QmitkTotalSegmentatorToolGUI::ShowErrorMessage(const std::string &message, QMessageBox::Icon icon)
{
this->setCursor(Qt::ArrowCursor);
QMessageBox *messageBox = new QMessageBox(icon, nullptr, message.c_str());
messageBox->exec();
delete messageBox;
MITK_WARN << message;
}
void QmitkTotalSegmentatorToolGUI::WriteStatusMessage(const QString &message)
{
m_Controls.statusLabel->setText(message);
m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: white");
}
void QmitkTotalSegmentatorToolGUI::WriteErrorMessage(const QString &message)
{
m_Controls.statusLabel->setText(message);
m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: red");
}
bool QmitkTotalSegmentatorToolGUI::IsTotalSegmentatorInstalled(const QString &pythonPath)
{
QString fullPath = pythonPath;
fullPath = fullPath.mid(fullPath.indexOf(" ") + 1);
- bool isPythonExists, isTotalSegExists = false;
+ bool isPythonExists = false;
#ifdef _WIN32
isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe"));
if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive)))
{
fullPath += QDir::separator() + QString("Scripts");
isPythonExists =
(!isPythonExists) ? QFile::exists(fullPath + QDir::separator() + QString("python.exe")) : isPythonExists;
}
#else
isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3"));
if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive)))
{
fullPath += QDir::separator() + QString("bin");
isPythonExists =
(!isPythonExists) ? QFile::exists(fullPath + QDir::separator() + QString("python3")) : isPythonExists;
}
#endif
bool isExists = QFile::exists(fullPath + QDir::separator() + QString("TotalSegmentator")) && isPythonExists;
return isExists;
}
void QmitkTotalSegmentatorToolGUI::AutoParsePythonPaths()
{
QString homeDir = QDir::homePath();
std::vector searchDirs;
#ifdef _WIN32
searchDirs.push_back(QString("C:") + QDir::separator() + QString("ProgramData") + QDir::separator() +
QString("anaconda3"));
#else
// Add search locations for possible standard python paths here
searchDirs.push_back(homeDir + QDir::separator() + "environments");
searchDirs.push_back(homeDir + QDir::separator() + "anaconda3");
searchDirs.push_back(homeDir + QDir::separator() + "miniconda3");
searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "miniconda3");
searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "anaconda3");
#endif
for (QString searchDir : searchDirs)
{
if (searchDir.endsWith("anaconda3", Qt::CaseInsensitive))
{
if (QDir(searchDir).exists())
{
m_Controls.sysPythonComboBox->insertItem(0, "(base): " + searchDir);
searchDir.append((QDir::separator() + QString("envs")));
}
}
for (QDirIterator subIt(searchDir, QDir::AllDirs, QDirIterator::NoIteratorFlags); subIt.hasNext();)
{
subIt.next();
QString envName = subIt.fileName();
if (!envName.startsWith('.')) // Filter out irrelevent hidden folders, if any.
{
m_Controls.sysPythonComboBox->insertItem(0, "(" + envName + "): " + subIt.filePath());
}
}
}
m_Controls.sysPythonComboBox->setCurrentIndex(-1);
}
void QmitkTotalSegmentatorToolGUI::OnPythonPathChanged(const QString &pyEnv)
{
if (pyEnv == QString("Select"))
{
+ m_Controls.previewButton->setDisabled(true);
QString path =
QFileDialog::getExistingDirectory(m_Controls.pythonEnvComboBox->parentWidget(), "Python Path", "dir");
if (!path.isEmpty())
{
this->OnPythonPathChanged(path); // recall same function for new path validation
bool oldState = m_Controls.pythonEnvComboBox->blockSignals(true); // block signal firing while inserting item
m_Controls.pythonEnvComboBox->insertItem(0, path);
m_Controls.pythonEnvComboBox->setCurrentIndex(0);
m_Controls.pythonEnvComboBox->blockSignals(
oldState); // unblock signal firing after inserting item. Remove this after Qt6 migration
}
}
else if (!this->IsTotalSegmentatorInstalled(pyEnv))
{
this->ShowErrorMessage(m_WARNING_TOTALSEG_NOT_FOUND);
m_Controls.previewButton->setDisabled(true);
}
else
{// Show positive status meeage
m_Controls.previewButton->setDisabled(false);
m_PythonPath = GetPythonPathFromUI(pyEnv);
}
}
QString QmitkTotalSegmentatorToolGUI::GetPythonPathFromUI(const QString &pyEnv)
{
QString pythonPath;
QString fullPath = pyEnv.mid(pyEnv.indexOf(" ") + 1);
bool isPythonExists = false;
#ifdef _WIN32
isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe"));
if (isPythonExists)
{
pythonPath = fullPath;
}
else if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive)))
{
fullPath += QDir::separator() + QString("Scripts");
pythonPath = fullPath;
}
#else
isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3"));
if (isPythonExists)
{
pythonPath = fullPath;
}
else if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive)))
{
fullPath += QDir::separator() + QString("bin");
pythonPath = fullPath;
}
#endif
return pythonPath;
}
void QmitkTotalSegmentatorToolGUI::OnOverrideChecked(int state)
{
bool isEnabled = false;
if (state == Qt::Checked)
{
isEnabled = true;
m_Controls.previewButton->setDisabled(true);
m_PythonPath.clear();
- connect(m_Controls.pythonEnvComboBox,
- SIGNAL(currentTextChanged(const QString &)),
- this,
- SLOT(OnPythonPathChanged(const QString &)));
}
else
{
m_PythonPath.clear();
- disconnect(m_Controls.pythonEnvComboBox,
- SIGNAL(currentTextChanged(const QString &)),
- this,
- SLOT(OnPythonPathChanged(const QString &)));
+ m_Controls.previewButton->setDisabled(true);
if (m_IsInstalled)
{
m_PythonPath = m_Installer.GetVirtualEnvPath();
this->EnableAll(m_IsInstalled);
}
}
m_Controls.pythonEnvComboBox->setEnabled(isEnabled);
}