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/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2025 Univ. Grenoble Alpes, CNRS, Grenoble INP - UGA, TIMC, 38000 Grenoble, France
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
#ifdef PYTHON_BINDING
#include "PythonManager.h"
#include "PythonHotPlugAction.h"
#include "Core.h"
#include "Application.h"
#include "AbortException.h"
#include <QRegularExpression>
#include <QProcess>
#include <QStandardPaths>
#include <QFile>
// manage ld_preload
#ifdef Q_OS_LINUX
#include <dlfcn.h>
#endif
#include "Log.h"
namespace camitk {
QString PythonManager::pythonStatusString;
QDir PythonManager::pythonCamitkModulePath;
QString PythonManager::pythonSoLib;
QString PythonManager::pythonVersion;
QString PythonManager::systemPythonExecutable;
bool PythonManager::isLocked;
QMap<QObject*, QPair<py::object, py::dict>> PythonManager::pythonStateMap;
QString PythonManager::currentVirtualEnvPath;
QString PythonManager::currentScriptPath;
py::module_ PythonManager::currentModule;
// -------------------- initPython --------------------
bool PythonManager::initPython() {
if (Py_IsInitialized() != 0) {
return true;
}
// check that python is installed
systemPythonExecutable = findPythonExecutable();
if (systemPythonExecutable.isNull()) {
pythonStatusString = "Python disabled: cannot find python executable anywhere on the system paths.";
CAMITK_TRACE_ALT(pythonStatusString)
return false;
}
// 1. load libpython at startup
//
// FIX for import c-module (such as numpy) from interpreter embedded in dlopen shared object
// raises undefined symbol (unix-only) / ImportError
//
// Analysis:
// When the interpreter is asked to import a Python script that contains "import numpy"
// (but that can happen with other python module), numpy is using cpython symbols.
// Unfortunately, and and least on Debian/Ubuntu Linux, these symbols are not available
// as the python executable is statically linked to the python library.
//
// Workaround:
// Use explicit dlopen to load the shared python library.
// Note: of course the shared library should be the same version as the one use
// to statically link the system python executable.
// We therefore need to:
// - 1. determine which version and where is the corresponding shared library
// - 2. manually load the python shared library
//
// When do we need this workaround?
// To check if python executable was linked statically to the python library,
// you need to run "python3 -m sysconfig | grep CONFIG_ARGS" and check if
// the flag "--disable-shared" is there.
// Alternatively (as this "disable-shared" is not present on Debian/Linux python),
// running "ldd /usr/bin/python" shows that that /usr/bin/python is not linked to
// any libpython.so shared object.
//
// Will this work?
// To be able to load the python shared library manually (so for this workaround to be
// efficient), run "python3 -m sysconfig | grep LINKFORSHARED" and check that
// LINKFORSHARED contains "-Xlinker -export-dynamic"
//
// References:
// [1] https://github.com/pybind/pybind11/issues/3555#issuecomment-996560050
// [2] https://github.com/pybind/pybind11/issues/3555#issuecomment-1736351976
// [3] https://github.com/NOAA-OWP/ngen/issues/655#issuecomment-1736273405
// [4] https://stackoverflow.com/a/60746446
// use python to determine the correct libpython shared object to load via sysconfig
resolvePythonSharedLibPathAndVersion();
if (pythonVersion.isNull() || pythonVersion.isEmpty()) {
pythonStatusString = "Python disabled: cannot determine python version.";
CAMITK_TRACE_ALT(pythonStatusString)
return false;
}
// use dl_open to load it first thing (simulate LD_PRELOAD)
if (!loadPythonSharedLibrary()) {
pythonStatusString = "Python disabled: could not load Python shared library. Check your installation.";
CAMITK_TRACE_ALT(pythonStatusString);
return false;
}
// 2. Determine the CamiTK directory that contains CamiTK python module
QString pythonCamitkModuleFilePath = findPythonModule("camitk");
if (pythonCamitkModuleFilePath.isNull()) {
pythonStatusString = "Python disabled: cannot find the CamiTK python module anywhere in the python system paths nor CamiTK install paths.";
CAMITK_TRACE_ALT(pythonStatusString)
return false;
}
else {
// use the directory
pythonCamitkModulePath = QFileInfo(pythonCamitkModuleFilePath).absoluteDir();
}
// 3. launch python interpreter inside CamiTK
// alternative to py::scoped_interpreter guard;
py::initialize_interpreter();
pythonStatusString = QString("Python %1 enabled.\nUsing camitk python module %2").arg(pythonVersion).arg(pythonCamitkModuleFilePath);
CAMITK_TRACE_ALT(pythonStatusString)
isLocked = false;
return true;
}
// -------------------- getPythonStatus --------------------
QString PythonManager::getPythonStatus() {
return pythonStatusString;
}
// -------------------- checkPythonPackageConflicts --------------------
void PythonManager::checkPythonPackageConflicts() {
py::module_ importlib_metadata = py::module_::import("importlib.metadata");
using PackageInfo = std::tuple<std::string, std::string>; // (version, location)
std::unordered_map<std::string, PackageInfo> seen;
for (auto dist : importlib_metadata.attr("distributions")()) {
std::string name = py::str(dist.attr("metadata")["Name"]);
std::string version = py::str(dist.attr("version"));
std::string location = py::str(dist.attr("locate_file")("").attr("__str__")());
auto it = seen.find(name);
if (it != seen.end()) {
const auto& [prev_version, prev_location] = it->second;
if ((prev_version != version || prev_location != location) && (name != "packaging")) {
// Already seen → conflict
QStringList errorMsg;
errorMsg << "[Conflict] " + QString::fromStdString(name) + ":";
errorMsg << " - " + QString::fromStdString(prev_version) + " at " + QString::fromStdString(prev_location);
errorMsg << " - " + QString::fromStdString(version) + " at " + QString::fromStdString(location);
QString errorString = errorMsg.join("\n");
CAMITK_ERROR_ALT(errorString)
}
}
else {
seen[name] = {version, location};
}
}
}
// -------------------- getPythonVersion --------------------
QString PythonManager::getPythonVersion() {
return pythonVersion;
}
// -------------------- resolvePythonSharedLibPath --------------------
void PythonManager::resolvePythonSharedLibPathAndVersion() {
py::scoped_interpreter guard{}; // start interpreter just for this
py::module_ sys = py::module_::import("sys");
if (!sys.is(py::module_())) {
pythonVersion = QString::fromStdString(py::str(sys.attr("version_info").attr("major"))) + "." + QString::fromStdString(py::str(sys.attr("version_info").attr("minor")));
}
#ifdef Q_OS_LINUX
py::module_ sysconfig = py::module_::import("sysconfig");
if (!sysconfig.is_none()) {
//PythonManager::dump(sysconfig.attr("__dict__"));
std::string libdir = py::str(sysconfig.attr("get_config_var")("LIBDIR"));
std::string ldlib = py::str(sysconfig.attr("get_config_var")("LDLIBRARY"));
pythonSoLib = QString::fromStdString(libdir + "/" + ldlib);
}
#endif
}
// -------------------- loadPythonSharedLibrary --------------------
bool PythonManager::loadPythonSharedLibrary() {
#ifdef Q_OS_LINUX
void* handle = dlopen(pythonSoLib.toUtf8().data(), RTLD_NOW | RTLD_GLOBAL);
if (!handle) {
CAMITK_WARNING_ALT(QString("dlopen failed: %1").arg(dlerror()));
return false;
}
#endif
return true;
}
//-------------------- importOrReload --------------------
py::module_ PythonManager::importOrReload(const QString& moduleName, bool clearAll) {
QString operation = "import/reload";
try {
py::module_ sys = py::module_::import("sys");
py::dict sys_modules = sys.attr("modules");
if (sys_modules.contains(moduleName.toStdString().c_str())) {
operation = "reload";
py::object existingModule = sys_modules[moduleName.toStdString().c_str()];
if (!py::isinstance<py::module_>(existingModule)) {
// not a module, probably a python error already happened previously
return py::module_();
}
if (clearAll) {
//--1. before reloading purge the __dict__ before reloading from
// all variables and functions, but do not delete dunders nor modules
QStringList keysToRemove;
py::dict existingModuledict = existingModule.attr("__dict__");
for (auto item : existingModuledict) {
QString key = QString::fromStdString(py::str(item.first));
// skip dunder and modules
if (!key.startsWith("__") && !py::isinstance<py::module_>(item.second)) {
// only remove variables and function, not import
keysToRemove.append(key);
}
}
for (auto key : keysToRemove) {
existingModuledict.attr("pop")(key.toStdString());
}
//--2. Force GC collection
try {
py::module_ gc = py::module_::import("gc");
gc.attr("collect")();
}
catch (...) {
CAMITK_WARNING_ALT("GC module not available or failed to run.")
}
}
py::module_ importlib = py::module_::import("importlib");
return importlib.attr("reload")(existingModule);
}
else {
operation = "import";
return py::module_::import(moduleName.toStdString().c_str());
}
}
catch (const std::bad_alloc& e) {
CAMITK_WARNING_ALT(QString("Caught a bad alloc exception, the application has run out of memory during %1 of module '%2':\n%3").arg(operation).arg(moduleName).arg(e.what()))
}
catch (const std::exception& e) {
py::module_ sys = py::module_::import("sys");
QStringList sysPath;
for (const auto& path : sys.attr("path")) {
sysPath << QString::fromStdString(py::str(path));
}
CAMITK_WARNING_ALT(QString("Error during %1 of module '%2':\n%3\nsys.path:\n- %4\n").arg(operation).arg(moduleName).arg(e.what()).arg(sysPath.join("\n- ")))
}
// something wrong happen
CAMITK_TRACE_ALT(QString("Error loading camitk module using the following python setup:\n %1").arg(pythonEnvironmentDebugInfo()))
return py::module_();
}
// -------------------- findPythonModuleDir --------------------
QString PythonManager::findPythonModule(const QString& moduleName) {
QSet<QString> searchPathSet;
// 1. add current build dir
// useful for non-conventional python installation (when testing directly from CamiTK SDK build or
// if CamiTK was manually locally/globally installed using the provided targets or package zip archive on windows)
QStringList camitkExtensionDir = Core::getExtensionDirectories("");
for (QString path : camitkExtensionDir) {
QDir installationLibPath;
installationLibPath.setPath(path);
installationLibPath.cdUp();
searchPathSet.insert(installationLibPath.absolutePath());
#ifdef Q_OS_LINUX
// check also python path inside installed path
installationLibPath.cd("python" + getPythonVersion().left(getPythonVersion().indexOf('.')) + "/dist-packages");
if (installationLibPath.exists()) {
searchPathSet.insert(installationLibPath.absolutePath());
}
#endif
}
// 2. Add system paths from Python itself
py::scoped_interpreter guard{}; // temporarily start python
py::module_ sys = py::module_::import("sys");
py::list sysPaths = sys.attr("path");
for (const auto& path : sysPaths) {
QDir pathDir;
pathDir.setPath(QString::fromStdString(py::str(path)));
if (pathDir.exists()) {
searchPathSet.insert(pathDir.absolutePath());
}
}
// 3. look for the module in all the path
QString modulePattern;
#ifdef Q_OS_WIN
modulePattern = "^" + moduleName + R"regex(\.cp.*\.pyd)regex";
#else
// on Q_OS_LINUX
modulePattern = "^" + moduleName + R"regex(\.cpython.*\.so.*)regex";
#endif
QRegularExpression moduleNameRegExp(modulePattern);
QStringList searchPaths = searchPathSet.values();
// Check for a file in searchPaths.at(i) that match the pattern
int i = 0;
QString foundModulePath;
while (i < searchPaths.size() && foundModulePath.isNull()) {
QStringList filesInPath = QDir(searchPaths.at(i)).entryList();
QStringList matchingFiles = filesInPath.filter(moduleNameRegExp);
if (matchingFiles.size() > 0) {
foundModulePath = QDir(searchPaths.at(i)).absoluteFilePath(matchingFiles.first());
}
i++;
}
return foundModulePath;
}
// -------------------- insertIfNotAlreadyInList --------------------
bool PythonManager::insertIfNotAlreadyInList(py::list* list, const QString& value) {
auto it = std::find_if(list->begin(), list->end(), [&](const py::handle & entry) {
return QString::fromStdString(py::str(entry).cast<std::string>().c_str()) == value;
});
if (it == list->end()) {
list->insert(0, value.toStdString());
return true;
}
else {
return false;
}
}
// -------------------- findPythonExecutable --------------------
QString PythonManager::findPythonExecutable() {
QString pythonPath;
#ifdef Q_OS_WIN
// Try finding the 'py' launcher first
pythonPath = QStandardPaths::findExecutable("py");
if (pythonPath.isEmpty()) {
// Fall back to python
pythonPath = QStandardPaths::findExecutable("python");
}
#else
// On Linux/macOS try python3 first
pythonPath = QStandardPaths::findExecutable("python3");
if (pythonPath.isEmpty()) {
// Fallback to python (for older systems)
pythonPath = QStandardPaths::findExecutable("python");
}
#endif
return pythonPath;
}
// -------------------- pythonEnvironmentDebugInfo --------------------
QString PythonManager::pythonEnvironmentDebugInfo() {
QStringList debugInfo;
try {
py::module_ sys = py::module_::import("sys");
py::module_ site = py::module_::import("site");
py::module_ metadata = py::module_::import("importlib.metadata");
py::module_ platform = py::module_::import("platform");
debugInfo << "# Python Environment Report\n";
debugInfo << "Python executable: " + QString::fromStdString(py::str(sys.attr("executable"))) + ", system python executable: " + systemPythonExecutable;
debugInfo << "Platform: " + QString::fromStdString(py::str(platform.attr("platform")()));
debugInfo << "Python version: " + QString::fromStdString(py::str(platform.attr("python_version")()));
debugInfo << "\n## sys.prefix info\n";
debugInfo << "sys.prefix: " + QString::fromStdString(py::str(sys.attr("prefix")));
debugInfo << "sys.base_prefix: " + QString::fromStdString(py::str(sys.attr("base_prefix")));
debugInfo << "sys.exec_prefix: " + QString::fromStdString(py::str(sys.attr("exec_prefix")));
debugInfo << "sys.base_exec_prefix: " + QString::fromStdString(py::str(sys.attr("base_exec_prefix")));
debugInfo << "\n## sys.path\n";
for (const auto& path : sys.attr("path")) {
debugInfo << " - " + QString::fromStdString(py::str(path));
}
debugInfo << "\n## Environment Variables\n";
QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
for (const QString& key : env.keys()) {
if (key.contains("PYTHON", Qt::CaseInsensitive) || key.contains("VIRTUAL", Qt::CaseInsensitive)) {
debugInfo << " - " + key + " = " + env.value(key);
}
}
debugInfo << "\n## Site info\n";
debugInfo << "site.getsitepackages():";
if (py::hasattr(site, "getsitepackages")) {
for (const auto& path : site.attr("getsitepackages")()) {
debugInfo << " - " + QString::fromStdString(py::str(path));
}
}
debugInfo << "site.getusersitepackages():" + QString::fromStdString(py::str(site.attr("getusersitepackages")()));
if (py::hasattr(site, "ENABLE_USER_SITE")) {
bool userSite = py::cast<bool>(site.attr("ENABLE_USER_SITE"));
debugInfo << "site.ENABLE_USER_SITE: " + QString(userSite ? "True" : "False");
}
debugInfo << "\n## sys.flags\n";
QStringList sysFlags;
py::object flags = sys.attr("flags");
const std::vector<std::string> flag_names = {
"debug", "inspect", "interactive", "optimize", "dont_write_bytecode", "no_user_site", "no_site", "ignore_environment", "verbose", "bytes_warning", "quiet", "hash_randomization", "isolated", "dev_mode", "utf8_mode", "warn_default_encoding", "safe_path", "int_max_str_digits"
};
for (const auto& flag : flag_names) {
sysFlags << QString::fromStdString(flag) + "=" + QString::fromStdString(py::str(flags.attr(flag.c_str())));
}
debugInfo << "sys.flags(" + sysFlags.join(", ") + ")";
debugInfo << "\n## Installed packages:";
py::list distributions = metadata.attr("distributions")();
for (const auto& dist : distributions) {
std::string name = py::str(dist.attr("metadata")["Name"]);
std::string version = py::str(dist.attr("metadata")["Version"]);
debugInfo << "- " + QString::fromStdString(name + "==" + version);
}
}
catch (const py::error_already_set& e) {
debugInfo << "Python error while attempting to get environment debug info: " + QString(e.what());
CAMITK_INFO_ALT(QString("Python error: %1").arg(e.what()))
}
return debugInfo.join("\n");
}
// -------------------- setupPython --------------------
bool PythonManager::setupPython(QString virtualEnvPath, QString scriptPath) {
try {
// load the sys module
py::module_ sys = py::module_::import("sys");
// create sys.path from scratch
py::list sys_path = py::list();
//-- 1. path to python CamiTK module
insertIfNotAlreadyInList(&sys_path, pythonCamitkModulePath.absolutePath());
//-- 2. path to the extension venv installed packages
#ifdef Q_OS_WIN
QString sitePackage = virtualEnvPath + "/Lib/site-packages";
#else
QString sitePackage = virtualEnvPath + "/lib/python" + getPythonVersion() + "/site-packages";
#endif
insertIfNotAlreadyInList(&sys_path, sitePackage);
//-- 3. common path (for global dll, but not for packages)
#ifdef Q_OS_WIN
QString sysBasePrefix = QString::fromStdString(py::str(sys.attr("base_prefix"))); // something like C:\Python312 (default install dir)
insertIfNotAlreadyInList(&sys_path, sysBasePrefix + "\\python" + getPythonVersion().remove('.') + ".zip");
insertIfNotAlreadyInList(&sys_path, sysBasePrefix + "\\DLLs");
insertIfNotAlreadyInList(&sys_path, sysBasePrefix + "\\Lib");
insertIfNotAlreadyInList(&sys_path, sysBasePrefix);
#else
insertIfNotAlreadyInList(&sys_path, "/usr/lib/python" + getPythonVersion() + "/lib-dynload");
insertIfNotAlreadyInList(&sys_path, "/usr/lib/python" + getPythonVersion());
insertIfNotAlreadyInList(&sys_path, "/usr/lib/python" + getPythonVersion().remove('.') + ".zip");
#endif
//-- 4. path to the extension directory to load the script as modules if given
if (!scriptPath.isNull()) {
insertIfNotAlreadyInList(&sys_path, QFileInfo(scriptPath).absoluteDir().path());
}
//-- 5. force the interpreter inside the action venv
sys.attr("path") = sys_path;
#ifdef Q_OS_WIN
sys.attr("executable") = virtualEnvPath.toStdString() + "/Scripts/python";
#else
sys.attr("executable") = virtualEnvPath.toStdString() + "/bin/python";
#endif
sys.attr("prefix") = virtualEnvPath.toStdString();
sys.attr("exec_prefix") = virtualEnvPath.toStdString();
//-- 6. set the ENABLE_USER_SITE to true as it is the case when inside a venv
// Note: this might have no real effect, but we want to mimic the venv as well as possible
py::module_ site = py::module_::import("site");
site.attr("ENABLE_USER_SITE") = py::bool_(false);
//-- 7. set VIRTUAL_ENV value
// Note: this might have no real effect, but we want to mimic the venv as well as possible
qputenv("VIRTUAL_ENV", virtualEnvPath.toUtf8());
//-- 8. monkey patch sitepackages
// this is using a lambda in Python that returns a fixed list of paths
py::list custom_paths;
custom_paths.append(sitePackage.toStdString());
#ifdef Q_OS_WIN
custom_paths.append(virtualEnvPath.toStdString());
#else
custom_paths.append(virtualEnvPath.toStdString() + "/local/lib/python" + getPythonVersion().toStdString() + "/dist-packages");
custom_paths.append(virtualEnvPath.toStdString() + "/lib/python" + getPythonVersion().mid(0, 1).toStdString() + "/dist-packages");
custom_paths.append(virtualEnvPath.toStdString() + "/lib/python" + getPythonVersion().toStdString() + "/dist-packages");
#endif
//-- 9. Replace site.getsitepackages with a lambda returning our list
// equivalent of site.getsitepackages = lambda: ['/path/to/dir/1', '/path/to/dir/2'])"
site.attr("getsitepackages") = py::cpp_function([custom_paths]() {
return custom_paths;
});
// Finally, load python camitk module
py::module_ pythonCamitkModule = importOrReload("camitk");
if (pythonCamitkModule.is(py::module_())) {
CAMITK_WARNING_ALT(QString("Cannot load camitk module required by virtual environment '%1'").arg(virtualEnvPath))
return false;
}
else {
// redirect python stdout and stderr to CamiTK
pythonCamitkModule.attr("redirectStandardStreams")();
}
}
catch (const std::exception& e) {
CAMITK_WARNING_ALT(QString("Error during Python setup to virtual environment '%1':\n%2").arg(virtualEnvPath).arg(e.what()))
return false;
}
// FIXME : should we do this only once per venv?
checkPythonPackageConflicts();
return true;
}
// -------------------- loadScript --------------------
py::module_ PythonManager::lockContext(QString virtualEnvPath, QString scriptPath) {
// check the venv and script exists first
if (!checkVirtualEnvPath(QFileInfo(virtualEnvPath).absoluteDir().absolutePath(), false)) {
// no need to print some warning, this is already done by calling checkVirtualEnvPath in non silent mode
return py::module_(); // uninitialized module
}
if (!QFileInfo(scriptPath).exists()) {
CAMITK_WARNING_ALT(QString("Python script '%1' not found").arg(scriptPath))
return py::module_(); // uninitialized module
}
if (isLocked) {
if (virtualEnvPath == currentVirtualEnvPath && scriptPath == currentScriptPath) {
return currentModule;
}
else {
CAMITK_TRACE_ALT("Python context already locked. Please call unlock() first.")
return py::module_(); // uninitialized module
}
}
// reset module
currentModule = py::module_();
if (setupPython(virtualEnvPath, scriptPath)) {
try {
QString scriptModuleName = QFileInfo(scriptPath).baseName();
// load user script as module
currentModule = importOrReload(scriptModuleName, true);
currentVirtualEnvPath = virtualEnvPath;
currentScriptPath = scriptPath;
isLocked = true;
}
catch (const std::exception& e) {
py::module_ sys = py::module_::import("sys");
py::list sysPaths = sys.attr("path");
QStringList sysPathList;
for (const auto& path : sysPaths) {
sysPathList.append(QString::fromStdString(py::str(path)));
}
QString executablePath = QString::fromStdString(py::str(sys.attr("executable")));
QString prefixPath = QString::fromStdString(py::str(sys.attr("prefix")));
CAMITK_WARNING_ALT(QString("Error importing Python script '%1':\n%2\nSystem path:\n- %3\nExecutable: %4\nPrefix: %5").arg(scriptPath).arg(e.what()).arg(sysPathList.join("\n- ")).arg(executablePath).arg(prefixPath))
}
}
return currentModule; // might be null/non initialized
}
// -------------------- unlock --------------------
void PythonManager::unlock() {
isLocked = false;
}
// -------------------- runScript --------------------
QMap<QString, QVariant> PythonManager::runScript(QString virtualEnvPath, const QString& pythonScript, QString& pythonError) {
QMap<QString, QVariant> scriptVariables;
// check the venv and script exists first
if (!checkVirtualEnvPath(QFileInfo(virtualEnvPath).absoluteDir().absolutePath(), false)) {
// no need to print some warning, this is already done by calling checkVirtualEnvPath in non silent mode
return scriptVariables;
}
// prevent mixing virtual env
if (isLocked) {
CAMITK_TRACE_ALT("Python context already locked. Please call unlock() first.")
return scriptVariables;
}
// Force clearing all references to modules and variables from `__main__`
// see https://github.com/pybind/pybind11/issues/5173#issuecomment-2185000795
// see https://github.com/pybind/pybind11/discussions/5171#discussioncomment-9857969
// Beware that this is a trick over pybind11, and might not work in the future
// if pybind11 team changes this behaviour
// PyDict_Clear(PyModule_GetDict(PyImport_AddModule("__main__")));
if (setupPython(virtualEnvPath)) {
try {
std::string script = pythonScript.toStdString();
// Use a dedicated namespace (dictionary) for script execution
py::dict locals;
py::exec(script, py::globals(), locals);
for (auto& item : locals) {
QString key = QString::fromStdString(py::str(item.first));
scriptVariables.insert(key, fromPython(item.second));
}
return scriptVariables;
}
catch (const py::error_already_set& e) {
CAMITK_WARNING_ALT(QString("Error when running script '%1':\n%2").arg(pythonScript).arg(e.what()))
pythonError = e.what();
return scriptVariables;
}
}
return scriptVariables;
}
// -------------------- fromPython --------------------
QVariant PythonManager::fromPython(const py::handle& value) {
// convert classic variable types
if (value.is_none()) {
return QVariant();
}
if (py::isinstance<py::bool_>(value)) {
return QVariant(static_cast<bool>(value.cast<py::bool_>()));
}
if (py::isinstance<py::int_>(value)) {
return QVariant(static_cast<qint64>(value.cast<py::int_>()));
}
if (py::isinstance<py::float_>(value)) {
return QVariant(static_cast<double>(value.cast<py::float_>()));
}
if (py::isinstance<py::str>(value)) {
return QVariant(QString::fromStdString(value.cast<std::string>()));
}
if (py::isinstance<py::bytes>(value)) {
std::string s = value.cast<std::string>();
return QVariant(QByteArray::fromRawData(s.data(), static_cast<int>(s.size())));
}
if (py::isinstance<py::list>(value) || py::isinstance<py::tuple>(value)) {
QVariantList list;
for (auto item : value) {
// beware: recurse
list.append(fromPython(item));
}
return list;
}
if (py::isinstance<py::dict>(value)) {
QVariantMap map;
py::dict dictValue = py::reinterpret_borrow<py::dict>(value);
for (auto item : dictValue) {
QString key = QString::fromUtf8(py::str(item.first).cast<std::string>().c_str());
// beware: recurse
map.insert(key, fromPython(item.second));
}
return map;
}
try {
py::object pythonObject = py::reinterpret_borrow<py::object>(value);
py::str pythonTypeName = py::str(py::type::of(pythonObject));
return QVariant(QString("<unsupported Python type '%1'>").arg(QString::fromStdString(pythonTypeName.cast<std::string>())));
}
catch (...) {
return QVariant(QString("<unsupported Python type>"));
}
}
// -------------------- checkVirtualEnvPath --------------------
bool PythonManager::checkVirtualEnvPath(QString virtualEnvRootPath, bool silent) {
QFileInfo venvRootPath(virtualEnvRootPath);
if (!venvRootPath.exists() || !venvRootPath.isDir() || !venvRootPath.isWritable()) {
CAMITK_WARNING_IF_ALT(!silent, "Invalid python virtual environment root directory '" + venvRootPath.absolutePath() + "': directory does not exist or is not writable.");
return false;
}
QDir checkDir;
checkDir.setPath(virtualEnvRootPath);
QDir venvDir = checkDir;
if (!venvDir.cd(".venv")) {
CAMITK_WARNING_IF_ALT(!silent, "Invalid python virtual environment root directory '" + checkDir.absolutePath() + "': missing or invalid '.venv' directory.");
return false;
}
QDir binDir = venvDir;
bool binDirExists;
#ifdef Q_OS_WIN
binDirExists = binDir.cd("Scripts");
#else
binDirExists = binDir.cd("bin");
#endif
if (!binDirExists) {
CAMITK_WARNING_IF_ALT(!silent, "Invalid python virtual environment directory '" + venvDir.absolutePath() + "': subdirectory 'bin' does not exist or is invalid.");
return false;
}
QDir sitePackageDir = venvDir;
#ifdef Q_OS_WIN
QString sitePackage = "Lib/site-packages";
#else
QString sitePackage = "lib/python" + PythonManager::getPythonVersion() + "/site-packages";
#endif
if (!sitePackageDir.cd(sitePackage)) {
CAMITK_WARNING_IF_ALT(!silent, "Invalid python virtual environment directory '" + venvDir.absolutePath() + "': missing '" + sitePackage + "' subdirectory.");
return false;
}
QString pipCommandPath;
#ifdef Q_OS_WIN
pipCommandPath = binDir.absoluteFilePath("pip.exe");
#else
pipCommandPath = binDir.absoluteFilePath("pip");
#endif
if (!QFile::exists(pipCommandPath)) {
CAMITK_WARNING_IF_ALT(!silent, "Invalid python virtual environment directory '" + venvDir.absolutePath() + "': missing 'pip' command.");
return false;
}
return true;
}
// -------------------- createVirtualEnv --------------------
bool PythonManager::createVirtualEnv(QString virtualEnvRootPath) {
if (!checkVirtualEnvPath(virtualEnvRootPath)) {
QStringList args = {"-m", "venv", virtualEnvRootPath + "/.venv"};
QProcess pythonCommand;
pythonCommand.setProgram(systemPythonExecutable);
pythonCommand.setWorkingDirectory(virtualEnvRootPath);
pythonCommand.setProcessChannelMode(QProcess::MergedChannels);
pythonCommand.setArguments(args);
pythonCommand.start();
if (!pythonCommand.waitForStarted()) {
CAMITK_WARNING_ALT("Command '" + systemPythonExecutable + " " + args.join(" ") + "' failed to start:\n" + QString(pythonCommand.errorString()))
}
if (!pythonCommand.waitForFinished(300000)) { // 5 min (default is 30s, but some Windows machine may be very slow)
CAMITK_WARNING_ALT("Command '" + systemPythonExecutable + " " + args.join(" ") + "' timed out (5 min):\n" + QString(pythonCommand.readAll()))
}
if (pythonCommand.exitCode() != 0) {
CAMITK_WARNING_ALT("Failed to create virtual environment using system python " + systemPythonExecutable + "\nExit code: " + QString::number(pythonCommand.exitCode()) + "\nOutput:\n" + QString(pythonCommand.readAll()))
}
return checkVirtualEnvPath(virtualEnvRootPath, false);
}
else {
return true;
}
}
// -------------------- installPackages --------------------
bool PythonManager::installPackages(QString virtualEnvPath, QStringList packages, int progressMinimum, int progressMaximum) {
// PyPI is case insensitive, ensure requirements are lowercase to simplify comparison
// see https://packaging.python.org/en/latest/specifications/
for (QString &req : packages) {
req = req.toLower();
}
// always add numpy (needed by CamiTK python module) and setuptools (needed by PythonManager itself)
if (packages.filter("setuptools").size() == 0) { // Note using filter(..) to take into account requirements with version number (e.g. "setuptools==68.1.2")
packages.append("setuptools");
}
if (packages.filter("numpy").size() == 0) {
packages.append("numpy");
}
//-- 0. prepare the pip command
QDir venvDir;
venvDir.setPath(virtualEnvPath);
#ifdef Q_OS_WIN
venvDir.cd("Scripts");
#else
venvDir.cd("bin");
#endif
QString pipCommandPath;
#ifdef Q_OS_WIN
pipCommandPath = venvDir.absoluteFilePath("pip.exe");
#else
pipCommandPath = venvDir.absoluteFilePath("pip");
#endif
QStringList output;
QProcess pipCommand;
pipCommand.setProgram(pipCommandPath);
pipCommand.setWorkingDirectory(virtualEnvPath);
pipCommand.setProcessChannelMode(QProcess::MergedChannels);
QString virtualEnvPackagePath = virtualEnvPath + "/lib/python" + getPythonVersion() + "/site-packages/";
QString systemPackagePath = "/usr/lib/python" + getPythonVersion().mid(0, 1) + "/dist-packages/";
//-- 1. Verify if all requirements are already installed
pipCommand.setArguments({ "list", "--format=freeze"});
pipCommand.start();
if (!pipCommand.waitForStarted()) {
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' failed to start:\n" + QString(pipCommand.errorString()))
return false;
}
if (!pipCommand.waitForFinished()) {
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' timed out (30 sec):\n" + QString(pipCommand.readAll()))
return false;
}
if (pipCommand.exitCode() != 0) {
CAMITK_WARNING_ALT("Failed to list already installed packages in " + virtualEnvPath + " (needed to verify the virtual env):\n" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "\nExit code: " + QString::number(pipCommand.exitCode()) + "\nOutput:\n" + QString(pipCommand.readAll()))
return false;
}
QByteArray rawData = pipCommand.readAll();
QString outputString = QString::fromUtf8(rawData);
QStringList installedPackages;
QStringList lines = outputString.split('\n', Qt::SkipEmptyParts);
for (const QString& line : lines) {
installedPackages.append(line.section("==", 0, 0).trimmed().toLower());
}
QStringList missingPackages;
for (const QString& req : packages) {
// Check lowercase version against our set
if (!installedPackages.contains(req.section("==", 0, 0).trimmed())) {
missingPackages.append(req);
}
}
if (missingPackages.isEmpty()) {
Application::showStatusBarMessage(QString("All requirements already installed."));
}
// Only install the missing packages
packages = missingPackages;
float progressValue = progressMinimum;
float progressStep = (progressMaximum - progressMinimum) / float(packages.size());
#ifdef Q_OS_LINUX
//-- 2. manage special case of VTK and Qt
// Note on virtual environment requiring VTK
// if vtk is needed, installing the package using pip will generate an application crash in case the
// installed version of the package differs from the version used to build camitkcore.
//
// Analysis:
// - camitkcore is linked with a specific version of vtk
// - on supported Linux OS, the vtk version is determined by the system packages available in the distribution
// (for instance on Ubuntu 24.04 LTS the system the packages provide vtk9.1)
// - on supported Linux OS, the system package automatically install the python vtk package (e.g. python-vtk9-9.1.0...)
// - the vtkCommon shared object is loaded when the application starts (e.g. libvtkCommonCore-9.1)
// - if vtk is installed using "pip" in the virtual environment, "import vtk" will load the package installed in the virtual env by pip
// - the available python vtk package might have a different version than the package version (system package and python
// packages are not synchronized/built by the same team).
// For instance on Ubuntu 24.04 LTS, "pip install vtk==9.1.0" will generate:
// ERROR: Could not find a version that satisfies the requirement vtk==9.1.0 (from versions: 9.3.0rc2, 9.3.0, 9.3.1, 9.4.0rc3, 9.4.0, 9.4.1, 9.4.2)
// - A std::bad exception will be generated by "import vtk", as it seems that the vtk python package will call some symbol in the
// system installed vtkCommon while it thinks it is calling symbol in the venv installed vtk (symptoms: huge memory allocation resulting in
// a crash).
// Although it can be potentially/theoretically caught, it seems quite fishy.
//
// Workaround:
// - Check that the workaround (see below) is not already in place
// - if not already applied:
// - uninstall vtk from the venv in case it was installed manually
// - add a symlink in the venv to thse system site package:
// ln -s /usr/lib/python3/dist-packages/vtk.py venv/lib/python3.12/site-packages
// ln -s /usr/lib/python3/dist-packages/vtkmodules venv/lib/python3.12/site-packages
// - trace it to let the user know
//
// The problem is the same with Qt python bindings with a supplementary degree of complexity as there are two sets of bindings, PyQt and PySide
// As CamiTK is distributed mostly through Debian and Ubuntu packages, the PySide packages are provided by the same team as QT packages
// PyQt being a different team, the releases of Qt and PyQt may not be synchronised.
// The other option that was explored was to force pip install PyQt==CAMITK_QT_VERSION but their is no certainty that the pip repo has all
// the versions of PyQt/PySide, including the one we will need.
// The solution here is to use the same workaround as VTK, using the system python3-vtk instead of the pip version,
// we will force here the use of the system PySide bindings.
QStringList vtkRequirements = packages.filter("vtk");
if (vtkRequirements.size() > 0) {
Application::showStatusBarMessage(QString("Verifying requirement 1/%1 (%2)...").arg(packages.size()).arg("vtk"));
//-- VTK workaround
bool vtkWorkaroundInPlace = false;
QFileInfo vtkSymLink(virtualEnvPackagePath + "vtk.py");
if (vtkSymLink.exists()) {
if (vtkSymLink.isSymLink()) { // note isSymbolicLink() has a different behaviour on Win and MacOS
QString existingTarget = vtkSymLink.symLinkTarget();
if (existingTarget == systemPackagePath + "vtk.py") {
vtkWorkaroundInPlace = true; // everything is ok, nothing to do
}
else {
CAMITK_WARNING_ALT("VTK workaround symlink exists but points to the wrong target. Removing it.")
}
}
else {
CAMITK_WARNING_ALT("VTK workaround path exists but is not a symlink. Removing it.")
}
}
if (!vtkWorkaroundInPlace) {
// remove the vtk package in case it was installed manually in the venv
pipCommand.setArguments({"uninstall", "--yes", "vtk"});
pipCommand.start();
if (!pipCommand.waitForStarted()) {
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' failed to start:\n" + QString(pipCommand.errorString()))
return false;
}
if (!pipCommand.waitForFinished(300000)) { // 5 min (default is 30s, but some Windows machine may be very slow)
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' timed out (5 min):\n" + QString(pipCommand.readAll()))
return false;
}
if (pipCommand.exitCode() != 0) {
CAMITK_WARNING_ALT("Failed to uninstall package 'vtk' (needed to install the Linux VTK symlink work around):\n" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "\nExit code: " + QString::number(pipCommand.exitCode()) + "\nOutput:\n" + QString(pipCommand.readAll()))
return false;
}
// start from scratch
QFile::remove(vtkSymLink.absoluteFilePath());
QFile::remove(virtualEnvPackagePath + "vtkmodules");
// add the symlink workaround
if (!QFile::link(systemPackagePath + "vtk.py", virtualEnvPackagePath + "vtk.py")) {
CAMITK_WARNING_ALT("Failed to create VTK workaround symlink from" + systemPackagePath + "to" + virtualEnvPackagePath + ": system-wide Vtk python module must be installed to use VTK from Python")
return false;
}
else {
if (!QFile::link(systemPackagePath + "vtkmodules", virtualEnvPackagePath + "vtkmodules")) {
CAMITK_WARNING_ALT("Failed to create VTK modules workaround symlink from" + systemPackagePath + "to" + virtualEnvPackagePath + ": system-wide Vtk python module must be installed to use VTK from Python")
return false;
}
else {
CAMITK_TRACE_ALT("VTK python workaround symlink created successfully.");
}
}
progressValue += progressStep;
Application::setProgressBarValue(progressValue);
}
// remove vtk requirements from the list of packages to install
for (QString req : vtkRequirements) {
packages.removeAll(req);
}
}
#endif
// Check Qt bindings : reject PyQt, check Qt version for PySide2/PySide6
if (packages.filter("pyqt").size() > 0) {
CAMITK_WARNING_ALT("Requirements contains PyQt, which is not supported. If you need Qt python bindings, you must use PySide.\nRationale: as CamiTK is linked to a specific version of Qt C++ library, Python bindings must use the same Qt version. This can only be guaranteed by using PySide instead of PyQt.\nPlease replace PyQt requirements by PySide.")
return false;
}
#if QT_VERSION < QT_VERSION_CHECK(6,0,0)
if (packages.filter("pyside6").size()>0) {
CAMITK_WARNING_ALT("Requirements contains PySide6 but this CamiTK version was built with Qt5. Please replace PySide6 by PySide2.")
return false;
}
#else
if (packages.filter("pyside2").size()>0) {
CAMITK_WARNING_ALT("Requirements contains PySide2 but this CamiTK version was built with Qt6. Please replace PySide2 by PySide6.")
return false;
}
#endif
#ifdef Q_OS_LINUX
// Like for vtk, use the system's PySide
QStringList qtRequirements = packages.filter("pyside");
if (qtRequirements.size() > 0) {
QString qtPackageName = qtRequirements.contains("pyside2") ? "PySide2" : "PySide6";
QString qtShibokenName = qtPackageName == "PySide2" ? "shiboken2" : "shiboken6";
Application::showStatusBarMessage(QString("Verifying requirement %1/%2 (%3)...").arg(vtkRequirements.size() > 0 ? "2" : "1").arg(packages.size()).arg(qtPackageName));
// The problem is the same as VTK with Qt python bindings
// As CamiTK is distributed mostly through Debian and Ubuntu packages, the PySide packages are provided by the same team as QT packages
// PyQt being a different team, the releases of Qt and PyQt may not be synchronised.
// The other option that was explored was to force pip install PyQt==CAMITK_QT_VERSION but their is no certainty that the pip repo has all
// the versions of PyQt/PySide, including the one we will need.
// The solution here is to use the same workaround as VTK, using the system bindings instead of the pip version,
// we will force here the use of the system PySide bindings.
//-- Qt/PySide workaround
bool qtWorkaroundInPlace = false;
QFileInfo qtSymLink(virtualEnvPackagePath + qtPackageName);
if (qtSymLink.exists()) {
if (qtSymLink.isSymLink()) { // note isSymbolicLink() has a different behaviour on Win and MacOS
QString existingTarget = qtSymLink.symLinkTarget();
if (existingTarget == systemPackagePath + qtPackageName) {
qtWorkaroundInPlace = true; // everything is ok, nothing to do
}
else {
CAMITK_WARNING_ALT("PySide workaround symlink exists but points to the wrong target. Removing it.")
}
}
else {
CAMITK_WARNING_ALT("PySide workaround path exists but is not a symlink. Removing it.")
}
}
if (!qtWorkaroundInPlace) {
// remove the qt package in case it was installed manually in the venv
pipCommand.setArguments({"uninstall", "--yes", qtPackageName});
pipCommand.start();
if (!pipCommand.waitForStarted()) {
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' failed to start:\n" + QString(pipCommand.errorString()))
return false;
}
if (!pipCommand.waitForFinished(300000)) { // 5 min (default is 30s, but some Windows machine may be very slow)
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' timed out (5 min):\n" + QString(pipCommand.readAll()))
return false;
}
if (pipCommand.exitCode() != 0) {
CAMITK_WARNING_ALT("Failed to uninstall package '" + qtPackageName + "' (needed to install the Linux Qt/PySide symlink work around):\n" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "\nExit code: " + QString::number(pipCommand.exitCode()) + "\nOutput:\n" + QString(pipCommand.readAll()))
return false;
}
// start from scratch
QFile::remove(qtSymLink.absoluteFilePath());
QFile::remove(virtualEnvPackagePath + qtShibokenName);
// check that proper pyside version is installed in the system
if (!QFile::exists(systemPackagePath + qtPackageName) || !QFile::exists(systemPackagePath + qtShibokenName) ) {
CAMITK_WARNING_ALT(qtPackageName + " not found in system path: " + systemPackagePath + ": system-wide PySide python module must be installed to use Qt/PySide from Python")
return false;
}
// add the symlink workaround
if (!QFile::link(systemPackagePath + qtPackageName, virtualEnvPackagePath + qtPackageName) || !QFile::link(systemPackagePath + qtShibokenName, virtualEnvPackagePath + qtShibokenName)) {
CAMITK_WARNING_ALT("Failed to create Qt/PySide workaround symlink from" + systemPackagePath + "to" + virtualEnvPackagePath + ": system-wide PySide python module must be installed to use Qt/PySide from Python")
return false;
}
else {
CAMITK_TRACE_ALT("Qt/PySide workaround symlink created successfully.");
}
progressValue += progressStep;
Application::setProgressBarValue(progressValue);
}
// remove PySide from the list of packages to install
for (QString req : qtRequirements) {
packages.removeAll(req);
}
}
#endif
//-- 3. install all remaining requirements
int i = 0;
bool exitCode = 0;
while (i < packages.size() && exitCode == 0) {
Application::showStatusBarMessage(QString("Verifying requirement %1/%2 (%3)...").arg(i + 1).arg(packages.size()).arg(packages.at(i)));
output << "Verifying " + packages.at(i) + " in " + virtualEnvPath + "...";
pipCommand.setArguments({"install", packages.at(i)});
pipCommand.start();
if (!pipCommand.waitForStarted()) {
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' failed to start:\n" + QString(pipCommand.errorString()))
return false;
}
if (!pipCommand.waitForFinished(300000)) { // 5 min (default is 30s, but some Windows machine may be very slow)
CAMITK_WARNING_ALT("Command '" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "' timed out (5 min):\n" + QString(pipCommand.readAll()))
return false;
}
exitCode = pipCommand.exitCode();
if (exitCode != 0) {
CAMITK_WARNING_ALT("Failed to install package:\n" + pipCommand.program() + " " + pipCommand.arguments().join(" ") + "\nExit code: " + QString::number(pipCommand.exitCode()) + "\nOutput:\n" + QString(pipCommand.readAll()))
}
else {
output << QString(pipCommand.readAll());
i++;
}
progressValue += progressStep;
Application::setProgressBarValue(progressValue);
}
CAMITK_TRACE_ALT(output.join("\n"))
// if all packages were not installed, return false
return !(i < packages.size());
}
// -------------------- dump --------------------
void PythonManager::dump(py::dict dict) {
py::module_ inspect = py::module::import("inspect");
for (auto item : dict) {
QString key = QString::fromStdString(py::str(item.first));
py::int_ address = py::int_(py::eval("id")(item.second));
if (key.startsWith("__")) {
CAMITK_INFO_ALT("- Dunder: " + key + ", " + CAMITK_PRINT_POINTER(address));
}
else {
if (py::isinstance<py::function>(item.second)) {
py::object functor = py::reinterpret_borrow<py::object>(item.second);
if (py::isinstance<py::function>(functor)) {
CAMITK_INFO_ALT("- Function/Method: " + key + ", pointer: " + CAMITK_PRINT_POINTER(functor.ptr()))
try {
py::str source = inspect.attr("getsource")(functor);
CAMITK_INFO_ALT(" Source code:\n" + QString::fromStdString(source) + "\n")
}
catch (const py::error_already_set& e) {
CAMITK_INFO_ALT(" Could not retrieve source code:\n" + QString::fromStdString(e.what()))
}
}
}
else {
QString valueType = QString::fromStdString(py::str(py::type::of(item.second)));
QString value = QString::fromStdString(py::str(item.second));
CAMITK_INFO_ALT("- Variable: " + key + ", type: " + valueType + ", value: '" + value + "'")
}
}
}
}
// ------------------- setPythonPointer -------------------
void PythonManager::setPythonPointer(QObject* qObject, py::object pythonPointer) {
if (!pythonStateMap.contains(qObject)) {
pythonStateMap.insert(qObject, qMakePair(pythonPointer, pythonPointer.attr("__dict__")));
}
}
// ------------------- restorePythonState -------------------
void PythonManager::restorePythonState(QObject* qObject) {
if (pythonStateMap.contains(qObject)) {
py::object pythonPointer = pythonStateMap.value(qObject).first;
py::dict pythonStateDict = pythonPointer.attr("__dict__");
for (auto item : pythonStateMap.value(qObject).second) {
pythonStateDict[item.first] = item.second;
}
}
}
// ------------------- backupPythonState -------------------
void PythonManager::backupPythonState(QObject* qObject) {
if (pythonStateMap.contains(qObject)) {
py::object pythonPointer = pythonStateMap.value(qObject).first;
py::dict pythonStateDict = pythonPointer.attr("__dict__");
for (auto item : pythonStateDict) {
std::string key = py::str(item.first);
if (key != "__builtins__" && key.rfind("__", 0) != 0) {
pythonStateMap.value(qObject).second[key.c_str()] = item.second;
}
}
}
}
} // namespace camitk
#endif // PYTHON_BINDING
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