mosamatic2 2.0.1__tar.gz → 2.0.2__tar.gz

mosamatic2-2.0.2/PKG-INFO

@@ -0,0 +1,31 @@
+Metadata-Version: 2.3
+Name: mosamatic2
+Version: 2.0.2
+Summary: 
+Author: Ralph Brecheisen
+Author-email: r.brecheisen@maastrichtuniversity.nl
+Requires-Python: >=3.11,<3.12
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Requires-Dist: nibabel (>=5.3.2)
+Requires-Dist: numpy (>=1.26.4)
+Requires-Dist: openpyxl (>=3.1.5)
+Requires-Dist: pandas (>=2.3.2)
+Requires-Dist: pendulum (>=3.1.0)
+Requires-Dist: pillow (>=11.3.0)
+Requires-Dist: pydicom (>=3.0.1)
+Requires-Dist: pyside6-essentials (>=6.9)
+Requires-Dist: python-gdcm (>=3.0.26)
+Requires-Dist: scipy (>=1.15.3)
+Requires-Dist: tensorboard (==2.15.2)
+Requires-Dist: tensorboard-data-server (==0.7.2)
+Requires-Dist: tensorflow (==2.15.*) ; platform_system == "Linux"
+Requires-Dist: tensorflow-intel (==2.15.0) ; platform_system == "Windows"
+Requires-Dist: tensorflow-io-gcs-filesystem (==0.31.0)
+Requires-Dist: tensorflow-macos (==2.15.0) ; platform_system == "Darwin" and platform_machine == "arm64"
+Requires-Dist: torch (>=2.8.0)
+Requires-Dist: torchvision (>=0.23.0)
+Requires-Dist: totalsegmentator (>=2.11.0)
+Description-Content-Type: text/markdown
+
+

mosamatic2-2.0.2/pyproject.toml

@@ -0,0 +1,47 @@
+[project]
+name = "mosamatic2"
+version = "2.0.2"
+description = ""
+authors = [
+    {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
+]
+readme = "README.md"
+requires-python = ">=3.11,<3.12"
+dependencies = [
+    "pyside6-essentials>=6.9",
+    "pydicom>=3.0.1",
+    "numpy>=1.26.4",
+    "pandas>=2.3.2",
+    "nibabel>=5.3.2",
+    "openpyxl>=3.1.5",
+    "pendulum>=3.1.0",
+    "pillow>=11.3.0",
+    "python-gdcm>=3.0.26",
+    "scipy>=1.15.3",
+    "torch>=2.8.0",
+    "torchvision>=0.23.0",
+    "tensorflow==2.15.*; platform_system == 'Linux'",
+    "tensorflow-intel==2.15.0; platform_system == 'Windows'",
+    "tensorflow-macos==2.15.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
+    "tensorboard==2.15.2",
+    "tensorboard-data-server==0.7.2",
+    "tensorflow-io-gcs-filesystem==0.31.0",
+    "totalsegmentator>=2.11.0",
+]
+
+[tool.poetry]
+packages = [
+    {include = "mosamatic2", from = "src"},
+    {include = "models.py", from = "src" },
+]
+
+[tool.poetry.scripts]
+mosamatic2 = "mosamatic2.app:main"
+mosamatic2-server = "mosamatic2.server:main"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.4.1"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"

mosamatic2-2.0.2/src/mosamatic2/app.py

@@ -0,0 +1,28 @@
+import sys
+import traceback
+import mosamatic2.constants as constants
+from PySide6 import QtWidgets
+from mosamatic2.ui.settings import Settings
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.splashscreen import SplashScreen
+
+LOG = LogManager()
+
+
+def main():
+    settings = Settings()
+    application_name = settings.get(constants.MOSAMATIC2_WINDOW_TITLE)
+    QtWidgets.QApplication.setApplicationName(application_name)
+    app = QtWidgets.QApplication(sys.argv)
+    app.setApplicationName(application_name)
+    try:
+        splash = SplashScreen()
+        splash.show()
+        sys.exit(app.exec())
+    except Exception as e:
+        LOG.error(str(e))
+        LOG.error(traceback.format_exc())
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

mosamatic2-2.0.2/src/mosamatic2/constants.py

@@ -0,0 +1,24 @@
+MOSAMATIC2_BUNDLE_IDENTIFIER = 'org.mumc'
+MOSAMATIC2_APP_NAME = 'mosamatic2'
+MOSAMATIC2_VERSION_FILE = 'mosamatic2/ui/resources/VERSION'
+MOSAMATIC2_IMAGES_DIR_PATH = 'mosamatic2/ui/resources/images'
+MOSAMATIC2_ICONS_DIR_PATH = 'mosamaticdesktop/resources/ui/images/icons'
+MOSAMATIC2_APP_ICON_FILE_NAME_WIN = 'mosamaticdesktop.ico'
+MOSAMATIC2_APP_ICON_FILE_NAME_MAC = 'mosamaticdesktop.icns'
+MOSAMATIC2_BACKGROUND_IMAGE_FILE_NAME = 'body-composition.jpg'
+MOSAMATIC2_BACKGROUND_IMAGE_OPACITY = 0.4
+
+MOSAMATIC2_WINDOW_TITLE = 'Mosamatic'
+MOSAMATIC2_WINDOW_W = 1000
+MOSAMATIC2_WINDOW_H = 600
+MOSAMATIC2_WINDOW_GEOMETRY_KEY = 'mainwindow/geometry'
+MOSAMATIC2_WINDOW_STATE_KEY = 'mainwindow/state'
+
+MOSAMATIC2_SPLASH_SCREEN_TITLE = MOSAMATIC2_WINDOW_TITLE
+MOSAMATIC2_SPLASH_SCREEN_TITLE_STYLESHEET = 'color: rgb(64, 64, 64); font-weight: bold; font-size: 32pt;'
+MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT = 'This software is for research only'
+MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT_STYLE_SHEET = 'color: rgb(64, 64, 64); font-style: italic; font-size: 10pt;'
+MOSAMATIC2_SPLASH_SCREEN_START_BUTTON_TEXT = 'Start Application'
+MOSAMATIC2_SPLASH_SCREEN_QUIT_BUTTON_TEXT = 'Quit'
+MOSAMATIC2_SPLASH_SCREEN_W = 600
+MOSAMATIC2_SPLASH_SCREEN_H = 300

mosamatic2-2.0.2/src/mosamatic2/core/managers/logmanager.py

@@ -0,0 +1,47 @@
+import os
+import atexit
+import datetime
+from pathlib import Path
+from mosamatic2.core.singleton import singleton
+
+
+@singleton
+class LogManager:
+    def __init__(self, suppress_print=False):
+        self._suppress_print = suppress_print
+        self._listeners = []
+        file_path = os.path.join(Path.home(), 'mosamatic2.log')
+        if os.path.isfile(file_path):
+            os.remove(file_path)
+        self._file_handle = open(file_path, 'w', buffering=1)
+        atexit.register(self.close_file)
+
+    def _log(self, level, message):
+        timestamp = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')
+        message = f'[{timestamp}] {level} : {message}'
+        if not self._suppress_print:
+            print(message)
+        self._file_handle.write(message + '\n')
+        self.notify_listeners(message)
+        return message
+
+    def info(self, message):
+        return self._log('INFO', message)
+
+    def warning(self, message):
+        return self._log('WARNING', message)
+
+    def error(self, message):
+        return self._log('ERROR', message)
+    
+    def add_listener(self, listener):
+        if listener not in self._listeners:
+            self._listeners.append(listener)
+
+    def notify_listeners(self, message):
+        for listener in self._listeners:
+            listener.new_message(message)
+
+    def close_file(self):
+        if self._file_handle:
+            self._file_handle.close()

mosamatic2-2.0.2/src/mosamatic2/core/managers/logmanagerlistener.py

@@ -0,0 +1,3 @@
+class LogManagerListener:
+    def new_message(self, message):
+        raise NotImplementedError()

mosamatic2-2.0.2/src/mosamatic2/core/singleton.py

@@ -0,0 +1,9 @@
+def singleton(cls):
+    _instances = {}
+
+    def instance(*args, **kwargs):
+        if cls not in _instances:
+            _instances[cls] = cls(*args, **kwargs)
+        return _instances[cls]
+    
+    return instance

mosamatic2-2.0.2/src/mosamatic2/server.py

@@ -0,0 +1,2 @@
+def main():
+    print('Running mosamatic2 server...')

mosamatic2-2.0.2/src/mosamatic2/ui/mainwindow.py

@@ -0,0 +1,62 @@
+import os
+import mosamatic2.constants as constants
+from PySide6.QtWidgets import (
+    QMainWindow,
+)
+from PySide6.QtGui import (
+    QGuiApplication,
+    QAction,
+    QIcon,
+)
+from PySide6.QtCore import Qt, QByteArray
+from mosamatic2.ui.utils import version, resource_path, is_macos
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.settings import Settings
+
+LOG = LogManager()
+
+
+class MainWindow(QMainWindow):
+    def __init__(self):
+        super(MainWindow, self).__init__()
+        self._settings = None
+        self.init_window()
+
+    def init_window(self):
+        self.setWindowTitle(f'{constants.MOSAMATIC2_WINDOW_TITLE} {version()}')
+        icon_file_name = constants.MOSAMATIC2_APP_ICON_FILE_NAME_MAC if is_macos() else constants.MOSAMATIC2_APP_ICON_FILE_NAME_WIN
+        self.setWindowIcon(QIcon(resource_path(os.path.join(constants.MOSAMATIC2_ICONS_DIR_PATH, icon_file_name))))
+        if not self.load_geometry_and_state():
+            self.set_default_size_and_position()
+
+    # GET
+
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+
+    # MISCELLANEOUS
+
+    def load_geometry_and_state(self):
+        geometry = self.settings().get(constants.MOSAMATIC2_WINDOW_GEOMETRY_KEY)
+        state = self.settings().get(constants.MOSAMATIC2_WINDOW_STATE_KEY)
+        if isinstance(geometry, QByteArray) and self.restoreGeometry(geometry):
+            if isinstance(state, QByteArray):
+                self.restoreState(state)
+            return True
+        return False
+
+    def save_geometry_and_state(self):
+        self.settings().set(constants.MOSAMATIC2_WINDOW_GEOMETRY_KEY, self.saveGeometry())
+        self.settings().set(constants.MOSAMATIC2_WINDOW_STATE_KEY, self.saveState())
+
+    def set_default_size_and_position(self):
+        self.resize(constants.MOSAMATIC2_WINDOW_W, constants.MOSAMATIC2_WINDOW_H)
+        self.center_window()
+
+    def center_window(self):
+        screen = QGuiApplication.primaryScreen().geometry()
+        x = (screen.width() - self.geometry().width()) / 2
+        y = (screen.height() - self.geometry().height()) / 2
+        self.move(int(x), int(y))

mosamatic2-2.0.2/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.2 

mosamatic2-2.0.2/src/mosamatic2/ui/settings.py

@@ -0,0 +1,62 @@
+import mosamatic2.constants as constants
+from PySide6.QtCore import QSettings
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class Settings(QSettings):
+    def __init__(self):
+        super(Settings, self).__init__(
+            QSettings.IniFormat, 
+            QSettings.UserScope, 
+            constants.MOSAMATIC2_BUNDLE_IDENTIFIER, 
+            constants.MOSAMATIC2_APP_NAME,
+        )
+
+    def prepend_bundle_identifier_and_name(self, name):
+        return '{}.{}.{}'.format(constants.MOSAMATIC2_BUNDLE_IDENTIFIER, constants.MOSAMATIC2_APP_NAME, name)
+
+    def get(self, name, default=None):
+        if not name.startswith(constants.MOSAMATIC2_BUNDLE_IDENTIFIER):
+            name = self.prepend_bundle_identifier_and_name(name)
+        value = self.value(name)
+        if value is None or value == '':
+            return default
+        return value
+    
+    def get_int(self, name, default=None):
+        try:
+            return int(self.get(name, default))
+        except ValueError as e:
+            return default
+        
+    def get_float(self, name, default=None):
+        try:
+            return float(self.get(name, default))
+        except ValueError as e:
+            return default
+        
+    def get_bool(self, name, default=None):
+        try:
+            value = self.get(name, default)
+            if value and isinstance(value, str):
+                if value == '0' or value.lower() == 'false':
+                    return False
+                elif value == '1' or value.lower() == 'true':
+                    return True
+                else:
+                    return default
+            if value and isinstance(value, bool):
+                return value
+        except ValueError as e:
+            return default
+    
+    def set(self, name, value):
+        name = self.prepend_bundle_identifier_and_name(name)
+        self.setValue(name, value)
+
+    def print(self):
+        LOG.info(f'Settings path: {self.fileName()}')
+        for key in self.allKeys():
+            LOG.info(f'Settings: {key}')

mosamatic2-2.0.2/src/mosamatic2/ui/utils.py

@@ -0,0 +1,36 @@
+import os
+import sys
+import mosamatic2.constants as constants
+from PySide6.QtGui import (
+    QPixmap, 
+    QPainter, 
+    QColor
+)
+
+
+def resource_path(relative_path):
+    base_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))
+    return os.path.join(base_path, relative_path)
+
+
+def version():
+    with open(resource_path(constants.MOSAMATIC2_VERSION_FILE), 'r') as f:
+        return f.readline().strip()
+
+
+def is_macos():
+    return sys.platform.startswith('darwin')
+
+
+def icon(parent, icon_type):
+    return parent.style().standardIcon(icon_type)
+
+
+def set_opacity(pixmap, opacity):
+    result = QPixmap(pixmap.size())
+    result.fill(QColor(0, 0, 0, 0))
+    painter = QPainter(result)
+    painter.setOpacity(opacity)
+    painter.drawPixmap(0, 0, pixmap)
+    painter.end()
+    return result

mosamatic2-2.0.2/src/mosamatic2/ui/widgets/splashscreen.py

@@ -0,0 +1,101 @@
+import os
+import mosamatic2.constants as constants
+from PySide6.QtWidgets import (
+    QWidget,
+    QVBoxLayout,
+    QPushButton,
+    QLabel,
+)
+from PySide6.QtCore import Qt
+from PySide6.QtGui import QPixmap
+from mosamatic2.ui.mainwindow import MainWindow
+from mosamatic2.ui.utils import resource_path, set_opacity, version
+
+
+class SplashScreen(QWidget):
+    def __init__(self):
+        super(SplashScreen, self).__init__()
+        self._main = None
+        self._background_label = None
+        self._background_pixmap = None
+        self._title_label = None
+        self._sub_text_label = None
+        self._start_app_button = None
+        self._donate_button = None
+        self._close_button = None
+        self.init_layout()
+
+    def main(self):
+        if not self._main:
+            self._main = MainWindow()
+        return self._main
+    
+    def background_label(self):
+        if not self._background_label:
+            self._background_label = QLabel(self)
+            self._background_label.setPixmap(self.background_pixmap())
+            self._background_label.setGeometry(0, 0, self.width(), self.height())
+            self._background_label.lower()
+        return self._background_label
+    
+    def background_pixmap(self):
+        if not self._background_pixmap:
+            self._background_pixmap = QPixmap(resource_path(os.path.join(
+                constants.MOSAMATIC2_IMAGES_DIR_PATH, constants.MOSAMATIC2_BACKGROUND_IMAGE_FILE_NAME,
+            ))).scaled(self.size(), Qt.IgnoreAspectRatio, Qt.SmoothTransformation)
+            self._background_pixmap = set_opacity(self._background_pixmap, constants.MOSAMATIC2_BACKGROUND_IMAGE_OPACITY)
+        return self._background_pixmap
+    
+    def title_label(self):
+        if not self._title_label:
+            self._title_label = QLabel(f'{constants.MOSAMATIC2_SPLASH_SCREEN_TITLE} {version()}')
+            self._title_label.setStyleSheet(constants.MOSAMATIC2_SPLASH_SCREEN_TITLE_STYLESHEET)
+            self._title_label.setAlignment(Qt.AlignCenter)
+        return self._title_label
+    
+    def sub_text_label(self):
+        if not self._sub_text_label:
+            message = constants.MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT
+            self._sub_text_label = QLabel(message)
+            self._sub_text_label.setStyleSheet(constants.MOSAMATIC2_SPLASH_SCREEN_SUB_TEXT_STYLE_SHEET)
+            self._sub_text_label.setAlignment(Qt.AlignCenter)
+        return self._sub_text_label
+    
+    def start_app_button(self):
+        if not self._start_app_button:
+            self._start_app_button = QPushButton(constants.MOSAMATIC2_SPLASH_SCREEN_START_BUTTON_TEXT)
+            self._start_app_button.clicked.connect(self.handle_start_app_button)
+        return self._start_app_button
+    
+    def close_button(self):
+        if not self._close_button:
+            self._close_button = QPushButton(constants.MOSAMATIC2_SPLASH_SCREEN_QUIT_BUTTON_TEXT)
+            self._close_button.clicked.connect(self.handle_close_button)
+        return self._close_button
+    
+    # LAYOUT
+
+    def init_layout(self):
+        layout = QVBoxLayout()
+        layout.addWidget(self.title_label())
+        layout.addWidget(self.sub_text_label())
+        layout.addWidget(self.start_app_button())
+        layout.addWidget(self.close_button())
+        self.setLayout(layout)
+        self.setFixedSize(constants.MOSAMATIC2_SPLASH_SCREEN_W, constants.MOSAMATIC2_SPLASH_SCREEN_H)
+        self.setWindowFlags(Qt.FramelessWindowHint)
+    
+    # EVENT HANDLERS
+
+    def handle_start_app_button(self):
+        self.close()
+        self.main().show()
+
+    def handle_close_button(self):
+        self.close()
+
+    def resizeEvent(self, event):
+        super().resizeEvent(event)
+        scaled = self.background_pixmap().scaled(self.size(), Qt.KeepAspectRatioByExpanding, Qt.SmoothTransformation)
+        self.background_label().setPixmap(scaled)
+        self.background_label().setGeometry(0, 0, self.width(), self.height())

mosamatic2-2.0.1/PKG-INFO

@@ -1,12 +0,0 @@
-Metadata-Version: 2.3
-Name: mosamatic2
-Version: 2.0.1
-Summary: 
-Author: Ralph Brecheisen
-Author-email: r.brecheisen@maastrichtuniversity.nl
-Requires-Python: >=3.11,<3.12
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Description-Content-Type: text/markdown
-
-

mosamatic2-2.0.1/pyproject.toml

@@ -1,28 +0,0 @@
-[project]
-name = "mosamatic2"
-version = "2.0.1"
-description = ""
-authors = [
-    {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}
-]
-readme = "README.md"
-requires-python = ">=3.11,<3.12"
-dependencies = [
-]
-
-[tool.poetry]
-packages = [
-    {include = "mosamatic2", from = "src"},
-    {include = "models.py", from = "src" },
-]
-
-[tool.poetry.scripts]
-mosamatic2 = "mosamatic2.app:main"
-mosamatic2-api = "mosamatic2.api:main"
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.4.1"
-
-[build-system]
-requires = ["poetry-core>=2.0.0,<3.0.0"]
-build-backend = "poetry.core.masonry.api"

mosamatic2-2.0.1/src/mosamatic2/api.py

@@ -1,2 +0,0 @@
-def main():
-    print('Running mosamatic2 API...')

mosamatic2-2.0.1/src/mosamatic2/app.py

@@ -1,2 +0,0 @@
-def main():
-    print('Running mosamatic2...')