mosamatic2 2.0.1__py3-none-any.whl → 2.0.3__py3-none-any.whl

mosamatic2/ui/widgets/panels/tasks/segmentmusclefatl3tensorflowtaskpanel.py

@@ -0,0 +1,216 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import SegmentMuscleFatL3TensorFlowTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'SegmentMuscleFatL3TensorFlowTask (TensorFlow)'
+PANEL_NAME = 'segmentmusclefatl3tensorflowtaskpanel'
+
+
+class SegmentMuscleFatL3TensorFlowTaskPanel(TaskPanel):
+    def __init__(self):
+        super(SegmentMuscleFatL3TensorFlowTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_button = None
+        self._model_files_dir_line_edit = None
+        self._model_files_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_button:
+            self._images_dir_select_button = QPushButton('Select')
+            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_button
+    
+    def model_files_dir_line_edit(self):
+        if not self._model_files_dir_line_edit:
+            self._model_files_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/model_files_dir'))
+        return self._model_files_dir_line_edit
+    
+    def model_files_dir_select_button(self):
+        if not self._model_files_dir_select_button:
+            self._model_files_dir_select_button = QPushButton('Select')
+            self._model_files_dir_select_button.clicked.connect(self.handle_model_files_dir_select_button)
+        return self._model_files_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        model_files_dir_layout = QHBoxLayout()
+        model_files_dir_layout.addWidget(self.model_files_dir_line_edit())
+        model_files_dir_layout.addWidget(self.model_files_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Model files directory', model_files_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_model_files_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.model_files_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = SegmentMuscleFatL3TensorFlowTask(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'model_files': self.model_files_dir_line_edit().text(),
+                },
+                params={'model_version': 1.0},
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if not os.path.isdir(self.images_dir_line_edit().text()):
+            errors.append('Images directory does not exist')
+        if self.model_files_dir_line_edit().text() == '':
+            errors.append('Empty model files directory path')
+        if not os.path.isdir(self.model_files_dir_line_edit().text()):
+            errors.append('Model files directory does not exist')
+        if len(os.listdir(self.model_files_dir_line_edit().text())) != 3:
+            errors.append('Model files directory should ONLY contain "model-1.1.zip", "contour_model-1.1.zip" and "params-1.1.json", nothing else!')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/model_files_dir', self.model_files_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2/ui/widgets/panels/tasks/selectslicefromscantaskpanel.py

@@ -0,0 +1,184 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QSpinBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamaticdesktop.core.utils.logmanager import LogManager
+from mosamaticdesktop.ui.panels.taskpanel import TaskPanel
+from mosamaticdesktop.ui.settings import Settings
+from mosamaticdesktop.ui.utils import is_macos
+from mosamaticdesktop.ui.worker import Worker
+
+from mosamatic.tasks import SelectSliceFromScanTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'Automatically select L3 or T4 slice from full CT scan'
+PANEL_NAME = 'selectslicefromscantaskpanel'
+
+
+class SelectSliceFromScanTaskPanel(TaskPanel):
+    def __init__(self):
+        super(SelectSliceFromScanTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._scans_dir_line_edit = None
+        self._scans_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def scans_dir_line_edit(self):
+        if not self._scans_dir_line_edit:
+            self._scans_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/scans_dir'))
+        return self._scans_dir_line_edit
+    
+    def scans_dir_select_button(self):
+        if not self._scans_dir_select_button:
+            self._scans_dir_select_button = QPushButton('Select')
+            self._scans_dir_select_button.clicked.connect(self.handle_scans_dir_select_button)
+        return self._scans_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        scans_dir_layout = QHBoxLayout()
+        scans_dir_layout.addWidget(self.scans_dir_line_edit())
+        scans_dir_layout.addWidget(self.scans_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Scans directory', scans_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_scans_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.scans_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = SelectSliceFromScanTask(
+                self.scans_dir_line_edit().text(), 
+                self.output_dir_line_edit().text(), 
+                'vertebrae_L3',
+                self.overwrite_checkbox().isChecked()
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.scans_dir_line_edit().text() == '':
+            errors.append('Empty scans directory path')
+        if not os.path.isdir(self.scans_dir_line_edit().text()):
+            errors.append('Scans directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/scans_dir', self.scans_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

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/ui/worker.py

@@ -0,0 +1,29 @@
+import traceback
+from PySide6.QtCore import (
+    QObject, 
+    Signal, 
+)
+from mosamatic2.core.managers.logmanager import LogManager
+
+LOG = LogManager()
+
+
+class Worker(QObject):
+    progress = Signal(int)
+    status = Signal(str)
+    finished = Signal()
+
+    def __init__(self, task):
+        super(Worker, self).__init__()
+        self._task = task
+
+    def run(self):
+        try:
+            self.status.emit('started')
+            self._task.run()
+            self.status.emit('done')
+            self.finished.emit()
+        except Exception as e:
+            self.status.emit('failed')
+            LOG.error(traceback.format_exc())
+            self.finished.emit()

mosamatic2-2.0.3.dist-info/METADATA

@@ -0,0 +1,34 @@
+Metadata-Version: 2.3
+Name: mosamatic2
+Version: 2.0.3
+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: antspyx (>=0.5.4)
+Requires-Dist: flask (>=3.1.2)
+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) ; platform_system == "Windows"
+Requires-Dist: tensorflow-io-gcs-filesystem (>=0.31.0) ; platform_system == "Darwin" and platform_machine == "arm64"
+Requires-Dist: tensorflow-macos (==2.15.0) ; platform_system == "Darwin" and platform_machine == "arm64"
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+Description-Content-Type: text/markdown
+
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mosamatic2-2.0.3.dist-info/RECORD

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mosamatic2-2.0.3.dist-info/entry_points.txt

@@ -0,0 +1,5 @@
+[console_scripts]
+mosamatic2=mosamatic2.app:main
+mosamatic2-cli=mosamatic2.cli:main
+mosamatic2-server=mosamatic2.server:main
+

mosamatic2/api.py

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

mosamatic2-2.0.1.dist-info/METADATA

@@ -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.dist-info/RECORD

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