ENH:Renaming application to Minder3D and packaging

.gitignore

@@ -1,6 +1,9 @@
+build
+*egg-info
 experiments
 venv*
 archive
 __pycache__
 *.swp
 *~
+*.zip

.pre-commit-config.yaml

@@ -30,4 +30,4 @@ repos:
     hooks:
       - id: prettier
         stages: [commit]
-exclude: "src/ui_*"
+exclude: ["src/ui_*", "*.md"]

README.md

@@ -1,3 +1,3 @@
-# pytubeview
+# Minder3D
 
-Analyze and visualize vessels in 3D
+Using AI to foster innovation in the exploration of radiological images.

README_Dev.md

@@ -1,5 +1,6 @@
-QT Designer was used to define the layout:
-qt6-tools.exe designer pytubeview.ui
+Prior to making a commit, please verify your code is compliant:
+    pre-commit run --all-files
 
-Then view the python code and same to
-ui_pytubeview.py
+QT Designer was used to define the layout.  On Windows, to launch
+designer, use this command:
+    qt6-tools.exe designer pytubeview.ui

pyproject.toml

@@ -1,9 +1,73 @@
-# Python
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "minder3d"
+description = "Using AI to foster innovation in the exploration of radiological images."
+license = {text = "Apache 2.0"}
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3"
+]
+dynamic = ["version", "readme"]
+
+dependencies = [
+  'PyQt6',
+  'PySide6',
+  'numpy',
+  'vtk',
+  #'itk',  # Do not install until ITK pypi is updated
+]
+
+[project.scripts]
+
+minder3d = "minder3d.main:main"
+
+[project.optional-dependencies]
+
+develop = [
+  'black',
+  'pylint',
+  'flake8'
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "minder3d.__version__"}
+readme = {file = ["README.md"]}
+
 [tool.black]
 line-length = 80
 skip-string-normalization = 1
-target_version = ["py311"]
+target_version = ['py311']
+exclude = '''
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | build
+    | dist
+  )/
+  | .gitignore
+)
+'''
 
 [tool.flake8]
 max-line-length = 80
 extend-ignore = ["E501"]
+
+[tool.isort]
+profile = "black"
+skip_glob = "src/ui_*"
+line_length = 80
+
+[tool.pylint]
+max-line-length = 80

src/minder3d/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.9.0"

src/minder3d/config.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+
+"""
+Helper utility to parse input parameters for a given run.
+"""
+
+import argparse
+
+
+def parse_config() -> argparse.Namespace:
+    """
+    Parse command line arguments to configure the run.
+    """
+
+    parser = argparse.ArgumentParser(
+        description="Enabling innovative AI for medical imaging.")
+
+    parser.add_argument(
+        "--load-image", type=str, required=False, help="Path to image"
+    )
+    parser.add_argument(
+        "--load-scene", type=str, required=False, help="Path to scene"
+    )
+
+    args = parser.parse_args()
+    print(args)
+
+    return args

src/sovChatPanelWidget.py → src/minder3d/lib/sovChatPanelWidget.py

@@ -1,7 +1,7 @@
 from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
-from ui_sovChatPanelWidget import Ui_ChatPanelWidget
+from .ui_sovChatPanelWidget import Ui_ChatPanelWidget
 
 
 class ChatPanelWidget(QWidget, Ui_ChatPanelWidget):

src/sovImageProcessPanelWidget.py → src/minder3d/lib/sovImageProcessPanelWidget.py

@@ -1,8 +1,8 @@
 from PySide6.QtWidgets import QWidget
 
-from sovImageProcessLogic import ImageProcessLogic
-from sovUtils import time_and_log
-from ui_sovImageProcessPanelWidget import Ui_ImageProcessPanelWidget
+from .sovImageProcessLogic import ImageProcessLogic
+from .sovUtils import time_and_log
+from .ui_sovImageProcessPanelWidget import Ui_ImageProcessPanelWidget
 
 
 class ImageProcessPanelWidget(QWidget, Ui_ImageProcessPanelWidget):

src/sovImageTablePanelWidget.py → src/minder3d/lib/sovImageTablePanelWidget.py

@@ -1,3 +1,4 @@
+"""This module provides the ImageTablePanelWidget class."""
 from PySide6.QtCore import QSize
 from PySide6.QtGui import QIcon, QPixmap
 from PySide6.QtWidgets import (
@@ -7,9 +8,9 @@
     QWidget,
 )
 
-from sovImageTablePanelUtils import get_qthumbnail_from_array
-from sovUtils import get_file_reccords_from_settings, time_and_log
-from ui_sovImageTablePanelWidget import Ui_ImageTablePanelWidget
+from .sovImageTablePanelUtils import get_qthumbnail_from_array
+from .sovUtils import get_file_reccords_from_settings, time_and_log
+from .ui_sovImageTablePanelWidget import Ui_ImageTablePanelWidget
 
 
 class ImageTablePanelWidget(QWidget, Ui_ImageTablePanelWidget):
@@ -60,7 +61,8 @@ def update_image(self):
     def redraw_image(self, img_num):
         """Redraws the image at the specified index in the image table widget.
 
-        This function updates the information displayed in the image table widget for the image at the specified index.
+        This function updates the information displayed in the image table
+        widget for the image at the specified index.
 
         Args:
             self: The object instance.
@@ -102,11 +104,13 @@ def redraw_image(self, img_num):
 
     @time_and_log
     def fill_table(self):
-        """Fill the image table with image records from the state and file records from settings.
+        """Fill the image table with images from the state and from settings.
 
-        This method clears the existing image table and fills it with image records from the state. It then retrieves file
-        records from the settings and adds them to the table if they are not already present. For each file record, it
-        populates the table with the file's thumbnail, filename, size, and spacing.
+        This method clears the existing image table and fills it with image
+        records from the state. It then retrieves file records from the
+        settings and adds them to the table if they are not already present.
+        For each file record, it populates the table with the file's thumbnail,
+        filename, size, and spacing.
 
         Args:
             self: The instance of the class.
@@ -131,13 +135,13 @@ def fill_table(self):
                 self.imageTableWidget.setItem(
                     img_num, 2, QTableWidgetItem(file.filename)
                 )
-                if type(file.file_size) == type([]) and len(file.file_size) > 0:
+                if type(file.file_size) is type([]) and len(file.file_size) > 0:
                     size_str = [str(i) for i in file.file_size]
                     self.imageTableWidget.setItem(
                         img_num, 3, QTableWidgetItem('x'.join(size_str))
                     )
                 if (
-                    type(file.file_spacing) == type([])
+                    type(file.file_spacing) is type([])
                     and len(file.file_spacing) > 0
                 ):
                     spacing_str = [f'{i:.4f}' for i in file.file_spacing]

src/sovInfoTablePanelWidget.py → src/minder3d/lib/sovInfoTablePanelWidget.py

@@ -5,8 +5,8 @@
     QWidget,
 )
 
-from sovUtils import time_and_log
-from ui_sovInfoTablePanelWidget import Ui_InfoTablePanelWidget
+from .sovUtils import time_and_log
+from .ui_sovInfoTablePanelWidget import Ui_InfoTablePanelWidget
 
 
 class InfoTablePanelWidget(QWidget, Ui_InfoTablePanelWidget):

src/sovLungCTALogic.py → src/minder3d/lib/sovLungCTALogic.py

@@ -4,8 +4,8 @@
 import itk
 import numpy as np
 
-from sovImageProcessLogic import ImageProcessLogic
-from sovUtils import time_and_log
+from .sovImageProcessLogic import ImageProcessLogic
+from .sovUtils import time_and_log
 
 
 class LungCTALogic:

src/sovLungCTAPanelWidget.py → src/minder3d/lib/sovLungCTAPanelWidget.py

@@ -2,9 +2,9 @@
 from PySide6.QtGui import QCloseEvent
 from PySide6.QtWidgets import QMessageBox, QWidget
 
-from sovLungCTALogic import LungCTALogic
-from sovUtils import add_objects_in_mask_image_to_scene, time_and_log
-from ui_sovLungCTAPanelWidget import Ui_LungCTAPanelWidget
+from .sovLungCTALogic import LungCTALogic
+from .sovUtils import add_objects_in_mask_image_to_scene, time_and_log
+from .ui_sovLungCTAPanelWidget import Ui_LungCTAPanelWidget
 
 
 class LungCTAPanelWidget(QWidget, Ui_LungCTAPanelWidget):

src/sovNewTaskPanelWidget.py → src/minder3d/lib/sovNewTaskPanelWidget.py

@@ -1,10 +1,10 @@
 from PySide6.QtWidgets import QWidget
 
-from sovImageProcessPanelWidget import ImageProcessPanelWidget
-from sovLungCTAPanelWidget import LungCTAPanelWidget
-from sovOtsuPanelWidget import OtsuPanelWidget
-from sovUtils import time_and_log
-from ui_sovNewTaskPanelWidget import Ui_NewTaskPanelWidget
+from .sovImageProcessPanelWidget import ImageProcessPanelWidget
+from .sovLungCTAPanelWidget import LungCTAPanelWidget
+from .sovOtsuPanelWidget import OtsuPanelWidget
+from .sovUtils import time_and_log
+from .ui_sovNewTaskPanelWidget import Ui_NewTaskPanelWidget
 
 
 class NewTaskPanelWidget(QWidget, Ui_NewTaskPanelWidget):

src/sovOtsuPanelWidget.py → src/minder3d/lib/sovOtsuPanelWidget.py

@@ -4,9 +4,9 @@
 from PySide6.QtGui import QCloseEvent
 from PySide6.QtWidgets import QWidget
 
-from sovOtsuLogic import OtsuLogic
-from sovUtils import add_objects_in_mask_image_to_scene, time_and_log
-from ui_sovOtsuPanelWidget import Ui_OtsuPanelWidget
+from .sovOtsuLogic import OtsuLogic
+from .sovUtils import add_objects_in_mask_image_to_scene, time_and_log
+from .ui_sovOtsuPanelWidget import Ui_OtsuPanelWidget
 
 
 class OtsuPanelWidget(QWidget, Ui_OtsuPanelWidget):

src/sovScreenCapturePanelWidget.py → src/minder3d/lib/sovScreenCapturePanelWidget.py

@@ -1,7 +1,7 @@
 from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
-from ui_sovScreenCapturePanelWidget import Ui_ScreenCapturePanelWidget
+from .ui_sovScreenCapturePanelWidget import Ui_ScreenCapturePanelWidget
 
 
 class ScreenCapturePanelWidget(QWidget, Ui_ScreenCapturePanelWidget):

src/sovTubesPanelWidget.py → src/minder3d/lib/sovTubesPanelWidget.py

@@ -1,7 +1,7 @@
 from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget
 
-from ui_sovPreProcessPanelWidget import Ui_PreProcessPanelWidget
+from .ui_sovPreProcessPanelWidget import Ui_PreProcessPanelWidget
 
 
 class PreProcessPanelWidget(QWidget, Ui_PreProcessPanelWidget):

src/sovUtils.py → src/minder3d/lib/sovUtils.py

@@ -22,7 +22,7 @@
 from PySide6.QtCore import QSettings, QStandardPaths
 from PySide6.QtWidgets import QMainWindow, QTextEdit
 
-from sovColorMapUtils import short_colormap, short_colormap_scale_factor
+from .sovColorMapUtils import short_colormap, short_colormap_scale_factor
 
 logging.basicConfig(level=logging.DEBUG)
 

src/sovView2DPanelWidget.py → src/minder3d/lib/sovView2DPanelWidget.py

@@ -2,13 +2,13 @@
 import numpy as np
 from PySide6.QtWidgets import QWidget
 
-from sovUtils import time_and_log
-from sovView2DRenderWindowInteractor import View2DRenderWindowInteractor
-from sovView2DUtils import (
+from .sovUtils import time_and_log
+from .sovView2DRenderWindowInteractor import View2DRenderWindowInteractor
+from .sovView2DUtils import (
     render_object_in_overlay_array,
     render_scene_in_overlay_array,
 )
-from ui_sovView2DPanelWidget import Ui_View2DPanelWidget
+from .ui_sovView2DPanelWidget import Ui_View2DPanelWidget
 
 
 class View2DPanelWidget(QWidget, Ui_View2DPanelWidget):

src/sovView2DRenderWindowInteractor.py → src/minder3d/lib/sovView2DRenderWindowInteractor.py

@@ -4,7 +4,7 @@
 from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 from vtk.util.numpy_support import numpy_to_vtk
 
-from sovUtils import time_and_log
+from .sovUtils import time_and_log
 
 
 class View2DRenderWindowInteractor(QVTKRenderWindowInteractor):

src/sovView2DUtils.py → src/minder3d/lib/sovView2DUtils.py

@@ -1,7 +1,7 @@
 import itk
 import numpy as np
 
-from sovUtils import get_children_as_list, time_and_log
+from .sovUtils import get_children_as_list, time_and_log
 
 
 @time_and_log

src/sovView3DPanelWidget.py → src/minder3d/lib/sovView3DPanelWidget.py

@@ -1,8 +1,8 @@
 from PySide6.QtWidgets import QWidget
 
-from sovUtils import time_and_log
-from sovView3DRenderWindowInteractor import View3DRenderWindowInteractor
-from ui_sovView3DPanelWidget import Ui_View3DPanelWidget
+from .sovUtils import time_and_log
+from .sovView3DRenderWindowInteractor import View3DRenderWindowInteractor
+from .ui_sovView3DPanelWidget import Ui_View3DPanelWidget
 
 
 class View3DPanelWidget(QWidget, Ui_View3DPanelWidget):

src/sovView3DRenderWindowInteractor.py → src/minder3d/lib/sovView3DRenderWindowInteractor.py

@@ -8,8 +8,8 @@
     vtkRenderer,
 )
 
-from sovUtils import get_tag_value_index_in_list_of_dict, time_and_log
-from sovView3DUtils import (
+from .sovUtils import get_tag_value_index_in_list_of_dict, time_and_log
+from .sovView3DUtils import (
     convert_scene_to_surfaces,
     get_closest_point_in_world_space,
 )

src/sovView3DUtils.py → src/minder3d/lib/sovView3DUtils.py

@@ -4,7 +4,7 @@
 from vtkmodules.vtkCommonDataModel import vtkCellArray, vtkPolyData, vtkPolyLine
 from vtkmodules.vtkFiltersCore import vtkSurfaceNets3D, vtkTubeFilter
 
-from sovUtils import get_children_as_list, time_and_log
+from .sovUtils import get_children_as_list, time_and_log
 
 
 @time_and_log