ENH: Updated Settings to use local files instead of registry

README.md

@@ -1,3 +1,16 @@
 # Minder3D
 
 Using AI to foster innovation in the exploration of radiological images.
+
+## Installing in a end-user system (without a python already installed)
+
+Download the installation package for current release from
+    [work-in-progress]
+
+## Installing and Running in a Python Environment
+
+    pip install minder3d
+
+### Running 
+
+    python -m minder3d

README_Dev.md

@@ -1,6 +1,12 @@
+Setup for editable installation. Changes to code in src are
+immediatelly reflected in the installed version.  Also installs
+all dependencies needed for development and testing:
+    pip install -e .[dev]
+
 Prior to making a commit, please verify your code is compliant:
     pre-commit run --all-files
 
+HINT:
 QT Designer was used to define the layout.  On Windows, to launch
 designer, use this command:
     qt6-tools.exe designer pytubeview.ui

pyproject.toml

@@ -28,15 +28,13 @@ dependencies = [
 [project.scripts]
 minder3d = "minder3d.__main__:main"
 
-[project.gui-scripts]
-minder3d = "minder3d.__main__:main"
-
 [project.urls]
 Homepage = "https://github.com/aylward/Minder3D"
 Aylward = "https://www.aylward.org"
 
 [project.optional-dependencies]
 dev = [
+  'qt6-tools',
   'black==24.4.2',
   'pylint',
   'flake8',
@@ -61,8 +59,8 @@ tag             = true
 push            = false
 
 [tool.bumpver.file_patterns]
-"pyproject.toml" = ['current_version = "{version}"', 'version = "{version}"']
-"src/minder3d/__init__.py" = ["{version}"]
+"pyproject.toml" = ['current_version = "{version}"']
+"src/minder3d/__init__.py" = ["__version__ = '{version}'"]
 
 [tool.black]
 line-length = 80

src/minder3d/__main__.py

@@ -9,7 +9,7 @@
 from PySide6.QtGui import QColor, QPalette
 from PySide6.QtWidgets import QApplication
 
-from .config import parse_config
+from .parse_args import parse_args
 from .minder3DWindow import Minder3DWindow
 
 
@@ -19,7 +19,7 @@ def main():
 
     Parse arguments and pass them to the application
     """
-    config = parse_config()
+    cli_args = parse_args()
 
     app = QApplication()
 
@@ -46,11 +46,11 @@ def main():
     app.setPalette(palette)
     app.setStyle('Fusion')
 
-    if config.load_image is not None:
-        minder3D.load_image(config.load_image)
+    if cli_args.load_image is not None:
+        minder3D.load_image(cli_args.load_image)
 
-    if config.load_scene is not None:
-        minder3D.load_scene(config.load_scene)
+    if cli_args.load_scene is not None:
+        minder3D.load_scene(cli_args.load_scene)
 
     minder3D.show()
 

src/minder3d/lib/sovImageTablePanelUtils.py

@@ -3,7 +3,7 @@
 
 
 def get_qthumbnail_from_array(thumb_array):
-    auto_range = np.quantile(thumb_array, [0.1, 0.9])
+    auto_range = np.quantile(thumb_array, [0.05, 0.95])
     thumb_array = np.clip(thumb_array, auto_range[0], auto_range[1])
     thumb_array = (
         (thumb_array - auto_range[0]) / (auto_range[1] - auto_range[0]) * 255

src/minder3d/lib/sovImageTablePanelWidget.py

@@ -136,13 +136,13 @@ def fill_table(self):
                 self.imageTableWidget.setItem(
                     img_num, 2, QTableWidgetItem(file.filename)
                 )
-                if isinstance(file.file_size, []) and len(file.file_size) > 0:
+                if isinstance(file.file_size, list) 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 (
-                    isinstance(file.file_spacing, [])
+                    isinstance(file.file_spacing, list)
                     and len(file.file_spacing) > 0
                 ):
                     spacing_str = [f'{i:.4f}' for i in file.file_spacing]

src/minder3d/lib/sovUtils.py

@@ -18,7 +18,7 @@
 
 import itk
 import numpy as np
-from PySide6.QtCore import QSettings, QStandardPaths
+from PySide6.QtCore import QSettings, QStandardPaths, QCoreApplication
 from PySide6.QtWidgets import QMainWindow, QTextEdit
 
 from .sovColorMapUtils import short_colormap, short_colormap_scale_factor
@@ -170,13 +170,23 @@ def wrapper(*args, **kwargs):
 def get_settings():
     """Get the application settings.
 
-    This function retrieves the application settings using QSettings from 'itkSpatialObjectsViewer' and 'QuantAIV'.
+    This function retrieves the application settings via QSettings.
+
+    The main application should set the CoreApplication variables, as shown
+    in the example below:
+        from PySide6.QtCore import QCoreApplication
+
+        QCoreApplication.setOrganizationName("aylward")
+        QCoreApplication.setApplicationName("Minder3D")
 
     Returns:
         QSettings: The application settings.
     """
+    settings_file = os.path.join(QStandardPaths.writableLocation(
+        QStandardPaths.AppDataLocation), "settings.ini")
+    os.makedirs(os.path.dirname(settings_file), exist_ok=True)
+    settings = QSettings(settings_file, QSettings.IniFormat)
 
-    settings = QSettings('itkSpatialObjectsViewer', 'QuantAIV')
     return settings
 
 
@@ -236,7 +246,8 @@ def get_file_reccords_from_settings():
 def add_file_to_settings(obj, filename, file_type, qthumbnail=None):
     """Add a file to the settings.
 
-    This function adds a file to the settings, including its filename, type, spacing, size, and thumbnail.
+    This function adds a file to the settings, including its filename, type,
+    spacing, size, and thumbnail.
 
     Args:
         obj: The object representing the file.

src/minder3d/minder3DWindow.py

@@ -3,6 +3,7 @@
 import itk
 import numpy as np
 import vtk
+from PySide6.QtCore import QCoreApplication
 from PySide6.QtWidgets import QFileDialog, QInputDialog, QMainWindow, QTabBar
 
 from .lib.sovColorMapUtils import get_nearest_color_index_and_name
@@ -38,6 +39,9 @@ def __init__(self, parent=None):
         super().__init__(parent)
         self.setupUi(self)
 
+        QCoreApplication.setOrganizationName("Aylward")
+        QCoreApplication.setApplicationName("Minder3D")
+
         self.state = Minder3DState()
 
         # File Menu
@@ -180,8 +184,9 @@ def log(self, message, level='info'):
     def load_image(self, filename=None):
         """Load an image from a file.
 
-        If filename is not provided, it opens a file dialog to select an image file.
-        It then creates a new image from the selected file and updates the image and overlay.
+        If filename is not provided, it opens a file dialog to select an image
+        file.  It then creates a new image from the selected file and updates
+        the image and overlay.
 
         Args:
             filename (str?): The path of the image file to be loaded.
@@ -201,7 +206,11 @@ def load_image(self, filename=None):
             self.update_image()
             self.update_overlay()
 
-            qthumb = get_qthumbnail_from_array(self.state.image_array[-1])
+            qthumb = get_qthumbnail_from_array(
+                self.state.image_array[-1][
+                    self.state.image_array[-1].shape[0] // 2, ::-1, :
+                ]
+            )
             add_file_to_settings(
                 self.state.image[-1], filename, 'image', qthumb
             )
@@ -210,8 +219,9 @@ def load_image(self, filename=None):
     def load_scene(self, filename=None):
         """Load a scene from a file and update the application state.
 
-        If filename is not provided, a file dialog is opened to select the file.
-        If a valid filename is provided, the scene is loaded from the file and added to the application state.
+        If filename is not provided, a file dialog is opened to select the
+        file.  If a valid filename is provided, the scene is loaded from the
+        file and added to the application state.
 
         Args:
             filename (str?): The name of the file to load the scene from.

src/minder3d/config.py → src/minder3d/parse_args.py

@@ -7,7 +7,7 @@
 import argparse
 
 
-def parse_config() -> argparse.Namespace:
+def parse_args() -> argparse.Namespace:
     """
     Parse command line arguments to configure the run.
     """