Merge branch 'cli_test' into 'main'

Cli test

See merge request !93

qim3d/__init__.py

@@ -11,6 +11,6 @@ from . import models
 from . import processing
 
 
-__version__ = "0.3.2"
+__version__ = "0.3.5"
 examples = io.ImgExamples()
 io.logger.set_level_info()

qim3d/utils/cli.py

@@ -8,39 +8,82 @@ from qim3d.utils import image_preview
 
 
 def main():
-    parser = argparse.ArgumentParser(description='Qim3d command-line interface.')
-    subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
+    parser = argparse.ArgumentParser(description="Qim3d command-line interface.")
+    subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
 
     # GUIs
-    gui_parser = subparsers.add_parser('gui', help = 'Graphical User Interfaces.')
-
-    gui_parser.add_argument('--data-explorer', action='store_true', help='Run data explorer.')
-    gui_parser.add_argument('--iso3d', action='store_true', help='Run iso3d.')
-    gui_parser.add_argument('--annotation-tool', action='store_true', help='Run annotation tool.')
-    gui_parser.add_argument('--local-thickness', action='store_true', help='Run local thickness tool.')
-    gui_parser.add_argument('--host', default='0.0.0.0', help='Desired host.')
-    gui_parser.add_argument('--platform', action='store_true', help='Use QIM platform address')
-    gui_parser.add_argument('--no-browser', action='store_true', help='Do not launch browser.')
-
-    # K3D 
-    viz_parser = subparsers.add_parser('viz', help = 'Volumetric visualization.')
-    viz_parser.add_argument('--source', default=False, help='Path to the image file')
-    viz_parser.add_argument('--destination', default='k3d.html', help='Path to save html file.')
-    viz_parser.add_argument('--no-browser', action='store_true', help='Do not launch browser.')
+    gui_parser = subparsers.add_parser("gui", help="Graphical User Interfaces.")
+
+    gui_parser.add_argument(
+        "--data-explorer", action="store_true", help="Run data explorer."
+    )
+    gui_parser.add_argument("--iso3d", action="store_true", help="Run iso3d.")
+    gui_parser.add_argument(
+        "--annotation-tool", action="store_true", help="Run annotation tool."
+    )
+    gui_parser.add_argument(
+        "--local-thickness", action="store_true", help="Run local thickness tool."
+    )
+    gui_parser.add_argument("--host", default="0.0.0.0", help="Desired host.")
+    gui_parser.add_argument(
+        "--platform", action="store_true", help="Use QIM platform address"
+    )
+    gui_parser.add_argument(
+        "--no-browser", action="store_true", help="Do not launch browser."
+    )
+
+    # K3D
+    viz_parser = subparsers.add_parser("viz", help="Volumetric visualization.")
+    viz_parser.add_argument("--source", default=False, help="Path to the image file")
+    viz_parser.add_argument(
+        "--destination", default="k3d.html", help="Path to save html file."
+    )
+    viz_parser.add_argument(
+        "--no-browser", action="store_true", help="Do not launch browser."
+    )
 
     # Preview
-    preview_parser = subparsers.add_parser('preview', help= 'Preview of the image in CLI')
-    preview_parser.add_argument('filename',type = str, metavar = 'FILENAME', help = 'Path to image that will be displayed')
-    preview_parser.add_argument('--slice',type = int, metavar ='S', default = None, help = 'Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.' )
-    preview_parser.add_argument('--axis', type = int, metavar = 'AX', default=0, help = 'Specifies from which axis will be the slice taken. Defaults to 0.')
-    preview_parser.add_argument('--resolution',type = int, metavar = 'RES', default = 80, help = 'Resolution of displayed image. Defaults to 80.')
-    preview_parser.add_argument('--absolute_values', action='store_false', help = 'By default set the maximum value to be 255 so the contrast is strong. This turns it off.')
+    preview_parser = subparsers.add_parser(
+        "preview", help="Preview of the image in CLI"
+    )
+    preview_parser.add_argument(
+        "filename",
+        type=str,
+        metavar="FILENAME",
+        help="Path to image that will be displayed",
+    )
+    preview_parser.add_argument(
+        "--slice",
+        type=int,
+        metavar="S",
+        default=None,
+        help="Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.",
+    )
+    preview_parser.add_argument(
+        "--axis",
+        type=int,
+        metavar="AX",
+        default=0,
+        help="Specifies from which axis will be the slice taken. Defaults to 0.",
+    )
+    preview_parser.add_argument(
+        "--resolution",
+        type=int,
+        metavar="RES",
+        default=80,
+        help="Resolution of displayed image. Defaults to 80.",
+    )
+    preview_parser.add_argument(
+        "--absolute_values",
+        action="store_false",
+        help="By default set the maximum value to be 255 so the contrast is strong. This turns it off.",
+    )
 
     args = parser.parse_args()
 
-    if args.subcommand == 'gui':
+    if args.subcommand == "gui":
         arghost = args.host
-        inbrowser = not args.no_browser # Should automatically open in browser
+        inbrowser = not args.no_browser  # Should automatically open in browser
         if args.data_explorer:
             if args.platform:
                 data_explorer.run_interface(arghost)
@@ -53,42 +96,74 @@ def main():
             else:
                 interface = iso3d.Interface()
                 interface.launch(inbrowser=inbrowser)
-        
+
         elif args.annotation_tool:
             if args.platform:
                 annotation_tool.run_interface(arghost)
             else:
                 interface = annotation_tool.Interface()
-                interface.launch(inbrowser=inbrowser)        
+                interface.launch(inbrowser=inbrowser)
         elif args.local_thickness:
             if args.platform:
                 local_thickness.run_interface(arghost)
             else:
                 interface = local_thickness.Interface()
                 interface.launch(inbrowser=inbrowser)
-
-
-    if args.subcommand == "viz":
+    elif args.subcommand == "viz":
         if not args.source:
-            print ("Please specify a source file using the argument --source")
+            print("Please specify a source file using the argument --source")
             return
         # Load the data
-        print (f"Loading data from {args.source}")
+        print(f"Loading data from {args.source}")
         volume = qim3d.io.load(str(args.source))
-        print (f"Done, volume shape: {volume.shape}")
+        print(f"Done, volume shape: {volume.shape}")
 
         # Make k3d plot
-        print ("\nGenerating k3d plot...")
+        print("\nGenerating k3d plot...")
         qim3d.viz.vol(volume, show=False, save=str(args.destination))
-        print (f"Done, plot available at <{args.destination}>")
+        print(f"Done, plot available at <{args.destination}>")
 
         if not args.no_browser:
             print("Opening in default browser...")
             webbrowser.open_new_tab(args.destination)
 
-    if args.subcommand == 'preview':
+    elif args.subcommand == "preview":
         image = DataLoader().load(args.filename)
-        image_preview(image, image_width = args.resolution, axis =  args.axis, slice = args.slice, relative_intensity= args.absolute_values)
-        
-if __name__ == '__main__':
-    main()
\ No newline at end of file
+        image_preview(
+            image,
+            image_width=args.resolution,
+            axis=args.axis,
+            slice=args.slice,
+            relative_intensity=args.absolute_values,
+        )
+
+    elif args.subcommand is None:
+        welcome_text = (
+            "\n"
+            "         _          _____     __ \n"
+            "  ____ _(_)___ ___ |__  /____/ / \n"
+            " / __ `/ / __ `__ \ /_ </ __  /  \n"
+            "/ /_/ / / / / / / /__/ / /_/ /   \n"
+            "\__, /_/_/ /_/ /_/____/\__,_/    \n"
+            "  /_/                            \n"
+            "\n"
+            "--- Welcome to qim3d command-line interface ---\n"
+            "qim3d is a Python package for 3D image processing and visualization.\n"
+            "For more information, please visit: https://platform.qim.dk/qim3d/\n"
+            f"Current version of qim3d: {qim3d.__version__}\n"
+            " \n"
+            "The qim3d command-line interface provides the following subcommands:\n"
+            "- gui: Graphical User Interfaces\n"
+            "- viz: Volumetric visualizations of volumes\n"
+            "- preview: Preview of an volume directly in the terminal\n"
+            " \n"
+            "For more information on each subcommand, type 'qim3d <subcommand> --help'.\n"
+        )
+        print(welcome_text)
+        print("--- Help page for qim3d command-line interface shown below ---\n")
+        parser.print_help()
+        print("\n")
+
+
+if __name__ == "__main__":
+    main()