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Cli test

Merged Cli test
cli_test into main
Merged s204159 requested to merge cli_test into main
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qim3d/utils/cli.py
+ 115
− 40
@@ -8,39 +8,82 @@ from qim3d.utils import image_preview
@@ -8,39 +8,82 @@ from qim3d.utils import image_preview
def main():
def main():
parser = argparse.ArgumentParser(description='Qim3d command-line interface.')
parser = argparse.ArgumentParser(description="Qim3d command-line interface.")
subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
# GUIs
# GUIs
gui_parser = subparsers.add_parser('gui', help = 'Graphical User Interfaces.')
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(
gui_parser.add_argument('--iso3d', action='store_true', help='Run iso3d.')
"--data-explorer", action="store_true", help="Run data explorer."
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("--iso3d", action="store_true", help="Run iso3d.")
gui_parser.add_argument('--host', default='0.0.0.0', help='Desired host.')
gui_parser.add_argument(
gui_parser.add_argument('--platform', action='store_true', help='Use QIM platform address')
"--annotation-tool", action="store_true", help="Run annotation tool."
gui_parser.add_argument('--no-browser', action='store_true', help='Do not launch browser.')
)
gui_parser.add_argument(
# K3D
"--local-thickness", action="store_true", help="Run local thickness tool."
viz_parser = subparsers.add_parser('viz', help = 'Volumetric visualization.')
)
viz_parser.add_argument('--source', default=False, help='Path to the image file')
gui_parser.add_argument("--host", default="0.0.0.0", help="Desired host.")
viz_parser.add_argument('--destination', default='k3d.html', help='Path to save html file.')
gui_parser.add_argument(
viz_parser.add_argument('--no-browser', action='store_true', help='Do not launch browser.')
"--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
preview_parser = subparsers.add_parser('preview', help= 'Preview of the image in CLI')
preview_parser = subparsers.add_parser(
preview_parser.add_argument('filename',type = str, metavar = 'FILENAME', help = 'Path to image that will be displayed')
"preview", help="Preview of the image in CLI"
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(
preview_parser.add_argument('--resolution',type = int, metavar = 'RES', default = 80, help = 'Resolution of displayed image. Defaults to 80.')
"filename",
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.')
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()
args = parser.parse_args()
if args.subcommand == 'gui':
if args.subcommand == "gui":
arghost = args.host
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.data_explorer:
if args.platform:
if args.platform:
data_explorer.run_interface(arghost)
data_explorer.run_interface(arghost)
@@ -53,42 +96,74 @@ def main():
@@ -53,42 +96,74 @@ def main():
else:
else:
interface = iso3d.Interface()
interface = iso3d.Interface()
interface.launch(inbrowser=inbrowser)
interface.launch(inbrowser=inbrowser)
elif args.annotation_tool:
elif args.annotation_tool:
if args.platform:
if args.platform:
annotation_tool.run_interface(arghost)
annotation_tool.run_interface(arghost)
else:
else:
interface = annotation_tool.Interface()
interface = annotation_tool.Interface()
interface.launch(inbrowser=inbrowser)
interface.launch(inbrowser=inbrowser)
elif args.local_thickness:
elif args.local_thickness:
if args.platform:
if args.platform:
local_thickness.run_interface(arghost)
local_thickness.run_interface(arghost)
else:
else:
interface = local_thickness.Interface()
interface = local_thickness.Interface()
interface.launch(inbrowser=inbrowser)
interface.launch(inbrowser=inbrowser)
elif args.subcommand == "viz":
if args.subcommand == "viz":
if not args.source:
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
return
# Load the data
# Load the data
print (f"Loading data from {args.source}")
print(f"Loading data from {args.source}")
volume = qim3d.io.load(str(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
# Make k3d plot
print ("\nGenerating k3d plot...")
print("\nGenerating k3d plot...")
qim3d.viz.vol(volume, show=False, save=str(args.destination))
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:
if not args.no_browser:
print("Opening in default browser...")
print("Opening in default browser...")
webbrowser.open_new_tab(args.destination)
webbrowser.open_new_tab(args.destination)
if args.subcommand == 'preview':
elif args.subcommand == "preview":
image = DataLoader().load(args.filename)
image = DataLoader().load(args.filename)
image_preview(image, image_width = args.resolution, axis = args.axis, slice = args.slice, relative_intensity= args.absolute_values)
image_preview(
image,
if __name__ == '__main__':
image_width=args.resolution,
main()
axis=args.axis,
\ No newline at end of file
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()