extract

The extract command measures pixel counts in selected regions of one or more GONet images.

Extraction can run in two modes:

  • Interactive mode, which opens the extraction GUI.

  • Direct mode, which performs extraction immediately from shape parameters supplied on the command line.

For the conceptual tool guide, see extraction tool guide.

Usage

GONet_Wizard extract [-h] [--blue] [--green] [--red]
                     [--shape {circle,rectangle,annulus,interactive}]
                     [--center CENTER] [--radius RADIUS] [--sides SIDES]
                     [--inner_radius INNER_RADIUS]
                     [--outer_radius OUTER_RADIUS]
                     [--angles ANGLES] [--output OUTPUT]
                     [--output_type {json,csv}] [--debug] [--port PORT]
                     [filenames ...]

Arguments

filenames

One or more GONet image files to extract.

The command supports files, folders, wildcards, and comma-separated lists.

Launch Behavior

The extract command has two different fallback behaviors, depending on how much information is provided.

Command Form Fallback

If the command is invoked without the required command-line inputs, GONet Wizard opens the Extract GUI form.

For example:

GONet_Wizard extract

This follows the same command-form fallback described in common CLI patterns.

Interactive Extraction Fallback

If input files are provided, but the command is not given enough information to perform a complete direct extraction, GONet Wizard launches the interactive extraction app.

For example:

GONet_Wizard extract image.jpg

This opens the interactive extraction app because files were provided, but no direct extraction shape and geometry were specified.

The same applies when the requested workflow is explicitly interactive:

GONet_Wizard extract image.jpg --shape interactive

Direct extraction only runs immediately when a non-interactive shape is selected and all parameters required by that shape are provided.

Channel Options

--blue

Extract the blue channel.

--green

Extract the green channel.

--red

Extract the red channel.

If no channel flags are provided, all channels are extracted.

Shape Options

--shape {circle,rectangle,annulus,interactive}

Select the extraction shape.

If the shape is interactive or no shape is provided, the interactive extraction GUI opens.

Circle Extraction

Circular extraction requires:

  • --shape circle

  • --center X,Y

  • --radius RADIUS

Example:

GONet_Wizard extract image.jpg --shape circle --center 1000,800 --radius 50

Rectangle Extraction

Rectangular extraction requires:

  • --shape rectangle

  • --center X,Y

  • --sides WIDTH,HEIGHT

Example:

GONet_Wizard extract image.jpg --shape rectangle --center 1000,800 --sides 300,400

Annulus Extraction

Annular extraction requires:

  • --shape annulus

  • --center X,Y

  • --inner_radius INNER_RADIUS

  • --outer_radius OUTER_RADIUS

Example:

GONet_Wizard extract image.jpg --shape annulus --center 1000,800 --inner_radius 40 --outer_radius 80

Interactive Extraction

Interactive extraction opens the dedicated extraction GUI.

Examples:

GONet_Wizard extract image.jpg
GONet_Wizard extract image.jpg --shape interactive

Angle Limits

--angles ANGLES

Optional angular range as start_angle,end_angle in degrees.

Angles are measured from the positive x axis and increase counter-clockwise.

Example:

GONet_Wizard extract image.jpg --shape circle --center 1000,800 --radius 100 --angles=-45,45

Output Options

--output OUTPUT

Output filename.

If omitted, a default filename based on the extraction shape is generated.

--output_type {json,csv}

Output format.

JSON is the default output type.

Examples:

GONet_Wizard extract image.jpg --shape circle --center 1000,800 --radius 50 --output counts.json

GONet_Wizard extract image.jpg --shape circle --center 1000,800 --radius 50 --output counts.csv --output_type csv

Interactive Runtime Options

--debug

Run the extraction GUI in debug mode.

--port PORT

Port for the extraction GUI Dash server.

These options only matter when the interactive extraction GUI is launched.

Examples

Extract all channels from a circular region:

GONet_Wizard extract image.jpg --shape circle --center 1000,800 --radius 50

Extract only the red channel:

GONet_Wizard extract image.jpg --red --shape circle --center 1000,800 --radius 50

Extract all matching files to CSV:

GONet_Wizard extract *.jpg --shape annulus --center 1000,800 --inner_radius 40 --outer_radius 80 --output annulus_counts.csv --output_type csv

Launch the interactive extraction GUI on a folder:

GONet_Wizard extract /path/to/images --shape interactive

GUI Equivalent

The graphical equivalent is Extract GUI guide.