http://imagej.net/ImageJ2_Python_Scripts

Z_Projection.py

# @ImageJ ij
# @Dataset data
# @String(label="Projection Type",choices={"Max","Mean","Median","Min", "StdDev", "Sum"}) proj_type


from net.imagej.axis import Axes
from net.imagej.ops import Ops


def proj_method(method):
    return {
        'Max': Ops.Stats.Max,
        'Mean': Ops.Stats.Mean,
        'Median': Ops.Stats.Median,
        'Min': Ops.Stats.Min,
        'StdDev': Ops.Stats.StdDev,
        'Sum': Ops.Stats.Sum,
    }.get(method, Ops.Stats.Max)

 
def main():
 
    # Select which dimension to project
    z_dim = data.dimensionIndex(Axes.Z)

    if z_dim == -1:
        print("Z dimension not found.")
        return
 
    if data.dimension(z_dim) < 2:
        print("Z dimension has only one frame.")
        return
 
    # Write the output dimensions
    projected_dimensions = [data.dimension(d) for d in range(0, data.numDimensions()) if d != z_dim]
 
    # Create the output image
    z_projected = ij.op().create().img(projected_dimensions)
 
    # Create the op and run it
    proj_op = ij.op().op(proj_method(proj_type), data)
    ij.op().transform().project(z_projected, data, proj_op, z_dim)
 
    # Create a dataset
    z_projected = ij.dataset().create(z_projected)
 
    # Set the correct axes (is that needed ?)
    axes = [data.axis(d) for d in range(0, data.numDimensions()) if d != z_dim]
    z_projected.setAxes(axes)
 
    print(z_projected)
    ij.ui().show("z_projected", z_projected)
 
main()