diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py index 6b23ca80badad8f65d6745c02b5e132bb1b82585..c3d2e84b2f66b3954717eaaaa8fb97d3ee31cd86 100644 --- a/extensions/chaeo/workflows.py +++ b/extensions/chaeo/workflows.py @@ -78,33 +78,19 @@ def export_patches_from_multichannel_zstack( ) ti.click('export_3d_patches') - # if export_2d_patches: - # files = export_patches_from_zstack( - # Path(where_output) / '2d_patches', - # stack.get_one_channel_data(patches_channel), - # zmask_meta, - # prefix=fstem, - # draw_bounding_box=False, - # rescale_clip=0.0, - # make_3d=False, - # focus_metric='max_sobel', - # ) - # ti.click('export_2d_patches') - if export_2d_patches: files = export_multichannel_patches_from_zstack( - Path(where_output) / '2d_patches_chlorophyl_contour', + Path(where_output) / '2d_patches', stack, zmask_meta, prefix=fstem, - draw_bounding_box=False, rescale_clip=0.0, make_3d=False, focus_metric='max_sobel', ch_white=4, ch_rgb_overlay=(3, None, None), - draw_contour=True, - contour_channel=1, + draw_bounding_box=True, + bounding_box_channel=1, overlay_gain=(0.1, 1.0, 1.0) ) ti.click('export_2d_patches')