Some issues with `landmark_atrium.py`

[keiyamamo]

Hi @hkjeldsberg

I tried to use landmark_atrium.py, but faced some issues. I found some fixes, but not for all of them.

The first problem is parsing the input file:

morphMan/src/morphman/landmark_atrium.py

Line 316 in aeeaa5b

return dict(input_path=args.input_path, resampling_step=args.resampling_step)

args do not have input_path, and this should be fixed as:

return dict(input_path=args.ifile, resampling_step=args.resampling_step) 

Secondly, I faced an issue with:

morphMan/src/morphman/landmark_atrium.py

Line 166 in aeeaa5b

line = extract_single_line(laa_centerline, 0, start_id=id_start, end_id=id_stop)

Changing the end_id=id_stop to end_id=None seemed to avoid the error.

However, I still get an error with:

morphMan/src/morphman/landmark_atrium.py

Line 170 in aeeaa5b

line = compute_splined_centerline(line, nknots=10, isline=True)

The error is as follows:

File “/morphMan/src/morphman/landmark_atrium.py", line 170, in separate_left_atrium_and_appendage
    line = compute_splined_centerline(line, nknots=10, isline=True)
  File “/morphMan/src/morphman/common/centerline_operations.py", line 932, in compute_splined_centerline
    misr = get_point_data_array(radiusArrayName, line)
  File “/morphMan/src/morphman/common/vtk_wrapper.py", line 328, in get_point_data_array
    data_array = line.GetPointData().GetArray(array_name).GetTuple1
AttributeError: 'NoneType' object has no attribute 'GetTuple1'

At this point, I stopped investigating further since it was not straightforward to identify the problem. Could you please look into this?

Best,
Kei