ValueError: Found array with 1 sample(s) (shape=(1, 2)) while a minimum of 2 is required by AgglomerativeClustering.

[timtsm]

Describe the bug
I'm trying to process the attached image. I get the error in the title (ValueError: Found array with 1 sample(s) (shape=(1, 2)) while a minimum of 2 is required by AgglomerativeClustering.) in the analyzing notehead boxes stage, and no output file. There are a few warnings beforehand so I am including the whole output. This is on a macbook pro (2022, M2).

Input Image

Full Traceback

2025-01-26 18:13:39 Extracting staffline and symbols
2025-01-26 18:13:39.606156 [W:onnxruntime:, coreml_execution_provider.cc:115 GetCapability] CoreMLExecutionProvider::GetCapability, number of partitions supported by CoreML: 86 number of nodes in the graph: 1577 number of nodes supported by CoreML: 102
2766 1328
Context leak detected, msgtracer returned -1
Context leak detected, msgtracer returned -1
2025-01-26 18:15:23 Extracting layers of different symbols
2025-01-26 18:15:23.490085 [W:onnxruntime:, coreml_execution_provider.cc:115 GetCapability] CoreMLExecutionProvider::GetCapability, number of partitions supported by CoreML: 94 number of nodes in the graph: 1619 number of nodes supported by CoreML: 107
2766 1328
Context leak detected, msgtracer returned -1
Context leak detected, msgtracer returned -1
2025-01-26 18:18:21 Extracting stafflines
/Users/tim/src/oemer/ve/lib/python3.12/site-packages/numpy/_core/fromnumeric.py:3596: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/Users/tim/src/oemer/ve/lib/python3.12/site-packages/numpy/_core/_methods.py:138: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)
70 404 4
405 739 4
740 1074 4
1075 1409 4
1410 1744 4
1745 2079 4
2080 2414 4
2415 2749 4
Centers of staff parts at the same row not aligned (Th: 0.1): [0.01716697 0.01716652 0.12034679 0.01715335 0.01735288 0.01711578
 0.01709273 0.01729857]
2025-01-26 18:18:22 Extracting noteheads
2025-01-26 18:18:22 Analyzing notehead bboxes
Traceback (most recent call last):
  File "/Users/tim/src/oemer/ve/bin/oemer", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/oemer/ete.py", line 287, in main
    mxl_path = extract(args)
               ^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/oemer/ete.py", line 184, in extract
    notes = note_extract()
            ^^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/oemer/notehead_extraction.py", line 440, in extract
    merged_box = merge_nearby_bbox(bboxes, distance=unit_size*max_whole_note_width_factor, y_factor=y_dist_factor)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/oemer/bbox.py", line 42, in merge_nearby_bbox
    model.fit(centers)
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/sklearn/base.py", line 1389, in wrapper
    return fit_method(estimator, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/sklearn/cluster/_agglomerative.py", line 988, in fit
    X = validate_data(self, X, ensure_min_samples=2)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/sklearn/utils/validation.py", line 2944, in validate_data
    out = check_array(X, input_name="X", **check_params)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/tim/src/oemer/ve/lib/python3.12/site-packages/sklearn/utils/validation.py", line 1130, in check_array
    raise ValueError(
ValueError: Found array with 1 sample(s) (shape=(1, 2)) while a minimum of 2 is required by AgglomerativeClustering.

Command You Execute
oemer -d ~/Downloads/ppmusic.png