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figure_1_dataset workflow fails #64

@pgarrison

Description

@pgarrison

I get the following error message when I run pdm run python run_all_manuscript_workflows.py --only figure_1_dataset.

Traceback (most recent call last):
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/.venv/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 3209, in ndim
    return a.ndim
AttributeError: 'list' object has no attribute 'ndim'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/nuc_morph_analysis/utilities/workflow_runner.py", line 38, in _runjob
    job()
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/run_all_manuscript_workflows.py", line 8, in figure_1_dataset
    import nuc_morph_analysis.analyses.dataset_images_for_figures.figure_1_workflow
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/nuc_morph_analysis/analyses/dataset_images_for_figures/figure_1_workflow.py", line 9, in <module>
    import nuc_morph_analysis.analyses.dataset_images_for_figures.figure_dataset_formation_and_breakdown
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/nuc_morph_analysis/analyses/dataset_images_for_figures/figure_dataset_formation_and_breakdown.py", line 35, in <module>
    df_fmb = figure_helper.process_images_and_add_to_dataframe(df_fmb, df, seg_img_list, raw_img_list)
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/nuc_morph_analysis/analyses/dataset_images_for_figures/figure_helper.py", line 1011, in process_images_and_add_to_dataframe
    df_fmb.loc[timepoint, f"seg_{yx_zx_zy}_contours"] = [contour_and_color_list]
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/.venv/lib/python3.9/site-packages/pandas/core/indexing.py", line 818, in __setitem__
    iloc._setitem_with_indexer(indexer, value, self.name)
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/.venv/lib/python3.9/site-packages/pandas/core/indexing.py", line 1795, in _setitem_with_indexer
    self._setitem_with_indexer_split_path(indexer, value, name)
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/.venv/lib/python3.9/site-packages/pandas/core/indexing.py", line 1833, in _setitem_with_indexer_split_path
    elif np.ndim(value) == 2:
  File "/home/philip.garrison/workspace/aics/nuc-morph-analysis/.venv/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 3211, in ndim
    return asarray(a).ndim
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 3 dimensions. The detected shape was (1, 1, 2) + inhomogeneous part.

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