[bug]: Graincrop __str__ method fails when skeleton is None

[SylviaWhittle]

Checklist

• Run using the main branch to check if the issue persists. Instructions on how to do this can be found here.
• Find the offending file in the output. If processing halts, re-run analysis with topostats --core 1 process.
• Describe the bug.
• Include the configuration file.
• Copy of the log-file from running with topostats --log-level debug <command>.
• The exact command that failed. This is what you typed at the command line, including any options.
• TopoStats version, this is reported by topostats --version
• Operating System and Python Version

Describe the bug

I encountered a badly processed grain in minicircle.spm from a bad config, where a skeleton is not produced.

This resulted in a crash when trying to print(grain_crop).

Copy of the log-file from running with topostats --log-level debug <command>

<class 'NoneType'>
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[24], [line 31](vscode-notebook-cell:?execution_count=24&line=31)
     29 skeleton = grain_crop.skeleton
     30 print(type(skeleton))
---> [31](vscode-notebook-cell:?execution_count=24&line=31) print(f"Grain {grain_index}: {grain_crop}")

File ~/src/TopoStats/topostats/classes.py:186, in GrainCrop.__str__(self)
    174 def __str__(self) -> str:
    175     """
    176     Representation function for useful statistics for the class.
    177 
   (...)
    181         Set of formatted statistics on matched branches.
    182     """
    183     return (
    184         f"filename : {self.filename}\n"
    185         f"image shape : {self.image.shape}\n"
--> [186](https://file+.vscode-resource.vscode-cdn.net/Users/sylvi/src/TopoStats/dev-scripts/__marimo__/session/~/src/TopoStats/topostats/classes.py:186)         f"skeleton shape : {self.skeleton.shape}\n"
    187         f"mask shape : {self.mask.shape}\n"
    188         f"padding : {self.padding}\n"
    189         f"thresholds : {self.thresholds}\n"
    190         f"threshold method : {self.threshold_method}\n"
    191         f"threshold index : {self.threshold_idx}\n"
    192         f"bounding box coords : {self.bbox}\n"
    193         f"pixel to nm scaling : {self.pixel_to_nm_scaling}\n"
    194         f"number of nodes : {len(self.nodes)}"
    195     )

AttributeError: 'NoneType' object has no attribute 'shape'

Include the configuration file

N/A

To Reproduce

No response

TopoStats Version

Git main branch

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

No response

[SylviaWhittle]

It also happens with number of nodes:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[5], [line 31](vscode-notebook-cell:?execution_count=5&line=31)
     29 skeleton = grain_crop.skeleton
     30 print(type(skeleton))
---> [31](vscode-notebook-cell:?execution_count=5&line=31) print(f"Grain {grain_index}: {grain_crop}")

File ~/src/TopoStats/topostats/classes.py:194, in GrainCrop.__str__(self)
    174 def __str__(self) -> str:
    175     """
    176     Representation function for useful statistics for the class.
    177 
   (...)
    181         Set of formatted statistics on matched branches.
    182     """
    183     return (
    184         f"filename : {self.filename}\n"
    185         f"image shape : {self.image.shape}\n"
    186         f"skeleton shape : {self.skeleton.shape}\n"
    187         f"mask shape : {self.mask.shape}\n"
    188         f"padding : {self.padding}\n"
    189         f"thresholds : {self.thresholds}\n"
    190         f"threshold method : {self.threshold_method}\n"
    191         f"threshold index : {self.threshold_idx}\n"
    192         f"bounding box coords : {self.bbox}\n"
    193         f"pixel to nm scaling : {self.pixel_to_nm_scaling}\n"
--> [194](https://file+.vscode-resource.vscode-cdn.net/Users/sylvi/src/TopoStats/branch-scripts/~/src/TopoStats/topostats/classes.py:194)         f"number of nodes : {len(self.nodes)}"
    195     )

TypeError: object of type 'NoneType' has no len()