AttributeError with deeptrack.Combine in cell counting

[Minh-Khang Le]

Hi. I'm trying to reproduce the code of 6_cell_counting.ipynb
When I run this cell:

normalization = dt.NormalizeMinMax()

blurred_validation_mask = validation_mask + png_to_mask 
normalized_validation_image = validation_image + normalization
validation_dataset = dt.Combine([normalized_validation_image, blurred_validation_mask]) 
blurred_test_mask = test_mask + png_to_mask
normalized_test_image = test_image + normalization
test_dataset = dt.Combine([normalized_test_image, blurred_test_mask])

I get the AttributeError:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Input In [13], in <cell line: 5>()
      3 blurred_validation_mask = validation_mask + png_to_mask 
      4 normalized_validation_image = validation_image + normalization
----> 5 validation_dataset = dt.Combine([normalized_validation_image, blurred_validation_mask]) 
      6 blurred_test_mask = test_mask + png_to_mask
      7 normalized_test_image = test_image + normalization

File ~/ideas/DeepTrack/venv/lib/python3.8/site-packages/deeptrack/features.py:999, in Combine.__init__(self, features, **kwargs)
    998 def __init__(self, features: List[Feature], **kwargs):
--> 999     self.features = [self.add_feature(f) for f in features]
   1000     super().__init__(**kwargs)

File ~/ideas/DeepTrack/venv/lib/python3.8/site-packages/deeptrack/features.py:999, in <listcomp>(.0)
    998 def __init__(self, features: List[Feature], **kwargs):
--> 999     self.features = [self.add_feature(f) for f in features]
   1000     super().__init__(**kwargs)

File ~/ideas/DeepTrack/venv/lib/python3.8/site-packages/deeptrack/features.py:274, in Feature.add_feature(self, feature)
    272 """Adds a feature to the dependecy graph."""
    273 feature.add_child(self)
--> 274 self.add_dependency(feature)
    275 return feature

File ~/ideas/DeepTrack/venv/lib/python3.8/site-packages/deeptrack/backend/core.py:160, in DeepTrackNode.add_dependency(self, other)
    159 def add_dependency(self, other):
--> 160     self.dependencies.add(other)
    162     return self

File ~/ideas/DeepTrack/venv/lib/python3.8/site-packages/deeptrack/features.py:460, in Feature.__getattr__(self, key)
    458         raise AttributeError
    459 else:
--> 460     raise AttributeError

AttributeError: 

Can you help me to define what is going on?
Thank you very much.

[BenjaminMidtvedt]

Hi! It seems like you are using a new version of deeptrack with an old version of the notebook. Either pull the latest version of the notebook from github or downgrade deeptrack to 0.x.x (0.11.5 should be fine)

[Minh-Khang Le]

Thank you! That works perfectly.