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Unable to install snap.yml environment because of depreciated Python3.6 #1

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nielverb opened this issue Aug 20, 2024 · 0 comments
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@nielverb
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I am unable to perform the steps described in the readme, because (mainly Tensorflow) cannot be installed anymore for python version 3.6 since it's end of life.

I tried installing all packages with python 3.10, which worked, but then the nodule_detector_example.ipynb file runs into the following error:

model_path_name='snap_nodule_dector_wts.h5'
# load retinanet model
model = models.load_model(model_path_name, backbone_name='resnet50')
model = models.convert_model(model)
labels_to_names = {0.0: 'N'}
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[2], [line 3](vscode-notebook-cell:?execution_count=2&line=3)
      [1](vscode-notebook-cell:?execution_count=2&line=1) model_path_name='snap_nodule_dector_wts.h5'
      [2](vscode-notebook-cell:?execution_count=2&line=2) # load retinanet model
----> [3](vscode-notebook-cell:?execution_count=2&line=3) model = models.load_model(model_path_name, backbone_name='resnet50')
      [4](vscode-notebook-cell:?execution_count=2&line=4) model = models.convert_model(model)
      [5](vscode-notebook-cell:?execution_count=2&line=5) labels_to_names = {0.0: 'N'}

File ~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:83, in load_model(filepath, backbone_name)
     [67](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:67) """ Loads a retinanet model using the correct custom objects.
     [68](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:68) 
     [69](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:69) Args
   (...)
     [80](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:80)     ValueError: In case of an invalid savefile.
     [81](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:81) """
     [82](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:82) import keras.models
---> [83](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:83) return keras.models.load_model(filepath, custom_objects=backbone(backbone_name).custom_objects)

File ~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:53, in backbone(backbone_name)
     [50](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:50) """ Returns a backbone object for the given backbone.
     [51](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:51) """
     [52](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:52) if 'resnet' in backbone_name:
---> [53](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:53)     from .resnet import ResNetBackbone as b
     [54](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/models/__init__.py:54) elif 'mobilenet' in backbone_name:
...
   (...)
     [30](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/utils/anchors.py:30)         scales  : List of scales to use per location in a feature map.
     [31](https://file+.vscode-resource.vscode-cdn.net/home/niel/OneDrive/07_projectjes/SNAP-master/nodule_detection/~/OneDrive/07_projectjes/SNAP-master/nodule_detection/keras_retinanet/utils/anchors.py:31)     """

ImportError: dynamic module does not define module export function (PyInit_compute_overlap)

It might point to a C module that is compiled for the older python version. I can't solve this myself. So the question is, could you maybe update the SNAP package so that it works with a supported python version?

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