YaleDHLab / pix-plot

A WebGL viewer for UMAP or TSNE-clustered images

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Tensorflow Issue? terminating due to uncaught exception of type google::protobuf::FatalException:

writingafterthedisaster opened this issue · comments

Am on an M1 Mac, and upon installing and running pix-plot, I receive the error:

0%| | 0/428 [00:00<?, ?it/s]2024-02-14 12:40:29.940019: I tensorflow/core/grappler/optimizers/custom_graph_optimizer_registry.cc:117] Plugin optimizer for device_type GPU is enabled. [libprotobuf FATAL google/protobuf/message_lite.cc:353] CHECK failed: target + size == res: libc++abi: terminating due to uncaught exception of type google::protobuf::FatalException: CHECK failed: target + size == res: /Users/jeff/miniforge3/envs/pixplot/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

Any ideas what this could be?

I downgraded to tensorflow 2.13.0 and it runs, but won't create a manifest. After analyzing the images, I get the error:
Traceback (most recent call last): File "/Users/jeff/miniforge3/envs/pixplot/bin/pixplot", line 33, in <module> sys.exit(load_entry_point('pixplot==0.0.113', 'console_scripts', 'pixplot')()) File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/pixplot-0.0.113-py3.9.egg/pixplot/pixplot.py", line 1375, in parse process_images(**config) File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/pixplot-0.0.113-py3.9.egg/pixplot/pixplot.py", line 159, in process_images get_manifest(**kwargs) File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/pixplot-0.0.113-py3.9.egg/pixplot/pixplot.py", line 417, in get_manifest layouts = get_layouts(**kwargs) File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/pixplot-0.0.113-py3.9.egg/pixplot/pixplot.py", line 557, in get_layouts 'layout': get_rasterfairy_layout(umap=umap, **kwargs), File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/pixplot-0.0.113-py3.9.egg/pixplot/pixplot.py", line 776, in get_rasterfairy_layout pos = rasterfairy.transformPointCloud2D(umap)[0] File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/yale_dhlab_rasterfairy-1.0.3-py3.9.egg/rasterfairy/rasterfairy.py", line 134, in transformPointCloud2D File "/Users/jeff/miniforge3/envs/pixplot/lib/python3.9/site-packages/numpy/__init__.py", line 305, in __getattr__ raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.floatwas a deprecated alias for the builtinfloat. To avoid this error in existing code, use floatby itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, usenp.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

Help is very much appreciated.