Comments (5)
Thank you. This solves the issue!
from tutorials.
Hi, it seems to be working for me. I'm using the master branch of MONAI, which required another bug fix (Project-MONAI/MONAI#1440), but I didn't see any problems regarding the CacheDataset
.
Would you be able to paste the error? And also the output of monai.config.print_debug_info()
?
from tutorials.
Hi, thank you for the fast response! Sorry for the formatting, it looks awful here. I hope it is readable although not optimal.
This the error output:
RuntimeError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/monai/transforms/utils.py in apply_transform(transform, data, map_items)
360 return [transform(item) for item in data]
--> 361 return transform(data)
362 except Exception as e:
9 frames
RuntimeError: can not find suitable reader for this file: /tmp/tmpy56jd7rb/MedNIST/Hand/001061.jpeg.
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/monai/transforms/utils.py in apply_transform(transform, data, map_items)
361 return transform(data)
362 except Exception as e:
--> 363 raise RuntimeError(f"applying transform {transform}") from e
364
365
RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7f614b16d4a8>`
I'm running it on colab. Here is the debug info:
================================
Printing MONAI config...
MONAI version: 0.4.0
Numpy version: 1.19.5
Pytorch version: 1.7.0+cu101
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 0563a4467fa602feca92d91c7f47261868d171a1
Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: 3.0.2
scikit-image version: 0.16.2
Pillow version: 7.0.0
Tensorboard version: 2.4.0
gdown version: 3.6.4
TorchVision version: 0.8.1+cu101
ITK version: NOT INSTALLED or UNKNOWN VERSION.
tqdm version: 4.56.0
lmdb version: 0.99
psutil version: 5.4.8
For details about installing the optional dependencies, please visit:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
================================
Printing system config...
System: Linux
Linux version: Ubuntu 18.04.5 LTS
Platform: Linux-4.19.112+-x86_64-with-Ubuntu-18.04-bionic
Processor: x86_64
Machine: x86_64
Python version: 3.6.9
Process name: python3
Command: ['/usr/bin/python3', '-m', 'ipykernel_launcher', '-f', '/root/.local/share/jupyter/runtime/kernel-e3bb8ea8-c3d8-4786-82c8-12db0bdb7b51.json']
Open files: []
Num physical CPUs: 1
Num logical CPUs: 2
Num usable CPUs: 2
CPU usage (%): [7.2, 6.7]
CPU freq. (MHz): UNKNOWN for given OS
Load avg. in last 1, 5, 15 mins (%): UNKNOWN for given OS
Disk usage (%): 47.7
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 12.7
Available memory (GB): 11.8
Used memory (GB): 0.7
Printing GPU config...
Num GPUs: 1
Has CUDA: True
CUDA version: 10.1
cuDNN enabled: True
cuDNN version: 7603
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_70', 'sm_75']
Info for GPU: 0
Name: Tesla T4
Is integrated: False
Is multi GPU board: False
Multi processor count: 40
Total memory (GB): 14.7
Cached memory (GB): 0.0
Allocated memory (GB): 0.0
CUDA capability (maj.min): 7.5`
from tutorials.
Hi, you're absolutely right. I think the problem relates to some changes caused by updates to how we read our images.
In colab, I modified the first line to be: %pip install -q "monai-weekly[pillow, tqdm]"
, and using the weekly release of MONAI solved that problem. You may need to restart the runtime after the pip install.
from tutorials.
Related update PR: Project-MONAI/MONAI#1448.
from tutorials.
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from tutorials.