Closed BirgerMoell closed 5 years ago
jpatrickpark
commented
5 years ago Hi,
It seems that src/heatmaps/run_producer.py was importing tensorflow even though it was not necessary. I removed this unnecessary import statement so it should work now. Please pull the changes.
mammoguy
commented
4 years ago Hi,
It seems that I'm experiencing the same issue as above. I can't get the run.sh to work with the sample data. Below is the output with error: unable to open the image
Also attached is the environment created in conda.
Thank you, Ioannis NanWu_env.txt
(NanWu) ioannis@ioannis-ML:~/Documents/models/errors/breast_cancer_classifier-master_NanWu$ ./run.sh
Stage 1: Crop Mammograms
/home/ioannis/anaconda3/envs/NanWu/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Stage 2: Extract Centers
/home/ioannis/anaconda3/envs/NanWu/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Stage 3: Generate Heatmaps
/home/ioannis/anaconda3/envs/NanWu/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "src/heatmaps/run_producer.py", line 376, in float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
100%|██████████████████████████████████████████████████████████████████████████████████| 4/4 [00:19<00:00, 4.88s/it]
Stage 4b: Run Classifier (Image+Heatmaps)
/home/ioannis/anaconda3/envs/NanWu/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
0%| | 0/4 [00:00<?, ?it/s]
Traceback (most recent call last):
File "src/modeling/run_model.py", line 238, in
jpatrickpark
commented
4 years ago @mammoguy, your stage 4B is failing because earlier stage 3 failed (the same error as #25 occurred). Heatmap files were not generated, therefore heatmap classifiers are not working.
According to @zphang in #25, our recommendation is to use Pytorch 0.4.1 and torchvision 0.2.0.
mammoguy
commented
4 years ago Hi @jpatrickpark
Thank you for your quick reply
@mammoguy, your stage 4B is failing because earlier stage 3 failed (the same error as #25 occurred). Heatmap files were not generated, therefore heatmap classifiers are not working.
According to @zphang in #25, our recommendation is to use Pytorch 0.4.1 and torchvision 0.2.0.
I am already using Pytorch 0.4.1 and torchvision 0.2.0. as you can see from the attached txt file in my original post.
What do you suggest I do next?
Thanks
Hi!
Thank you for a great project.
I'm trying to run the project on a K80 on Google Cloud using their provided Pytorch image.
The model fails when trying to create the heatmats with the following error.
I've tried creating the missing directories and reading through the source code.
Any help would be greatly appreciated. Stage 1: Crop Mammograms Error: the directory to save cropped images already exists. Stage 2: Extract Centers Stage 3: Generate Heatmaps Traceback (most recent call last): File "src/heatmaps/run_producer.py", line 29, in
import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'
Stage 4a: Run Classifier (Image)
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:19<00:00, 5.10s/it]
Stage 4b: Run Classifier (Image+Heatmaps)
0%| | 0/4 [00:00<?, ?it/s]
Traceback (most recent call last):
File "src/modeling/run_model.py", line 195, in
main()
File "src/modeling/run_model.py", line 190, in main
parameters=parameters,
File "src/modeling/run_model.py", line 148, in load_run_save
predictions = run_model(model, exam_list, parameters)
File "src/modeling/run_model.py", line 80, in run_model
horizontal_flip=datum["horizontal_flip"],
File "/home/birgermoell/chexnet/breast_cancer_classifier/src/data_loading/loading.py", line 72, in load_heatmaps
benign_heatmap = load_image(benign_heatmap_path, view, horizontal_flip)
File "/home/birgermoell/chexnet/breast_cancer_classifier/src/data_loading/loading.py", line 59, in load_image
image = read_image_mat(image_path)
File "/home/birgermoell/chexnet/breast_cancer_classifier/src/utilities/reading_images.py", line 37, in read_image_mat
data = h5py.File(file_name, 'r')
File "/opt/anaconda3/lib/python3.7/site-packages/h5py/_hl/files.py", line 312, in init
fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
File "/opt/anaconda3/lib/python3.7/site-packages/h5py/_hl/files.py", line 142, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 78, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = 'sample_output/heatmaps/heatmap_benign/0_L_CC.hdf5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)