jacobkie / 2018dsb Goto Github PK

label_mask = remove_small_holes(label_mask)
label_mask = basin(label_mask, wall)
label_mask = remove_small_holes(label_mask)

Are these function working on instance labels or semantic labels
@jacobkie

when I'm trying to run predict_auto.py in the folder script_final, there occurs an error:

from keras import Model, optimizers,losses, activations, models
ImportError: cannot import name 'Model'

It may due to the version of keras I installed do not fit the project. But the project didn't provide the required package version(maybe I do not find?)😭。 I tried to search in the Internet but still cannot solve the problem...
So could you please tell me what's the version need to run the project? Thank you so much!

I am trying to use your pre-trained weights to run predict_auto.py, but it complains that there is no hdf5 file in the cache folder. If I run merge_model_weight.sh in said folder first, then it will load the merged h5 file. But, this process takes a very long time (~30min??) in 25 stages, i.e. the terminal output from the first stage looks like
0/25 2 (205, 694, 3) 704
19-02-22 23:58:35 INFO| loading weights form /home/ubuntu/git_repos/2018DSB/cache/UnetRCNN_180410-221747/71_0.4155.hdf5

Is this what I should be doing and expect to see?

Can you share links to weights you have trained?

when run 'python3 train_ext.py', meet some issues, is my environment not correct?
can you help to provide your running environment? by running the 'pip3 list'.

`
Epoch 1/100
Traceback (most recent call last):
File "train_ext.py", line 62, in
train_1s()
File "train_ext.py", line 59, in train_1s
model.train_generator(tr_ms1, val_ms1, 1e-3, 100, 'all')
File "/2th-DSB2018/script_final/model_rcnn_weight.py", line 495, in train_generator
use_multiprocessing=False,
File "/usr/local/lib/python3.5/dist-packages/keras/legacy/interfaces.py", line 91, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.5/dist-packages/keras/engine/training.py", line 2145, in fit_generator
generator_output = next(output_generator)
File "/usr/local/lib/python3.5/dist-packages/keras/utils/data_utils.py", line 770, in get
six.reraise(value.class, value, value.traceback)
File "/usr/lib/python3/dist-packages/six.py", line 686, in reraise
raise value
File "/usr/local/lib/python3.5/dist-packages/keras/utils/data_utils.py", line 635, in _data_generator_task
generator_output = next(self._generator)
File "/medical_data/yunhai/2th-DSB2018/script_final/model_ms1.py", line 42, in generator_1s_v11
image, mask = next(gen)
File "train_ext.py", line 34, in train_generator
image, mask = next(gen)
File "/2th-DSB2018/script_final/generator.py", line 64, in data_generator_multi
zoom_range = config.ZOOM_RANGE)
File "/2th-DSB2018/script_final/preprocess.py", line 198, in affine_transform_batch
xt = scipy.ndimage.affine_transform(x, matrix, order=1, cval=-512)
File "/usr/local/lib/python3.5/dist-packages/scipy/ndimage/interpolation.py", line 449, in affine_transform
raise RuntimeError('affine matrix has wrong number of rows')
RuntimeError: affine matrix has wrong number of rows

`