python src/deep/unet/unet_trainer.py config/unet_splits/split01.ini？

[langbin2014]

nothing？why？Anyone can help me？

[microljy]

I found that there is only Class definition in src/deep/unet/unet_trainer.py. No running command. So nothing is done. There are something remained to be done src/deep/unet/unet_trainer.py. I did not have idea how to do it yet.

[langbin2014]

train部分可以参考里面的一个脚本，但是还是有问题

发自我的 iPhone

在 2017年3月12日，15:16，Junying Li notifications@github.com 写道：

I found that there is only Class definition in src/deep/unet/unet_trainer.py. No running command. So nothing is done. There are something remained to be done src/deep/unet/unet_trainer.py. I did not have idea how to do it yet.

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[microljy]

我也看到了，改了下，可以运行。O(∩_∩)O谢谢哈

[langbin2014]

你好，我是在训练的时候出现一个batch分母为零的错误，不知道你有没有碰到，你也是跑的肺结节检测的么？能否把你训练的代码发我参考一下？ 另外，这边是一个kaggle的教程你可以参考一下https://pythonprogramming.net/3d-convolutional-neural-network-machine-learning-tutorial/

发自我的 iPhone

在 2017年3月13日，10:40，Junying Li notifications@github.com 写道：

我也看到了，改了下，可以运行。O(∩_∩)O谢谢哈

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[JianqiaoAirport]

@langbin2014 我也遇到了batch分母为零的错误！发现是这样的，default.ini里面的文件路径，需要在后面加上 _ALL 才匹配，加上之后就好了！

[langbin2014]

@JianqiaoAirport 谢谢，我试试

[JianqiaoAirport]

@langbin2014 发现后面还是有各种问题搞不定，如果你调好了能不能给@我我讲一下呀？谢谢！

[galactica147]

have you guys figured out how to call src/deep/unet/unet_trainer.py config/unet_splits/split01.ini??

1. UNetTrainer.init() doesn't take a config path as a parameter so far.

2. The train() method in unet_trainer.py takes parameters 'train_splits, filenames_val, train_generator, val_generator'. How to properly set up these?

please advise. Thanks!

[galactica147]

looking at scripts/split01.sh, the training command should really be something like:

python train.py ../../config/titan_x_default.ini ../../config/split01.ini

although this seems to be in conflict with hard-coded line in params.py:

params = Params(['../../config/default.ini']+sys.argv[1:])

Really hope the author could clarify how to run a basic training procedure using the 10 subsets of data on CPU and GPU respectively...

[gzuidhof]

Hi galactica147,

It's not in conflict with the line you found in params.py, it forms a list of the default configurations and the other script arguments, and loads them in that order (so your last configuration file overwrites earlier ones).

After the DSB competition is over (less than a month now), I can share the code of that. It features a 3D segmentation network for candidate generation, which I found to work quite a bit better. It's also faster in every way (A U-net implementation that is 10x as fast).

[galactica147]

that'd be great @gzuidhof! Thanks and look forward to that

[yezifeiafei]

I met the same problem. Have this issue been solved yet？

[yezifeiafei]

@langbin2014 @JianqiaoAirport 求问如何解决这个问题？

[guyucowboy]

@JianqiaoAirport 如何修改路径,在路径中加_all阿? 谢谢阿! How can I change the path in default.ini to avoid ZeroDivisionError? How to add "_all" to path? Thanks!

[MoonBunnyZZZ]

@gzuidhof how to run Unet training process?Thank you

[MoonBunnyZZZ]

@gzuidhof 1.In Preprocessing, I run src/data_processing/create_same_spacing_data_NODULE.py, but the error seems to tell me creat many dir first, such as '1_1_1mm_slices_lung/subset0' .However, I don't know how to use the 'set of segmentations of the lungs' that you talked about.

2.When I run ./src/deep/train.py config/unet_splits/split01.ini, error occur: Loaded configurations from (in order) ['config/unet_splits/split01.ini'] Traceback (most recent call last): File "./src/deep/train.py", line 4, in from params import params as P File "/home/ubuntu/Documents/project/luna16/luna16-master/src/deep/params.py", line 95, in params = Params(['../../config/default.ini']+sys.argv[1:]) File "/home/ubuntu/Documents/project/luna16/luna16-master/src/deep/params.py", line 25, in init self.PIXELS = cf.getint('dataset','pixels') File "/home/ubuntu/anaconda2/lib/python2.7/ConfigParser.py", line 359, in getint return self._get(section, int, option) File "/home/ubuntu/anaconda2/lib/python2.7/ConfigParser.py", line 356, in _get return conv(self.get(section, option)) File "/home/ubuntu/anaconda2/lib/python2.7/ConfigParser.py", line 618, in get raise NoOptionError(option, section) ConfigParser.NoOptionError: No option 'pixels' in section: 'dataset'

[Arno-Wen]

@microljy 请问lung_masks的数据在哪下呢，我运行他的第一个文件create_same_spacing_data_NODULE.py就出错。谢谢！