error when I try to run ./train_model.sh dna 0

[sll513]

loaded all the data to /data/ folder. and run ./train_model.sh dna 0, got the following error. does anyone know the reason? Thanks,

Using existing train/test split. DEBUG: Initializing new model! Model fnet.nn_modules.fnet_nn_3d.Net(**{}) iter: 0 gpu: [0]

0%| | 0/1 [00:00<?, ?it/s] 100%|██████████| 1/1 [00:18<00:00, 18.49s/it] {'buffer_size': 1, 'npatches': 1200000} Traceback (most recent call last): File "train_model.py", line 147, in main() File "train_model.py", line 119, in main args, n_remaining_iterations, validation=True File "train_model.py", line 22, in get_dataloader ds = str_to_class(args.dataset_class)(dataset_kwargs) File "/local_disk0/fnet/pytorch_fnet-master/fnet/data/czidataset.py", line 13, in init super().init(kwargs) File "/local_disk0/fnet/pytorch_fnet-master/fnet/data/fnetdataset.py", line 45, in init self.df = pd.read_csv(self.path_csv) File "/databricks/python/lib/python3.6/site-packages/pandas/io/parsers.py", line 678, in parser_f return _read(filepath_or_buffer, kwds) File "/databricks/python/lib/python3.6/site-packages/pandas/io/parsers.py", line 424, in _read filepath_or_buffer, encoding, compression) File "/databricks/python/lib/python3.6/site-packages/pandas/io/common.py", line 218, in get_filepath_or_buffer raise ValueError(msg.format(_type=type(filepath_or_buffer))) ValueError: Invalid file path or buffer object type: <class 'NoneType'>

[sll513]

all data is under pytorch_fnet-master/data

3500000427_100X_20170120_F05_P27.czi alpha_tubulin beta_actin csvs desmoplakin dic_lamin_b1 EM_low.tif fibrillarin lamin_b1 MBP_low.tif membrane_caax_63x myosin_iib sec61_beta st6gal1 timelapse_wt2_s2 tom20 zo1

[gregjohnso]

hi @sll513 I fixed a bug in the download script. Please re-download and make sure you are using our release_1 branch as well.

[sll513]

Thanks. tried release_1. But get new error while running ./scripts/test_run. sh (which was fine if I used master)

• BUFFER_SIZE=1
• N_ITER=8
• RUN_DIR=saved_models/TEST
• PATH_DATASET_CSV=data/csvs/test_run.csv
• GPU_IDS=0 +++ dirname ./scripts/test_run.sh ++ cd ./scripts ++ pwd
• cd /local_disk0/fnet/pytorch_fnet-release_1/scripts/..
• rm -r saved_models/TEST rm: cannot remove 'saved_models/TEST': No such file or directory
• python train_model.py --n_iter 8 --path_dataset_csv data/csvs/test_run.csv --path_dataset_val_csv data/csvs/test_run.csv --interval_save 6 --buffer_size 1 --path_run_dir saved_models/TEST --gpu_ids 0 Traceback (most recent call last): File "train_model.py", line 2, in import fnet.data File "/local_disk0/fnet/pytorch_fnet-release_1/fnet/data/init.py", line 1, in from fnet.data.czidataset import CziDataset File "/local_disk0/fnet/pytorch_fnet-release_1/fnet/data/czidataset.py", line 2, in from fnet.data.czireader import CziReader File "/local_disk0/fnet/pytorch_fnet-release_1/fnet/data/czireader.py", line 1, in import aicsimage.io as io File "/local_disk0/fnet/pytorch_fnet-release_1/aicsimage/io/init.py", line 1, in from . import cziReader File "/local_disk0/fnet/pytorch_fnet-release_1/aicsimage/io/cziReader.py", line 1, in from . import czifile File "/local_disk0/fnet/pytorch_fnet-release_1/aicsimage/io/czifile.py", line 119, in from tifffile.tifffile import FileHandle, decode_lzw, lazyattr, stripnull ImportError: cannot import name 'decode_lzw'

[gregjohnso]

@sll513 Did you use the release_1 conda environment?

[sll513]

I just installed all the needed libs on python 3.6, anaconda3.

Then download release_1.zip and unzip it.

Then I just run the test.

It was ok with master.zip before.

Thanks,

-Lingling

Sent from my iPhone

On Dec 18, 2018, at 12:18 PM, Gregory Johnson notifications@github.com wrote:

@sll513 Did you use the release_1 conda environment?

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