environment and import fix

sara-nl · Jan 11, 2022 · 0b2148f · 0b2148f
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diff --git a/environment.yml b/environment.yml
@@ -1,158 +1,153 @@
-name: pytorch1.7
+name: py38
 channels:
-  - simpleitk
-  - pytorch-nightly
-  - conda-forge
+  - pytorch
   - defaults
+  - conda-forge
 dependencies:
   - _libgcc_mutex=0.1=main
-  - _pytorch_select=0.2=gpu_0
-  - absl-py=0.9.0=py38h32f6830_1
+  - _openmp_mutex=4.5=1_gnu
+  - absl-py=0.15.0=pyhd3eb1b0_0
+  - aiohttp=3.8.1=py38h7f8727e_0
+  - aiosignal=1.2.0=pyhd3eb1b0_0
+  - async-timeout=4.0.1=pyhd3eb1b0_0
+  - attrs=21.2.0=pyhd3eb1b0_0
   - blas=1.0=mkl
-  - blinker=1.4=py_1
-  - brotlipy=0.7.0=py38h1e0a361_1000
+  - blinker=1.4=py38h06a4308_0
+  - brotli=1.0.9=he6710b0_2
+  - brotlipy=0.7.0=py38h27cfd23_1003
   - bzip2=1.0.8=h7b6447c_0
-  - c-ares=1.16.1=h516909a_2
-  - ca-certificates=2021.1.19=h06a4308_0
-  - cachetools=4.1.1=py_0
-  - certifi=2020.12.5=py38h06a4308_0
-  - cffi=1.14.1=py38he30daa8_0
-  - chardet=3.0.4=py38h32f6830_1006
-  - click=7.1.2=pyh9f0ad1d_0
-  - cryptography=3.0=py38h766eaa4_0
-  - cudatoolkit=11.0.221=h6bb024c_0
-  - cycler=0.10.0=py_2
-  - dbus=1.13.16=hb2f20db_0
-  - einops=0.3.0=py_0
-  - expat=2.2.9=he6710b0_2
-  - ffmpeg=4.2.2=h20bf706_0
-  - filelock=3.0.12=pyhd3eb1b0_1
-  - fontconfig=2.13.0=h9420a91_0
-  - freetype=2.10.4=h5ab3b9f_0
-  - future=0.18.2=py38h32f6830_1
-  - gdcm=2.8.9=py38h138f8cb_1
-  - glib=2.65.0=h3eb4bd4_0
-  - gmp=6.1.2=h6c8ec71_1
-  - gnutls=3.6.5=h71b1129_1002
-  - google-auth=1.20.1=py_0
-  - google-auth-oauthlib=0.4.1=py_2
-  - grpcio=1.31.0=py38h2c89da0_0
-  - gst-plugins-base=1.14.0=hbbd80ab_1
-  - gstreamer=1.14.0=hb31296c_0
-  - h5py=2.10.0=py38hd6299e0_1
-  - hdf5=1.10.6=hb1b8bf9_0
+  - c-ares=1.17.1=h27cfd23_0
+  - ca-certificates=2021.10.26=h06a4308_2
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cachetools=4.2.2=pyhd3eb1b0_0
+  - certifi=2021.10.8=py38h06a4308_0
+  - cffi=1.14.6=py38h400218f_0
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - click=8.0.3=pyhd3eb1b0_0
+  - cryptography=3.4.8=py38hd23ed53_0
+  - cudatoolkit=11.3.1=h2bc3f7f_2
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - dataclasses=0.8=pyh6d0b6a4_7
+  - dbus=1.13.18=hb2f20db_0
+  - einops=0.3.2=pyhd8ed1ab_0
+  - expat=2.4.1=h2531618_2
+  - ffmpeg=4.3=hf484d3e_0
+  - filelock=3.4.2=pyhd8ed1ab_1
+  - fontconfig=2.13.1=h6c09931_0
+  - fonttools=4.25.0=pyhd3eb1b0_0
+  - freetype=2.11.0=h70c0345_0
+  - frozenlist=1.2.0=py38h7f8727e_0
+  - fsspec=2021.10.1=pyhd3eb1b0_0
+  - future=0.18.2=py38_1
+  - giflib=5.2.1=h7b6447c_0
+  - glib=2.69.1=h5202010_0
+  - gmp=6.2.1=h2531618_2
+  - gnutls=3.6.15=he1e5248_0
+  - google-auth=1.33.0=pyhd3eb1b0_0
+  - google-auth-oauthlib=0.4.4=pyhd3eb1b0_0
+  - grpcio=1.42.0=py38hce63b2e_0
+  - gst-plugins-base=1.14.0=h8213a91_2
+  - gstreamer=1.14.0=h28cd5cc_2
+  - h5py=3.6.0=py38ha0f2276_0
+  - hdf5=1.10.6=nompi_h3c11f04_101
   - icu=58.2=he6710b0_3
-  - idna=2.10=pyh9f0ad1d_0
-  - importlib-metadata=1.7.0=py38h32f6830_0
-  - intel-openmp=2020.1=217
-  - jpeg=9b=h024ee3a_2
-  - json-c=0.13.1=h1bed415_0
-  - kiwisolver=1.2.0=py38hbf85e49_0
+  - idna=3.3=pyhd3eb1b0_0
+  - importlib-metadata=4.8.2=py38h06a4308_0
+  - intel-openmp=2021.4.0=h06a4308_3561
+  - jpeg=9d=h7f8727e_0
+  - kiwisolver=1.3.1=py38h2531618_0
   - lame=3.100=h7b6447c_0
-  - lcms2=2.11=h396b838_0
-  - ld_impl_linux-64=2.33.1=h53a641e_7
-  - libedit=3.1.20181209=hc058e9b_0
-  - libffi=3.3=he6710b0_1
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - libjpeg-turbo=2.0.5=h516909a_0
-  - libopus=1.3.1=h7b6447c_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.35.1=h7274673_9
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=9.3.0=h5101ec6_17
+  - libgfortran-ng=7.5.0=ha8ba4b0_17
+  - libgfortran4=7.5.0=ha8ba4b0_17
+  - libgomp=9.3.0=h5101ec6_17
+  - libiconv=1.15=h63c8f33_5
+  - libidn2=2.3.2=h7f8727e_0
   - libpng=1.6.37=hbc83047_0
-  - libprotobuf=3.13.0=h8b12597_0
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - libtiff=4.1.0=h2733197_1
-  - libuuid=1.0.3=h1bed415_2
+  - libprotobuf=3.19.1=h4ff587b_0
+  - libstdcxx-ng=9.3.0=hd4cf53a_17
+  - libtasn1=4.16.0=h27cfd23_0
+  - libtiff=4.2.0=h85742a9_0
+  - libunistring=0.9.10=h27cfd23_0
+  - libuuid=1.0.3=h7f8727e_2
   - libuv=1.40.0=h7b6447c_0
-  - libvpx=1.7.0=h439df22_0
+  - libwebp=1.2.0=h89dd481_0
+  - libwebp-base=1.2.0=h27cfd23_0
   - libxcb=1.14=h7b6447c_0
-  - libxml2=2.9.10=he19cac6_1
-  - lz4-c=1.9.2=he6710b0_0
-  - markdown=3.2.2=py_0
-  - matplotlib=3.1.3=py38_0
-  - matplotlib-base=3.1.3=py38hef1b27d_0
-  - mkl=2020.1=217
-  - mkl-service=2.3.0=py38he904b0f_0
-  - mkl_fft=1.1.0=py38h23d657b_0
-  - mkl_random=1.1.1=py38h0573a6f_0
-  - ncurses=6.2=he6710b0_1
-  - nettle=3.4.1=hbb512f6_0
-  - ninja=1.9.0=py38hfd86e86_0
-  - numpy=1.18.1=py38h4f9e942_0
-  - numpy-base=1.18.1=py38hde5b4d6_1
-  - oauthlib=3.0.1=py_0
-  - olefile=0.46=py_0
-  - openh264=2.1.0=hd408876_0
-  - openjpeg=2.3.1=h981e76c_3
-  - openssl=1.1.1i=h27cfd23_0
-  - packaging=20.4=py_0
-  - pcre=8.44=he6710b0_0
-  - pillow=8.0.1=py38he98fc37_0
-  - protobuf=3.13.0=py38h950e882_0
-  - pyasn1=0.4.8=py_0
-  - pyasn1-modules=0.2.7=py_0
-  - pycparser=2.20=pyh9f0ad1d_2
-  - pydicom=2.1.0=pyhd3deb0d_0
-  - pyjwt=1.7.1=py_0
+  - libxml2=2.9.12=h03d6c58_0
+  - lz4-c=1.9.3=h295c915_1
+  - markdown=3.3.4=py38h06a4308_0
+  - matplotlib=3.5.0=py38h06a4308_0
+  - matplotlib-base=3.5.0=py38h3ed280b_0
+  - mkl=2021.4.0=h06a4308_640
+  - mkl-service=2.4.0=py38h7f8727e_0
+  - mkl_fft=1.3.1=py38hd3c417c_0
+  - mkl_random=1.2.2=py38h51133e4_0
+  - monai=0.8.0=pyhd8ed1ab_1
+  - multidict=5.2.0=py38h7f8727e_2
+  - munkres=1.1.4=py_0
+  - ncurses=6.3=h7f8727e_2
+  - nettle=3.7.3=hbbd107a_1
+  - numpy=1.21.2=py38h20f2e39_0
+  - numpy-base=1.21.2=py38h79a1101_0
+  - oauthlib=3.1.1=pyhd3eb1b0_0
+  - olefile=0.46=pyhd3eb1b0_0
+  - openh264=2.1.1=h4ff587b_0
+  - openssl=1.1.1l=h7f8727e_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pcre=8.45=h295c915_0
+  - pillow=8.4.0=py38h5aabda8_0
+  - pip=21.2.4=py38h06a4308_0
+  - protobuf=3.19.1=py38h295c915_0
+  - pyasn1=0.4.8=pyhd3eb1b0_0
+  - pyasn1-modules=0.2.8=py_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pydicom=2.2.2=pyh6c4a22f_0
+  - pyjwt=2.1.0=py38h06a4308_0
   - pynrrd=0.4.2=pyh95af2a2_0
-  - pyopenssl=19.1.0=py_1
-  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pyopenssl=21.0.0=pyhd3eb1b0_1
+  - pyparsing=3.0.4=pyhd3eb1b0_0
   - pyqt=5.9.2=py38h05f1152_4
-  - pysocks=1.7.1=py38h32f6830_1
-  - python=3.8.3=hcff3b4d_0
-  - python-dateutil=2.8.1=py_0
-  - python-lmdb=0.98=py38he6710b0_0
-  - python_abi=3.8=1_cp38
-  - pytorch=1.8.0.dev20210122=py3.8_cuda11.0.221_cudnn8.0.5_0
-  - pyyaml=5.3.1=py38h1e0a361_0
+  - pysocks=1.7.1=py38h06a4308_0
+  - python=3.8.12=h12debd9_0
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python-lmdb=0.99=py38h709712a_0
+  - python_abi=3.8=2_cp38
+  - pytorch=1.10.1=py3.8_cuda11.3_cudnn8.2.0_0
+  - pytorch-lightning=1.2.10=pyhd8ed1ab_0
+  - pytorch-mutex=1.0=cuda
+  - pyyaml=6.0=py38h7f8727e_1
   - qt=5.9.7=h5867ecd_1
-  - readline=8.0=h7b6447c_0
-  - requests=2.24.0=pyh9f0ad1d_0
-  - requests-oauthlib=1.3.0=pyh9f0ad1d_0
-  - rsa=4.6=pyh9f0ad1d_0
-  - setuptools=51.0.0=py38h06a4308_2
-  - simpleitk=2.0rc3=py38hf484d3e_0
+  - readline=8.1.2=h7f8727e_0
+  - requests=2.27.1=pyhd3eb1b0_0
+  - requests-oauthlib=1.3.0=py_0
+  - rsa=4.7.2=pyhd3eb1b0_1
+  - scipy=1.7.3=py38hc147768_0
+  - setuptools=58.0.4=py38h06a4308_0
   - sip=4.19.13=py38he6710b0_0
-  - six=1.15.0=py_0
-  - sqlite=3.31.1=h62c20be_1
-  - tensorboard=2.3.0=pyh4dce500_0
-  - tensorboard-plugin-wit=1.6.0=pyh9f0ad1d_0
-  - tk=8.6.8=hbc83047_0
-  - torchvision=0.9.0.dev20210122=py38_cu110
-  - tornado=6.0.4=py38h1e0a361_1
-  - tqdm=4.48.2=pyh9f0ad1d_0
-  - typing_extensions=3.7.4.3=py_0
-  - urllib3=1.25.10=py_0
-  - werkzeug=1.0.1=pyh9f0ad1d_0
-  - wheel=0.36.2=pyhd3eb1b0_0
-  - x264=1!157.20191217=h7b6447c_0
+  - six=1.16.0=pyhd3eb1b0_0
+  - sqlite=3.37.0=hc218d9a_0
+  - tensorboard=2.4.0=pyhc547734_0
+  - tensorboard-plugin-wit=1.6.0=py_0
+  - tk=8.6.11=h1ccaba5_0
+  - torchaudio=0.10.1=py38_cu113
+  - torchmetrics=0.6.2=pyhd8ed1ab_0
+  - torchvision=0.11.2=py38_cu113
+  - tornado=6.1=py38h27cfd23_0
+  - tqdm=4.62.3=pyhd3eb1b0_1
+  - typing-extensions=3.10.0.2=hd3eb1b0_0
+  - typing_extensions=3.10.0.2=pyh06a4308_0
+  - urllib3=1.26.7=pyhd3eb1b0_0
+  - werkzeug=2.0.2=pyhd3eb1b0_0
+  - wheel=0.37.1=pyhd3eb1b0_0
   - xz=5.2.5=h7b6447c_0
-  - yaml=0.2.5=h516909a_0
-  - zipp=3.1.0=py_0
-  - zlib=1.2.11=h7b6447c_3
-  - zstd=1.4.4=h0b5b093_3
-  - pip:
-    - aiohttp==3.7.3
-    - async-timeout==3.0.1
-    - attrs==20.3.0
-    - dataclasses==0.6
-    - fairscale==0.1.5
-    - fsspec==0.8.4
-    - itk==5.1.1
-    - itk-core==5.1.1
-    - itk-filtering==5.1.1
-    - itk-io==5.1.1
-    - itk-numerics==5.1.1
-    - itk-registration==5.1.1
-    - itk-segmentation==5.1.1
-    - monai==0.3.0
-    - multidict==5.1.0
-    - nibabel==3.1.1
-    - omegaconf==2.0.5
-    - onnxruntime==1.6.0
-    - pip==21.0.1
-    - python-graphviz==0.16
-    - pytorch-lightning==1.2.0.dev0
-    - torchviz==0.0.1
-    - yarl==1.6.3
-prefix: /home/robertsc/.conda/envs/pytorch1.7
-
+  - yaml=0.2.5=h7b6447c_0
+  - yarl=1.6.3=py38h27cfd23_0
+  - zipp=3.7.0=pyhd3eb1b0_0
+  - zlib=1.2.11=h7f8727e_4
+  - zstd=1.4.9=haebb681_0
+prefix: /home/robertsc/.conda/envs/py38
diff --git a/pixel-model/layers.py → pixel_model/layers.py b/pixel-model/layers.py → pixel_model/layers.py
diff --git a/pixel-model/pixelcnn.py → pixel_model/pixelcnn.py b/pixel-model/pixelcnn.py → pixel_model/pixelcnn.py
@@ -17,10 +17,10 @@
 from pytorch_lightning.metrics import Accuracy, Precision, Recall
 from tqdm import tqdm
 
-from layers import FixupCausalResBlock, PreActFixupCausalResBlock, input_to_stack, stack_to_output, GatedResBlock
+from pixel_model.layers import FixupCausalResBlock, PreActFixupCausalResBlock, input_to_stack, stack_to_output, GatedResBlock
+from pixel_model.train_helpers import idx_to_one_hot, bits_per_dim, mixup_data, mixup_criterion
 from utils.logging_helpers import sub_metric_log_dict
 from utils.argparse_helpers import booltype
-from train_helpers import idx_to_one_hot, bits_per_dim, mixup_data, mixup_criterion
 
 
 

diff --git a/pixel-model/pixelsnail.py → pixel_model/pixelsnail.py b/pixel-model/pixelsnail.py → pixel_model/pixelsnail.py
@@ -17,10 +17,10 @@
 from pytorch_lightning.metrics import Accuracy, Precision, Recall
 from tqdm import tqdm
 
-from layers import CausalAttentionPixelBlock, PreActFixupCausalResBlock, input_to_stack, stack_to_output, GatedResBlock
+from pixel_model.layers import CausalAttentionPixelBlock, PreActFixupCausalResBlock, input_to_stack, stack_to_output, GatedResBlock
+from pixel_model.train_helpers import idx_to_one_hot, bits_per_dim, mixup_data, mixup_criterion
 from utils.logging_helpers import sub_metric_log_dict
 from utils.argparse_helpers import booltype
-from train_helpers import idx_to_one_hot, bits_per_dim, mixup_data, mixup_criterion
 
 
 

diff --git a/pixel-model/sample_embeddings.py → pixel_model/sample_embeddings.py b/pixel-model/sample_embeddings.py → pixel_model/sample_embeddings.py
@@ -12,8 +12,8 @@
 from tqdm import tqdm
 from filelock import FileLock
 
-from pixelcnn import PixelCNN
-from pixelsnail import PixelSNAIL
+from pixel_model.pixelcnn import PixelCNN
+from pixel_model.pixelsnail import PixelSNAIL
 
 GPU = torch.device('cuda')
 

diff --git a/pixel-model/test.py → pixel_model/test.py b/pixel-model/test.py → pixel_model/test.py
@@ -2,7 +2,7 @@
 import matplotlib.pyplot as plt
 from torchvision.utils import make_grid
 
-from model import CausalConv3dAdd
+from pixel_model.layers import CausalConv3dAdd
 
 if __name__ == '__main__':
     inp = torch.zeros((1, 3, 20,20,20))

diff --git a/pixel-model/train.py → pixel_model/train.py b/pixel-model/train.py → pixel_model/train.py
@@ -4,8 +4,8 @@
 import torch
 import pytorch_lightning as pl
 
-from pixelcnn import PixelCNN
-from pixelsnail import PixelSNAIL
+from pixel_model.pixelcnn import PixelCNN
+from pixel_model.pixelsnail import PixelSNAIL
 from utils.load_lmdb_dataset import LMDBDataModule
 
 def parse_arguments():

diff --git a/pixel-model/train_helpers.py → pixel_model/train_helpers.py b/pixel-model/train_helpers.py → pixel_model/train_helpers.py
diff --git a/vqvae/calc_ssim_from_checkpoint.py b/vqvae/calc_ssim_from_checkpoint.py
@@ -10,7 +10,7 @@
 from einops import rearrange
 import torch.nn as nn
 
-from model import VQVAE
+from vqvae.model import VQVAE
 from utils import CTDataModule
 from metrics.evaluate import SSIM3DSlices
 

diff --git a/vqvae/decode_embeddings.py b/vqvae/decode_embeddings.py
@@ -8,7 +8,7 @@
 import torch.nn.functional as F
 from torch.utils.data import DataLoader
 
-from model import VQVAE
+from vqvae.model import VQVAE
 from utils import CTScanDataset, DepthPadAndCrop
 
 def inverse_softplus(x):

diff --git a/vqvae/extract_embeddings.py b/vqvae/extract_embeddings.py
@@ -7,7 +7,7 @@
 import numpy as np
 from tqdm import tqdm
 
-from model import VQVAE
+from vqvae.model import VQVAE
 from utils import CTDataModule
 
 

diff --git a/vqvae/layers.py b/vqvae/layers.py
@@ -8,7 +8,7 @@
 import torch.nn.functional as F
 from torch import nn
 
-from evonorm import EvoNorm3DS0
+from vqvae.evonorm import EvoNorm3DS0
 
 
 class EvonormResBlock(nn.Module):

diff --git a/vqvae/model.py b/vqvae/model.py
@@ -8,7 +8,7 @@
 from torch import nn
 from torch.distributions.normal import Normal
 
-from layers import Encoder, Decoder, FixupResBlock, PreActFixupResBlock, EvonormResBlock, Encoder2
+from vqvae.layers import Encoder, Decoder, FixupResBlock, PreActFixupResBlock, EvonormResBlock, Encoder2
 from utils import ExtractCenterCylinder
 from metrics.distribution import Logistic, mixture_nll_loss, generic_nll_loss
 from metrics.evaluate import nmse, psnr, SSIM3DSlices