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tibuch
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Merge pull request #13 from juglab/merger
v0.1.17
2 parents e8ef4c0 + 90db96c commit 89dc8ec

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‎README.md‎

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@@ -6,7 +6,7 @@ Build Python package:
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`python setup.py bdist_wheel`
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Build singularity recipe:
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`neurodocker generate singularity -b nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04 -p apt --copy /home/tibuch/Gitrepos/FourierImageTransformer/dist/fourier_image_transformers-0.1.16-py3-none-any.whl /fourier_image_transformers-0.1.16-py3-none-any.whl --miniconda create_env=fit conda_install='python=3.7 astra-toolbox pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch -c astra-toolbox/label/dev' pip_install='/fourier_image_transformers-0.1.16-py3-none-any.whl' activate=true --entrypoint "/neurodocker/startup.sh python" > v0.1.16.Singularity`
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`neurodocker generate singularity -b nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04 -p apt --copy /home/tibuch/Gitrepos/FourierImageTransformer/dist/fourier_image_transformers-0.1.17-py3-none-any.whl /fourier_image_transformers-0.1.17-py3-none-any.whl --miniconda create_env=fit conda_install='python=3.7 astra-toolbox pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch -c astra-toolbox/label/dev' pip_install='/fourier_image_transformers-0.1.17-py3-none-any.whl' activate=true --entrypoint "/neurodocker/startup.sh python" > v0.1.17.Singularity`
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Build singularity container:
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`sudo singularity build fit_v0.1.16.simg v0.1.16.Singularity`
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`sudo singularity build fit_v0.1.17.simg v0.1.17.Singularity`

‎fit/modules/TRecTransformerModule.py‎

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@@ -229,11 +229,10 @@ def validation_epoch_end(self, outputs):
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phi_loss = [d['phi_loss'] for d in outputs]
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mean_val_mse = torch.mean(torch.stack(val_mse))
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mean_val_psnr = torch.mean(torch.stack(val_psnr))
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mean_bin_mse = torch.mean(torch.stack(bin_mse))
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if self.bin_count > self.hparams.bin_factor_cd and mean_val_mse < (
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self.hparams.alpha * mean_bin_mse) and self.bin_factor > 1:
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bin_factor_threshold = torch.mean(torch.stack(bin_mse)) * self.bin_factor
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if self.bin_count > self.hparams.bin_factor_cd and mean_val_mse < bin_factor_threshold and self.bin_factor > 1:
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self.bin_count = 0
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self.bin_factor = max(1, self.bin_factor - 1)
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self.bin_factor = max(1, self.bin_factor // 2)
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self.register_buffer('mask', psfft(self.bin_factor, pixel_res=self.hparams.img_shape).to(self.device))
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print('Reduced bin_factor to {}.'.format(self.bin_factor))
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@@ -245,7 +244,7 @@ def validation_epoch_end(self, outputs):
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self.log('Train/avg_val_loss', torch.mean(torch.stack(val_loss)), logger=True, on_epoch=True)
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self.log('Train/avg_val_mse', mean_val_mse, logger=True, on_epoch=True)
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self.log('Train/avg_val_psnr', mean_val_psnr, logger=True, on_epoch=True)
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self.log('Train/avg_bin_mse', mean_bin_mse, logger=True, on_epoch=True)
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self.log('Train/avg_bin_mse', bin_factor_threshold, logger=True, on_epoch=True)
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self.log('Train/avg_val_amp_loss', torch.mean(torch.stack(amp_loss)), logger=True, on_epoch=True)
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self.log('Train/avg_val_phi_loss', torch.mean(torch.stack(phi_loss)), logger=True, on_epoch=True)
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‎fit/version.py‎

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__version__ = '0.1.16'
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__version__ = '0.1.17'

‎singularity/v0.1.17.Singularity‎

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# Generated by: Neurodocker version 0.7.0
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# Latest release: Neurodocker version 0.7.0
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# Timestamp: 2021/01/26 06:27:03 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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#
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# https://github.com/ReproNim/neurodocker
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Bootstrap: docker
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From: nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04
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%post
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su - root
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
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apt-utils \
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bzip2 \
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ca-certificates \
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curl \
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locales \
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unzip
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apt-get clean
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rm -rf /var/lib/apt/lists/*
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sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
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dpkg-reconfigure --frontend=noninteractive locales
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update-locale LANG="en_US.UTF-8"
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chmod 777 /opt && chmod a+s /opt
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mkdir -p /neurodocker
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if [ ! -f "$ND_ENTRYPOINT" ]; then
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echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
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echo 'set -e' >> "$ND_ENTRYPOINT"
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echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
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echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
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fi
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chmod -R 777 /neurodocker && chmod a+s /neurodocker
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export PATH="/opt/miniconda-latest/bin:$PATH"
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echo "Downloading Miniconda installer ..."
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conda_installer="/tmp/miniconda.sh"
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curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash "$conda_installer" -b -p /opt/miniconda-latest
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rm -f "$conda_installer"
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conda update -yq -nbase conda
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conda config --system --prepend channels conda-forge
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conda config --system --set auto_update_conda false
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conda config --system --set show_channel_urls true
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sync && conda clean -y --all && sync
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conda create -y -q --name fit
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conda install -y -q --name fit \
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"python=3.7" \
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"astra-toolbox" \
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"pytorch" \
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"torchvision" \
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"torchaudio" \
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"cudatoolkit=10.2" \
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"-c" \
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"pytorch" \
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"-c" \
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"astra-toolbox/label/dev"
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sync && conda clean -y --all && sync
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bash -c "source activate fit
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pip install --no-cache-dir \
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"/fourier_image_transformers-0.1.17-py3-none-any.whl""
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rm -rf ~/.cache/pip/*
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sync
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sed -i '$isource activate fit' $ND_ENTRYPOINT
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echo '{
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\n "pkg_manager": "apt",
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\n "instructions": [
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\n [
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\n "base",
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\n "nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04"
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\n ],
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\n [
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\n "user",
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\n "root"
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\n ],
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\n [
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\n "_header",
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\n {
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\n "version": "generic",
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\n "method": "custom"
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\n }
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\n ],
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\n [
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\n "copy",
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\n [
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\n "/home/tibuch/Gitrepos/FourierImageTransformer/dist/fourier_image_transformers-0.1.17-py3-none-any.whl",
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\n "/fourier_image_transformers-0.1.17-py3-none-any.whl"
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\n ]
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\n ],
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\n [
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\n "miniconda",
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\n {
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\n "create_env": "fit",
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\n "conda_install": [
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\n "python=3.7",
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\n "astra-toolbox",
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\n "pytorch",
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\n "torchvision",
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\n "torchaudio",
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\n "cudatoolkit=10.2",
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\n "-c",
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\n "pytorch",
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\n "-c",
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\n "astra-toolbox/label/dev"
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\n ],
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\n "pip_install": [
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\n "/fourier_image_transformers-0.1.17-py3-none-any.whl"
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\n ],
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\n "activate": true
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\n }
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\n ],
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\n [
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\n "entrypoint",
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\n "/neurodocker/startup.sh python"
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\n ]
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\n ]
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\n}' > /neurodocker/neurodocker_specs.json
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%environment
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export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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%files
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/home/tibuch/Gitrepos/FourierImageTransformer/dist/fourier_image_transformers-0.1.17-py3-none-any.whl /fourier_image_transformers-0.1.17-py3-none-any.whl
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%runscript
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/neurodocker/startup.sh python

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