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tibuch
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Merge pull request #8 from juglab/dev
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2 parents b8115d1 + 7ae928d commit 9b3f66b

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‎README.md‎

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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-0.1.5-py3-none-any.whl /fourier_image_transformers-0.1.5-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-0.1.5-py3-none-any.whl' activate=true --entrypoint "/neurodocker/startup.sh python" > v0.1.5.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-0.1.6-py3-none-any.whl /fourier_image_transformers-0.1.6-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-0.1.6-py3-none-any.whl' activate=true --entrypoint "/neurodocker/startup.sh python" > v0.1.6.Singularity`
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Build singularity container:
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`sudo singularity build fit_v0.1.5.simg v0.1.5.Singularity`
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`sudo singularity build fit_v0.1.6.simg v0.1.6.Singularity`

‎fit/modules/TRecTransformerModule.py‎

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def criterion(self, pred_fc, target_fc, target_real, mag_min, mag_max):
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fc_loss, amp_loss, phi_loss = self._fc_loss(pred_fc=pred_fc, target_fc=target_fc, mag_min=mag_min, mag_max=mag_max)
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# real_loss = self._real_loss(pred_fc=pred_fc, target_fc=target_fc, target_real=target_real, mag_min=mag_min,
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# mag_max=mag_max)
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# return fc_loss + real_loss
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return fc_loss, amp_loss, phi_loss
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real_loss = self._real_loss(pred_fc=pred_fc, target_fc=target_fc, target_real=target_real, mag_min=mag_min,
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mag_max=mag_max)
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return fc_loss + real_loss, amp_loss, phi_loss
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def _bin_data(self, x_fc, y_fc):
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shells = (self.hparams.detector_len // 2 + 1) / self.bin_factor

‎fit/version.py‎

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__version__ = '0.1.5'
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__version__ = '0.1.6'

‎singularity/v0.1.6.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: 2021/01/11 22:18:13 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 "$conda_installer"
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conda update -yq -nbase conda
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conda config --system --prepend channels conda-forge
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conda config --system --set auto_update_conda false
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conda config --system --set show_channel_urls true
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sync && conda clean -y --all && sync
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conda create -y -q --name fit
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conda install -y -q --name fit \
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"python=3.7" \
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"astra-toolbox" \
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"pytorch" \
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"torchvision" \
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"torchaudio" \
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"cudatoolkit=10.2" \
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"-c" \
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"pytorch" \
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"-c" \
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"astra-toolbox/label/dev"
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sync && conda clean -y --all && sync
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bash -c "source activate fit
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pip install --no-cache-dir \
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"/fourier_image_transformers-0.1.6-py3-none-any.whl""
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rm -rf ~/.cache/pip/*
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sync
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sed -i '$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-0.1.6-py3-none-any.whl",
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\n "/fourier_image_transformers-0.1.6-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-0.1.6-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-0.1.6-py3-none-any.whl /fourier_image_transformers-0.1.6-py3-none-any.whl
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%runscript
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/neurodocker/startup.sh python

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