Merge pull request #13 from juglab/merger

v0.1.17

README.md

@@ -6,7 +6,7 @@ Build Python package:
 `python setup.py bdist_wheel`
 
 Build singularity recipe:
-`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`
+`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`
 
 Build singularity container:
-`sudo singularity build fit_v0.1.16.simg v0.1.16.Singularity`
+`sudo singularity build fit_v0.1.17.simg v0.1.17.Singularity`

fit/modules/TRecTransformerModule.py

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

fit/version.py

@@ -1 +1 @@
-__version__ = '0.1.16'
+__version__ = '0.1.17'

singularity/v0.1.17.Singularity

@@ -0,0 +1,138 @@
+# Generated by: Neurodocker version 0.7.0
+# Latest release: Neurodocker version 0.7.0
+# Timestamp: 2021/01/26 06:27:03 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/ReproNim/neurodocker
+
+Bootstrap: docker
+From: nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04
+
+%post
+su - root
+
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    apt-utils \
+    bzip2 \
+    ca-certificates \
+    curl \
+    locales \
+    unzip
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
+dpkg-reconfigure --frontend=noninteractive locales
+update-locale LANG="en_US.UTF-8"
+chmod 777 /opt && chmod a+s /opt
+mkdir -p /neurodocker
+if [ ! -f "$ND_ENTRYPOINT" ]; then
+  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
+  echo 'set -e' >> "$ND_ENTRYPOINT"
+  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
+  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
+fi
+chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+export PATH="/opt/miniconda-latest/bin:$PATH"
+echo "Downloading Miniconda installer ..."
+conda_installer="/tmp/miniconda.sh"
+curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash "$conda_installer" -b -p /opt/miniconda-latest
+rm -f "$conda_installer"
+conda update -yq -nbase conda
+conda config --system --prepend channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+sync && conda clean -y --all && sync
+conda create -y -q --name fit
+conda install -y -q --name fit \
+    "python=3.7" \
+    "astra-toolbox" \
+    "pytorch" \
+    "torchvision" \
+    "torchaudio" \
+    "cudatoolkit=10.2" \
+    "-c" \
+    "pytorch" \
+    "-c" \
+    "astra-toolbox/label/dev"
+sync && conda clean -y --all && sync
+bash -c "source activate fit
+  pip install --no-cache-dir  \
+      "/fourier_image_transformers-0.1.17-py3-none-any.whl""
+rm -rf ~/.cache/pip/*
+sync
+sed -i '$isource activate fit' $ND_ENTRYPOINT
+
+
+echo '{
+\n  "pkg_manager": "apt",
+\n  "instructions": [
+\n    [
+\n      "base",
+\n      "nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04"
+\n    ],
+\n    [
+\n      "user",
+\n      "root"
+\n    ],
+\n    [
+\n      "_header",
+\n      {
+\n        "version": "generic",
+\n        "method": "custom"
+\n      }
+\n    ],
+\n    [
+\n      "copy",
+\n      [
+\n        "/home/tibuch/Gitrepos/FourierImageTransformer/dist/fourier_image_transformers-0.1.17-py3-none-any.whl",
+\n        "/fourier_image_transformers-0.1.17-py3-none-any.whl"
+\n      ]
+\n    ],
+\n    [
+\n      "miniconda",
+\n      {
+\n        "create_env": "fit",
+\n        "conda_install": [
+\n          "python=3.7",
+\n          "astra-toolbox",
+\n          "pytorch",
+\n          "torchvision",
+\n          "torchaudio",
+\n          "cudatoolkit=10.2",
+\n          "-c",
+\n          "pytorch",
+\n          "-c",
+\n          "astra-toolbox/label/dev"
+\n        ],
+\n        "pip_install": [
+\n          "/fourier_image_transformers-0.1.17-py3-none-any.whl"
+\n        ],
+\n        "activate": true
+\n      }
+\n    ],
+\n    [
+\n      "entrypoint",
+\n      "/neurodocker/startup.sh python"
+\n    ]
+\n  ]
+\n}' > /neurodocker/neurodocker_specs.json
+
+%environment
+export LANG="en_US.UTF-8"
+export LC_ALL="en_US.UTF-8"
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
+
+%files
+/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
+
+%runscript
+/neurodocker/startup.sh python