DenoisET

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.6 (Blue Onyx)
 
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64  570.181  Release Build  (dvs-builder@U22-I3-AF02-20-5)  Wed Jul 30 18:41:07 UTC 2025
GCC version:  gcc version 11.5.0 20240719 (Red Hat 11.5.0-5) (GCC)
 
[root@rockylinux9 ~]#

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2025.06-1
pyenv global anaconda3-2025.06-1
source /apps/pyenv/versions/anaconda3-2025.06-1/etc/profile.d/conda.sh
conda update conda
 
(既に環境があるなら)
 
source /apps/pyenv/versions/anaconda3-2025.06-1/etc/profile.d/conda.sh

[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/apeck12/denoiset.git
 
[root@rockylinux9 apps]# cd denoiset/
 
[root@rockylinux9 denoiset]# ls -CF
LICENSE  models/  pyproject.toml  README.md  src/  tests/
 
[root@rockylinux9 denoiset]# conda create --name denoiset python=3.11.4
 
[root@rockylinux9 denoiset]# conda activate denoiset
 
(denoiset) [root@rockylinux9 denoiset]# pip install .
 
[ちょいと確認]
(denoiset) [root@rockylinux9 denoiset]# conda list
 :
denoiset                    0.1.0            pypi_0           pypi
 :
numpy                       1.26.4           pypi_0           pypi
nvidia-cublas-cu12          12.8.4.1         pypi_0           pypi
nvidia-cuda-cupti-cu12      12.8.90          pypi_0           pypi
nvidia-cuda-nvrtc-cu12      12.8.93          pypi_0           pypi
nvidia-cuda-runtime-cu12    12.8.90          pypi_0           pypi
nvidia-cudnn-cu12           9.10.2.21        pypi_0           pypi
nvidia-cufft-cu12           11.3.3.83        pypi_0           pypi
nvidia-cufile-cu12          1.13.1.3         pypi_0           pypi
nvidia-curand-cu12          10.3.9.90        pypi_0           pypi
nvidia-cusolver-cu12        11.7.3.90        pypi_0           pypi
nvidia-cusparse-cu12        12.5.8.93        pypi_0           pypi
nvidia-cusparselt-cu12      0.7.1            pypi_0           pypi
nvidia-nccl-cu12            2.27.3           pypi_0           pypi
nvidia-nvjitlink-cu12       12.8.93          pypi_0           pypi
nvidia-nvtx-cu12            12.8.90          pypi_0           pypi
 :
python                      3.11.4           h955ad1f_0
 :
torch                       2.8.0            pypi_0           pypi
 :
(denoiset) [root@rockylinux9 denoiset]# conda deactivate
[root@rockylinux9 denoiset]#

#%Module1.0
 
module load AreTomo3
set root /apps/pyenv/versions/anaconda3-2025.06-1/envs/denoiset
prepend-path PATH $root/bin

[root@rockylinux9 ~]# ls -l /apps/denoiset/models/
total 56736
-rw-r--r--. 1 root root 11615396 Aug  9 01:44 cilia.pth
-rw-r--r--. 1 root root 11617622 Aug  9 01:44 lysosome.pth
-rw-r--r--. 1 root root 11617622 Aug  9 01:44 minicell.pth
-rw-r--r--. 1 root root 11618002 Aug  9 01:44 phantom.pth
-rw-r--r--. 1 root root 11617736 Aug  9 01:44 synaptosome.pth
[root@rockylinux9 ~]#

[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load DenoisET
 
[saber@rockylinux9 ~]$ denoise3d --help
usage: denoise3d [-h] --input INPUT [--model MODEL] --output OUTPUT [--pattern PATTERN] [--metrics_file METRICS_FILE] [--min_selected MIN_SELECTED]
                 [--max_selected MAX_SELECTED] [--sort_by SORT_BY] [--tilt_axis TILT_AXIS] [--thickness THICKNESS] [--global_shift GLOBAL_SHIFT]
                 [--bad_patch_low BAD_PATCH_LOW] [--bad_patch_all BAD_PATCH_ALL] [--ctf_res CTF_RES] [--ctf_score CTF_SCORE] [--odd_pattern ODD_PATTERN]
                 [--odd_extension ODD_EXTENSION] [--n_extract N_EXTRACT] [--seed SEED] [--optimizer OPTIMIZER] [--learning_rate LEARNING_RATE]
                 [--batch_size BATCH_SIZE] [--val_fraction VAL_FRACTION] [--n_epochs N_EPOCHS] [--n_denoise N_DENOISE] [--length LENGTH] [--train_only]
                 [--ch_threshold CH_THRESHOLD] [--train_all_epochs] [--exclude_tags EXCLUDE_TAGS [EXCLUDE_TAGS ...]] [--inf_length INF_LENGTH]
                 [--inf_padding INF_PADDING] [--live] [--t_interval T_INTERVAL] [--t_exit T_EXIT]
 
options:
  -h, --help            show this help message and exit
  --input INPUT         Input directory of tomograms or a text file specifying their full path (minus extension)
  --model MODEL         Pre-trained UNet3d model file
  --output OUTPUT       Output directory for denoised volumes
  --pattern PATTERN     Glob pattern for file basename
  --metrics_file METRICS_FILE
                        AreTomo3 TiltSeries_Metrics.csv file
  --min_selected MIN_SELECTED
                        Minimum number of selected tomograms if in_path is a metrics file
  --max_selected MAX_SELECTED
                        Maximum number of selected tomograms if in_path is a metrics file
  --sort_by SORT_BY     Metric for sorting tomograms if selected set exceeds max_selected
  --tilt_axis TILT_AXIS
                        Maximum deviation from median tilt axis in degrees
  --thickness THICKNESS
                        Minimum sample thickness in Angstrom
  --global_shift GLOBAL_SHIFT
                        Maximum global shift in Angstrom
  --bad_patch_low BAD_PATCH_LOW
                        Maximum fraction of bad patches at low tilt angles
  --bad_patch_all BAD_PATCH_ALL
                        Maximum fraction of bad patches across the full tilt range
  --ctf_res CTF_RES     Maximum resolution of CTF score in Angstrom
  --ctf_score CTF_SCORE
                        Minimum CTF score
  --odd_pattern ODD_PATTERN
                        Glob pattern for ODD tomograms
  --odd_extension ODD_EXTENSION
                        suffix for ODD tomograms
  --n_extract N_EXTRACT
                        Number of subvolumes to extract per tomogram
  --seed SEED           Fixed random seed value
  --optimizer OPTIMIZER
                        Optimizer
  --learning_rate LEARNING_RATE
                        Learning rate
  --batch_size BATCH_SIZE
                        Number of paired subvolumes per batch
  --val_fraction VAL_FRACTION
                        Fraction of tomograms for validation
  --n_epochs N_EPOCHS   Number of training epochs
  --n_denoise N_DENOISE
                        Number of tomograms to denoise per epoch for visual inspection
  --length LENGTH       Side length of cubic subvolumes to extract in pixels
  --train_only          Only perform training and not inference on the full dataset
  --ch_threshold CH_THRESHOLD
                        Checkerboard metric threshold for terminating training
  --train_all_epochs    Continue training past ch_threshold for diagnostic purposes
  --exclude_tags EXCLUDE_TAGS [EXCLUDE_TAGS ...]
                        Volumes containing these substring(s) will not be denoised
  --inf_length INF_LENGTH
                        Side length of cubic subvolumes to extract in pixels during inference
  --inf_padding INF_PADDING
                        Padding length in pixels during inference
  --live                Live processing mode to denoise tomograms on-the-fly
  --t_interval T_INTERVAL
                        Interval in seconds between checking for new files
  --t_exit T_EXIT       Exit after this period in seconds if new files are not found
[saber@rockylinux9 ~]$

conda env remove --name denoiset
conda create --name denoiset python=3.11.4
cd /apps/denoiset/
pip install .
pip install torch==2.7.1 --index-url https://download.pytorch.org/whl/cu118
 
conda list
  torch                       2.7.1+cu118      pypi_0           pypi