DenoisET をテンプレートにして作成
[
トップ
] [
新規
|
一覧
|
検索
|
最終更新
|
ヘルプ
|
ログイン
]
開始行:
本家様 [[https://github.com/apeck12/denoiset>+https://git...
「An implementation of Noise2Noise for cryoET data」
***環境 [#f4d588ca]
#code(nonumber){{
[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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]#
}}
***pyenv-anacondaの設置 [#t1c137a6]
#code(nonumber){{
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/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/anaconda3-2025.06-1/etc/profi...
}}
っと準備を終わらせます
***構築 [#f9053361]
gitのドキュメントの記載通りに作ります
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/ape...
[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...
[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 ...
:
numpy 1.26.4 pypi_0 ...
nvidia-cublas-cu12 12.8.4.1 pypi_0 ...
nvidia-cuda-cupti-cu12 12.8.90 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.8.93 pypi_0 ...
nvidia-cuda-runtime-cu12 12.8.90 pypi_0 ...
nvidia-cudnn-cu12 9.10.2.21 pypi_0 ...
nvidia-cufft-cu12 11.3.3.83 pypi_0 ...
nvidia-cufile-cu12 1.13.1.3 pypi_0 ...
nvidia-curand-cu12 10.3.9.90 pypi_0 ...
nvidia-cusolver-cu12 11.7.3.90 pypi_0 ...
nvidia-cusparse-cu12 12.5.8.93 pypi_0 ...
nvidia-cusparselt-cu12 0.7.1 pypi_0 ...
nvidia-nccl-cu12 2.27.3 pypi_0 ...
nvidia-nvjitlink-cu12 12.8.93 pypi_0 ...
nvidia-nvtx-cu12 12.8.90 pypi_0 ...
:
python 3.11.4 h955ad1f_0
:
torch 2.8.0 pypi_0 ...
:
(denoiset) [root@rockylinux9 denoiset]# conda deactivate
[root@rockylinux9 denoiset]#
}}
***environment-modules [#n897664f]
「/apps/modulefiles/DenoisET」
#code(nonumber){{
#%Module1.0
module load AreTomo3
set root /apps/pyenv/versions/anaconda3-2025.06-1/envs/de...
prepend-path PATH $root/bin
}}
***Run [#yd3d0464]
事前学習済みモデルは git に同封されているようで、この場合は
「/apps/denoiset/models/」に用意されています
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/denoiset/models/
total 56736
-rw-r--r--. 1 root root 11615396 Aug 9 01:44 cilia.pth
-rw-r--r--. 1 root root 11617622 Aug 9 01:44 lysosome.pth
-rw-r--r--. 1 root root 11617622 Aug 9 01:44 minicell.pth
-rw-r--r--. 1 root root 11618002 Aug 9 01:44 phantom.pth
-rw-r--r--. 1 root root 11617736 Aug 9 01:44 synaptosome...
[root@rockylinux9 ~]#
}}
っでコマンド denoise3d を使用します
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load DenoisET
[saber@rockylinux9 ~]$ denoise3d --help
usage: denoise3d [-h] --input INPUT [--model MODEL] --out...
[--max_selected MAX_SELECTED] [--sort_by...
[--bad_patch_low BAD_PATCH_LOW] [--bad_p...
[--odd_extension ODD_EXTENSION] [--n_ext...
[--batch_size BATCH_SIZE] [--val_fractio...
[--ch_threshold CH_THRESHOLD] [--train_a...
[--inf_padding INF_PADDING] [--live] [--...
options:
-h, --help show this help message and exit
--input INPUT Input directory of tomograms or a...
--model MODEL Pre-trained UNet3d model file
--output OUTPUT Output directory for denoised vol...
--pattern PATTERN Glob pattern for file basename
--metrics_file METRICS_FILE
AreTomo3 TiltSeries_Metrics.csv f...
--min_selected MIN_SELECTED
Minimum number of selected tomogr...
--max_selected MAX_SELECTED
Maximum number of selected tomogr...
--sort_by SORT_BY Metric for sorting tomograms if s...
--tilt_axis TILT_AXIS
Maximum deviation from median til...
--thickness THICKNESS
Minimum sample thickness in Angst...
--global_shift GLOBAL_SHIFT
Maximum global shift in Angstrom
--bad_patch_low BAD_PATCH_LOW
Maximum fraction of bad patches a...
--bad_patch_all BAD_PATCH_ALL
Maximum fraction of bad patches a...
--ctf_res CTF_RES Maximum resolution of CTF score i...
--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 p...
--seed SEED Fixed random seed value
--optimizer OPTIMIZER
Optimizer
--learning_rate LEARNING_RATE
Learning rate
--batch_size BATCH_SIZE
Number of paired subvolumes per b...
--val_fraction VAL_FRACTION
Fraction of tomograms for validat...
--n_epochs N_EPOCHS Number of training epochs
--n_denoise N_DENOISE
Number of tomograms to denoise pe...
--length LENGTH Side length of cubic subvolumes t...
--train_only Only perform training and not inf...
--ch_threshold CH_THRESHOLD
Checkerboard metric threshold for...
--train_all_epochs Continue training past ch_thresho...
--exclude_tags EXCLUDE_TAGS [EXCLUDE_TAGS ...]
Volumes containing these substrin...
--inf_length INF_LENGTH
Side length of cubic subvolumes t...
--inf_padding INF_PADDING
Padding length in pixels during i...
--live Live processing mode to denoise t...
--t_interval T_INTERVAL
Interval in seconds between check...
--t_exit T_EXIT Exit after this period in seconds...
[saber@rockylinux9 ~]$
}}
***めも [#rb126f65]
DenoisETに使用される torch に cuda 12.8 のライブラリが用...
もし動かない場合は nvidia driver を 570.xx 以上に上げるか...
#code(nonumber){{
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.pyt...
conda list
torch 2.7.1+cu118 pypi_0 ...
}}
終了行:
本家様 [[https://github.com/apeck12/denoiset>+https://git...
「An implementation of Noise2Noise for cryoET data」
***環境 [#f4d588ca]
#code(nonumber){{
[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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]#
}}
***pyenv-anacondaの設置 [#t1c137a6]
#code(nonumber){{
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/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/anaconda3-2025.06-1/etc/profi...
}}
っと準備を終わらせます
***構築 [#f9053361]
gitのドキュメントの記載通りに作ります
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/ape...
[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...
[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 ...
:
numpy 1.26.4 pypi_0 ...
nvidia-cublas-cu12 12.8.4.1 pypi_0 ...
nvidia-cuda-cupti-cu12 12.8.90 pypi_0 ...
nvidia-cuda-nvrtc-cu12 12.8.93 pypi_0 ...
nvidia-cuda-runtime-cu12 12.8.90 pypi_0 ...
nvidia-cudnn-cu12 9.10.2.21 pypi_0 ...
nvidia-cufft-cu12 11.3.3.83 pypi_0 ...
nvidia-cufile-cu12 1.13.1.3 pypi_0 ...
nvidia-curand-cu12 10.3.9.90 pypi_0 ...
nvidia-cusolver-cu12 11.7.3.90 pypi_0 ...
nvidia-cusparse-cu12 12.5.8.93 pypi_0 ...
nvidia-cusparselt-cu12 0.7.1 pypi_0 ...
nvidia-nccl-cu12 2.27.3 pypi_0 ...
nvidia-nvjitlink-cu12 12.8.93 pypi_0 ...
nvidia-nvtx-cu12 12.8.90 pypi_0 ...
:
python 3.11.4 h955ad1f_0
:
torch 2.8.0 pypi_0 ...
:
(denoiset) [root@rockylinux9 denoiset]# conda deactivate
[root@rockylinux9 denoiset]#
}}
***environment-modules [#n897664f]
「/apps/modulefiles/DenoisET」
#code(nonumber){{
#%Module1.0
module load AreTomo3
set root /apps/pyenv/versions/anaconda3-2025.06-1/envs/de...
prepend-path PATH $root/bin
}}
***Run [#yd3d0464]
事前学習済みモデルは git に同封されているようで、この場合は
「/apps/denoiset/models/」に用意されています
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/denoiset/models/
total 56736
-rw-r--r--. 1 root root 11615396 Aug 9 01:44 cilia.pth
-rw-r--r--. 1 root root 11617622 Aug 9 01:44 lysosome.pth
-rw-r--r--. 1 root root 11617622 Aug 9 01:44 minicell.pth
-rw-r--r--. 1 root root 11618002 Aug 9 01:44 phantom.pth
-rw-r--r--. 1 root root 11617736 Aug 9 01:44 synaptosome...
[root@rockylinux9 ~]#
}}
っでコマンド denoise3d を使用します
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load DenoisET
[saber@rockylinux9 ~]$ denoise3d --help
usage: denoise3d [-h] --input INPUT [--model MODEL] --out...
[--max_selected MAX_SELECTED] [--sort_by...
[--bad_patch_low BAD_PATCH_LOW] [--bad_p...
[--odd_extension ODD_EXTENSION] [--n_ext...
[--batch_size BATCH_SIZE] [--val_fractio...
[--ch_threshold CH_THRESHOLD] [--train_a...
[--inf_padding INF_PADDING] [--live] [--...
options:
-h, --help show this help message and exit
--input INPUT Input directory of tomograms or a...
--model MODEL Pre-trained UNet3d model file
--output OUTPUT Output directory for denoised vol...
--pattern PATTERN Glob pattern for file basename
--metrics_file METRICS_FILE
AreTomo3 TiltSeries_Metrics.csv f...
--min_selected MIN_SELECTED
Minimum number of selected tomogr...
--max_selected MAX_SELECTED
Maximum number of selected tomogr...
--sort_by SORT_BY Metric for sorting tomograms if s...
--tilt_axis TILT_AXIS
Maximum deviation from median til...
--thickness THICKNESS
Minimum sample thickness in Angst...
--global_shift GLOBAL_SHIFT
Maximum global shift in Angstrom
--bad_patch_low BAD_PATCH_LOW
Maximum fraction of bad patches a...
--bad_patch_all BAD_PATCH_ALL
Maximum fraction of bad patches a...
--ctf_res CTF_RES Maximum resolution of CTF score i...
--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 p...
--seed SEED Fixed random seed value
--optimizer OPTIMIZER
Optimizer
--learning_rate LEARNING_RATE
Learning rate
--batch_size BATCH_SIZE
Number of paired subvolumes per b...
--val_fraction VAL_FRACTION
Fraction of tomograms for validat...
--n_epochs N_EPOCHS Number of training epochs
--n_denoise N_DENOISE
Number of tomograms to denoise pe...
--length LENGTH Side length of cubic subvolumes t...
--train_only Only perform training and not inf...
--ch_threshold CH_THRESHOLD
Checkerboard metric threshold for...
--train_all_epochs Continue training past ch_thresho...
--exclude_tags EXCLUDE_TAGS [EXCLUDE_TAGS ...]
Volumes containing these substrin...
--inf_length INF_LENGTH
Side length of cubic subvolumes t...
--inf_padding INF_PADDING
Padding length in pixels during i...
--live Live processing mode to denoise t...
--t_interval T_INTERVAL
Interval in seconds between check...
--t_exit T_EXIT Exit after this period in seconds...
[saber@rockylinux9 ~]$
}}
***めも [#rb126f65]
DenoisETに使用される torch に cuda 12.8 のライブラリが用...
もし動かない場合は nvidia driver を 570.xx 以上に上げるか...
#code(nonumber){{
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.pyt...
conda list
torch 2.7.1+cu118 pypi_0 ...
}}
ページ名:
1
![[PukiWiki]](image/picc.png "[PukiWiki]")
