![[PukiWiki]](image/picc.png "[PukiWiki]")
#author("2024-07-06T17:24:30+00:00","default:sysosa","sysosa") #author("2024-07-06T17:27:38+00:00","default:sysosa","sysosa") 本家様 [[https://github.com/asarnow/pyem>+https://github.com/asarnow/pyem]] pyemのwiki [[https://github.com/asarnow/pyem/wiki>+https://github.com/asarnow/pyem/wiki/]] 「A collection of Python modules and command-line utilities for electron microscopy of biological samples.」とある。 deepL先生訳 「生物試料の電子顕微鏡観察用のPythonモジュールとコマンドラインユーティリティのコレクション」 ***pyenv/anaconda [#s1f1f4c4] [[crYOLO]]と同じように pyenv を敷いて anaconda か miniforge でconda環境を用意してます &color(red){*};&size(10){既に [[crYOLO]] とかで構築済みなら不要。その環境を使い回します}; #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 --list <-- 最新版らを確認 pyenv install anaconda3-2024.06-1 (あるいは pyenv install miniforge3-23.11.0-0 ) }} &size(10){サイトでは miniforge を進めてます. まぁmambaが使えますからね.}; その後にconda環境を作れるようにするために #code(nonumber){{ source /apps/pyenv/versions/anaconda3-2024.06-1/etc/profile.d/conda.sh (あるいは source /apps/pyenv/versions/miniforge3-23.11.0-0/etc/profile.d/conda.sh }} とします ***PyEM 向けの仮想実行環境を作って、PyEMをインストールします [#i88a2992] PyEMの仮想環境名ですが単純に「PyEM」としてます. &size(10){まぁ、pyemでも構いません};l #code(nonumber){{ [root@rockylinux ~]# conda create -n PyEM python=3.9 -c conda-forge -y [root@rockylinux ~]# conda activate PyEM (PyEM) [root@rockylinux ~]# conda install numba numpy scipy matplotlib seaborn pandas pathos pyfftw healpy natsort starfile ipython -c conda-forge -y (PyEM) [root@rockylinux ~]# cd /apps (PyEM) [root@rockylinux apps]# git clone https://github.com/asarnow/pyem.git (PyEM) [root@rockylinux apps]# cd pyem/ (PyEM) [root@rockylinux pyem]# which pip /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/pip (PyEM) [root@rockylinux pyem]# pip install --no-dependencies -e . (PyEM) [root@rockylinux pyem]# pip install cs2star (ついでです) }} 一応確認 &size(10){ついでに cs2star も入れてます. 参照[[https://pypi.org/project/cs2star/>+https://pypi.org/project/cs2star/]]}; #code(nonumber){{ (PyEM) [root@rockylinux ~]# ls /apps/pyem/pyem/cli/ angdist.py ctf2star.py __init__.py mcstar.py projection_subtraction.py reconstruct.py star2bild.py subset.py cfsc.py disparticle.py map.py par2star.py project.py sort.py star.py varmap.py csparc2star.py emcalc.py mask.py pose.py recenter.py stack.py subparticles.py (PyEM) [root@rockylinux ~]# (PyEM) [root@rockylinux ~]# ls /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/*.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/cfsc.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/csparc2star.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/ctf2star.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/disparticle.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/emcalc.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/map.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/mask.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/mcstar.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/par2star.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/projection_subtraction.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/project.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/stack.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/star2bild.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/star.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/subparticles.py /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/varmap.py (PyEM) [root@rockylinux ~]# }} 「/apps/pyem/pyem/cli」にあって、「/apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM/bin/*.py」にないものとかある( angdist.py, recenter.py, reconstruct.py, sort.py, subset.py ) なので、EnvironmentModulesは下記のようにします ***EnvironmentModules [#se252f32] 「/apps/modulefiles/PyEM」 #code(nonumber){{ #%Module1.0 set PyEM /apps/pyem/ set root /apps/pyenv/versions/anaconda3-2024.06-1/envs/PyEM prepend-path PATH $root/bin:$PyEM/pyem/cli }} ***実行するには [#b065a49a] みんな大好き csparc2star.py のヘルプを出してみた. #code(nonumber){{ [saber@rockylinux ~]$ module use /apps/modulefiles/ [saber@rockylinux ~]$ module load PyEM [saber@rockylinux ~]$ csparc2star.py -h usage: csparc2star.py [-h] [--movies] [--boxsize BOXSIZE] [--class CLS] [--minphic MINPHIC] [--stack-path STACK_PATH] [--micrograph-path MICROGRAPH_PATH] [--copy-micrograph-coordinates COPY_MICROGRAPH_COORDINATES] [--swapxy] [--noswapxy] [--invertx] [--inverty] [--flipy] [--cached] [--transform TRANSFORM] [--relion2] [--strip-uid [STRIP_UID]] [--10k] [--loglevel LOGLEVEL] [input ...] output positional arguments: input Cryosparc metadata .csv (v0.6.5) or .cs (v2+) files output Output .star file optional arguments: -h, --help show this help message and exit --movies Write per-movie star files into output directory --boxsize BOXSIZE Cryosparc refinement box size (if different from particles) --class CLS Keep this class in output, may be passed multiple times --minphic MINPHIC Minimum posterior probability for class assignment --stack-path STACK_PATH Path to single particle stack --micrograph-path MICROGRAPH_PATH Replacement path for micrographs or movies --copy-micrograph-coordinates COPY_MICROGRAPH_COORDINATES Source for micrograph paths and particle coordinates (file or quoted glob) --swapxy Swap X and Y axes when converting particle coordinates from normalized to absolute --noswapxy Do not swap X and Y axes when converting particle coordinates --invertx Invert particle coordinate X axis --inverty Invert particle coordinate Y axis --flipy Invert refined particle Y shifts --cached Keep paths from the Cryosparc 2+ cache when merging coordinates --transform TRANSFORM Apply rotation matrix or 3x4 rotation plus translation matrix to particles (Numpy format) --relion2, -r2 Relion 2 compatible outputs --strip-uid [STRIP_UID] Strip all leading UIDs from file names --10k Only read first 10,000 particles for rapid testing. --loglevel LOGLEVEL, -l LOGLEVEL Logging level and debug output [saber@rockylinux ~]$ [saber@rockylinux ~]$ [saber@rockylinux ~]$ cs2star -h Usage: cs2star [OPTIONS] JOB_DIR [DEST_DIR] Copy and convert a cryosparc dir into a relion-ready dir. \b Parameters ========== JOB_DIR: a cryosparc job containing particles files. DEST_DIR: the destination directory. [default: '.'] WARNING! This script will use --swapxy by default. This is because *usually* this is the convention change between cryosparc and relion. However, your mileage may vary, so you are encouraged to check you data after conversion. Note that if -p/-m are not passed, those columns are not usable (due to the mrc extension and broken path). Options: -f, --overwrite overwrite the existing destination directory if present.Passed once, overwrite star file only. Twice, also files/symlinks [default: 0] -d, --dry-run do not perform the command, simply check inputs and show what will be done. -c, --copy / -s, --symlink copy the images or symlink to them [default: s] -m, --micrographs copy/link the full micrographs -p, --patches copy/link the particle patches, if available --sets TEXT only use these sets (only used if job is Particle Sets Tool). Comma-separated list. --classes TEXT only use particles from these classes. Comma- separated list. --swapxy / --no-swapxy swap x and y axes [default: swapxy] --inverty / --no-inverty invert y axis [default: no-inverty] --invertx / --no-invertx invert x axis [default: no-invertx] --version Show the version and exit. -h, --help Show this message and exit. [saber@rockylinux ~]$ }} とかで ~ ただ、、 ***recenter.py [#r0c5bc60] 「recenter.py」スクリプトを実行すると #code(nonumber){{ [saber@rockylinux ~]$ recenter.py Traceback (most recent call last): File "/apps/pyem//pyem/cli/recenter.py", line 24, in <module> from star import parse_star, write_star ImportError: cannot import name 'parse_star' from 'star' (/apps/pyem/pyem/cli/star.py) [saber@rockylinux ~]$ }} と言われる. 強引な方法だけどこのPyEM仮想実行環境に eman-dev をcondaで入れてしまう #code(nonumber){{ [root@rockylinux ~]# source /apps/pyenv/versions/anaconda3-2024.06-1/etc/profile.d/conda.sh [root@rockylinux ~]# conda activate PyEM (PyEM) [root@rockylinux ~]# conda install eman-dev -c cryoem -c conda-forge }} そのうえで、ちょっと「recenter.py」を弄る #code(diff,nonumber){{ --- /apps/pyem/pyem/cli/recenter.py.orig 2024-07-07 01:41:51.218929388 +0900 +++ /apps/pyem/pyem/cli/recenter.py 2024-07-07 02:13:10.286641708 +0900 @@ -21,7 +21,7 @@ import logging import sys import numpy as np -from star import parse_star, write_star +from pyem.star import parse_star, write_star from EMAN2 import EMData, Vec3f, Transform }} そうすると、 #code(nonumber){{ [saber@rockylinux ~]$ module use /apps/modulefiles/ [saber@rockylinux ~]$ module load PyEM [saber@rockylinux ~]$ [saber@rockylinux ~]$ [saber@rockylinux ~]$ recenter.py -h usage: recenter.py [-h] [--class-2d CLASS_2D] [--class-3d CLASS_3D] [--zero-origin ZERO_ORIGIN] input output positional arguments: input Input .star file output Output .star file optional arguments: -h, --help show this help message and exit --class-2d CLASS_2D 2D class images for recentering (pass glob in quotes for multiple files) --class-3d CLASS_3D 3D class images for recentering (pass glob in quotes for multiple files) --zero-origin ZERO_ORIGIN Subtract particle origin from particle coordinates in output [saber@rockylinux ~]$ }} と動くようになる ***めも [#wa819621] eman-dev を入れてしまうので、eman2 向けとしてアプリを用意して、その中にPyEMを入れたほうがいいのかも.
