Cinderella をテンプレートにして作成
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開始行:
本家様 [[http://sphire.mpg.de/wiki/doku.php?id=auto_2d_cl...
Automatic 2D class selection
***インストール [#h6b44929]
まずはpyenv環境を構築する[[crYOLO#w789c07e]]
その次に
Cinderella 向けの仮想実行環境を作る
#code(nonumber){{
[root@c ~]# conda create -n cinderella-gpu -c anaconda py...
(h5pyのバージョンを固定しないと動かないみたい)
[root@c ~]# source activate cinderella-gpu
(cinderella-gpu) [root@c ~]# pip install cinderella[gpu]
(cinderella-gpu) [root@c ~]# which sp_cinderella_predict.py
/apps/pyenv/versions/anaconda3-2021.11/envs/cinderella-0....
(cinderella-gpu) [root@c ~]#
(cinderella-gpu) [root@c ~]# conda deactivate
[root@c ~]#
}}
***EnvironmentModules [#a77b2f7e]
[[EnvironmentModules]]で実行環境を整備するならmodiilefile...
&color(red){*};&size(10){普通は「/etc/modulefiles/cindere...
#code(nonumber){{
[root@c ~]# vi /home/Common/modules/cinderella
#%Module -*- tcl -*-
proc ModulesHelp { } {
puts stderr "\tAdds anaconda to your environment variab...
}
module-whatis "Adds anaconda to your environment variables"
set root /Appl/pyenv/versions/anaconda3-5.3.1/en...
prepend-path PATH $root/bin
[root@c ~]#
}}
ロード方法は「module load cinderella」
***使い方 [#j8202fe4]
参照[[http://sphire.mpg.de/wiki/doku.php?id=auto2d_tutori...
Pretrained modelが提供されているので、それを取得します。
「relion40_tutorial_precalculated_results/Class2D/job008...
#code(nonumber){{
(cinderella) [saber@c cinderella]$ cp ../relion40_tutoria...
(cinderella) [saber@c cinderella]$ sp_cinderella_predict....
Using TensorFlow backend.
2019-09-13 00:40:33.505544: I tensorflow/core/platform/cp...
2019-09-13 00:40:33.518586: E tensorflow/stream_executor/...
2019-09-13 00:40:33.519113: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519131: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519178: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519230: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519244: I tensorflow/stream_executor/...
Model: "model_2"
_________________________________________________________...
Layer (type) Output Shape Pa...
=========================================================...
input_1 (InputLayer) (None, 75, 75, 1) 0
_________________________________________________________...
model_1 (Model) (None, 4, 4, 1024) 50...
_________________________________________________________...
global_average_pooling2d_1 ( (None, 1024) 0
_________________________________________________________...
denseL1 (Dense) (None, 64) 65...
_________________________________________________________...
denseL2 (Dense) (None, 10) 650
_________________________________________________________...
denseL3 (Dense) (None, 1) 11
=========================================================...
Total params: 50,712,693
Trainable params: 50,691,637
Non-trainable params: 21,056
_________________________________________________________...
2019-09-13 00:40:37.687003: W tensorflow/core/framework/a...
2019-09-13 00:40:37.687099: W tensorflow/core/framework/a...
2019-09-13 00:40:37.728333: W tensorflow/core/framework/a...
2019-09-13 00:40:37.808678: W tensorflow/core/framework/a...
2019-09-13 00:40:37.826402: W tensorflow/core/framework/a...
Try to list images on run_it025_classes.mrcs
100%|????????????????????????????????????????????????????...
Good classes: 2 / 50 ( 4 % )
Bad classes: 48 / 50 ( 96 % )
(cinderella) [saber@c cinderella]$
}}
「relion_display --gui」でoutputのファイルを開いてみる。
***メモ [#d7017857]
#code(nonumber){{
line 1224, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].dec...
AttributeError: 'str' object has no attribute 'decode'
}}
とエラーが発生した場合は、pythonモジュールの「h5py」が新...
#code(nonumber){{
pip uninstall h5py
pip install h5py==2.10.0
}}
あとRTX 30x0 でcinderellaを動かすには crYOLO と同じように...
終了行:
本家様 [[http://sphire.mpg.de/wiki/doku.php?id=auto_2d_cl...
Automatic 2D class selection
***インストール [#h6b44929]
まずはpyenv環境を構築する[[crYOLO#w789c07e]]
その次に
Cinderella 向けの仮想実行環境を作る
#code(nonumber){{
[root@c ~]# conda create -n cinderella-gpu -c anaconda py...
(h5pyのバージョンを固定しないと動かないみたい)
[root@c ~]# source activate cinderella-gpu
(cinderella-gpu) [root@c ~]# pip install cinderella[gpu]
(cinderella-gpu) [root@c ~]# which sp_cinderella_predict.py
/apps/pyenv/versions/anaconda3-2021.11/envs/cinderella-0....
(cinderella-gpu) [root@c ~]#
(cinderella-gpu) [root@c ~]# conda deactivate
[root@c ~]#
}}
***EnvironmentModules [#a77b2f7e]
[[EnvironmentModules]]で実行環境を整備するならmodiilefile...
&color(red){*};&size(10){普通は「/etc/modulefiles/cindere...
#code(nonumber){{
[root@c ~]# vi /home/Common/modules/cinderella
#%Module -*- tcl -*-
proc ModulesHelp { } {
puts stderr "\tAdds anaconda to your environment variab...
}
module-whatis "Adds anaconda to your environment variables"
set root /Appl/pyenv/versions/anaconda3-5.3.1/en...
prepend-path PATH $root/bin
[root@c ~]#
}}
ロード方法は「module load cinderella」
***使い方 [#j8202fe4]
参照[[http://sphire.mpg.de/wiki/doku.php?id=auto2d_tutori...
Pretrained modelが提供されているので、それを取得します。
「relion40_tutorial_precalculated_results/Class2D/job008...
#code(nonumber){{
(cinderella) [saber@c cinderella]$ cp ../relion40_tutoria...
(cinderella) [saber@c cinderella]$ sp_cinderella_predict....
Using TensorFlow backend.
2019-09-13 00:40:33.505544: I tensorflow/core/platform/cp...
2019-09-13 00:40:33.518586: E tensorflow/stream_executor/...
2019-09-13 00:40:33.519113: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519131: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519178: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519230: I tensorflow/stream_executor/...
2019-09-13 00:40:33.519244: I tensorflow/stream_executor/...
Model: "model_2"
_________________________________________________________...
Layer (type) Output Shape Pa...
=========================================================...
input_1 (InputLayer) (None, 75, 75, 1) 0
_________________________________________________________...
model_1 (Model) (None, 4, 4, 1024) 50...
_________________________________________________________...
global_average_pooling2d_1 ( (None, 1024) 0
_________________________________________________________...
denseL1 (Dense) (None, 64) 65...
_________________________________________________________...
denseL2 (Dense) (None, 10) 650
_________________________________________________________...
denseL3 (Dense) (None, 1) 11
=========================================================...
Total params: 50,712,693
Trainable params: 50,691,637
Non-trainable params: 21,056
_________________________________________________________...
2019-09-13 00:40:37.687003: W tensorflow/core/framework/a...
2019-09-13 00:40:37.687099: W tensorflow/core/framework/a...
2019-09-13 00:40:37.728333: W tensorflow/core/framework/a...
2019-09-13 00:40:37.808678: W tensorflow/core/framework/a...
2019-09-13 00:40:37.826402: W tensorflow/core/framework/a...
Try to list images on run_it025_classes.mrcs
100%|????????????????????????????????????????????????????...
Good classes: 2 / 50 ( 4 % )
Bad classes: 48 / 50 ( 96 % )
(cinderella) [saber@c cinderella]$
}}
「relion_display --gui」でoutputのファイルを開いてみる。
***メモ [#d7017857]
#code(nonumber){{
line 1224, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].dec...
AttributeError: 'str' object has no attribute 'decode'
}}
とエラーが発生した場合は、pythonモジュールの「h5py」が新...
#code(nonumber){{
pip uninstall h5py
pip install h5py==2.10.0
}}
あとRTX 30x0 でcinderellaを動かすには crYOLO と同じように...
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