Command line tools¶
This page gives instructions on how to launch DeepFinder steps from the terminal.
Set up¶
First, add DeepFinder to your path with following command: export PATH="/path/to/deep-finder/bin:$PATH"
You can add this command to your ~/.bash_profile
Note
Running these commands without any argument will launch the graphical user interface.
Target generation¶
For generate_target
and train
, it is not possible to pass all necessary parameters as terminal arguments. Therefore, they have to be passed as an xml file.
Usage:
generate_target -p /path/to/parameters.xml
Parameter file:
<paramsGenerateTarget>
<path_objl path="/path/to/objl.xml"/>
<path_initial_vol path=""/>
<tomo_size>
<X size="400"/>
<Y size="400"/>
<Z size="200"/>
</tomo_size>
<strategy strategy="spheres"/>
<radius_list>
<class1 radius="1"/>
<class2 radius="2"/>
<class3 radius="3"/>
</radius_list>
<path_mask_list>
<class1 path=""/>
</path_mask_list>
<path_target path="/path/to/target.mrc"/>
</paramsGenerateTarget>
Note
You can find classes with methods for automatically reading and writing these parameter files in utils/params.py
Training¶
Usage:
train -p /path/to/parameters.xml
Parameter file:
<paramsTrain>
<path_out path="./"/>
<path_tomo>
<tomo0 path="/path/to/tomo0.mrc"/>
<tomo1 path="/path/to/tomo1.mrc"/>
<tomo2 path="/path/to/tomo2.mrc"/>
</path_tomo>
<path_target>
<target0 path="/path/to/target0.mrc"/>
<target1 path="/path/to/target1.mrc"/>
<target2 path="/path/to/target2.mrc"/>
</path_target>
<path_objl_train path="/path/to/objl_train.xml"/>
<path_objl_valid path="/path/to/objl_valid.xml"/>
<number_of_classes n="3"/>
<patch_size n="48"/>
<batch_size n="20"/>
<number_of_epochs n="100"/>
<steps_per_epoch n="100"/>
<steps_per_validation n="10"/>
<flag_direct_read flag="False"/>
<flag_bootstrap flag="True"/>
<random_shift shift="13"/>
</paramsTrain>
Segmentation¶
Usage:
segment -t /path/tomogram.mrc
-w /path/net_weights.h5
-c NCLASS
-p PSIZE
-o /path/output/segmentation.mrc
With NCLASS and PSIZE integer values. See Guide for parameter description.
Clustering¶
Usage:
cluster -l /path/to/segmentation.mrc
-r clusterRadius
-o /path/to/output/object_list.xml