pipeline:window:sp_cryolo_predict

This version (2019/04/02 11:40) is a draft.
Approvals: 0/1

crYOLO - predict: Prediction with crYOLO, a deep learning high accuracy particle picking procedure.


Usage in command line

sp_cryolo_predict.py config_path target_dir model_path output_dir --cryolo_predict_path=CRYOLO_PATH --confidence_threshold=confidence_threshold --gpu=gpu --gpu=GPU_NUMBER --filament_mode --filament_width=FILAMENT_WIDTH --min_box_per_filament=MIN_BOX_PER_FILAMENT --box_distance=BOX_DISTANCE --gpu_fraction=GPU_FRACTION --num_cpu=NUM_CPU --nosplit --nomerging


To pick with crYOLO one have to specifiy the config file, the target folder containing the images and the output folder for writing the box files. Optionally one can specify the confidence threshold and which GPUs should be used.


Prediction:

sp_cryolo_predict.py config_path target_dir model_path output_dir --confidence_threshold=0.3 --gpu=0

\


Main Parameters

--cryolo_predict_path
crYOLO predict executeable
Path to the crYOLO prediction executeable (default none)
config_path
Config file: Path of the crYOLO config file. (default required)
target_dir
Image directory
Folder which contain all images. (default none)
model_path
Model path
Path to the trained model. (default required)
output_dir
Output directory
Folder to write the box files. (default none)


Advanced Parameters

--confidence_threshold
Confidence threshold [0-1]
Confidence threshold for picking. Particles with a confidence threshold lower than this value will be discarded. (default 0.3)
--gpu
GPUs
List of GPUs to use. (default 0)
--gpu_fraction: GPU memory fraction
Specify the fraction of memory per GPU used by crYOLO during prediction. Only values between 0.0 and 1.0 are allowed. (default 1.0)
--num_cpu: Number of CPUs
Number of CPUs used during prediction. By default it will use half of the available CPUs. (default 1.0)
--filament_mode
Filament mode [True/False]
Check if you want to use the filament mode. (default False)
--filament_width
Filament width [Pixel]
Width of your filament in pixel. (default 100)
--filament_mode==True
--min_box_per_filament
Minimum number of boxes per filament
Specifies the minimum number of boxes per filament. (default 6)
--filament_mode==True
--box_distance
Box distance
Distance between two boxes in pixel. (default 20)
--filament_mode==True
--nosplit: Don't split curved filaments
If checked, the filament mode does not split to curved filaments. (default False)
--filament_mode==True
--nomerging: Don't merge filaments
If checked, the filament mode does not merge filaments. (default False)
--filament_mode==True


It will write box and star files into your output directory.


List of Output Files

Write box and star files into the output directory


See the reference below.


Picking is very fast with up to 8 micrographs / s.


2019/09/24 Thorsten Wagner

  • Initial creation of the document


Thorsten Wagner


Category 1:: APPLICATIONS


sparx/bin/sp_cryolo_predict.py


Stable


None right now.


  • pipeline/window/sp_cryolo_predict.txt
  • Last modified: 2019/04/02 11:40
  • by lusnig