pipeline:window:sp_cryolo_predict

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pipeline:window:sp_cryolo_predict [2019/04/02 11:40] (current)
lusnig created
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 +~~NOTOC~~
 +
 +===== sp_cryolo_predict =====
 +crYOLO - predict: Prediction with crYOLO, a deep learning high accuracy particle picking procedure.
 +
 +\\
 +===== Usage =====
 +
 +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
 +
 +\\
 +===== Typical usage =====
 +
 +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
 +
 +\
 +
 +\\
 +===== Input =====
 +=== 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
 +
 +
 +
 +\\
 +===== Output =====
 +It will write box and star files into your output directory.
 +
 +\\
 +=== List of Output Files ===
 +Write box and star files into the output directory
 +
 +
 +\\
 +==== Method ====
 +See the reference below.
 +
 +\\
 +==== Time and Memory ===
 +Picking is very fast with up to 8 micrographs / s.
 +
 +
 +\\
 +==== Developer Notes ====
 +=== 2019/09/24 Thorsten Wagner ===
 +  * Initial creation of the document
 +
 +\\
 +==== Reference ====
 + ​https://​doi.org/​10.1101/​356584
 +
 +\\
 +==== Author / Maintainer ====
 +Thorsten Wagner
 +
 +\\
 +==== Keywords ====
 +Category 1:: APPLICATIONS
 +
 +\\
 +==== Files ====
 +sparx/​bin/​sp_cryolo_predict.py
 +
 +\\
 +==== See also ====
 +[[pipeline:​window:​cryolo|crYOLO]]
 +
 +\\
 +==== Maturity ====
 +Stable
 +
 +\\
 +==== Bugs ====
 +None right now.
 +
 +\\
  
  • pipeline/window/sp_cryolo_predict.txt
  • Last modified: 2019/04/02 11:40
  • by lusnig