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

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===== Usage =====

Usage in command line

  sp_cryolo_predict.py config_path target_dir model_path output_directory --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

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===== Typical usage =====

To pick with crYOLO, one has to specify 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.

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

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===== Input =====
=== Main Parameters ===
  ; %%--%%cryolo_predict_path : crYOLO predict executable : Path to the cryolo_predict.py in your crYOLO environment (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_directory : Output directory : Folder to write the box files. (default none)


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=== 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, separated by commas if more than one. If no GPU is present, be sure to supply the non-GPU executable. (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)::
  ; %%--%%filament_mode : Filament mode [Yes/No] : Check if you want to use the filament mode. (default False)::True;Main
  ; %%--%%filament_width : Filament width [Pixel] : Width of your filament in pixel. (default 100) : %%--%%filament_mode==True:100;Main
  ; %%--%%min_box_per_filament : Minimum number of boxes per filament : Specifies the minimum number of boxes per filament. (default 6) : %%--%%filament_mode==True:6;Main
  ; %%--%%box_distance : Box distance : Distance between two boxes in pixels. (default -1) : %%--%%filament_mode==True:-1;Main
  ; %%--%%nosplit: Don't split curved filaments : If checked, the filament mode does not split 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:



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

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=== List of Output Files ===
Write box and star files into the output directory


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==== Method ====
See the reference below.

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==== Time and Memory ===
Picking is very fast with up to 8 micrographs / s.


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==== Developer Notes ====
=== 2019/09/24 Thorsten Wagner ===
  * Initial creation of the document

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==== Reference ====
 https://doi.org/10.1101/356584

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==== Author / Maintainer ====
Thorsten Wagner

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_cryolo_predict.py

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==== See also ====
[[pipeline:window:cryolo|crYOLO]]

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==== Maturity ====
Stable

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==== Bugs ====
None right now.

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