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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.
+\\

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