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pipeline:window:cryolo [2019/03/18 14:58]
twagner [Picking particles - Without training using a general model] 		pipeline:window:cryolo [2019/03/28 07:47]
twagner [Configuration]
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 to the training command. to the training command.
 ==== Picking ==== ==== Picking ====
-You can now use the model weights saved in ''model.h5'' to pick all your images in the directory ''full_data''. To do this, run: +You can now use the model weights saved in ''model.h5'' (//if you come to this section from another point of the tutorial, this filename might be different like ''gmodel_phosnet_X_Y.h5''//) to pick all your images in the directory ''full_data''. To do this, run: 
 <code> <code>
 cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/ cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/
 </code> </code>
  
-You will find the picked particles in the directory ''boxfiles''+You will find the picked particles in the directory ''boxfiles''.
  
 If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter: If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter:
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 ==== Configuration ==== ==== Configuration ====
-You can configure it the same way as for a "normal" project. We recommend to use [[:cryolo_nets#network_2_yolo_with_patches|YOLO in "patch mode" with 3x3 patches]]:+You can configure it the same way as for a "normal" project. 
 <code json config.json> <code json config.json>
 { {
     "model" : {     "model" : {
-        "architecture":         "YOLO", +        "architecture":         "PhosaurusNet", 
-        "input_size":           768, +        "input_size":           1024, 
-        "anchors":              [200,200],+        "anchors":              [160,160],
         "max_box_per_image":    600,         "max_box_per_image":    600,
-        "num_patches":          3, +        "num_patches":          1, 
-        "filter":               [0.1,"tmp_filtered"]+        "filter":               [0.1,"filtered"]
     },     },
  
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 } }
 </code> </code>
 +
 //[[:cryolo_config|Click here to get more information about the configuration file]]// //[[:cryolo_config|Click here to get more information about the configuration file]]//
  
pipeline/window/cryolo.txt · Last modified: 2021/02/19 10:00 by twagner

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