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downloads:cryolo_1 [2019/07/29 09:37]
twagner [Installation] 		downloads:cryolo_1 [2019/07/29 15:58]
twagner [Known issues]
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 ====crYOLO==== ====crYOLO====
-Version: 1.4.0+Version: 1.4.1
  
-Uploaded:  11. July 2019+Uploaded:  29. July 2019
  
-[[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_4_0/cryolo-1.4.0.tar.gz|DOWNLOAD]]+[[https://pypi.org/project/cryolo/#files|DOWNLOAD]]
  
 Please see [[downloads:cryolo_1#installation|install instructions]] how to get it running on the CPU. Please see [[downloads:cryolo_1#installation|install instructions]] how to get it running on the CPU.
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 ====crYOLO boxmanager==== ====crYOLO boxmanager====
  
-Version: 1.2.3+Version: 1.2.6
  
-Uploaded: 11. July 2019+Uploaded: 29. July 2019
  
-[[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_2_3/cryoloBM-1.2.3.tar.gz|DOWNLOAD]]+[[https://pypi.org/project/cryoloBM/#files|DOWNLOAD]]
  
 [{{ :downloads:cryolophosaurusdb.jpg?150|**crYOLO Phosauraus**Net's eponym}}] [{{ :downloads:cryolophosaurusdb.jpg?150|**crYOLO Phosauraus**Net's eponym}}]
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   * Issue 0: Training on multiple GPUs sometimes lead to worse performance (higher loss). We currently recommend to train on single gpus.   * Issue 0: Training on multiple GPUs sometimes lead to worse performance (higher loss). We currently recommend to train on single gpus.
   * Issue 17: On the fly filtering (%%--%%otf) is slower than using it not, as the filtering is not parallelized in this case.    * Issue 17: On the fly filtering (%%--%%otf) is slower than using it not, as the filtering is not parallelized in this case. 
-  * Issue 22: Since crYOLO 1.4.0 it sometimes take long until it starts picking. The reason seems to be the tensorflow update. + 
-  * Issue 23: Fine-tune mode does not start (cannot find layer model_3). Will be fixed in 1.4.1.+
 <hidden Closed issues> <hidden Closed issues>
   * <del>  Issue 1: crYOLO sometimes not exit properly after training finished. Has to be killed manually.</del>   * <del>  Issue 1: crYOLO sometimes not exit properly after training finished. Has to be killed manually.</del>
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   * <del>Issue 21: The search range for filament tracing is too low for many datasets. To check if you are affected: Use your trained model and pick without the filament options. Check if your filaments a nicely picked (many consecutive boxes on a filament). In the next version, the search range will be increased and added as an optional parameter.</del>   * <del>Issue 21: The search range for filament tracing is too low for many datasets. To check if you are affected: Use your trained model and pick without the filament options. Check if your filaments a nicely picked (many consecutive boxes on a filament). In the next version, the search range will be increased and added as an optional parameter.</del>
   * <del>Issue 22: If absolute paths are used in the field "train_image" in your configuration file, filtering is skipped.</del>   * <del>Issue 22: If absolute paths are used in the field "train_image" in your configuration file, filtering is skipped.</del>
 +  * <del>Issue 23: Since crYOLO 1.4.0 it sometimes take long until it starts picking. The reason seems to be the tensorflow update.<del>
 +  * <del>Issue 24: Fine-tune mode does not start (cannot find layer model_3). Will be fixed in 1.4.1.<del>
 </hidden> </hidden>
  
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 After that, create a new virtual environment: After that, create a new virtual environment:
 <code> <code>
-conda create -n cryolo -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 cython+conda create -n cryolo -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython
 </code> </code>
  
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 <code> <code>
 source activate cryolo source activate cryolo
-</code> 
- 
-Install fast numpy from conda: 
-<code> 
-conda install numpy==1.14.5 
 </code> </code>
  
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 pip install 'cryolo[cpu]'  pip install 'cryolo[cpu]' 
 </code> </code>
 +
 +<note>
 +During the installtion of crYOLO you will see the following error message:
 +''ERROR: imagecodecs-lite 2019.2.22 has requirement numpy>=1.15.4, but you'll have numpy 1.14.5 which is incompatible.''
 +However, you can ignore it. It is actually also working with numpy==1.14.5
 +</note>
  
 **That's it!** **That's it!**
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 ====crYOLO==== ====crYOLO====
 +
 +**crYOLO 1.4.1:**
 +  * Downgrade the dependencies to tensorflow 1.10.1 and numpy 1.14.5 as some users reported long initialization times. (Thanks to Shaun Rawson)
 +  * The initialization weights are not longer shipped with the package and downloaded on-the-fly (because they are big and pypi does not allow such big packages)
 +  * crYOLO is installed through pypi
 +  * crYOLO box manager is installed through pypi and automatically shipped with the crYOLO package
 +  * Fix fine-tune mode (Thanks to Antoine Koehl)
 +  * Fixed normalization function for YOLO backend (Thanks to Wolfgang Lugmayr)
 +
 +<hidden **Old crYOLO change logs**>
  
 **crYOLO 1.4.0:** **crYOLO 1.4.0:**
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   * Update numpy from 1.14.5 to 1.15.4 to make crYOLO compatible with JANNI   * Update numpy from 1.14.5 to 1.15.4 to make crYOLO compatible with JANNI
  
-<hidden **Old crYOLO change logs**> 
 **crYOLO 1.3.6:** **crYOLO 1.3.6:**
   * Changed filament search radius factor from 0.8 to 1.41 (this fixed issue 21)   * Changed filament search radius factor from 0.8 to 1.41 (this fixed issue 21)
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 </hidden> </hidden>
 ====crYOLO Boxmanager==== ====crYOLO Boxmanager====
-**crYOLO Boxmanager Version 1.2.3:**+**crYOLO Boxmanager Version 1.2.6:**
   * Make it compatible with current new environment   * Make it compatible with current new environment
  
 <hidden **Old crYOLO Boxmanager change logs**> <hidden **Old crYOLO Boxmanager change logs**>
 +
 +**crYOLO Boxmanager Version 1.2.3:**
 +  * Make it compatible with current new environment
 +
 **crYOLO Boxmanager Version 1.2.2:** **crYOLO Boxmanager Version 1.2.2:**
   * Makes sure that the correct version of MatplotLib is used.   * Makes sure that the correct version of MatplotLib is used.
downloads/cryolo_1.txt · Last modified: 2021/02/19 09:43 by twagner

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