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downloads:cryolo_1 [2019/07/23 10:31] twagner [Known issues] |
downloads:cryolo_1 [2019/09/06 14:04] twagner [crYOLO] |
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====crYOLO==== | ====crYOLO==== | ||
- | Version: 1.4.0 | + | Version: 1.5.0 |
- | Uploaded: | + | Uploaded: |
- | [[ftp://ftp.gwdg.de/pub/misc/sphire/ | + | [[https://pypi.org/project/cryolo/#files|DOWNLOAD]] |
Please see [[downloads: | Please see [[downloads: | ||
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====crYOLO boxmanager==== | ====crYOLO boxmanager==== | ||
- | Version: 1.2.3 | + | Version: 1.2.6 |
- | Uploaded: | + | Uploaded: |
- | [[ftp://ftp.gwdg.de/pub/misc/sphire/ | + | [[https://pypi.org/project/cryoloBM/#files|DOWNLOAD]] |
[{{ : | [{{ : | ||
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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> | ||
* < | * < | ||
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* < | * < | ||
* < | * < | ||
+ | * < | ||
+ | * < | ||
</ | </ | ||
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After that, create a new virtual environment: | After that, create a new virtual environment: | ||
< | < | ||
- | 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 |
</ | </ | ||
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< | < | ||
source activate cryolo | source activate cryolo | ||
- | </ | ||
- | |||
- | Install fast numpy from conda: | ||
- | < | ||
- | conda install numpy==1.15.4 | ||
</ | </ | ||
In case you run **crYOLO on a GPU** run: | In case you run **crYOLO on a GPU** run: | ||
< | < | ||
- | pip install ' | + | pip install ' |
</ | </ | ||
But if you want to run **crYOLO on a CPU** run: | But if you want to run **crYOLO on a CPU** run: | ||
< | < | ||
- | pip install ' | + | pip install ' |
</ | </ | ||
- | Finally | + | < |
- | < | + | During the installtion of crYOLO |
- | pip install cryoloBM-X.Y.Z.tar.gz | + | '' |
- | </code> | + | However, you can ignore it. It is actually also working with numpy==1.14.5 |
+ | </note> | ||
**That' | **That' | ||
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====crYOLO==== | ====crYOLO==== | ||
+ | |||
+ | **crYOLO 1.5.0:** | ||
+ | * Added a GUI for crYOLO (start with cryoloo.py) | ||
+ | * Add rotation as data augmentation | ||
+ | * Number of layers for fine tuning are now changeable (-lft) | ||
+ | * cryolo_evaluation.py will now output a html file with the results. | ||
+ | * Set patch argument as deprecated | ||
+ | * Remove warmup as config file option. Please specify it with -w. | ||
+ | |||
+ | **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 | ||
+ | * Fixed 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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</ | </ | ||
====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. |