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janni_tutorial [2019/09/16 13:22] shaikh [Start JANNI] |
janni_tutorial [2020/09/24 14:46] twagner [Training a model for your data] |
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It will tell you if something goes wrong. Pressing " | It will tell you if something goes wrong. Pressing " | ||
==== Training a model for your data ==== | ==== Training a model for your data ==== | ||
- | In case you want to use the general model ([[janni# | + | In case you want to use the general model ([[janni# |
- | In case you would like to train a model for your data, you need to copy a couple of movie files into a separate directory. We typically use at least 30 movies (unaligned) to train the model. | + | In case you would like to train a model for your data, you need to copy a few movie files into a separate directory. We typically use at least 30 movies (unaligned) to train the model. |
+ | |||
+ | <note important> | ||
+ | ** Setup binning ** | ||
+ | In case your movies are superresolution and you later want to denoise binned micrographs, | ||
+ | </ | ||
+ | |||
+ | The next thing you have to do is to create a configuration file for JANNI. | ||
=== Configuration === | === Configuration === | ||
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{{ :: | {{ :: | ||
- | Press "start" and the config will be written in the specified // | + | Press "Start," and the config |
<hidden **Generate the configuration file with the command line**> | <hidden **Generate the configuration file with the command line**> | ||
If you would like to use the command line, you can get a description of all parameters with: | If you would like to use the command line, you can get a description of all parameters with: | ||
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=== Training === | === Training === | ||
- | In principle you just have to specify the config file. However, you might want to specify the GPU ID as well. You find the GPU option in the //Optional arguments// tab. | + | In principle, you simply |
{{: | {{: | ||
- | Press " | + | Press " |
<hidden **Run the training with the command line**> | <hidden **Run the training with the command line**> | ||
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</ | </ | ||
</ | </ | ||
- | |||
==== Denoise ==== | ==== Denoise ==== | ||
- | With a trained model (either trained by you or the general model ([[janni# | + | With a trained model (either |
{{ :: | {{ :: | ||
- | You might also want to change the GPU ID in //Optional arguments// tab. After that press the //Start// button. JANNI will denoise your images | + | You might also want to change the GPU ID in //Optional arguments// tab. Then, press the //Start// button. JANNI will denoise your images |
<hidden **Run prediction in the command line**> | <hidden **Run prediction in the command line**> | ||
- | In case you need a description of all available parameters type: | + | In case you need a description of all available parameters, type: |
< | < | ||
- | janni_denoise.py | + | janni_denoise.py |
</ | </ | ||
- | The following command will run the denoise the images in ''/ | + | The following command will run the denoise the images in ''/ |
< | < | ||
- | janni_denoise.py | + | janni_denoise.py |
</ | </ | ||
</ | </ |