# Processing Toolkit
This tutorial provides step-by-step guidance for pre- and post- processing toolkit.
> Please use it as needed. If you have any new requirements, please [let me know](zhen.zhang.zz545@yale.edu). 

#### Main Menu

Run ```python -m magneton``` to start the CLI.
This interface displays the basic information of the current system. The main interface consists of 3 functional modules: processing toolkit, affinity map inference module and instance segmentation module.
![Main](../_static/main.png)


Input ```1``` and ```Enter```, enter the **processing toolkit** menu:
![affinity map inference module](../_static/toolkit.png)


#### Options

This module can be used for configuration, data preprocessing and postprocessing. 

##### Global Configuration
Input ```18``` and ```Enter```, view current **global configuration**:
![global configuration](../_static/gc.png)

For the title:
- ```Section```: the configuration file for which module.
- ```Parameter```: the key in configuration file.
- ```Value```: the value of key

For the keys in toolkit module:
> The details of the keys are specified in the YAML files.
- ```split```: the config file path for split tool.
- ```merge```: the config file path for merge tool.
- ```prec```: the config file path for the precomputed format converter.
- ```downsample```: the config file path for the precomputed data downsampling.
- ```gen_mask```: the config file path for mask generator of precomputed data.
- ```mask_prec```:  the config file path for masking of precomputed data.
- ```mask_tif```: the config file path for masking of tif data.
- ```resize_tif```: the config file path for resizing of tif data.


Input ```17``` and ```Enter```, edit current **global configuration**:
> Currently, only modifications are permitted; additions are not allowed.

You can select a value to change:
![select a value to change](../_static/gc1.png)


##### Data preprocessing and postprocessing
The **tool menu**:
![tool menu](../_static/toolkit.png)
###### Split tool
Input ```1``` and ```Enter```, using ***local resources*** to split tif volume to tif blocks with overlap. 

Input ```2``` and ```Enter```, using ***HPC resources*** to split tif volume to tif blocks with overlap. 

The tool is based on the configuration files (```split``` in global configuration file).Before start the training, you can modify the configuration by CLI or any tools:
![split](../_static/toolkit1.png)

###### Merge tool
Input ```3``` and ```Enter```, using ***local resources*** to merge h5 blocks (inference) to tif volume with overlap. 

Input ```4``` and ```Enter```, using ***HPC resources*** to merge h5 blocks (inference) to tif volume with overlap. 

The tool is based on the configuration files (```merge``` in global configuration file).Before start the training, you can modify the configuration by CLI or any tools:
![merge](../_static/tool2.png)

###### Convert tool
Input ```5``` and ```Enter```, using ***local resources*** to convert tif/h5 data to precomputed format. 

Input ```6``` and ```Enter```, using ***HPC resources*** to convert tif/h5 data to precomputed format. 

These tools are based on the configuration files (```prec``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.

###### Downsample tool
Input ```7``` and ```Enter```, using ***local resources*** to create lower-resolution mipmap levels using voxel downsampling for precomputed data.

Input ```8``` and ```Enter```, using ***HPC resources*** to create lower-resolution mipmap levels using voxel downsampling for precomputed data.

These tools are based on the configuration files (```downsample``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.

###### Mask tool
Input ```9``` and ```Enter```, using ***local resources*** to generate binary masks from affinity maps.

Input ```10``` and ```Enter```, using ***HPC resources*** to generate binary masks from affinity maps.

These tools are based on the configuration files (```gen_mask``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.

###### Mask Prec tool
Input ```11``` and ```Enter```, using ***local resources*** to apply a mask to prec images, preserving structure.

Input ```12``` and ```Enter```, using ***HPC resources*** to apply a mask to prec images, preserving structure.

These tools are based on the configuration files (```mask_prec``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.

###### Mask Tif tool
Input ```13``` and ```Enter```, using ***local resources*** to apply a mask to tif images, preserving structure.

Input ```14``` and ```Enter```, using ***HPC resources*** to apply a mask to tif images, preserving structure.

These tools are based on the configuration files (```mask_tif``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.

###### Resize TIf tool
Input ```15``` and ```Enter```, using ***local resources*** to resize tif volumes to new voxel size or dimension.

Input ```16``` and ```Enter```, using ***HPC resources*** to resize tif volumes to new voxel size or dimension.

These tools are based on the configuration files (```resize_tif``` in global configuration file).Before start the converting, you can modify the configuration by CLI or any tools.