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## NanoLocz User Guide <img src="https://github.com/George-R-Heath/NanoLocz/assets/90329395/36d664a6-38e2-4405-b5cc-a962093cf13b" width="30">

<a href="installation.html">Installation</a> - - <a href="getting_started.html">Getting Started</a> - - <a href="saving_data.html">Saving Data</a> \
<a href="image_levelling.html" style="color: red;">Level</a> - - 
<a href="particle_detection.html" style="color: lightblue;">Detect</a> - - 
<a href="fine_align.html" style="color: orange;">FineAlign</a> - - 
<a href="localize.html" style="color: pink;">Localize</a>\
<a href="area_analysis.html" style="color: limegreen;">Area Analysis</a> - - <a href="keyboard_shortcuts.html">Keyboard Shortcuts</a>\
<a href="simulation_afm.html" style="color: orange;">Simulation AFM</a> - - <a href="general_use.html">YouTube Video Tutorials</a> 

# Saving Data
This section explains how to save data in NanoLocz. Data can either be saved/processed in bulk and for later use or by exporting the current views in the plots for figures/presentations.\
[1. Save or Batch Process Data](#1-save-or-batch-process-data)\
[2. Export Images, Videos and Data](#2-exporting-images-videos-and-data) 

## 1. Save or Batch Process Data
The following describes saving and batch processing options so that raw and processed data can be quickly reopened in NanoLocz or other software. See section 2 for export of images / movies for publication quality figures or presentations. 

### Single or Batch Save 
- To save one or multiple files open the Save Options using save <img src="https://github.com/George-R-Heath/NanoLocz/assets/90329395/6e6c149b-85c8-46d2-9d31-4152f5415854" width="25">
- Select the format, to retain all image and analysis data use combined file format options. To access the images and data analysis in other software use separate Image/video and Analysis tables formats.
- Select Files to save using the Save dropdown box:\
**Current File:** Selects the currently open image\
**All Files:** Selects all files in the open folder\
**All Processed:** Selects and displays only files that have been processed (levelled, filtered or analysed)\
**Session:** Saves all processed data in a single .mat file which can be reopened in NanoLocz 
- Use the checkboxes next to each file name to select which files to Save.
- To level unprocessed data select the 'Level unprocessed data' option and images will be levelled using the current level settings in the main NanoLocz window.
- Select the Output folder you want NanoLocz to save to.
- Select subfolder preferences:\
**Create a new subfolder:** Generates 1 subfolder in the Output folder with the name: ‘xxxxxxx NanoLocz Output’ where xxxxxx is the name of the current open folder. Recommended for general use.\
**Create multiple subfolder(s):** Generates 1 subfolder per image/movie in the Output folder with the name: ‘Image Name’. Recommended if saving many separate tables and images.   
- Press Save to run the save
![save](https://github.com/George-R-Heath/NanoLocz/assets/90329395/c2e197c7-def9-4347-ba4b-89874aa0edaa)

### Format Options 
![Format table](https://github.com/George-R-Heath/NanoLocz/assets/90329395/dd2755a1-09c7-4d26-9dbc-4ee9ce17c5db)

### AutoSave
By turning on AutoSave - files will automatically be saved to the output folder according to the settings in Preferences. To change these setting - open the preferences window using the Cog icon or Settings option. 
![pref](https://github.com/George-R-Heath/NanoLocz/assets/90329395/ee3f646d-4075-405f-afeb-ada44420036f)

## 2. Exporting Images, Videos and Data
This section describes how to export data based on the current view - useful for publication quality figures, presentations, or exporting raw data in manual way. See section 1 for batch export options. 
### 2.1 Image and Video export
**Option 1:**
* Select ‘Plot 1’ (left image panel) or ‘Plot 2’ (right Image panel) from the dropdown box
![export](https://github.com/George-R-Heath/NanoLocz/assets/90329395/b5143548-f448-4614-9816-6bf05a907b9a)
* Select the desired format from the dropdown box (.tiff, .csv, .txt, .xls, gif, .avi, .png, .jpeg or .pdf)
* Press the Export button, then select file name and save location.
* Don’t close the image window that pops up until after the file has saved

Note: Exporting as .tiff, .csv, .txt, or .xls enables export without loss of image information whereas export as .gif, .avi, .png, .jpeg or .pdf gives movies/images at presentation or publication quality with automatic scale bars and timestamps. 

**Option 2** (good for creating publication quality figures or grabbing images quickly):
* Press the Pop Out button <img src="https://github.com/George-R-Heath/NanoLocz/assets/90329395/c1e4a884-38cd-49f9-b71a-1d7925d73cc3" width="20">
* Resize the image 
* Go to the top right hand side of the image and select the far left button from the toolbar
* For making figures choose ‘Copy as vector graphic’ Or for quickly copying an image choose ‘Copy as image’, the image can then be pasted into another program.
* Once pasted vector files can be ungrouped to enable movement and formatting of any labels (eg. scale bars, timestamps…) 
* Only works for single images\
   ![snip](https://github.com/George-R-Heath/NanoLocz/assets/90329395/bf909586-d6b3-4c50-82ae-9ce813b126c6)

### 2.2 Analysis data export
* Open the data Viewer 
* With Plot type table selected, choose the table of data required for export 
* Select format (.txt, .csv, .xls) and press export
* Alternatively, manually select entries from the table and copy (ctrl+c)

### 2.3 MATLAB data export (MATLAB app only)
* From the ‘Plot 1’ dropdown select ‘data’ 
* From the desired format dropdown box select ‘MATLAB Workspace’
* Press the Export button
* Data will appear in the MATLAB workspace