The respective sections go into further details; alternatively issues can be raised on the project’s GitHub-Page.
+
+ Main Script
+To make things easier, I will establish a few rules used throughout this section.
+Anytime text is formatted like this (X), it refers to a button, editable field, drop-down menu, or in general a control on the GUI. The number at the end, here an (X) signifies which section of the GUI this control is located in. As an example, csv2xlsx (4) is the button used to convert csv-files to xlsx-files, located under 4. Auxiliary Utilities.
+
+ Selecting a configuration
+The main task of this program is to generate a suitable configuration file which can be used with the R-Script GFA_Evaluation.R bundled alongside this program. For details on its functioning, see documentation on GFA_Evaluation.R
+Configuration files can be handled by this program in three ways: 1. New Config in Folder (1)
+This allows you to create a config-file for a new project 2. Edit existing Config (1)
+This allows you to load an existing config file for editing 3. Double-clicking a configuration previously used under Configurations and Image-renaming (4)
+This effectively works the same as Number 2. 4. You may also drag and drop a config file onto the greyed-out field (1) to the right of those two buttons.
+Under curr. loaded Config (3), the path to a configuration-file will be visible if the user has chosen a path already - by loading a config, or by manually selecting a config’s location when clicking New Config in Folder. When saving or previewing a configuration, the program will attempt to validate the inputs given by the user. Certain inputs however cannot be validated with certainty by the program. In these cases, the user is asked to manually confirm or discard their choices. These popups differentiate between mild warnings (yellow warning signs) and severe warnings (red x-crosses). This depends on how severe a false decision may be, or how vital it is for GFA_main()’s functioning to have correct inputs. ### Selecting and Editing an R-Script
+To complement the config-files generated, the user may generate a barebones “starter”-R-Script which will call GFA_main().
+R-Scripts can be handled by this program in three ways: 1. New R-StarterScript (2)
+This allows you to create a new R-Script for a new project 2. Edit existing R-StarterScript (2)
+This allows you to load an existing R-Script for editing 3. Double-clicking an R-Script previously used under R Scripts (4)
+This effectively works the same as Number 2. 4. You may also drag and drop a config file onto the greyed-out field (2) to the right of those two buttons.
1 Note that this is not the same greyed-out field that is used for dropping configurations.
Under curr. loaded R-Script (3), an R-Script is visible. If the field is empty, attempting to write to a file will result in the program asking the user to select an appropriate location.
+
+
+ Editing a configuration
+First off it makes sense to take a look at the example configurations and how the results of them look. Examples can be found under XX\res\Examples, where XX is the folder in which this program resides. They are not meant to display sensible data, the data may be unrealistic. The intention of the reference files is mostly to give simple visualisation of a configuration. They also don’t showcase all potential cases, as those are just too many.
+Configurations can be edited after being loaded (see section on config-selection).
+If a configuration is leaded, its path will be visible under curr. loaded Config (3)
+Alternatively, the user can create a config file first.
+
+
+
+ csv2xlsx
+After selecting a configuration file (see Section 1.1.1), you may use the button csv2xlsx (4) to run the csv-to-xlsx-converter embedded into the program. It will parse through all _*.csv_-files in any subfolder of the config’s location, check if there is a xlsx-equivalent present, and create it if it is not.
+Note This program will cease to function if the csv’s are not delimited using either , or ;.
+The program will
+
+- replace the cell-delimiter (
, or ;) with ;
+- replace dots
. with ,
+- save this transformed version to the csv-file, effectively overwriting it.
+- Afterwards, it will create an xlsx-copy.
+This functionality requires the program Excel to be installed on the user’s machine, as it takes advantage of Excel’s ComObject-Interface to do its work.
+
+Program Configuration options:
+As with all program-configuration options, these affect the behaviour of the Configurator-Program, not the R-Script.
+Options can be accessed by pressing Alt+P on the Configurator’s main window. It is not recommended to modify the raw config files of this program by hand.
2 You can, obviously. It is just very easy to disrupt or destroy data if you do not know how AutoHotKey handles config files, and more importantly how this program itself handles them. Just use the GUI please.
Rename images
+Program Configuration options:
+After selecting a configuration file (see [Selecting a configuration|here]), you may use the button rename Images (4) to run the image-renamer embedded into the program.
+The program will use the currently loaded configuration to retrieve data required, namely the number of pots per group & groups names. These variables can be changed before submitting. The user can then choose a folder containing images they want to rename. The folder must not contain subfolders which also contain images, or those will also be considered.
+Upon submission, the program will open a preview in which the user can check that each image was associated with its correct name; then submit to rename the images.
+Images are never renamed in-place, instead a set of working copies is made which get renamed instead. They will be located in a GFAR_WD-subfolder of the initially chosen directory, alongside a textfile associating original filenames with their renamed counterparts.
+As with all program-configuration options, these affect the behaviour of the Configurator-Program, not the R-Script.
+Options can be accessed by pressing Alt+P on the Configurator’s main window. It is not recommended to modify the raw config files of this program by hand.
3 You can, obviously. It is just very easy to disrupt or destroy data if you do not know how AutoHotKey handles config files, and more importantly how this program itself handles them. Just use the GUI please.
+
+
+
+
+
+
+
+
+
+| filetype |
+Select if the script should consider JPG- or PNG-files for renaming. |
+
+
+| PutFilesOnClipboard |
+Do you want to have the renamed images put on your clipboard at the end? Suggested if you need to move them all to a different computer. |
+
+
+| CopyFiles |
+Select if you want to copy Ctrl+C the files to your clipboard. Uncheck if you want to cut Ctrl+X them instead |
+
+
+| CopyParentDirectory |
+Select if you want to copy/cut the parent directory, instead of all files. Generally suggested to ease batch-renaming of multiple sets at once. |
+
+
+
+
+
