Helicon Focus Batch Processing Workflow

This repository provides an automated workflow for batch processing focus stacking tasks using Helicon Focus software. It also includes scripts to parse metadata from folder structures and save it for downstream processing.

Workflow Overview

1. Folder Validation:

   • Python script identifies valid folders containing .ARW files.
   • It excludes invalid folders (e.g., those with CaptureOne subdirectories).

2. Batch Processing:

   • A .bat script processes valid folders, generating .dng stacked images.
   • Each .dng file is saved at the parent folder level with a robust name.

3. Metadata Extraction:

   • A second Python script extracts metadata from processed folders and saves it to a CSV file.
   • Metadata includes:
     • Collection object or photographer.
     • Hash value (if available).
     • Species name.
     • View type (e.g., dorsal, lateral).
     • Extra details (e.g., magnification).

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Repository Structure

|-- *\[INPUT_DIR]\[Folder_With_ARW]\*.ARW
|-- generate_valid_folders.py # Validates folders and generates folders_to_process.txt 
|-- process_folders_master.bat # Master batch script orchestrating Python and .bat scripts 
|-- process_valid_folders.bat # Processes folders using Helicon Focus 
|-- postprocess_file_metadata.py # Parses metadata from processed folders (Unfinished)
|-- *\[INPUT_DIR]\folders_to_process.txt # List of valid folders (generated) 
|-- *\[INPUT_DIR]\parsed_metadata.csv # Final metadata in tabular format (output)

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Usage

Setup

Install "HeliconFocus" and the "Adobe DNG Converter" plugin from the [Helicon Soft website][https://www.heliconsoft.com/software-downloads/]

Step 1 (only first time):

Activate the licence with a valid licence key for the software.

LICENSE_KEY=12345678                                                              :: Replace with your activation key
HF_EXE="C:\Program Files\Helicon Software\Helicon Focus 8\HeliconFocus.exe"       :: Define path to Helicon Focus executable and main directory containing subfolders
%HF_EXE% --activationCode %LICENSE_KEY% --register-global

Step 2: generate valid folders to batch process them for Focus stacking within the .ARW images in those folders.

Step 2.1: generate valid folders

Run the following command to generate a folders_to_process.txt file within the [INPUT_DIR] :

process_folders_master.bat -d [INPUT_DIR] -t [all|keep]

[INPUT_DIR]: Root directory containing subfolders with .ARW files. [all|keep]: a flagg to determine if all valid folders need to be stacked or just the ones without a .dng stacked image in their parent folder (default is all)

Example Directory Structure

Before Running the Script

C:\path_to_images
├── Folder1
│   ├── file1.ARW
│   ├── file2_label.ARW
├── Folder2
│   ├── file3.ARW
│   ├── file4.ARW
│   └── SubFolder1
│       ├── file5.ARW
│       └── file6.ARW
├── CaptureOne
│   ├── file7.ARW
│   └── file8.ARW

After Running the Script

Content of folders_to_process.txt:

C:\path_to_images\Folder2
C:\path_to_images\Folder2\SubFolder1

Step 2.2: to batch process them for Focus stacking within the .ARW images in those folders.

Helicon Focus processes the folders listed in folders_to_process.txt. Output .dng files are saved in the parent folder.

Example Directory Structure

Before Processing:

C:\path_to_images
├── Folder1
│   ├── Image1.ARW
│   ├── Image2.ARW
│   └── Image3.ARW
├── Folder2
│   ├── Image1.ARW
│   └── Image2.ARW
├── folders_to_process.txt

After Processing:

C:\path_to_images
├── Folder1
│   ├── Image1.ARW
│   ├── Image2.ARW
│   ├── Image3.ARW
│   └── Folder1.dng
├── Folder2
│   ├── Image1.ARW
│   ├── Image2.ARW
│   └── Folder2.dng
├── folders_to_process.txt

Step 3: Extract Metadata (Unfinished)

Run the postprocess_file_metadata.py script to parse folder metadata:

python postprocess_file_metadata.py