FFMPEG_workaround_hack.py

# User Inputs and Documentation:
# - debug_mode: Enable or disable debug mode for verbose output. Set to True or False.
# - ffmpeg_path: The path to the FFMPEG executable. Adjust according to your FFMPEG installation.
ffmpeg_path = "C:/tools/ffmpeg-master-latest-win64-gpl/bin/ffmpeg.exe"  # Default FFMPEG path
# - output_directory: The directory where the output video will be saved. This is chosen by the user at runtime.
# - frame_rate: The frame rate of the output video. Adjust as needed.
frame_rate = 24  # Default frame rate for video generation
# - The script assumes the image stack is in RGB format. Ensure your image stack is RGB before running.




# FFMPEG Installation on Windows:
# 1. Download the latest version of FFMPEG from https://ffmpeg.org/download.html#build-windows
# 2. Extract the downloaded ZIP file to a location of your choice (e.g., C:/tools/ffmpeg)
# 3. Add the bin folder within the extracted FFMPEG folder to your system's PATH environment variable
#    - Right-click on 'This PC' or 'My Computer' and select 'Properties'
#    - Click on 'Advanced system settings' and then 'Environment Variables'
#    - Under 'System Variables', find the 'Path' variable and click 'Edit'
#    - Add the path to the FFMPEG bin folder (e.g., C:/tools/ffmpeg/bin) and click 'OK'

# Running Jython Plugins in Fiji:
# 1. Download and install Fiji from https://fiji.sc/
# 2. Start Fiji and select 'Plugins' > 'Scripts' > 'New' > 'Script...'
# 3. Choose 'Python' as the language for the new script
# 4. Copy and paste this script into the script editor window
# 5. Save the script with a .py extension to the Fiji plugins folder or any subfolder
# 6. Run the script by selecting it from 'Plugins' > 'Scripts'



from ij import IJ, WindowManager
from ij.io import DirectoryChooser
from java.io import File
import os
import subprocess
import time

# Enable debug mode (set to True for verbose output)
debug_mode = True

# Function to print debug messages with timestamp
def debug(message):
    if debug_mode:
        timestamp = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
        IJ.log(timestamp + " DEBUG: " + message)

# Set default FFMPEG path (hardcoded)
ffmpeg_path = "C:/tools/ffmpeg-master-latest-win64-gpl/bin/ffmpeg.exe"

# Verify that ffmpeg_path exists before proceeding
if not os.path.exists(ffmpeg_path):
    IJ.showMessage("Error", "FFMPEG executable not found at: " + ffmpeg_path + " Please verify the path and try again.")
    raise SystemExit("FFMPEG path verification failed.")
debug("FFMPEG path: " + ffmpeg_path)

# Prompt the user for output directory
output_directory = DirectoryChooser("Choose output directory").getDirectory()
if not output_directory:
    IJ.showMessage("Error", "No output directory selected.")
    raise SystemExit("No output directory selected.")
debug("Output directory: " + output_directory)

# Verify if an active image stack is present
if WindowManager.getImageCount() < 1:
    IJ.showMessage("Error", "No open images found.")
    raise SystemExit("No images found.")

# Get the currently active image and its title before duplicating
original_imp = IJ.getImage()  # Get the original image
original_title = original_imp.getTitle()  # Get the title of the original image

# Duplicate the image for processing to avoid modifying the original
imp = original_imp.duplicate()

stack_size = imp.getStackSize()
debug("Original title: " + original_title)
debug("Number of slices in stack: " + str(stack_size))

# Assumption: The image stack is an RGB color stack
# The script assumes that each frame in the stack is a full-color (RGB) image.
# This is important because FFMPEG will expect the input frames to have color information
# when creating the video output. If the image stack is not RGB (e.g., grayscale or single-channel),
# the resulting video may not be correct, or FFMPEG may fail.
# Make sure that your input image stack is in RGB format before running this script.

# Set parameters for video generation
frame_rate = 24
output_filename = original_title + ".mp4"
output_file = os.path.join(output_directory, output_filename)
debug("Output file: " + output_file)

# Set temporary directory for frames
temp_directory = IJ.getDirectory("temp")
debug("Temporary directory for frames: " + temp_directory)

# Extract frames from the stack
if stack_size > 1:
    for i in range(1, stack_size + 1):
        imp.setSlice(i)
        frame_path = os.path.join(temp_directory, "frame_" + str(i).zfill(5) + ".png")
        IJ.saveAs(imp, "PNG", frame_path)
        debug("Saved frame: " + frame_path)    
else:
    IJ.showMessage("Error", "The current image is not a stack.")
    raise SystemExit("No stack available to convert.")

# Construct the FFMPEG command to convert image stack to MP4
ffmpeg_command = [
    ffmpeg_path,
    "-r", str(frame_rate),
    "-i", os.path.join(temp_directory, "frame_%05d.png"),
    "-c:v", "libx264",
    "-pix_fmt", "yuv420p",
    output_file
]

# Execute the command and redirect output to a log file
temp_log_file = os.path.join(temp_directory, "ffmpeg_conversion_output.log")
with open(temp_log_file, "w") as log_file:
    process = subprocess.Popen(ffmpeg_command, stdout=log_file, stderr=subprocess.STDOUT)
    process.wait()

# Read and log the output of FFMPEG
with open(temp_log_file, "r") as log_file:
    ffmpeg_log = log_file.read()
    IJ.log("FFMPEG command output: " + ffmpeg_log)

# Notify the user that the command has been executed
IJ.log("FFMPEG conversion command executed: " + ' '.join(ffmpeg_command))

# Cleanup: Delete temporary frame files after FFMPEG completes
deleted_count = 0
for file_name in os.listdir(temp_directory):
    if file_name.startswith("frame_") and file_name.endswith(".png"):
        frame_path = os.path.join(temp_directory, file_name)
        try:
            os.remove(frame_path)
            deleted_count += 1
        except Exception as e:
            debug("Failed to delete file: " + frame_path + ", error: " + str(e))

debug("Deleted " + str(deleted_count) + " temporary frame files")

# Show a completion message to the user
if os.path.exists(output_file):
    IJ.showMessage("Video Creation Complete", "The video has been saved to: " + output_file)
else:
    IJ.showMessage("Error", "Failed to create the video. Check the log for details.")

debug("Script execution completed")

# Print final debug message to console
if debug_mode:
    IJ.log("DEBUG: Script execution summary:")
    IJ.log("  - Input: " + original_title + " (" + str(stack_size) + " frames)")
    IJ.log("  - Output: " + output_file)
    IJ.log("  - Frame rate: " + str(frame_rate) + " fps")
    IJ.log("  - Temporary files created and deleted: " + str(deleted_count))

IJ.log("Script finished. Check the log for details.")