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create_thumbnail.py
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create_thumbnail.py
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#!/usr/bin/env python3
import argparse
import os
import random
import subprocess
import sys
import logging
def setup_logging():
"""Configure logging for the script."""
logger = logging.getLogger("CreateThumbnail")
logger.setLevel(logging.DEBUG)
# Create console handler with a higher log level
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
# Create file handler for detailed logs
fh = logging.FileHandler("create_thumbnail.log")
fh.setLevel(logging.DEBUG)
# Create formatter and add it to the handlers
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s'
)
ch.setFormatter(formatter)
fh.setFormatter(formatter)
# Add handlers to the logger
logger.addHandler(ch)
logger.addHandler(fh)
return logger
def run_subprocess(command, logger):
"""
Run a subprocess command and handle errors.
Parameters:
command (list): Command and arguments to execute.
logger (logging.Logger): Logger instance for logging messages.
Returns:
bool: True if command succeeds, False otherwise.
"""
logger.debug(f"Executing command: {' '.join(command)}")
try:
result = subprocess.run(
command,
check=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
text=True
)
logger.debug(f"Command output: {result.stdout}")
if result.stderr:
logger.warning(f"Command stderr: {result.stderr}")
return True
except subprocess.CalledProcessError as e:
logger.error(f"Command failed: {' '.join(command)}")
logger.error(f"Return code: {e.returncode}")
logger.error(f"Output: {e.output}")
logger.error(f"Error Output: {e.stderr}")
return False
def create_thumbnail(template_file, signal_file, output_file, cache_template=False, max_scale=False, logger=None):
"""
Create a thumbnail by processing template and signal NRRD files.
Parameters:
template_file (str): Path to the Template.nrrd file.
signal_file (str): Path to the Signal.nrrd file.
output_file (str): Path to the output thumbnail.png file.
cache_template (bool): Whether to cache template MIPs.
max_scale (bool): Whether to use max scale for colorization.
logger (logging.Logger): Logger instance for logging messages.
"""
if logger is None:
logger = logging.getLogger("CreateThumbnail")
# Verify input files exist
if not os.path.isfile(template_file):
logger.error(f"Template file does not exist: {template_file}")
sys.exit(1)
if not os.path.isfile(signal_file):
logger.error(f"Signal file does not exist: {signal_file}")
sys.exit(1)
# Set up paths to the necessary scripts
scripts_dir = os.path.dirname(os.path.abspath(__file__))
merge_images_path = os.path.join(scripts_dir, "merge_images.py")
colorize_image_stack_path = os.path.join(scripts_dir, "colorize_image_stack.py")
create_mip_path = os.path.join(scripts_dir, "create_mip.py")
# Verify that the scripts exist
for script in [merge_images_path, colorize_image_stack_path, create_mip_path]:
if not os.path.isfile(script):
logger.error(f"Required script not found: {script}")
sys.exit(1)
# Generate a random number for temporary file names
rand_num = str(random.randint(1000, 9999))
# Determine the template MIP file name
if cache_template:
template_id = os.path.basename(os.path.dirname(template_file))
template_mip = f"template_mip_{template_id}.png"
else:
template_mip = f"template_mip_{rand_num}.png"
# Create the maximum intensity projection of the template
if not cache_template or not os.path.exists(template_mip):
logger.info(f"Creating MIP for template: {template_file} -> {template_mip}")
mip_command = [
sys.executable, create_mip_path, template_file, template_mip
]
if not run_subprocess(mip_command, logger):
logger.error("Failed to create template MIP.")
sys.exit(1)
else:
logger.info(f"Using cached template MIP: {template_mip}")
# Colorize the signal image
signal_colorized = f"signal_colorized_{rand_num}.png"
if max_scale:
logger.info("Producing with max scale...")
colorize_command = [
sys.executable, colorize_image_stack_path,
"--nrrd", signal_file,
"--png", signal_colorized,
"--scale",
"--max"
]
else:
colorize_command = [
sys.executable, colorize_image_stack_path,
"--nrrd", signal_file,
"--png", signal_colorized,
"--scale"
]
if not run_subprocess(colorize_command, logger):
logger.error("Failed to colorize signal image.")
# Clean up and exit
if not cache_template and os.path.exists(template_mip):
os.remove(template_mip)
logger.debug(f"Removed temporary file: {template_mip}")
sys.exit(1)
# Merge the template and colorized signal images
merge_command = [
sys.executable, merge_images_path,
template_mip,
signal_colorized,
output_file
]
if not run_subprocess(merge_command, logger):
logger.error("Failed to merge images.")
# Clean up and exit
if not cache_template and os.path.exists(template_mip):
os.remove(template_mip)
logger.debug(f"Removed temporary file: {template_mip}")
if os.path.exists(signal_colorized):
os.remove(signal_colorized)
logger.debug(f"Removed temporary file: {signal_colorized}")
sys.exit(1)
logger.info(f"Successfully created thumbnail: {output_file}")
# Clean up temporary files
try:
if not cache_template and os.path.exists(template_mip):
os.remove(template_mip)
logger.debug(f"Removed temporary file: {template_mip}")
except Exception as e:
logger.warning(f"Could not remove template MIP file: {template_mip}. Error: {e}")
try:
if os.path.exists(signal_colorized):
os.remove(signal_colorized)
logger.debug(f"Removed temporary file: {signal_colorized}")
except Exception as e:
logger.warning(f"Could not remove signal colorized file: {signal_colorized}. Error: {e}")
def main():
# Set up logging
logger = setup_logging()
# Create argument parser
parser = argparse.ArgumentParser(
description="Create a thumbnail image from a Template.nrrd file and a Signal.nrrd file."
)
# Add arguments
parser.add_argument(
"template_file",
help="Path to Template.nrrd file"
)
parser.add_argument(
"signal_file",
help="Path to Signal.nrrd file"
)
parser.add_argument(
"output_file",
help="Path to output thumbnail.png file"
)
parser.add_argument(
'--cache',
action='store_true',
help='If added then the template mips are cached'
)
parser.add_argument(
'--max_scale',
action='store_true',
help='If the colour scale should use the full stack rather than fit only data depth'
)
# Parse arguments
args = parser.parse_args()
# Create thumbnail
create_thumbnail(
args.template_file,
args.signal_file,
args.output_file,
cache_template=args.cache,
max_scale=args.max_scale,
logger=logger
)
if __name__ == "__main__":
main()