I’m working on a Python script that processes images and saves them as TIFF files using the tifffile library. The script runs as part of a larger pipeline where I use the ashlar tool to process these TIFF files further. However, I’m encountering an issue related to ASCII encoding when saving the TIFF files.

Context:

Python Environment: I am using Python 3.9 along with the tifffile library for TIFF file handling.

Error Trigger: The error arises during the execution of the save_tiff function, which is responsible for saving TIFF files with a description.

Description Handling: The ashlar tool requires all descriptions in TIFF files to be ASCII-compliant for proper functioning in subsequent processing steps.

Python Code Snippet:

import numpy as np
import tifffile

def save_tiff(image, path, description='Generated by process_tile'):
    """
    Save the image as a TIFF file with an ASCII-compliant description.
    
    Args:
    - image: The image array to save.
    - path: The file path to save the TIFF file.
    - description: Optional description string (default is 'Generated by process_tile').
    """
    description_ascii = description.encode('ascii', 'ignore').decode('ascii')
    
    with tifffile.TiffWriter(path, imagej=True) as tif:
        tif.save(image, description=description_ascii)

Bash Script Snippet:

#!/usr/bin/env bash


module load jupyter/python_3.9
ashlar --version

# Function to check consistency of input images
check_images() {
    local input_path=$1
    find $input_path -name 'mask*.tif' -type f -print0 | sort -z | xargs -0 ashlar -o $OUTPUT_PATH/ashlar_output_mask.ome.tif -c 0 --stitch-alpha 0.01 --filter-sigma 1.0
}

# Function to modify TIFF descriptions to ensure ASCII compliance
modify_tiff_description() {
    local input_path=$1
    local temp_path=$2
    find $input_path -name 'overlay*.tif' -type f -print0 | sort -z | xargs -0 ashlar -o $OUTPUT_PATH/ashlar_output_overlay.ome.tif -c 0 --stitch-alpha 0.01 --filter-sigma 1.0
}

# Create temporary directories for modified images
TEMP_PATH_MASK="${INPUT_PATH_MASK}/temp"
TEMP_PATH_OVERLAY="${INPUT_PATH_OVERLAY}/temp"
mkdir -p $TEMP_PATH_MASK $TEMP_PATH_OVERLAY  # Create temp directories

# Check consistency of mask images
echo "Checking mask images..."
check_images $TEMP_PATH_MASK

# Check consistency of overlay images
echo "Checking overlay images..."
check_images $TEMP_PATH_OVERLAY

# Modify TIFF descriptions to ensure ASCII compliance
echo "Modifying TIFF descriptions for mask images..."
modify_tiff_description $INPUT_PATH_MASK $TEMP_PATH_MASK

echo "Modifying TIFF descriptions for overlay images..."
modify_tiff_description $INPUT_PATH_OVERLAY $TEMP_PATH_OVERLAY

# Clean up temporary directories
rm -rf $TEMP_PATH_MASK $TEMP_PATH_OVERLAY

Error Message:

Traceback (most recent call last):
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 7552, in overwrite
    value = value.encode('ascii')
UnicodeEncodeError: 'ascii' codec can't encode character 'xb5' in position 552: ordinal not in range(128)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/scg/apps/software/jupyter/python_3.9/bin/ashlar", line 8, in <module>
    sys.exit(main())
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/ashlar/scripts/ashlar.py", line 226, in main
    return process_single(
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/ashlar/scripts/ashlar.py", line 296, in process_single
    writer.run()
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/ashlar/reg.py", line 1307, in run
    print()
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 2809, in __exit__
    self.close()
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 2802, in close
    self._write_image_description()
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 2791, in _write_image_description
    self._descriptiontag.overwrite(self, description, erase=False)
  File "/scg/apps/software/jupyter/python_3.9/lib/python3.9/site-packages/tifffile/tifffile.py", line 7554, in overwrite
    raise ValueError(
ValueError: TIFF strings must be 7-bit ASCII