slideCompare - swvanderlaan/slideToolKit GitHub Wiki

slideCompare is designed to compare two images using ImageMagick's compare function. Here's a breakdown of its functionality:

Display Functions Several functions are defined to format text output with different colors, styles, and effects. Required | General Variables IMG_FILE: The variable is set to the first argument provided when running the script, representing the slidenumber with stain. Log File A log file (slideCompare.logfile.txt) is created or updated for recording relevant information during script execution. Module Loading The script activates the CellProfiler-Anaconda3.8 environment. Message Functions Functions for displaying copyright information and script arguments error are defined. Script Execution Argument Check: The script checks if the correct number of arguments is provided. If not, it displays an error message and exits. Loading Required Modules: The script loads the required Anaconda environment containing the slideToolKit-CellProfiler4.1.3 installation. Comparing Images: If the image file has a .ndpi extension, the script proceeds to create macro images and compares them using ImageMagick's compare function. The results of the comparison are stored in the log file. If the image file has a different extension (.tif, .TIF), an error message is displayed, and the script exits. Logging: Information about the comparison duration is recorded in the log file.

Example usage:

python slideExtract --input AE1234.SR.ndpi --levels m,6

Argument(s):

  • -i, --input Input (directory containing files). Try: IMG012.ndpi (or .TIF or /path_to/images/.ndpi). Required.
  • -l, --levels Comma seperated list of magnification levels to extract, with 'm' as thumbnail and '6' as level 6. Try: m,6. Required.

Optional argument(s):

  • -o, --outdir Output dir, default is present working directory. Optional.
  • -s, --suffix Suffix to append to end of file, default is 'm' for thumbnail and '#' for a given level. Optional.
  • -t, --type Output file type, default is png (which is slower), other options are tif. Optional.
  • -f, --force Force output even if it exists. Optional.
  • -v, --verbose While writing images also display image properties. Optional.
  • -h, --help Show this help message and exit. Optional.