README.md

Image_Viewer_Data_Converter

Scripts for converting images to the compatible format for the CIL Image Viewer

Requirements

• Python3
  • numpy
  • sckit-image
  • joblib
• PHP 7.2+
  • Sqlite
• IMOD
• ImageMagick
• GDAL (gdal2tiles.py)

Convert images to the sqlite files for the CIL Image Viewer

python3 conver2galNsqlite.py INPUT_IMAGE_FOLDER OUTPUT_GDAL_FOLDER OUTPUT_SQLITE_FOLDER

Assumption: The image name contains the Z slice index number. For example, "temp.0000.tif"

Convert images to the GDAL tile images only

python3 conver2gal.py INPUT_IMAGE_FOLDER OUTPUT_GDAL_FOLDER

Convert the GDAL tile images to the Sqlite files only

python3 conver2Sqlite3.py INPUT_GDAL_FOLDER OUTPUT_SQLITE_FOLDER

Invert the image color

python3 invertImages.py INPUT_IMAGE_FOLDER OUTPUT_INVERTED_FOLDER

Rescale image contrast

python3 conv2uint8-sph.py INPUT_IMAGE_FOLDER OUTPUT_ENHANCED_FOLDER

• This script requires a huge amount of RAM if the image size is in the Gigabyte range

python3 conv2uint8-ww.py INPUT_IMAGE_FOLDER OUTPUT_ENHANCED_FOLDER

• This script rescales the images using ImagMagick