ij-plugins / ijp-imageio Goto Github PK

Adjust branch names to more typically used in GitHub projects, with default development branch being "master"

Java 9 and newer includes most of the JAI ImageIO support natively (except JPEG 2000). Most customization in ijp-imageio is around TIFF that is part of the new Java 9+ ImageIO. External ImageIO dependencies can be removed. They can be added by the user, if user needs them, without changes in the ijp-imageio code.

When opening a PNG image that has an alpha channel (transparency) ask user how to interpret:

• load only RGB
• load as 4 channel image
• load RGB into one image and transparency into a separate image

Can this also handle 16-bit per channel images?

Similar to saving with build in ImageJ functions, Image title should reflect name under which image was saved.

Exception when using:

IJImageIO.readAsBufferedImages(file).get(0).image

Class ImageAndMetadata should be public.

Save spatial calibration units in a way that is comparable with ImageJ. For instance, if ImageJ is using 'mm' do not translate it to TIFF supported 'cm'. Save as ImageJ "unitless" and add "unit=mm" in ImageDescription

Metadata in image saved by ImageJ:

TIFF Directory ...
  Resolution: 31.25, 31.25 (unitless)
  ...
  ImageDescription: ImageJ=1.52v unit=mm

Metadata in image saved by ijp-imageio in a way that is incompatible with ImageJ

TIFF Directory ...)
  Resolution: 0.03125, 0.03125 pixels/cm
  ...
  ImageDescription: ImageJ=1.52v unit=mm

When an 8-bit gray level image is saved as compressed TIFF the Photometric Interpretation tag is set to palette color but it should be the min-is-black. When OpenCV reads that image it interprets it as an RGB image not an 8-bit gray level image.

Here is an info of an image saves by "Save as TIFF":

  Image Width: 186 Image Length: 226
  Resolution: 1, 1 (unitless)
  Bits/Sample: 8
  Compression Scheme: AdobeDeflate
  Photometric Interpretation: palette color (RGB from colormap)
  Samples/Pixel: 1
  Rows/Strip: 44
  Planar Configuration: single image plane
  Color Map: (present)
  ImageDescription: ImageJ=1.53o

  Software: ij-plugins/ijp-imageio

For comparison the same image saved by ImageJ build-in encoder:

  Subfile Type: (0 = 0x0)
  Image Width: 186 Image Length: 226
  Bits/Sample: 8
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 226
  Planar Configuration: single image plane
  ImageDescription: ImageJ=1.53o

Migrate from defunct Travis CI to GitHub Actions