Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Use correct image alignment information and not the identity matrix #4

Open
eriksjolund opened this issue Jun 15, 2016 · 0 comments
Open
Labels

Comments

@eriksjolund
Copy link
Owner

Right now the crickconvert command does not store a correct imageAlignment (that relates
to micrometers in the physical world).

$ grep "imageAlignment =" protobuf_schema/st_exp_protobuf/fullsize_image.proto 
  repeated float imageAlignment = 5;
$ 

It just uses an identity matrix.

$ grep identity_matrix{ c++/serialize_to_st_exp_protobuf/serialize_to_st_exp_protobuf.cc
  const std::array<float, 4> identity_matrix{1.0, 0.0, 0.0, 1.0};
$ 

The reason for this is that the crick file format does not contain any information about how the photo pixels relate to the physical real world. This should be fixed.

As long as there is incorrect information in the imageAlignment, it doesn't make sense to introduce
any scalebar (e.g. https://pages.nist.gov/OpenSeadragonScalebar/) in a viewer.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant