Command line tool for slicing image into channel dimension

Requirement

We would like to have a command line interface that can be used like this:

scitiff_values input_tiff_with_multi_channel.tiff /path/to/output_tiff_only_with_intensities_channel.tiff

Expected Input

Any tiff file including scitiff flie that has multiple channel (variances and mask).

Expected Output

A new Scitiff file that does not have extra channel other than values(intentisites) of the input file.

• INFO if the image is already single channel and do nothing.
• INFO about the result if succeeded.

About the Project

Scitiff stands for scientific tiff.

It aims to encode scientific metadata as a plain text along with the image data in tiff.

See our scitiff documentation for more details.

Development Environment

See Developer Guide to set up the local environment.

Setting up a remote repository

Go to the base branch, channel-slicer, and fork the repo.

TODO list of this issue

• Complete the implementation of the values API.
  https://github.com/scipp/scitiff/blob/f76534453b028c9471e6ef70fb78a2e64a87c926/src/scitiff/executables.py#L226-L238

  It should probably use python `values` API:
  https://github.com/scipp/scitiff/blob/bea312571bbcfc9d6c3609d8f1ecbf3c408c42a3/src/scitiff/_img_processors.py#L9-L11
  

• Expose the executables values api as a command line interface.
  https://github.com/scipp/scitiff/blob/f76534453b028c9471e6ef70fb78a2e64a87c926/pyproject.toml#L48-L52
  See how other scripts are exposed and add scitiff_values command there!

• Write documentation page. Under user-guide, Could be a separate sub-issue

• Write unit tests. Could be a separate sub-issue
  
  https://github.com/scipp/scitiff/blob/f76534453b028c9471e6ef70fb78a2e64a87c926/tests/scitiff_values_test.py#L1-L3

  Writing unit test for this command line interface might be challenging. We can skip it from this issue.
  

• Test with ImageJ (Optional)

• Open a PR (Pull Request)
  
  Set the base branch to channel-slicer.

Related Information for Implementation

Scipp User Guide for Slicing

https://scipp.github.io/user-guide/slicing.html

We are going to learn more about scipp on Wednesday, so no need to dig in too deep 😁

IO module documentation

IO Helper Tutorial
Good starting point to see what scitiff do and to see what helper functions there are for development.

Meaning of Channel in Scitiff

This section of IO tutorial explains what channels mean in scitiff.