Loaded images are gray scale

[aknckaan]

I am reading the nd2 file with the library however RGB channel doesn't show up.

[FrickTobias]

Hi aknckaan,

Could you give more information about your situation?

Remember that someone else will not know anything about your system, versions, whether you are interpreting your traceback correctly, etc. Here is an example issue I made up, where someone more experienced could either help the programmer understand what they have done wrong or find the problem in the package.

In this case it turns out the programmer has mistakenly added () at the end of images.sizes which tries to call on a function instead of a variable (or technically you would call it method since we're dealing with an instance here but it's very similar).

Example issue: images.sizes doesn't work

Problem description

I am trying to print images.sizes but I just get a TypeError. Can someone help me?

Code snippet

from nd2reader import ND2Reader
with ND2Reader(input) as images:
    print(images.sizes())

Traceback

Traceback (most recent call last):
  File "/Users/tobiasfrick/miniconda3/envs/ndt/bin/nd2tools", line 33, in <module>
    sys.exit(load_entry_point('nd2tools', 'console_scripts', 'nd2tools')())
  File "/Users/tobiasfrick/PycharmProjects/nd2tools/src/nd2tools/__main__.py", line 70, in main
    module.main(args)
  File "/Users/tobiasfrick/PycharmProjects/nd2tools/src/nd2tools/cli/movie.py", line 87, in main
    print(images.sizes())
TypeError: 'dict' object is not callable

Environment*

*This could be harder to make yourself if you are new to programming and are not using virtual environments, but if you can include it I would highly recommend it.

conda info

     active environment : ndt
    active env location : /Users/tobiasfrick/miniconda3/envs/ndt
            shell level : 2
       user config file : /Users/tobiasfrick/.condarc
 populated config files : /Users/tobiasfrick/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.8.10.final.0
       virtual packages : __osx=10.16=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/tobiasfrick/miniconda3  (writable)
      conda av data dir : /Users/tobiasfrick/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/tobiasfrick/miniconda3/pkgs
                          /Users/tobiasfrick/.conda/pkgs
       envs directories : /Users/tobiasfrick/miniconda3/envs
                          /Users/tobiasfrick/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.10 Darwin/20.6.0 OSX/10.16
                UID:GID : 501:20
             netrc file : None
           offline mode : False

[rbnvrw]

Thank you for your report @aknckaan and thanks @FrickTobias for the help.

Could you provide some more information on the problem as @FrickTobias suggested? Is your problem maybe already solved in the meantime?