mic-dkfz / niicat Goto Github PK

This is a tool to quickly preview nifti images on the terminal

License: GNU General Public License v2.0

Python 74.46% Shell 25.54%

niicat's Introduction

niicat

This is a tool to quickly preview nifti images on the terminal. This can be helpful if you are working on a remote server via SSH and do not have a -X connection. It uses libsixel to display the images. Niicat can also display png, jpg or similar images.

Install:

pip install niicat

Usage:

niicat T1.nii.gz

Possible problems

If nothing is displayed check if your terminal supports sixel.

Per default niicat is trying to use libsixel-python. If this is causing problems you can also try using niicat with the option -ic if you are using iterm2 (this will use imgcat from iterm2) or with the option -lb (this will use libsixel-bin which can be installed via sudo apt install libsixel-bin).

Niicat was only tested on python >= 3.5.

Copyright

niicat's People

Contributors

Stargazers

Watchers

Forkers

nahomagidew yarikoptic tingsterx yoaman weberlab ostfor wahyurahmaniar sophmrtn ysl2

niicat's Issues

AttributeError: type object 'Path' has no attribute 'home'

I've pip3 installed niicat on my Ubuntu 18 machine, but I am having trouble running it.

$ niicat t1.nii.gz 
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/niicat/resources/niipre.py", line 17, in <module>
    home = str(Path.home())
AttributeError: type object 'Path' has no attribute 'home'

I am using

$ python3 --version
Python 3.6.8

Cool project!

UnboundLocalError: local variable 'oL' referenced before assignment

$ niicat t1.nii.gz                                                                                                        ✓  29% (0:52) 🔋  00:42:40
Traceback (most recent call last):
  File "/Users/fernando/miniconda3/envs/episurg/bin/niicat", line 50, in <module>
    main()
  File "/Users/fernando/miniconda3/envs/episurg/bin/niicat", line 46, in main
    plot(args.nifti_file, dpi=args.dpi)
  File "/Users/fernando/miniconda3/envs/episurg/lib/python3.6/site-packages/niicat/plotter.py", line 248, in plot
    return _plot_nifti_preview(iFile, return_fig=return_fig, dpi=dpi)
  File "/Users/fernando/miniconda3/envs/episurg/lib/python3.6/site-packages/niicat/plotter.py", line 159, in _plot_nifti_preview
    plt.text(-10, mY + 5, oL, fontsize=9, color='red')  # Label on left side
UnboundLocalError: local variable 'oL' referenced before assignment

You might want to check nibabel docs for some high-level utilities to get image orientation.

`libsixel-python` is missing.

$ niicat icbm_avg_152_t1_tal_nlin_symmetric_VI.nii.gz 
`libsixel-python` is missing. See https://github.com/saitoha/libsixel

$ pip install libsixel-python    
Requirement already satisfied: libsixel-python in /Users/fernando/miniconda3/envs/episurg/lib/python3.6/site-packages (0.5.0)

$ niicat icbm_avg_152_t1_tal_nlin_symmetric_VI.nii.gz 
`libsixel-python` is missing. See https://github.com/saitoha/libsixel

$ ipython                  
Python 3.6.7 | packaged by conda-forge | (default, Jul  2 2019, 02:07:37)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.6.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import libsixel
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-7b2ccdc20b41> in <module>
----> 1 import libsixel

~/miniconda3/envs/episurg/lib/python3.6/site-packages/libsixel/__init__.py in <module>
    350
    351 if not find_library('sixel'):
--> 352     raise ImportError("libsixel not found.")
    353
    354 # load shared library

ImportError: libsixel not found.

name 'libsixel' is not defined

I have started work on making your software automatically accessible on Gentoo Linux. However there seems to be an issue with the installation:

chymera@darkhost ~ $ niicat /usr/share/mouse-brain-atlases/dsurqec_200micron.nii 
Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.6/niicat", line 34, in <module>
    main()
  File "/usr/lib/python-exec/python3.6/niicat", line 30, in main
    plot_preview(args.nifti_file)
  File "/usr/lib64/python3.6/site-packages/niicat/niipre.py", line 222, in plot_preview
    plot_sixel(fig)
  File "/usr/lib64/python3.6/site-packages/niicat/niipre.py", line 26, in plot_sixel
    if not libsixel:
NameError: name 'libsixel' is not defined

This is surprising, because the libsixel package is installed, providing the following files:

darkhost ~ # equery f media-libs/libsixel
 * Searching for libsixel in media-libs ...
 * Contents of media-libs/libsixel-1.8.2:
/usr
/usr/bin
/usr/bin/img2sixel
/usr/bin/libsixel-config
/usr/bin/sixel2png
/usr/include
/usr/include/sixel.h
/usr/lib64
/usr/lib64/libsixel.so -> libsixel.so.1.0.6
/usr/lib64/libsixel.so.1 -> libsixel.so.1.0.6
/usr/lib64/libsixel.so.1.0.6
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/libsixel.pc
/usr/share
/usr/share/bash-completion
/usr/share/bash-completion/completions
/usr/share/bash-completion/completions/img2sixel
/usr/share/doc
/usr/share/doc/libsixel-1.8.2
/usr/share/doc/libsixel-1.8.2/ChangeLog.bz2
/usr/share/doc/libsixel-1.8.2/NEWS.bz2
/usr/share/doc/libsixel-1.8.2/README.md.bz2
/usr/share/doc/libsixel-1.8.2/images
/usr/share/doc/libsixel-1.8.2/images/egret.jpg
/usr/share/doc/libsixel-1.8.2/images/map16.png
/usr/share/doc/libsixel-1.8.2/images/map8.png
/usr/share/doc/libsixel-1.8.2/images/snake.jpg
/usr/share/doc/libsixel-1.8.2/images/vimperator3.png
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/img2sixel.1.bz2
/usr/share/man/man1/sixel2png.1.bz2
/usr/share/man/man5
/usr/share/man/man5/sixel.5.bz2
/usr/share/zsh
/usr/share/zsh/site-functions
/usr/share/zsh/site-functions/_img2sixel

Any idea what's going wrong?

be able to specify coords for cross-cut

ATM there is no way to adjust AFAIK

$> niicat --help
usage: niicat [-h] [-ic] [-lb] [--dpi N] [--version] nifti_file

Generate previews of nifti image and png/jpeg images on the terminal.

positional arguments:
  nifti_file

optional arguments:
  -h, --help  show this help message and exit
  -ic         Use iTerm2's imgcat instead of libsixel-python to plot the image.
  -lb         Use libsixel-bin instead of libsixel-python to plot the image.
  --dpi N     resolution for plotting (default: 150).
  --version   show program's version number and exit

AttributeError: 'FigureCanvasGTK3Agg' object has no attribute 'renderer'

I get the following error when trying to run niicat — any ideas what could be wrong?

Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.7/niicat", line 50, in <module>
    main()
  File "/usr/lib/python-exec/python3.7/niicat", line 46, in main
    plot(args.nifti_file, dpi=args.dpi)
  File "/usr/lib/python3.7/site-packages/niicat/plotter.py", line 254, in plot
    return _plot_nifti_preview(iFile, return_fig=return_fig, dpi=dpi)
  File "/usr/lib/python3.7/site-packages/niicat/plotter.py", line 233, in _plot_nifti_preview
    _plot_sixel(fig)
  File "/usr/lib/python3.7/site-packages/niicat/plotter.py", line 36, in _plot_sixel
    res = _sixel_encode(fig.canvas.buffer_rgba(), fig.get_figwidth()* dpi, fig.get_figheight() * dpi)
  File "/usr/lib/python3.7/site-packages/matplotlib/backends/backend_agg.py", line 444, in buffer_rgba
    return self.renderer.buffer_rgba()
AttributeError: 'FigureCanvasGTK3Agg' object has no attribute 'renderer'

My matplotlib installation has gtk3 support enabled (though the error remains the same with it disabled):

[U] dev-python/matplotlib
     Available versions:  3.2.2-r2^t (~)3.3.0-r1^t (~)3.3.1-r2^t {cairo doc examples excel gtk3 latex qt5 test tk wxwidgets PYTHON_TARGETS="python3_6 python3_7 python3_8 python3_9"}
     Installed versions:  3.2.2-r2^t(03:19:33 PM 09/18/2020)(cairo gtk3 latex wxwidgets -doc -examples -excel -qt5 -test -tk PYTHON_TARGETS="python3_7 -python3_6 -python3_8 -python3_9")
     Homepage:            https://matplotlib.org/
     Description:         Pure python plotting library with matlab like syntax

error in plotter: `ctypes.ArgumentError: argument 2: TypeError: wrong type`

I get the following error when trying to run niicat on a nifti file:

Traceback (most recent call last):
  File "/raid/shared/tbartczak/conda/envs/tb/bin/niicat", line 50, in <module>
    main()
  File "/raid/shared/tbartczak/conda/envs/tb/bin/niicat", line 46, in main
    plot(args.nifti_file, dpi=args.dpi)
  File "/raid/shared/tbartczak/conda/envs/tb/lib/python3.11/site-packages/niicat/plotter.py", line 254, in plot
    return _plot_nifti_preview(iFile, return_fig=return_fig, dpi=dpi)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/raid/shared/tbartczak/conda/envs/tb/lib/python3.11/site-packages/niicat/plotter.py", line 233, in _plot_nifti_preview
    _plot_sixel(fig)
  File "/raid/shared/tbartczak/conda/envs/tb/lib/python3.11/site-packages/niicat/plotter.py", line 36, in _plot_sixel
    res = _sixel_encode(fig.canvas.buffer_rgba(), fig.get_figwidth()* dpi, fig.get_figheight() * dpi)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/raid/shared/tbartczak/conda/envs/tb/lib/python3.11/site-packages/niicat/plotter.py", line 23, in _sixel_encode
    libsixel.sixel_dither_initialize(dither, data, w, h, libsixel.SIXEL_PIXELFORMAT_RGBA8888)
  File "/raid/shared/tbartczak/conda/envs/tb/lib/python3.11/site-packages/libsixel/__init__.py", line 503, in sixel_dither_initialize
    status = _sixel.sixel_dither_initialize(dither, data, width, height, pixelformat,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ctypes.ArgumentError: argument 2: TypeError: wrong type

I've installed niicat from source from the version in #8 as I got nibabel issues with pypi version.

From the stacktracie it seems that wrong datatype is passed to sixel when encoding figure?

My env:
Python 3.11
matplotlib==3.7.1
matplotlib-inline==0.1.6
numpy==1.24.3
nibabel==5.1.0