Matplotlib Error

AFNI Message Board
1

Hi AFNI team,

I’m trying to switch from using the basic html_review_style to pythonic. I am getting some errors during that portion of the processing though and I’m not sure why. Here is the terminal output:


++ FOR: motion_AS1108_enorm.1D: 1 arrays with 512 pts
++ FOR: outcount_rall.1D: 1 arrays with 512 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..511]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
Traceback (most recent call last):
  File "/nfs/pkg64/afni_ubuntu_16_20230101/1dplot.py", line 65, in <module>
    ok_fig  = lpod.make_1dplot_figure(bigfig)
  File "/nfs/pkg64/afni_ubuntu_16_20230101/afnipy/lib_plot_1D.py", line 497, in make_1dplot_figure
    plt.savefig( bf.fname, dpi=bf.dpi, facecolor=bf.bkgd_color,
  File "/usr/lib/python3/dist-packages/matplotlib/pyplot.py", line 722, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/matplotlib/figure.py", line 2180, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/usr/lib/python3/dist-packages/matplotlib/backend_bases.py", line 2021, in print_figure
    canvas = self._get_output_canvas(format)
  File "/usr/lib/python3/dist-packages/matplotlib/backend_bases.py", line 1961, in _get_output_canvas
    raise ValueError(
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
++ FOR: dfile_rall.1D: 6 arrays with 512 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..511]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
Traceback (most recent call last):
  File "/nfs/pkg64/afni_ubuntu_16_20230101/1dplot.py", line 65, in <module>
    ok_fig  = lpod.make_1dplot_figure(bigfig)
  File "/nfs/pkg64/afni_ubuntu_16_20230101/afnipy/lib_plot_1D.py", line 497, in make_1dplot_figure
    plt.savefig( bf.fname, dpi=bf.dpi, facecolor=bf.bkgd_color,
  File "/usr/lib/python3/dist-packages/matplotlib/pyplot.py", line 722, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/matplotlib/figure.py", line 2180, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/usr/lib/python3/dist-packages/matplotlib/backend_bases.py", line 2021, in print_figure
    canvas = self._get_output_canvas(format)
  File "/usr/lib/python3/dist-packages/matplotlib/backend_bases.py", line 1961, in _get_output_canvas
    raise ValueError(
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)

And I am also attaching my afni_system_check output:


architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              5.4.0-139-generic
version:              #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023
distribution:         ubuntu 20.04 focal
number of CPUs:       96
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /nfs/pkg64/afni_ubuntu_16_20230101/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Jan 18 2023 
                     : AFNI_23.0.01 'Commodus'
AFNI_version.txt     : AFNI_23.0.01, linux_ubuntu_16_64, Jan 18 2023
which python         : /bin/python
python version       : 3.8.10
which R              : /bin/R
R version            : R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/nfs/pkg64/afni_ubuntu_16_20230101/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.8)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/usr/bin/python3.8)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /usr/lib/R

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
   module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
   matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /nfs/pkg64/afni_ubuntu_16_20230101:/home/farnsworth/bin:/home/farnsworth/.local/bin:/usr/local/cuda/bin:/bin:/usr/bin:/opt/thinlinc/bin:/usr/local/bin:/usr/bin/X11:/sbin:/usr/sbin:/usr/local/sbin:/snap/bin

PYTHONPATH = 
R_LIBS = /home/farnsworth/R

LD_LIBRARY_PATH = /usr/local/cuda/lib64:/opt/thinlinc/lib64:/opt/thinlinc/lib

DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /nfs/pkg64/afni_ubuntu_16_20230101

------------------------------ OS specific -------------------------------
which apt-get        : /bin/apt-get
apt-get version      : apt 2.0.9 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Jan 18 2023 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  'afni' executable is owned by root
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)

Thanks in advance for your help!

Sincerely,
Ian

2

Hi, Ian-

I think you will be happier with the full pythonic version, yes! But indeed, we need to fix that error message.

So, the default package manager in Ubuntu 20.04 (Aptitude) distributes a version of Matplotlib, 3.1.2, that contains this error when trying to make JPGs:
https://bugs.launchpad.net/ubuntu/+source/matplotlib/+bug/1897283
I don’t know why they haven’t fixed it, and it is the root cause of the error here.

The good news: there is a fix. Can you please run the following on your computer (requires the admin/sudo password):


sudo apt-get install pip
sudo apt-get remove python3-matplotlib
pip install matplotlib

That should get you matplotlib ver=3.6.2 (or so), and Python can now generate JPG images. (Why Ubuntu didn’t make the bug-free version of matplotlib its default… I don’t know.)

If you want to test this fix without rerunning the full afni_proc.py command, you can do this:
Go into an afni_proc.py (AP) results directory, and do:


curl -O [https://raw.githubusercontent.com/afni/afni/master/src/ptaylor/supplement/redo_apqc.tcsh](https://raw.githubusercontent.com/afni/afni/master/src/ptaylor/supplement/redo_apqc.tcsh)
tcsh redo_apqc.tcsh

… to regenerate the QC directory there. Under the ‘mot’ block, you should now see lots of line plots.

Please let me know how that goes.

–pt

3

Hi Paul,

So, our server admin didn’t want to change any of the Python/Matplotlib versions tied to the server Linux distributions. However, they recommended a very simple fix to create a virtual environment using Python’s venv module to install a newer matplotlib version, which worked perfectly! Thanks for your help and info about that specific Matplotlib version being bugged.

Sincerely,
Ian

4

Hi, Ian-

Glad it got sorted.

I’ll just note that using conda/miniconda to make a local environment (I use this to manage Python on my own systems) is useful, modular and doesn’t require sudo/admin privileges. There are other ways to go, certainly, and it sounds like you are set, but I note this for anyone with similar constraints reading this thread. Here are notes about using miniconda specifically, with recipes for AFNI dependencies:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/miniconda.html

–pt