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
