org-mode inline images not working (remotely with TRAMP) - matplotlib

I am working with emacs org-mode on a remote machine using TRAMP. I connect code cells to a jupyter server (on that remote machine) where I start a python 3 kernel. Code execution works perfectly fine, I can also create plots with matplotlib. While a .png is generated in the right temp file location, the output of the code cell is a (relative) link to the file without displaying it inline as expected.
An example code-block look like this:
#+BEGIN_SRC jupyter-python :session /jpy:localhost#9090:TEST
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(range(10), range(10))
#+END_SRC
#+RESULTS:
:RESULTS:
| <matplotlib.lines.Line2D | at | 0x7f1c43a289a0> |
[[file:./.ob-jupyter/e1eecf5d59de9bfa1d3468867a64aadf4b1a6261.png]]
:END:
C-c C-x C-v gives the message: 'No images to display inline'
C-c o opens and displays the file in a different buffer correctly.
I would expect the file to display correctly inline in the org-mode buffer.
I tried to change the link manually to a TRAMP path, looking something like this:
[[file:/ssh:MYSERVER:/PATH_TO_TEMP_FOLDER/.ob-jupyter/e1eecf5d59de9bfa1d3468867a64aadf4b1a6261.png]]
which also allows me to open the file with C-c o, but won't display the file inline (Same behavior as described above)
If I open the jupyter-repl session directly and type fig (after executing the above code block) The figure displays as expected in the jupyter-repl buffer
If I run the jupyter session locally, inline plotting works as expected
Update:
I realized if I C-f on the link to open the file, the link expands to an invalid tramp link, which throws the following error message:
File is missing: /ssh:bih:/PATH_TO_CORRECT_FOLDER/00_test/file:./.ob-jupyter/
Note the file:./ at the end of the link that doesn't belong there. So I think something is going wrong somewhere between TRAMP and org-mode (or emacs-jupyter). Any ideas how to fix this?

C-h v org-display-remote-inline-images says:
org-display-remote-inline-images is a variable defined in ‘org.el’.
Its value is ‘skip’
How to display remote inline images.
Possible values of this option are:
skip Don’t display remote images.
download Always download and display remote images.
cache Display remote images, and open them in separate buffers
for caching. Silently update the image buffer when a file
change is detected.
Check the value and maybe customize the variable to do something other than skip.

Related

IntelliJ console output with multiple (source.java:line) links on a line

When my logging system outputs the source and line number in the proper format (name.java:linenumber), it appears in the output console like a link you can click on, taking you to the corresponding line number of that source code, which works great. Except my logging system prints like a stack trace, a series of source location on a single line, like this:
date/time - a logging statement - (Source1.java:123) (Source2.java:321) (Source5.java:11)
The thing is that IntelliJ only makes the first one a link. The remaining ones don't become clickable links.
Is there a way to configure IntelliJ to scan all source location for each line in the console output, and not just the first one for each line?
This feature is not available at the moment and the progress can be tracked at:
Highlight links with multiple (source.java:line) per line in the output console

Creating image retention test im builder view

I just downloaded psychopy this morning and have spent the day trying to figure out how to work with builder view. I watched the youtube video "Build your first PsychoPy experiment (Stroop task)" by Jon Pierce. In his video he was explaining how to make a conditions file with excel that would be used in his experiment. I wanted to make a very similar test where images would appear and subjects would be required to give a yes or no answer to them (the correct answer is already predefined). In his conditions file he had the columns 'word' 'colour' and 'corrANS'. I was wondering if instead of a 'word' column, I can have an 'image' column. In this column I would like to upload all my images to them in the same way I would words, and have them correlated to a correct answer of either 'yes' or 'no'. We tried doing this and uploaded images to the conditions file, but we haven't had any success in running the test successfully and were hoping somebody could help us.
Thank you in advance.
P.S. we are not familiar with python, or code in general, so we were hoping to get this running using the builder view.
EDIT: Here is the error message we are receiving when running the program
#### Running: C:\Users\mr00004\Desktop\New folder\1_lastrun.py
4.8397 ERROR Couldn't find image file 'C:/Users/mr00004/Desktop/New folder/PPT Retention 1/ Slide102.JPG'; check path?
Traceback (most recent call last):
File "C:\Users\mr00004\Desktop\New folder\1_lastrun.py", line 174, in
image.setImage(images)
File "C:\Program Files (x86)\PsychoPy2\lib\site-packages\psychopy-1.80.03-py2.7.egg\psychopy\visual\image.py", line 271, in setImage
maskParams=self.maskParams, forcePOW2=False)
File "C:\Program Files (x86)\PsychoPy2\lib\site-packages\psychopy-1.80.03-py2.7.egg\psychopy\visual\basevisual.py", line 652, in createTexture
% (tex, os.path.abspath(tex))#ensure we quit
OSError: Couldn't find image file 'C:/Users/mr00004/Desktop/New folder/PPT Retention 1/ Slide102.JPG'; check path? (tried: C:\Users\mr00004\Desktop\New folder\PPT Retention 1\ Slide102.JPG)
Yes, certainly, that is exactly how PsychoPy is designed to work. Simply place the image names in a column in your conditions file. You can then use the name of that column in the Builder Image component's "Image" field. The appropriate image file for a given trial will be selected.
It is difficult to help you further, though, as you haven't specified what went wrong. "we haven't had any success" doesn't give us much to go on.
Common problems:
(1) Make sure you use full filenames, including extensions (.jpg, .png, etc). These aren't always visible in Windows at least I think, but they are needed by Python.
(2) Have the images in the right place. If you just use a bare filename (e.g. image01.jpg), then PsychoPy will expect that the file is in the same directory as your Builder .psyexp file. If you want to tidy the images away, you could put them in a subfolder. If so, you need to specify a relative path along with the filename (e.g. images/image01.jpg).
(3) Avoid full paths (starting at the root level of your disk): they are prone to errors, and stop the experiment being portable to different locations or computers.
(4) Regardless of platform, use forward slashes (/) not backslashes (\) in your paths.
make a new folder in H drive and fill in the column of image in psychopy as e.g. 'H:\psych\cat.jpg' it works for me

Ansys multiphysics: blank output file

I have a model of a heating process on Ansys Multiphysics, V11.
After running the simulation, I have a script to plot a temperature profile:
!---------------- POST PROCESSING -----------------------
/post1 ! tdatabase postprocessor
!---define profile temperature
path,s_temp1,2,,100 ! define a path
ppath,1,,dop/2,0,0 ! create a path point
ppath,2,,dop/2,1.5,0 ! create a path point
PDEF,surf_t1,TEMP, ,noav ! print a path
plpath,surf_t1 ! plot a path
What I now need, is to save the resulting path in a text file. I have already looked online for a solution, and found the following code to do it, which I appended after the lines above:
/OUTPUT,filename,extension
PRPATH,surf_t1
/OUTPUT
Ansys generates the file filename.extension but it is empty. I tried to place the OUTPUT command in a few locations in the script, but without any success.
I suspect I need to define something else, but I have no idea where to look, as Ansys documentation online is terribly chaotic, and all internet pages I've opened before writing this question are not better.
A final note: Ansys V11 is an old version of the software, but I don't want to upgrade it and fit the old model to the new software.
For the output of the simulation (which includes all calculation steps, and sub-steps description and node-by-node results) the output must be declared in the beginning of the code, and not in the postprocessing phase.
Declaring
/OUTPUT,filename,extension
in the preamble of the main script makes such that the output is stored in the right location, with the desired extension. At the end of the scripts, you must then declare
/OUTPUT
to reset the output file location for ANSYS.
The output to the PATH call made in the postprocessing script is however not printed in the file.
It is convenient to use
*CFOPEN,file,ext
*VWRITE,Vector(1,1).Vector(1,2)
(2F12.6)
*CFCLOSE
where Vector(1,1) is a two column array created by *DIM, and stores your data to output to file
As this is a special command, run it from file i.e. macro_output.mac

doxygen latex make fails for input encoding error

I have a git repo project in eclipse which I have been documenting using doxygen (v1.8.4).
If I run the latex make ion a fresh clone of the project it runs fine and the PDF is made.
However, if I then run a doxy build, which completes OK, then attempt to run the latex make, it fails for
! Package inputenc Error: Keyboard character used is undefined
(inputenc) in inputencoding `utf8'.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
I have tried switching the encoding of the doxyfile by setting DOXYFILE_ENCODING to ISO-8859-1 with no change in the result... How can I fix this?? Thanks.
EDIT: I have used no non-UTF-8 chars as far as I know in my files, the file referenced before the error is very short and definitely doesn't have non-UTF-8 chars in it. I've even tried clearing my latex output dir and building from scratch with no luck...
EDIT: Irealised that the doxy build only appears to run correctly. It doesnt show any errors, but it should, for example run DOT and build about 10 graphs. The console output says Running dot, but it doesn't say generating graph (n/x) like it should when it actually makes the graphs...
Short answer: So by a slow process of elimination I found that this was caused by a single apostrophe in a file that had appeared to be already built and made without error!!
Long answer: Firstly I used used the project properties to flip the encoding from the default Cp1252 to UTF-8. Then I started removing files one-by-one until rebuilding and remaking after each removal, until the make ran successfully. I re-added all files, but deleted the content in the most recently removed file and tested the make - to confirm it was this file and only this file that caused the issue. the make ran fine. So I pasted the content back into the empty file, and started deleting smaller and smaller sections of the file, again rebuilding and remaking each time until I was left with a good make without the apostrophe and a bad one with it... I simply retyped the apostrophe (as this would then force it to be a UTF-8 char) and success!! Such an annoying bug!
Dude you made it a hard way. Why not use python to do the work for you:
f = open(fn,"rb")
data = f.read()
f.close()
for i in range(len(data)):
ch = data[i]
if(ch > 0x7F): # non ASCII character
print("char: %c, idx: %d, file: %s"%(ch,i,fn))
str2 = str(data[i-30:i+30])#.decode("utf-8")
print("txt: %s" % (str2))

.png and .eps files generated by matplotlib won't print on RHEL 5

I'm using matplotlib.pyplot to plot some data, and after running plt.show() I save the image as either a PNG image or encapsulated postscript.
When I open these saved files with evince and try to print them, a job is sent to the printer but nothing is printed. The plots display on the screen with no problems.
Is there something specific I need to do in matplotlib to generate printable PNGs and EPSes? Is this a bug in matplotlib?
Here are a few steps to start debugging this situation:
(1) Stop your cupsd (CUPS daemon).
(2) Change in cupsd.conf: LogLevel debug (instead of LogLevel info.
(3) Delete your log file /var/log/cups/error_log.
(4) Start your cupsd again.
(5) Print your problem EPS.
(6) Check your cupsd.conf logfile for errors.
Report the errors here. (Errors may be recognized by the prefixed E on each line.) Also, what is the result of the Auto-typing step?
Alternatively: can you provide a link to a sample of your problem EPS?