* Output result of source block to a file
@ 2019-06-05 10:41 Roger Mason
2019-06-05 13:17 ` stardiviner
2019-06-05 13:33 ` Ken Mankoff
0 siblings, 2 replies; 12+ messages in thread
From: Roger Mason @ 2019-06-05 10:41 UTC (permalink / raw)
To: Org-Mode
Hello,
I want to output the result of the evaluation of a (python) source block
to a (graphics) file and have a link to the file inserted in the buffer.
Here is the code:
#+begin_src python :results value file :file scaleplot02.pdf :exports results :var data=test
import matplotlib.pyplot as plt
import csv
scale = []
lescale = []
cdscale = []
energy = []
leenergy = []
cdenergy = []
for row in data:
scale.append(float(row[0]))
energy.append(float(row[1]))
if int(row[2]) != 0:
lescale.append(float(row[0]))
leenergy.append(float(row[1]))
if int(row[3]) != 0:
cdscale.append(float(row[0]))
cdenergy.append(float(row[1]))
plt.plot(scale,energy, 'r+')
plt.plot(lescale,leenergy, 'go')
plt.plot(cdscale,cdenergy, 'bo')
plt.xlabel('scale')
plt.ylabel('energy (Ha)')
plt.title('Energy vs scale')
plt.legend()
plt.savefig(file)
print ("[[./%s]]" % file)
#+end_src
This is the error:
NameError: name 'file' is not defined
Obviously the syntax on the begin_src line is wrong, but what should it
be instead?
Thanks,
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-05 10:41 Output result of source block to a file Roger Mason
@ 2019-06-05 13:17 ` stardiviner
2019-06-06 11:36 ` Roger Mason
2019-06-06 18:04 ` Roger Mason
2019-06-05 13:33 ` Ken Mankoff
1 sibling, 2 replies; 12+ messages in thread
From: stardiviner @ 2019-06-05 13:17 UTC (permalink / raw)
To: emacs-orgmode
Roger Mason <rmason@mun.ca> writes:
> Hello,
>
> I want to output the result of the evaluation of a (python) source block
> to a (graphics) file and have a link to the file inserted in the buffer.
For this, you should try updated header arguments like ":results graphics link"
or ":results file link".
>
> Here is the code:
>
> #+begin_src python :results value file :file scaleplot02.pdf :exports results :var data=test
> import matplotlib.pyplot as plt
> import csv
>
> scale = []
> lescale = []
> cdscale = []
>
> energy = []
> leenergy = []
> cdenergy = []
>
> for row in data:
> scale.append(float(row[0]))
> energy.append(float(row[1]))
> if int(row[2]) != 0:
> lescale.append(float(row[0]))
> leenergy.append(float(row[1]))
> if int(row[3]) != 0:
> cdscale.append(float(row[0]))
> cdenergy.append(float(row[1]))
>
> plt.plot(scale,energy, 'r+')
> plt.plot(lescale,leenergy, 'go')
> plt.plot(cdscale,cdenergy, 'bo')
> plt.xlabel('scale')
> plt.ylabel('energy (Ha)')
> plt.title('Energy vs scale')
> plt.legend()
> plt.savefig(file)
> print ("[[./%s]]" % file)
> #+end_src
>
> This is the error:
>
> NameError: name 'file' is not defined
>
> Obviously the syntax on the begin_src line is wrong, but what should it
> be instead?
>
> Thanks,
> Roger
--
[ stardiviner ]
I try to make every word tell the meaning what I want to express.
Blog: https://stardiviner.github.io/
IRC(freenode): stardiviner, Matrix: stardiviner
GPG: F09F650D7D674819892591401B5DF1C95AE89AC3
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-05 10:41 Output result of source block to a file Roger Mason
2019-06-05 13:17 ` stardiviner
@ 2019-06-05 13:33 ` Ken Mankoff
2019-06-06 11:48 ` Roger Mason
1 sibling, 1 reply; 12+ messages in thread
From: Ken Mankoff @ 2019-06-05 13:33 UTC (permalink / raw)
To: Roger Mason; +Cc: Org-Mode
On 2019-06-05 at 12:41 +02, Roger Mason <rmason@mun.ca> wrote...
> I want to output the result of the evaluation of a (python) source
> block to a (graphics) file and have a link to the file inserted in the
> buffer.
>
> Here is the code:
>
> #+begin_src python :results value file :file scaleplot02.pdf :exports results :var data=test
> print ("[[./%s]]" % file)
> #+end_src
What about :var file="scaleplot02.pdf".
-k.
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-05 13:17 ` stardiviner
@ 2019-06-06 11:36 ` Roger Mason
2019-06-07 11:05 ` stardiviner
2019-06-06 18:04 ` Roger Mason
1 sibling, 1 reply; 12+ messages in thread
From: Roger Mason @ 2019-06-06 11:36 UTC (permalink / raw)
To: numbchild; +Cc: emacs-orgmode
Hello,
stardiviner <numbchild@gmail.com> writes:
> Roger Mason <rmason@mun.ca> writes:
>
>> Hello,
>>
>> I want to output the result of the evaluation of a (python) source block
>> to a (graphics) file and have a link to the file inserted in the buffer.
>> #+begin_src python :results value file :file scaleplot02.pdf :exports results :var data=test
...snip...
>> plt.savefig(file)
>> print ("[[./%s]]" % file)
>> #+end_src
> For this, you should try updated header arguments like ":results graphics link"
> or ":results file link".
Thanks for your reply.
The current incarnation:
#+begin_src python :results graphics link :exports results :var data=test :var file="scaleplot2.pdf"
The output:
#+RESULTS: scaleplot02
: None
I'm guessing I have the syntax wrong. Is it documented somewhere? I'm
on Org mode version 9.1.13 (release_9.1.13-784-ged7d1d @
/home/rmason/.emacs.d/org-git/lisp/).
Cheers,
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-05 13:33 ` Ken Mankoff
@ 2019-06-06 11:48 ` Roger Mason
0 siblings, 0 replies; 12+ messages in thread
From: Roger Mason @ 2019-06-06 11:48 UTC (permalink / raw)
To: Ken Mankoff; +Cc: Roger Mason, Org-Mode
Hello,
Ken Mankoff <mankoff@gmail.com> writes:
>
> What about :var file="scaleplot02.pdf".
That was my starting point, but the resulting link is prefixed by ':'
Perhaps I should upgrade org.
Cheers,
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-05 13:17 ` stardiviner
2019-06-06 11:36 ` Roger Mason
@ 2019-06-06 18:04 ` Roger Mason
2019-06-06 21:12 ` John Kitchin
1 sibling, 1 reply; 12+ messages in thread
From: Roger Mason @ 2019-06-06 18:04 UTC (permalink / raw)
To: numbchild; +Cc: emacs-orgmode
Hello again,
stardiviner <numbchild@gmail.com> writes:
> Roger Mason <rmason@mun.ca> writes:
>
>> Hello,
>>
>> I want to output the result of the evaluation of a (python) source block
>> to a (graphics) file and have a link to the file inserted in the buffer.
>
> For this, you should try updated header arguments like ":results graphics link"
> or ":results file link".
I updated to Org mode version 9.2.3 (release_9.2.3-390-gfb5091 @ /home/rmason/.emacs.d/org-git/lisp/)
This works but sets the results to verbatim, hence the exported &
compiled code does not include the graphic.
#+name: scaleplot03
#+begin_src python :results output graphics link :exports results :var data=test :var file="scaleplot03.pdf"
import matplotlib.pyplot as plt
import csv
scale = []
lescale = []
cdscale = []
energy = []
leenergy = []
cdenergy = []
for row in data:
scale.append(float(row[0]))
energy.append(float(row[1]))
if int(row[2]) != 0:
lescale.append(float(row[0]))
leenergy.append(float(row[1]))
if int(row[3]) != 0:
cdscale.append(float(row[0]))
cdenergy.append(float(row[1]))
plt.plot(scale,energy, 'r+')
plt.plot(lescale,leenergy, 'go')
plt.plot(cdscale,cdenergy, 'bo')
plt.xlabel('scale')
plt.ylabel('energy (Ha)')
plt.title('Energy vs scale')
plt.legend()
plt.savefig(file)
print ("./%s" % file)
#+end_src
#+RESULTS: scaleplot03
: ./scaleplot03.pdf
This header does not work either:
#+name: scaleplot04
#+begin_src python :results file link :exports results :var data=test :var file="scaleplot04.pdf"
( same pythone code here)
#+RESULTS: scaleplot04
[[file:None]]
]]
#+end_src
Thank you for your help.
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-06 18:04 ` Roger Mason
@ 2019-06-06 21:12 ` John Kitchin
2019-06-07 10:00 ` Roger Mason
0 siblings, 1 reply; 12+ messages in thread
From: John Kitchin @ 2019-06-06 21:12 UTC (permalink / raw)
To: Roger Mason; +Cc: org-mode-email
[-- Attachment #1: Type: text/plain, Size: 2427 bytes --]
I think you can use something like this:
#+BEGIN_SRC python :results output file :var fname="test.png"
import matplotlib.pyplot as plt
import io
f = io.StringIO()
plt.plot([1, 2, 3, 17])
plt.savefig(fname)
print(fname, end='')
#+END_SRC
It is in Python3.
John
-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu
On Thu, Jun 6, 2019 at 2:27 PM Roger Mason <rmason@mun.ca> wrote:
> Hello again,
>
> stardiviner <numbchild@gmail.com> writes:
>
> > Roger Mason <rmason@mun.ca> writes:
> >
> >> Hello,
> >>
> >> I want to output the result of the evaluation of a (python) source block
> >> to a (graphics) file and have a link to the file inserted in the buffer.
> >
> > For this, you should try updated header arguments like ":results
> graphics link"
> > or ":results file link".
>
> I updated to Org mode version 9.2.3 (release_9.2.3-390-gfb5091 @
> /home/rmason/.emacs.d/org-git/lisp/)
>
> This works but sets the results to verbatim, hence the exported &
> compiled code does not include the graphic.
>
> #+name: scaleplot03
> #+begin_src python :results output graphics link :exports results :var
> data=test :var file="scaleplot03.pdf"
> import matplotlib.pyplot as plt
> import csv
>
> scale = []
> lescale = []
> cdscale = []
>
> energy = []
> leenergy = []
> cdenergy = []
>
> for row in data:
> scale.append(float(row[0]))
> energy.append(float(row[1]))
> if int(row[2]) != 0:
> lescale.append(float(row[0]))
> leenergy.append(float(row[1]))
> if int(row[3]) != 0:
> cdscale.append(float(row[0]))
> cdenergy.append(float(row[1]))
>
> plt.plot(scale,energy, 'r+')
> plt.plot(lescale,leenergy, 'go')
> plt.plot(cdscale,cdenergy, 'bo')
> plt.xlabel('scale')
> plt.ylabel('energy (Ha)')
> plt.title('Energy vs scale')
> plt.legend()
> plt.savefig(file)
> print ("./%s" % file)
> #+end_src
>
> #+RESULTS: scaleplot03
> : ./scaleplot03.pdf
>
> This header does not work either:
> #+name: scaleplot04
> #+begin_src python :results file link :exports results :var data=test :var
> file="scaleplot04.pdf"
> ( same pythone code here)
>
> #+RESULTS: scaleplot04
> [[file:None]]
> ]]
> #+end_src
>
> Thank you for your help.
>
> Roger
>
>
>
>
[-- Attachment #2: Type: text/html, Size: 3633 bytes --]
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-06 21:12 ` John Kitchin
@ 2019-06-07 10:00 ` Roger Mason
2019-06-07 15:01 ` John Kitchin
0 siblings, 1 reply; 12+ messages in thread
From: Roger Mason @ 2019-06-07 10:00 UTC (permalink / raw)
To: John Kitchin; +Cc: Roger Mason, org-mode-email
Hello John,
John Kitchin <jkitchin@andrew.cmu.edu> writes:
> I think you can use something like this:
>
> #+BEGIN_SRC python :results output file :var fname="test.png"
> import matplotlib.pyplot as plt
> import io
>
> f = io.StringIO()
> plt.plot([1, 2, 3, 17])
> plt.savefig(fname)
> print(fname, end='')
> #+END_SRC
>
> It is in Python3.
Thank you. That works.
Best wishes,
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-06 11:36 ` Roger Mason
@ 2019-06-07 11:05 ` stardiviner
0 siblings, 0 replies; 12+ messages in thread
From: stardiviner @ 2019-06-07 11:05 UTC (permalink / raw)
To: Roger Mason; +Cc: emacs-orgmode
Roger Mason <rmason@mun.ca> writes:
> Hello,
>
> stardiviner <numbchild@gmail.com> writes:
>
>> Roger Mason <rmason@mun.ca> writes:
>>
>>> Hello,
>>>
>>> I want to output the result of the evaluation of a (python) source block
>>> to a (graphics) file and have a link to the file inserted in the buffer.
>
>>> #+begin_src python :results value file :file scaleplot02.pdf :exports results :var data=test
>
> ...snip...
>
>>> plt.savefig(file)
>>> print ("[[./%s]]" % file)
>>> #+end_src
>
>> For this, you should try updated header arguments like ":results graphics link"
>> or ":results file link".
>
> Thanks for your reply.
>
> The current incarnation:
>
> #+begin_src python :results graphics link :exports results :var data=test :var file="scaleplot2.pdf"
>
> The output:
> #+RESULTS: scaleplot02
> : None
>
First, check out =org-manual.org= documentation.
And you don't need ~print ("[[./%s]]" % file)~ in Python code if you use ~:results graphics link~.
> I'm guessing I have the syntax wrong. Is it documented somewhere? I'm
> on Org mode version 9.1.13 (release_9.1.13-784-ged7d1d @
> /home/rmason/.emacs.d/org-git/lisp/).
>
> Cheers,
> Roger
--
[ stardiviner ]
I try to make every word tell the meaning what I want to express.
Blog: https://stardiviner.github.io/
IRC(freenode): stardiviner, Matrix: stardiviner
GPG: F09F650D7D674819892591401B5DF1C95AE89AC3
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-07 10:00 ` Roger Mason
@ 2019-06-07 15:01 ` John Kitchin
2019-06-08 10:51 ` Roger Mason
0 siblings, 1 reply; 12+ messages in thread
From: John Kitchin @ 2019-06-07 15:01 UTC (permalink / raw)
To: Roger Mason; +Cc: org-mode-email
you probably figured out the "import io" and "f = io..." line are not
necessary here.
I couldn't figure out a reasonable way to use :results graphics link
that didn't result in repeating the filename more than desired. These
also both work, but seem to both require repeating the filename twice.
#+BEGIN_SRC python :results graphics link :var fname="test.png" :file "test.png"
import matplotlib.pyplot as plt
plt.plot([1, 2, 3, 1])
plt.savefig(fname)
#+END_SRC
#+BEGIN_SRC python :results graphics link :file "test.png"
import matplotlib.pyplot as plt
plt.plot([1, 2, 3])
plt.savefig("test.png")
#+END_SRC
Something like this should work, but there seem to be some extra bytes
getting put in the png file from the decoding, and latin-1 is the only
one I can get to work. If anyone knows how to get this to work, I am
interested in seeing it!
#+BEGIN_SRC python :results value :file "io.png"
import matplotlib.pyplot as plt
import io
buf = io.BytesIO()
plt.plot([1, 2, 3])
plt.savefig(buf, format='png')
s = buf.getvalue()
return s.decode('latin-1')
#+END_SRC
In general though, all of these are much more work than using
ob-ipython, which just puts images in the buffer for you.
Roger Mason <rmason@mun.ca> writes:
> Hello John,
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
>> I think you can use something like this:
>>
>> #+BEGIN_SRC python :results output file :var fname="test.png"
>> import matplotlib.pyplot as plt
>> import io
>>
>> f = io.StringIO()
>> plt.plot([1, 2, 3, 17])
>> plt.savefig(fname)
>> print(fname, end='')
>> #+END_SRC
>>
>> It is in Python3.
>
> Thank you. That works.
>
> Best wishes,
> Roger
--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-07 15:01 ` John Kitchin
@ 2019-06-08 10:51 ` Roger Mason
2019-06-08 20:40 ` John Kitchin
0 siblings, 1 reply; 12+ messages in thread
From: Roger Mason @ 2019-06-08 10:51 UTC (permalink / raw)
To: John Kitchin; +Cc: Roger Mason, org-mode-email
Hello John,
John Kitchin <jkitchin@andrew.cmu.edu> writes:
> you probably figured out the "import io" and "f = io..." line are not
> necessary here.
Indeed.
> I couldn't figure out a reasonable way to use :results graphics link
> that didn't result in repeating the filename more than desired. These
> also both work, but seem to both require repeating the filename twice.
>
> #+BEGIN_SRC python :results graphics link :var fname="test.png" :file "test.png"
> import matplotlib.pyplot as plt
>
> plt.plot([1, 2, 3, 1])
> plt.savefig(fname)
> #+END_SRC
>
> #+BEGIN_SRC python :results graphics link :file "test.png"
> import matplotlib.pyplot as plt
>
> plt.plot([1, 2, 3])
> plt.savefig("test.png")
> #+END_SRC
>
> Something like this should work, but there seem to be some extra bytes
> getting put in the png file from the decoding, and latin-1 is the only
> one I can get to work. If anyone knows how to get this to work, I am
> interested in seeing it!
>
> #+BEGIN_SRC python :results value :file "io.png"
> import matplotlib.pyplot as plt
> import io
> buf = io.BytesIO()
>
> plt.plot([1, 2, 3])
> plt.savefig(buf, format='png')
>
> s = buf.getvalue()
> return s.decode('latin-1')
> #+END_SRC
>
>
> In general though, all of these are much more work than using
> ob-ipython, which just puts images in the buffer for you.
I will investigate that, thanks for the tip. I began this bit of work
using gnuplot for making x-y plots, but I find that gnuplot syntax gets
messy for anything but simple data. I am not a particular fan
of python so I'm also looking into guile & racket for plotting.
Thanks for your help, it is much appreciated.
Roger
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Output result of source block to a file
2019-06-08 10:51 ` Roger Mason
@ 2019-06-08 20:40 ` John Kitchin
0 siblings, 0 replies; 12+ messages in thread
From: John Kitchin @ 2019-06-08 20:40 UTC (permalink / raw)
To: Roger Mason; +Cc: org-mode-email
[-- Attachment #1: Type: text/plain, Size: 2394 bytes --]
A similar approach as the last one should work, the problem I was having is
that to print the binary string from python you have to decode it, and
latin-1 seems close to right, but it puts a bunch of extra bytes in it that
lead to a bad png file. I feel like this worked in Python2 with StringIO,
but not in Python3 with BytesIO.
John
-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu
On Sat, Jun 8, 2019 at 6:52 AM Roger Mason <rmason@mun.ca> wrote:
> Hello John,
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > you probably figured out the "import io" and "f = io..." line are not
> > necessary here.
>
> Indeed.
>
> > I couldn't figure out a reasonable way to use :results graphics link
> > that didn't result in repeating the filename more than desired. These
> > also both work, but seem to both require repeating the filename twice.
> >
> > #+BEGIN_SRC python :results graphics link :var fname="test.png" :file
> "test.png"
> > import matplotlib.pyplot as plt
> >
> > plt.plot([1, 2, 3, 1])
> > plt.savefig(fname)
> > #+END_SRC
> >
> > #+BEGIN_SRC python :results graphics link :file "test.png"
> > import matplotlib.pyplot as plt
> >
> > plt.plot([1, 2, 3])
> > plt.savefig("test.png")
> > #+END_SRC
> >
> > Something like this should work, but there seem to be some extra bytes
> > getting put in the png file from the decoding, and latin-1 is the only
> > one I can get to work. If anyone knows how to get this to work, I am
> > interested in seeing it!
> >
> > #+BEGIN_SRC python :results value :file "io.png"
> > import matplotlib.pyplot as plt
> > import io
> > buf = io.BytesIO()
> >
> > plt.plot([1, 2, 3])
> > plt.savefig(buf, format='png')
> >
> > s = buf.getvalue()
> > return s.decode('latin-1')
> > #+END_SRC
> >
> >
> > In general though, all of these are much more work than using
> > ob-ipython, which just puts images in the buffer for you.
>
> I will investigate that, thanks for the tip. I began this bit of work
> using gnuplot for making x-y plots, but I find that gnuplot syntax gets
> messy for anything but simple data. I am not a particular fan
> of python so I'm also looking into guile & racket for plotting.
>
> Thanks for your help, it is much appreciated.
>
> Roger
>
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^ permalink raw reply [flat|nested] 12+ messages in thread
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Thread overview: 12+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2019-06-05 10:41 Output result of source block to a file Roger Mason
2019-06-05 13:17 ` stardiviner
2019-06-06 11:36 ` Roger Mason
2019-06-07 11:05 ` stardiviner
2019-06-06 18:04 ` Roger Mason
2019-06-06 21:12 ` John Kitchin
2019-06-07 10:00 ` Roger Mason
2019-06-07 15:01 ` John Kitchin
2019-06-08 10:51 ` Roger Mason
2019-06-08 20:40 ` John Kitchin
2019-06-05 13:33 ` Ken Mankoff
2019-06-06 11:48 ` Roger Mason
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