I am trying to create a plot in Octave using the LaTeX interpreter for the axis labels, but whenever I try to do so, using the following code:
figure()
xlabel('The $x$ axis','interpreter','latex')
Octave returns the following message:
warning: latex_renderer: a run-time test failed and the 'latex' interpreter has been disabled.
According to the online Octave documentation, it requires some external tools, all of which are present on my system.
The "latex" interpreter only works if an external LaTeX tool chain is present. Three binaries are needed: latex, dvipng, and dvisvgm. If those binaries are installed but not on the path, one can still provide their respective path using the following environment variables: OCTAVE_LATEX_BINARY, OCTAVE_DVIPNG_BINARY, and OCTAVE_DVISVG_BINARY.
I even tried manually setting the aforementioned environment variables, using Octave's setenv() function, but no dice. I'm using Octave version 7.3.0, running on OpenSUSE. If there is a way I can get some more verbose output from Octave to help debug the issue I'm all ears.
Related
I would like to visualize pointcloud in drake-visualizer using python binding.
I imitated how to publish images through lcm from here, and checked out these two issues (14985, 14991). The snippet is as follows :
point_cloud_to_lcm_point_cloud = builder.AddSystem(PointCloudToLcm())
point_cloud_to_lcm_point_cloud.set_name('pointcloud_converter')
builder.Connect(
station.GetOutputPort('camera0_point_cloud'),
point_cloud_to_lcm_point_cloud.get_input_port()
)
point_cloud_lcm_publisher = builder.AddSystem(
LcmPublisherSystem.Make(
channel="DRAKE_POINT_CLOUD_camera0",
lcm_type=lcmt_point_cloud,
lcm=None,
publish_period=0.2,
# use_cpp_serializer=True
)
)
point_cloud_lcm_publisher.set_name('point_cloud_publisher')
builder.Connect(
point_cloud_to_lcm_point_cloud.get_output_port(),
point_cloud_lcm_publisher.get_input_port()
)
However, I got the following runtime error:
RuntimeError: DiagramBuilder::Connect: Mismatched value types while connecting output port lcmt_point_cloud of System pointcloud_converter (type drake::lcmt_point_cloud) to input port lcm_message of System point_cloud_publisher (type drake::pydrake::Object)
When I set 'use_cpp_serializer=True', the error becomes
LcmPublisherSystem.Make(
File "/opt/drake/lib/python3.8/site-packages/pydrake/systems/_lcm_extra.py", line 71, in _make_lcm_publisher
serializer = _Serializer_[lcm_type]()
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 90, in __getitem__
return self.get_instantiation(param)[0]
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 159, in get_instantiation
raise RuntimeError("Invalid instantiation: {}".format(
RuntimeError: Invalid instantiation: _Serializer_[lcmt_point_cloud]
I saw the cpp example here, so maybe this issue is specific to python binding.
I also saw this python example, but thought using 'PointCloudToLcm' might be more convenient.
P.S.
I am aware of the development in recent commits on MeshcatVisualizerCpp and MeshcatPointCloudVisualizerCpp, but I am still on the drake-dev stable build 0.35.0-1 and want to stay on drake visualizer until the meshcat c++ is more mature.
The old version in pydrake.systems.meshcat_visualizer.MeshcatVisualizer is a bit too slow on my current use-case (multiple objects drop). I can visualize the pointcloud with this visualization setting, but it took too much machine resources.
Only the message types that are specifically bound in lcm_py_bind_cpp_serializers.cc can be used on an LCM message input/output port connection between C++ and Python. For all other LCM message types, the input/output port connection must be from a Python system to a Python system or a C++ System to a C++ System.
The lcmt_image_array is listed there, but not the lcmt_point_cloud.
If you're stuck using Drake's v0.35.0 capabilities, then I don't see any great solutions. Some options:
(1) Write your own PointCloudToLcm system in Python (by re-working the C++ code into Python, possibly with a narrower set of supported features / channels for simplicity).
(2) Write your own small C++ helper function MakePointCloudPublisherSystem(...) that calls LcmPublisherSystem::Make<lcmt_point_cloud> function in C++, and bind it into Python. Then your Python code can call MakePointCloudPublisherSystem() and successfully connect that to the existing C++ PointCloudToLcm.
From the GraalVM examples, they have code like this to run a single line of Python code:
context.eval("python", "\nprint('Hello polyglot world Python!');");
Yes that works fine in a Java program.
I can also run a Python program from the command line using the "graalpython" program.
My question is how do I run a python program from the Java example I mentioned above?
context.eval("python", "\nprint('Hello polyglot world Python!');");
I tried using the "file:" argument, but that didn't work or I'm doing something wrong.
For example, this did not work:
context.eval("python", "file: /path_to_python/test.py");
This line of code gives me:
Original Internal Error:
java.lang.RuntimeException: not implemented
So, maybe that answers my question, but I have to believe you can run a python script from a GRAAL program like you can a single line of code. Hence, this posting.
--
Is running a python program from within a Java program using graal "eval" supported? If so, I would very much appreciate an example of usage.
Thanks very much.
You need to build a Source object in order to eval a file:
File file = new File("/path_to_python/test.py");
Source source = Source.newBuilder("python", file).build();
context.eval(source);
I'm fresh to python/biopython and tried blast using biopython like this:
from Bio.Blast import NCBIWWW
fasta_string = open("C:\\xxxx\\xxxx\\xxxx\\abc.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
print result_handle.read()
I was wondering if it is possible to run igblast using biopython. I have searched for this but it seems no one is really doing this.
I haven't tried them, but I have found:
pyigblast.
PyIgBlast - Open source Parser to call IgBlast and parse results for
high-throughput sequencing. Uses Python multi-processing to get around
bottlenecks of IgBlast multi-threading. Parses blast output to
deliminated files (csv,json) for uploading to databases. Can connect
directly with mysql and mongo instances to insert directly.
The code uses Python 2.7 and BioPython.
PyIR
Immunoglobulin and T-Cell receptor rearrangement software. A Python wrapper for IgBLAST that scales to allow for the parallel processing of millions of reads on shared memory computers. All output is stored in a convenient JSON format.
The code uses Python 3.6 and BioPython.
Both tools use a locally installed igblastn executable. You can install igblastn locally with conda install igblast.
I have my emacs set up so that colors in shell buffers work great. I also use the compile command to run individual test files in my ruby on rails environment But when I do that, the ror test functionality puts lots of shell/terminal escape characters into my compilation buffer. Is there any way to get that stuff to display in terminal colors?
BTW: I searched around and tried some things, but they didn't work.
Thanks!
Here's what I have in my .emacs file now. It does not work until the end, but that's OK.
;; This stuff is to ansi-colorize the compilation buffer after a rails test so the terminal colors come through.
(define-derived-mode ansi-compilation-mode compilation-mode "ansi compilation"
"Compilation mode that understands ansi colors."
(require 'ansi-color)
(toggle-read-only 0)
(ansi-color-apply-on-region (point-min) (point-max)))
(defun colorize-compilation (one two)
"ansi colorize the compilation buffer."
(ansi-compilation-mode))
(setq compilation-finish-function 'colorize-compilation)
EDIT
I have switched from using the compile mode to using an async shell command. Here's the code:
(defun run-it ()
"Run it on the current file."
(interactive)
(save-buffer)
(shell-command
(format "my_command %s &"
(shell-quote-argument (buffer-name)))))
(global-set-key "\C-ct" 'run-it)
It saves the buffer first. The & makes it actually interactive so I can enter text in the buffer and the command will get that input. And it colors the command output on the fly, which my compile buffer was not doing.
Backing the comment by Alex Vorobiev, which delivered the answer.
Seems you've put a comint-mode aside and with that the ansi-color-process-output filter.
AFAIU fontifying is done on a per-buffer-base, run from an idle-timer resp. triggered by buffer-changes. If enabled in a output-shell, Emacs might hang, as a lot of changes may occur in short time. Therefor fontification is commonly off here. An alternative approach: M-x MY-MODE at the shell-buffer. Which might need some reset to shell environment or re-start then.
I recently had to move my site from one server to another and it appears Fred's 3Drotate script creates files that have Imagemagick settings in them instead of image data. When I first ran the script I received the following error:
expr: warning: unportable BRE: `^[0-9][0-9]*$': using `^' as the first character of the basic regular expression is not portable; it is being ignored
expr: warning: unportable BRE: `^[+-][0-9][0-9]*$': using `^' as the first character of the basic regular expression is not portable; it is being ignored
expr: warning: unportable BRE: `^[0-9]*[\\.][0-9]*$': using `^' as the first character of the basic regular expression is not portable; it is being ignored
expr: warning: unportable BRE: `^[+-][0-9]*[\\.][0-9]*$': using `^' as the first character of the basic regular expression is not portable; it is being ignored
I was able to resolve this by removing each instance of the '^' character. The script runs and it creates a file of a few hundred KB, but the contents appear to be a configuration such as:
id=MagickCache
quantum-depth=16
class=DirectClass colors=0 matte=False
columns=500 rows=500 depth=8
colorspace=sRGB
compression=JPEG quality=75
units=PixelsPerInch
resolution=72x72
page=500x500+0+0
rendering-intent=Perceptual
gamma=0.454545
red-primary=0.64,0.33 green-primary=0.3,0.6 blue-primary=0.15,0.06
white-point=0.3127,0.329
date:create=2012-08-10T20:44:21-07:00
date:modify=2012-08-10T20:44:21-07:00
jpeg:colorspace=2
jpeg:sampling-factor=2x2,1x1,1x1
Any ideas? I'm running imagemagick version 6.7.8-9 which is newer than what was on my original server, however I don't know which version that was.
Update:
I'm on a CentOS box using 3DRotate revised by Fred on 3/11/10. ImageMagick is version 6.7.8-9 whereas my old server, also CentOS was using version 6.7.6-0.
Fred's 3Drotate script still works fine for me. I have no reason to complain.
This is on Mac OS X Lion, with Bash version GNU bash, Version 4.2.37(2)-release....
You are strongly advised to re-download the script and try again. If you want to report a bug, you should give info about your OS, your Bash and your ImageMagick versions...
Oh, and see also this page, which states...
...you need ImageMagick v6.3.5.0 or higher for the script to work,
...gives some hints about troubleshooting and
...tells you the eMail address of the author so you can contact him to discuss your problems.
With recent changes to ImageMagick between IM 6.7.6.7 and IM 6.7.8.3 for colorspace changes and grayscale becoming linear, I have had to go through recently all my scripts and make appropriate changes. I am only part way through my scripts as of this date, but have fixed about 1/3 to 1/2, but 3Drotate did not need any changes since the last one on 11/26/2011. But your version is to old, so you will need to get an update. The problems you seem to have may or may not be related. But appear to be related to the unix utility expr. I would make sure that you have a current version of that installed. The following works perfectly fine for me on both IM 6.7.6.0 and 6.7.8.9 on my Mac OSX Snow Leopard
3Drotate pan=45 tilt=45 auto=zc mandril.jpg mandril_test.jpg
The first question I would ask is what was your exact command line. As you can see the arguments are a bit different from my other scripts as they include equal signs.
If you still have trouble, report them to me or on the ImageMagick Discourse forum at http://www.imagemagick.org/discourse-server/viewforum.php?f=1
Fred