I am trying to load an mrc file, generate the map of it and then save the image, the problem is that it only saves a blank image, the code I run is the following:
from pymol import cmd
cmd.load('./6vof.mrc', ' 6vof')
cmd.volume( '6vof _volume', ' 6vof')
cmd.png('./test.png', 300, 200)
The equivalent code in the interface does work, I wanted to know how I can make the save method wait for the rendering of everything.
Hi Luis José Castillo,
it seems I encountered the same problem as you did.
I wanted to use Pymol from within a Ruby on Rails application and always got his message, when I launched it from within ruby:
CmdLoad: "mypol/4hhb.pdb" loaded as "4hhb".
Ray: render time: 0.02 sec. = 178776.9 frames/hour (0.02 sec. accum.).
The result was a blank transparent png. If I ran it in the command line with the same script I got this message and a perfect png:
CmdLoad: "4hhb.pdb" loaded as "4hhb".
Ray: render time: 4.04 sec. = 890.8 frames/hour (4.04 sec. accum.).
I got this behavoir on Ubuntu 20, Ubuntu 18 Server and in Docker.
I figured out, that the only difference was, I used relative paths from within ruby, but was always running everything in the same folder in the command line.
Well, so I just make this detour for my Rails application and now it does work:
def get_protein_image(pdb_id)
dir_path = get_pdb_file(pdb_id)
`cp lib/png_from_pdb.py #{dir_path} && cd #{dir_path} && pymol protein.pdb png_from_pdb.py -qc`
end
Sorry for the ruby code here, but here the essential solution, try to run everything inside the same folder (I simply delete the tmp subfolder after png generation).
cp lib/png_from_pdb.py #{dir_path} && cd #{dir_path} && pymol protein.pdb png_from_pdb.py -qc
I hope this trick will help you too!
Best regards,
Stephan
Related
I just tried the standalone PyQGIS application by running the custom script "Proximity.py"* in a VS Code project without the need of a GUI (such as QGIS).
But, when I run the python-program I get the following message:
proj_create_from_database: C:\Program Files\PostgreSQL\14\share\contrib\postgis-3.2\proj\proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 0 whereas a number >= 2 is expected. It comes from another PROJ installation. (see also: Error Message after launching the configuration (launch.json) from VS Code (when pressing F5))
I'm trying this online example with the following installations:
PostgreSQL 14
Python39
.vscode\extensions\ms-python.python-2022.4.1\pythonFiles\lib\python\debugpy\launcher
osgeo4w-setup.exe (including QGIS LTR)
I read that there is a solution by undefining [PROJ_LIB] before importing pyproj or osgeo: del os.environ ['PROJ_LIB'] as described under this link. If this is also supposed to be the correct solution in this case, can someone help me with step-by-step instructions (for dummies)?
. * The "Proximity.py" script is a pyqgis standalone example from "https://github.com/MarByteBeep/pyqgis-standalone"
Finally, I got a solution to be able to run the "standalone PyQGIS"* example "Proximity" (provided by MarByteBeep).
This solution was possible without needing to launch the configuration file "launch.json" as above described. And so, avoiding the need to make any configuration to the environment variable "PROJ_LIB" by trying to circumvent the above issue.
I just first added the following two code-lines (see here line 2 and 3) in the python file "main.py" so as to be able to use the plugin "PROCESSING" (initially line 8 of the "main.py" file), then I store it and finally I ran it.
Line 1: from qgis.core import
Line 2: import sys
Line 3: sys.path.append('C:\Program Files\QGIS 3.24.1\apps\qgis\python\plugins')
Line 4: qgs = QgsApplication([], False)
Line 5: ...
The Proximity example is based on the answer of "Mar Tjin" to the following Question: "Looking for manual on how to properly setup standalone PyQGIS without GUI"
. * By "Standalone PyQGIS" I refer to code/scripts that can be run outside the QGIS-GUI (=> QGIS-Desktop/Server Application). In my case under the external Editor VS Code
While a binary works with bazel run, when I run a test using bazel test, such as:
$ bazel test //systems/sensors:rgbd_camera_test
I encounter a slew of errors from VTK / OpenGL:
ERROR: In /vtk/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 820
vtkXOpenGLRenderWindow (0x55880715b760): failed to create offscreen window
ERROR: In /vtk/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 816
vtkXOpenGLRenderWindow (0x55880715b760): GLEW could not be initialized.
ERROR: In /vtk/Rendering/OpenGL2/vtkShaderProgram.cxx, line 453
vtkShaderProgram (0x5588071d5aa0): Shader object was not initialized, cannot attach it.
ERROR: In /vtk/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 1858
vtkXOpenGLRenderWindow (0x55880715b760): Hardware does not support the number of textures defined.
May I ask why this happens?
(Note: This post is a means to migrate from http://drake.mit.edu/faq.html to StackOverflow for user-based questions.)
The best workaround at the moment is to first mark the test as as local in the BUILD.bazel file, either with local = 1, or tags = [.., "local"]. Doing so will make the specific target run without sandboxing, such that it has an environment similar to that of bazel run.
As an example, in systems/sensors/BUILD.bazel:
drake_cc_googletest(
name = "rgbd_camera_test",
# ...
local = 1,
# ...
)
If this does not work, then try running the test in Bazel without sandboxing:
$ bazel test --spawn_strategy=standalone //systems/sensors:rgbd_camera_test
Please note that you can possibly add --spawn_strategy=standalone to your ~/.bazelrc, but be aware that this means your development testing environment may deviate even more from other developer's testing environments.
Update 2
I think #faré is right, it's an output translation problem.
So I declared the evironment variable ASDF_OUTPUT_TRANSLATIONS and set it to E:/. Now (asdf:require-system "my-system") yields a different error: Uneven number of components in source to destination mapping: "E:/" which led me to this SO-topic.
Unfortunately, his solution doesn't work for me. So I tried the other answer and set ASDF_OUTPUT_TRANSLATIONS to (:output-translations (t "E:/")). Now I get yet another error:
Invalid source registry (:OUTPUT-TRANSLATIONS (T "E:/")).
One and only one of
:INHERIT-CONFIGURATION or
:IGNORE-INHERITED-CONFIGURATION
is required.
(will be skipped)
Original Posting
I have a simple system definition but can't get ASDF to load it.
(asdf-version 3.1.5, sbcl 1.3.12 (upgraded to 1.3.18 AMD64), slime 2.19, Windows 10)
What I have tried so far
Following the ASDF manual: "4.1 Configuring ASDF to find your systems"
There it says:
For Windows users, and starting with ASDF 3.1.5, start from your
%LOCALAPPDATA%, which is usually ~/AppData/Local/ (but you can ask in
a CMD.EXE terminal echo %LOCALAPPDATA% to make sure) and underneath
create a subpath config/common-lisp/source-registry.conf.d/
That's exactly what I did:
Echoing %LOCALAPPDATA% which evaluates to C:\Users\my-username\AppData\Local
Underneath I created the subfolders config\common-lisp\source-registry.conf.d\ (In total: C:\Users\my-username\AppData\Local\config\common-lisp\source-registry.conf.d\
The manual continues:
there create a file with any name of your choice but with the type conf, for instance 50-luser-lisp.conf; in this file, add the following line to tell ASDF to recursively scan all the subdirectories under /home/luser/lisp/ for .asd files: (:tree "/home/luser/lisp/")
That’s enough. You may replace /home/luser/lisp/ by wherever you want to install your source code.
In the source-registry.conf.d folder I created the file my.conf and put in it (:tree "C:/Users/my-username/my-systems/"). This folder contains a my-system.asd.
And here comes the weird part:
If I now type (asdf:require-system "my-system") in the REPL I get the following error:
Can't create directory C:\Users\my-username\AppData\Local\common-lisp\sbcl-1.3.12-win-x86\C\Users\my-username\my-systems\C:\
So the problem is not that ASDF doesn't find the file, it does -- but (whatever the reason) it tries to create a really weird subfolder hierarchy which ultimately fails because at the end it tries to create the folder C: but Windows doesn't allow foldernames containing a colon.
Another approach: (push path asdf:*central-registry*)
If I try
> (push #P"C:/Users/my-username/my-systems/" asdf:*central-registry*)
(#P"C:/Users/my-username/my-systems/"
#P"C:/Users/my-username/AppData/Roaming/quicklisp/quicklisp/")
> (asdf:require-system "my-system")
I get the exact same error.
I don't know what to do.
Update
Because of the nature of the weird path ASDF was trying to create I thought maybe I could bypass the problem by specifying a relative path instead of an absolute one.
So I tried
(:tree "\\Users\\my-username\\my-systems")
in my conf file. Still the same error.
Ahem. It looks like an output-translations problem.
I don't have a Windows machine right now, but this all used to work last time I tried.
Can you setup some ad hoc output-translations for now that will make it work?
I've searched a lot for this and have not yet found a definitive solution. The closest thing I've found is this:
import shutil
from os.path import join
import os
import time
import sys
minecraft_dir = ('server diectory')
world_dir = ('server world driectory')
def server_command(cmd):
os.system('screen -S -X stuff "{}\015"'.format(cmd))
on = "1"
while True:
command=input()
command=command.lower()
if on == "1":
if command==("start"):
os.chdir(minecraft_dir)
os.system('"C:\Program Files\Java\jre1.8.0_111\bin\java.exe" -Xms4G -Xmx4G -jar craftbukkit-1.10.2.jar nogui java')
print("Server started.")
on = "0"
else:
server_command(command)
When I launch this program and type 'start' the CMD flashes up and closes instantly. Instead I want the CMD to stay open with the minecraft sever running from it. I'm not sure why this happens or what the problem is, any help would be greatly appreciated.
p.s. I have edited this to my needs (such as removing a backup script that was unnecessary) but it didn't work before. The original link is: https://github.com/tschuy/minecraft-server-control
os.system will simply run the command then return to your python script with no way to further communicate with it.
On the other hand using subprocess.Popen gives you access to the process while it runs, including writing to it's .stdin which is how you send data to the server:
def server_command(cmd):
process.stdin.write(cmd+"\n") #just write the command to the input stream
process = None
executable = '"C:\Program Files\Java\jre1.8.0_111\bin\java.exe" -Xms4G -Xmx4G -jar craftbukkit-1.10.2.jar nogui java'
while True:
command=input()
command=command.lower()
if process is not None:
if command==("start"):
os.chdir(minecraft_dir)
process = subprocess.Popen(executable, stdin=subprocess.PIPE)
print("Server started.")
else:
server_command(command)
you can also pass stdout=subprocess.PIPE so you can also read it's output and stderr=subprocess.PIPE to read from it's error stream (if any)
As well instead of process.stdin.write(cmd+"\n") you could also use the file optional parameter of the print function, so this:
print(cmd, file=process.stdin)
Will write the data to process.stdin formatted in the same way that print normally does, like ending with newline for you unless passing end= to override it etc.
Both of the above answers do not work in the environment I tried them in.
I think the best way is to use RCON, not sending keys to a window.
RCON is the protocol used by games to run commands.
Many python libraries support Minecraft RCON, and the default server.properties file has an option for RCON.
We will use the python module: MCRON.
Install it. It works for windows, mac, linux.
Type:
pip install mcrcon
Lets configure your server to allow RCON.
In server.properties, find the line 'enable-rcon' and make it look like this:
enable-rcon=true
Restart and stop your server.
Find the line 'rcon.password' and set it to any password you will remember.
You can leave the port default at 25575.
Now, open your terminal and type:
mcron localhost
Or your server ip.
You will be prompted to enter the password you set.
Then you can run commands and will get the result.
But we are doing this with python, not the PYPI MCRON scripts - so do this.
from mcrcon import MCRcon as r
with r('localhost', 'insertyourpasswordhere') as mcr:
resp = mcr.command('/list')
print(resp) #there are 0/20 players online: - This will be different for you.
I've developed a node.js tool which uses imagemagick from the command line. That is, exec('my_imagemagick_commands'). What's the best way to deliver that tool to a client using Windows? That is, how can I make a Windows installer that'll install node.js, imagemagick and the tool - preferably as a binary, not the source - in a specific folder?
If you want an easy bundle... Zip the list below, deploy on client and drag/drop images to be processed onto the yourtool.cmd file (I'm doing something similar for image optimizers)
Bundle: (put these in one directory)
yourtool.cmd
yourtool.js
node.exe
node_modules/ (if applicable)
yourtool.cmd
REM Get the drive/path the batch file is in
set batchdir=%~d0%~p0
REM Run tool for items dragged over...
"%batchdir%node.exe" "%batchdir%yourtool.js" %*
yourtool.js
// start at 2 for arguments passed...
// 0 is node.exe
// 1 is the js file run
for (var i=2; i<process.argv.length; i++) {
var imagePath = process.argv[i];
//do something with image...
}
For others interested in imagemagick with node, you should check out node-imagemagick