I am trying to find a way to convert a 3dm file into ply format. I found a number of online converters but no library which I could use to write my own python script helping me to be more flexible.
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I have a lammps_file.data and I need to convert it to Gromacs files (gro and top) to run my simulations.
Does anyone know how to do this?
Another choice is to convert from lammps to charmm files (psf and pdb). Once I get the charmm files I can just use Topotools to get the gromacs files I need.
Thanks
Indeed, NOW I am trying to do the same myself.
So far, you can use intermol , this should work fine to convert LAMMPS data files to Gromacs files. Once you install intermol, and you ceate a path to the intermol converter, you can use a command like:
python2.7 $conv/convert.py --lmp_in topology.data --gromacs -v
CHECK the format of your data file, I still having problemst to convert it.
If you wish to create the psf file,
you would need VMD (google it), then open the tcl terminal and write :
topo readlammpsdata topology.data full
animate write psf topology.psf
The 1st line is for loading yur LAMMPS data file, if you are in the folder where
that files is located
2nd convert the data to psf CHARMM
Also, you could try this. In this paper, they provide a tood to conver
CHARMM topologies to gromacs here. Thus, you convert to psf, then to gro top.
Need to read .dat files (binary files) from local and write the output in console using scala IDE,
Is it required first convert .dat file to .txt/.csv file then we can read and apply if any transformation and again need to convert .txt/.csv to .dat
tried with some existing code
ref:http://alvinalexander.com/scala/how-to-read-write-binary-files-in-scala-examples
still getting error ,Please share any suggestion
Thanks in advance.
I want to open my 3D point cloud in MATLAB. But they are in .las files. How can I display them in MATLAB???
I heard about .ply file can open 3D point data on MATLAB. So I want to know how to convert las files to ply files.
There is a .las file reader for matlab here:
https://es.mathworks.com/matlabcentral/fileexchange/48073-lasdata
Once you have the data in matlab you can use these point cloud tools, which are part of the computer vision toolbox:
https://es.mathworks.com/help/vision/3-d-point-cloud-processing.html
If you want to embrace the open source force, I'm writing a Python (easy transition from matlab) library for point cloud processing:
https://github.com/daavoo/pyntcloud
You can use the free and open-source CloudCompare software.
On the command line:
CloudCompare -O file_to_convert.las -C_EXPORT_FMT PLY -SAVE_CLOUDS
Take care to the order of the options: it seems that -SAVE_CLOUDS must be at the end.
That will result in a binary-format PLY file in the same directory as the file to convert, named using the original filename and the date of export, like: file_to_convert_2019-07-18_13h32_06_751.ply
I found no way to specify the output file name (should you find one please comment below).
Should you want a more predictable name, add option -NO_TIMESTAMP before the option -SAVE_CLOUDS (but then you risk overwriting files so be careful).
More help (such as how to export in ASCII-format) in the documentation.
I timed this on powerful PC, it took 170s to convert a 2.7GB LAS file with 102M points (XYZ,intensity,time).
if you have LAStools installed, you can use las2txt to convert your *.las/*.laz files into *.xyz format which MeshLab can import natively as a point cloud, which may then be converted into a Mesh.
There are a multitude of caveats to that depending on the source of your data-set.
Has anyone ever heard of something that might facilitate the work with XMP metadata in Matlab?
For instance, EXIF metadata can be read simply by using the exifread command -
output = exifread(filename);
I've found this thread, but it seems to be dead.
Currently I am thinking about the following options:
Writing MEX file using C++ XMP SDK
Calling Java routines using JAVA XMP SDK
To summarize, the question is:
Do you have any idea on how XMP can be read/written in Matlab?
XMP is just XML, so you can use any MATLAB XML toolbox. My personal favourite is xml_io_tools.
If you want to use the SDK to avoid having to manually interpret what bits of the XML means, then of your two options the Java one sounds preferable. Calling Java from MATLAB is straightforward, and you avoid the hassle of building things that MEX entails.
I have found the answer. The best way is to download ExifTool and any Matlab JSON parser. It is possible to extract it from any file format, including .DNG, .XMP, .JPEG, .TIFF.
Step 1: Extract the info into temporary JSON file by using
system(['exiftool -struct -j ' fileName '>' tempFile]);
Step 2: Call the JSON parser on the tempFile
Step 3: You have the data in Matlab struct.
I have some data generated in MATLAB that I want to process using Perl. I saved the data from MATLAB in a .mat file. Is there any way to read it in Perl?
One option would be to save the binary MAT file as ASCII from inside MATLAB using something like:
load('test_data.mat');
save('test_data.asc', 'var1', 'var2', '-ascii');
Then you would have ASCII data to process in Perl.
If you need a solution completely written in Perl, then you should be able to automate the process using the Math::MATLAB package on CPAN.
NOTE: If Python is an option, you could use the loadmat function in the SciPy Python library.
The Java library JMatIO has worked well for me. Maybe you can try using inline Java.