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.
Related
I have a simulation which produces a bunch of vtu (also pvtu) and vti (also pvti) files which, as I understand, represent the configuration of points in one timestamp. But is there a way to group them into one close-to-vtk file to be able to visualize a simulation, which consists of many timestamps, in an app like paraview (but not only)?
ParaView can natively open many files as a time series, see the doc.
If your file names contains a number, the ParaView "open file" dialog will collapse them under a dummy filename containing dots instead of number. Open it to open the whole series.
edit: conversion
To be close to the vtk format, you may use .pvd that is a ParaView format described here or the .series from VTK (doc here )
To read it with another software, well, you will need to check the supported file formats by the application you want to use. VTK can write several other formats, including Exodus, XDMF or CGNS for instance.
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.
Anybody knows how to export an Ansys structural data file to ParaView?
It is read that ParaView has an Ansys reader, but it does not work. Errors always come up when loading the *.inp file.
Is there any script to convert .inp files to .vtk?
Thanks
Based on the video from Czech-based SVS FEM s.r.o., I wrote an input file for Ansys Mechanical APDL, that creates a VTK file, which can be opened in ParaView.
In the input file vtk.inp, the user has to specify the argument arg1, for which the nodal values are to be written to the vtk file via the command *get,my_results(j),NODE,n_j,..., p.e.
arg1='S,EQV' ! for equivalent stress or
arg1='TEMP' ! for temperature
For further nodal results, refer to the specifications of the *GET command in the Ansys Commands Reference.
The vtk.inp file should be placed in the current working directory. It is called with the APDL command /input,vtk,inp. In Ansys Mechanical, this command can directly be inserted in the command line. In Ansys Workbench, the command can be pasted in the feature Commands (APDL) under Solution.
The output file output.vtk is written in the same location as the input file.
The code was tested with a structural analysis in Ansys Mechanical APDL 17.2 and Ansys Workbench 17.2. The vtk file was tested with ParaView 5.4.1.
Explanation:
The array e_types_Ansys_to_VTK maps the Ansys element types (p. e. SOLID186) to VTK cell types (see also Ansys Element Types).
Limitations:
The input file is yet limited to write only one scalar parameter result in the vtk file, but it can easily be extended for vector or tensor results as well as for multiple results in one vtk file, following the VTK File Format Specification.
Since Ansys stores nodal results only in the corner nodes, only linear VTK elements are used. There could still be some minor mistakes in the e_types_Ansys_to_VTK map, since I could only test some element types. Please feel free to report any corrections or extensions to the code in the comments.
Here is the link to the source code. Use at your own risk.
In case you would like to export a vtk file directly from Ansys Workbench, a Python result converter was introduced in a Youtube video here. Unfortunately, the source code only appears in the video and is explained in Czech language.
Thus, I typewrote the code from screenshots and made some minor improvements.
You will need two files to install the macro as an Ansys ACT extension:
main.py and vtk.xml.
Place the file vtk.xml in the folder C:\Program Files\ANSYS Inc\v###\Addins\ACT\extensions, where ### is your Ansys version, p.e. 172
Create a new folder vtk in C:\Program Files\ANSYS Inc\v###\Addins\ACT\extensions.
Place the file main.py in the created folder.
Start Ansys Workbench.
Register the path C:\Program Files\ANSYS Inc\v###\Addins\ACT\extensions as additional extension path under Tools > Options > Extensions.
Restart Ansys Workbench, go to Extensions > ACT start page > Extension manager > VTK and load the extension.
In a structural analysis, go to Results, right-click and insert My results. Three inputs have to made by the user:
Under *get,my_results(j),NODE,N,..., , give the desired nodal result according to the Ansys Commands Reference, p.e. S,EQV for equivalent stress.
Under VTF file name, give the full path to the vtk output file to be created, p.e. C:\temp\output.vtk
Under Load step, give the load step number (p.e. 1 for last load step unless not stated otherwise).
For larger models, I experienced that the automatically generated file makeresult.mac is not instantly transferred from the project_pending folder to the actual working directory, thus, causing the macro to throw an error. Maybe, anyone can make a suggestion on how to fix this?
ParaView cannot read .inp structure files (I guess this is the Abaqus file format). You could try to export your files as Nastran (.nas) files, since ParaView has a Nastran reader.
I am a biology graduate student trying to export these files so that they can be used with a matlab based automated behavior classification software JAABA. It looks like there is no direct way to save .trc files as .mat (http://www.mediacy.com/imageproplus/specifications). At the very least I would like to figure out a way to read the format of the .trc files so that I could write a script to get them to make sense for JAABA. If anyone is familiar with either of these programs or both, or could simply point to a good way to write an importer (definitely outside of my skill set) I would be very grateful.
I've downloaded a data set that I am interested in. However, it is in .mat format and I do not have access to Matlab.
I've done some googling and it says I can open it in SciLab.
I tried a few things, but I haven't found any good tutorials on this.
I did
fd = matfile_open("file.mat")
matfile_listvar(fd)
and that prints out the filename without the extension. I tried
var1 = matfile_varreadnext(fd)
and that just gives me "var1 = "
I don't really know how the data is organized. The repository described the data it contains, but not how it is organized.
So, my question is, what am I doing wrong in extracting/viewing this data? I'm not committed to SciLab, if there is a better tool for this I am open to that.
One options is to use Octave, which can read .mat files and run most Matlab .m files. Octave is open source with binaries available for Linux, Mac, and Windows. Inside of Octave you can load the file using:
load file
See Octave's manual section 14.1.3 Simple File I/O for more details.
In Scilab:
loadmatfile('file.mat');
(Source)
I had this same interest a few years back. I used this question as a guide. It uses Python and SciPy. There are options for NumPy and hd5f as well. Another option is to write your own reader for the .mat format in whatever language you need. Here is the link to the mat file format definition.