Converter#

class up4.Converter#

Bases: object

Convert particle data from a given format to HDF5 (H5Part-like).

Methods

vtk:	Convert VTK file to a HDF5 file
vtk_from_folder:	Convert all VTK files in a folder to a HDF5 file
csv:	Convert CSV file to a HDF5 file

static csv(filename, outname, columns=..., delimiter=',', header=True, comment='#', vel=False, interpolate=False, radius=0.0, sampling_steps=9)#

```ignore Convert CSV file to a HDF5 file.

Parameters:

filenamestr: Path to the CSV file
outnamestr: Name of the output HDF5 file
columnslist[int], optional: List of columns to convert containing t,x,y,z,(optional vx,vy,vz), by default [0,1,2,3]
delimiterstr, optional: Pattern for separating numbers in a csv file, by default ‘,’
headerbool, optional: True if the CSV file contains a header, by default True
commentstr, optional: Comment character to ignore, by default ‘#’
velbool, optional: If true the velocity will be computed from the position using the savitzky-golay filter, by default False
interpolatebool, optional: If true the particle positions will be interpolated in order to have a constant timestep, by default False
radiusfloat, optional: Particle radius, by default 0.0
sampling_stepsint, optional: Number of sampling steps for the savitzky-golay filter to calculate the velocity, by default 9

Returns:

None

static csv_multi(filename, outname, columns=..., delimiter='","', header=True, comment='"#"', vel=False, interpolate=False, radius=0.0, method='"id_line"')#

```ignore Convert CSV file containing multiple particles into a HDF5 file.

There can be different ways how this is achieved, therefore the function takes an argument called method which can be one of the following:

chain: The particles are chained in the file, i.e. the first particle
is followed by the second, the second by the third, etc. all particles are stored in one file
id_line: This algorithm sorts the particles by their id column and
their time column. The columns argument must contain the id column as the first element.

no other method is implemented yet. If you want to use another method, please contact the developers.

Parameters:

filenamestr

Path to the CSV file

outnamestr

Name of the output HDF5 file

columnslist[int], optional

List of columns to convert containing t,x,y,z, (optional vx,vy,vz), by default [0,1,2,3]

headerbool, optional

True if the CSV file contains a header, by default True

commentstr, optional

Comment character to ignore, by default “#”

velbool, optional

If true the velocity will be computed from the position using the savitzky-golay filter, by default False

interpolatebool, optional

If true the particle positions will be interpolated in order to have a constant timestep, by default False

radiusfloat, optional

Radius of the particle, by default 0.0

methodstr, optional

Method to use to convert the CSV file. Can be one of the following:

chain`: The particles are chained in the file, i.e. the first particle
is followed by the second, the second by the third, etc. all particles are stored in one file
id_line`: This algorithm sorts the particles by their id column and
their time column. The columns argument must contain the id column as the first element.

, by default chain

static csv_multi_files(filenames, outname, times, columns=..., delimiter=',', header=True, comment='#', vel=False, interpolate=False, radius=0.0)#

Convert CSV file containing multiple particles into a HDF5 file.

There can be different ways how this is achieved, therefore the function takes an argument called method which can be one of the following:

chain: The particles are chained in the file, i.e. the first particle
is followed by the second, the second by the third, etc. all particles are stored in one file.

id_line: This algorithm sorts the particles by their id column and
their time column. The columns argument must contain the id column as the first element.

no other method is implemented yet. If you want to use another method, please contact the developers.

Parameters:

filenamesstr: Path to the CSV files
outnamestr: Name of the output HDF5 file
columnslist[int], optional: List of columns to convert containing pid,x,y,z,(optional vx,vy,vz) Default: [0,1,2,3]
headerbool, optional: True if the CSV file contains a header Default: True
commentstr, optional: Comment character to ignore Default: “#”
velbool, optional: If true the velocity will be computed from the position using the savitzky-golay filter Default: False
interpolatebool, optional: If true the particle positions will be interpolated in order to have a constant timestep Default: False
radiusfloat, optional: Radius of the particle

static vtk(filenames, timestep, outname, filter='(\\d+).vtk', velocity_field_name='v', radius_field_name='radius', id_field_name='id', type_field_name='type', diameter_field_name=None)#

Convert VTK file to a HDF5 file.

Parameters:

filenameslist[str]: List of VTK files to convert, the list must be ordered by time and filenames must contain the timestep.
timestepfloat: Time between two timesteps.
outnamestr: Name of the output HDF5 file.
filterstr, optional: Regex Filter to apply to the data in order to extract the time for each file, by default r”(d+).vtk”. up4 dispatches the correct converter based on the filter extension.
velocity_field_namestr, optional: Name of the velocity field in the vtk files, by default “v”.
radius_field_namestr, optional: Name of the radius field in the vtk files, by default “radius”.
id_field_namestr, optional: Name of the id field in the vtk files, by default “id”.
type_field_namestr, optional: Name of the type field in the vtk files, by default “type”.
diameter_field_namestr, optional: Name of the diameter field in the vtk files, by default None.

Returns:

None

Examples

Convert legacy VTK files to HDF5

>>> from up4 import Converter
>>>
>>> Converter.vtk(
>>>     filenames=["file1.vtk", "file2.vtk"],
>>>     timestep=1e-5,
>>>     outname="output.hdf5",
>>>     filter=r"(\d+).vtk",
>>>     velocity_field_name="v",
>>>     radius_field_name="radius",
>>>     id_field_name="id",
>>>     type_field_name="type",
>>>     diameter_field_name=None,
>>> )

Convert XML VTK (unstructured grid format) files to HDF5

>>> from up4 import Converter
>>>
>>> Converter.vtk(
>>>     filenames=["file1.vtu", "file2.vtu"],
>>>     timestep=1e-5,
>>>     outname="output.hdf5",
>>>     filter=r"(\d+).vtu",
>>>     velocity_field_name="v",
>>>     id_field_name="id",
>>>     type_field_name="type",
>>>     diameter_field_name="diameter",
>>> )

static vtk_from_folder(folder, timestep, outname, filter='(\\d+).vtk', velocity_field_name='v', radius_field_name='radius', id_field_name='id', type_field_name='type', diameter_field_name=None)#

Convert all VTK files in a folder to a HDF5 file.

Parameters:

folderstr: Path to the folder containing the VTK files Folder must only contain one type of vtk files
timestepfloat: Time between two timesteps
outnamestr: Name of the output HDF5 file
filterstr, optional: Regex Filter to apply to the data in order to extract the time for each file, by default r”(d+).vtk”
velocity_field_namestr, optional: Name of the velocity field in the vtk files, by default “v”
radius_field_namestr, optional: Name of the radius field in the vtk files, by default “radius”
id_field_namestr, optional: Name of the id field in the vtk files, by default “id”
type_field_namestr, optional: Name of the type field in the vtk files, by default “type”
diameter_field_namestr, optional: Name of the diameter field in the vtk files, by default None

Returns:

None

Examples

Convert legacy VTK files to HDF5

>>> from up4 import Converter
>>>
>>> Converter.vtk_from_folder(
>>>     folder="folder",
>>>     timestep=1e-5,
>>>     outname="output.hdf5",
>>>     filter=r"(\d+).vtk",
>>>     velocity_field_name="v",
>>>     radius_field_name="radius",
>>>     id_field_name="id",
>>>     type_field_name="type",
>>>     diameter_field_name=None,
>>> )

Convert XML VTK (unstructured grid format) files to HDF5

>>> from up4 import Converter
>>>
>>> Converter.vtk_from_folder(
>>>     folder="folder",
>>>     timestep=1e-5,
>>>     outname="output.hdf5",
>>>     filter=r"(\d+).vtu",
>>>     velocity_field_name="v",
>>>     id_field_name="id",
>>>     type_field_name="type",
>>>     diameter_field_name="diameter",
>>> )