waltsims / k-wave-python Goto Github PK

Following dependencies are missing from the requirements file:

uff.py
gdown

And following dependencies are not used:

flask

Hi Walter,
Sorry to bother you again.
I would like to implement a project that only include k-wave simulation about the transducer/sensor receive the acoustic signal from source.
BTW, is this the definition of transducer in your code is the device can transmmit signal and sensor : the device only receive signal?
When I try to save the sensor_data in a similar way as your example in your 'bmode_reconstruction_example.py'
Some error retruns about 'kSensor' object has no attribute 'combine_sensor_data'

Code info:
`
import os
from tempfile import gettempdir

from kwave.ksource import kSource
from kwave.kspaceFirstOrder2D import kspaceFirstOrder2DC
from kwave.kspaceFirstOrder2D import kspaceFirstOrder2DG
from kwave.utils.maputils import makeDisc, makeCartCircle
from kwave.utils import dotdict
from kwave.ktransducer import *
from kwave.kmedium import kWaveMedium
from copy import deepcopy

pathname = '/home/wx/hdd1/k-wave-python/examples'

Nx = 128 # number of grid points in the x (row) direction
Ny = 128 # number of grid points in the y (column) direction
dx = 0.1e-3 # grid point spacing in the x direction [m]
dy = 0.1e-3 # grid point spacing in the y direction [m]
kgrid = kWaveGrid([Nx, Ny], [dx, dy])

t_end = (Nx * dx) * 2.2 / 1500 # [s]
kgrid.makeTime(1500, t_end=t_end)

medium = kWaveMedium(sound_speed=1500, alpha_coeff=0.75, alpha_power=1.5)

disc_magnitude = 5 # [Pa]
disc_x_pos = 50 # [grid points]
disc_y_pos = 50 # [grid points]
disc_radius = 8 # [grid points]
disc_1 = disc_magnitude * makeDisc(Nx, Ny, disc_x_pos, disc_y_pos, disc_radius)

disc_magnitude = 3 # [Pa]
disc_x_pos = 80 # [grid points]
disc_y_pos = 60 # [grid points]
disc_radius = 5 # [grid points]
disc_2 = disc_magnitude * makeDisc(Nx, Ny, disc_x_pos, disc_y_pos, disc_radius)

source = kSource()
source.p0 = disc_1 + disc_2

sensor_radius = 4e-3 # [m]
num_sensor_points = 50
sensor_mask = makeCartCircle(sensor_radius, num_sensor_points)
sensor = kSensor(sensor_mask)
input_filename = f'example_input.h5'
input_file_full_path = os.path.join(pathname, input_filename)
print(input_file_full_path)

input_args = {
'SaveToDisk':input_file_full_path,
'SaveToDiskExit': False
}
sensor_data = kspaceFirstOrder2DG(**{
'medium': medium,
'kgrid': kgrid,
'source': source,
'sensor': sensor,
**input_args
})
Error info: File "/home/wx/anaconda3/envs/py39k-wave/lib/python3.9/site-packages/kwave/kspaceFirstOrder2D.py", line 386, in kspaceFirstOrder2D
return k_sim.sensor.combine_sensor_data(sensor_data)
AttributeError: 'kSensor' object has no attribute 'combine_sensor_data'`

Thanks for you help again, and I would like to become the beta tester of windows. Thank you agagin.

Best Regards
Chenzhe Li

Publish package to PyPI and update the installation guide in Readme.

The number of branches keeps increasing. I suggest we update the branch policy in GitHub so that branches get deleted when respective PR is merged.

It would be awesome if this worked on windows!

The use of @dataclass is not applied consistently throughout. For example, kSource uses @dataclass but the attributes are declared as class attributes instead so there is no benefit for kwarg instantiation or repr. There are several other classes that use @dataclass with no benefit. On the other hand, kWaveMedium uses @dataclass in the standard way. It would be nice to have all the classes with MATLAB k-wave analogs to have proper implementations as dataclasses.

Shipping kWave binaries with the package results in larger package sizes. As the kWave source code is under 1MB, it might better to compile kWave from scratch during installation. However, this might expand the dependency list. We should exemine the process and see if it is feasible to do.

Ruff is orders of magnitude faster than alternatives and supports pyproject.toml

Hi, I was trying to run the exmaple and installed the requirments yet.
After precomputation.
sensor_data = kspaceFirstOrder3DG/3DC
raise error.
'Running on Windows and Mac is not implemented yet'
The version of python is 3.9.13.
Thank you!

https://stackoverflow.com/a/58930304 Allow for so specific downloads

Something like this could be helpful:

import numpy as np

class Vector(np.ndarray):
    def __new__(cls, x, y, z):
        obj = np.array([x, y, z], dtype=float).view(cls)
        obj.x = obj[0]
        obj.y = obj[1]
        obj.z = obj[2]
        return obj
    
    def __array_finalize__(self, obj):
        if obj is None: return
        self.x = getattr(obj, 'x', None)
        self.y = getattr(obj, 'y', None)
        self.z = getattr(obj, 'z', None)

Add GitHub actions to auto-generate documentation from the source code.

Traceback (most recent call last):
  File "C:\Users\nhl08\code\k-wave-python\examples\bmode_reconstruction_example.py", line 207, in <module>
    beamform(channel_data)
  File "C:\Users\nhl08\code\k-wave-python\kwave\reconstruction\beamform.py", line 73, in beamform
    transform = ShiftedTransform.deserialize(probe.transform.serialize())
  File "C:\Users\nhl08\miniconda3\envs\kwave\lib\site-packages\uff\uff_io.py", line 58, in deserialize
    assert k in fields, f'Class {cls} does not have property named {k}.'
AssertionError: Class <class 'kwave.reconstruction.shifted_transform.ShiftedTransform'> does not have property named translation.

fresh install of k-wave-python with the example dependencies.

Seems to be caused by the Serializable mechanism in uff. Opened an issue in uff to discuss.

Hello team! I was playing with a fresh install and following the example, however I believe that this line is not correct anymore?

https://github.com/waltsims/k-wave-python/blob/12db9efda690aa552adf99c692ae9589651e27f6/examples/bmode_reconstruction_example.py#LL6C52-L6C52

I don't see SimulationExecutionOptions in kwave.options anymore.

Related to this, I believe that the entire kwave.options module failed to render in the documentation: https://waltersimson.com/k-wave-python/kwave.options.html

Thanks for the great work again!

Vision here is to have something like the k-Wave-example pages in Jupyter notebooks.

Add an example that loads the BMode simulation output and displays the reconstruction of it.

Hey there,

Within the standardised image reconstruction project of the international photoacoustic standardisation consortium (IPASC) we were looking for a way to use the k-wave provided time reversal algorithm for image reconstruction from Python without having to invoke MATLAB.

https://github.com/IPASC/standardised-image-reconstruction

It seems that this project might be a solution to our problem. Fantastic! Either I or someone else from the project group will take a look in the next few weeks. It would be great if we could approach you with any questions we may have.

Kind regards,
Janek

Add kWave binaries to the packaging so that it is not required to download them separately.

If I do pip install k-wave-python, no dependencies are installed. Must install {numpy, scipy, h5py, opencv-python, etc.} manually.

I feel sorry to disturbe your work. Because I got a problem. When I run bmode_reconstruction_example.py, there was interrruption.

there are the packages:


I wonder the package uff is not from the command 'pip install uff'?
Hope you can help me in your free time, thanks!

k-Wave fails to select a device and outputs no data on my system.

Setting up the k-wave grid...
Defining the input signal...
Setting up the transducer configuration...
Fetching phantom data...
RUN_SIMULATION set to True
Running simulation locally...
Computing scan line 1 of 96
/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/kwave/kspaceFirstOrder.py:99: UserWarning: 
                    The binary file kspaceFirstOrder-OMP could not be found in None. 
                    To use the C++ code, the C++ binaries for your operating system must be downloaded 
                    from www.k-wave.org/download.php and placed in the binaries folder.
  warn(f'''
  start time: 04-May-2022-13-11-33
Running k-Wave simulation...
  start time: 04-May-2022-13-11-33
  reference sound speed:  1600.7033686418115 m/s
  reference sound speed:  1600.7033686418115 m/s
  prepending transducer.input_signal with 17 leading zeros
  appending transducer.input_signal with 17 trailing zeros
  dt:  36.075ns , t_end: 57.1429us , time steps: 1585
  input grid size: 216 by 108 by 108 grid points (40.0 by 20.0 by 20.0 m)
  maximum supported frequency:  3.78MHz
  expanding computational grid...
  computational grid size: 256 by 128 by 128 grid points
  precomputation completed in  3.8572562130284496 s
  saving input files to disk...
  completed in  0.3157105499994941 s
┌───────────────────────────────────────────────────────────────┐
│                  kspaceFirstOrder-CUDA v1.3                   │
├───────────────────────────────────────────────────────────────┤
│ Reading simulation configuration:                        Done │
│ Selected GPU device id:                                Failed │
└───────────────────────────────────────────────────────────────┘
┌───────────────────────────────────────────────────────────────┐
│            !!! K-Wave experienced a fatal error !!!           │
├───────────────────────────────────────────────────────────────┤
│ Error: All CUDA-capable devices are busy or unavailable.      │
├───────────────────────────────────────────────────────────────┤
│                      Execution terminated                     │
└───────────────────────────────────────────────────────────────┘
Traceback (most recent call last):
  File "examples/bmode_reconstruction_example.py", line 174, in <module>
    sensor_data = kspaceFirstOrder3DC(**{
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/kwave/kspaceFirstOrder.py", line 283, in wrapper
    res = func(kgrid=kgrid, medium=medium, source=source, sensor=sensor, **args, **kwargs)
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/kwave/kspaceFirstOrder3D.py", line 92, in kspaceFirstOrder3DC
    sensor_data = kspaceFirstOrder3D(**kwargs)
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/kwave/kspaceFirstOrder3D.py", line 412, in kspaceFirstOrder3D
    sensor_data = executor.run_simulation(input_filename, output_filename, options='--p_raw')
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/kwave/executor.py", line 55, in run_simulation
    with h5py.File(output_filename, 'r') as hf:
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/h5py/_hl/files.py", line 507, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "/media/thurston/home/thurston/Projects/k-wave-python/venv_debug/lib/python3.8/site-packages/h5py/_hl/files.py", line 220, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 106, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/tmp/output.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

As mentioned in #11, when running k-Wave binaries, k-wave-python erroneously warns that no binaries can be found:

<directory>/lib/python3.8/site-packages/kwave/kspaceFirstOrder.py:99: UserWarning:
                    The binary file kspaceFirstOrder-OMP could not be found in None.
                    To use the C++ code, the C++ binaries for your operating system must be downloaded
                    from www.k-wave.org/download.php and placed in the binaries folder.
  warn(f'''

This should be fixed in a patch release.

50a6c5e reverts changes to makeCircle that broke testing.

This patch needs to be re-evaluated for correctness.

If the changes from 5ffde2d are correct, then test hash files must be updated accordingly for failing tests.

When I run the example file the first time, it fails and gives an access denied error. I tried again and it worked. Possibly related to gdown.

Setting up the k-wave grid...
Defining the input signal...
Setting up the transducer configuration...
Fetching phantom data...
Access denied with the following error:

 	Cannot retrieve the public link of the file. You may need to change
	the permission to 'Anyone with the link', or have had many accesses. 

You may still be able to access the file from the browser:

	 https://drive.google.com/uc?id=1ZfSdJPe8nufZHz0U9IuwHR4chaOGAWO4 

Any plans to support k-wave elastic simulations?

Hi Walter,
Thank you for your fascinating work on implying k-wave in python.
But when i want to use k-wave-python to produce some images, I found it is not esay. The examples of k-wave in matlab can't be applied directly in your project. Because there are much difference between your work and k-wave in matlab.
So I expect that your could add complete examples, not only a part. Especially, 2D photoacoustic reconstrction.
Thanks a lot!

Trying to run the example but getting a type error in the uff dependency.

Using the latest version of k-wave-python from github on Ubuntu (WSL2).

(sim) ~ python3 bmode_reconstruction_example.py
Traceback (most recent call last):
  File "/home/tnie/code/sim/k-wave-python/examples/bmode_reconstruction_example.py", line 4, in <module>
    from kwave.reconstruction.beamform import beamform
  File "/home/tnie/code/sim/k-wave-python/kwave/reconstruction/beamform.py", line 4, in <module>
    from uff import UFF, ChannelData
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/__init__.py", line 48, in <module>
    from uff import converters, model  # noqa
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/model/__init__.py", line 48, in <module>
    from . import uff_pb2 as uff_pb  # noqa
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/uff/model/uff_pb2.py", line 33, in <module>
    _descriptor.EnumValueDescriptor(
  File "/home/tnie/miniconda3/envs/sim/lib/python3.10/site-packages/google/protobuf/descriptor.py", line 755, in __new__
    _message.Message._CheckCalledFromGeneratedFile()
TypeError: Descriptors cannot not be created directly.
If this call came from a _pb2.py file, your generated code is out of date and must be regenerated with protoc >= 3.19.0.
If you cannot immediately regenerate your protos, some other possible workarounds are:
 1. Downgrade the protobuf package to 3.20.x or lower.
 2. Set PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python (but this will use pure-Python parsing and will be much slower).

More information: https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates