Version incompatibility and packages problems

[MarcoRafaelSilvaGomes]

Description of the bugs

There are two problems with the PyTissueOptics package in this moment:

• Version incompatibilities: The other packages that PyTissueOptics uses (Numpy, Mayavi, and VTK) are not compatible on 3D visualisation, and I don't know a other way to make a 3D view of the results;
• Packages: I found that in some files of the PyTissueOptics package cannot detect other files, like 'scene.solids' or 'scene.viewer.abstract3DViewer' on the null3DViewer.py

To Reproduce

Just run the given example on the webpage https://pypi.org/project/pytissueoptics/ :

from pytissueoptics import *

# Define (scene, source, logger)
N = 500_000
scene = samples.PhantomTissue()
source = DivergentSource(
   position=Vector(0, 0, -0.1), direction=Vector(0, 0, 1), N=N, diameter=0.2, divergence=0.78
)
logger = EnergyLogger(scene)

# Run
source.propagate(scene, logger=logger)

# Stats & Visualizations
viewer = Viewer(scene, source, logger)
viewer.reportStats()

viewer.show2D(View2DProjectionX())
viewer.show2D(View2DProjectionX(solidLabel="middleLayer"))
viewer.show2D(View2DSurfaceZ(solidLabel="middleLayer", surfaceLabel="interface0"))
viewer.show1D(Direction.Z_POS)
viewer.show3D()

Expected behavior

It was expected to give every plot of the results, but only gave the 2D plots.

Screenshots

Desktop

• Windows 11
• Python Version 3.13.0

Packages versions

• Numpy: 2.4.2
• Mayavi: 4.8.3.dev0
• PyTissueOptics: 2.0.0
• VTK: 9.4.2

Output of the running program

PS C:\Users\mrafa\Desktop\Universidade\Disciplinas\3ºano-2ºsem\Projeto final\Codigo> & C:\Users\mrafa\AppData\Local\Programs\Python\Python313\python.exe "c:/Users/mrafa/Desktop/Universidade/Disciplinas/3ºano-2ºsem/Projeto final/Codigo/Tests/example1.py"
Propagating 500000 photons with hardware acceleration on device Intel(R) Iris(R) Xe Graphics...

=============================== SIMULATION PROGRESS ===============================
[BATCH #] ::  [PHOTON COUNT]  :: [SPEED (ph/ms)] :: [TIME ELAPSED] :: [TIME LEFT]
Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
    1     ::   82833 (16.6%)  ::      288.60     ::      0.29 s    ::    1.45 s   
    2     ::   174983 (35.0%) ::      356.28     ::      0.49 s    ::    0.91 s   
    3     ::   268857 (53.8%) ::      385.67     ::      0.70 s    ::    0.60 s   
    4     ::   362856 (72.6%) ::      391.53     ::      0.93 s    ::    0.35 s   
    5     ::   464309 (92.9%) ::      412.37     ::      1.13 s    ::    0.09 s   
    6     ::   497077 (99.4%) ::      383.64     ::      1.30 s    ::    0.01 s   
    7     ::  500000 (100.0%) ::      348.20     ::      1.44 s    ::    0.00 s   

Computation splits:
        Propagation: 29.6%
        Data transfer: 16.2%
        Data conversion: 46.4%
==================================================================================

Report of solid 'frontLayer'
  Absorbance: 60.82% (59.91% of total power)
  Absorbance + Transmittance: 100.0%
    Transmittance at 'frontLayer_front': 1.3%
    Transmittance at 'frontLayer_left': 0.2%
    Transmittance at 'frontLayer_right': 0.2%
    Transmittance at 'frontLayer_bottom': 0.2%
    Transmittance at 'frontLayer_top': 0.2%
    Transmittance at 'interface1': 37.0%
Report of solid 'backLayer'
  Absorbance: 86.68% (13.44% of total power)
  Absorbance + Transmittance: 100.0%
    Transmittance at 'backLayer_back': 9.5%
    Transmittance at 'backLayer_left': 0.4%
    Transmittance at 'backLayer_right': 0.4%
    Transmittance at 'backLayer_bottom': 0.4%
    Transmittance at 'backLayer_top': 0.4%
    Transmittance at 'interface0': 2.2%
Report of solid 'middleLayer'
  Absorbance: 53.03% (19.49% of total power)
  Absorbance + Transmittance: 100.0%
    Transmittance at 'middleLayer_left': 0.3%
    Transmittance at 'middleLayer_right': 0.3%
    Transmittance at 'middleLayer_bottom': 0.3%
    Transmittance at 'middleLayer_top': 0.3%
    Transmittance at 'interface0': 42.2%
    Transmittance at 'interface1': 3.5%

Mayavi is not available. Falling back to a null 3D viewer. Fix the following error to use the Mayavi backend or select another backend by setting the PTO_3D_BACKEND environment variable (available backends: ('mayavi', 'null')).
module 'numpy' has no attribute 'in1d'
Traceback (most recent call last):
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\pytissueoptics\scene\viewer\provider.py", line 13, in get3DViewer
    from .mayavi.mayavi3DViewer import Mayavi3DViewer
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\pytissueoptics\scene\viewer\mayavi\mayavi3DViewer.py", line 2, in <module>
    from mayavi import mlab
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\mlab.py", line 16, in <module>
    from mayavi.tools.camera import view, roll, yaw, pitch, move
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\tools\camera.py", line 24, in <module>
    from .engine_manager import get_engine
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\tools\engine_manager.py", line 14, in <module>
    from mayavi.core.registry import registry
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\core\registry.py", line 16, in <module>
    from mayavi.core.metadata import Metadata, import_symbol
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\core\metadata.py", line 11, in <module>
    from mayavi.core.pipeline_info import PipelineInfo
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\core\pipeline_info.py", line 12, in <module>
    from .utils import get_tvtk_dataset_name
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\mayavi\core\utils.py", line 4, in <module>
    from vtk.numpy_interface import algorithms as algs
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\vtkmodules\numpy_interface\algorithms.py", line 984, in <module>
    in1d = _make_ufunc(numpy.in1d)
                       ^^^^^^^^^^
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\numpy\__init__.py", line 805, in __getattr__
    raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
AttributeError: module 'numpy' has no attribute 'in1d'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "c:\Users\mrafa\Desktop\Universidade\Disciplinas\3ºano-2ºsem\Projeto final\Codigo\Tests\example1.py", line 22, in <module>
    viewer.show3D()
    ~~~~~~~~~~~~~^^
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\pytissueoptics\rayscattering\display\viewer.py", line 123, in show3D
    self._viewer3D = get3DViewer()
                     ~~~~~~~~~~~^^
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\pytissueoptics\scene\viewer\provider.py", line 22, in get3DViewer
    from .null3DViewer import Null3DViewer
  File "C:\Users\mrafa\AppData\Local\Programs\Python\Python313\Lib\site-packages\pytissueoptics\scene\viewer\null3DViewer.py", line 4, in <module>
    from scene.solids import Solid
ModuleNotFoundError: No module named 'scene'
PS C:\Users\mrafa\Desktop\Universidade\Disciplinas\3ºano-2ºsem\Projeto final\Codigo> 

[MarcoRafaelSilvaGomes]

I think that I solved the problem.

I replaced the line 984 of the file vtkmodules\numpy_interface\algorithms.py:

in1d = _make_ufunc(numpy.in1d)

for:

in1d = _make_ufunc(numpy.isin)

And now it only gives this warning when I try to use 3D on the example:

dtype(): align should be passed as Python or NumPy boolean but got `align=0`. Did you mean to pass a tuple to create a subarray type? (Deprecated NumPy 2.4)

The output is exactly the same of what was supposed to be.

And strangelly, the ModuleNotFoundError disapeared. Maybe was the other error that make the other happening, I guess...?

But in vtkmodules package used by PyTissueOptics the VS Code still launches some warnings, for example, packages or files that couldn't be solved.