Problems with alpaca

aventador17 · June 23, 2025, 5:13pm

Hello, this is my first time using 3d slicer. I write to community 'cause I have had some problem with ALPACA, it does not run . The phyton console showes this:

In the future np.bool will be defined as the corresponding NumPy scalar.
Traceback (most recent call last):
File “C:/Users/USUARIO/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/SlicerMorph/lib/Slicer-5.8/qt-scripted-modules/ALPACA.py”, line 105, in setup
from itk import Fpfh
File “C:\Users\USUARIO\AppData\Local\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\itk_init_.py”, line 59, in
from itk.support.extras import *
File “C:\Users\USUARIO\AppData\Local\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\itk\support\extras.py”, line 37, in
import itk.support.types as itkt
File “C:\Users\USUARIO\AppData\Local\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\itk\support\types.py”, line 178, in
) = itkCType.initialize_c_types_once()
File “C:\Users\USUARIO\AppData\Local\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\itk\support\types.py”, line 143, in initialize_c_types_once
B: “itkCType” = itkCType(“bool”, “B”, np.dtype(np.bool))
File "C:\Users\USUARIO\AppData\Local\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\numpy_init.py", line 353, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module ‘numpy’ has no attribute ‘bool’.
np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.bool_ here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
NumPy 1.20.0 Release Notes — NumPy v2.4.dev0 Manual

I hope someone could help me, I would be very grateful

muratmaga · June 23, 2025, 5:15pm

please see the workaround in this thread:

aventador17 · June 24, 2025, 2:09am

Thenks a lot for your answer. I have installed numpy as you said, but a new error has appeared, it says: “AttributeError: np.Inf was removed in the NumPy 2.0 release. Use np.inf instead.”

jamesobutler · June 24, 2025, 8:26am

FYI @smrolfe

github.com/SlicerMorph/SlicerMorph

ALPACA/ALPACA.py

4b3234c5c


      
              transform.SetIdentity()
              return [transform, transform]
          
          import time
          
          bransac = time.time()
          
          maxAttempts = 1
          attempt = 0
          best_fitness = -1
          best_rmse = np.Inf
          while attempt < maxAttempts:
              # Perform Initial alignment using Ransac parallel iterations with no scaling
              transform_matrix, fitness, rmse = self.ransac_using_package(
                  movingMeshPoints=sourcePoints,
                  fixedMeshPoints=targetPoints,
                  movingMeshFeaturePoints=moving_corr.T,
                  fixedMeshFeaturePoints=fixed_corr.T,
                  number_of_iterations=parameters["maxRANSAC"],
                  number_of_ransac_points=3,
                  inlier_value=float(parameters["distanceThreshold"]) * voxelSize,

I would suggest adding the ruff hook to SlicerMorph’s pre-commit-config like in Slicer as ruff includes a numpy 2 deprecation rule that can auto apply fixes ( numpy2-deprecation (NPY201) | Ruff).

github.com/Slicer/Slicer

.pre-commit-config.yaml

406beac7a


      
              - id: check-yaml
              - id: debug-statements
                exclude: "Base/QTGUI/Testing/Data/Input/qSlicerScriptedLoadableModuleSyntaxErrorTestWidget.py|Base/QTGUI/Testing/Data/Input/qSlicerScriptedLoadableModuleSyntaxErrorTest.py"
              - id: end-of-file-fixer
                exclude: "\\.(md5|svg|vtk|vtp)$|^Resources\\/[^\\/]+\\.h$|\\/ColorFiles\\/.+\\.txt$|Data\\/Input\\/.+$"
              - id: mixed-line-ending
                exclude: "\\.(svg|vtk|vtp)$"
              - id: trailing-whitespace
                exclude: "\\.(svg|vtk|vtp)$"
          
          - repo: https://github.com/astral-sh/ruff-pre-commit
            rev: v0.12.0
            hooks:
              - id: ruff
                args: ["--fix", "--show-fixes"]
          
          - repo: https://github.com/asottile/pyupgrade
            rev: v3.20.0
            hooks:
              - id: pyupgrade
                args: [--py312-plus]

muratmaga · June 24, 2025, 4:57pm

Thanks @jamesobutler

When is Slicer going to officially transition to numpy 2?

jamesobutler · June 24, 2025, 6:04pm

Slicer preview already comes with numpy 2 bundled. This was updated as part of the transition to Python 3.12. Most latest Python packages have numpy binary compatibility with numpy 1 and 2.

github.com/Slicer/Slicer

SuperBuild/External_python-numpy.cmake

6afc5bc94


      
          # Hashes correspond to the following packages:
          #  - numpy-2.0.2-cp312-cp312-macosx_10_9_x86_64.whl
          #  - numpy-2.0.2-cp312-cp312-macosx_11_0_arm64.whl
          #  - numpy-2.0.2-cp312-cp312-macosx_14_0_arm64.whl
          #  - numpy-2.0.2-cp312-cp312-macosx_14_0_x86_64.whl
          #  - numpy-2.0.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
          #  - numpy-2.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
          #  - numpy-2.0.2-cp312-cp312-musllinux_1_1_x86_64.whl
          #  - numpy-2.0.2-cp312-cp312-musllinux_1_2_aarch64.whl
          #  - numpy-2.0.2-cp312-cp312-win_amd64.whl
          numpy==2.0.2 --hash=sha256:df55d490dea7934f330006d0f81e8551ba6010a5bf035a249ef61a94f21c500b \
                       --hash=sha256:8df823f570d9adf0978347d1f926b2a867d5608f434a7cff7f7908c6570dcf5e \
                       --hash=sha256:9a92ae5c14811e390f3767053ff54eaee3bf84576d99a2456391401323f4ec2c \
                       --hash=sha256:a842d573724391493a97a62ebbb8e731f8a5dcc5d285dfc99141ca15a3302d0c \
                       --hash=sha256:c05e238064fc0610c840d1cf6a13bf63d7e391717d247f1bf0318172e759e692 \
                       --hash=sha256:0123ffdaa88fa4ab64835dcbde75dcdf89c453c922f18dced6e27c90d1d0ec5a \
                       --hash=sha256:96a55f64139912d61de9137f11bf39a55ec8faec288c75a54f93dfd39f7eb40c \
                       --hash=sha256:ec9852fb39354b5a45a80bdab5ac02dd02b15f44b3804e9f00c556bf24b4bded \
                       --hash=sha256:cfd41e13fdc257aa5778496b8caa5e856dc4896d4ccf01841daee1d96465467a
          # [/numpy]
          ]===])

aventador17 · June 25, 2025, 1:35am

Muchas gracias por tu repsuesta, el problema fue solucionado. Ten un maravilloso día.

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