dipy / cudipy

cupy-accelerated DIPY

DIPY [DIPYREF] is a python library for the analysis of MR diffusion imaging.

DIPY is for research only; please contact [email protected] if you plan to deploy in clinical settings.

Website

Current information can always be found from the DIPY website - http://dipy.org

Mailing Lists

Please see the DIPY community list at https://mail.python.org/mailman3/lists/dipy.python.org/

Please see the users' forum at https://github.com/dipy/dipy/discussions

Please join the gitter chatroom here.

Code

You can find our sources and single-click downloads:

• Main repository on Github.
• Documentation for all releases and current development tree.
• Download as a tar/zip file the current trunk.

Installing DIPY

DIPY can be installed using pip:

pip install dipy

or using conda:

conda install -c conda-forge dipy

For detailed installation instructions, including instructions for installing from source, please read our installation documentation.

Python versions and dependencies

DIPY follows the Scientific Python SPEC 0 — Minimum Supported Versions recommendation as closely as possible, including the supported Python and dependencies versions.

Further information can be found in Toolchain Roadmap.

License

DIPY is licensed under the terms of the BSD license. Please see the LICENSE file.

Contributing

We welcome contributions from the community. Please read our Contributing guidelines.

Reference

[DIPYREF]

E. Garyfallidis, M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, I. Nimmo-Smith and DIPY contributors, "DIPY, a library for the analysis of diffusion MRI data", Frontiers in Neuroinformatics, vol. 8, p. 8, Frontiers, 2014.

cudipy's Issues

Affine Registration Support

Hi,
I am using DIPY for some image registration. My current registration pipeline involves center of mass , translation, rigid, affine, and SymmetricDiffeomorphic registrations. From the CuDIPY readme, I understand that currently I can only implement the SymmetricDiffeomorphic registration in cudipy. Is that correct? Are you planning on adding gpu support to other registrations (affine) soon?

conversion of cudipy.align.imwarp.DiffeomorphicMap to dipy.align.imwarp.DiffeomorphicMap

Hi...Can we transform cudipy.align.imwarp.DiffeomorphicMap to dipy.align.imwarp.DiffeomorphicMap?

GPU requirement

cuDipy failed to install: Cupy rebuild failed

im trying to install the cudipy using pip. but the installer doing cupy rebuild.

i have no problem installing cupy for cuda 11.7 separately.

i have cuda running with tensorflow and works flawlessly.

but for this install is error on cupy rebuild

here the config summary

 ************************************************************
      * CuPy Configuration Summary                               *
      ************************************************************

      Build Environment:
        Include directories: ['C:\\Users\\gsiha\\AppData\\Local\\Temp\\pip-install-emb7ru0o\\cupy_c408cdb7fdc84a05a7f5b3ac01e3f362\\cupy/_core/include\\cupy/_cccl/libcudacxx', 'C:\\Users\\gsiha\\AppData\\Local\\Temp\\pip-install-emb7ru0o\\cupy_c408cdb7fdc84a05a7f5b3ac01e3f362\\cupy/_core/include\\cupy/_cccl/thrust', 'C:\\Users\\gsiha\\AppData\\Local\\Temp\\pip-install-emb7ru0o\\cupy_c408cdb7fdc84a05a7f5b3ac01e3f362\\cupy/_core/include\\cupy/_cccl/cub', 'C:\\Users\\gsiha\\AppData\\Local\\Temp\\pip-install-emb7ru0o\\cupy_c408cdb7fdc84a05a7f5b3ac01e3f362\\cupy/_core/include', 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.7\\include', 'C:\\Program Files\\NVIDIA Corporation\\Nsight Systems 2022.1.3\\target-windows-x64\\nvtx\\include']
        Library directories: ['C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.7\\bin', 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.7\\lib\\x64']
        nvcc command       : ['C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.7\\bin/nvcc.exe']
        hipcc command      : (not found)

      Environment Variables:
        CFLAGS          : (none)
        LDFLAGS         : (none)
        LIBRARY_PATH    : (none)
        CUDA_PATH       : C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.7
        NVCC            : (none)
        HIPCC           : (none)
        ROCM_HOME       : (none)

      Modules:
        cuda      : Yes (version 11070)
        cusolver  : Yes
        cudnn     : No
          -> Include files not found: ['cudnn.h']
          -> Check your CFLAGS environment variable.
        nccl      : No
          -> Include files not found: ['nccl.h']
          -> Check your CFLAGS environment variable.
        nvtx      : Yes
        cutensor  : No
          -> Include files not found: ['cutensor.h']
          -> Check your CFLAGS environment variable.
        cub       : Yes (version 200200)
        jitify    : Yes (version <unknown>)
        random    : Yes
        thrust    : Yes (version 200200)
        cusparselt: No
          -> Include files not found: ['cusparseLt.h']
          -> Check your CFLAGS environment variable.
        dlpack    : Yes

      WARNING: Some modules could not be configured.
      CuPy will be installed without these modules.
      Please refer to the Installation Guide for details:
      https://docs.cupy.dev/en/stable/install.html

      ************************************************************

and this is the error

error install cupy in cudipy.txt

my expectation : "when i install cupy separately, it use the other installation and not rebuilding it"