3D shape analysis using deep learning
Project description
Cellshape-helper provides the ability to convert 3D masks to point clouds.
To install
Step 1: Install PyMesh:
This package relies on PyMesh which needs to be installed first. To install, check out the source code from GitHub:
- Clone the PyMesh repo into a directory of your choice:
git clone https://github.com/PyMesh/PyMesh.git
cd PyMesh
git submodule update --init
export PYMESH_PATH=`pwd`
- On Linux, the system dependencies can be installed with apt-get:
apt-get install \
libeigen3-dev \
libgmp-dev \
libgmpxx4ldbl \
libmpfr-dev \
libboost-dev \
libboost-thread-dev \
libtbb-dev \
python3-dev
- On MacOS, the system dependencies can be installed with MacPorts:
port install
python36 \
eigen3 \
gmp \
mpfr \
tbb \
boost
- Python dependencies such as NumPy and SciPy can be installed using pip:
pip install -r $PYMESH_PATH/python/requirements.txt
- Build PyMesh with setuptools:
./setup.py build
- Install PyMesh:
./setup.py install # May require root privilege
- Alternatively, one can install PyMesh locally:
./setup.py install --user
- Check if PyMesh was installed correctly:
python -c "import pymesh; pymesh.test()"
- Please refer to the PyMesh installation guide if there are any issues.
Step 2: Install cellshape-helper
pip install cellshape-helper
Usage
import cellshape_helper as helper
PATH_TO_TIF_FILES = "path/to/tif/files/"
PATH_TO_SAVE_MESH = "path/to/save/mesh/files/"
PATH_TO_SAVE_PC = "path/to/save/pointcloud/files/"
NUM_POINTS = 2048
helper.tif_to_pc_directory(PATH_TO_TIF_FILES,
PATH_TO_SAVE_MESH,
PATH_TO_SAVE_PC,
NUM_POINTS)
Parameters
PATH_TO_TIF_FILES
: str.
The path to you binary masks of cells or nuclei.PATH_TO_SAVE_MESH
: str.
The path where you want to save the mesh objects to.PATH_TO_SAVE_PC
: str.
The path where you want to save your point clouds to.NUM_POINTS
: str.
The number of points to sample from the mesh object when creating a point cloud.
For developers
- Fork the repository
- Clone your fork
git clone https://github.com/USERNAME/cellshape-helper
- Install an editable version (
-e
) with the development requirements (dev
)
cd cellshape-voxel
pip install -e .[dev]
- To install pre-commit hooks to ensure formatting is correct:
pre-commit install
- To release a new version:
Firstly, update the version with bump2version (bump2version patch
,
bump2version minor
or bump2version major
). This will increment the
package version (to a release candidate - e.g. 0.0.1rc0
) and tag the
commit. Push this tag to GitHub to run the deployment workflow:
git push --follow-tags
Once the release candidate has been tested, the release version can be created with:
bump2version release
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Close
Hashes for cellshape_helper-0.0.13-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f621f6f4a76dfd903ea5da538b9ab167e6a3b4d1be34eb9ff562c96af179fc1a |
|
MD5 | 303dc4dae1fc4a626f6fb98f4a685f5b |
|
BLAKE2b-256 | 248475c12cdf04ec358cce65c8fc6cf5e9bb4de8d553893ce3da1b1066917177 |