Phenomenal
stable
Installation
Installation with Miniconda (Windows, linux, OSX)
0. Install Miniconda
1. Install conda-build if not already installed
2. Create virtual environment and activate it
3. Build and install openalea.phenomenal package
Developer Install - Ubuntu (linux)
1. Install linux dependencies
2. Miniconda installation
4. Install dependencies with conda
2. Install openalea.phenomenal
3. Test if installation is well installed (with nosetests package)
Windows
1. Install dependencies
2. Install openalea.phenomenal
3. Test if installation is well installed (with nosetests package)
Questions and Answers
How solve the server certificate verification failed problem on a ubuntu VM ?
How solve the hostnanme on a ubuntu VM ?
How to install Python-Irodsclient ?
How launch a Notebook Server on a cloud VM ?
API References
Acces to plant’s data
openalea.phenomenal.data.path_bin_images
openalea.phenomenal.data.path_raw_images
openalea.phenomenal.data.path_chessboard_images
openalea.phenomenal.data.raw_images
openalea.phenomenal.data.bin_images
openalea.phenomenal.data.chessboard_images
openalea.phenomenal.data.chessboards
openalea.phenomenal.data.calibrations
openalea.phenomenal.data.voxel_grid
openalea.phenomenal.data.tutorial_data_binarization_mask
Synthetic data (for test)
openalea.phenomenal.data.bin_images_with_circle
openalea.phenomenal.data.build_cube
Image Methods
Threshold
openalea.phenomenal.image.threshold_meanshift
openalea.phenomenal.image.threshold_hsv
openalea.phenomenal.image.mean_image
openalea.phenomenal.image.phenoarch_side_binarization
Image Skeleton
openalea.phenomenal.image.skeletonize_thinning
openalea.phenomenal.image.skeletonize_erode_dilate
Morphologic Operation
openalea.phenomenal.image.dilate_erode
openalea.phenomenal.image.erode_dilate
openalea.phenomenal.image.close
Input / Output
openalea.phenomenal.image.read_image
openalea.phenomenal.image.write_image
Calibration
Target & Chessboard
openalea.phenomenal.calibration.Target
openalea.phenomenal.calibration.Chessboard
Calibration
openalea.phenomenal.calibration.CalibrationCamera
openalea.phenomenal.calibration.CalibrationCameraTop
openalea.phenomenal.calibration.CalibrationCameraSideWith2TargetYXZ
Frame
openalea.phenomenal.calibration.Frame
openalea.phenomenal.calibration.x_axis
openalea.phenomenal.calibration.y_axis
openalea.phenomenal.calibration.z_axis
Data Structure
openalea.phenomenal.object.Image3D
openalea.phenomenal.object.ImageView
openalea.phenomenal.object.VoxelGrid
openalea.phenomenal.object.VoxelSegment
openalea.phenomenal.object.VoxelOrgan
openalea.phenomenal.object.VoxelSkeleton
openalea.phenomenal.object.VoxelSegmentation
Display
Image
openalea.phenomenal.display.show_image
openalea.phenomenal.display.show_images
openalea.phenomenal.display.show_image_with_chessboard_corners
openalea.phenomenal.display.show_chessboard_3d_projection_on_image
3D Data
openalea.phenomenal.display.Display
openalea.phenomenal.display.Scene
Multi-View Reconstruction
Main’s function
openalea.phenomenal.multi_view_reconstruction.reconstruction_3d
openalea.phenomenal.multi_view_reconstruction.project_voxel_centers_on_image
openalea.phenomenal.multi_view_reconstruction.project_voxels_position_on_image
openalea.phenomenal.multi_view_reconstruction.image_error
openalea.phenomenal.multi_view_reconstruction.reconstruction_error
Mesh
Algorithms
openalea.phenomenal.mesh.algorithms.meshing
openalea.phenomenal.mesh.algorithms.marching_cubes
openalea.phenomenal.mesh.algorithms.smoothing
openalea.phenomenal.mesh.algorithms.decimation
Formats
openalea.phenomenal.mesh.write_vertices_faces_to_ply_file
openalea.phenomenal.mesh.write_vtk_poly_data_to_ply_file
Routines
openalea.phenomenal.mesh.normals
openalea.phenomenal.mesh.centers
VTK Transformation
openalea.phenomenal.mesh.from_vertices_faces_to_vtk_poly_data
openalea.phenomenal.mesh.from_vtk_poly_data_to_vertices_faces
openalea.phenomenal.mesh.from_voxel_centers_to_vtk_image_data
openalea.phenomenal.mesh.from_numpy_matrix_to_vtk_image_data
3D Segmentation
Skeletonization
openalea.phenomenal.segmentation.connect_all_node_with_nearest_neighbors
openalea.phenomenal.segmentation.create_graph
openalea.phenomenal.segmentation.graph_from_voxel_grid
openalea.phenomenal.segmentation.skeletonize
openalea.phenomenal.segmentation.segment_reduction
Maize Segmentation
openalea.phenomenal.segmentation.maize_segmentation
openalea.phenomenal.segmentation.maize_analysis
Phenomenal
Docs
»
API References
»
Acces to plant’s data
»
openalea.phenomenal.data.bin_images_with_circle
Edit on GitHub
openalea.phenomenal.data.bin_images_with_circle
¶
openalea.phenomenal.data.
bin_images_with_circle
(
shape_image=(2454
,
2056)
,
circle_position=(1227
,
1028)
,
circle_radius=100
)
[source]
¶
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