Skip to main content
Ctrl+K
phenomenal 1.10.5.dev0+g2df28ca14.d20260127 documentation - Home phenomenal 1.10.5.dev0+g2df28ca14.d20260127 documentation - Home
  • Home
  • Installation
  • Usage
  • AUTHORS
  • API References
  • GitHub
  • Home
  • Installation
  • Usage
  • AUTHORS
  • API References
  • GitHub

Section Navigation

  • openalea.phenomenal
    • openalea.phenomenal.calibration
      • openalea.phenomenal.calibration.chessboard
      • openalea.phenomenal.calibration.calibration
      • openalea.phenomenal.calibration.calibration_manual
      • openalea.phenomenal.calibration.calibration_opencv
      • openalea.phenomenal.calibration.frame
      • openalea.phenomenal.calibration.transformations
      • openalea.phenomenal.calibration.calibration
        • openalea.phenomenal.calibration.calibration.angle3
        • openalea.phenomenal.calibration.calibration.find_frame
        • openalea.phenomenal.calibration.calibration.find_position_3d_points
        • openalea.phenomenal.calibration.calibration.find_position_3d_points_soil
        • openalea.phenomenal.calibration.calibration.normalise_angle
        • openalea.phenomenal.calibration.calibration.CalibrationSetup
        • openalea.phenomenal.calibration.calibration.CalibrationSolver
        • openalea.phenomenal.calibration.calibration.Calibrator
      • openalea.phenomenal.calibration.calibration_manual
        • openalea.phenomenal.calibration.calibration_manual.CalibrationCameraManual
        • openalea.phenomenal.calibration.calibration_manual.EnvironmentCamera
      • openalea.phenomenal.calibration.calibration_opencv
        • openalea.phenomenal.calibration.calibration_opencv.CalibrationCameraOpenCv
      • openalea.phenomenal.calibration.chessboard
        • openalea.phenomenal.calibration.chessboard.compass_position
        • openalea.phenomenal.calibration.chessboard.detect_checkerboards
        • openalea.phenomenal.calibration.chessboard.Chessboard
        • openalea.phenomenal.calibration.chessboard.Chessboards
        • openalea.phenomenal.calibration.chessboard.Target
        • openalea.phenomenal.calibration.chessboard.TargetFinder
      • openalea.phenomenal.calibration.frame
        • openalea.phenomenal.calibration.frame.change_frame_tensor2
        • openalea.phenomenal.calibration.frame.local_to_global3d
        • openalea.phenomenal.calibration.frame.mean_frame
        • openalea.phenomenal.calibration.frame.tetrahedron_frame
        • openalea.phenomenal.calibration.frame.triangle_frame
        • openalea.phenomenal.calibration.frame.Frame
      • openalea.phenomenal.calibration.object
        • openalea.phenomenal.calibration.object.normalise_angle
        • openalea.phenomenal.calibration.object.Calibration
        • openalea.phenomenal.calibration.object.CalibrationCamera
        • openalea.phenomenal.calibration.object.CalibrationFrame
        • openalea.phenomenal.calibration.object.OldCalibration
        • openalea.phenomenal.calibration.object.OldCalibrationCamera
      • openalea.phenomenal.calibration.transformations
        • openalea.phenomenal.calibration.transformations.affine_matrix_from_points
        • openalea.phenomenal.calibration.transformations.angle_between_vectors
        • openalea.phenomenal.calibration.transformations.arcball_constrain_to_axis
        • openalea.phenomenal.calibration.transformations.arcball_map_to_sphere
        • openalea.phenomenal.calibration.transformations.arcball_nearest_axis
        • openalea.phenomenal.calibration.transformations.clip_matrix
        • openalea.phenomenal.calibration.transformations.compose_matrix
        • openalea.phenomenal.calibration.transformations.concatenate_matrices
        • openalea.phenomenal.calibration.transformations.decompose_matrix
        • openalea.phenomenal.calibration.transformations.euler_from_matrix
        • openalea.phenomenal.calibration.transformations.euler_from_quaternion
        • openalea.phenomenal.calibration.transformations.euler_matrix
        • openalea.phenomenal.calibration.transformations.identity_matrix
        • openalea.phenomenal.calibration.transformations.inverse_matrix
        • openalea.phenomenal.calibration.transformations.is_same_transform
        • openalea.phenomenal.calibration.transformations.orthogonalization_matrix
        • openalea.phenomenal.calibration.transformations.projection_from_matrix
        • openalea.phenomenal.calibration.transformations.projection_matrix
        • openalea.phenomenal.calibration.transformations.quaternion_about_axis
        • openalea.phenomenal.calibration.transformations.quaternion_conjugate
        • openalea.phenomenal.calibration.transformations.quaternion_from_euler
        • openalea.phenomenal.calibration.transformations.quaternion_from_matrix
        • openalea.phenomenal.calibration.transformations.quaternion_imag
        • openalea.phenomenal.calibration.transformations.quaternion_inverse
        • openalea.phenomenal.calibration.transformations.quaternion_matrix
        • openalea.phenomenal.calibration.transformations.quaternion_multiply
        • openalea.phenomenal.calibration.transformations.quaternion_real
        • openalea.phenomenal.calibration.transformations.quaternion_slerp
        • openalea.phenomenal.calibration.transformations.random_quaternion
        • openalea.phenomenal.calibration.transformations.random_rotation_matrix
        • openalea.phenomenal.calibration.transformations.random_vector
        • openalea.phenomenal.calibration.transformations.reflection_from_matrix
        • openalea.phenomenal.calibration.transformations.reflection_matrix
        • openalea.phenomenal.calibration.transformations.rotation_from_matrix
        • openalea.phenomenal.calibration.transformations.rotation_matrix
        • openalea.phenomenal.calibration.transformations.scale_from_matrix
        • openalea.phenomenal.calibration.transformations.scale_matrix
        • openalea.phenomenal.calibration.transformations.shear_from_matrix
        • openalea.phenomenal.calibration.transformations.shear_matrix
        • openalea.phenomenal.calibration.transformations.superimposition_matrix
        • openalea.phenomenal.calibration.transformations.translation_from_matrix
        • openalea.phenomenal.calibration.transformations.translation_matrix
        • openalea.phenomenal.calibration.transformations.unit_vector
        • openalea.phenomenal.calibration.transformations.vector_norm
        • openalea.phenomenal.calibration.transformations.vector_product
        • openalea.phenomenal.calibration.transformations.Arcball
    • openalea.phenomenal.clean_build_artefacts
      • openalea.phenomenal.clean_build_artefacts.clean_project_tree
    • openalea.phenomenal.data
      • openalea.phenomenal.data.data
      • openalea.phenomenal.data.synthetic_data
      • openalea.phenomenal.data.data
        • openalea.phenomenal.data.data.bin_images
        • openalea.phenomenal.data.data.calibrations
        • openalea.phenomenal.data.data.chessboard_images
        • openalea.phenomenal.data.data.chessboards
        • openalea.phenomenal.data.data.do_calibration
        • openalea.phenomenal.data.data.image_points
        • openalea.phenomenal.data.data.mesh_mccormik_plant
        • openalea.phenomenal.data.data.new_calibrations
        • openalea.phenomenal.data.data.path_bin_images
        • openalea.phenomenal.data.data.path_chessboard_images
        • openalea.phenomenal.data.data.path_raw_images
        • openalea.phenomenal.data.data.raw_images
        • openalea.phenomenal.data.data.synthetic_plant
        • openalea.phenomenal.data.data.tutorial_data_binarization_mask
        • openalea.phenomenal.data.data.voxel_grid
      • openalea.phenomenal.data.synthetic_data
        • openalea.phenomenal.data.synthetic_data.bin_images_with_circle
        • openalea.phenomenal.data.synthetic_data.build_cube
        • openalea.phenomenal.data.synthetic_data.random_voxel_grid
    • openalea.phenomenal.display
      • openalea.phenomenal.display.image
      • openalea.phenomenal.display.calibration
      • openalea.phenomenal.display.scene
      • openalea.phenomenal.display.show_basic
      • openalea.phenomenal.display.show_segmentation
      • openalea.phenomenal.display.show_skeleton
      • openalea.phenomenal.display.calibration
        • openalea.phenomenal.display.calibration.show_chessboard_3d_projection_on_image
        • openalea.phenomenal.display.calibration.show_image_with_chessboard_corners
      • openalea.phenomenal.display.display
        • openalea.phenomenal.display.display.Display
      • openalea.phenomenal.display.image
        • openalea.phenomenal.display.image.show_image
        • openalea.phenomenal.display.image.show_images
      • openalea.phenomenal.display.notebook
        • openalea.phenomenal.display.notebook.plot_voxel
        • openalea.phenomenal.display.notebook.show_mesh
        • openalea.phenomenal.display.notebook.show_point_cloud
        • openalea.phenomenal.display.notebook.show_segmentation
        • openalea.phenomenal.display.notebook.show_skeleton
        • openalea.phenomenal.display.notebook.show_synthetic_plant
        • openalea.phenomenal.display.notebook.show_voxel_grid
      • openalea.phenomenal.display.peak
        • openalea.phenomenal.display.peak.show_values
      • openalea.phenomenal.display.scene
        • openalea.phenomenal.display.scene.Scene
      • openalea.phenomenal.display.show_basic
        • openalea.phenomenal.display.show_basic.record_voxel_grids
        • openalea.phenomenal.display.show_basic.show_mesh
        • openalea.phenomenal.display.show_basic.show_voxel_grid
        • openalea.phenomenal.display.show_basic.show_vtk_poly_data
      • openalea.phenomenal.display.show_segmentation
      • openalea.phenomenal.display.show_skeleton
    • openalea.phenomenal.image
      • openalea.phenomenal.image.threshold
      • openalea.phenomenal.image.skeletonize
      • openalea.phenomenal.image.morphology
      • openalea.phenomenal.image.io
      • openalea.phenomenal.image.io
        • openalea.phenomenal.image.io.read_image
        • openalea.phenomenal.image.io.write_image
      • openalea.phenomenal.image.morphology
        • openalea.phenomenal.image.morphology.close
        • openalea.phenomenal.image.morphology.dilate_erode
        • openalea.phenomenal.image.morphology.erode_dilate
      • openalea.phenomenal.image.routines
        • openalea.phenomenal.image.routines.mean_image
        • openalea.phenomenal.image.routines.phenoarch_side_binarization
      • openalea.phenomenal.image.skeletonize
        • openalea.phenomenal.image.skeletonize.skeletonize_erode_dilate
        • openalea.phenomenal.image.skeletonize.skeletonize_thinning
      • openalea.phenomenal.image.threshold
        • openalea.phenomenal.image.threshold.threshold_hsv
        • openalea.phenomenal.image.threshold.threshold_meanshift
        • openalea.phenomenal.image.threshold.threshold_meanshift_enhance
    • openalea.phenomenal.mesh
      • openalea.phenomenal.mesh.algorithms.meshing
      • openalea.phenomenal.mesh.algorithms.marching_cubes
      • openalea.phenomenal.mesh.algorithms.smoothing
      • openalea.phenomenal.mesh.algorithms.decimation
      • openalea.phenomenal.mesh.formats
      • openalea.phenomenal.mesh.routines
      • openalea.phenomenal.mesh.vtk_transformation
      • openalea.phenomenal.mesh.algorithms
        • openalea.phenomenal.mesh.algorithms.decimation
        • openalea.phenomenal.mesh.algorithms.from_vertices_faces_to_voxels_position
        • openalea.phenomenal.mesh.algorithms.marching_cubes
        • openalea.phenomenal.mesh.algorithms.mesh_surface_area
        • openalea.phenomenal.mesh.algorithms.meshing
        • openalea.phenomenal.mesh.algorithms.smoothing
        • openalea.phenomenal.mesh.algorithms.voxelization
      • openalea.phenomenal.mesh.formats
        • openalea.phenomenal.mesh.formats.read_ply_to_vertices_faces
        • openalea.phenomenal.mesh.formats.read_ply_to_vtk_poly_data
        • openalea.phenomenal.mesh.formats.write_vertices_faces_to_ply_file
        • openalea.phenomenal.mesh.formats.write_vtk_poly_data_to_ply_file
      • openalea.phenomenal.mesh.routines
        • openalea.phenomenal.mesh.routines.centers
        • openalea.phenomenal.mesh.routines.median_color_from_images
        • openalea.phenomenal.mesh.routines.normals
        • openalea.phenomenal.mesh.routines.project_mesh_on_image
      • openalea.phenomenal.mesh.vtk_transformation
        • openalea.phenomenal.mesh.vtk_transformation.from_numpy_matrix_to_vtk_image_data
        • openalea.phenomenal.mesh.vtk_transformation.from_vertices_faces_to_vtk_poly_data
        • openalea.phenomenal.mesh.vtk_transformation.from_voxel_centers_to_vtk_image_data
        • openalea.phenomenal.mesh.vtk_transformation.from_vtk_image_data_to_voxels_center
        • openalea.phenomenal.mesh.vtk_transformation.from_vtk_poly_data_to_vertices_faces
        • openalea.phenomenal.mesh.vtk_transformation.voxel_grid_to_vtk_poly_data
    • openalea.phenomenal.multi_view_reconstruction
      • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction
      • openalea.phenomenal.multi_view_reconstruction._multi_view_reconstruction_octree
      • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.check_groups
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.create_groups
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.get_bounding_box_voxel_projected
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.get_integrale_image
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.get_voxels_corners
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.have_image_ref
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.image_error
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.kept_visible_voxel
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.project_voxel_centers_on_image
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.project_voxels_position_on_image
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.reconstruction_3d
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.reconstruction_error
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.reconstruction_inconsistent
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.split_voxels_in_eight
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.voxels_is_visible_in_image
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.Voxels
        • openalea.phenomenal.multi_view_reconstruction.multi_view_reconstruction.VoxelsStage
    • openalea.phenomenal.object
      • 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
      • openalea.phenomenal.object.image3D
        • openalea.phenomenal.object.image3D.Image3D
      • openalea.phenomenal.object.imageView
        • openalea.phenomenal.object.imageView.ImageView
      • openalea.phenomenal.object.voxelGrid
        • openalea.phenomenal.object.voxelGrid.NumpyEncoder
        • openalea.phenomenal.object.voxelGrid.VoxelGrid
      • openalea.phenomenal.object.voxelOctree
        • openalea.phenomenal.object.voxelOctree.VoxelNode
        • openalea.phenomenal.object.voxelOctree.VoxelOctree
      • openalea.phenomenal.object.voxelOrgan
        • openalea.phenomenal.object.voxelOrgan.VoxelOrgan
      • openalea.phenomenal.object.voxelSegment
        • openalea.phenomenal.object.voxelSegment.VoxelSegment
      • openalea.phenomenal.object.voxelSegmentation
        • openalea.phenomenal.object.voxelSegmentation.VoxelSegmentation
      • openalea.phenomenal.object.voxelSkeleton
        • openalea.phenomenal.object.voxelSkeleton.VoxelSkeleton
    • openalea.phenomenal.optional_deps
      • openalea.phenomenal.optional_deps.extra_map
      • openalea.phenomenal.optional_deps.require_dependency
      • openalea.phenomenal.optional_deps.OptionalDependencyError
    • openalea.phenomenal.segmentation
      • openalea.phenomenal.segmentation.graph
      • openalea.phenomenal.segmentation.image_3d_routines
      • openalea.phenomenal.segmentation._skeleton_octree
      • openalea.phenomenal.segmentation.skeleton_phenomenal
      • openalea.phenomenal.segmentation.skeleton_thinning
      • openalea.phenomenal.segmentation.peak_detection
      • openalea.phenomenal.segmentation.plane_interception
      • openalea.phenomenal.segmentation.maize_segmentation
      • openalea.phenomenal.segmentation.maize_stem_detection
      • openalea.phenomenal.segmentation.maize_analysis
      • openalea.phenomenal.segmentation.graph
        • openalea.phenomenal.segmentation.graph.connect_all_node_with_nearest_neighbors
        • openalea.phenomenal.segmentation.graph.create_graph
        • openalea.phenomenal.segmentation.graph.graph_from_voxel_grid
      • openalea.phenomenal.segmentation.image_3d_routines
        • openalea.phenomenal.segmentation.image_3d_routines.kept_biggest_connected_component
        • openalea.phenomenal.segmentation.image_3d_routines.labeling_connected_component
        • openalea.phenomenal.segmentation.image_3d_routines.remove_internal
      • openalea.phenomenal.segmentation.maize_analysis
      • openalea.phenomenal.segmentation.maize_segmentation
      • openalea.phenomenal.segmentation.maize_stem_detection
        • openalea.phenomenal.segmentation.maize_stem_detection.get_nodes_radius
        • openalea.phenomenal.segmentation.maize_stem_detection.maize_stem_peak_detection
        • openalea.phenomenal.segmentation.maize_stem_detection.stem_detection
      • openalea.phenomenal.segmentation.peak_detection
      • openalea.phenomenal.segmentation.plane_interception
        • openalea.phenomenal.segmentation.plane_interception.compute_plane_equation
        • openalea.phenomenal.segmentation.plane_interception.connected_points_with_point
        • openalea.phenomenal.segmentation.plane_interception.connected_voxel_with_point
        • openalea.phenomenal.segmentation.plane_interception.intercept_points_along_path_with_planes
        • openalea.phenomenal.segmentation.plane_interception.intercept_points_along_polyline_with_ball
        • openalea.phenomenal.segmentation.plane_interception.intercept_points_from_src_point_with_plane_equation
        • openalea.phenomenal.segmentation.plane_interception.intercept_points_with_ball
        • openalea.phenomenal.segmentation.plane_interception.max_distance_from_point_to_points
        • openalea.phenomenal.segmentation.plane_interception.max_distance_in_points
        • openalea.phenomenal.segmentation.plane_interception.orientation_vector_of_point_in_polyline
      • openalea.phenomenal.segmentation.skeleton_phenomenal
        • openalea.phenomenal.segmentation.skeleton_phenomenal.compute_all_shorted_path
        • openalea.phenomenal.segmentation.skeleton_phenomenal.find_base_stem_position
        • openalea.phenomenal.segmentation.skeleton_phenomenal.segment_reduction
        • openalea.phenomenal.segmentation.skeleton_phenomenal.skeletonize
      • openalea.phenomenal.segmentation.skeleton_thinning
        • openalea.phenomenal.segmentation.skeleton_thinning.skeletonize_thinning
    • openalea.phenomenal.tracking
      • openalea.phenomenal.tracking.alignment
        • openalea.phenomenal.tracking.alignment.alignment_score
        • openalea.phenomenal.tracking.alignment.insert_gaps
        • openalea.phenomenal.tracking.alignment.multi_alignment
        • openalea.phenomenal.tracking.alignment.needleman_wunsch
        • openalea.phenomenal.tracking.alignment.scoring_function
      • openalea.phenomenal.tracking.alignment_postprocessing
        • openalea.phenomenal.tracking.alignment_postprocessing.detect_abnormal_ranks
        • openalea.phenomenal.tracking.alignment_postprocessing.leaf_polylines_distance
      • openalea.phenomenal.tracking.display
        • openalea.phenomenal.tracking.display.plot_polylines
      • openalea.phenomenal.tracking.leaf_extension
        • openalea.phenomenal.tracking.leaf_extension.compute_extension
        • openalea.phenomenal.tracking.leaf_extension.leaf_extension
        • openalea.phenomenal.tracking.leaf_extension.skeleton_branches
      • openalea.phenomenal.tracking.median_stem
        • openalea.phenomenal.tracking.median_stem.get_median_polyline
        • openalea.phenomenal.tracking.median_stem.normal_stem_shape
        • openalea.phenomenal.tracking.median_stem.z_to_xy
      • openalea.phenomenal.tracking.phenomenal_coupling
        • openalea.phenomenal.tracking.phenomenal_coupling.phm_leaf_features
        • openalea.phenomenal.tracking.phenomenal_coupling.phm_to_phenotrack_input
      • openalea.phenomenal.tracking.polyline_utils
        • openalea.phenomenal.tracking.polyline_utils.polyline_length
        • openalea.phenomenal.tracking.polyline_utils.polyline_quantile_coordinate
        • openalea.phenomenal.tracking.polyline_utils.polyline_simplification
        • openalea.phenomenal.tracking.polyline_utils.polyline_until_z
      • openalea.phenomenal.tracking.trackedPlant
        • openalea.phenomenal.tracking.trackedPlant.check_time_intervals
        • openalea.phenomenal.tracking.trackedPlant.TrackedLeaf
        • openalea.phenomenal.tracking.trackedPlant.TrackedPlant
        • openalea.phenomenal.tracking.trackedPlant.TrackedSnapshot
  • API References
  • openalea.phenomenal
  • openalea.phenomenal.data

openalea.phenomenal.data#

Acces to plant’s data#

data

Synthetic data (for test)#

synthetic_data

Modules

data

synthetic_data

previous

openalea.phenomenal.clean_build_artefacts.clean_project_tree

next

openalea.phenomenal.data.data
On this page
  • Acces to plant’s data
    • Synthetic data (for test)

This Page

  • Show Source

© Copyright Cecill-C INRAE / INRIA / CIRAD.

Created using Sphinx 9.1.0.

Built with the PyData Sphinx Theme 0.16.1.