microdraw.py

Functions for working with MicroDraw

Import using

from microdraw import microdraw as mic

FUNCTIONS

Download and upload datasets from microdraw

download_all_regions_from_dataset(source, project, token, microdraw_url='https://microdraw.pasteur.fr') Download all regions in all slices in a dataset.

download_all_regions_from_dataset_slice(source, project, slce, token, backups=False, microdraw_url='https://microdraw.pasteur.fr') Download all regions in a slice in a dataset.

download_dataset_definition(source) Download a dataset. A dataset can contain several slices, each with several regions

download_microdraw_contours_as_polygons(source, project, sliceIndex, token, width) Download microdraw contours as polygons, taking care of childrens, lines and bezier curves.

download_project_definition(project, token) Download a project. A project can contain several datasets.

upload_polygons_to_microdraw_slice(source, project, slice_index, token, polygons, name, rgb, host="https://microdraw.pasteur.fr/api/upload") Upload polygons to a microdraw slice.

Load and save datasets locally

load_dataset(path) load dataset stored in json format

save_dataset(data, path) save dataset in json format

Conversion between MicroDraw json and polygons

convert_polygons_to_microdraw_json(lines, name, rgb) Convert an array of lines (a series of vertices) into Microdraw JSON format (which is the default Paper.js format)

paperjs_path_to_polygon(co) Convert Paper.js paths to a polygon (a line made of consecutive vertices).

Note: Paper.js Bézier curves are encoded as px, py, ax, ay, bx, by,
where px, py is an anchor point, ax, ay is the previous handle and
bx, by the next handle. SVG path tools use a more standard encoding:
p1x,p1y, b1x, b1y, a2x, a2y, p2x, p2y, where p1x, p1y is the start
anchor point, p2x, p2y the end anchor point, b1x, b1y is the
handle coming out from p1x, p1y, and a2x, a2y is the handle entering
into the end anchor point.

Others

assignments(a, b, P, projection_type='line')

assignments_indices(a, b, P)

b_to_a_projection(a, b, scale)

color_from_string(my_string) Create a random color based on a hash of the input string

compute_inner_contour(coords_arr, delta)

compute_inner_contours_for_polygons(polygons, iterations=10, projection='maxcoupling', scale=1000, nodeinterval=10, distCont=-3)

compute_inner_contours_for_polygons_inwards(polygons, iterations=3, scale=5000, distCont=-5, nodeinterval=10)

compute_inner_contours_for_polygons_outwards(polygons, iterations=3, scale=5000, distCont=-5, nodeinterval=10)

continuous_contours(edge_soup) Obtain contiuous lines from the unordered list of edges in edge_soup. Returns an array of lines where each element is a continuous line composed of string of neighbouring vertices

dataset_as_volume(dataset, filter=None) Combine all regions into a single mesh. This mesh does not have triangles, only region contours. dataset: the dataset from which to obtain the region contours filter: an optional array of strings with the names of the regions to include in the mesh

dataset_to_nifti(dataset, voxdim=[0.1, 0.1, 1.25], region_name=None) convert dataset to nifti volume. Returns a nifti object

draw_all_dataset(dataset, ncol=13, width=800, alpha=0.5, path=None) draw all dataset

draw_slice(v, f, slice_index, path, scale_x=3, scale_yz=0.25, slice_offset=0)

filter_offdiagonal(P, D=10, freq=0.4)

find_compound_regions(regions) combine regions into compound regions

find_contour_correspondences(manual, auto, min_pct=0.7, max_pct=1.4)

find_mesh_contour_to_profile_contour_correspondence(mesh_contour, registered_manual_contour, profile_contour)

get_points_from_segment(seg) get points from segment

get_regions_from_dataset_slice(dataset) get regions from dataset slice

icp(ref, mov)

icp_step(mov, ref)

interp(a, b, x) Obtain a vector between a and b at the position a[2]<=x<=b[2]

is_reference_orientation_a_hole(regions, sub_regions) determine the orientation of sub regions in a compound region

no_duplicates_contour(vert_point_and_coord, contour) Remove duplicate vertices from the contour given by vertices vert_point_and_coord and edges in contour. The indices in contour are re-indexed accordingly.

raw_contour(v, f, x) Obtain the contour produced by slicing the mesh with vertices v and faces f at coordinate x in the last dimension. Produces a list of vertices and a list of edges. The vertices for each edge are unique which means that vertices at connecting edges will be duplicated. Each vertex includes a reference to the edge where it comes from. This reference contains the index of the triangle, the number of the edge withing the triangle (0, 1 or 2), and the distance from the beginning of the edge.

register_contours(manual, auto, corresp)

register_microdraw_contours_to_mesh_contours_for_slice(source, project, sliceIndex, token, v, f, width, height, scale_x, scale_yz, slice_offset)

save_contour(path, ver, con) A contour is a list of vertices and a list of edges. A contour can contain multiple independent closed contours, but the list of vertices and edges is always unique. This function saves the contour in a format readable by MeshSurgery.

save_dataset_as_nifti(dataset, path, voxdim=[0.1, 0.1, 1.25], region_name=None) save dataset as a nifti volume

save_dataset_as_text_mesh(dataset, path, voxdim=[0.1, 0.1, 1.25]) save dataset as a text mesh

save_slice_contours_in_svg(path, contours, width, height)

scale_contours_to_image(v, width, height, scale_yz)

slice_mesh(v, f, z, min_contour_length=10) Slices the mesh of vertices v and faces f with the plane of given z coordinate. Returns: * unique_verts_point_and_coord: a list of unique vertices, * mesh_relative_vertex_coords: their coordinates relative to the mesh. Each row has 3 values: index of the mesh triangle that was sliced, index of the edge within that triangle, position of the vertex within that edge. The value of the position of the vertex within the edge is 0 if the vertex is at the beginning of the edge, and 1 if it is at the end. * edges: a list of edges, * lines: and a list of continuous lines.

Data types

Annotation: Any type of data added by the user, in particular, regions
Bézier curve: A curve composed of a series of polynomial curves, each determined by a start anchor, an end anchor, and two control points.
Color: A combination of red, green and blue components, plus an alpha value, encoded in hexadecimal.
Contour, continuous:
Contour, raw:
Contour: Same as a region?
Dataset: Annotations for a series of slices
Image: The image being annotated, encoded in .dzi format.
Inner contour:
Inner polygon:
Label: A name and a color.
Mesh contour: Contour obtained by slicing a mesh.
Mesh: Collection of vertices and triangles.
Microdraw contour:
Microdraw JSON:
Nifti: Volume encoded in Nifti 1 format, contains the volume data and metadata.
Outer contour:
Outer polygon:
Paper.js path: A simple or compound path encoded in Paper.js format.
Point: A position in space described by its coordinates.
Polygon: A curve composed of straight lines.
Profile contour: A contour used for computing profiles.
Profile: Grey level profile along a line going from the outer contour to the inner contour.
Project: A Microdraw project, containing a dataset plus information about collaborators, permissions, list of features to annotate, project description, project URL.
Region: a path enclosing a part of the image. Can be a simple path or a compound path. Can be a Bézier curve or a polygon. It is associated to a label.
Segment:
Slice (noun): An image and its annotations, identified by the index in the dataset it belongs.
Slice (verb): To intersecting a volumetric object with a plane.
SVG: A standard format for encoding 2D vectorial graphics.
Text mesh: A mesh encoded in plain text. The first row contains number of vertices followed by number of triangles. The following rows contain the x, y and z coordinates for each of the vertices. The next rows contain each of the mesh triangles, where each triangle contains the indices of its 3 vertices. The 1st vertex has index 0.
Volume: Same as Nifti?