wsi-dicom-annotations 0.2.1

DICOM WSI ANN, SEG, SR, and Parametric Map interoperability
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142

use super::feature::ProfiledFeature;
use super::geometry::ProfiledGeometry;
use crate::Point2;

#[derive(Debug, Clone)]
pub struct PathologyPreview {
    features: Vec<PathologyPreviewFeature>,
}

impl PathologyPreview {
    pub(super) fn from_owned_features(features: Vec<ProfiledFeature>) -> Self {
        Self {
            features: features
                .into_iter()
                .map(PathologyPreviewFeature::from)
                .collect(),
        }
    }

    #[must_use]
    pub fn features(&self) -> &[PathologyPreviewFeature] {
        &self.features
    }
}

#[derive(Debug, Clone)]
pub struct PathologyPreviewFeature {
    tracking_id: String,
    label: String,
    classification: String,
    recommended_display_cielab: [u16; 3],
    bounds: [f64; 4],
    geometry: PathologyPreviewGeometry,
}

impl PathologyPreviewFeature {
    #[must_use]
    pub fn tracking_id(&self) -> &str {
        &self.tracking_id
    }

    #[must_use]
    pub fn label(&self) -> &str {
        &self.label
    }

    #[must_use]
    pub fn classification(&self) -> &str {
        &self.classification
    }

    #[must_use]
    pub const fn recommended_display_cielab(&self) -> [u16; 3] {
        self.recommended_display_cielab
    }

    #[must_use]
    pub const fn bounds(&self) -> [f64; 4] {
        self.bounds
    }

    #[must_use]
    pub const fn geometry(&self) -> &PathologyPreviewGeometry {
        &self.geometry
    }
}

impl From<ProfiledFeature> for PathologyPreviewFeature {
    fn from(feature: ProfiledFeature) -> Self {
        let bounds = geometry_bounds(&feature.geometry);
        let geometry = match feature.geometry {
            ProfiledGeometry::Points(points) => PathologyPreviewGeometry::Points(points),
            ProfiledGeometry::Lines(lines) => PathologyPreviewGeometry::Lines(lines),
            ProfiledGeometry::Polygons(polygons) => PathologyPreviewGeometry::Polygons(
                polygons
                    .into_iter()
                    .map(|polygon| PathologyPreviewPolygon {
                        exterior: polygon.outer,
                        holes: polygon.holes,
                    })
                    .collect(),
            ),
        };
        Self {
            tracking_id: feature.tracking_id,
            label: feature.name,
            classification: feature.classification,
            recommended_display_cielab: feature.semantics.finding.recommended_display_cielab(),
            bounds,
            geometry,
        }
    }
}

fn geometry_bounds(geometry: &ProfiledGeometry) -> [f64; 4] {
    let mut bounds = [
        f64::INFINITY,
        f64::INFINITY,
        f64::NEG_INFINITY,
        f64::NEG_INFINITY,
    ];
    let mut observe = |point: &Point2| {
        bounds[0] = bounds[0].min(point.x);
        bounds[1] = bounds[1].min(point.y);
        bounds[2] = bounds[2].max(point.x);
        bounds[3] = bounds[3].max(point.y);
    };
    match geometry {
        ProfiledGeometry::Points(points) => points.iter().for_each(&mut observe),
        ProfiledGeometry::Lines(lines) => lines.iter().flatten().for_each(&mut observe),
        ProfiledGeometry::Polygons(polygons) => polygons.iter().for_each(|polygon| {
            polygon.outer.iter().for_each(&mut observe);
            polygon.holes.iter().flatten().for_each(&mut observe);
        }),
    }
    bounds
}

#[derive(Debug, Clone)]
pub enum PathologyPreviewGeometry {
    Points(Vec<Point2>),
    Lines(Vec<Vec<Point2>>),
    Polygons(Vec<PathologyPreviewPolygon>),
}

#[derive(Debug, Clone)]
pub struct PathologyPreviewPolygon {
    exterior: Vec<Point2>,
    holes: Vec<Vec<Point2>>,
}

impl PathologyPreviewPolygon {
    #[must_use]
    pub fn exterior(&self) -> &[Point2] {
        &self.exterior
    }

    #[must_use]
    pub fn holes(&self) -> &[Vec<Point2>] {
        &self.holes
    }
}