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Merge pull request #61 from arcadelab/sean_branch
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@benjamindkilleen
benjamindkilleen authored Dec 2, 2021
2 parents 6b7240f + b38f1f9 commit dc8d8ea
Showing 1 changed file with 105 additions and 105 deletions.
210 changes: 105 additions & 105 deletions deepdrr/annotations/line_annotation.py
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
from __future__ import annotations

import logging
from typing import Optional
from typing import List, Optional
from pathlib import Path
import numpy as np
import json
import pyvista as pv

from .. import geo
from .. import geo, utils
from ..vol import Volume, AnyVolume

logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -65,109 +65,109 @@ def from_markup(cls, path: str, volume: AnyVolume) -> LineAnnotation:

return cls(*points, volume)

def save(self, path: str):
# todo(sean): save markups with color options based on the following template
# markup = {
# "@schema": "https://raw.githubusercontent.com/slicer/slicer/master/Modules/Loadable/Markups/Resources/Schema/markups-schema-v1.0.0.json#",
# "markups": [
# {
# "type": "Line",
# "coordinateSystem": "LPS",
# "locked": false,
# "labelFormat": "%N-%d",
# "controlPoints": [
# {
# "id": "1",
# "label": "entry",
# "description": "",
# "associatedNodeID": "",
# "position": [
# 3.980233907699585,
# -40.96451187133789,
# -1392.0523681640626,
# ],
# "orientation": [
# -1.0,
# -0.0,
# -0.0,
# -0.0,
# -1.0,
# -0.0,
# 0.0,
# 0.0,
# 1.0,
# ],
# "selected": true,
# "locked": false,
# "visibility": true,
# "positionStatus": "defined",
# },
# {
# "id": "2",
# "label": "exit",
# "description": "",
# "associatedNodeID": "",
# "position": [
# 100.19214630126953,
# -2.4773364067077638,
# -1322.3232421875,
# ],
# "orientation": [
# -1.0,
# -0.0,
# -0.0,
# -0.0,
# -1.0,
# -0.0,
# 0.0,
# 0.0,
# 1.0,
# ],
# "selected": true,
# "locked": false,
# "visibility": true,
# "positionStatus": "defined",
# },
# ],
# "measurements": [
# {
# "name": "length",
# "enabled": true,
# "value": 124.90054351814699,
# "printFormat": "%-#4.4gmm",
# }
# ],
# "display": {
# "visibility": true,
# "opacity": 1.0,
# "color": [0.5, 0.5, 0.5],
# "selectedColor": [1.0, 0.5000076295109484, 0.5000076295109484],
# "activeColor": [0.4, 1.0, 0.0],
# "propertiesLabelVisibility": true,
# "pointLabelsVisibility": true,
# "textScale": 3.0,
# "glyphType": "Sphere3D",
# "glyphScale": 5.800000000000001,
# "glyphSize": 5.0,
# "useGlyphScale": true,
# "sliceProjection": false,
# "sliceProjectionUseFiducialColor": true,
# "sliceProjectionOutlinedBehindSlicePlane": false,
# "sliceProjectionColor": [1.0, 1.0, 1.0],
# "sliceProjectionOpacity": 0.6,
# "lineThickness": 0.2,
# "lineColorFadingStart": 1.0,
# "lineColorFadingEnd": 10.0,
# "lineColorFadingSaturation": 1.0,
# "lineColorFadingHueOffset": 0.0,
# "handlesInteractive": false,
# "snapMode": "toVisibleSurface",
# },
# }
# ],
# }

raise NotImplementedError
def save(self, path: str, color: List[float] = [0.5, 0.5, 0.5]):
"""Save the Line annotation to a mrk.json file, which can be opened by 3D Slicer.
Args:
path (str): Output path to the file.
color (List[int], optional): The color of the saved annotation.
"""
path = Path(path).expanduser()

markup = {
"@schema": "https://raw.githubusercontent.com/slicer/slicer/master/Modules/Loadable/Markups/Resources/Schema/markups-schema-v1.0.0.json#",
"markups": [
{
"type": "Line",
"coordinateSystem": self.volume.anatomical_coordinate_system,
"locked": True,
"labelFormat": "%N-%d",
"controlPoints": [
{
"id": "1",
"label": "entry",
"description": "",
"associatedNodeID": "",
"position": utils.jsonable(self.startpoint),
"orientation": [
-1.0,
-0.0,
-0.0,
-0.0,
-1.0,
-0.0,
0.0,
0.0,
1.0,
],
"selected": True,
"locked": False,
"visibility": True,
"positionStatus": "defined",
},
{
"id": "2",
"label": "exit",
"description": "",
"associatedNodeID": "",
"position": utils.jsonable(self.endpoint),
"orientation": [
-1.0,
-0.0,
-0.0,
-0.0,
-1.0,
-0.0,
0.0,
0.0,
1.0,
],
"selected": True,
"locked": False,
"visibility": True,
"positionStatus": "defined",
},
],
"measurements": [
{
"name": "length",
"enabled": True,
"value": 124.90054351814699,
"printFormat": "%-#4.4gmm",
}
],
"display": {
"visibility": True,
"opacity": 1.0,
"color": color,
"selectedColor": [1.0, 0.5000076295109484, 0.5000076295109484],
"activeColor": [0.4, 1.0, 0.0],
"propertiesLabelVisibility": True,
"pointLabelsVisibility": True,
"textScale": 3.0,
"glyphType": "Sphere3D",
"glyphScale": 5.800000000000001,
"glyphSize": 5.0,
"useGlyphScale": True,
"sliceProjection": False,
"sliceProjectionUseFiducialColor": True,
"sliceProjectionOutlinedBehindSlicePlane": False,
"sliceProjectionColor": [1.0, 1.0, 1.0],
"sliceProjectionOpacity": 0.6,
"lineThickness": 0.2,
"lineColorFadingStart": 1.0,
"lineColorFadingEnd": 10.0,
"lineColorFadingSaturation": 1.0,
"lineColorFadingHueOffset": 0.0,
"handlesInteractive": False,
"snapMode": "toVisibleSurface",
},
}
],
}

with open(path, "w") as file:
json.dump(markup, file)

@property
def startpoint_in_world(self) -> geo.Point:
Expand Down

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