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@benjamindkilleen
benjamindkilleen committed Dec 2, 2021
1 parent 08e1328 commit b38f1f9
Showing 1 changed file with 104 additions and 113 deletions.
217 changes: 104 additions & 113 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 @@ -65,118 +65,109 @@ def from_markup(cls, path: str, volume: AnyVolume) -> LineAnnotation:

return cls(*points, volume)

#sean 11/23/21
def save(self, fileName: str, breachDetected: bool, startPt: geo, endPt: geo):
start = startPt
end = endPt

#determine line color and path based on cortical breach detected
if breachDetected :
#RGB red if breach
lineColor = [1.0, 0.0, 0.0]
path = './savedLineAnnotations/breachDetected'
else :
#RGB green if no breach
lineColor = [0.0, 1.0, 0.0]
path = './savedLineAnnotations/noBreachDetected'

# todo(sean): save markups with color options based on the following template
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": "LPS",
"locked": false,
"labelFormat": "%N-%d",
"controlPoints": [
{
"id": "1",
"label": "entry",
"description": "",
"associatedNodeID": "",
"position": start,
"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": end,
"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": lineColor,
"selectedColor": lineColor,
"activeColor": lineColor,
"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",
},
}
],
}

#the actual saving
savePath = path + '/' + fileName + '.json'
with open(savePath, 'w') as outfile:
json.dump(markup, outfile)
"@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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