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chhsiao1981chhsiao1981
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Merge pull request #1393 from chhsiao1981/mipav-colormap
mipav colormap
2 parents 633e402 + bdf8af9 commit fc4f1ba

29 files changed

+2107
-34
lines changed

‎.gitmodules‎

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@@ -7,3 +7,9 @@
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[submodule "third-party/fs2NiiVueColormaps"]
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path = third-party/fs2NiiVueColormaps
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url = [email protected]:niivue/fs2NiiVueColormaps.git
10+
[submodule "third-party/mipav"]
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path = third-party/mipav
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url = [email protected]:JaneliaSciComp/mipav.git
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[submodule "third-party/mipav-to-niivue"]
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path = third-party/mipav-to-niivue
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url = [email protected]:chhsiao1981/mipav-to-niivue.git

‎package.json‎

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@@ -37,7 +37,8 @@
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"__helper_functions": "",
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"get-running-url": "./testing/get_running_url.sh",
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"print-version": "node printVersion.js",
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"fs2niivue": "if [ -d third-party/fs2NiiVueColormaps ]; then cd third-party/fs2NiiVueColormaps; python3 fs2niivue.py; cp FreesurferColorLUT.v7.4.1.json ../../src/components/Preview/displays; rm *.json; cd ../..; else echo '[WARN] need to git submodule fs2NiiVueColormaps first'; fi"
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"fs2niivue": "if [ -d third-party/fs2NiiVueColormaps ]; then cd third-party/fs2NiiVueColormaps; python3 fs2niivue.py; cp FreesurferColorLUT.v7.4.1.json ../../src/components/Preview/displays; rm *.json; cd ../..; else echo '[WARN] need to git submodule fs2NiiVueColormaps first'; fi",
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"mipav2niivue": "mipav-to-niivue -d third-party/mipav -o src/components/Preview/displays/mipav"
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},
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"dependencies": {
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"@ant-design/icons": "^5.5.1",

‎src/components/Preview/displays/NiiVueDisplay.tsx‎

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@@ -1,11 +1,9 @@
1-
import { SLICE_TYPE } from "@niivue/niivue";
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import { Switch } from "@patternfly/react-core";
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import { InputNumber, Select } from "antd";
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import { type CSSProperties, useState } from "react";
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import type { IFileBlob } from "../../../api/model.ts";
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import SizedNiivueCanvas from "../../SizedNiivueCanvas";
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import { getFileResourceUrl } from "./dicomUtils/utils.ts";
8-
import FreeSurferColorLUT from "./FreesurferColorLUT.v7.4.1.json";
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import styles from "./NiiVueDisplay.module.css";
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import {
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type CrosshairLocation,
@@ -15,13 +13,6 @@ import {
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SliceType,
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} from "./types.ts";
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18-
const SLICE_TYPE_MAP = {
19-
[SliceType.Axial]: SLICE_TYPE.AXIAL,
20-
[SliceType.Coronal]: SLICE_TYPE.CORONAL,
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[SliceType.Sagittal]: SLICE_TYPE.SAGITTAL,
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[SliceType.Multiplanar]: SLICE_TYPE.MULTIPLANAR,
23-
};
24-
2516
const SLICE_TYPE_LIST = [
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SliceType.Multiplanar,
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SliceType.Axial,
@@ -32,15 +23,36 @@ const SLICE_TYPE_LIST = [
3223
const COLOR_MAP_LIST = [
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DisplayColorMap.Gray,
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DisplayColorMap.NIH,
26+
DisplayColorMap.NIH2,
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DisplayColorMap.Plasma,
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DisplayColorMap.Viridis,
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DisplayColorMap.Freesurfer,
30+
DisplayColorMap.BlackBody,
31+
DisplayColorMap.Cardiac,
32+
DisplayColorMap.Flow,
33+
DisplayColorMap.GEColor,
34+
DisplayColorMap.GrayRainbow,
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DisplayColorMap.HotGreen,
36+
DisplayColorMap.HotIron,
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DisplayColorMap.HotMetal,
38+
DisplayColorMap.Hue1,
39+
DisplayColorMap.Hue2,
40+
DisplayColorMap.IRed,
41+
DisplayColorMap.Rainbow,
42+
DisplayColorMap.Rainbow2,
43+
DisplayColorMap.Rainbow3,
44+
DisplayColorMap.Ratio,
45+
DisplayColorMap.Spectrum,
46+
DisplayColorMap.Stern,
47+
DisplayColorMap.UCLA,
48+
DisplayColorMap.VRBones,
49+
DisplayColorMap.VRMusclesBones,
50+
DisplayColorMap.VRRedVessels,
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];
3952

4053
const DISPLAY_TYPE_LIST = [
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DisplayType.IMG4096,
42-
DisplayType.ZMap5,
43-
DisplayType.ZMap10,
55+
DisplayType.ZMap,
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DisplayType.Label,
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DisplayType.IMG256,
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DisplayType.IMG65536,
@@ -52,16 +64,11 @@ const DISPLAY_TYPE_MAP: DisplayTypeMap = {
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calMin: 0,
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calMax: 4096,
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},
55-
[DisplayType.ZMap5]: {
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colorMap: DisplayColorMap.NIH,
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[DisplayType.ZMap]: {
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colorMap: DisplayColorMap.Rainbow2,
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calMin: -5,
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calMax: 5,
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},
60-
[DisplayType.ZMap10]: {
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colorMap: DisplayColorMap.NIH,
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calMin: -10,
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calMax: 10,
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},
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[DisplayType.Label]: {
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colorMap: DisplayColorMap.Freesurfer,
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calMin: 0,
@@ -99,10 +106,7 @@ export default (props: Props) => {
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100107
const urls = selectedFile ? [getFileResourceUrl(selectedFile)] : [];
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102-
const colormapLabel =
103-
colorMap === DisplayColorMap.Freesurfer ? FreeSurferColorLUT : null;
104-
const theColorMap =
105-
colorMap === DisplayColorMap.Freesurfer ? "gray" : colorMap;
109+
const theColorMap = colorMap;
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107111
const selectStyle = { width: "9em" };
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@@ -239,7 +243,6 @@ export default (props: Props) => {
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size={8}
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urls={urls}
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colormap={theColorMap}
242-
colormapLabel={colormapLabel}
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calMax={calMax}
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calMin={calMin}
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onLocationChange={(c: CrosshairLocation) => {

‎src/components/Preview/displays/mipav/black_body.json‎

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‎src/components/Preview/displays/mipav/cardiac.json‎

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77+
59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
78+
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,
79+
97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
80+
113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127,
81+
128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
82+
143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157,
83+
158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
84+
173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187,
85+
188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,
86+
203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,
87+
218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232,
88+
233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,
89+
248, 249, 250, 251, 252, 253, 254, 255
90+
]
91+
}

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