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Colormap wasn't being applied #3464

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merged 12 commits into from
Jul 4, 2023
Merged

Colormap wasn't being applied #3464

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1a5ae5c
fix(tmtv): Fix the tmtv colormap settings
wayfarer3130 Jun 9, 2023
0febe3e
Fix colormap menu
wayfarer3130 Jun 9, 2023
7dd9f4a
Merge remote-tracking branch 'origin/master' into fix/colormap-tmtv
wayfarer3130 Jun 29, 2023
fb72037
Update CS3D
wayfarer3130 Jun 29, 2023
5df9c51
Remove port change
wayfarer3130 Jun 29, 2023
60e2975
Merge remote-tracking branch 'origin/master' into fix/colormap-tmtv
wayfarer3130 Jun 29, 2023
04cbba6
Merge remote-tracking branch 'origin/master' into fix/colormap-tmtv
wayfarer3130 Jun 29, 2023
92f11a2
Merge remote-tracking branch 'origin/master' into fix/colormap-tmtv
wayfarer3130 Jun 29, 2023
b3a92e5
PR comments
wayfarer3130 Jun 29, 2023
1233d3a
Merge branch 'master' of github.com:OHIF/Viewers into remotes/origin/…
sedghi Jul 4, 2023
3845818
fix(colormap): opacity was renamed recently
sedghi Jul 4, 2023
5cfbdc5
Merge branch 'master' of github.com:OHIF/Viewers into remotes/origin/…
sedghi Jul 4, 2023
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6 changes: 3 additions & 3 deletions extensions/cornerstone-dicom-sr/package.json
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Expand Up @@ -44,9 +44,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.2.4",
"@cornerstonejs/core": "^1.2.4",
"@cornerstonejs/tools": "^1.2.4",
"@cornerstonejs/adapters": "^1.2.8",
"@cornerstonejs/core": "^1.2.8",
"@cornerstonejs/tools": "^1.2.8",
"classnames": "^2.3.2"
}
}
10 changes: 5 additions & 5 deletions extensions/cornerstone/package.json
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Expand Up @@ -36,7 +36,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.2.4",
"@cornerstonejs/dicom-image-loader": "^1.2.8",
"@ohif/core": "3.7.0-beta.21",
"@ohif/ui": "3.7.0-beta.21",
"dcmjs": "^0.29.6",
Expand All @@ -52,10 +52,10 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.2.4",
"@cornerstonejs/core": "^1.2.4",
"@cornerstonejs/streaming-image-volume-loader": "^1.2.4",
"@cornerstonejs/tools": "^1.2.4",
"@cornerstonejs/adapters": "^1.2.8",
"@cornerstonejs/core": "^1.2.8",
"@cornerstonejs/streaming-image-volume-loader": "^1.2.8",
"@cornerstonejs/tools": "^1.2.8",
"@kitware/vtk.js": "27.3.1",
"html2canvas": "^1.4.1",
"lodash.debounce": "4.0.8",
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1 change: 0 additions & 1 deletion extensions/cornerstone/src/index.tsx
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Expand Up @@ -24,7 +24,6 @@ import { toolNames } from './initCornerstoneTools';
import { getEnabledElement, reset as enabledElementReset } from './state';
import dicomLoaderService from './utils/dicomLoaderService';
import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement';
import { registerColormap } from './utils/colormap/transferFunctionHelpers';

import { id } from './id';
import * as csWADOImageLoader from './initWADOImageLoader.js';
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2 changes: 1 addition & 1 deletion extensions/default/src/Toolbar/Toolbar.tsx
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Expand Up @@ -29,7 +29,7 @@ export default function Toolbar({ servicesManager }) {

return (
<>
{toolbarButtons.map((toolDef, index) => {
{toolbarButtons.map(toolDef => {
const { id, Component, componentProps } = toolDef;
// TODO: ...

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4 changes: 2 additions & 2 deletions extensions/measurement-tracking/package.json
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Expand Up @@ -30,8 +30,8 @@
"start": "yarn run dev"
},
"peerDependencies": {
"@cornerstonejs/core": "^1.2.4",
"@cornerstonejs/tools": "^1.2.4",
"@cornerstonejs/core": "^1.2.8",
"@cornerstonejs/tools": "^1.2.8",
"@ohif/core": "3.7.0-beta.21",
"@ohif/extension-cornerstone-dicom-sr": "3.7.0-beta.21",
"@ohif/ui": "3.7.0-beta.21",
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11 changes: 10 additions & 1 deletion extensions/tmtv/src/commandsModule.js
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Expand Up @@ -553,7 +553,16 @@ const commandsModule = ({
commandsManager.runCommand('setViewportColormap', {
viewportIndex,
displaySetInstanceUID: ptDisplaySet.displaySetInstanceUID,
colormap,
colormap: {
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name: colormap,
// TODO: This opacity mapping matches that in hpViewports, but
// ideally making this editable in a side panel would be useful
opacity: [
{ value: 0, opacity: 0 },
{ value: 0.1, opacity: 0.9 },
{ value: 1, opacity: 0.95 },
],
},
});

viewports.push(
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24 changes: 18 additions & 6 deletions extensions/tmtv/src/utils/hpViewports.ts
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Expand Up @@ -254,16 +254,20 @@ const fusionAXIAL = {
id: 'ctDisplaySet',
},
{
id: 'ptDisplaySet',
options: {
colormap: {
name: 'hsv',
opacityMapping: [{ value: 0.1, opacity: 0.9 }],
opacity: [
{ value: 0, opacity: 0 },
{ value: 0.1, opacity: 0.9 },
{ value: 1, opacity: 0.95 },
],
},
voi: {
custom: 'getPTVOIRange',
},
},
id: 'ptDisplaySet',
},
],
};
Expand Down Expand Up @@ -310,16 +314,20 @@ const fusionSAGITTAL = {
id: 'ctDisplaySet',
},
{
id: 'ptDisplaySet',
options: {
colormap: {
name: 'hsv',
opacityMapping: [{ value: 0.1, opacity: 0.9 }],
opacity: [
{ value: 0, opacity: 0 },
{ value: 0.1, opacity: 0.9 },
{ value: 1, opacity: 0.95 },
],
},
voi: {
custom: 'getPTVOIRange',
},
},
id: 'ptDisplaySet',
},
],
};
Expand Down Expand Up @@ -366,16 +374,20 @@ const fusionCORONAL = {
id: 'ctDisplaySet',
},
{
id: 'ptDisplaySet',
options: {
colormap: {
name: 'hsv',
opacityMapping: [{ value: 0.1, opacity: 0.9 }],
opacity: [
{ value: 0, opacity: 0 },
{ value: 0.1, opacity: 0.9 },
{ value: 1, opacity: 0.95 },
],
},
voi: {
custom: 'getPTVOIRange',
},
},
id: 'ptDisplaySet',
},
],
};
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16 changes: 4 additions & 12 deletions modes/tmtv/src/toolbarButtons.js
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Expand Up @@ -24,9 +24,8 @@ function _createButton(type, id, icon, label, commands, tooltip) {

function _createColormap(label, colormap) {
return {
id: label.toString(),
title: label,
subtitle: label,
id: label,
label,
type: 'action',
commands: [
{
Expand All @@ -36,13 +35,6 @@ function _createColormap(label, colormap) {
colormap,
},
},
{
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Duplicated unnecessarily redundant.

commandName: 'setFusionPTColormap',
commandOptions: {
toolGroupId: toolGroupIds.Fusion,
colormap,
},
},
],
};
}
Expand Down Expand Up @@ -313,7 +305,8 @@ const toolbarButtons = [
commandName: 'displayNotification',
commandOptions: {
title: 'RectangleROI Threshold Tip',
text: 'RectangleROI Threshold tool should be used on PT Axial Viewport',
text:
'RectangleROI Threshold tool should be used on PT Axial Viewport',
type: 'info',
},
},
Expand Down Expand Up @@ -345,7 +338,6 @@ const toolbarButtons = [
tooltip: 'PET Image Colormap',
},
isAction: true, // ?
renderer: WindowLevelMenuItem,
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This was causing the menu to have numbers beside it, causing it to look like it was appliable from the keyboard.

items: [
_createColormap('HSV', 'hsv'),
_createColormap('Hot Iron', 'hot_iron'),
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2 changes: 1 addition & 1 deletion package.json
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Expand Up @@ -149,7 +149,7 @@
]
},
"resolutions": {
"@cornerstonejs/core": "^1.2.4",
"@cornerstonejs/core": "^1.2.8",
"**/@babel/runtime": "^7.20.13",
"commander": "8.3.0",
"nth-check": "^2.1.1",
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2 changes: 1 addition & 1 deletion platform/app/package.json
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Expand Up @@ -51,7 +51,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.2.4",
"@cornerstonejs/dicom-image-loader": "^1.2.8",
"@ohif/core": "3.7.0-beta.21",
"@ohif/extension-cornerstone": "3.7.0-beta.21",
"@ohif/extension-cornerstone-dicom-rt": "3.7.0-beta.21",
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2 changes: 1 addition & 1 deletion platform/core/package.json
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Expand Up @@ -35,7 +35,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.2.4",
"@cornerstonejs/dicom-image-loader": "^1.2.8",
"@ohif/ui": "3.7.0-beta.21",
"cornerstone-math": "0.1.9",
"dicom-parser": "^1.8.21"
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49 changes: 25 additions & 24 deletions platform/core/src/defaults/hotkeyBindings.js
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Expand Up @@ -173,30 +173,31 @@ const bindings = [
label: 'W/L Preset 5',
keys: ['5'],
},
{
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commandName: 'setWindowLevel',
commandOptions: windowLevelPresets[6],
label: 'W/L Preset 6',
keys: ['6'],
},
{
commandName: 'setWindowLevel',
commandOptions: windowLevelPresets[7],
label: 'W/L Preset 7',
keys: ['7'],
},
{
commandName: 'setWindowLevel',
commandOptions: windowLevelPresets[8],
label: 'W/L Preset 8',
keys: ['8'],
},
{
commandName: 'setWindowLevel',
commandOptions: windowLevelPresets[9],
label: 'W/L Preset 9',
keys: ['9'],
},
// These don't exist, so don't try applying them....
// {
// commandName: 'setWindowLevel',
// commandOptions: windowLevelPresets[6],
// label: 'W/L Preset 6',
// keys: ['6'],
// },
// {
// commandName: 'setWindowLevel',
// commandOptions: windowLevelPresets[7],
// label: 'W/L Preset 7',
// keys: ['7'],
// },
// {
// commandName: 'setWindowLevel',
// commandOptions: windowLevelPresets[8],
// label: 'W/L Preset 8',
// keys: ['8'],
// },
// {
// commandName: 'setWindowLevel',
// commandOptions: windowLevelPresets[9],
// label: 'W/L Preset 9',
// keys: ['9'],
// },
];

export default bindings;
4 changes: 2 additions & 2 deletions platform/docs/docs/platform/extensions/modules/hpModule.md
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Expand Up @@ -246,7 +246,7 @@ A list of criteria for the protocol along with the provided points for ranking.

- `constraint`: the constraint that needs to be satisfied for the attribute. It accepts a `validator` which can be
[`equals`, `doesNotEqual`, `contains`, `doesNotContain`, `startsWith`, `endsWidth`]

- | Rule | Single Value | Array Value | Example |
|--- |--- |--- |--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| equals | === | All members are === in same order | value = ['abc', 'def', 'GHI']<br/>testValue = 'abc' (Fail)<br/><br/> = ['abc'] (Fail)<br/><br/> = ['abc', 'def', 'GHI'] (Valid)<br/><br/> = ['abc', 'GHI', 'def'] (Fail)<br/><br/> = ['abc', 'def'] (Fail)<br/><br/>value = 'Attenuation Corrected'<br/>testValue = 'Attenuation Corrected' (Valid)<br/> = 'Attenuation' (Fail)<br/><br/> value = ['Attenuation Corrected'] <br/> testValue = ['Attenuation Corrected'] (Valid)<br/> = 'Attenuation Corrected' (Valid) <br/> = 'Attenuation' (Fail) <br/> |
Expand Down Expand Up @@ -439,7 +439,7 @@ As you can see in the hanging protocol we defined three viewports (but only show
- `options` (optional): options for the display set
- voi: windowing options for the display set (optional: windowWidth, windowCenter)
- voiInverted: whether the VOI is inverted or not (optional)
- colormap: colormap for the display set (optional, it is an object with `{ name }` and optional extra `opacityMapping` property)
- colormap: colormap for the display set (optional, it is an object with `{ name }` and optional extra `opacity` property)
- displayPreset: display preset for the display set (optional, used for 3D volume rendering. e.g., 'CT-Bone')


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46 changes: 23 additions & 23 deletions yarn.lock
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Expand Up @@ -1589,10 +1589,10 @@
resolved "https://registry.yarnpkg.com/@colors/colors/-/colors-1.5.0.tgz#bb504579c1cae923e6576a4f5da43d25f97bdbd9"
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"@cornerstonejs/adapters@^1.2.4":
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resolved "https://registry.npmjs.org/@cornerstonejs/adapters/-/adapters-1.2.4.tgz#9920ca4cae2acf064ba3165cde6da67123fbc25e"
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"@cornerstonejs/adapters@^1.2.8":
version "1.2.8"
resolved "https://registry.yarnpkg.com/@cornerstonejs/adapters/-/adapters-1.2.8.tgz#26e584971b917dd099a73511abde32f236655915"
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dependencies:
"@babel/runtime-corejs2" "^7.17.8"
dcmjs "^0.29.5"
Expand Down Expand Up @@ -1640,43 +1640,43 @@
resolved "https://registry.yarnpkg.com/@cornerstonejs/codec-openjph/-/codec-openjph-2.4.2.tgz#e96721d56f6ec96f7f95c16321d88cc8467d8d81"
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dependencies:
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detect-gpu "^5.0.22"
gl-matrix "^3.4.3"
lodash.clonedeep "4.5.0"

"@cornerstonejs/dicom-image-loader@^1.2.4":
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dependencies:
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"@cornerstonejs/codec-libjpeg-turbo-8bit" "^1.2.2"
"@cornerstonejs/codec-openjpeg" "^1.2.2"
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pako "^2.0.4"
uuid "^9.0.0"

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dependencies:
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"@cornerstonejs/core" "^1.2.8"

"@cornerstonejs/tools@^1.2.4":
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dependencies:
"@cornerstonejs/core" "^1.2.4"
"@cornerstonejs/core" "^1.2.8"
lodash.clonedeep "4.5.0"
lodash.get "^4.4.2"

Expand Down