Difference between revisions of "Documentation/Nightly/Modules/Colors"
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The Colors Module manages color look up tables. | The Colors Module manages color look up tables. | ||
− | Color look up tables are used by mappers to translate between an integer and a | + | Color look up tables are used by mappers to translate between an integer and a color value for display of models and volumes. |
Slicer supports three kinds of tables: | Slicer supports three kinds of tables: | ||
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* Discrete | * Discrete | ||
− | ** [[image:Discretelabels.png]] Labels: A legacy | + | ** [[image:Discretelabels.png]] Labels: A legacy color table that contains some anatomical mapping |
− | ** [[image:DiscreteFullRainbow.png ]] FullRainbow: A full rainbow of 256 colors, goes from red to red with all rainbow colors in between. Useful for | + | ** [[image:DiscreteFullRainbow.png ]] FullRainbow: A full rainbow of 256 colors, goes from red to red with all rainbow colors in between. Useful for colorful display of a label map. |
** [[image:DiscreteGrey.png]] Grey: A grey scale ranging from black at 0 to white at 255. Useful for displaying MRI volumes. | ** [[image:DiscreteGrey.png]] Grey: A grey scale ranging from black at 0 to white at 255. Useful for displaying MRI volumes. | ||
− | ** [[image:DiscreteIron.png]] Iron: A scale from red to yellow, 157 | + | ** [[image:DiscreteIron.png]] Iron: A scale from red to yellow, 157 colors. |
− | ** [[image:DiscreteRainbow.png]] Rainbow: Goes from red to purple, passing through the colors of the rainbow in between. Useful for a colorful display of a label map | + | ** [[image:DiscreteRainbow.png]] Rainbow: Goes from red to purple, passing through the colors of the rainbow in between. Useful for a colorful display of a label map. |
** [[image:DiscreteOcean.png]] Ocean: A lighter blue scale of 256 values, useful for showing registration results. | ** [[image:DiscreteOcean.png]] Ocean: A lighter blue scale of 256 values, useful for showing registration results. | ||
− | ** [[image:DiscreteDesert.png]] Desert: Red to yellow/orange scale, 256 | + | ** [[image:DiscreteDesert.png]] Desert: Red to yellow/orange scale, 256 colous. |
− | ** [[image:DiscreteInvertedGrey.png]] InvertedGrey: A white to black scale, 256 | + | ** [[image:DiscreteInvertedGrey.png]] InvertedGrey: A white to black scale, 256 colors, useful to highlight negative versions, or to flip intensities of signal values. |
− | ** [[image:DiscreteReverseRainbow.png]] ReverseRainbow: A | + | ** [[image:DiscreteReverseRainbow.png]] ReverseRainbow: A colorful display option, 256 colors going from purple to red |
** [[image:DiscretefMRI.png]] fMRI: A combination of Ocean (0-22) and Desert (23-42), useful for displaying functional MRI volumes (highlights activation) | ** [[image:DiscretefMRI.png]] fMRI: A combination of Ocean (0-22) and Desert (23-42), useful for displaying functional MRI volumes (highlights activation) | ||
** [[image:DiscretefMRIPA.png]] fMRIPA: A small fMRI positive activation scale going from red to yellow from 0-19, useful for displaying functional MRI volumes when don't need the blue of the fMRI scale. | ** [[image:DiscretefMRIPA.png]] fMRIPA: A small fMRI positive activation scale going from red to yellow from 0-19, useful for displaying functional MRI volumes when don't need the blue of the fMRI scale. | ||
− | ** [[image:DiscreteRandom.png]] Random: A random selection of 256 rgb | + | ** [[image:DiscreteRandom.png]] Random: A random selection of 256 rgb colors, useful to distinguish between a small number of labeled regions (especially outside of the brain) |
** [[image:DiscreteRed.png]] Red: A red scale of 256 values. Useful for layering with Cyan | ** [[image:DiscreteRed.png]] Red: A red scale of 256 values. Useful for layering with Cyan | ||
** [[image:DiscreteGreen.png]] Green: A green scale of 256 values, useful for layering with Magenta | ** [[image:DiscreteGreen.png]] Green: A green scale of 256 values, useful for layering with Magenta | ||
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** [[image:DiscreteCyan.png]] Cyan: A cyan ramp of 256 values, from black to cyan, complementary ramp to red, layering yeilds gray | ** [[image:DiscreteCyan.png]] Cyan: A cyan ramp of 256 values, from black to cyan, complementary ramp to red, layering yeilds gray | ||
** [[image:DiscreteMagenta.png]] Magenta: A magenta scale of 256 colors from black to magenta, complementary ramp to green, layering yeilds gray | ** [[image:DiscreteMagenta.png]] Magenta: A magenta scale of 256 colors from black to magenta, complementary ramp to green, layering yeilds gray | ||
− | ** [[image:DiscreteWarm1.png]] Warm1: A scale from yellow to red, of 256 colors, ramp of warm | + | ** [[image:DiscreteWarm1.png]] Warm1: A scale from yellow to red, of 256 colors, ramp of warm colors that's complementary to Cool1 |
− | ** [[image:DiscreteWarm2.png]] Warm2: A scale from green to yellow, 256 | + | ** [[image:DiscreteWarm2.png]] Warm2: A scale from green to yellow, 256 colors, ramp of warm colors that's complementary to Cool2 |
− | ** [[image:DiscreteWarm3.png]] Warm3: A scale from cyan to green, 256 | + | ** [[image:DiscreteWarm3.png]] Warm3: A scale from cyan to green, 256 colors, ramp of warm colors that's complementary to Cool3 |
− | ** [[image:DiscreteCool1.png]] Cool1: A scale from blue to cyan, 256 | + | ** [[image:DiscreteCool1.png]] Cool1: A scale from blue to cyan, 256 colors, ramp of cool colors that's complementary to Warm1 |
− | ** [[image:DiscreteCool2.png]] Cool2: A scale from magenta to blue, 256 | + | ** [[image:DiscreteCool2.png]] Cool2: A scale from magenta to blue, 256 colous, ramp of cool colors that's complementary to Warm2 |
− | ** [[image:DiscreteCool3.png]] Cool3: A scale from red to magenta, ramp of cool | + | ** [[image:DiscreteCool3.png]] Cool3: A scale from red to magenta, ramp of cool colors that's complementary to Warm3 |
** [[image:DiscreteRandomIntegers.png]] RandomIntegers: A random scale with 1000 entries. | ** [[image:DiscreteRandomIntegers.png]] RandomIntegers: A random scale with 1000 entries. | ||
* Shade: | * Shade: | ||
** [[image:ShadeWarmShade1.png]] WarmShade1: A scale from black to red, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade1 | ** [[image:ShadeWarmShade1.png]] WarmShade1: A scale from black to red, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade1 | ||
** [[image:ShadeWarmShade2.png]] WarmShade2: A scale from black to yellow, through green, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade2 | ** [[image:ShadeWarmShade2.png]] WarmShade2: A scale from black to yellow, through green, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade2 | ||
− | ** [[image:ShadeWarmShade3.png]] WarmShade3: A scale from black to green, of 256 | + | ** [[image:ShadeWarmShade3.png]] WarmShade3: A scale from black to green, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade3 |
− | ** [[image:ShadeCoolShade1.png]] CoolShade1: A scale from black to cyan, 256 | + | ** [[image:ShadeCoolShade1.png]] CoolShade1: A scale from black to cyan, 256 colors, ramp of cool colors with variation in value that is complementary to WarmShade1 |
− | ** [[image:ShadeCoolShade2.png]] CoolShade2: A scale from black to blue through purple, 256 colors, ramp of cool | + | ** [[image:ShadeCoolShade2.png]] CoolShade2: A scale from black to blue through purple, 256 colors, ramp of cool colors with variation in value that is complementary to WarmShade2 |
− | ** [[image:ShadeCoolShade3.png]] CoolShade3: A scale from black to magenta, 256 | + | ** [[image:ShadeCoolShade3.png]] CoolShade3: A scale from black to magenta, 256 colors, ramp of cool colors with variation in value that is complementary to WarmShade3 |
* Tint: | * Tint: | ||
− | ** [[image:TintWarmTint1.png]] WarmTint1: A scale from white to red, 256 | + | ** [[image:TintWarmTint1.png]] WarmTint1: A scale from white to red, 256 colors, ramp of warm colors with variation in saturation that's complementary to CoolTint1 |
− | ** [[image:TintWarmTint2.png]] WarmTint2: A scale from white to yellow, 256 | + | ** [[image:TintWarmTint2.png]] WarmTint2: A scale from white to yellow, 256 colors, ramp of warm colors with variation in saturation that's complementary to CoolTint2 |
− | ** [[image:TintWarmTint3.png]] WarmTint3: A scale from white to green, 256 | + | ** [[image:TintWarmTint3.png]] WarmTint3: A scale from white to green, 256 colors, ramp of warm colors with variation in saturation that's complementary to CoolTint3 |
− | ** [[image:TintCoolTint1.png]] CoolTint1: A scale from white to cyan, 256 | + | ** [[image:TintCoolTint1.png]] CoolTint1: A scale from white to cyan, 256 colors, ramp of cool colors with variations in saturation that's complementary to WarmTint1 |
− | ** [[image:TintCoolTint2.png]] CoolTint2: A scale from white to blue, 256 | + | ** [[image:TintCoolTint2.png]] CoolTint2: A scale from white to blue, 256 colors, ramp of cool colors with variations in saturation that's complementary to WarmTint2 |
− | ** [[image:TintCoolTint3.png]] CoolTint3: A scale from white to magenta, 256 | + | ** [[image:TintCoolTint3.png]] CoolTint3: A scale from white to magenta, 256 colors, ramp of cool colors with variations in saturation that's complementary to WarmTint3 |
* FreeSurfer | * FreeSurfer | ||
− | ** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer | + | ** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation |
− | ** [[image:FreeSurferBlueRed.png]] BlueRed: A FreeSurfer color scale, 256 | + | ** [[image:FreeSurferBlueRed.png]] BlueRed: A FreeSurfer color scale, 256 colors, from blue to red |
− | ** [[image:FreeSurferRedBlue.png]] RedBlue: A FreeSurfer color scale, 256 | + | ** [[image:FreeSurferRedBlue.png]] RedBlue: A FreeSurfer color scale, 256 colors, from red to blue |
− | ** [[image:FreeSurferRedGreen.png]] RedGreen: A FreeSurfer color scale, 256 | + | ** [[image:FreeSurferRedGreen.png]] RedGreen: A FreeSurfer color scale, 256 colors, from red to green, used to highlight sulcal curvature |
− | ** [[image:FreeSurferGreenRed.png]] GreenRed: A FreeSurfer color scale, 256 | + | ** [[image:FreeSurferGreenRed.png]] GreenRed: A FreeSurfer color scale, 256 colors, from green to red, used to highlight sulcal curvature |
** FreeSurferLabels: A color table read in from a text file, each line of the format: IntegerLabel Name R G B Alpha | ** FreeSurferLabels: A color table read in from a text file, each line of the format: IntegerLabel Name R G B Alpha | ||
* PET | * PET | ||
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The Colors module Dispay panel can be popped up as a stand alone widget and used to select colors in other modules of Slicer4. | The Colors module Dispay panel can be popped up as a stand alone widget and used to select colors in other modules of Slicer4. | ||
− | * The Models module uses it to select surface model | + | * The Models module uses it to select surface model colors. |
* The Volumes module uses it to select color maps for label map volumes to control which colors are used to display the scalar values at each voxel | * The Volumes module uses it to select color maps for label map volumes to control which colors are used to display the scalar values at each voxel | ||
* The Editor uses it to select colors with which to paint on label map volumes. | * The Editor uses it to select colors with which to paint on label map volumes. | ||
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**Table of currently selected colors: | **Table of currently selected colors: | ||
***1st Column: Index: the integer value giving the index of this color in the look up table, used to match it up with a scalar value in a volume voxel. | ***1st Column: Index: the integer value giving the index of this color in the look up table, used to match it up with a scalar value in a volume voxel. | ||
− | ***2nd Column: Color: a box showing the current | + | ***2nd Column: Color: a box showing the current color. When viewing an editable table, double click on it to bring up a color picker. |
***Label: the text description of the color, often an anatomical label. For some tables, the name is automatically generated from the RGBA values. | ***Label: the text description of the color, often an anatomical label. For some tables, the name is automatically generated from the RGBA values. | ||
***Opacity: a value between 0 and 1 describing how opaque this color is. The background color at index 0 is usually set to 0 and other colors to 1. | ***Opacity: a value between 0 and 1 describing how opaque this color is. The background color at index 0 is usually set to 0 and other colors to 1. | ||
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{{documentation/{{documentation/version}}/module-section|Similar Modules}} | {{documentation/{{documentation/version}}/module-section|Similar Modules}} | ||
− | * The Volumes, Editor and Models modules use the | + | * The Volumes, Editor and Models modules use the colors to adjust the display properties for label map volumes and surface models |
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Revision as of 19:44, 14 November 2013
Home < Documentation < Nightly < Modules < Colors
For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
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Module Description
The Colors Module manages color look up tables. Color look up tables are used by mappers to translate between an integer and a color value for display of models and volumes. Slicer supports three kinds of tables:
You can load a color table file from the File -> Add Data dialog. File formatThe color file format is a plain text file with the .txt or .ctbl extension. Each line in the file has: label name R G B A label is an integer, name a string, and RGBA are 0-255. File example: # Comments if the line start with # 0 air 0 0 0 0 1 bone 255 255 255 255 whatever after the Alpha value is discarded 2 tumor 255 128 0 255 ... Custom LUTsYou can create custom LUTs by creating a table with the colors on the wiki, saving to file and then loading them into Slicer. CategoriesThe colors are divided up into categories:
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Use Cases
The Colors module Dispay panel can be popped up as a stand alone widget and used to select colors in other modules of Slicer4.
- The Models module uses it to select surface model colors.
- The Volumes module uses it to select color maps for label map volumes to control which colors are used to display the scalar values at each voxel
- The Editor uses it to select colors with which to paint on label map volumes.
Tutorials
N/A
Panels and their use
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
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Similar Modules
- The Volumes, Editor and Models modules use the colors to adjust the display properties for label map volumes and surface models
References
N/A
Information for Developers
Section under construction. |