Difference between revisions of "Documentation/Nightly/Modules/Colors"
Line 72: | Line 72: | ||
The colors are divided up into categories: | The colors are divided up into categories: | ||
+ | {|style="width: 100%" | ||
+ | | | ||
* Discrete | * Discrete | ||
** [[image:Discretelabels.png]] Labels: A legacy color table that contains some anatomical mapping | ** [[image:Discretelabels.png]] Labels: A legacy color table that contains some anatomical mapping | ||
Line 113: | Line 115: | ||
** [[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 | ** [[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 | ||
* Continuous | * Continuous | ||
− | ** [[image:ContinuousRedGreenBlue.png]] RedGreenBlue: A scale defined from -6.0 to 6.0 that maps to a rainbow from | + | ** [[image:ContinuousRedGreenBlue.png]] RedGreenBlue: A scale defined from -6.0 to 6.0 that maps to a rainbow from red to blue through green. |
* FreeSurfer | * FreeSurfer | ||
** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation | ** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation | ||
Line 143: | Line 145: | ||
**LightPaleChartColors: A light pale palette from Stephen Few, useful for charts. | **LightPaleChartColors: A light pale palette from Stephen Few, useful for charts. | ||
**SPL-BrainAtlas-2009-ColorFile: an updated brain segmentation color node | **SPL-BrainAtlas-2009-ColorFile: an updated brain segmentation color node | ||
+ | * File | ||
+ | ** If you load a color file from File -> Add Data, it will appear here | ||
* User Generated: A user defined color table, use the editor to specify it | * User Generated: A user defined color table, use the editor to specify it | ||
** Copies of other color tables get displayed in this category | ** Copies of other color tables get displayed in this category | ||
** If you create a new color node, it will appear here | ** If you create a new color node, it will appear here | ||
− | |||
− | |||
*GenericAnatomyColors: a list of whole body anatomy labels and useful colors for them, the default for the Editor module creating new label map volumes | *GenericAnatomyColors: a list of whole body anatomy labels and useful colors for them, the default for the Editor module creating new label map volumes | ||
*Generic Colors: a list of colors with the names being the same as the integer value for each entry | *Generic Colors: a list of colors with the names being the same as the integer value for each entry | ||
Line 160: | Line 162: | ||
[[Image:Slicer43-Colors-3D.jpeg|thumb|300px|Colors]] | [[Image:Slicer43-Colors-3D.jpeg|thumb|300px|Colors]] | ||
− | The Colors module | + | The Colors module Color Table Display 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 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 | ||
Line 172: | Line 174: | ||
<!-- ---------------------------- --> | <!-- ---------------------------- --> | ||
{{documentation/{{documentation/version}}/module-section|Panels and their use}} | {{documentation/{{documentation/version}}/module-section|Panels and their use}} | ||
− | |||
− | |||
− | |||
{|style="width: 100%" | {|style="width: 100%" | ||
| | | | ||
− | * | + | *'''Colors''': a drop down menu from which to select from the list of loaded color nodes |
− | + | **[image:Slicer43-Colors-FolderPlus.jpeg]] Copy Color Node button: Duplicate the current color node to edit the color entries, built-in color nodes don't allow user editing. | |
− | **[image:Slicer43-Colors-FolderPlus.jpeg]] Copy Color Node button: Duplicate the current color | + | * '''Color Table Display panel:''' |
**Number of Colors: the number of colors in the currently selected table. | **Number of Colors: the number of colors in the currently selected table. | ||
**Hide empty Colors: When checked, hide the unnamed color entries in the list below. | **Hide empty Colors: When checked, hide the unnamed color entries in the list below. | ||
− | ** | + | **Scalar Range: The range of scalar values that are mapped to to the full range of colors. This only changes the display range, not the values in the table. |
**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. | ||
Line 190: | Line 189: | ||
***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. | ||
| align="right" | | | align="right" | | ||
− | [[Image: | + | [[Image:Slicer44-Colors-ColorTableDisplay.jpeg|thumb|280px|Color Table Display panel]] |
+ | |- | ||
+ | | | ||
+ | * '''Continuous Display Panel''' | ||
+ | ** For Slicer default nodes this panel is not editable, make a copy to inspect the color values by clicking on the circles that determine the points of the continuous function. Click elsewhere in the color display to add new points. | ||
+ | ** Point: the index of this point | ||
+ | ** Color box: click on this to edit the color for this point | ||
+ | ** Floating point number: the scalar value that maps to this color | ||
+ | |||
+ | | align="right" | | ||
+ | [[Image:Slicer44-Colors-ContinuousDisplay.jpeg|thumb|280px|Continuous Display panel]] | ||
|- | |- | ||
| | | | ||
− | * Scalar Bar panel: | + | * '''Scalar Bar panel:''' |
+ | **Use color names for labels: check this box if you wish to use the names of the colors for the labels in the scalar bar widget, uncheck if you wish to use the scalar values. | ||
**Display scalar bar: check this box if you wish to see a scalar bar in the 3d view that shows the range of colors for this color look up table. You can drag the widget around in the 3D window, it will resize and switch between horizontal and vertical alignments. | **Display scalar bar: check this box if you wish to see a scalar bar in the 3d view that shows the range of colors for this color look up table. You can drag the widget around in the 3D window, it will resize and switch between horizontal and vertical alignments. | ||
**'''Title properties''' control the display of the scalar bar's title text. | **'''Title properties''' control the display of the scalar bar's title text. | ||
− | ***Text: Title text, often showing the measurement units of mm. | + | ***Text: Title text with the color node name, often showing the measurement units of mm. |
***Color: the color to use for the title text. | ***Color: the color to use for the title text. | ||
***Opacity: the opacity of the title text. | ***Opacity: the opacity of the title text. | ||
Line 216: | Line 226: | ||
**Number of labels: how many labels to display along the length of the scalar bar. | **Number of labels: how many labels to display along the length of the scalar bar. | ||
| align="right" | | | align="right" | | ||
− | [[Image: | + | [[Image:Slicer44-Colors-ScalarBar.jpeg|thumb|280px|Scalar bar panel]] |
|} | |} | ||
Revision as of 21:29, 13 November 2014
Home < Documentation < Nightly < Modules < Colors
For the latest Slicer documentation, visit the read-the-docs. |
Introduction and Acknowledgements
| |||||||
|
Module Description
The Colors Module manages MRML color nodes. Color nodes can contain discrete color look up tables or procedurally defined color transfer functions. 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:
Color transfer functions are used to map scalar values, which can be integers or float/double numbers, into color values for display of models and volumes.
You can load a color table file from the File -> Add Data dialog. File formatThe color table 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 ... A procedurally defined color node has the file extension .txt (coming soon: an xm version with the extension .cxml). It defines a number of points in a color transfer function using the following format: position R G B position is a floating point number that defines the scalar range over which the mapping is valid. RGB are color values from 0.0 to 1.0. 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: Use CasesThe Colors module Color Table Display panel can be popped up as a stand alone widget and used to select colors in other modules of Slicer4.
TutorialsN/A Panels and their use
Similar Modules
ReferencesInformation for Developers
|