Documentation/Nightly/Modules/Colors - Revision history

Nicole: /* Categories */

2014-11-13T21:33:46Z

Categories

Nicole: /* Categories */

2014-11-13T21:29:59Z

Categories

Nicole: /* Categories */

2014-11-13T21:00:20Z

Categories

Nicole: /* Categories */

2014-11-13T20:35:03Z

Categories

Nicole at 20:31, 13 November 2014

2014-11-13T20:31:32Z

Nicole at 20:10, 14 November 2013

2013-11-14T20:10:37Z

Nicole at 20:07, 14 November 2013

2013-11-14T20:07:19Z

Nicole at 19:48, 14 November 2013

2013-11-14T19:48:57Z

Nicole at 19:44, 14 November 2013

2013-11-14T19:44:03Z

Nicole at 19:31, 14 November 2013

2013-11-14T19:31:36Z

@@ Line 200: / Line 200: @@
 | align="right" |
 [[Image:Slicer44-Colors-ContinuousDisplay.jpeg|thumb|280px|Continuous Display panel]]
 |-
+|

@@ Line 72: / Line 72: @@
 The colors are divided up into categories:
 * Discrete
 ** [[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
 * Continuous
-** [[image:ContinuousRedGreenBlue.png]] RedGreenBlue: A scale defined from -6.0 to 6.0 that maps to a rainbow from Red to Blue through green.
+** [[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
 ** [[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.
 **SPL-BrainAtlas-2009-ColorFile: an updated brain segmentation color node
 * User Generated: A user defined color table, use the editor to specify it
 ** Copies of other color tables get displayed in this category
 ** 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
 *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]]
-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 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 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}}
 {|style="width: 100%"
+|
-* Display panel:
+*'''Colors''': a drop down menu from which to select from the list of loaded color nodes
-**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 table to edit the color entrees as built-in color tables don't allow user editing.
+* '''Color Table Display panel:'''
 **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.
-**Lookup Range: Only change the display range, not the values in the table.
+**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:
 ***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.
 | align="right" |
-[[Image:Slicer4-Colors-Display.jpeg|thumb|280px|Display panel]]
+[[Image:Slicer44-Colors-ColorTableDisplay.jpeg|thumb|280px|Color Table Display panel]]
 |-
+|
-* Scalar Bar panel:
+* '''Scalar Bar panel:'''
 **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.
-***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.
 ***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.
 | align="right" |
-[[Image:Slicer4-Colors-ScalarBar.jpeg|thumb|280px|Scalar bar panel]]
+[[Image:Slicer44-Colors-ScalarBar.jpeg|thumb|280px|Scalar bar panel]]
 |}

← Older revision		Revision as of 21:00, 13 November 2014
Line 152:		Line 152:


−	\|[[Image:~~Slicer43~~-Colors-~~Tables~~.jpeg\|thumb\|280px\|Drop down menu showing current color tables]]	+	\|[[Image:Slicer44-Colors-Nodes.jpeg\|thumb\|280px\|Drop down menu showing current color tables]]
	\|}		\|}

@@ Line 113: / Line 113: @@
 ** [[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
-** [[image:ContinuousRedGreenBlue.tiff]] RedGreenBlue: A scale defined from -6.0 to 6.0 that maps to a rainbow from Red to Blue through green.
+** [[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
 ** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation

@@ Line 26: / Line 26: @@
+|
-The Colors Module manages color look up tables.
+The Colors Module manages MRML color nodes.
 Color look up tables are used by mappers to translate between an integer and a color value for display of models and volumes.
@@ Line 34: / Line 36: @@
 # Parametric tables, defined by an equation, such as the fMRIPA table.
 # Discrete tables, such as those read in from a file.
 <!--
 You can specify a directory from which to read color files using the Edit -> Application Settings window, Module Settings frame, in the User defined color file paths section. -->
-You can create a duplicate of a color table to allow editing the names, values and color by clicking on the [[image:Slicer43-Colors-FolderPlus.jpeg]] icon next to the drop down meny of color table nodes. You can then save the new color table via the File -> Save interface.
+You can create a duplicate of a color table to allow editing the names, values and color by clicking on the [[image:Slicer43-Colors-FolderPlus.jpeg]] icon next to the drop down menu of color table nodes. You can then save the new color table via the File -> Save interface.
 You can load a color table file from the File -> Add Data dialog.
 ===File format===
-The color file format is a plain text file with the .txt or .ctbl extension. Each line in the file has:
+The 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
@@ Line 55: / Line 59: @@
 tumor 255 128 0 255
   ...
 ===Custom LUTs===
@@ Line 102: / Line 112: @@
 ** [[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 colors, ramp of cool colors with variations in saturation that's complementary to WarmTint3
 * FreeSurfer
 ** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation
@@ Line 167: / Line 179: @@
+|
 * Display panel:
-**Color Tables: a drop down menu from which to select from the list of installed color look up tables.
+**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 table to edit the color entrees as built-in color tables don't allow user editing.
 **Number of Colors: the number of colors in the currently selected table.

@@ Line 192: / Line 192: @@
 ****shadow
 **'''Labels properties''' control the display of the scalar bar's label text, displayed along the length of the scalar bar.
-***Format: a string format that controls the number of digits in the values displayed as the scalar bar labels, uses [http://www.cplusplus.com/reference/cstdio/printf/ | standared C++ string format notation].
+***Format: a string format that controls the number of digits in the values displayed as the scalar bar labels, uses [http://www.cplusplus.com/reference/cstdio/printf/ standared C++ string format notation].
 ***Color: the color to use for the label text.
 ***Opacity: the opacity of the label text.

@@ Line 28: / Line 28: @@
 The Colors Module manages color look up tables.
-Color look up tables are used by mappers to translate between an integer and a colour value for display of models and volumes.
+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:
@@ Line 63: / Line 63: @@
 * Discrete
-** [[image:Discretelabels.png]] Labels: A legacy colour table that contains some anatomical mapping
+** [[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 colourful display of a label map
+** [[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:DiscreteIron.png]] Iron: A scale from red to  yellow, 157 colours, useful for
+** [[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:DiscreteDesert.png]] Desert: Red to yellow/orange scale, 256 colours, useful for
+** [[image:DiscreteDesert.png]] Desert: Red to yellow/orange scale, 256 colous.
-** [[image:DiscreteInvertedGrey.png]] InvertedGrey: A white to black scale, 256 colours, useful to highlight negative versions, or to flip intensities of signal values.
+** [[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 colourful display option, 256 colours going from purple to red
+** [[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: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 colours, useful to distinguish between a small number of labeled regions (especially outside of the brain)
+** [[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:DiscreteGreen.png]] Green: A green scale of 256 values, useful for layering with Magenta
@@ Line 81: / Line 81: @@
 ** [[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:DiscreteWarm1.png]] Warm1: A scale from yellow to red, of 256 colors, ramp of warm colours that's complementary to Cool1
+** [[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 colours, ramp of warm colours that's complementary to Cool2
+** [[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 colours, ramp of warm colours that's complementary to Cool3
+** [[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 colours, ramp of cool colours that's complementary to Warm1
+** [[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 colours, ramp of cool colours that's complementary to Warm2
+** [[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 colours that's complementary to Warm3
+** [[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.
 * 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: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 colours, ramp of warm colors with variation in value that's complementary to CoolShade3
+** [[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 colours, ramp of cool colours with variation in value that is complementary to WarmShade1
+** [[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 colours with variation in value that is complementary to WarmShade2
+** [[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 colours, ramp of cool colours with variation in value that is complementary to WarmShade3
+** [[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:
-** [[image:TintWarmTint1.png]] WarmTint1: A scale from white to red, 256 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint1
+** [[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 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint2
+** [[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 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint3
+** [[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 colours, ramp of cool colours with variations in saturation that's complementary to WarmTint1
+** [[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 colours, ramp of cool colours with variations in saturation that's complementary to WarmTint2
+** [[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 colours, ramp of cool colours 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
 * FreeSurfer
-** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer colour table, shows hot spots with high activation
+** [[image:FreeSurferHeat.png]] Heat: The Heat FreeSurfer color table, shows hot spots with high activation
-** [[image:FreeSurferBlueRed.png]] BlueRed: A FreeSurfer color scale, 256 colours, from blue to red
+** [[image:FreeSurferBlueRed.png]] BlueRed: A FreeSurfer color scale, 256 colors, from blue to red
-** [[image:FreeSurferRedBlue.png]] RedBlue: A FreeSurfer color scale, 256 colours, from red to blue
+** [[image:FreeSurferRedBlue.png]] RedBlue: A FreeSurfer color scale, 256 colors, from red to blue
-** [[image:FreeSurferRedGreen.png]] RedGreen: A FreeSurfer color scale, 256 colours, from red to green, used to highlight sulcal curvature
+** [[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 colours, from green to red, used to highlight sulcal curvature
+** [[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
 * PET
@@ Line 149: / Line 149: @@
 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 colours.
+* 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.
@@ Line 173: / Line 173: @@
 **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.
-***2nd Column: Color: a box showing the current colour. When viewing an editable table, double click on it to bring up a color picker.
+***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.
 ***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.
@@ Line 208: / Line 208: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-* The Volumes, Editor and Models modules use the colours to adjust the display properties for label map volumes and surface models
+* The Volumes, Editor and Models modules use the colors to adjust the display properties for label map volumes and surface models
 <!-- ---------------------------- -->