Dipole set models - Revision history

Raffaele Coray at 12:58, 2 December 2024

2024-12-02T12:58:50Z

Daniel Castaño: /* Sets of vesicles */

2017-02-24T16:20:23Z

Sets of vesicles

Daniel Castaño: /* Walkthrough */

2017-02-23T11:08:57Z

Walkthrough

Daniel Castaño: /* Edition in dtmslice */

2017-02-23T11:05:42Z

Edition in dtmslice

Daniel Castaño: /* Walkthrough */

2017-02-23T11:05:08Z

Walkthrough

Daniel Castaño: /* Walkthrough */

2017-02-23T10:53:43Z

Walkthrough

Daniel Castaño: /* Walkthrough */

2017-02-23T10:49:49Z

Walkthrough

Daniel Castaño at 10:43, 23 February 2017

2017-02-23T10:43:20Z

Daniel Castaño at 10:35, 23 February 2017

2017-02-23T10:35:59Z

Daniel Castaño: /* Edition in dtmslice */

2017-02-22T17:11:43Z

Edition in dtmslice

← Older revision		Revision as of 12:58, 2 December 2024
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		+	[[Category:Walkthroughs]]
		+
	The <tt>dipole set</tt> model allows to gather sets of <tt>dipoles</tt>, each one being an assemble of 3d points called <tt>center</tt>,<tt>north</tt>, <tt>south</tt> and <tt>west</tt>. Not every point needs to be defined.		The <tt>dipole set</tt> model allows to gather sets of <tt>dipoles</tt>, each one being an assemble of 3d points called <tt>center</tt>,<tt>north</tt>, <tt>south</tt> and <tt>west</tt>. Not every point needs to be defined.

@@ Line 13: / Line 13: @@
 === Sets of vesicles ===
-Each dipole has four points available, which can be used with full flexibility as geometrical markers. We frequently use the <tt>north</tt> and the <tt>center</tt> to mark vesicular entities in a given tomogram (each dipole being a separate vesicle, and using a single <tt>dipole set<tt> model to encompass all the models). Some manipulation [[Vesicle_models#From_dipole_set_models | from the command line ]] allows then to create a real <tt>vesicle</tt> model for ach dipole in the dipole set model.
+Each dipole has four points available, which can be used with full flexibility as geometrical markers. We frequently use the <tt>north</tt> and the <tt>center</tt> to mark vesicular entities in a given tomogram (each dipole being a separate vesicle, and using a single <tt>dipole set</tt> model to encompass all the models). Some manipulation [[Vesicle_models#From_dipole_set_models | from the command line ]] allows then to create a real <tt>vesicle</tt> model for ach dipole in the dipole set model.
 == Edition in <tt>dtmslice</tt> ==

@@ Line 75: / Line 75: @@
   You can also click on [>], which moves a dipole up without the popup window. It just creates a message in the information window of <tt>dtmslice</tt>. You can always click on [?] to get a readout on which dipole number is the current one inside the dipole set.
-[[File:DipoleVesicleExampleNewDipolePopUp.png|thumb|center|400px|  Information window in <tt>dtmslice</tt> reports the number of the current dipole, i.e., the one in which the clicks on [c],[n],[s] and [w] will be assigned.]]
+[[File:DipoleVesicleExampleNewDipoleMessage.png|thumb|center|400px|  Information window in <tt>dtmslice</tt> reports the number of the current dipole, i.e., the one in which the clicks on [c],[n],[s] and [w] will be assigned.]]
 You can create now a new dipole. Note that now the current dipole number is two: this dipole appears represented with bigger marks, and with a selection mark (two floating squares).

← Older revision		Revision as of 11:05, 23 February 2017
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	The points on the currently dipole appear bigger than in the other dipoles. The current dipole has a green square selection mark, so that you can see it while it is ocluded by other elements in the scene (like the tomogram slice). A dipole that comprises the <tt>center</tt> and at least other point will be shown inside a transparent enclosing sphere. If this sphere shadows the dipole, you can secondary click on it and then press the option to hide the graphical depiction. When the enclosing sphere is not visible, you can secondary click on the dipole itself to delete it.		The points on the currently dipole appear bigger than in the other dipoles. The current dipole has a green square selection mark, so that you can see it while it is ocluded by other elements in the scene (like the tomogram slice). A dipole that comprises the <tt>center</tt> and at least other point will be shown inside a transparent enclosing sphere. If this sphere shadows the dipole, you can secondary click on it and then press the option to hide the graphical depiction. When the enclosing sphere is not visible, you can secondary click on the dipole itself to delete it.
−

	=== Select points in the current dipole ===		=== Select points in the current dipole ===

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 |}
-Ok, we solved the problem. Now, in order to proceed you need to click on [enter]. This will briefly announce with a popup window that a new dipole has been opened. You can also click on [>], which moves a dipole up without the popup window. It just creates a message in the information window of <tt>dtmslice</tt>. You can always click on [?] to get a readout on which dipole number is the current one inside the dipole set.
+Ok, we solved the problem. Now, in order to proceed you need to click on [enter]. This will briefly announce with a popup window that a new dipole has been opened.
-{|style="margin: 0 auto;"
+[[File:DipoleVesicleExampleNewDipolePopUp.png|thumb|center|400px|  Click on [enter] to force open a new dipole]]
-| [[File:DipoleVesicleExampleNewDipolePopUp.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
-| [[File:DipoleVesicleExampleNewDipoleMessage.png|thumb|center|400px| Set [C] back.]]
+ You can also click on [>], which moves a dipole up without the popup window. It just creates a message in the information window of <tt>dtmslice</tt>. You can always click on [?] to get a readout on which dipole number is the current one inside the dipole set.
-|}

@@ Line 65: / Line 65: @@
 {|style="margin: 0 auto;"
-| [[File:DipoleVesicleExampleHideSpheresMenu.png|thumb|center|300px|[ Hide sphere with menu option after secondary click on one sphere.]]
+| [[File:DipoleVesicleExampleHideSpheresMenu.png|thumb|center|300px| Hide sphere with menu option after secondary click on one sphere.]]
 | [[File:DipoleVesicleExampleHideSpheresScene.png|thumb|center|300px| Scene is free for clicking.]]
 | [[File:DipoleVesicleExampleNorth.png|thumb|center|300px| After clicking [C], dipole is restored.]]
@@ Line 73: / Line 73: @@
 {|style="margin: 0 auto;"
-| [[File:.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
+| [[File:DipoleVesicleExampleNewDipolePopUp.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
-| [[File:.png|thumb|center|400px| Set [C] back.]]
+| [[File:DipoleVesicleExampleNewDipoleMessage.png|thumb|center|400px| Set [C] back.]]
 |}

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 Consider a single tomogram containing several vesicles. We want to define a single dipole set model, and capture each vesicle as a different dipole, by picking the center of the vesicle, and then one point as the <tt>north</tt> of the dipole, which will later define the <tt>radius</tt> of the vesicle.
-[[File:VesiclePickGlobal.png|thumb|center|500px| A tomogram with several vesicles shown in <tt>dtmslice</tt>]]
+[[File:DipoleVesicleExampleScene.png|thumb|center|500px| A tomogram with several vesicles shown in <tt>dtmslice</tt>]]
 We create first a dipole set model, which automatically becomes active. Whenever the active model if of <tt>dipoleSet</tt> class, the keyboard shortcuts for dipole sets are working.
-[[File:VesiclePickGlobal.png|thumb|center|300px|  Selecting the creation of a new dipole set in <tt>dtmslice</tt>]]
+[[File:DipoleVesicleExampleSelection.png|thumb|center|300px|  Selecting the creation of a new dipole set in <tt>dtmslice</tt>]]
 We can then use [C] and [N] to mark the <tt>center</tt> and <tt>north</tt> points. The second one should create a transparent sphere enclosing the dipole.
 {|style="margin: 0 auto;"
-| [[File:VesicleClickMenuFitting.png|thumb|center|400px|[C] creates the <tt>center</tt> point in the current dipole.]]
+| [[File:DipoleVesicleExampleCenter.png|thumb|center|400px|[C] creates the <tt>center</tt> point in the current dipole.]]
-| [[File:VesicleClickMenuFittingDetail.png|thumb|center|400px|Addition of <tt>north</tt> with [N] creates a sphere.]]
+| [[File:DipoleVesicleExampleNorth.png|thumb|center|400px|Addition of <tt>north</tt> with [N] creates a sphere.]]
 |}
 New clicks on [C],[N],[S],or [W] will be referred to the '''current''' dipole. If you forget to open a new dipole and click one of them, you will just mess the dipole you just created. In this example, if you just click [C] on the center of the vesicle on the left, you will just move the current center.
-[[File:VesiclePickGlobal.png|thumb|center|300px|  Wrong: attempt to create a new dipole without creating one.]]
+[[File:.png|thumb|center|300px|  Wrong: attempt to create a new dipole without creating one.]]
 If something like this happens you need to move the point [C] to its right position. You may need to hide the transparent spheres for this, y secondary clicking on one sphere and then selecting the option.
 {|style="margin: 0 auto;"
-| [[File:VesicleClickMenuFitting.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
+| [[File:.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
-| [[File:VesicleClickMenuFittingDetail.png|thumb|center|400px| Set [C] back.]]
+| [[File:.png|thumb|center|400px| Set [C] back.]]
 |}
@@ Line 72: / Line 72: @@
 {|style="margin: 0 auto;"
-| [[File:VesicleClickMenuFitting.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
+| [[File:.png|thumb|center|400px|[ Hide sphere with menu option after secondary click on one sphere.]]
-| [[File:VesicleClickMenuFittingDetail.png|thumb|center|400px| Set [C] back.]]
+| [[File:.png|thumb|center|400px| Set [C] back.]]
 |}

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 === Select points in the current dipole ===
-* <tt>[c]</tt> creates or shifts the <tt>center</tt> point in the current dipole.
+* <tt>[c]</tt> creates or shifts the <tt>center</tt> point in the current dipole (cyan).
-* <tt>[n]</tt> creates or shifts the <tt>north</tt> point in the current dipole.
+* <tt>[n]</tt> creates or shifts the <tt>north</tt> point in the current dipole (blue).
-* <tt>[s]</tt> creates or shifts the <tt>south</tt> point in the current dipole.
+* <tt>[s]</tt> creates or shifts the <tt>south</tt> point in the current dipole (red).
-* <tt>[w]</tt> creates or shifts the <tt>west</tt> point in the current dipole.
+* <tt>[w]</tt> creates or shifts the <tt>west</tt> point in the current dipole (magenta).
 While you remain in the same dipole, pressing any of this keys will redefine the corresponding point.
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 ** It briefly shows a window announcing the label of the created dipole.
 * <tt>[?]</tt> Writes the labels of the dipoles that have been defined.