Construction of masks - Revision history

Daniel Castaño: /* Combination of masks */

2017-09-14T09:58:09Z

Combination of masks

2017-09-14T09:57:55Z

Combination of masks

2017-09-14T09:57:27Z

Combination of masks

2016-05-19T11:47:55Z

Depicting mask overlays

2016-05-19T10:32:26Z

2016-05-19T10:26:23Z

By thresholding and smoothing

2016-05-19T10:22:52Z

By thresholding and smoothing

2016-05-19T10:16:01Z

Slide by slide

2016-05-19T10:08:36Z

Revolution solids

2016-05-19T10:03:32Z

@@ Line 85: / Line 85: @@
 The flag {{t|delete}} can be used to define parts of the final mask that need to be set to zero (black).
-   <nowiki % deletion
+ <nowiki> % deletion
 a = dynamo_sphere(60,128);
 b = dynamo_sphere(20,128);

@@ Line 77: / Line 77: @@
 Alternatively, you can use the compact syntax in {{t|dynamo_mask_combine}} on a cell array of masks defined independently.
-    <nowiki>% adds the different masks
+    <nowiki>% adds two different masks
-  a{1} = dynamo_sphere(20,128,[64,64,40]);
+a{1} = dynamo_sphere(20,128,[64,64,40]);
-  a{2} = dynamo_sphere(20,128,[64,64,80]);
+a{2} = dynamo_sphere(20,128,[64,64,80]);
- finalMask = dynamo_mask_combine(a);
+finalMask = dynamo_mask_combine(a);
 dview(finalMask)</nowiki>
@@ Line 86: / Line 86: @@
     <nowiki % deletion
-  a = dynamo_sphere(60,128);
+a = dynamo_sphere(60,128);
-  b = dynamo_sphere(20,128);
+b = dynamo_sphere(20,128);
- % deletes mask b from mask a
+% deletes mask b from mask a
-  finalMaskWithoutCenter = dynamo_mask_combine(a,'delete',b);
+finalMaskWithoutCenter = dynamo_mask_combine(a,'delete',b);
-  dview(finalMaskWithoutCenter)</nowiki>
+dview(finalMaskWithoutCenter)</nowiki>
 == Depicting mask overlays ==

@@ Line 75: / Line 75: @@
 It is easy to create combinations of masks using logical operators: {{t|or}} just "adds" masks.
-Alternatively, you can use the compact syntax in {{t|dynamo_mask_combine}} on a cell array of masks defined independently. The flag {{t|delete}} can be used to define parts of the final mask that need to be set to zero (black).
+Alternatively, you can use the compact syntax in {{t|dynamo_mask_combine}} on a cell array of masks defined independently.
 == Depicting mask overlays ==

← Older revision		Revision as of 11:47, 19 May 2016
Line 89:		Line 89:
	{{t\|ov}} or {{t\|overlay}} is the overlaying volume (in this case the just created file {{t\|mask.em}}), {{t\|ovas}} or {{t\|overlay_as}} indicates that the overlaying volume is to be understood as a solid mask (i.e., we are interested in showing the bright pixels in the mask as a solid color). You can choose color and transparency with {{t\|ovc}}/{{t\|overlay_color}} and {{t\| alpha}}.		{{t\|ov}} or {{t\|overlay}} is the overlaying volume (in this case the just created file {{t\|mask.em}}), {{t\|ovas}} or {{t\|overlay_as}} indicates that the overlaying volume is to be understood as a solid mask (i.e., we are interested in showing the bright pixels in the mask as a solid color). You can choose color and transparency with {{t\|ovc}}/{{t\|overlay_color}} and {{t\| alpha}}.

−	[[File:overlayed_mask_dslices.png\|thumb\|center\|~~300px~~\| Mask overlay with {{t\|dslices}}]]	+	[[File:overlayed_mask_dslices.png\|thumb\|center\|500px\| Mask overlay with {{t\|dslices}}]]

@@ Line 59: / Line 59: @@
 <tt> threshold = -0.003; </tt>
 <tt> mask(find(template<threshold))=1;  </tt>
 This procedure frequently needs some auxiliary steps like:

@@ Line 53: / Line 53: @@
 Create an all black cube:
-<tt> mask = zeros(size(template)) </tt>
+<tt> mask = zeros(size(template)); </tt>
-puts ones (mask is bright) on the pixels where the template has lowest values:
+puts ones (mask is bright) on the pixels where the template has lowest values, in this case below a predefined template:
 <tt> mask(find(template<threshold))=1;  </tt>

@@ Line 43: / Line 43: @@
 == By thresholding and smoothing==
-A mask can be defined to XXXXX
+A mask can be defined by thresholding the intensity of a given template.
 == Combination of masks ==

@@ Line 29: / Line 29: @@
 === Slide by slide ===
-You can edit a volume as a montage of orthoslices, and handdraw on each of them, or onto a selection of them an let ''Dynamo'' interpolate on the other sections:
+You can edit a volume as a montage of orthoslices, and handdraw on each of them, or onto a selection of them an let ''Dynamo'' interpolate on the other sections. This interpolation is purely geometrical and doesn't take the graymap into account.
 <tt>dpkvol.montage('template.em');</tt>
-Then choose the <tt>Mask</tt> tab to created a control for free handdraw of shapes on each slice. Secondary click on a drawn level will offer a menu of options, like interpolating between user-marked levels, or converting the current work into a cube.
+Then choose the <tt>Mask</tt> tab to created a control for free handdraw of shapes on each slice. It will appear as a small icon on the toolbar (see figure below). Secondary click on a drawn level will offer a menu of options, like interpolating between user-marked levels, or converting the current set of lines into a file.
 [[File:mask_handdraw_montage.png|thumb|center|300px| The blue square is the control for the handdrawn shape. Solid red are levels interpolated between the user-drawn light levels]]

@@ Line 19: / Line 19: @@
 Here, you would enclose an area on a 2d slice that includes the Z axis (i.e., a section from an X-view or a Z-view), and then let ''Dynamo'' rotate the area around the central Z axis to create a revolution solid.
-This can be done with {{t|dynamo_mapview}}.  Open your template, go to an X view, select one slice and press on [shift+S]. A second window will pop up, zooming into the selected slice. When you finish, the message area will tell you the name of the file containing the the created revolution solid.
+This can be done with {{t|dynamo_mapview}}.  Open your template, go to an X view, select one slice and press on [shift+S]. A second window will pop up, zooming into the selected slice. When you finish, the message area will tell you the name of the file containing the the created revolution solid, by default {{t|temp_drawn_revolution_mask.em}}.  You can secondary click on it to directly show in Chimera.
 [[File: mapview_select_slice_for_revolution.png|thumb|center|600px| Select a central section representing an x-view and click shift+S]]
 [[File: mapview_handdraw_slice_zoom.png|thumb|center|300px| Draw the line and click secondary click to close the line]]
 === Slide by slide ===