Prebinned tomograms - Revision history

Daniel Castaño: /* Through the catalogue */

2017-04-28T14:19:27Z

Through the catalogue

2017-02-23T17:05:56Z

Through the catalogue

2017-02-23T16:57:16Z

2017-02-23T16:57:03Z

2017-02-23T16:50:11Z

2017-02-23T16:47:28Z

2017-02-23T16:44:56Z

Use

2017-02-23T16:30:35Z

Creation

2017-02-23T16:20:50Z

Through the catalogue

2017-02-23T16:11:58Z

Through the catalogue

@@ Line 96: / Line 96: @@
 You need to secondary click on the <tt>index</tt> field of the tomogram inside the [[dcm GUI]]. If prebinned versions are avaialable, they will show. You can then click on the <tt>open with tmslice</tt> option for the binning factor that you wish.
-[[File:PrebinningSelectContextCatalogue.png|thumb|center|400px|BOpening the binning options]]
+[[File:PrebinningSelectContextCatalogue.png|thumb|center|400px|Opening the binning options]]
 ==== From the command line ====

← Older revision		Revision as of 17:05, 23 February 2017
Line 96:		Line 96:
	You need to secondary click on the <tt>index</tt> field of the tomogram inside the [[dcm GUI]]. If prebinned versions are avaialable, they will show. You can then click on the <tt>open with tmslice</tt> option for the binning factor that you wish.		You need to secondary click on the <tt>index</tt> field of the tomogram inside the [[dcm GUI]]. If prebinned versions are avaialable, they will show. You can then click on the <tt>open with tmslice</tt> option for the binning factor that you wish.

−	~~PrebinningSelectContextCatalogue~~
	[[File:PrebinningSelectContextCatalogue.png\|thumb\|center\|400px\|BOpening the binning options]]		[[File:PrebinningSelectContextCatalogue.png\|thumb\|center\|400px\|BOpening the binning options]]

@@ Line 1: / Line 1: @@
 Prebinned tomograms are files that contained binned versions of a tomogram. The filename of a prebinned tomogram must be derived from the original tomogram following a specific [[#convention | convention]].
-Prebinning the tomograms in a [[catalogue]] before starting to annotate them in [[dtmslice]] '''is strongly adviced''
+Prebinning the tomograms in a [[catalogue]] before starting to annotate them in [[dtmslice]] '''is strongly adviced'''.
 ==Motivation==

@@ Line 1: / Line 1: @@
-Prebinned tomograms are files that contained binned versions of a tomogram.
+Prebinned tomograms are files that contained binned versions of a tomogram. The filename of a prebinned tomogram must be derived from the original tomogram following a specific [[#convention | convention]].
 The filename of a prebinned tomogram must be derived from the original tomogram following a specific [[#convention | convention]]
 ==Motivation==
@@ Line 8: / Line 9: @@
 For this reason, it is frequently necessary to keep one or several binned versions of the same tomogram in disk. Some programs in ''Dynamo'' can use a prebinned tomogram as a proxy for the full defined tomogram, keeping track of all the coordinate coventions. The most used one is <tt>dtmslice</tt>. A tomogram with  original sidelengths of 4000 x 4000 x 800 pixels will probably make the interaction with <tt>dtmslice</tt>sluggish and inconvenient. It's more convenient to send to <tt>dtmslice</tt> a 2 times binned tomogram, with a sidelength of 1000x1000x200 pixels, which can be comfortably navigated. Annotations will be automatically kept in the scale of the original tomogram.
-===Quick access in viewers===
+===Better depiction===
 ===Storage considerations===

@@ Line 1: / Line 1: @@
 Big tomograms are difficult to fit in memory. Even if they fit, their visualization can be difficult inside browsers as [[dtmslice|<tt>dtmsice</tt>]], which load volumetric data in memory.
 For this reason, it is frequently necessary to keep one or several binned versions of the same tomogram in disk. Some programs in ''Dynamo'' can use a prebinned tomogram as a proxy for the full defined tomogram, keeping track of all the coordinate coventions. The most used one is <tt>dtmslice</tt>. A tomogram with  original sidelengths of 4000 x 4000 x 800 pixels will probably make the interaction with <tt>dtmslice</tt>sluggish and inconvenient. It's more convenient to send to <tt>dtmslice</tt> a 2 times binned tomogram, with a sidelength of 1000x1000x200 pixels, which can be comfortably navigated. Annotations will be automatically kept in the scale of the original tomogram.
 Storage of prebinned tomograms is normally not problematic in terms of disk space: a 2x binned tomogram has 64 times less voxels than the original one.

@@ Line 76: / Line 76: @@
 === In tmslice ===
 ==== Through the catalogue ====
 ==== From the command line ====
-=== With custom commands ===
+You can open the tomograms using the flag 'pb' or 'prebinned' to detail that you want the prebinned version. If not available, it will be computed on the fly:

@@ Line 41: / Line 41: @@
 [[File:PrebinningChangeParameters.png|thumb|center|400px|BOpening the binning options]]
- Your most important options are the slab size and the number of processors acting in parallel (called matlab workers).
+Your most important options are the slab size and the number of processors acting in parallel (called matlab workers). If the slab size is set to zero, then the size will be determined in runtime so as not to exceed the maximum number of Mb in memory. This number is indicated per processor.
 [[File:PrebinningParameters.png|thumb|center|400px|editing the binning options]]
@@ Line 60: / Line 59: @@
 ==== Dedicated tools ====
 ==== Generic tools ====
 == Use ==

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 The [[dcm GUI| catalogue GUI]] allows to select a binning factor that will be applied to all the tomograms in the catalogue.
 If you add new tomograms and then use this option later, by default the tomograms that were already prebinned won't be processed again.
-[[File:PrebinningCatalogueMenu.png|thumb|center|400px|Binning factors in the dcm GUI]]
+[[File:PrebinningCatalogueMenu.png|thumb|center|400px|Binning options in the dcm GUI]]
-The GUI allows to change the parameters used for the binning, mainly the slab size and the number of processors acting in parallel (called matlab workers).
+The GUI allows to change the parameters used for the binning:
 === Through dtmslice ===