Operations on volumes - Revision history

Daniel Castaño at 09:45, 20 April 2017

2017-04-20T09:45:33Z

2017-04-19T11:44:32Z

Equivalent in Imod

2017-04-12T16:56:59Z

Flipping along a direction

2017-04-12T16:56:48Z

Equivalent in Imod

2017-04-12T16:55:09Z

Equivalent in Imod

2017-04-12T16:54:50Z

Functionalities

2017-04-12T14:50:23Z

2017-04-12T14:48:17Z

Flipping along a direction

2017-02-15T11:05:51Z

Flipping along a direction

2017-02-15T11:05:30Z

Flipping along a direction

← Older revision		Revision as of 09:45, 20 April 2017
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	== Advanced functions==		== Advanced functions==

−	A (somewhat) GUI version is available as the command {{t\|dvolume}}. The command line counterpart is {{docfunction\| dynamo_particle\|dparticle}}, which accepts several operators (binning, symmetrization, etc). The notation of the operators in {{t\|dparticle}} is the same used in other instances of ''Dynamo'' (normally under the name {{t\|actions}} or {{t\|particle actions}}) when volumetric transformations are operated on the fly. For instance when depicting the contents of [[data folder]]s with {{t\|ddbrowse}}.	+	A (somewhat complicated) GUI version is available as the command {{t\|dvolume}}. The command line counterpart is {{docfunction\| dynamo_particle\|dparticle}}, which accepts several operators (binning, symmetrization, etc). The notation of the operators in {{t\|dparticle}} is the same used in other instances of ''Dynamo'' (normally under the name {{t\|actions}} or {{t\|particle actions}}) when volumetric transformations are operated on the fly. For instance when depicting the contents of [[data folder]]s with {{t\|ddbrowse}}.

@@ Line 38: / Line 38: @@
 <tt>binvol -i original.mrc -o binned.mrc -b 4 </tt>
-would correspond to a binning factor of 2 in <tt>dbin</tt> (or any other binning tool inisde ''Dynamo'').
+would correspond to a binning factor of 2 in <tt>dbin</tt> (or any other binning tool inside ''Dynamo'').
 ===Normalization===

← Older revision		Revision as of 16:56, 12 April 2017
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	Also, you can use the ''Dynamo'' command {{t\|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.		Also, you can use the ''Dynamo'' command {{t\|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.
−

	=== Flipping two directions===		=== Flipping two directions===

@@ Line 67: / Line 67: @@
 ====Equivalent in Imod====
-Imod provides the <tt>flipyz</tt> option in its command for flipping files, with the syntax:
+For flipping tomograms, Imod provides the <tt>flipyz</tt> option in its command [http://bio3d.colorado.edu/imod/doc/man/clip.html clip], with the syntax:
 <tt>clip flipyz original.mrc flipped.mrc</tt>

@@ Line 34: / Line 34: @@
 ==== Equivalent in Imod ====
-Imod provides the <tt>binvol</tt> [ http://bio3d.colorado.edu/imod/doc/man/binvol.html command]. The binning factor follows a different convention. In Imod, the syntax:
+Imod provides the <tt>binvol</tt> [http://bio3d.colorado.edu/imod/doc/man/binvol.html command]. The binning factor follows a different convention. In Imod, the syntax:
 <tt>binvol -i original.mrc -o binned.mrc -b 4 </tt>

@@ Line 30: / Line 30: @@
 ===Binning===
-Command {{docfunction|dynamo_bin|dbin}}.
+Command {{docfunction|dynamo_bin|dbin}}. See also {{t|dpktomo.tools.flipYZ}} for larger volumes.
 ===Normalization===
@@ Line 56: / Line 64: @@
 === Flipping two directions===
-You can use the Matlab commad {{t|permute}} to interchange two directions in a volume.
+You can use the Matlab commad {{t|permute}} to interchange two directions in a volume. Take into account that this causes a swap of handedness.
 ====Equivalent in Imod====

@@ Line 54: / Line 54: @@
 Also, you can use the ''Dynamo'' command {{t|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.
 === Flipping two directions===
 You can use the Matlab commad {{t|permute}} to interchange two directions in a volume.
 ===Rotations and shifts===

← Older revision		Revision as of 14:48, 12 April 2017
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	Also, you can use the ''Dynamo'' command {{t\|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.		Also, you can use the ''Dynamo'' command {{t\|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.
		+
		+
		+	==== Equivalent in Imod ===
		+	Imod provides the flipyz option for flipping files, with the syntax:
		+	clip flipyz original.mrc flipped.mrc

	=== Flipping two directions===		=== Flipping two directions===

@@ Line 50: / Line 50: @@
 ===Flipping  along a direction===
-You can use the Matlab command {{t|flip}}. This requires using {{t|dread}} <tt>dread</tt> dread to bring the contents of a file into the Matlab workspace.
+You can use the Matlab command {{t|flip}}. This requires using {{t|dread}} to bring the contents of a file into the Matlab workspace.
 Also, you can use the ''Dynamo'' command {{t|dpktomo.tools.flipYZ}} to flip the contains of a file controlling the maximum amount of memory used as a given time.