Cropping table - Revision history

Daniel Castaño: /* On several volumes */

2018-05-23T12:49:59Z

On several volumes

Daniel Castaño: /* Scaling cropping tables */

2018-04-03T13:40:15Z

Scaling cropping tables

Daniel Castaño: /* Scaling cropping tables */

2018-04-03T13:39:23Z

Scaling cropping tables

Daniel Castaño at 13:38, 3 April 2018

2018-04-03T13:38:47Z

Daniel Castaño: /* On several volumes */

2017-04-26T10:25:16Z

On several volumes

Daniel Castaño: /* Generation of cropping tables */

2017-04-26T10:24:21Z

Generation of cropping tables

Daniel Castaño: /* On several volumes */

2017-04-26T10:24:10Z

On several volumes

Daniel Castaño: /* On several volumes */

2017-04-26T10:22:18Z

On several volumes

Daniel Castaño: /* On a single volume */

2017-04-26T10:19:20Z

On a single volume

Daniel Castaño: /* On a single volume */

2016-04-27T12:04:12Z

On a single volume

@@ Line 23: / Line 23: @@
 === On several volumes ===
-You need provide a [[Tomogram-table map file| text file]] that maps the column 20 in the table with a tomogram file. Such a file is generated automatically when using the catalogue tools for cropping particles, but you can generate your won file manually.
+You need provide a [[Tomogram-table map file| text file]] that maps the column 20 in the table with a tomogram file. Such a file is generated automatically when using the catalogue tools for cropping particles, but you can generate your own file manually.
 == Generation of cropping tables==

← Older revision		Revision as of 13:40, 3 April 2018
Line 74:		Line 74:
	<tt>tFullCentered = dpktbl.centerCropPoints(tFullRaw); </tt>		<tt>tFullCentered = dpktbl.centerCropPoints(tFullRaw); </tt>

−	For each row in <tt>tFullCentered</tt> and <tt>tFullRaw</tt>, the total ''xyz'' position should be exactly the same. It means that the ''N''x3 matrices (''N'' being the number of particles) <tt>tFullCentered(:,4:6)+ tFullCentered(:24:26)</tt> and <tt>tFullRaw(:,4:6)+ tFullRaw(:24:26)</tt>, which express the 3d position of the particles, will be the same. The difference is that columns 24:26 in <tt>tFullCentered</tt> have been set to the semiinteger value closest to the ''xyz'' position of the particle. ~~The~~ shifts in columns 4:6 in <tt>tFullCentered</tt> will ~~consequently~~ have values ~~below~~ 0.5;	+	For each row in <tt>tFullCentered</tt> and <tt>tFullRaw</tt>, the total ''xyz'' position should be exactly the same. It means that the ''N''x3 matrices (''N'' being the number of particles) <tt>tFullCentered(:,4:6)+ tFullCentered(:24:26)</tt> and <tt>tFullRaw(:,4:6)+ tFullRaw(:24:26)</tt>, which express the 3d position of the particles, will be the same. The difference is that columns 24:26 in <tt>tFullCentered</tt> have been set to the semiinteger value closest to the ''xyz'' position of the particle. Notice that, in consequence, the shifts in columns 4:6 in <tt>tFullCentered</tt> will have values between -0.5 and 0.5;

@@ Line 55: / Line 55: @@
 A typical situation is the reuse of cropping tables generated for binned versions of tomograms to recrop particles on full sized (or less binned tomograms).
 For such a task, one needs to
- *first scale the coordinates. This includes the cropping positions in columns 24 to 26, but  also the shifts in positions 4 to 6. Including the shifts is crucial if the table expresses the result of an alignment project, as the final ''xyz'' position of the particles will be the addition of columns 24:26 to columns 4:6
+*first scale the coordinates. This includes the cropping positions in columns 24 to 26, but  also the shifts in positions 4 to 6. Including the shifts is crucial if the table expresses the result of an alignment project, as the final ''xyz'' position of the particles will be the addition of columns 24:26 to columns 4:6
- *then, balance the final positions of the centers, so that positions 24 to 26 contain ''semintegers'' positions.
+*then, balance the final positions of the centers, so that positions 24 to 26 contain ''semintegers'' positions.
 Both steps can be performed with simple matlab operations, or using the commands <tt>dynamo_table_rescale</tt> and  <tt>dpktbl.centerCropPoints</tt>.

← Older revision		Revision as of 13:38, 3 April 2018
Line 50:		Line 50:
	#: t = m.grepTable();		#: t = m.grepTable();
	</tt>		</tt>
		+
		+	== Scaling cropping tables==
		+
		+	A typical situation is the reuse of cropping tables generated for binned versions of tomograms to recrop particles on full sized (or less binned tomograms).
		+	For such a task, one needs to
		+	*first scale the coordinates. This includes the cropping positions in columns 24 to 26, but also the shifts in positions 4 to 6. Including the shifts is crucial if the table expresses the result of an alignment project, as the final ''xyz'' position of the particles will be the addition of columns 24:26 to columns 4:6
		+	*then, balance the final positions of the centers, so that positions 24 to 26 contain ''semintegers'' positions.
		+
		+	Both steps can be performed with simple matlab operations, or using the commands <tt>dynamo_table_rescale</tt> and <tt>dpktbl.centerCropPoints</tt>.
		+
		+	=== Example ===
		+
		+	Let's imagine you have a variable <tt>tBin2</tt> representing the results of a subtomogram averaging experiment performed on a tomogram called <tt>vBin2.mrc</tt>. This tomogram is the two-times binned version of the full resolution tomogram <tt>vFull.mrc</tt>. Now, you want to crop particles from <tt>vFull.mrc</tt> using the information in <tt>tBin2</tt>.
		+
		+	First, you rescale the table to the correct size. If <tt>vBin2.mrc</tt> is the result of binning <tt>vFull.mrc</tt> twice, it means that the physical sidelength of the voxels in <tt>vFull.mrc</tt> if '''four''' times smaller. Coordinates in <tt>tBin2</tt> must then be multiplied by four.
		+
		+	<tt>tFullRaw = dynamo_table_rescale(tBin2,'factor',2); </tt>
		+
		+	This command creates a variable <tt>tFullRaw</tt> in the workspace, with the same entries as <tt>tBin2</tt> except for columns 4 to 6 (shifts) and 24 to 26 (positions in tomogram).
		+
		+	Then, we redefine the positions in columns 24:26 to point to ''semiintegers'' coordinates, so that they point at the physical centers of voxels.
		+
		+	<tt>tFullCentered = dpktbl.centerCropPoints(tFullRaw); </tt>
		+
		+	For each row in <tt>tFullCentered</tt> and <tt>tFullRaw</tt>, the total ''xyz'' position should be exactly the same. It means that the ''N''x3 matrices (''N'' being the number of particles) <tt>tFullCentered(:,4:6)+ tFullCentered(:24:26)</tt> and <tt>tFullRaw(:,4:6)+ tFullRaw(:24:26)</tt>, which express the 3d position of the particles, will be the same. The difference is that columns 24:26 in <tt>tFullCentered</tt> have been set to the semiinteger value closest to the ''xyz'' position of the particle. The shifts in columns 4:6 in <tt>tFullCentered</tt> will consequently have values below 0.5;

@@ Line 23: / Line 23: @@
 === On several volumes ===
-You need provide a [[Tomogram-table map file| text file]] that maps the column 20 in the table with a tomogram file. Such a file is generated automatically when using the catalogue tools for cropping particles.
+You need provide a [[Tomogram-table map file| text file]] that maps the column 20 in the table with a tomogram file. Such a file is generated automatically when using the catalogue tools for cropping particles, but you can generate your won file manually.
 == Generation of cropping tables==

← Older revision		Revision as of 10:24, 26 April 2017
Line 32:		Line 32:

	Note that the list of tags inside {{t\|crop.tbl}} can be smaller that the tags originally in the input table: during the extraction procedure, some particles might be too close to the boundaries of the respective tomograms, and will not be cropped. Thus, it is always useful to use the produced {{t\|crop.tbl}} table to initialize an alignment project, as it contains the identities of the particles actually on the data folder.		Note that the list of tags inside {{t\|crop.tbl}} can be smaller that the tags originally in the input table: during the extraction procedure, some particles might be too close to the boundaries of the respective tomograms, and will not be cropped. Thus, it is always useful to use the produced {{t\|crop.tbl}} table to initialize an alignment project, as it contains the identities of the particles actually on the data folder.
−

	=== By the user ===		=== By the user ===

@@ Line 10: / Line 10: @@
 <tt>
-dtcrop <myVolumeFile>  <tableFile> sidelength <folderToBeCreated>;
+dtcrop <myVolumeFile>  <tableFile> <folderToBeCreated> <sidelength>;
 </tt>
@@ Line 16: / Line 16: @@
 <tt>
-dtcrop example.mrc  crop.tbl 64 data;
+dtcrop example.mrc  crop.tbl data 64;
 </tt>

@@ Line 7: / Line 7: @@
 === On a single volume ===
-Cropping particles from a volume in
+Cropping particles from a single volume is
 <tt>
-dtcrop <myVolumeFile> <tableFile> sidelength <folderToBeCreated>;
+dtcrop example.mrc  crop.tbl 64 data;
 </tt>
-look at  for the full syntax.
+look at {{docfunction|dynamo_table_crop|dtcrop}}  for the full syntax.
 === On several volumes ===