Particle extraction - Revision history

Daniel Castaño: /* Non-integer positions in tomogram */

2018-04-24T14:46:38Z

Non-integer positions in tomogram

Daniel Castaño: /* Non-integer positions in tomogram */

2018-04-24T14:46:28Z

Non-integer positions in tomogram

Daniel Castaño: /* Non-integer positions in tomogram */

2018-04-17T14:19:43Z

Non-integer positions in tomogram

Daniel Castaño: /* Extract from different tomograms */

2017-12-12T17:11:46Z

Extract from different tomograms

Daniel Castaño: /* Using the catalogue */

2017-12-12T17:07:53Z

Using the catalogue

Daniel Castaño: /* From the command line */

2017-05-02T08:52:20Z

From the command line

Daniel Castaño: /* Volume table index */

2017-04-26T10:20:27Z

Volume table index

Daniel Castaño: /* Extract from different tomograms */

2017-04-14T07:52:55Z

Extract from different tomograms

Daniel Castaño at 13:50, 2 March 2017

2017-03-02T13:50:16Z

Daniel Castaño: /* From the command line */

2017-02-23T15:03:56Z

From the command line

← Older revision		Revision as of 14:46, 24 April 2018
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	Tomogram positions in a [[cropping table\|table]] are indicated by the addition of columns 4 to 6 (shifts from physical [[Volume center\|subtomogram center]]) and 24 to 26 (position of the physical center of the subtomogram). These numbers are defined with respect to an origin (0,0,0) located on the bottom corner of the voxel of the tomogram pixel indexed as [1,1,1] (and centered at coordinate (0.5,0.5,0.5) in this system of coordinates ).		Tomogram positions in a [[cropping table\|table]] are indicated by the addition of columns 4 to 6 (shifts from physical [[Volume center\|subtomogram center]]) and 24 to 26 (position of the physical center of the subtomogram). These numbers are defined with respect to an origin (0,0,0) located on the bottom corner of the voxel of the tomogram pixel indexed as [1,1,1] (and centered at coordinate (0.5,0.5,0.5) in this system of coordinates ).

−		+	This convention, explained [[Volume_center#While_particle_cropping\| here]], ensures that particles are cropped ''without any interpolation'' from the original tomogram. The intensities of tomogram voxels will fill verbatim the voxels of the cropped particle. If the center of the central voxel of a particle does not correspond to the center of a voxel of a tomogram, the general policy in ''Dynamo'' is to register the distance between the two centers and store it as a "shift" in columns 4 to 6 of a table.
−	This convention, explained [[Volume_center#While_particle_cropping\| here]], ensures that particles are cropped ''without any interpolation'' from the original tomogram. The intensities of tomogram voxels will fill verbatim the voxels of the cropped particle. If the center of the central voxel of a particle does not correspond to the center of a voxel of a tomogram, the general policy in ''Dynamo'' is to register the distance between the two centers and store it as a "shift" in columns 4 to 6 of a table.

← Older revision		Revision as of 14:46, 24 April 2018
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	== Non-integer positions in tomogram ==		== Non-integer positions in tomogram ==

−	Tomogram positions in a [[cropping table\|table]] are indicated by the addition of columns 4 to 6 (shifts from physical [[Volume center\|subtomogram center]]) and 24 to 26 (position of the physical center of the subtomogram). This convention, explained [[Volume_center#While_particle_cropping\| here]], ensures that particles are cropped ''without any interpolation'' from the original tomogram. The intensities of tomogram voxels will fill verbatim the voxels of the cropped particle. If the center of the central voxel of a particle does not correspond to the center of a voxel of a tomogram, the general policy in ''Dynamo'' is to register the distance between the two centers and store it as a "shift" in columns 4 to 6 of a table.	+	Tomogram positions in a [[cropping table\|table]] are indicated by the addition of columns 4 to 6 (shifts from physical [[Volume center\|subtomogram center]]) and 24 to 26 (position of the physical center of the subtomogram). These numbers are defined with respect to an origin (0,0,0) located on the bottom corner of the voxel of the tomogram pixel indexed as [1,1,1] (and centered at coordinate (0.5,0.5,0.5) in this system of coordinates ).
		+
		+
		+	This convention, explained [[Volume_center#While_particle_cropping\| here]], ensures that particles are cropped ''without any interpolation'' from the original tomogram. The intensities of tomogram voxels will fill verbatim the voxels of the cropped particle. If the center of the central voxel of a particle does not correspond to the center of a voxel of a tomogram, the general policy in ''Dynamo'' is to register the distance between the two centers and store it as a "shift" in columns 4 to 6 of a table.

← Older revision		Revision as of 14:19, 17 April 2018
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	== Non-integer positions in tomogram ==		== Non-integer positions in tomogram ==

−	Tomogram positions ~~that~~ are ~~not integer are rounded off before cropping. Internally, this means that~~ columns 24 to 26 in the [[~~table~~]] are ~~rounded with~~ the ~~Matlab command <tt>round</tt>~~. ~~However,~~ the ~~created crop~~.~~tbl table will still contain~~ the ~~non-rounded double precision digits (in case~~ the ~~user needs them later for some reason).~~	+	Tomogram positions in a [[cropping table\|table]] are indicated by the addition of columns 4 to 6 (shifts from physical [[Volume center\|subtomogram center]]) and 24 to 26 (position of the physical center of the subtomogram). This convention, explained [[Volume_center#While_particle_cropping\| here]], ensures that particles are cropped ''without any interpolation'' from the original tomogram. The intensities of tomogram voxels will fill verbatim the voxels of the cropped particle. If the center of the central voxel of a particle does not correspond to the center of a voxel of a tomogram, the general policy in ''Dynamo'' is to register the distance between the two centers and store it as a "shift" in columns 4 to 6 of a table.
−
−	~~The reason for this policy is~~ to ~~ensure that subtomograms are extracted from~~ the ~~tomogram as cubes~~ of ~~voxels as originally defined in the~~ tomogram, ~~without any interpolation due~~ to ~~non-integer centering.~~
−
−	~~This has no effect when running alignment or classification projects. However, this~~ "~~mean half-pixel offset~~" ~~needs~~ to ~~taken into account when creating graphical depictions using the~~ table ~~to place the averages back into the tomograms~~.

@@ Line 31: / Line 31: @@
 You can use the coordinates picked in a set of tomogram to extract particles on a different set of tomograms. This can be done automatically using the  [[Viewing tomograms#Explicite volume pairs | catalogue]] to explicite pairs of tomograms, or you can do it manually using [[dtcrop]]:
-<tt> dtcrop <tomogram_table_map.doc> <mytable>  <outputfolder> <sidelength> </tt>
+ <tt> dtcrop <tomogram_table_map.doc> <tableForAllTomograms>  <outputfolder> <sidelength> </tt>
-You could create a table with the previous tomograms in the [[tomogram-table map file]] , and then edit the names of the tomogram files.
+You could create a table with the previous tomograms in the [[tomogram-table map file]] , and then edit the names of the tomogram files. If you use this option, the number that identifies the tomogram in <tt>tomogram_table_map.doc</tt> should match column 20 of the table.
 ==From the command line==

@@ Line 27: / Line 27: @@
 * a file called [[Tomogram-table map file | <tt>‎‎indices_column20.doc</tt>]] doc file with the full name of each tomogram coded by an integer in column 20 of <tt>crop.tbl</tt>
 * a file called <tt>‎‎indices_column21.doc</tt> with the full name of each model coded by an integer in column 21 of <tt>crop.tbl</tt>
 ===Extract from different tomograms ===

@@ Line 44: / Line 44: @@
 #: Here, the first argument of <tt>dtcrop</tt> is the name of a [[volume list file]], the second is the code word <tt>reorder</tt>.
 #: In this case, the volume list file contains all the cropping information in a text file: a list of tomogram files, and a list of models or tables to be used on each tomogram. For instance:
-#: <tt>dtcrop myfile.vll reorder 64 myDataFolder </tt>
+#: <tt>dtcrop myfile.vll reorder myDataFolder 64</tt>
 # A table  and a [[volume table index file]]
-#: T.B.I. In this case, the table stores explicitely the coordinates of the particles (cols 24 to 26), and in column 20 it stores an integer. The [[volume table index file]] is a text file that contains on each row an index and a tomogram file name
+#:  In this case, the table stores explicitely the coordinates of the particles (cols 24 to 26), and in column 20 it stores an integer. The [[volume table index file]] is a text file that contains on each row an index and a tomogram file name.
 ==On each model separately==

@@ Line 16: / Line 16: @@
 === Volume table index ===
 The [[volume table index file]] is generated when several tomograms have been used. It is generated inside the data folder with the name {{t|indices_column20.doc}} and its a text file with two columns. Each row is an integer number and a filename. The numbers are the ''tomogram number'' used in the column 20 of  the [[#Table|produced table]] {{t|crop.tbl}}. This file, jointly with the table, makes possible to track from which tomogram a particle has been cropped.
 ==Using the catalogue==

← Older revision		Revision as of 13:50, 2 March 2017
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	If you are working in <tt>dtmview</tt>, <tt>dtmslice</tt>, <tt>Montage</tt> or any other tomogram browser connected with the [[model pool]], you just need to select the model as the "actual" in the [[model pool]] menu tab (or right clicking on any point in the model), click on the <tt>update table points</tt> option and then on <tt> crop points on active model</tt>. This will bring you to the [[dtcrop GUI]] already pointing to the correct tomogram and to a temporary [[table]] containing the crop_points and <tt>crop_angles</tt> induces by your model.		If you are working in <tt>dtmview</tt>, <tt>dtmslice</tt>, <tt>Montage</tt> or any other tomogram browser connected with the [[model pool]], you just need to select the model as the "actual" in the [[model pool]] menu tab (or right clicking on any point in the model), click on the <tt>update table points</tt> option and then on <tt> crop points on active model</tt>. This will bring you to the [[dtcrop GUI]] already pointing to the correct tomogram and to a temporary [[table]] containing the crop_points and <tt>crop_angles</tt> induces by your model.
		+
		+
		+	== Non-integer positions in tomogram ==
		+
		+	Tomogram positions that are not integer are rounded off before cropping. Internally, this means that columns 24 to 26 in the [[table]] are rounded with the Matlab command <tt>round</tt>. However, the created crop.tbl table will still contain the non-rounded double precision digits (in case the user needs them later for some reason).
		+
		+	The reason for this policy is to ensure that subtomograms are extracted from the tomogram as cubes of voxels as originally defined in the tomogram, without any interpolation due to non-integer centering.
		+
		+	This has no effect when running alignment or classification projects. However, this "mean half-pixel offset" needs to taken into account when creating graphical depictions using the table to place the averages back into the tomograms.