Data folder - Revision history

Daniel Castaño at 15:48, 30 September 2019

2019-09-30T15:48:28Z

2018-03-09T08:44:21Z

Typical operations on data folders

2018-03-09T08:43:46Z

Typical operations on data folders

2018-03-09T08:43:10Z

Averaging

2017-05-03T14:39:12Z

2017-05-03T14:37:02Z

2017-05-02T08:42:50Z

2016-05-02T08:29:45Z

2016-05-02T08:28:36Z

Deep check

2016-05-02T08:28:20Z

← Older revision		Revision as of 15:48, 30 September 2019
Line 1:		Line 1:
−	The data folder is the easiest way to store subtomograms.	+	The data folder is the easiest way to store subtomograms. Other formats are [[DBox folder \| dBoxes]] or [[Particle List File \| Particle List File]]

	A correctly formated data folder is the minimal input that the [[dcp GUI]] needs in order to create an alignment project.		A correctly formated data folder is the minimal input that the [[dcp GUI]] needs in order to create an alignment project.

@@ Line 54: / Line 54: @@
 Averaging all the particles in a data folder is frequently a useful sanity check to check that the contents of the mulitiple, noisy looking files do contain signal. This is specially useful when some apriori knowledge on the particles is available. The basic syntax is:
-  <tt> daverage <data> -t <mytable> -ws o </tt>
+  <tt> daverage <mydata> -t <mytable> -ws o </tt>
 which will save in the workspace variable <tt>o</tt> all the outputs of an average experiment.

@@ Line 54: / Line 54: @@
 Averaging all the particles in a data folder is frequently a useful sanity check to check that the contents of the mulitiple, noisy looking files do contain signal. This is specially useful when some apriori knowledge on the particles is available. The basic syntax is:
-  <tt> daverage <data> -t <table> -ws o <\tt>
+  <tt> daverage <data> -t <mytable> -ws o </tt>
 which will save in the workspace variable <tt>o</tt> all the outputs of an average experiment.

@@ Line 54: / Line 54: @@
 Averaging all the particles in a data folder is frequently a useful sanity check to check that the contents of the mulitiple, noisy looking files do contain signal. This is specially useful when some apriori knowledge on the particles is available. The basic syntax is:
-  <tt> daverage <data> -t <table> -ws o </tt>
+  <tt> daverage <data> -t <table> -ws o <\tt>
 which will save in the workspace variable <tt>o</tt> all the outputs of an average experiment.

@@ Line 19: / Line 19: @@
 ==Creating data folders==
 Data folders with the correct format are automatically created when cropping particles out of tomograms with ''Dynamo''.
 ==Inspecting data folders==

@@ Line 30: / Line 30: @@
 {{docfunction|dynamo_data_check|ddcheck}} is slower but more exhaustive. It reads each particle in the [[data folder]] to check coherence in dimensions or presence of corrupted pixels (NaN values). It also computes the mean and std values of each particle.
-=== Visualization of a individual particles ===
+=== Visualization of individual particles ===
 ====  Easy GUI: <tt>ddbrowse</tt> ====
@@ Line 44: / Line 44: @@
 === Normalization ===
 Normalization is not stricitly necessary for operating an alignment, as ''Dynamo'' will normalize the particles internally. However, you might want to normalize your data for visualization purposes.
 == Fourier Mask on particles==

@@ Line 2: / Line 2: @@
 A correctly formated data folder is the minimal input that the [[dcp GUI]] needs in order to create an alignment project.
 ==Basic Format==
@@ Line 35: / Line 34: @@
 ====  Easy GUI: <tt>ddbrowse</tt> ====
 {{docfunction|dynamo_data_browse| ddbrowse}}  is an easy-to-use browser. Many ''Dynamo'' GUIs link to it, and can also be initiated through the command line. Passing a [[data folder]] and a [[table]], one can see projections of a selected set of particles and check how they behave when they are aligned with the table. Secondary click on each particle will allow to visualize it through [[dview]] or [[dmapview]] or linked external tools like Chimera.
 ====  A complexer GUI: dgallery ====
 {{docfunction|dynamo_gallery| dgallery}} allows keeping in memory large sets of particles. This allows for quick visualization of the same area of sets of particles very quickly.
 <tt> dgallery </tt> is commonly used for [manual alignment]
 == Typical operations on data folders ==
@@ Line 47: / Line 44: @@
 === Normalization ===
 Normalization is not stricitly necessary for operating an alignment, as ''Dynamo'' will normalize the particles internally. However, you might want to normalize your data for visualization purposes.
 == Fourier Mask on particles==

@@ Line 29: / Line 29: @@
 === Deep check ===
-{{docfunction| dynamo_data_check|ddcheck}} is slower but more exhaustive. It reads each particle in the [[data folder]] to check coherence in dimensions or presence of corrupted pixels (NaN values). It also computes the mean and std values of each particle.
+{{docfunction|dynamo_data_check|ddcheck}} is slower but more exhaustive. It reads each particle in the [[data folder]] to check coherence in dimensions or presence of corrupted pixels (NaN values). It also computes the mean and std values of each particle.
 === Visualization of a individual particles ===

@@ Line 23: / Line 23: @@
 ==Inspecting data folders==
-Several tools are available for different levels of detail.
+Several tools are available for different check depths.
 === Quick check ===
-[http://{{SERVERNAME}}/w/doc/dynamo_data_browse.html <tt>ddinfo</tt>] checks if the contents of a folder are files with the correct naming convention, and reports their number and expected sidelength.
+{{docfunction|dynamo_data_info|ddinfo}} checks if the contents of a folder are files with the correct naming convention, and reports their number and expected sidelength.
 === Deep check ===
-[http://{{SERVERNAME}}/w/doc/dynamo_data_browse.html <tt>ddcheck</tt>] is slower but more exhaustive. It reads each particle in the [[data folder]] to check coherence in dimensions or presence of corrupted pixels (NaN values). It also computes the mean and std values of each particle.
+{{docfunction| dynamo_data_check|ddcheck}} is slower but more exhaustive. It reads each particle in the [[data folder]] to check coherence in dimensions or presence of corrupted pixels (NaN values). It also computes the mean and std values of each particle.
 === Visualization of a individual particles ===