Binning tomograms - Revision history

Daniel Castaño: /* Creating chunks */

2016-05-20T08:49:25Z

Creating chunks

2016-05-20T08:27:57Z

Binning tomograms for catalogue

2016-05-20T08:27:23Z

Binning tomograms for catalogue

2016-05-20T08:26:44Z

2016-05-19T16:43:58Z

Loading the full tomogram into memory

2016-05-19T16:35:34Z

Creating chunks

2016-05-19T16:35:02Z

Creating chunks

2016-05-19T16:31:49Z

Creating chunks

2016-05-19T16:31:09Z

2016-05-19T16:28:47Z

Creating chunks

@@ Line 27: / Line 27: @@
 An example of use is:
-  <tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','binned.mrc','slabSize',100);</tt>
+  <tt>o = dpktomo.partition.bin(myFile.mrc,2,'of','binned.mrc','slabSize',100);</tt>
 Here, {{t|slabSize}} determines that {{t|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels.  {{t|of}} determines the output file. This procedure can be accelerated using the flag {{t|mw}} to engage several Matlab workers in parallet. However, this will only make sense if the total  memory occupied by all the slabs simultaneously in memory in a given time fits in the RAM of the machine.
@@ Line 42: / Line 44: @@
 You can create them directly with the <tt>dpktomo.partition.bin</tt> command, by using the option {{t|cat}} on the {{t|outputFile}} flag:
-  <tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','cat','mb',1000);</tt>
+  <tt>o = dpktomo.partition.bin(myFile.mrc,2,'of','cat','mb',1000);</tt>

@@ Line 40: / Line 40: @@
 The [[Catalogue]] uses an [[Viewing_tomograms#Prebinned_tomograms |specific convention]] that allows to store for each catalogued tomogram a binned version (or several). This allows a quicker visualization.
- You can create them directly with the <tt>dpktomo.partition.bin</tt> command, by using the option {{t|cat}} on the {{t|outputFile}} flag;
+You can create them directly with the <tt>dpktomo.partition.bin</tt> command, by using the option {{t|cat}} on the {{t|outputFile}} flag:
-<tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','cat','mb',1000);</tt>
+ <tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','cat','mb',1000);</tt>

@@ Line 39: / Line 39: @@
 === Binning tomograms for catalogue ===
-The [[Catalogue]] uses an [[Viewing_tomograms#Prebinned_tomograms |specific convention]] that allows to store for each catalogued tomogram a binned version (or severals). You can create them directly with the <tt>dpktomo.partition.bin</tt> command, by using the option {{t|cat}} on the {{t|outputFile}} flag;
+The [[Catalogue]] uses an [[Viewing_tomograms#Prebinned_tomograms |specific convention]] that allows to store for each catalogued tomogram a binned version (or several). This allows a quicker visualization.
 <tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','cat','mb',1000);</tt>

← Older revision		Revision as of 08:26, 20 May 2016
Line 32:		Line 32:

	The extension of the output file needs to be {{t\|mrc}}. Target precision can be chosen with flag {{t\|type}} (i.e, can be set to {{t\|float}} or {{t\|double}}).		The extension of the output file needs to be {{t\|mrc}}. Target precision can be chosen with flag {{t\|type}} (i.e, can be set to {{t\|float}} or {{t\|double}}).
		+
		+	=== Controlling the size of the chunk===
		+
		+	You can use the flag {{t\|mb}} to set a maximum size in Megabytes for each slab. This is a comfortable way to create a chunk partition, as it does not require knowing a priori the size of the original tomogram.
		+
		+	=== Binning tomograms for catalogue ===
		+
		+	The [[Catalogue]] uses an [[Viewing_tomograms#Prebinned_tomograms \|specific convention]] that allows to store for each catalogued tomogram a binned version (or severals). You can create them directly with the <tt>dpktomo.partition.bin</tt> command, by using the option {{t\|cat}} on the {{t\|outputFile}} flag;
		+
		+	<tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','cat','mb',1000);</tt>

@@ Line 9: / Line 9: @@
   <tt> dread myVolume.mrc a </tt>
-reads the file {{t|myVolume.mrc}} into the variable {{t|a}}. For a volume (), it takes 6 minutes on a MacBookPro (i5), during which the computer is close to frozen.
+reads the file {{t|myVolume.mrc}} into the variable {{t|a}}. For a volume {{t|4k x 4k x 400}}, it takes 6 minutes on a MacBookPro (i5), during which the computer is close to frozen.
 After reading the full tomogram, you still need to bin it. You can do it with the command {{docfunction|dynamo_bin|dbin}}
@@ Line 15: / Line 15: @@
   <tt> b=dbin(a,2); </tt>
-... which will also take some time to complete.
+... which will also take 12 minutes to complete. You can then write the result as
 == Creating chunks ==

← Older revision		Revision as of 16:35, 19 May 2016
Line 28:		Line 28:
	Here, {{t\|slabSize}} determines that {{t\|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels. {{t\|of}} determines the output file. This procedure can be accelerated using the flag {{t\|mw}} to engage several Matlab workers in parallet. However, this will only make sense if the total memory occupied by all the slabs simultaneously in memory in a given time fits in the RAM of the machine.		Here, {{t\|slabSize}} determines that {{t\|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels. {{t\|of}} determines the output file. This procedure can be accelerated using the flag {{t\|mw}} to engage several Matlab workers in parallet. However, this will only make sense if the total memory occupied by all the slabs simultaneously in memory in a given time fits in the RAM of the machine.

−	The extension of the output file needs to be {{t\|mrc}}. Target precision can be chosen with flag {{t\|type}} (i.e, can be set to {{t\|float}})	+	The extension of the output file needs to be {{t\|mrc}}. Target precision can be chosen with flag {{t\|type}} (i.e, can be set to {{t\|float}} or {{t\|double}}).

@@ Line 26: / Line 26: @@
   <tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','binned.mrc','slabSize',100);</tt>
-Here, {{t|slabSize}} determines that {{t|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels.  {{t|of}} determines the output file. This procedure can be accelerated using the flag {{t|mw}} to engage several Matlab workers. However, this will only make sense if the total memory of
+Here, {{t|slabSize}} determines that {{t|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels.  {{t|of}} determines the output file. This procedure can be accelerated using the flag {{t|mw}} to engage several Matlab workers in parallet. However, this will only make sense if the total  memory occupied by all the slabs simultaneously in memory in a given time fits in the RAM of the machine.
-The extension needs to be {{t|mrc}}
+The extension of the output file needs to be {{t|mrc}}. Target precision can be chosen with flag {{t|type}} (i.e, can be set to  {{t|float}})

← Older revision		Revision as of 16:28, 19 May 2016
Line 24:		Line 24:
	An example of use is:		An example of use is:

−	<tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','binned.em','slabSize',100);</tt>	+	<tt>o = dpktomo.partition.bin(myFile.mrc,1,'of','binned.mrc','slabSize',100);</tt>
		+
		+	Here, {{t\|slabSize}} determines that {{t\|myFile.mrc}} will be read in vertical slabs, each one of 100 pixels. {{t\|of}} determines the output file
		+
		+	The extension needs to be {{t\|mrc}}