Module: Extract Subvolume ()

Description:

This module can be attached to data objects providing a Lattice interface. The Lattice interface is designed to access large data sets in a block-by-block fashion on different resolution levels. However, many modules require data sets to be stored completely in memory. The Extract Subvolume modules makes is possible to use such modules by converting a subblock of a large volume into a traditional memory-resident data object.

You may select the subblock either by typing numbers in the ports or by using a dragger in the viewer. Additionally, it is possible to request a subsampled version of the data. Depending on the actual data object providing the Lattice interface lower resolution levels are stored on disk and might be accessed rather quickly or they are calculated on the fly, which might take some time. After selecting a subblock you should press the load button. A memory-resident data object is created and filled with the data from disk. All standard visualization techniques may now be applied on the subblock.

Press the Apply button to load the subblock. If you check the auto-refresh box, the subblock will be immediately reloaded once the selection has been modified. This is useful for interactively exploring a large volume.

Connections:

Data [required]
A data object providing a Lattice interface.

Time [optional]
Optional connection to a time object, only useful if the input object provides time-dependent data. If the port is connected to a time object the time of that object is used. In this way multiple modules with a time port can be synchronized.

Select ROI [optional]
This port allows you to select a ROI to select a subset to extract.
By using this port, draggers are hidden and the user cannot set manually Minimum, Size and Units ports. The Minimum and Size ports are set to ROI values and the Units port is set to global.

Ports:

Info

This port displays the size of the subblock to be loaded.

Dataset

If the input object provides multiple data sets this port allows you to select the data set to be converted into a memory-resident data object.

Timestep

If the input object provides time-dependent data, this port allows you to select the time step to be loaded.

Memory Info

Displays the memory amount to be extracted and the available system memory.

Units

This port allows you to select the coordinates system to apply on the box min and box size ports. By default, is set to lattice index coordinates system.

Minimum

This port is no longer displayed. However, it is still synchronized with the Box Min Units port in order to be able to load previously saved projects.

Minimum

The coordinates of the lower corner of the subblock. Depending on the coordinates system chosen using the Box Units port, these coordinates will be displayed as lattice indexes, global coordinates or local coordinates. Note that this port is only used for displaying the coordinates, it is not saved.

Size

This port is no longer displayed. However, it is still synchronized with the Box Size Units port in order to be able to load previously saved projects.

Size

The size of the subblock to be loaded. The size is in the same coordinates system as the Box Min Units port. The numbers will not change if you select subsampling but the real size of the subblock to be loaded will change. This is indicated in the Info port. Note that this port is only used for displaying the coordinates, it is not saved.

Set

Convenience buttons to use the maximum box size for the width, height and depth, respectively. Also enables the subsampling open to quickly load a coarse version of the whole volume.

Advanced

Options

Hides the dragger and/or enables subsampling.

Subsample

The number of voxels to be averaged in each dimension, if subsampling is enabled. If subsampling is used on a LDA dataset, only the minimal dimension factor will be editable. This is done because there is a limitation about LDA dataset. The factor must be the same on all dimensions not equal to 1 and it is capped by the maximal value for the minimal dimension.

Commands:

setInteractive
When the volume in input is large, there is a warning to cancel the computation. To disable this warning, call this command with 0.