The Segment Read module is available as a part of Segment Volume package. The module is a Chimera extension module. To use this module, the Segment Menu module of the Segment Volume package is required. You will need the Chimera software package to use this module. The module interacts with Volume Viewer, a Chimera module for visualizing 3D volume data.
Segment Read uses Chimera's VolumeData data objects (see Volume Data module in Chimera) and reads volume data in different file formats.
Note: This version of the Segment Volume package is a pre-release version.
The module files are stored in the directory SegmentRead. To list the module under Chimera's Tools menu, add the directory - containing - the SegmentRead directory to Chimera's list of Tools.
To do so, open Chimera's main window, choose Perferences under Favorites menu, then choose the Tools category and then Add the directory - containing - the SegmentRead directory. This will list the tool under AIRS on the Tools menu.
To start the module from the Chimera menu, first you will need to ensure that the module is listed under Chimera's Tools menu. Then, click on Segment Read in the AIRS menu, under Chimera's Tools menu.
Alternatively, you can use the command line tool in Chimera's IDLE tool (under Programming tools on the Tools menu), and type:
>>> import SegmentRead
>>> SegmentRead.show_seg_read_dialog()
The Segment Read module currently supports all of Chimera's VolumeData data types, handled by the Volume Data module of Chimera.
Additional formats supported by the Segment Read module include the following:
The Segment Read dialog panel has two main sections. The first section is the Input data section. The Data file menu automatically lists available data regions in Chimera's Volume Viewer. To select a data set, simply pick an entry from this menu. The size of the data set in pixels is automatically displayed on the dialog, below the menu. If the data set is displayed in Chimera, then the Displayed value is set to Yes.
To open new models, click the Open button below the menu. This will open Chimera's Volume Viewer dialog and an Open file browser dialog. After adding the models, if the models are not listed on the data menu, click the Refresh menu button, next to the Open button on the Segment Read dialog.
Alternatively, you can directly open new models using Chimera's Volume Viewer. Once again, if the newly opened models are not displayed on the data menu, hit the Refresh menu button.
To read additional datat formats, pick the format from this section, and the click on the Open button next to the format name. This will open an Open file browser.
The file will be listed on the Input data menu of this dialog as well as the Volume Viewer data menu. If the file is not already displayed, use the Show button on the Volume Viewer dialog.
The Close button closes the Segment Read dialog. The Help button opens this help page.
The command line options can be used in Chimera's IDLE tool (under Programming tools on the Tools menu).
Volume data in Chimera is handled by the Volume Data module in Chimera, and is represented as a grid object. The grid object essentially contains the header info. To creata a VolumeData grid data object, simply type:
>>> import SegmentRead
>>> data = SegmentRead.rawiv_read.open_rawiv(path)
# RawIV data format
For further help, type:
>>> help(SegmentRead.rawiv_read.open_rawiv)
# RawIV data format
Volume data in Chimera is handled by the Volume Data module in Chimera, and is represented as a grid object. To open the file in Volume Viewer, simply type:
>>> import SegmentRead
>>> data, region = SegmentRead.rawiv_read.display_rawiv(path)
# RawIV data format
For further help, type:
>>> help(SegmentRead.rawiv_read.display_rawiv) # RawIV data format
Currently, only the RawIV input data format is supported.