# readAnalyze

### Synopsis

> The readAnalyze user macro reads Mayo Analyze data files and outputs a uniform field representing the volume of data.

> #### Parameters

> The following lists all of the parameters used by the readAnalyze user macro.

> Name | Type | Description | UI Control
> filename_in | string | name of Analyze file to read | Filename text box

> #### Output Ports

> Name | Type | Description
> out_fld | uniform field | read 3D volume
> out_obj | DataObject | directly renderable output object

### Description

> The readAnalyze macro reads a set of Mayo Analyze files and outputs a uniform field representing the data. The Analyze file format consists of at least two file. For the image named foo the files need by this module are foo.hdr and foo.img. This module reads the foo.hdr file and prints all the information from the header to the standard output. It then uses this information to read in the file foo.img and converts it into the appropriate uniform field.

> The output field is stretched in the z axis to account for the difference in the interslice resolution. The module performs byte swapping as appropriate so that it works correctly on little and big endian platforms. Volumes containing RGB or Complex data cannot be dealt with.

### Parameters

> filename_in

> The name of the file that should be read from. This parameter is of type string and can be specified through either a text-box or a file browser. If the file is not valid then module should correctly detect this and report the error that has occured.

### Output Ports

> out_fld

> The most primitive output field of the readAnalyze macro. This contains the generated 3D volume in the form of a uniform field. The field has node data of the type specified in the Analyze header file. The resultant field data is automatically stretched in the z axis to account for the difference in the interslice distance. This scaling should normally be correct. However it can be changed by altering the `out_points` array in the field object.

> out_obj

> The directly renderable output field of the readAnalyze macro. This contains a DataObject object that can be rendered by the standard data viewers. The DataObject is generated directly from the field data created from the Analyze image file.

### Utility Macros

> The User Macro readAnalyze uses the low-level module ReadAnalyzeFile. It also makes use of the ReadAnalyzeUI UI macro.

### Example

> An example application ReadAnalyzeEg is provided that reads a set of Analyze files and renders three orthoslices through the volume. A sample set of Analyze files, head.hdr and head.img, are provided with the distribution of this module.

### Files

> iac_proj/rd_anlyz/rdanmacs.v contains the readAnalyze User Macro, the ReadAnalyzeUI UI Macro, and the example application ReadAnalyzeEg V definitions.

### Other Notes

> The ReadAnalyzeMacs library inherits its process. As this library contains no procedural code, the process is not important.

> The ReadAnalyzeFile module was designed to work on a 32-bit system. In particular it assumes that the short variable type is 16 bits long, the int and float variable types are 32 bits long and the double variable type is 64 bits long. If this is not the case then it is unlikely that the data will be read correctly. Correcting this problem will require alterations to the `rd_anlyz.c` source code file.

> Information for this module was obtained from David Clunies Medical Image File Format web site, it can currently be accessed from:

> http://idt.net/~dclunie/medical-image-faq/html/index.html

> Analyze is the file format of the software produced by the Biomedical Imageing Resource Group at the Mayo Clinic/Foundation.

> http://www.mayo.edu/bir/

### Authors

>     Joanna Leng

### Modifications

>     Andrew Dodd

### Contact

>     International AVS Centre
>     Manchester Visualization Centre
>     Manchester Computing
>     University of Manchester
>     Oxford Road
>     Manchester
>     United Kingdom
>     M13 9PL

### See Also

> readAnalyze, ReadAnalyzeUI and ReadAnalyzeEg