Manual readimx 2.2.0

Overview

Reading all LaVision file formats: IMG/IMX, VEC/VC7, Set
Access to all data from the files
Organized data in a hierarchical structure
No data conversion/copying

Download

Download from our webpage: www.lavision.de
Requirements:
- Matlab 2024a or higher on Windows 11
- Matlab 2024a or higher on macOS 12 or higher

Installation

Unzip download in folder of your choice
On macOS the security policy doesn’t allow simply executing files downloaded from a third-party website. You have to open the terminal inside the folder and run the following command:

find . \( -name "*.mexmaca64" -o -name "*.mexmaci64" -o -name "*.dylib" \) -exec xattr -d com.apple.quarantine {} \;

If you forget do that, you’ll get the “library load disallowed by system policy” error and the system will suggest to move readimx to trash (please refuse).

Open Matlab and add the path to the search path:

>>addpath <MY_READIMX_PATH>

or use

>>pathtool

Buffer data model

The Matlab command

>> B=readimx('B00001.im7') % Reads an image from a file

loads an image file and creates a Buffer structure with two fields:

B=
    Frames: {[1x1 struct]}
    Attributes: {19x1 cell}

The field Frames is a cell array of frame structures and holds all frame data of the file.

The field Attributes is a cell array of attribute structures and holds all buffer attributes from the file.

Frame data model

The Matlab command

>>F=B.Frames{1} % Access 1. frame

returns a Frame structure with the following fields:

F=
    Components: {[1x1 struct]}
    Attributes: {13x1 cell}
    Scales: [1x1 struct]
    ComponentNames: {'PIXEL'}
    IsVector: 0
    Grids: [1x1 struct]

The field Components is a cell array of Component structures and holds the image or vector data.

The field Attributes is a cell array of Attribute structures and holds the frame attributes.

The field Scales is a structure holding the X, Y, Z, I scale information of the image or vector data.

The field ComponentNames is a cell array of names, giving the meanings of the components.

The field IsVector indicates whether the frame contains vector components or image planes.

The field Grids is a structure for grid spaces in X, Y, Z direction.

Component data model

The Matlab command

>>C=B.Frames{1}.Components{1} % Access 1. component of 1. frame

returns a Component structure with the following fields:

C=
    Scale: [1x1 struct]
    Planes: {[1152x896 uint16]}
    Name: 'PIXEL'

The field Scale is a Scale structure for intensity scaling of image or component data.

The field Planes is a cell array of Plane structures and holds the components data.

The field Name is the component name of this component.

Other data models

A Plane is a 2-dimensional data array containing data for image planes or vector components.

The Scale structure provides data for linear mapping plane data to physical quantities. It has the following fields: Slope, Offset, Unit, Description. The mapping is done by f(I) = A*I + B, with slope A and offset B. Unit and Description are simple strings.

The Attribute structure has two fields: Name, Value. The Name field is always a string and gives the attribute an identifier. The Value field holds the attribute data and has different type: double, string, array.

Scripts

File	Description
`showimx.m`	get a frame, display the data, return compiled data
`show2DVec.m`	get a frame, display the vectors, return compiled 2D vector data
`show3DVec.m`	get a frame, display the vectors, return compiled 3D vector data
`showPlane.m`	get plane and scales, display the image, return compiled 2D image data
`showVolume.m`	get plane and scales, display slices, return compiled 3D image data
`create2DVec.m`	get a frame, return compiled 2D vector data
`create3DVec.m`	get a frame, return compiled 3D vector data
`createPlane.m`	get plane and scales, return compiled 2D image data
`createVolume.m`	get plane and scales, return compiled 3D image data
`makeFrameInfo.m`	get frame, return frame information
`readimxdemo.m`	read demo files, display results

writeimx

A function for storing LaVision’s IM7/VC7 file format is added to the readimx package. The function is called writeimx and allows to store 2D/3D arrays and structs from the readimx (V.2) function.

Example usage:

>>A=rand(222,333)*1023;
>>V=rand(111,444,5)*1023;
>>S=readimx('testdata.vc7')
>>writeimx(uint16(A),'myimage.im7'); % writing a 2D image A
>>writeimx(uint16(V),'myvolume.im7'); % writing a 3D volume V
>>writeimx(S,'mystruct.vc7'); % writing a struct (with changed data fields) from the readimx function

The following data formats for plain image and volume data or in structs are supported:

Double
Single
UINT8
UINT16
UINT32
INT32

Sets

Since version 2.1.7, readimx allows the reading of buffer from set. The signature is extended to Set access and a new function for reading the number buffer in a Set.

Example:

>> n = lvsetsize('example.set'); % Get the number of buffers in a set
>> last = readimx('example.set',n); % Reads the last image of a set
>> showimx(last.Frames{1});  % Shows the image

Since version 2.1.8, readimx supports MultiSets. The function lvsetsize now returns two sizes (optional, the recent calling is still working).

The first one gives the number of images in a subset and the second one gives the number of subsets.

Example:

>> [n,m] = lvsetsize('example.set'); % Get the size of a (multi) set
>> last = readimx('example.set',n,m); % Reads the last image of a (multi) set
>> showimx(last.Frames{1});  % Shows the image