AIMS-specific file formats¶

`.ima` GIS volume format¶

Todo

to be continued…

`.mesh` surfacic mesh format¶

1. Introduction¶

This document describes the main format used by BrainVISA and Anatomist to represent surfaces (composed of polygons such as triangles) and segment set. The aimed audience is programmers who wish to generate surfaces and/or segments with their own software and use them with BrainVISA / Anatomist.

2. Syntax¶

The format description is written with the following elements. A field (written in bold) represent an element that can be split in other elements. All fields are described in section 4. In ascii mode fields can be separated by one or more space.

Characters strings are represented in verbatim between quotes. For example, ’string’ represent six ascii characters (each one coded on one byte).

3. Format description¶

A mesh file contains the following fields:

mode
textureType
polygonDimension
numberOfTimeSteps
timeSteps

4. Fields description¶

mode: The format can be written either as an ascii text file or as a binary file. The mode is used to identify the representation it can have three values:

’ascii’: the file is in text format.
’binarABCD’: the file is in binary format and uses big-endian byte order for numbers (such as Motorola or Sun processors for example).
’binarDCBA’: the file is in binary format and uses little-endian byte order for numbers (such as Intel processors for example).

textureType: The file format was created with the possibility to include a texture. But this is never used since textures are represented in a separate format. In ascii mode his field should always contain ’VOID’ or, in binary mode, a U32 containing 4 (which is the size of the following string) followed by the four characters ’VOID’.

polygonDimension: This field is a U32 containing the number of points of each polygon. The following values are supported in Anatomist and Aims:

3: Polygons are composed of three points (they are triangles). This is the recomanded value for surfaces because other values may not be supported by all BrainVISA processing tools.
4: Polygon are composed of four points. This is supported in Anatomist but may not be supported in every BrainVISA processing tools.
2: This value is used to represent segments in a 3D space. Each ”polygon” is composed of two 3D points.

numberOfTimeSteps: The mesh format can represent several meshes at different time steps. This is a U32 representing the number of time steps.

timeSteps: This field contains numberOfTimeSteps times the following structure:

instant: a U32 representing a time instant.
vectorOf<vertex>: contains all the vertices which are used to build polygons.
vectorOf<normal>: contains the normals of the surface at each vertex. It must have the same size as vectorOf<vertex> or be empty.
vectorOf<texture>: must be an empty vector (i.e a U32 containing 0).
vectorOf<polygon>: contains the polygons which represent the surface.

vertex: is 3D a point.

In ascii mode it has the following syntax: ’(’ FLOAT ’,’ FLOAT ’,’ FLOAT ’)’.
In binary mode it is represented by three FLOAT.

normal: is a normalized vector.

In ascii mode it has the following syntax: ’(’ FLOAT ’,’ FLOAT ’,’ FLOAT ’)’.
In binary mode it is represented by three FLOAT.

polygon: is a set of polygonDimension points. Each point is represented by a U32 which is an index in vectorOf<vertex>. The first vertex index is zero, the second is one, etc.

In ascii mode it has the following syntax: ’(’ U32 ’,’ U32 ’,’ … ’,’ U32 ’)’.
In binary mode it is represented by a series of polygonDimension elements of type U32.

U32: A 32 bits wide unsigned integer (between 0 and 4294967295).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

FLOAT: A 32 bits wide real number (maximum 3.40282347e+38).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

vectorOf<field>: where field is a field type. It represents a fixed length vector of elements of type field. It contains the size of the vector (i.e. the number of elements) as a U32 followed by the elements.

space: A byte with one of the ascii value for a space, a tabulation or a carriage-return.

5. Examples¶

Here is an example of an ascii mesh file containing a tetrahedron.

ascii
VOID
3
1
0
4 (-0.8,0.8,0) (0.8,8e-1,0) (-1,-1,0) (0,0,1)
4 (-0.8,0.8,0) (0.8,8e-1,0) (-1,-1,0) (0,0,1)
0
4 (0,1,2) (0,3,1) (1,3,2) (2,3,0)

Here is an example of an ascii mesh file containing a linear spiral.

ascii
VOID
2
1
0
16
(10, 0, 0) (7.07, 7.07, 0.4) (0, 10, 0.8)
(-7.07, 7.07, 1.2) (-10, 0, 1.6) (-7.07, -7.07, 2.0)
(0, -10, 2.4) (7.07, -7.07, 2.8) (10, 0, 3.2)
(7.07, 7.07, 3.6) (0, 10, 4.0) (-7.07, 7.07, 4.4)
(-10, 0, 4.8) (-7.07, -7.07, 5.2) (0, -10, 5.6)
(7.07, -7.07, 6.0)
0
0
15
(0,1) (1,2) (2,3) (3,4) (4,5) (5,6) (6,7) (7,8) (8,9)
(9,10) (10,11) (11,12) (12,13) (13,14) (14,15)

Additional example data can be found here.

`.tex` texture format¶

1. Syntax¶

The format description is written with the following elements. A field (written in bold) represent an element that can be split in other elements. All fields are described in section 3. In ascii mode fields can be separated by one or more space.

Characters strings are represented in verbatim between quotes. For example, ’string’ represent six ascii characters (each one coded on one byte).

2. Format description¶

A tex file contains the following fields:

mode
textureType
numberOfTimeSteps
timeSteps

3. Fields description¶

mode: The format can be written either as an ascii text file or as a binary file. The mode is used to identify the representation it can have three values :

’ascii’: the file is in text format.
’binarABCD’: the file is in binary format and uses big-endian byte order for numbers (such as Motorola or Sun processors for example).
’binarDCBA’: the file is in binary format and uses little-endian byte order for numbers (such as Intel processors for example).

textureType:

In ascii mode his field should contain the name of the texture type (’FLOAT’, ’S16’, ’U32’, ’POINT2DF’),
In binary mode, a U32 containing the size of the typename string followed by the string itself (’FLOAT’ etc).

numberOfTimeSteps: The texture format can represent several textures at different time steps. This is a U32 representing the number of time steps.

timeSteps: This field contains numberOfTimeSteps times the following structure :

instant: a U32 representing a time instant.
vectorOf<texture>: contains all the texture values, each associated to a mesh vertex (in the same order).

U32: A 32 bits wide unsigned integer (between 0 and 4294967295).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

S16: A 16 bits wide signed integer (between -32768 and 32767).

In ascii mode it is written as a decimal number. In binary mode it is represented on two bytes with the chosen byte order (see mode above).

FLOAT: A 32 bits wide real number (maximum 3.40282347e+38).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

vectorOf<field>: where field is a field type. It represents a fixed length vector of elements of type field. It contains the size of the vector (i.e. the number of elements) as a U32 followed by the elements.

POINT2DF: A POINT2DF is a couple of floating point numbers, ie 2 texture coords for a 2D texture. It is coded as a vector of two 32 bits wide real (FLOAT) numbers.

4. Example¶

Here is an example of an ascii tex file containing a 2D texture of 2 timesteps, for a mesh of 4 vertices.

ascii
POINT2DF
2
0
4 (-0.2,0.8) (0.8,8e-1) (-1,0) (0,0)
1
4 (-0.8,0.7) (0.7,-0.3) (-0.9,0.1) (0.2,0.3)

`.bck` “bucket” (voxels list) format¶

1. Introduction¶

This document describes the main format used by BrainVISA and Anatomist to represent a series of 3D voxel coordinates along with corresponding values. For historical reason this format is called bucket format. The aimed audience is programmers who wish to read or generate buckets files with their own software.

2. Syntax¶

The format description is written with the following elements. A field (written in bold) represent an element that can be splitted in other elements. All fields are described in section 4. In ascii mode fields can be separated by spaces.

Characters strings are represented in verbatim between quotes. For example, ’string’ represent six ascii characters (each one coded on one byte).

3. Format description¶

A bucket file contains the following fields:

mode
textureType
voxelSize
numberOfTimeSteps
timeSteps

4. Fields description¶

mode: The format can be written either as an ascii text file or as a binary file. The mode is used to identify the representation it can have three values:

’ascii’: the file is in text format.
’binarABCD’: the file is in binary format and uses big-endian byte order for numbers (such as Motorola or Sun processors for example).
’binarDCBA’: the file is in binary format and uses little-endian byte order for numbers (such as Intel processors for example).

dataType: The file format was created with the possibility to store several data types. However, in a single bucket file, all values must be of the same type. Recognized types are described below. The dataType field defines the data type.

In ascii mode his field contains ’-type’ followed by spaces and the data type name (see below).
In binary mode, it is a string containing the data type name.

voxelSize: Contains x, y, z and t voxel sizes.

In ascii it is ’-dx’ FLOAT ’-dy’ FLOAT ’-dz’ FLOAT ’-dt’ FLOAT.
In binary, it is four FLOAT.

numberOfTimeSteps: The bucket format can represent several series of coordinate/value at different time steps. numberOfTimeSteps contains the number of time steps.

In ascii mode, it is ’-dimt’ U32
In binary mode, it is a U32

timeSteps: This field contains numberOfTimeSteps times the following structure:

instant: A U32 representing a time instant.
In ascii: ’-time’ U32.
In binary: a U32

numberOfPoints: Number of (coordinate, value) pairs.

In ascii: ’-dim’ U32.
In binary: a U32

pointsAndValues: a series containing numberOfPoints times a coordinate value pair (space-separated in ascii mode).

coordinate: A 3D coordinate.

In ascii mode it has the following syntax: ’(’ S32 ’,’ S32 ’,’ S32 ’)’.
In binary it is three S32.

value: The content of this field depends on the value of dataType. See below.

U32: A 32 bits wide unsigned integer (between 0 and 4294967295).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

S32: A 32 bits wide signed integer (between -2147483648 and 2147483647).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

FLOAT: A 32 bits wide real number (maximum 3.40282347e+38).

In ascii mode it is written as a decimal number.
In binary mode it is represented on four bytes with the chosen byte order (see mode above).

string: * In ascii mode it is a serie of non-space ascii bytes * in binary mode it is a U32 containing the string size followed by the string content (ascii bytes series).

vectorOf<field>: where field is a field type. It represents a fixed length vector of elements of type field. It contains the size of the vector (i.e. the number of elements) as a U32 followed by the elements.

spaces: Valid only in ascii mode (in binary, a space can be considered as an empty string). One or more byte with one of the ascii value for a space, a tabulation or a carriage-return.

5. Data types¶

The field dataType defines the type of value associated to each coordinate. Here is a list of the possible values for dataType and the corresponding value structure.

VOID
FLOAT
DOUBLE
U32
S32
U16
S16
POINT2DF

6. Examples¶

Here should be an example of an ascii bucket file.

Todo

To be continued…

`.arg` graph format¶

Todo

To be continued…

`.hie` tree format¶

Todo

To be continued…

`.bundles` bundles / fibers format¶

Definition of curve bundles format (*.bundles) used in Brainvisa

1. Introduction¶

This document describes the main format used by brainvisa and anatomist to represent named sets of curves.

2. Format description¶

The bundle format is composed of two files. One human readable file with the extension .bundles and one data file with the extension .bundlesdata. The *.bundles file contains a generic header with the same format as *.minf files of brainvisa.

A *.bundles file contains the following fields :

format: (required): Format identifier. A format identifier uses the following pattern: <format_name>.<major_version>.<minor_version>. To date, bundles_1.0 value is required.
space_dimension: (optional, default = 3): Space dimension. Must be 3 for bundles_1.0.
curves_count: (required): Number of fibers in data file (required). Must be > 0 for bundles_1.0.
data_file_name: (optional, default = *.bundlesdata): File where to find the data. Must be *.bundlesdata for bundles_1.0.

A star (*) in the file name is replaced by the header file name without its extension. This file contains a series of curves. Each curve is a series of points. Each point is a series of space_dimension coordinates.

In ascii mode:

coordinate is a decimal number.
A point is space_dimension space-separated coordinates.
A curve is a comma separated series of points.
There is one and only one curve per line.

In binary mode:

A coordinate is a 8 bytes floating point number (a double in C or C++).
A point is the concatenation of space_dimension coordinates.
A curve is a 4 bytes integer representing the number of points and a series of points.

AIMS-specific file formats¶

`.ima` GIS volume format¶

`.mesh` surfacic mesh format¶

1. Introduction¶

2. Syntax¶

3. Format description¶

4. Fields description¶

5. Examples¶

`.tex` texture format¶

1. Syntax¶

2. Format description¶

3. Fields description¶

4. Example¶

`.bck` “bucket” (voxels list) format¶

1. Introduction¶

2. Syntax¶

3. Format description¶

4. Fields description¶

5. Data types¶

6. Examples¶

`.arg` graph format¶

`.hie` tree format¶

`.bundles` bundles / fibers format¶

1. Introduction¶

2. Format description¶

Table of Contents

Previous topic

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This Page

AIMS-specific file formats¶

.ima GIS volume format¶

.mesh surfacic mesh format¶

1. Introduction¶

2. Syntax¶

3. Format description¶

4. Fields description¶

5. Examples¶

.tex texture format¶

1. Syntax¶

2. Format description¶

3. Fields description¶

4. Example¶

.bck “bucket” (voxels list) format¶

1. Introduction¶

2. Syntax¶

3. Format description¶

4. Fields description¶

5. Data types¶

6. Examples¶

.arg graph format¶

.hie tree format¶

.bundles bundles / fibers format¶

1. Introduction¶

2. Format description¶

`.ima` GIS volume format¶

`.mesh` surfacic mesh format¶

`.tex` texture format¶

`.bck` “bucket” (voxels list) format¶

`.arg` graph format¶

`.hie` tree format¶

`.bundles` bundles / fibers format¶