CIBC:Documentation:SCIRun:Reference:MatlabInterface:InterfaceWithMatlab

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InterfaceWithMatlab

Information

Package: MatlabInterface
Category: Interface
Author(s): Jeroen Stinstra
Status: Supported in latest version
Version: 3.0

Description

Summary

Interactive InterfaceWithMatlab Interface: This module accomplishes a number of steps to integrate MATLAB code into SCIRun, (1) it translates a SCIRun object (field/matrix/nrrd) into a matlabarray and puts the object in the current workspace of matlab, (2) it executes MATLAB code that can be provided within the interface, (3) it translates back the matlabarrays in MATLAB's workspace into SCIRun objects.

Detailed Description

This module launches MATLAB as a separate process under control of SCIRun. The process can be on a remote machine or a local machine. In case the module is running on a remote machine the communication with matlab will be through sockets. In the latter case the entry fields in the middle panel of the GUI will need to be filled out with the IP address (it will automatically do a DNS lookup), the port number and a password. A password is only necessary for a remote MATLAB engine that is configured to require a password when launching MATLAB. The current implementation has an optional password in the matlabegine.rc, if this field is left empty no password check is done. The current implementation does not make use of secure sockets, this implementation is still under development. In order to run multiple MATLAB processes simultaneously different sessions can be launched. Each session on the same machine will share the global workspace in MATLAB and code is being executed sequentially for all modules making use of that session. Hence variables declared in the global workspace can be shared between these matlab modules.

Once matlab is launched the intro message will appear in the MATLAB OUTPUT window. The module needs to be executed in order to launch matlab, but will then remain active until the module is destroyed. Alternatively MATLAB can be launched from the InterfaceWithMatlabEngine Status panel in the right lower corner. It can be disconnected using the 'disconnect' button in the same panel. That the MATLAB process is kept alive between executions is done to smoothen the executing of matlab networks and as well to be able to store variables in matlab's workspace for later usage. However before the module is executed the translation table of SCIRun objects to matlab objects needs to be setup. This is accomplished by connecting the SCIRun object to one of the input ports on the module. Note that there are ports for Matrices, Fields and Nrrds. In the translation menu the Field section deals with the translation of fields, the Matrix section with the translation of Matrices and the Nrrd section with the translation of the nrrds. Each line in this translation table refers to one set of input and output ports. First of all the module will need to know how the object should be called in MATLAB, it is going to be a matlab array and thus needs to have a name. Then depending on the SCIRun object the object can be translated into structured arrays or numeric arrays, whose numeric format can be set as well. See the sections below for more details. Then at the end of the line the name of the matlab array that needs to be translated back into a SCIRun object. Here a name is sufficient as the translation process will do the rest. The name can be the same as the input array, but it might refer to another array as well.

The process of running code in MATLAB is accomplished as follows: SCIRun will translate the SCIRun objects into matlab compatible objects and write them in a file and then instructs matlab to read this file. Since all communication is through the stdin of matlab, using files makes sure that the data does not have to be written out in ASCII readable code. The module is smart enough to recognize that it translated objects before. If this is the case it will not do the translation again and it will use the file already generated. When loading data into matlab the objects that were already there with the same name will be overwritten. Subsequently the module will take the code the user entered in the GUI and wrap it in a 'try/catch' environment and execute it in matlab. All output generated on the stdout will be displayed in the module. It will write a tag of when the code starts executing as well one on when the code finished executing. These are markers for the module to keep track of when matlab finishes executing code. Please make sure that your progam does NOT generate output that resembles these markers as it will confuse the InterfaceWithMatlab Interface. Once the end marker is encountered, the module will instruct matlab to save the variables in the workspace so they can be read in by SCIRun.

The third window on the bottom will show the current status of the matlab engine. Note: when session 0 is requested a new session number will be assigned to the matlab process, which has not been used before. The new session number will appear in this status window. This option can be used to give each InterfaceWithMatlabInterface Module its own matlab process running in the background.

Local configuration

Before the module can be used, SCIRun needs to know how to run matlab on the local machine. This is accomplished by the configuration file 'matlabengine.rc', which will be created in the SCIRun/services directory in your local HOME directory. This file is copied out of the src tree the first time SCIRun is run. This file configures how matlab should be run. Edit the line 'startmatlab=' to instruct SCIRun how matlab should be started from an 'sh'-compatible shell. If matlab can already be found using the PATH settings in the shell launching SCIRun, this line probably does not need to be altered. All other fields in this file refer to running matlab on a remote machine. In case SCIRun will not be able to launch matlab a message will be displayed asking to check the configuration file.

To open a matlab process on the local machine the 'MATLAB ENGINE ADDRESS' in the GUI needs to have an empty Address and does not require a port. SCIRun will in this case automatically launch matlab locally. In the latter case no password checks are done. The local manager does support multiple sessions. To clarify the word session: a session is a matlab process. When multiple InterfaceWithMatlab modules make use of the same session the workspace in matlab is shared. Hence one module can be used to load a large matrix into matlab, whereas another one can be used to iterate over a process with small matrices, while using the big matrix stored by the first one. This will allow for some efficiency improvements.

Remote configuration

In order to run matlab on a different machine then SCIRun, a small server program needs to be run on the remote machine. The latter is called 'scirunremote', this program sets up a socket for listening and launches matlab when a request is made on its socket. This program uses the same 'matlabengine.rc' file as the module (though it will look in the local HOME directory of the remote machine). This configuration file can be used to set a password, restrict login to only certain machines in a certain domain. Currently the communication is over an open socket in the future an openssl implementation will be used for secure connections. In order to launch the scirunremote program, type 'scirunremote -port 5678', or which ever port you want to use. The latter program must be run on the remote system and serves as a daemon for starting all kinds of external programs. When launching this application a list of services will be displayed. For the matlab engine to work properly two services need to be switched on: matlabengine and matlabenginefiletransfer. The currently implementation requires the last one even if there is a shared home directory. In the latter case no files are transfered, and only the names of the directories in which temporary files are stored are exchanged. The latter mechanism will reduce the amount of network traffic and hopefully speed up the function of this module.


Configuration file

This section shortly lists the different options that can be set in the configuration file 'SCIRun/services/matlabengine.rc'

START MATLAB: This line describes how a sh-shell should start matlab. This instruction is executed to launch matlab

DISABLE: This will disable the matlabengine in scirunremote. The service cannot be launched and any request for starting the matlabengine will be denied.

PASSWORD: A simple password, as a first line of defense. Better ways will follow.

RHOSTS: A list of machines that are allowed to log into scirunremote to request the matlabengine service. This list should contain all the machines you want to use for running SCIRun. Any machine not on the list will be denied access. If no machine is listed all machines are welcome to log in.

MATLABTIMEOUT: How long should we wait before giving up. Note that matlab often needs a couple of minutes to startup. The time entered here is in seconds.


How to use the GUI

The three main panels of the GUI and what they represent

The GUI is subdivided into three mainparts. The top panel controls the translation from SCIRun objects into matlab objects and vice versa. The middle panel controls where the matlab engine is started and whether a matlab engine is shared with another InterfaceWithMatlab module. The lower panel displays the matlab code that needs to be executed and the output from matlab. The subdivision is shown in figure CROSS REFERENCE.

The SCIRun to matlab translation panel

The first panel configures the matlabconverter which is used to translate SCIRun objects into matlab objects and vice versa. This matlabconverter is the same as used by the modules MODULE REFERENCE, MODULE REFERENCE, MODULE REFERENCE, MODULE REFERENCE, MODULE REFERENCE, MODULE REFERENCE. The SCIRun objects are translated into matlab files which are stored in a temparory directory that is automatically generated and are subsequently read by matlab. For the translation back into SCIRun a similar mechanism is used which tells matlab to write out the results in matlab files and these files are subsequently loaded into SCIRun. The input options are the same as for the other modules: the first field on the left controls the name that an object has in matlab. This name has to be alphanumeric and needs to adhere to InterfaceWithMatlab's naming convention. When writing matlab code this name can be used to access the object. The second parameter in the list controls the data format used for the matlab objects, i.e. whether the data is written as doubles, floats, or ints; the third parameter controls what kind of object is created. For matrices and nrrd the most logical translation is a multi dimensional matrix, which is thence the default. All the properties and axis settings are lost in such a translation. Hence the option is offered to translate the SCIRun object into a structured array in which each field represents one of the dataelements stored in that SCIRun object. The documentation on which fieldnames are used and how the object is translated, can be found in the documentation of the individual modules doing this translation. A summary of how geometrical data is represented is given below. Concerning the output variables, only the name needs to be known. If the object is not compatible an error message will be generated in the error message GUI of module. This message will also explain why the object could not be translated.

GUI for determining where MATLAB should be run

The second panel tells SCIRun where to launch MATLAB. For a matlab engine on the local machine leave the Address field empty. For a remote engine enter the DNS or IP address of the remote server. The engine should support IPv6 addresses, although the support has not fully been tested. The second field is the port number for a remote matlab process. Currently the program scirunremote needs to be run on the remote side. This program will allow SCIRun to connect to this machine and run all kinds of remote applications. The program scirunremote needs to be run with a port number, this is the number that needs to be entered here. Optionally a password protection can be added. Currently the implementation of the password is a weak protection and will need some more adjustments in the future.

The fourth entry is a session number. Each matlabengine on a certain host is identified by a unique number. This number is stored by the program launching matlab (scirun on the local machine and scirunremote on the remote machine) and is used to see whether a session is already open. If multiple InterfaceWithMatlab modules refer to the same session, no new matlab engine will be opened in stead these modules will share the use of the matlab engine. If session '0' is used a new non existing session number will be assigned by the matlab engine.

The panel for running code in matlab

The lower panel contains there parts: the first for setting the code matlab needs to execute, the second for displaying matlab's output and the third for displaying the current status of the matlab engine. The code to be entered should assume that the matrices that have been created out of SCIRun objects already reside in the work space of matlab. In the code that maintains this absolute paths are used to ensure that the matrices can be found. The code will also be embedded in a try-catch statement to make sure that an end marker is generated even if the code crashes. All these measures to run code are hidden in the engine and the user should not worry about them for simple code. The code in that needs to be execute can be loaded and saved as well. So for more complex tasks the matlab code can be written in a different more userfriendly text editor. The extension of the filenames need to .m and are similar to matlab scripts. Please do not confuse these with functions. The latter will not work as functions need the input to be parsed to them. If a function call is desired, put the instruction that calls the function in the matlab code field and not the function code itself.

The second part of the lower panel contains the matlab output. It will display all the output generated by matlab. Currently, it can parse input as well, though that is limited to normal keystrokes. Simple commands may be given, but still the full functionality as found in a shell is not present yet. This latter feature is still experimental and will be expanded in future versions.

The third part of the lower panel, displays the current status of the matlab engine. The information stored here can be used for debugging and to see whether the matlab engine is running properly. The connection to matlab engine can be closed here as well and new connections can be made without the need of executing the module.


Translation of FIELDS

The following is an incomplete overview of the translation between SCIRun and MATLAB field objects. The following describes how fields are to be prepared in matlab for it to be used in SCIRun. The opposite process will be done for the input ports. Note that there one can specify whether one ones a structured or numerical matlab array. In case of numerical array only the data from the field is taken and the rest is thrown away. In case of a structured matlab array the data is fitted into a structure with the same fields as described below.

The following sections describe the fields of the structure matrix can be defined and are recognized by the module.


Unstructured Meshes

FIELDNAME .node (or .pts) This field is required for unstructured meshes and defines the position of the nodes within the mesh. This matrix should be a dense 3 by M matrix, where M is the number of nodes.

FIELDNAME .edge This field is required for curve meshes and defines the line elements in the mesh. This matrix should be a dense 2 by N matrix, where N is the number of line segments. The numbers in this mesh refer to the node positions in the NODE matrix. By default it is assumed that the numbering of nodes starts at one. However if one of the indices in this EDGE matrix is zero, a zero base is assumed.

FIELDNAME .face (or .fac) This field is required for surfaces meshes and defines the surface elements in the mesh. This matrix should be a dense 3 by N matrix for triangulated meshes and a 4 by N matrix for quadsurf meshes. Here N is the number of surface elements. The numbers in this mesh refer to the node positions in the NODE matrix. By default it is assumed that the numbering of nodes starts at one. However if one of the indices in this FACE matrix is zero, a zero base is assumed.

FIELDNAME .cell This field is required for volume meshes and defines the volume elements in the mesh. This matrix should be a dense 4 by N matrix for tetrahedral meshes, or a 6 by N matrix for prism shaped volume elements, or a 8 by N matrix for hexahedral elements. Here N is the number of volume elements. The numbers in this mesh refer to the node positions in the NODE matrix. By default it is assumed that the numbering of nodes starts at one. However if one of the indices in this CELL matrix is zero, a zero base is assumed.


Structured Meshes

FIELDNAMES x , y , AND z The fields X, Y, and Z form the description of a structured mesh. These fields are 1D, 2D, or 3D matrices defining the structured line, surface, or volume data. The connectivity of these meshes is defined by the position of the matrix, neighboring elements are connected. In this definition matrix X defines the x cartesian co-ordinate of each node, matrix Y the y cartesian co-ordinate and matrix Z the z cartesian co-ordinate. This kind of definition is compatible with MATLAB functions such as ndmesh() and sphere().


Structured regular Meshes

As structured matlab arrays:

FIELDNAME .dims This field describes the dimensions of the regular grid and is required for making a regular structured mesh. This field is a vector with 1, 2, or 3 elements describing the dimensions in each direction. Hence depending on this field the module creates a line, a surface, or a volume. This field is required for structured regular meshes.

FIELDNAME .transform This field describes a 4x4 matrix which defines an affine transformation, which is applied to the mesh. This matrix describes rotation, translation and scaling of each node in the regular mesh. This field is optional and does not need to be supplied. In case on transform matrix is defined a regular grid with spacing of 1 in each direction will be generated. [NEED TO ADD MORE DETAILS]

As regular dense matrices:

ImageFields and LatVolFields can be entered as well as dense matrices. A 2D matrix will be translated into an ImageField, and a 3D matrix will be translated into a LatVolField. When entering data as regular matrices, the data is assumed to be on the nodes and to be a scalar double field.

Note: The displaying dimensions between matlab and SCIRun are flipped, in matlab the first dimension is along the vertical axis, whereas in SCIRun it is along the horizontal axis. Depending on the application the data may need to be transposed, in order to make to obtain the proper vertical alignment.


Field Data

FIELDNAME .field A matrix specifying scalar/vector/tensor data for each node/element in the mesh. Each subsequent element in this vector is added to the next node/element in the field. Use the field FIELDLOCATION to specify where the data should be located. The module detects the type of data. The tensor and respectively the vector dimension is assumed to be the first one.

FIELDNAME .fieldtype A string specifying the type of data stored in field. Currently three value are accepted: 'scalar', 'vector', and 'tensor'. If this type information is omitted it defaults to 'scalar'

FIELDNAME .fieldat The location of the data. This field is a string describing where the data should be located. The default field location is assumed to be the nodes, meaning each node has a scalar, vector, or tensor value. In case the data is at the nodes, this field does not to be specified. This field is a string with the following options: "node", "edge", "face", or "cell". This field can be a number as well, which will describe the basis order of the element.

The way of specifying a field was different in version 1.22 of SCIRun. The modules still support input through the fields 'vectorfield', 'tensorfield', and 'scalarfield'. However to be compatible with future additions this has been changed to a combination of 'field' and 'fieldtype'. The new fieldwriters will use this convention instead of the old one.

The module will try to reconstruct data, for instance if a matrix is transposed, it will detect this and read the data properly. Most of the fields mentioned are optional and are not necessary. Only choose those fields from the list that are needed to describe your data. Currently not every field type supported by SCIRun is implemented in this module. Hopefully future versions will support more data types and have even less restrictive converters.


Example 1: preparing MATLAB file

The following lines of MATLAB code demonstrate how to structure a matrix for the use in SCIRun. Assuming that the nodes are specified in nodematrix and the connectivity of these nodes is specified in facematrix

>> geom.node = nodematrix 
>> geom.face = facematrix 

Opening the file with the InterfaceWithMatlabFieldsReader module will show that there is one data matrix called "geom" whose contents is a TRISURFMESH with no data on any of the node points

In case MATLAB is not available to structure the data, use the MODULE REFERENCE module to read a MATLAB matrix data directly and use the MODULE REFERENCE module to construct a Field out of the Nrrd object.


Example 2: Creating a structured mesh

The following lines of MATLAB code demonstrate the creation of a matlab file with the matlab logo on a structured mesh:

>> [X,Y,DATA] = peaks(100); 
>> field.x = X; 
>> field.y = Y; 
>> field.z = DATA; 
>> field.scalarfield = DATA; 

This will create a surface mesh in the shape of the peaks logo and uses the z value as its data values. Be sure to specify all the three cartensian coordinates, omitting one will result in the module not to recognise the mesh and it will not display the object in its selection box.


Exampe 3: Creating an unstructured mesh

The following lines of MATLAB code demonstrate the creation of a matlab field with an unstructured tessellated surface:

>> [X,Y,Z] = ndmesh(1:10,1:10,0); 
>> field.node = [X(:)'; Y(:)'; Z(:)']; 
>> field.face = delauney(X,Y); 
>> field.scalarfield = X(:).^2; 

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