BatchMake is a cross platform tool for batch processing of large amount of data. BatchMake can process datasets locally or on distributed systems using Condor.

Common Features:

BSD License
CMake like scripting langage
Distributed Scripting via Condor
Central remote website for online statistical analysis
User Interface using FLTK
Cross platform

BatchMake

List of available commands:

AppendFile Add a string to the end of a file
CloseTCPSocket Close a TCP/IP socket
DashboardExperiment Specify the encrypted name of the experiment to report on
DashboardHost Specify the hostname of the central database manager
DashboardNotify Specify the hostname of the central database manager
DashboardSend Send the results of a program to the central database for data collection
DeleteFile Delete a file on disk
Echo Print messages on the standard output
ExtractSlice Extract a slice from a 3D image volume
ExtractString Extract a string from a string chain
ForEach Create a "for" loop
GetParam Access directly a parameter from a sequence
If Defines a conditional statement
Inc Increment a number by a certain amount
Include Include another batchmake script
Int Convert a variable to integer
ListDirInDir List all the directories in a specified directory
ListFileInDir List all the files in a specified directory
OpenTCPSocket Open a TCP/IP socket
Randomize Create a random number
Run Execute a program in a thread
Sequence Create a sequence of numbers
Set Assign a value to a variable
SetApp Assign a variable to an Application defined by the Application Wrapper
SetAppOption Assign a value to a predefined option of a program
SendTCP Send a message via TCP socket
Sin Evaluate the sin() function
WriteFile Write variables into a file

How to use each command:

AppendFile - Add a string to the end of a file

AppendFile( <filename> <value1> <value2> ... )

The first parameter is the name of the file and all the others parameters will be added at the end of this file.

Example :

sequence(seq 1 3 1)
foreach(value ${seq})
appendFile('C:/bmtest.txt' 'value: ${value}\n')
endforeach(value)

This script will add the following strings at the end of the file entitled "C:/bmtest.txt" :

"value: 1"
"value: 2"
"value: 3"

CloseTCPSocket - Close a TCP/IP socket

CloseTCPSocket( <SocketName> )

Example :

CloseTCPSocket(MySocket)

DashboardExperiment - Specify the encrypted name of the experiment to report on

DashboardExperiment( <encryptedExperiment> )

The encryptedExperiment is given when creating a new experiment online (this requires a login/pass)

Example :

DashboardExperiment( 7YF04vELWW4m1B88t)

DashboardHost - Specify the hostname of the central database manager

DashboardHost( <hostname> )

Example :

DashboardHost(www.kitware.com)

DashboardNotify - Add a new string to the central database

DashboardNotify( <message> )

Example :

DashboardNotify('End of first experiment')

DashboardSend - Send the results of a program to the central database for data collection

DashboardSend( <methodid> <value1> <value2> )

Example :

DashboardSend(1,${value1},${value2})

DeleteFile - Delete a file on disk

DeleteFile( <filename> )

Example :

DeleteFile('myfile.txt')

Echo - Print messages on the standard output

Echo( <value1> <value2> ... )

Example :

sequence(seq 1 2 1)
sequence(seq2 1 2 1)
foreach(value ${seq})
foreach(value2 ${seq2})
Echo(value: ${value} ${value2})
endforeach(value2)
endforeach(value)

This script will print the following lines on the screen :

value: 1 1
value: 1 2
value: 2 1
value: 2 2

ExtractSlice - Extract a slice from a 3D image volume

ExtractSlice( <3D image filename> <2D image filename> <orientation> <slice> )

Example :

ExtractSlice('head.mha','slice.jpg',0,23)

This command extracts the saggital slice #23 from the volume head.mha and write the extracted slice to slice.jpg

ExtractString - Extract a string from a string chain

ExtractString( <output> <input> <lenght> [FROMEND] [KEEPEND] )

The parameter <output> will contain the <lenght> first characters of <input> if FROMEND is not set. With FROMEND the <lenght> last characters won't be copied. if KEEPEND is specified then the end of the string is returned.

Example :

set(example 'hello')
extractstring(result ${example} 1)
extractstring(result2 ${example} 2 FROMEND)
extractstring(result3 ${example} 2 KEEPEND)
extractstring(result4 ${example} 2 FROMEND KEEPEND) 
echo(${result})
echo(${result2})
echo(${result3})
echo(${result4})

This script will print the following lines on the screen :

h
hel
llo
lo

ForEach / EndForEach - Create a "for" loop

ForEach( <variable> <sequence> )

EndForEach( <variable> )

During the ith iteration, <variable> contains the ith parameter of <sequence>. The EndForEach command allows to define the end of the loop.

Example :

set(seq a b c d e f)
ForEach(letter ${seq})
echo(${letter})
EndForEach(letter)

This script will print the following lines on the screen :

a
b
c
d
e
f

GetParam - Access directly a parameter from a sequence

GetParam( <new variable> <sequence> <number> [<number2>] ... )

<number> corresponds to the argument of <sequence> to copy into <new variable>. We can copy as many arguments of <sequence> as we want adding at the end the rank of the argument in <sequence>.

Example :

sequence(seq 1 7 2)
echo(${seq})
GetParam(new1 ${seq} 0)
GetParam(new2 ${seq} 3)
echo(${new1})
echo(${new2})
GetParam(new ${seq} 0 2)
echo(${new})

This script will print the following lines on the screen :

If / EndIf - Defines a conditional statement=

If( <variable1> == or <= or >= or != <variable2> ) EndIf( <variable> )

Example :

set(var1 2)
set(var2 4)
If(${var1} <= ${var2})
echo(${var1} <= ${var2})
EndIf(${var1})

set(char1 test)
set(char2 test)
If(${char1} == ${char2})
echo(${char1} == ${char2})
EndIf(${char1})

This script will print the following lines on the screen :

2 <= 4
test == test

Inc Increment a number by a certain amount

Inc( <variable> <number> )

<variable> = <variable> + <number>

Example :

Set(value 2)
Inc(${value} 5)
echo(2 + 5 = ${value})

This script will print the following lines on the screen :

2 + 5 = 7.000000

Include - Include another batchmake script

Include( <ScriptFilename> )

Example :

#Script1 : F:\Script1.bms
echo('Script1')

#Script2 : F:\Script2.bms
echo('Script2')

#Script3 :
Include(F:\Script1.bms)
Include(F:\Script2.bms)

When we execute Script3 the following lines will be printed on the screen :

Script1
Script2

Int - Convert a variable to integer

Int( <variable> )

Example :

Set(value 2)
Inc(${value} 5)
Int(${value})
echo(2 + 5 = ${value})

This script prints the following lines on the screen:

2 + 5 = 7  ( instead of 7.000000 if we Int() is not used)

ListDirInDir - List all the directories in a specified directory

ListDirInDir( <dirlist> <directory> [ *.* ] )

<dirlist> contains the name of all the subdirectories included in <directory>. We can also list only the subdirectories with a specific string in their names : for instance if 'doc*' is added at the end of ListDirInDir only the subdirectories started wtih 'doc' will be listed.

Example :

Structure of the Hard Drive :
 F:\
    Example
         number1
         number2
         number3

set(dir F:\Example)
ListDirInDir(example ${dir})
echo(${example})

This script will print the following lines on the screen:

number1/ number2/ number3/

ListFileInDir - List all the files in a specified directory

ListFileInDir( <filelist> <directory> [ *.* ] )

<filelist> contains the name of all the files included in <directory>. We can also list only the files with a specific string in their names : for instance if *.txt' is added at the end of ListFileInDir only the files wtih the '.txt' extension will be listed.

Example :

Structure of the Hard Drive :
 F:\
    Example
        number1.txt
        number2.txt
        number3.txt

set(dir F:\Example)
ListFileInDir(example ${dir})
echo(${example})

This script will print the following lines on the screen:

number1.txt number2.txt number3.txt

OpenTCPSocket - Open a TCP/IP socket

OpenTCPSocket( <SocketName> <IPAddress> <Port> )

Example :

OpenTCPSocket(MySocket,10.0.0.1,8081)

Randomize - Create a random number

Randomize( <variable> <uniform | gaussian | categorical> <min> <max> )

<variable> contains the result. The distribtion can be set thanks to one of these 3 words : uniform, gaussian or categorical. The range an be set thanks to <min> and <max>.

Example :

Randomize(result uniform 0 1)
echo(${result})

This script will print on the screen a random number between 0 and 1 following a uniform distribution.

Run - Execute a program in a thread

Run( <output variable> <'program.exe param1 param2 ....'> )

The program called 'program.exe' will be launched with the parameters 'param1 param2' ... Note that the Application Wrapper can be used to defined the parameters as names.

Example :

Run( output 'MyProgram.exe -in input -out output' )

This script will run the program called MyProgram.exe with the parameters input and output.

BatchMake

Contents

BatchMake

List of available commands:

How to use each command:

AppendFile - Add a string to the end of a file

CloseTCPSocket - Close a TCP/IP socket

DashboardExperiment - Specify the encrypted name of the experiment to report on

DashboardHost - Specify the hostname of the central database manager

DashboardNotify - Add a new string to the central database

DashboardSend - Send the results of a program to the central database for data collection

DeleteFile - Delete a file on disk

Echo - Print messages on the standard output

ExtractSlice - Extract a slice from a 3D image volume

ExtractString - Extract a string from a string chain

ForEach / EndForEach - Create a "for" loop

GetParam - Access directly a parameter from a sequence

If / EndIf - Defines a conditional statement=

Inc Increment a number by a certain amount

Include - Include another batchmake script

Int - Convert a variable to integer

ListDirInDir - List all the directories in a specified directory

ListFileInDir - List all the files in a specified directory

OpenTCPSocket - Open a TCP/IP socket

Randomize - Create a random number

Run - Execute a program in a thread

Distributed Computing

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