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| BatchMake can process datasets locally or on distributed systems using Condor. | | BatchMake can process datasets locally or on distributed systems using Condor. |
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| Common Features:
| | = Documentation = |
| | *[[batchmake_install|Install BatchMake]] |
| | *[[batchmake_documentation|Functions]] |
| | *[[batchmake_grid|Grid]] |
| | *[[batchmake_faq|FAQ]] |
| | *[[batchmake_tutorial|Tutorial]] |
| | *[[MetaIO|MetaIO]] |
| | *[[batchmake_slicer|BatchMake in Slicer]] |
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| |
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| * BSD License
| | = Developers = |
| * CMake like scripting langage
| | *[[batchmake_developers|For Developers]] |
| * Distributed Scripting via Condor
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| * Central remote website for online statistical analysis
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| * User Interface using FLTK
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| * Cross platform
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| | |
| = BatchMake =
| |
| ==List of available commands:==
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| | |
| *'''''AppendFile''''' Add a string to the end of a file
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| *'''''CloseTCPSocket''''' Close a TCP/IP socket
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| *'''''DashboardExperiment''''' Specify the encrypted name of the experiment to report on
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| *'''''DashboardHost''''' Specify the hostname of the central database manager
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| *'''''DashboardNotify''''' Specify the hostname of the central database manager
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| *'''''DashboardSend''''' Send the results of a program to the central database for data collection
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| *'''''DeleteFile''''' Delete a file on disk
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| *'''''Echo''''' Print messages on the standard output
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| *'''''ExtractSlice''''' Extract a slice from a 3D image volume
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| *'''''ExtractString''''' Extract a string from a string chain
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| *'''''ForEach''''' Create a "for" loop
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| *'''''GetParam''''' Access directly a parameter from a sequence
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| *'''''If''''' Defines a conditional statement
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| *'''''Inc''''' Increment a number by a certain amount
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| *'''''Include''''' Include another batchmake script
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| *'''''Int Convert''''' a variable to integer
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| *'''''ListDirInDir''''' List all the directories in a specified directory
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| *'''''ListFileInDir''''' List all the files in a specified directory
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| *'''''OpenTCPSocket''''' Open a TCP/IP socket
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| *'''''Randomize''''' Create a random number
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| *'''''Run''''' Execute a program in a thread
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| *'''''Sequence''''' Create a sequence of numbers
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| *'''''Set''''' Assign a value to a variable
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| *'''''SetApp''''' Assign a variable to an Application defined by the Application Wrapper
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| *'''''SetAppOption''''' Assign a value to a predefined option of a program | |
| *'''''SendTCP''''' Send a message via TCP socket
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| *'''''Sin''''' Evaluate the sin() function
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| *'''''WriteFile''''' Write variables into a file
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| | |
| ==How to use each command:==
| |
| ===AppendFile - Add a string to the end of a file===
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| '''AppendFile( <filename> <value1> <value2> ... )'''
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| | |
| The first parameter is the name of the file and all the others parameters will be added at the end of this file.
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| '''Example :'''
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| sequence(seq 1 3 1)
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| foreach(value ${seq})
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| appendFile('C:/bmtest.txt' 'value: ${value}\n')
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| endforeach(value)
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| This script will add the following strings at the end of the file entitled "C:/bmtest.txt" :
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| "value: 1"
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| "value: 2"
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| "value: 3"
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| | |
| ===CloseTCPSocket - Close a TCP/IP socket===
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| '''CloseTCPSocket( <SocketName> )'''
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| | |
| '''Example :'''
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| CloseTCPSocket(MySocket)
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| | |
| ===DashboardExperiment - Specify the encrypted name of the experiment to report on===
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| '''DashboardExperiment( <encryptedExperiment> )'''
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| The encryptedExperiment is given when creating a new experiment online (this requires a login/pass)
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| | |
| '''Example :'''
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| DashboardExperiment( 7YF04vELWW4m1B88t)
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| | |
| | |
| ===DashboardHost - Specify the hostname of the central database manager===
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| '''DashboardHost( <hostname> )'''
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| '''Example :'''
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| DashboardHost(www.kitware.com)
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| | |
| ===DashboardNotify - Add a new string to the central database===
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| '''DashboardNotify( <message> )'''
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| | |
| '''Example :'''
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| DashboardNotify('End of first experiment')
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| | |
| ===DashboardSend - Send the results of a program to the central database for data collection===
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| '''DashboardSend( <methodid> <value1> <value2> )'''
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| | |
| '''Example :'''
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| DashboardSend(1,${value1},${value2})
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| | |
| | |
| ===DeleteFile - Delete a file on disk ===
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| '''DeleteFile( <filename> )'''
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| '''Example :'''
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| DeleteFile('myfile.txt')
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| | |
| | |
| ===Echo - Print messages on the standard output===
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| '''Echo( <value1> <value2> ... )'''
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| '''Example :'''
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| sequence(seq 1 2 1)
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| sequence(seq2 1 2 1)
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| foreach(value ${seq})
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| foreach(value2 ${seq2})
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| Echo(value: ${value} ${value2})
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| endforeach(value2)
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| endforeach(value)
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| This script will print the following lines on the screen :
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| value: 1 1
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| value: 1 2
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| value: 2 1
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| value: 2 2
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| | |
| | |
| ===ExtractSlice - Extract a slice from a 3D image volume===
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| '''ExtractSlice( <3D image filename> <2D image filename> <orientation> <slice> )'''
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| '''Example :'''
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| ExtractSlice('head.mha','slice.jpg',0,23)
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| This command extracts the saggital slice #23 from the volume head.mha and write the extracted slice to slice.jpg
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| | |
| | |
| ===ExtractString - Extract a string from a string chain===
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| '''ExtractString( <output> <input> <lenght> [FROMEND] [KEEPEND] )'''
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| 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.
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| | |
| '''Example :'''
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| set(example 'hello')
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| extractstring(result ${example} 1)
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| extractstring(result2 ${example} 2 FROMEND)
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| extractstring(result3 ${example} 2 KEEPEND)
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| extractstring(result4 ${example} 2 FROMEND KEEPEND)
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| echo(${result})
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| echo(${result2})
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| echo(${result3})
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| echo(${result4})
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| This script will print the following lines on the screen :
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| h
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| hel
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| llo
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| lo
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| | |
| | |
| ===ForEach / EndForEach - Create a "for" loop===
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| '''ForEach( <variable> <sequence> )'''
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| '''EndForEach( <variable> )'''
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| During the ith iteration, <variable> contains the ith parameter of <sequence>. The EndForEach command allows to define the end of the loop.
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| '''Example :'''
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| set(seq a b c d e f)
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| ForEach(letter ${seq})
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| echo(${letter})
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| EndForEach(letter)
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| This script will print the following lines on the screen :
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| a
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| b
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| c
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| d
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| e
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| f
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| ===GetParam - Access directly a parameter from a sequence===
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| '''GetParam( <new variable> <sequence> <number> [<number2>] ... )'''
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| <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>.
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| '''Example :'''
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| sequence(seq 1 7 2)
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| echo(${seq})
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| GetParam(new1 ${seq} 0)
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| GetParam(new2 ${seq} 3)
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| echo(${new1})
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| echo(${new2})
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| GetParam(new ${seq} 0 2)
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| echo(${new})
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| This script will print the following lines on the screen :
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| 1 3 5 7
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| 1
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| 7
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| 1 5
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| | |
| | |
| ===If / EndIf - Defines a conditional statement====
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| '''If( <variable1> == or <= or >= or != <variable2> )'''
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| '''EndIf( <variable> )'''
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| '''Example :'''
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| set(var1 2)
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| set(var2 4)
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| If(${var1} <= ${var2})
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| echo(${var1} <= ${var2})
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| EndIf(${var1})
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|
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| set(char1 test)
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| set(char2 test)
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| If(${char1} == ${char2})
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| echo(${char1} == ${char2})
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| EndIf(${char1})
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| This script will print the following lines on the screen :
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| 2 <= 4
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| test == test
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| | |
| | |
| ===Inc Increment a number by a certain amount===
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| '''Inc( <variable> <number> )'''
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| '''<variable> = <variable> + <number>'''
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| '''Example :'''
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| Set(value 2)
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| Inc(${value} 5)
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| echo(2 + 5 = ${value})
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| This script will print the following lines on the screen :
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| 2 + 5 = 7.000000
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| | |
| ===Include - Include another batchmake script===
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| '''Include( <ScriptFilename> )'''
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| '''Example :'''
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| #Script1 : F:\Script1.bms
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| echo('Script1')
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|
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| #Script2 : F:\Script2.bms
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| echo('Script2')
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|
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| #Script3 :
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| Include(F:\Script1.bms)
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| Include(F:\Script2.bms)
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| When we execute Script3 the following lines will be printed on the screen :
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| Script1
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| Script2
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| | |
| ===Int - Convert a variable to integer===
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| '''Int( <variable> )'''
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| '''Example :'''
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| Set(value 2)
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| Inc(${value} 5)
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| Int(${value})
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| echo(2 + 5 = ${value})
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| This script prints the following lines on the screen:
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| 2 + 5 = 7 ( instead of 7.000000 if we Int() is not used)
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| ===ListDirInDir - List all the directories in a specified directory===
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| '''ListDirInDir( <dirlist> <directory> [ *.* ] )'''
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| <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.
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| | |
| '''Example :'''
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| Structure of the Hard Drive :
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| F:\
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| Example
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| number1
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| number2
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| number3
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| set(dir F:\Example)
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| ListDirInDir(example ${dir})
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| echo(${example})
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| This script will print the following lines on the screen:
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| number1/ number2/ number3/
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| | |
| ===ListFileInDir - List all the files in a specified directory===
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| '''ListFileInDir( <filelist> <directory> [ *.* ] )'''
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| <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.
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| | |
| '''Example :'''
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| Structure of the Hard Drive :
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| F:\
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| Example
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| number1.txt
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| number2.txt
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| number3.txt
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| set(dir F:\Example)
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| ListFileInDir(example ${dir})
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| echo(${example})
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| This script will print the following lines on the screen:
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| number1.txt number2.txt number3.txt
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| | |
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| ===OpenTCPSocket - Open a TCP/IP socket===
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| '''OpenTCPSocket( <SocketName> <IPAddress> <Port> )'''
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| '''Example :'''
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| OpenTCPSocket(MySocket,10.0.0.1,8081)
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| ===Randomize - Create a random number===
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| '''Randomize( <variable> <uniform | gaussian | categorical> <min> <max> )'''
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| <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>.
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| '''Example :'''
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| Randomize(result uniform 0 1)
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| echo(${result})
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| This script will print on the screen a random number between 0 and 1 following a uniform distribution.
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| ===Run - Execute a program in a thread===
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| '''Run( <output variable> <'program.exe param1 param2 ....'> )'''
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| The program called 'program.exe' will be launched with the parameters 'param1 param2' ...
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| Note that the Application Wrapper can be used to defined the parameters as names.
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| '''Example :'''
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| Run( output 'MyProgram.exe -in input -out output' )
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| This script will run the program called MyProgram.exe with the parameters input and output.
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| ===SendTCP - Send a message thru a TCP socket===
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| '''SendTCP( <SocketName> <message> )'''
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| The socket should be open using OpenTCPSocket and closed via CloseTCPSocket
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| '''Example :'''
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| SendTCP(MySocket 'my message to send')
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| ===Sequence - Create a sequence of numbers===
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| '''Sequence( <variable> <From> <To> <Step> )'''
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| A sequence starting at <From> ending at <To> with a step of <Step> is generated and stored in <variable>.
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| '''Example :'''
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| sequence(seq 0 10 2)
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| echo(${seq})
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| This script will print the following lines on the screen :
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| 0 2 4 6 8 10
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| ===Set - Assign a value to a variable===
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| '''Set( <variable> <name1> <name2> ... )'''
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| '''Example :'''
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| Set(example name1 name2 name3)
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| echo(${example})
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| This script will print the following lines on the screen :
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| name1 name2 name3
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| ===SetApp - Assign a variable to an Application defined by the Application Wrapper===
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| ''''SetApp( <variable> <application> )
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| Before using this command we must declare the program we want to execute in Application Wraper ( clic on the Application Wrapper button -> new ).
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| '''Example :'''
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| SetApp( prog @MyProgam)
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| Run(output ${prog})
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|
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| This script will run the software called MyProgram.
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| '''NOTE''' : When the @ key is pressed the list of the programs known by Application Wrapper is displayed.
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| ===SetAppOption - Assign a value to a predefined option of a program===
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| '''SetAppOption( <application.option> <value> )'''
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| Before using this command we must use the SetApp command to set an application.
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| Warning : We can only use this command if the software use the MetaCommand library to parse its arguments.
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| '''Example :'''
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| SetApp(prog @MyProgam)
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| SetAppOption( prog.input MyInput )
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| SetAppOption( prog.output MyOutput )
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| Run(output ${prog})
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| This script is equivalent to : MyProgram.exe -in MyInput -out MyOutput.
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| '''NOTE''' : When the "." key is pressedafter the nam eof the application the list of the option available is displayed.
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| ===Sin - Evaluate the sin() function===
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| '''Sin( <output variable> <input> )'''
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| The input number must be given in radian.
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| '''Example :'''
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| Sin(result 1.57)
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| echo(${result})
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| This script wiill print the following lines on the screen :
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| 1.000000
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| ===WriteFile - Write variables into a file===
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| '''WriteFile( <filename> <variable1> <variable2> ... )'''
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| '''Example :'''
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| sequence(seq 1 10 1)
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| set(end 'end')
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| WriteFile(F:\example.txt ${seq} ${end})
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| This script will print the following lines into the file : F:\example.txt :
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| 12345678910end
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| = Distributed Computing =
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| | |
| = BatchBoards =
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