Difference between revisions of "Batchmake documentation"

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Line 98: Line 98:
  Set(url_filename "${url};${filename}")
  Set(url_filename "${url};${filename}")
  Set(path 'C://Download')
  Set(path 'C://Download')
  DownloadXnatDataSet(${filename} ${url} ${path} 'myLogin' 'myPassword')
  DownloadXnatDataSet(${url_filename} ${path} 'myLogin' 'myPassword')
or
or
  GetXnatDataSets(xnatDatas ${xnatCatalog} 'myLogin' 'myPassword')
  GetXnatDataSets(xnatDatas ${xnatCatalog} 'myLogin' 'myPassword')

Revision as of 22:39, 30 January 2008

<back to main page

Main Commands

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')

DownloadXcedeDataSet - Download a DataSet from an URL

DownloadXcedeDataSet ( <xcedeData> <directory> [login] [password])

The first parameter is a XcedeDataSet which is a camiantion between the url and the name of the file. It looks like : url;filename.

The directory is the path where the file will be downloaded.

The two last one are the parameters of connection. Sometimes you need them to be allowed to access to an XcedetDataBase.

Attention : If your filename looks like 'dir1/dir2/filename.img', and if dir1 exists, but dir2 doesn't : it will be created.

Example :

Set(url 'http://www.insight-journal.org/dspace/view_item.php?itemid=118#')
Set(filename MyImage.mha)
Set(url_filename "${url};${filename}")
Set(path 'C://Download')
DownloadXcedeDataSet(${url_filename} 'C:/Downloads' myLogin myPassword)

or

GetXcedeDataSets(xcedeDatas 'Catalog.xcede' '11' 'myLogin'   'myPassword')
ForEach(xcedeData ${xcedeDatas})
DownloadXcedeDataSet(${xcedeData} 'C:/Downloads' 'myLogin'  'myPassword')
EndForEach(${xcedeData})

DownloadXnatDataSet - Download a DataSet from an URL

DownloadXnatDataSet ( <XnatDataSet> <directory> [login] [password])

The first parameter is a XnatDataSet which is a camiantion between the url and the name of the file. It looks like : url;filename.

The directory is the path where the file will be downloaded.

The two last one are the parameters of connection. Sometimes you need them to be allowed to access to an XnatDataBase.

Attention : If your filename looks like 'dir1/dir2/filename.img', and if dir1 exists, but dir2 doesn't : it will be created.

Example :

Set(url 'http://central.xnat.org:8080/archive/cache/VQYPEjndn96JMCiRVniaAwA3K4Wtv2useiTCuyTkDVSjtPBvqEwPqNhFaV34LQLF')
Set(filename MyImage.img)
Set(url_filename "${url};${filename}")
Set(path 'C://Download')
DownloadXnatDataSet(${url_filename} ${path} 'myLogin' 'myPassword')

or

GetXnatDataSets(xnatDatas ${xnatCatalog} 'myLogin' 'myPassword')
ForEach(xnatData ${xnatDatas})
DownloadXnatDataSet(${xnatData} 'C:/Downloads' 'myLogin' 'myPassword')
EndForEach(${xnatData})

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

GetListSize - Return the size of sequence/list

GetListSize( <new variable> <sequence>)

Example : sequence(seq 1 9 1) GetListSize(size ${seq}) echo(${size})

will return:

10

GetParam - Access directly a parameter from a sequence/list

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:

1 3 5 7
1
7
1 5


GetXcedeDataSets - Get the DataSets form an XcedeCatalog

GetXcedeFilename( <urls> <xcedeCatalog> [catalogID] [login] [password])

The first parameter is a list which will contain all the urls of the catalog.

The second one is an xcedeCatalog : catalog.xcede or catalog.xml for example.

The third one (which is an option) is the ID of the catalog you are looking for, if you don't want all the catalogs in the main one.

login et password are sometimes required to connect to an xcede database.

Example :

GetXcedeDataSets(xcedeUrls 'Catalog.xcede' 'ID02')

After that you will be able to access to each filename and url that your catalog contain.

GetXnatDataSets - Get the DataSets form an XcedeCatalog

GetXnatFilename( <urls> <xcedeCatalog> [login] [password])

The first parameter is a list which will contain all the urls of the catalog.

The second one is an xnatCatalog : catalog.xml for example.

login et password are sometimes required to connect to an xnat database.

Example :

GetXcedeDataSets(xnatUrls 'Catalog.xml' 'myLogin' 'mYPassword')
ForEach(url ${xnatUrls})
echo(${url})
GetXnatFilename(xnatFilename ${url})
echo(${xnatFilename})
DownloadXnatDataSet(${xnatFilename} ${url} 'C:/')
EndForEach(${url})

This script will print the following lines on the screen:

arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-2_anon.img
http://central.xnat.org:8080/archive/cache/ozlOTU6wIPZz5ZMNUvQpZyl4ZgtT2hkymb5D25uPSemKizxu19ejyoO2w5FQ5yMH
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-2_anon_sag_66.gif
http://central.xnat.org:8080/archive/cache/kjy0nYMAng80CHgDGTACJJa2USCjm4liJddnWJF5JNLmBqhv0b5GI3LZw7iDk2pn
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-3_anon.hdr
http://central.xnat.org:8080/archive/cache/m7jStt2LKug1rVG5RIysbQbfGIGsqCnh6aVTQJDbEE0XcAwLuQfiPipeCvtYfFfU
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-3_anon.img
http://central.xnat.org:8080/archive/cache/0Gm5UOjCMnqXr8bfNSfmnt29k4lHyoncvLOR8M28QacTRy6ublyOQq3XkzLpuX6e
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-3_anon_sag_66.gif
http://central.xnat.org:8080/archive/cache/dpLzQ8hM61vwj2RWKUOpEBgyEoKTYW8C9dBgYmtP1Gi6QlMdtQyijRlWkJUonkBo
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-4_anon.img
http://central.xnat.org:8080/archive/cache/19ntONbyxdUPdAnaLVyupWm3zdWg7R1lFSeUN7RnIZS2J9XwZXbGUScOuAnYzaDK
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-4_anon.hdr
http://central.xnat.org:8080/archive/cache/MRsIDez3d3O5WvXL2iPFZOrodSf4BsAcSEtpeY881ItrLof1WsPSXvFikDEkE1gZ
arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-4_anon_sag_66.gif

GetXcedeFilename - Get the filename of an URL

GetXcedeFilename( <filename> <URL> )

If you want to use this command, you have to launch the "GetXcedeDataSets" command first. Example :

Set(url 'http://www.insight-journal.org/dspace/view_item.php?itemid=118#')
GetXcedeFilename(filename ${url})
echo(Filename : ${filename })

This script will print the following line on the screen:

Filename : JelloPhantom001_CT_000004_0.48x0.48x3.00.mha

GetXnatFilename - Get the filename of an URL

GetXnatFilename( <filename> <URL> )

If you want to use this command, you have to launch the "GetXnatDataSets" command first. Example :

Set(url 'http://'http://central.xnat.org:8080/archive/cache/VQYPEjndn96JMCiRVniaAwA3K4Wtv2useiTCuyTkDVSjtPBvqEwPqNhFaV34LQLF')
GetXcedeFilename(filename ${url})
echo(Filename : ${filename })

This script will print the following line on the screen:

Filename : arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-1_anon.img

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.


SendTCP - Send a message thru a TCP socket

SendTCP( <SocketName> <message> )

The socket should be open using OpenTCPSocket and closed via CloseTCPSocket

Example :

SendTCP(MySocket 'my message to send')


Sequence - Create a sequence of numbers

Sequence( <variable> <From> <To> <Step> )

A sequence starting at <From> ending at <To> with a step of <Step> is generated and stored in <variable>.

Example :

sequence(seq 0 10 2)
echo(${seq})

This script will print the following lines on the screen :

0 2 4 6 8 10


Set - Assign a value to a variable

Set( <variable> <name1> <name2> ... )

Example :

Set(example name1 name2 name3)
echo(${example})

This script will print the following lines on the screen :

name1 name2 name3 


SetApp - Assign a variable to an Application defined by the Application Wrapper

'SetApp( <variable> <application> )

Before using this command we must declare the program we want to execute in Application Wraper ( clic on the Application Wrapper button -> new ).

Example :

SetApp( prog @MyProgam)
Run(output ${prog})
 

This script will run the software called MyProgram.

NOTE : When the @ key is pressed the list of the programs known by Application Wrapper is displayed.


SetAppOption - Assign a value to a predefined option of a program

SetAppOption( <application.option> <value> )

Before using this command we must use the SetApp command to set an application.

Warning : We can only use this command if the software use the MetaCommand library to parse its arguments.

Example :

SetApp(prog @MyProgam)
SetAppOption( prog.input MyInput )
SetAppOption( prog.output MyOutput )
Run(output ${prog})

This script is equivalent to : MyProgram.exe -in MyInput -out MyOutput.

NOTE : When the "." key is pressedafter the nam eof the application the list of the option available is displayed.


Sin - Evaluate the sin() function

Sin( <output variable> <input> )

The input number must be given in radian.

Example :

Sin(result 1.57)
echo(${result})

This script wiill print the following lines on the screen :

1.000000

WriteFile - Write variables into a file

WriteFile( <filename> <variable1> <variable2> ... )

Example :

sequence(seq 1 10 1)
set(end 'end')
WriteFile(F:\example.txt ${seq} ${end})

This script will print the following lines into the file : F:\example.txt :

12345678910end