Batchmake documentation
Main Commands
AddError - Manually generates an error
AddError( [<description>] ... )
Manually generates an error. Display the error description on the output via the ProgressManager ( std::cerr ). If ExitOnError() has been previously set to true, the script is stopped.
Example :
If( ${my_var} != '0' )
AddError( 'Error in segmentation. Error number:' ${my_var} )
EndIf( ${my_var} )
See Also:
ClearErrors() Exit() ExitOnError() GetErrorCount()
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"
See also
WriteFile()
ClearErrors - Reset the number of errors
ClearErrors( )
Example :
ClearErrors( )
... # A failing action
GetErrorCount( errorcount )
echo( ${errorcount} )
ClearErrors( )
GetErrorCount( errorcount )
Echo( ${errorcount} )
Displays on screen:
1 0
See Also:
AddError() Exit() ExitOnError() GetErrorCount()
CloseTCPSocket - Close a TCP/IP socket
CloseTCPSocket( <SocketName> )
Example :
CloseTCPSocket(MySocket)
CopyFile - Copy a file from disk to disk
CopyFile( <src filename> <dst filename> [<dst2 filename>] ... )
Copy a file on disk to one or many files. It can also copy directories.
Example :
CopyFile('myfile.txt' 'copyofmyfile.txt' 'anothercopyofmyfile.txt')
See Also:
DeleteFile() ListFileInDir() FileExists()
DashboardExperiment - Specify the encrypted name of the experiment to report on
DashboardExperiment( <encryptedExperiment> )
The encryptedExperiment is given when creating a new experiment online (this requires a login/pass)
Example :
DashboardExperiment( 7YF04vELWW4m1B88t)
DashboardHost - Specify the hostname of the central database manager
DashboardHost( <hostname> )
Example :
DashboardHost(www.kitware.com)
DashboardNotify - Add a new string to the central database
DashboardNotify( <message> )
Example :
DashboardNotify('End of first experiment')
DashboardSend - Send the results of a program to the central database for data collection
DashboardSend( <methodid> <value1> <value2> )
Example :
DashboardSend(1,${value1},${value2})
DeleteFile - Delete a file on disk
DeleteFile( <filename> )
Note: It also deletes directories.
Example :
DeleteFile('myfile.txt')
See also
CopyFile() FileExists() GetFilename()
DownloadXcedeDataSet - Download a DataSet from an URL
DownloadXcedeDataSet ( <xcedeData> <directory> [login] [password])
The first parameter is a XcedeDataSet which is a camiantion between the url and the name of the file. It looks like : url;filename.
The directory is the path where the file will be downloaded.
The two last one are the parameters of connection. Sometimes you need them to be allowed to access to an XcedetDataBase.
Attention : If your filename looks like 'dir1/dir2/filename.img', and if dir1 exists, but dir2 doesn't : it will be created.
Example :
Set(url '//www.insight-journal.org/dspace/view_item.php?itemid=118#')
Set(filename MyImage.mha)
Set(url_filename "${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(${xcedeData})
DownloadXnatDataSet - Download a DataSet from an URL
DownloadXnatDataSet ( <XnatDataSet> <directory> [login] [password])
The first parameter is a XnatDataSet which is a camiantion between the url and the name of the file. It looks like : url;filename.
The directory is the path where the file will be downloaded.
The two last one are the parameters of connection. Sometimes you need them to be allowed to access to an XnatDataBase.
Attention : If your filename looks like 'dir1/dir2/filename.img', and if dir1 exists, but dir2 doesn't : it will be created.
Example :
Set(url '//central.xnat.org:8080/archive/cache/VQYPEjndn96JMCiRVniaAwA3K4Wtv2useiTCuyTkDVSjtPBvqEwPqNhFaV34LQLF')
Set(filename MyImage.img)
Set(url_filename "${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} ${value2})
endforeach(value2)
endforeach(value)
This script will print the following lines on the screen :
value: 1 1 value: 1 2 value: 2 1 value: 2 2
Note : Single quotes prevents the variables to be expanded:
Set( foo My car is red )
Echo( '${foo}' <- ${foo} )
This script will print the following line on the screen :
${foo} <- My car is red
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> <length> [FROMEND] [KEEPEND] )
The parameter <output> will contain the <length> first characters of <input> if FROMEND is not set. With FROMEND the <length> 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
Exit - Stop the running script
Exit( )
Example :
If( ${my_var} == '0' )
Exit()
EndIf( ${my_var} )
See also
AddError() ExitOnError()
ExitOnError - Stop the script if an action returns an error
ExitOnError( '1' or '0' or 'true' or 'false' or 'TRUE' or ... )
Example :
ExitOnError( 'TrUe' )
WriteFile( ${my_file} ${my_data}) # -> WriteFile fails to write on disk. An error is returned
CopyFile( ${my_file} ${my_duplicate_file} ) # -> won't be executed
See also
AddError() GetErrorCount() ClearErrors()
FileExists - check if a file exists on disk
FileExists(<myvar> <filename>)
Example :
FileExists(fileCreated 'myfile.mha')
If( ${myvar} == 1 )
...
EndIf
See also
AppendFile() CopyFile() DeleteFile() GetFilename() ListDirInDir() ListFileInDir() WriteFile()
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
GetErrorCount - Return the number of errors found
GetErrorCount( <variable> )
Example :
AddError( )
WriteFile( ${my_file} ${my_data} ) # -> WriteFile fails to write ${my_file}
GetErrorCount( errorcount )
echo(${errorcount})
Displays on screen:
2
See also
AddError() ClearErrors() ExitOnError()
GetFilename - Get some information about a file
GetFilename(<outputvariale> <input> [NAME PATH PARENT_PATH EXTENSION NAME_WITHOUT_EXTENSION])
Example :
Set( my_file 'foo.txt' )
GetFilename( filewithnoextension ${my_file} NAME_WITHOUT_EXTENSION )
Echo( ${filewithnoextension} )
Prints on screen
foo
See also
FileExists() ListDirInDir() ListFileInDir()
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
GetParamCount - Return the number of items in a set
GetParamCount( <variable count> <variable> )
Example :
sequence(seq 1 10 1)
echo(${seq})
GetParamCount(seqSize ${seq})
echo(${seqSize})
This script will print the following lines on the screen:
1 2 3 4 5 6 7 8 9 10 11
See also:
GetParam() Sequence() GetErrorCount() ForEach()
GetXcedeDataSets - Get the DataSets form an XcedeCatalog
GetXcedeDataSets( <urls;filenames> <xcedeCatalog> [catalogID] [login] [password])
The first parameter is a list which will contain all the DataSets (url;filename) 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(xcedeDatas 'Catalog.xcede' '11')
After that you will be able to access to each filename and url that your catalog contain.
ForEach(xcedeData ${xcedeDatas})
echo(${xcedeData})
EndForEach(${xcedeData})
This script will print the following lines on the screen:
//rigel/midas/download_bitstream?bitstreamid=23;ellipse4.mha //rigel/midas/download_bitstream?bitstreamid=24;ellipse5.mha //rigel/midas/download_bitstream?bitstreamid=25;ellipse6.mha
GetXnatDataSets - Get the DataSets form an XcedeCatalog
GetXnatDataSets( <urls;filenames> <xcedeCatalog> [login] [password])
The first parameter is a list which will contain all the DataSets (url;filename) 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 :
GetXnatDataSets(xnatDatas 'Catalog.xml' ${xnatLogin} ${psw})
ForEach(xnatData ${xnatDatas})
echo(${xnatData})
EndForEach(${xnatData})
This script will print the following lines on the screen:
//central.xnat.org:8080/archive/emKizxu19ejyoO2w5FQ5yMH;arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-2_anon.img //central.xnat.org:8080/archive/A5JNLmBqhv0b5GI3LZw7iDn;arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-2_anon_sag_66.gif //central.xnat.org:8080/archive/m7jStt2fGIGs0XcAwtYfFfU;arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-3_anon.hdr //central.xnat.org:8080/archive/0GoncvLOR8M28QaczLpuX6e;arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-3_anon.img
GetXcedeFilename - Get the filename of an URL
GetXcedeFilename( <filename> <XcedeData> )
The first parameter is your new varaiable : the filename.
The second one is A XcedeData which lokks like : url;filename.
Basically, this function will cut the url and will return only the filename.
Example :
Set(dataSet '//www.insight-journal.org/dspace/view_item.php?itemid=118#;JelloPhantom001_CT_000004_0.48x0.48x3.00.mha')
GetXcedeFilename(filename ${dataSet})
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> <dataSet> )
The first parameter is your new varaiable : the filename.
The second one is A XnatData which looks like : url;filename.
Basically, this function will cut the url and will return only the filename.
Example :
Set(dataSet '//central.xnat.org:8080/archive/FaV34LQLF;arc001/OAS1_0289_MR1/RAW/OAS1_0289_MR1_mpr-1_anon.img')
GetXcedeFilename(filename ${dataSet})
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> ==|<=|>=|!= <$variable2> [ || <condition> ] [ && <condition> ]) ... EndIf(<condition>)
Example :
set(var1 2)
set(var2 4)
If(${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 or variable> )
<variable> = <variable> + <number or variable>
Example :
Set(value 2)
Set(value2 3)
Inc(${value} 5)
Inc(${value} ${value2})
echo( 2 + 5 + ${value2} = ${value})
This script will print the following lines on the screen :
2 + 5 + 3 = 10.000000
Include - Include another batchmake script
Include( <ScriptFilename> )
Example :
#Script1 : F:\Script1.bms
echo('Script1')
#Script2 : F:\Script2.bms
echo('Script2')
#Script3 :
Include(F:\Script1.bms)
Include(F:\Script2.bms)
When we execute Script3 the following lines will be printed on the screen :
Script1 Script2
Int - Convert a variable to integer
Int( <variable> )
Example :
Set(value 2)
Inc(${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/
See also
FileExists() ListFileInDir()
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
See also
FileExists() ListDirInDir()
MakeDirectory - Create a directory
MakeDirectory( <dirname> ) Create a directory at the path dirname on your system.
Example
MakeDirectory( ${project_dir}/test )
See also
AppendFile() CopyFile() DeleteFile() ListDirInDir() ListFileInDir() WriteFile()
Math - Compute an algebra expression
Math(<result> <var1> <operator> <var2>)
Example
Set( val 18 )
MakeDirectory( res ${val} / 2 )
Echo( ${res} )
This script will print the following line on the screen:
9
See also
Inc()
OpenTCPSocket - Open a TCP/IP socket
OpenTCPSocket( <SocketName> <IPAddress> <Port> )
Example :
OpenTCPSocket(MySocket,10.0.0.1,8081)
Randomize - Create a random number
Randomize( <variable> <uniform | gaussian | categorical> <min> <max> )
<variable> contains the result. The distribtion can be set thanks to one of these 3 words : uniform, gaussian or categorical. The range an be set thanks to <min> and <max>.
Example :
Randomize(result uniform 0 1)
echo(${result})
This script will print on the screen a random number between 0 and 1 following a uniform distribution.
RegEx - Apply regular expressions on a variable
RegEx(<newvar> <variable> <RegularExpression> <MATCH or REPLACE> [replacevar]) Below are the metacharacters recognized by the regular expression engine
^ Matches at beginning of a line $ Matches at end of a line . Matches any single character [ ] Matches any character(s) inside the brackets [^ ] Matches any character(s) not inside the brackets - Matches any character in range on either side of a dash * Matches preceding pattern zero or more times + Matches preceding pattern one or more times ? Matches preceding pattern zero or once only () Saves a matched expression and uses it in a later match
Example :
RegEx( result 'foo' 'o' REPLACE 'a' )
Set to result the value 'faa'
RegEx( result 'the car is green' 'c.*e' MATCH )
Set 'car is gree' to result
Run - Execute a program in a thread
Run( <output variable> <'program.exe param1 param2 ....'> [<error variable>] [<exit status variable>])
The program called 'program.exe' will be launched with the parameters 'param1 param2 ...'
<output> and <error> are filled with the std::cout and std::cerr streams of the program.
<exit status> is set with the return value of the program.
Note that the Application Wrapper can be used to defined the parameters as names.
Example :
Run( prog_output 'MyProgram.exe -in input -out output' prog_error prog_status)
Or
Set( my_program MyProgram.exe)
Set( my_input input)
Set( my_output output)
Set( command_line ${my_program} -in ${my_input} -out ${my_output} )
Run( prog_output ${command_line} prog_error)
Or:
Set( my_program MyProgram.exe)
Set( my_input input)
Set( my_output output)
Run( prog_output ${my_program}' -in '${my_input}' -out '${my_output} prog_error prog_exit_status)
In this last example, make sure you do not have space between ${my_program} and the parameter 'quote'.
Or using the Application Wrapper (if MyProgram.exe is already wrapped ):
SetApp( my_program @MyProg )
SetAppOption( my_program.in ${my_input} )
SetAppOption( my_program.out ${my_output} )
Run( prog_output ${my_program} prog_error)
This script will run the program called MyProgram.exe with the parameters input and output.
SendTCP - Send a message thru a TCP socket
SendTCP( <SocketName> <message> )
The socket should be open using OpenTCPSocket and closed via CloseTCPSocket
Example :
SendTCP(MySocket 'my message to send')
Sequence - Create a sequence of numbers
Sequence( <variable> <From> <To> <Step> )
A sequence starting at <From> ending at <To> with a step of <Step> is generated and stored in <variable>.
Example :
sequence(seq 0 10 2)
echo(${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 line on the screen :
name1 name2 name3
Set( foo name )
Set( bar ${foo} )
Echo( ${bar} )
This script will print the following line on the screen :
name
Note Single quotes prevents the variables to be expanded:
Set( foo name )
Set( bar '${foo}' )
Echo( ${bar} )
This script will print the following line on the screen :
${bar}
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
See also
AppendFile() CopyFile() DeleteFile()
