Guide to madagascar API - Revision history

Fomels: typos

2024-11-26T04:05:20Z

typos

Sfomel: /* Mines JTK */ syntax highlighting

2021-10-11T19:45:26Z

Mines JTK: syntax highlighting

← Older revision		Revision as of 19:45, 11 October 2021
Line 1,065:		Line 1,065:
	How to read a file:		How to read a file:

	<java>		<syntaxhighlight lang="java">

	import rsf.Header;		import rsf.Header;
	import rsf.Reader;		import rsf.Reader;
Line 1,080:		Line 1,079:
	}		}
	}		}
			</syntaxhighlight>
	</~~java~~>

	How to write a file:		How to write a file:

	<java>		<syntaxhighlight lang="java">
	import rsf.Header;		import rsf.Header;
	import rsf.Reader;		import rsf.Reader;
Line 1,102:		Line 1,100:
	}		}
	}		}
			</syntaxhighlight>
	</~~java~~>

	If you want to create a dataset from scratch from within Java, then you can create an array of data, modify the values, create a header, and then write it out to rsf:		If you want to create a dataset from scratch from within Java, then you can create an array of data, modify the values, create a header, and then write it out to rsf:

	<java>		<syntaxhighlight lang="java">
	import rsf.Header;		import rsf.Header;
	import rsf.Reader;		import rsf.Reader;
Line 1,135:		Line 1,132:
	}		}
	}		}
			</syntaxhighlight>
	</~~java~~>

	==References==		==References==
	<references/>		<references/>

Sfomel: /* Mines JTK */ syntax highlighting

2021-10-11T19:43:20Z

Mines JTK: syntax highlighting

← Older revision		Revision as of 19:43, 11 October 2021
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	There are two ways to access the API:		There are two ways to access the API:

	1 - From the command line: point the classpath at BOTH compile and runtime to this location on the command line.		1. From the command line: point the classpath at BOTH compile and runtime to this location on the command line.
	<bash>		<syntaxhighlight lang="bash">
	javac -cp $MINESJTK:$RSFROOT/lib/rsf.jar:. Test.java		javac -cp $MINESJTK:$RSFROOT/lib/rsf.jar:. Test.java
	java -cp $MINESJTK:$RSFROOT/lib/rsf.jar:. Test arg1=... arg2=... arg3=...		java -cp $MINESJTK:$RSFROOT/lib/rsf.jar:. Test arg1=... arg2=... arg3=...
	</~~bash~~>		</syntaxhighlight>

	2 - From within a SConstruct script: BOTH the path for the API ($RSFROOT/lib) and the path to the Mines JTK ($MINESJTK) are automatically added to the environment variable CLASSPATH and JAVACLASSPATH for executions made within an SConstruct. Additionally, any additional classes that are already in the CLASSPATH environmental variable in the shell that you launch from will be added to your classpath. This allows you to include additional libraries automatically within your Java programs. The local directory (.) is also included in the CLASSPATH.		2. From within a SConstruct script: BOTH the path for the API ($RSFROOT/lib) and the path to the Mines JTK ($MINESJTK) are automatically added to the environment variable CLASSPATH and JAVACLASSPATH for executions made within an SConstruct. Additionally, any additional classes that are already in the CLASSPATH environmental variable in the shell that you launch from will be added to your classpath. This allows you to include additional libraries automatically within your Java programs. The local directory (.) is also included in the CLASSPATH.

	<python>		<syntaxhighlight lang="python">
	from rsf.proj import *		from rsf.proj import *

Line 999:		Line 999:

	End()		End()
	</~~python~~>		</syntaxhighlight>

	The interface itself is fairly straightforward. More details on the methods exposed by the API can be found at the [[Library_Reference#Java_API \| Library Reference]].		The interface itself is fairly straightforward. More details on the methods exposed by the API can be found at the [[Library_Reference#Java_API \| Library Reference]].
Line 1,005:		Line 1,005:
	Data clipping, argument parsing, and IO example:		Data clipping, argument parsing, and IO example:

	<java>		<syntaxhighlight lang="java">
	import rsf.Par;		import rsf.Par;
	import rsf.Reader;		import rsf.Reader;
Line 1,061:		Line 1,061:
	}		}
	}		}
			</syntaxhighlight>
	</~~java~~>

	How to read a file:		How to read a file:

Sfomel: /* SWIG */

2021-10-11T19:39:50Z

SWIG

← Older revision		Revision as of 19:39, 11 October 2021
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	To compile on the command line:		To compile on the command line:
	<bash>		<syntaxhighlight lang="bash">
	javac -cp $RSFROOT/lib Clip.java		javac -cp $RSFROOT/lib Clip.java
	</~~bash~~>		</syntaxhighlight>

	To include this as part of a SCons script (SConstruct):		To include this as part of a SCons script (SConstruct):

Sfomel: /* SWIG */ syntax highlighting

2021-10-11T19:38:23Z

SWIG: syntax highlighting

← Older revision		Revision as of 19:38, 11 October 2021
Line 865:		Line 865:

	2. Create the JAVA_HOME environment variable for your shell. This should point to the directory where the JDK was installed. Example (for Ubuntu 10.04):		2. Create the JAVA_HOME environment variable for your shell. This should point to the directory where the JDK was installed. Example (for Ubuntu 10.04):
	<bash>		<syntaxhighlight lang="bash">
	export JAVA_HOME=/usr/lib/jvm/java-6-opensdk		export JAVA_HOME=/usr/lib/jvm/java-6-opensdk
	</~~bash~~>		</syntaxhighlight>

	3. Reconfigure Madagascar:		3. Reconfigure Madagascar:
	<bash>		<syntaxhighlight lang="bash">
	./configure API=java		./configure API=java
	</~~bash~~>		</syntaxhighlight>

	4. Reinstall Madagascar (Ignore the compilation warnings for Java files):		4. Reinstall Madagascar (Ignore the compilation warnings for Java files):
	<bash>		<syntaxhighlight lang="bash">
	scons; scons install		scons; scons install
	</~~bash~~>		</syntaxhighlight>

	~~The installation creates two files: $RSFROOT/lib/libjrsf.so and $RSFROOT/lib/rsf.jar .~~

	~~Make sure that you set your LD_LIBRARY_PATH to include $RSFROOT/lib.~~

			The installation creates two files: <tt>$RSFROOT/lib/libjrsf.so</tt> and <tt>$RSFROOT/lib/rsf.jar</tt>.

			Make sure that you set your LD_LIBRARY_PATH to include <tt>$RSFROOT/lib</tt>.

	A short demonstration of the interface follows:		A short demonstration of the interface follows:
Line 931:		Line 931:
	There are only three classes in the interface:		There are only three classes in the interface:

	1. RSF - The command line argument parser, and the initializer for the native interface. An RSF object MUST be instantiated BEFORE instantiating an Input or Output object.		1.'''RSF''' - The command line argument parser, and the initializer for the native interface. An RSF object MUST be instantiated BEFORE instantiating an Input or Output object.

	2. Input - An object that provides read access to an RSF file.		2. '''Input''' - An object that provides read access to an RSF file.

	3. Output - An object that provides write access to an RSF file.		3. '''Output''' - An object that provides write access to an RSF file.

	Additionally, the shared library (libjrsf.so or libjrsf.dll) must be included via the System.loadLibrary("jrsf"); as the first command in the file.		Additionally, the shared library (libjrsf.so or libjrsf.dll) must be included via the System.loadLibrary("jrsf"); as the first command in the file.

Sfomel: /* SWIG */ syntax highlighting

2021-10-11T19:35:29Z

SWIG: syntax highlighting

← Older revision		Revision as of 19:35, 11 October 2021
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	To install the SWIG interface:		To install the SWIG interface:

	1 - Download the Java Standard Development Kit (JDK). Installation varies by platform.		1. Download the Java Standard Development Kit (JDK). Installation varies by platform.

	2 - Create the JAVA_HOME environment variable for your shell. This should point to the directory where the JDK was installed. Example (for Ubuntu 10.04):		2. Create the JAVA_HOME environment variable for your shell. This should point to the directory where the JDK was installed. Example (for Ubuntu 10.04):
	<bash>		<bash>
	export JAVA_HOME=/usr/lib/jvm/java-6-opensdk		export JAVA_HOME=/usr/lib/jvm/java-6-opensdk
	</bash>		</bash>
	3 - Reconfigure Madagascar:		3. Reconfigure Madagascar:
	<bash>		<bash>
	./configure API=java		./configure API=java
	</bash>		</bash>
	4 - Reinstall Madagascar (Ignore the compilation warnings for Java files):		4. Reinstall Madagascar (Ignore the compilation warnings for Java files):
	<bash>		<bash>
	scons; scons install		scons; scons install
Line 885:		Line 885:
	A short demonstration of the interface follows:		A short demonstration of the interface follows:

	<java>		<syntaxhighlight lang="java">
	import rsf.RSF;		import rsf.RSF;
	import rsf.Input;		import rsf.Input;
Line 927:		Line 927:
	}		}
	}		}
	</~~java~~>		</syntaxhighlight>

	There are only three classes in the interface:		There are only three classes in the interface:

	1 -- RSF - The command line argument parser, and the initializer for the native interface. An RSF object MUST be instantiated BEFORE instantiating an Input or Output object.		1. RSF - The command line argument parser, and the initializer for the native interface. An RSF object MUST be instantiated BEFORE instantiating an Input or Output object.

	2 -- Input - An object that provides read access to an RSF file.		2. Input - An object that provides read access to an RSF file.

	3 -- Output - An object that provides write access to an RSF file.		3. Output - An object that provides write access to an RSF file.

	Additionally, the shared library (libjrsf.so or libjrsf.dll) must be included via the System.loadLibrary("jrsf"); as the first command in the file.		Additionally, the shared library (libjrsf.so or libjrsf.dll) must be included via the System.loadLibrary("jrsf"); as the first command in the file.
Line 945:		Line 945:

	To include this as part of a SCons script (SConstruct):		To include this as part of a SCons script (SConstruct):
	<python>		<syntaxhighlight lang="python">
	from rsf.proj import *		from rsf.proj import *

Line 957:		Line 957:
	''' % WhereIs('java'))		''' % WhereIs('java'))
	Flow('test.attr','clipd','sfattr')		Flow('test.attr','clipd','sfattr')
			</syntaxhighlight>

	~~</python>~~		Note, that we compile <tt>Clip.java</tt> using the SCons Java builder. To execute the command, we have to locate the "java" command, which we do using <tt>WhereIs('java')</tt>. Then we execute the class name, and pass any command line arguments as usual. The files are read from standard in for this program and written to standard out.

	Note, that we compile Clip.java using the SCons Java builder. To execute the command, we have to locate the "java" command, which we do using WhereIs('java'). Then we execute the class name, and pass any command line arguments as usual. The files are read from standard in for this program and written to standard out.

	Please see the [[Library Reference]] for more details on the functions available in the SWIG API.		Please see the [[Library Reference]] for more details on the functions available in the SWIG API.

Sfomel: /* MATLAB interface */

2019-06-14T19:20:40Z

MATLAB interface

← Older revision		Revision as of 19:20, 14 June 2019
Line 801:		Line 801:

	The MATLAB clip function is listed below.		The MATLAB clip function is listed below.
	<matlab>		<syntaxhighlight lang="matlab">
	function clip(in,out,clip)		function clip(in,out,clip)
	%CLIP Clip the data		%CLIP Clip the data
Line 817:		Line 817:
	rsf_write(trace,out,'same');		rsf_write(trace,out,'same');
	end		end
			</syntaxhighlight>
	</~~matlab~~>

	Let us examine it in detail.		Let us examine it in detail.
	<matlab>		<syntaxhighlight lang="matlab">
	dims = rsf_dim(in);		dims = rsf_dim(in);
	</~~matlab~~>		</syntaxhighlight>

	We start by figuring out the input file dimensions.		We start by figuring out the input file dimensions.
	<matlab>		<syntaxhighlight lang="matlab">
	n1 = dims(1); % trace length		n1 = dims(1); % trace length
	n2 = prod(dims(2:end)); % number of traces		n2 = prod(dims(2:end)); % number of traces
	</~~matlab~~>		</syntaxhighlight>

	The first dimension is the trace length, the product of all other		The first dimension is the trace length, the product of all other
	dimensions correspond to the number of traces.		dimensions correspond to the number of traces.
	<matlab>		<syntaxhighlight lang="matlab">
	trace = 1:n1; % allocate trace		trace = 1:n1; % allocate trace
	rsf_create(out,in) % create an output file		rsf_create(out,in) % create an output file
	</~~matlab~~>		</syntaxhighlight>

	Next, we allocate the trace array and create an output file.		Next, we allocate the trace array and create an output file.
	<matlab>		<syntaxhighlight lang="matlab">
	for i2 = 1:n2 % loop over traces		for i2 = 1:n2 % loop over traces
	rsf_read(trace,in,'same');		rsf_read(trace,in,'same');
Line 846:		Line 845:
	rsf_write(trace,out,'same');		rsf_write(trace,out,'same');
	end		end
	</~~matlab~~>		</syntaxhighlight>

	Finally, we do the actual work: loop over input traces, reading,		Finally, we do the actual work: loop over input traces, reading,

Karl: /* Python interface */

2018-12-14T21:33:12Z

Python interface

← Older revision		Revision as of 21:33, 14 December 2018
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	\|simple_m8r_create_write_filter_read.ipynb \|\| numpy, write rsf, Madagascar commands, read rsf, plot		\|simple_m8r_create_write_filter_read.ipynb \|\| numpy, write rsf, Madagascar commands, read rsf, plot
	\|-		\|-
	\| ~~synthetic_for_tle_Edge-preserving~~.ipynb \|\| reproduces a paper from TLE with numpy and Matplotlib		\| tle_edge_preserve.ipynb \|\| reproduces a paper from TLE with numpy and Matplotlib
	\|-		\|-
	\| file_filter_scons_example.ipynb \|\| advanced m8r options; File, filter, and scons from python		\| file_filter_scons_example.ipynb \|\| advanced m8r options; File, filter, and scons from python

Karl: /* Python interface */

2018-12-14T17:18:56Z

Python interface

@@ Line 694: / Line 694: @@
 The python script does not require compilation. Simply make sure that
 <tt>&#36;RSFROOT/lib</tt> is in <tt>PYTHONPATH</tt> and <tt>LD_LIBRARY_PATH</tt>.
 ===Interactive mode usage without graphics===

Karl: /* Python interface */

2018-12-13T21:08:32Z

Python interface

← Older revision		Revision as of 21:08, 13 December 2018
Line 699:		Line 699:

	<pre>		<pre>
	sfmath n1=10 n2=5 output=x1+x2*100 > test.rsf		sfmath n1=10 n2=9 output=x1+x2 > test.rsf
	</pre>		</pre>

Line 720:		Line 720:

	<pre>		<pre>
	[[ 0. ~~100~~. ~~200~~. ~~300~~. ~~400~~.]		[[ 0. 1. 2. 3. 4. 5. 6. 7. 8.]
	[ 1. ~~101~~. ~~201. 301. 401~~.]		[ 1. 2. 3. 4. 5. 6. 7. 8. 9.]
	[ 2. ~~102~~. ~~202~~. ~~302~~. ~~402~~.]		[ 2. 3. 4. 5. 6. 7. 8. 9. 10.]
	[ 3. ~~103~~. ~~203~~. ~~303~~. ~~403~~.]		[ 3. 4. 5. 6. 7. 8. 9. 10. 11.]
	[ 4. ~~104~~. ~~204~~. ~~304~~. ~~404~~.]		[ 4. 5. 6. 7. 8. 9. 10. 11. 12.]
	[ 5. ~~105~~. ~~205~~. ~~305~~. ~~405~~.]		[ 5. 6. 7. 8. 9. 10. 11. 12. 13.]
	[ 6. ~~106~~. ~~206~~. ~~306~~. ~~406~~.]		[ 6. 7. 8. 9. 10. 11. 12. 13. 14.]
	[ 7. ~~107~~. ~~207~~. ~~307~~. ~~407~~.]		[ 7. 8. 9. 10. 11. 12. 13. 14. 15.]
	[ 8. ~~108~~. ~~208~~. ~~308~~. ~~408~~.]		[ 8. 9. 10. 11. 12. 13. 14. 15. 16.]
	[ 9. ~~109~~. ~~209~~. ~~309~~. ~~409~~.]]		[ 9. 10. 11. 12. 13. 14. 15. 16. 17.]]
	</pre>		</pre>