cutout: modifies SodaImpl to use vlkb-cutout instead on two calls to vlkb-overlap + vlkb-imcopy (1dc0d2ea) · Commits · ViaLactea / vlkb-soda

data-access/engine/src/vlkb/src/imcopy.cpp

+438 −440

Original line number	Diff line number	Diff line
		@@ -32,13 +32,12 @@ int stream_cutout(string pathname, int extnum, string region)
		string pixfilter{ to_cfitsio_format(bnds) };

		imcopy(pathname, extnum, pixfilter);
		return EXIT_SUCCESS;

		// pixfilter must be within NAXIS[] otherwise cfitsio-error
		return 0; // EXIT_SUCCESS
		}
		else if((ov_code == 1) \|\| (ov_code == 6))
		{
		// no overlap
		return EXIT_SUCCESS;
		return 1; // no overlap EXIT_SUCCESS
		}
		else
		{
		@@ -47,7 +46,6 @@ int stream_cutout(string pathname, int extnum, string region)
		}



		// ----------------------------------------------------------------------------------

		int fits_copy_image_section2(

data-access/engine/src/vlkb/src/main.cpp

+12 −6

Original line number	Diff line number	Diff line
		@@ -259,10 +259,16 @@ int cmd_cutout(int argc, char * argv[])
		if (argc != 4)
		{
		std::cerr
		<< "Usage: cutout <filename.fits> <extnum> <region>\n"
		<< "\n"
		<< "Calculate overlap between HDU in file and region.\n\nregion in JSON form of VO-SODA params. For example 'POS=CIRCLE 21.4458 -1.373 0.1' :\n"
		" \'{\"pos\":{\"circle\":{\"lat\":-1.373,\"lon\":21.4458,\"radius\":0.1},\"system\":\"ICRS\"},\"service\":\"SUBIMG\"}\'\n";
		<< "Usage: cutout <filename.fits> <extnum> <region>"
		<< endl
		<< endl
		<< "Calculate overlap between HDU in file and region. Returns 0 (ok), 1 (no overlap) or EXIT_FAILURE"
		<< endl
		<< endl
		<< "region in JSON form of VO-SODA params. For example 'POS=CIRCLE 21.4458 -1.373 0.1' :"
		<< endl
		<< " \'{\"pos\":{\"circle\":{\"lat\":-1.373,\"lon\":21.4458,\"radius\":0.1},\"system\":\"ICRS\"},\"service\":\"SUBIMG\"}\'"
		<< endl;
		return EXIT_FAILURE;
		}
		else
		@@ -272,8 +278,8 @@ int cmd_cutout(int argc, char * argv[])
		string region{argv[3]};

		int rc = stream_cutout(pathname, extnum, region);
		if(!rc)
		return EXIT_SUCCESS;
		if( (rc == 0) \|\| (rc == 1))
		return rc; // OK or no overlap
		}
		return EXIT_FAILURE;
		}

data-access/servlet/src/main/java/cutout/Soda.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ import vo.parameter.*;
		public interface Soda
		{

		public void doStream(String relPathname, int hdunum,
		public int doStream(String relPathname, int hdunum,
		Pos pos, Band band, Time time, Pol pol, String pixels,
		OutputStream outputStream) throws IOException, InterruptedException;

data-access/servlet/src/main/java/cutout/SodaImpl.java

+53 −223

Original line number	Diff line number	Diff line
		@@ -43,32 +43,28 @@ class SodaImpl implements Soda
		}


		public void doStream(String relPathname, int hdunum,
		public int doStream(String relPathname, int hdunum,
		Pos pos, Band band, Time time, Pol pol, String pixels,
		OutputStream outputStream) throws IOException, InterruptedException
		{
		LOGGER.fine("trace");

		Instant start = Instant.now();
		LOGGER.fine("trace");

		boolean has_overlap = false;
		boolean pixels_valid = (pixels != null);

		String boundsString = "";
		if(outputStream == null)
		LOGGER.finest("supplied outputStream for cut-file is null");
		// FIXME throw excpetion here

		final boolean isDavCall = relPathname.startsWith("http://") \|\| relPathname.startsWith("https://");
		final boolean isAbsPath = relPathname.startsWith("/"); // Resolver removes schema from file://
		//boolean pixels_valid = (pixels != null);
		//final boolean isDavCall = relPathname.startsWith("http://")
		// \|\| relPathname.startsWith("https://");
		//final boolean isAbsPath = relPathname.startsWith("/"); // Resolver removes schema from file://
		// file:///some_abs_path -> /soma_abs_path
		// file://some_rel_path -> some_rel_path
		//String absPathname = (isDavCall \|\| isAbsPath) ? relPathname
		// : (fitsPaths.surveys() +"/"+ relPathname);

		String absPathname = (isDavCall \|\| isAbsPath) ? relPathname : (fitsPaths.surveys() +"/"+ relPathname);

		if( !pixels_valid )
		{
		ByteArrayOutputStream bos = new ByteArrayOutputStream();
		if(bos == null)
		throw new AssertionError("byte output stream for bounds was not created, is null");

		boolean has_overlap = false;
		String boundsString = "";
		JsonEncoder jReq = new JsonEncoder();
		jReq.add(pos);
		jReq.add(band);
		@@ -77,203 +73,37 @@ class SodaImpl implements Soda
		String coordString = jReq.toString();
		LOGGER.finest("coordString: " + coordString);

		/* calc bounds */

		String[] cmdBounds = new String[4];
		cmdBounds[0] = "/usr/local/bin/vlkb";
		cmdBounds[1] = "overlap";
		cmdBounds[2] = absPathname;
		cmdBounds[3] = coordString;

		LOGGER.finest(String.join(" ", cmdBounds));
		String[] cmd = new String[5];
		cmd[0] = "/usr/local/bin/vlkb";
		cmd[1] = "cutout";
		cmd[2] = fitsPaths.surveys() + "/" + relPathname;
		cmd[3] = String.valueOf(hdunum);
		cmd[4] = coordString;
		LOGGER.finest(String.join(" ", cmd));

		ExecCmd execBounds = new ExecCmd();
		execBounds.doRun(bos, cmdBounds);
		LOGGER.finest("execBounds exitValue: " + execBounds.exitValue);

		boolean has_result = (execBounds.exitValue == 0);

		if(has_result)
		{
		boundsString = new String(bos.toByteArray());
		StringBuilder errorStrBuilder = new StringBuilder();

		/* FIXME disable GRID not supported
		boundsString = replaceWithGrid(boundsString, pos, band, time, pol);
		LOGGER.finest("boundsString(with GRID): " + boundsString);
		*/
		LOGGER.warning("GRID support was disabled");
		has_overlap = !((boundsString != null) && boundsString.trim().isEmpty());
		ExecCmd exec = new ExecCmd();
		exec.doRun(outputStream, cmd, errorStrBuilder);
		int rc = exec.exitValue;
		LOGGER.finest("exec cutout exitValue: " + rc);
		LOGGER.finer("EXECTIME cutoutDone: " + Duration.between(start, Instant.now()));

		if( !has_overlap )
		if(rc == 0)
		{
		throw new IllegalArgumentException(
		"region in file does not overlap with region defined by SODA parameters");
		}
		return rc; // OK
		}
		bos.close();

		Instant boundsDone = Instant.now();
		LOGGER.finer("EXECTIME boundsDone: " + Duration.between(start, boundsDone));
		}

		if(has_overlap \|\| pixels_valid)
		else if(rc == 1)
		{
		/* cutout -> outputStream */

		String pixFilterString = pixels_valid ? pixels : boundsString;

		String[] cmdCut = new String[5];
		cmdCut[0] = "/usr/local/bin/vlkb";
		cmdCut[1] = isDavCall ? "imcopydav" : "imcopy";
		cmdCut[2] = absPathname;
		cmdCut[3] = String.valueOf(hdunum-1);
		cmdCut[4] = pixFilterString;

		LOGGER.finest(String.join(" ", cmdCut));

		if(outputStream == null)
		LOGGER.finest("supplied outputStream for cut-file is null");

		ExecCmd execCut = new ExecCmd();
		execCut.doRun(outputStream, cmdCut);

		LOGGER.finest("execCut exitValue: " + execCut.exitValue);

		boolean cut_successful = (execCut.exitValue == 0);

		if(!cut_successful)
		{
		throw new IllegalArgumentException("cut by pixels not completed for pixels : " + pixFilterString);
		}

		Instant cutDone = Instant.now();
		LOGGER.finer("EXECTIME cutDone: " + Duration.between(start, cutDone));
		return rc; // OK, but no overlap
		}
		else
		{
		throw new IllegalArgumentException(
		"overlap computation could not be completed with the given arguments");
		"overlap computation could not be completed with the given arguments. "
		+ errorStrBuilder.toString());
		}
		}


		private String genRegionForVlkbOverlapCmd(Pos pos, Band band)
		{
		LOGGER.fine("trace");

		String region = "";

		if(pos != null)
		{
		String skySystem = pos.system.name();

		if(pos.shape.equals("CIRCLE"))
		{
		double l = pos.circle.lon;
		double b = pos.circle.lat;
		double r = pos.circle.radius;
		region = region + "skysystem=" + skySystem + "&l=" + String.valueOf(l) + "&b=" + String.valueOf(b)
		+ "&r=" + String.valueOf(r);
		}
		else if(pos.shape.equals("RANGE"))
		{
		double l = (pos.range.lon1 + pos.range.lon2)/2.0;
		double b = (pos.range.lat1 + pos.range.lat2)/2.0;
		double dl = (pos.range.lon2 - pos.range.lon1);
		double db = (pos.range.lat2 - pos.range.lat1);
		region = region + "skysystem=" + skySystem + "&l=" + String.valueOf(l) + "&b=" + String.valueOf(b)
		+ "&dl=" + String.valueOf(dl) + "&db=" + String.valueOf(db);
		}
		else
		{
		LOGGER.finest("FIXME here Exception: POLYGON not supported or pos.shape invalid: " + pos.shape);
		}

		}

		if(band != null)
		{
		String specSystem = band.system.name();
		double vl = band.min;
		double vu = band.max;

		region =region + "specsystem=" + specSystem + "&vl=" + String.valueOf(vl) + "&vu=" + String.valueOf(vu);
		}

		return region;
		}

		/*
		private String replaceWithGrid(String wcsBounds, Pos pos, Band band, Time time, Pol pol)
		{
		// remove end-of-line (was added by vlkb_ast.cpp: cout << ... << endl)
		String lineSeparator = System.lineSeparator();
		wcsBounds = wcsBounds.replace(lineSeparator, "");
		LOGGER.finest("BOUNDS: " + wcsBounds);

		// replace in wcsBounds those bounds where pos,band,time or pol has system=GRID

		String[] substr = wcsBounds.split("(?=AXES)", 2);
		for(String ss : substr) LOGGER.finest("boundsResult: " + ss);

		String boundsString = substr[0];
		boolean noOverlap = ((boundsString != null) && boundsString.trim().isEmpty());
		if(noOverlap)
		{
		boundsString = ""; // no overlap
		}
		else
		{
		String axesTypes = "";
		if(substr.length > 1)
		{
		axesTypes = substr[1].replace("AXES"," ").trim();
		LOGGER.finest("AXES TYPES: " + axesTypes);

		String[] bnds = normalize(boundsString);
		String[] types = normalize(axesTypes);
		// assert: bnds.length == types.length
		LOGGER.finest("boundsCount: " + bnds.length + " typesCount: " + types.length);

		if(bnds.length == types.length)
		boundsString = replaceBounds(bnds, types, pos, band);
		}
		}
		return boundsString;
		}

		private String replaceBounds(String[] bnds, String[] types, Pos pos, Band band)
		{
		int ix;
		for(ix=0; ix<bnds.length; ix++)
		{
		if( types[ix].equals("LON") && ((pos != null) && (pos.system == Pos.System.GRID)) )
		{
		bnds[ix] = pos.lonBoundsString();
		}
		else if(types[ix].equals("LAT") && ((pos != null) && (pos.system == Pos.System.GRID)))
		{
		bnds[ix] = pos.latBoundsString();
		}
		else if(types[ix].equals("BAND") && ((band != null) && (band.system == Band.System.GRID)))
		{
		bnds[ix] = band.boundsString();
		}
		}

		LOGGER.finest("replaced: " + String.join(" ", bnds)) ;

		return "[" + String.join(" ", bnds) + "]";
		}

		// MAKE SURE vlkb overlap returns space delimited bounds: [ a:b c:d ]
		// normalize: strip [,] if any, and split into array by space
		private String[] normalize(String spaceStr)
		{
		String other = spaceStr.replace("[","").replace("]","");
		LOGGER.finest("normalize: " + other);
		return other.split("\\s+");
		}
		*/
		}

data-access/servlet/src/main/java/cutout/engine/cli/ExecCmd.java

+11 −5

Original line number	Diff line number	Diff line
		@@ -11,10 +11,14 @@ class StreamGobbler extends Thread
		InputStream is;
		String type;
		OutputStream os;
		StringBuilder sb;

		StreamGobbler(InputStream is, String type)
		StreamGobbler(InputStream is, String type, StringBuilder sb)
		{
		this(is, type, null);
		this.is = is;
		this.type = type;
		this.os = null;
		this.sb = sb;
		}

		StreamGobbler(InputStream is, String type, OutputStream redirect)
		@@ -48,7 +52,9 @@ class StreamGobbler extends Thread
		}
		else
		{
		LOGGER.finest(type + ">" + new String(buffer, 0, nread, "utf-8"));
		String str = new String(buffer, 0, nread, "utf-8");
		LOGGER.finest(type + ">" + str);//new String(buffer, 0, nread, "utf-8"));
		sb.append(str);
		}
		}

		@@ -69,7 +75,7 @@ class ExecCmd

		public int exitValue;

		public void doRun(OutputStream outputStream, String[] cmd)
		public void doRun(OutputStream outputStream, String[] cmd, StringBuilder error)
		throws IOException, InterruptedException
		{
		LOGGER.fine("trace CMD: " + Arrays.toString(cmd));
		@@ -82,7 +88,7 @@ class ExecCmd
		Process proc = rt.exec(cmd);

		// any error message?
		StreamGobbler errorGobbler = new StreamGobbler(proc.getErrorStream(), "ERROR");
		StreamGobbler errorGobbler = new StreamGobbler(proc.getErrorStream(), "ERROR", error);

		// any output?
		StreamGobbler outputGobbler = new StreamGobbler(proc.getInputStream(), "OUTPUT", outputStream);