data-access/engine/src/Makefile

@@ -12,10 +12,10 @@ RPM_ROOT = rpmbuild
 
 .PHONY: all clean
 
-all: vlkb vlkb-obscore vlkbd
+all: vlkb vlkb-obscore
 
-.PHONY: vlkb vlkb-obscore vlkbd
-vlkb vlkb-obscore vlkbd:
+.PHONY: vlkb vlkb-obscore
+vlkb vlkb-obscore:
 	make -C common
 	make -C $@
 	make  EXEC_NAME=$@ $(PACK_EXT)
@@ -23,7 +23,6 @@ vlkb vlkb-obscore vlkbd:
 clean:
 	make -C vlkb clean
 	make -C vlkb-obscore clean
-	make -C vlkbd clean
 	make -C common clean
 
 

data-access/engine/src/common/include/ast4vl.hpp

@@ -21,13 +21,6 @@ struct Bounds
    int naxis;
 };
 
-struct uint_bounds
-{
-   unsigned int pix1;
-   unsigned int pix2;
-   unsigned char type;
-};
-
 struct double_xy
 {
    double x;

data-access/engine/src/common/include/cutout.hpp

@@ -12,6 +12,14 @@ enum class specsystem {NONE, VELO_LSRK, WAVE_Barycentric};
 enum class timesystem {NONE, MJD_UTC};
 
 
+struct uint_bounds
+{
+   unsigned int pix1;
+   unsigned int pix2;
+   unsigned char type;
+};
+
+
 /* SODA */
 
 struct circle
@@ -68,25 +76,27 @@ struct coordinates
 {
    coordinates();
 
-   skysystem skysys;               // mandatory: "GALACTIC"|"ICRS"
-   double lon_deg, lat_deg;        // mandatory
-   area  shape;                    // mandatory: CIRCLE dlon=dlat=2xRadius, RECT dlon may differ from dlat
-   double dlon_deg, dlat_deg;      // mandatory
-   std::vector<double> p_lon_deg;  // mandatory polygon arrry
-   std::vector<double> p_lat_deg;  // mandatory polygon array
+   skysystem skysys;               // mandatory: NONE GALACTIC ICRS
+   double lon_deg, lat_deg;        // optional, check skysys == NONE
+   area  shape;                    // optional: CIRCLE dlon=dlat=2xRadius, RECT dlon may differ dlat
+   double dlon_deg, dlat_deg;      // optional
+   std::vector<double> p_lon_deg;  // optional polygon arrry
+   std::vector<double> p_lat_deg;  // optional polygon array
 
-   specsystem specsys;             // mandatory NONE VELO-LSRK WAVE-Bary
+   specsystem specsys;             // mandatory NONE VELO_LSRK WAVE_Barycentric
    double vl_kmps, vu_kmps;        // optional, check specsystem == NONE
 
    timesystem timesys;
    double time_value[2];           // time interval (MJD in UTC)
 
    std::vector<std::string> pol;   // polarization states FIXME pol should be Set<enums>
+
+   std::vector<uint_bounds> pixel_i;   // PIXEL_i for non-standard axes allow direct cut without WCS
 };
 
  coordinates parse_coordinates(const std::string region_string);
  coordinates to_coordinates(const position pos, const band bnd, const time_axis time,
-       const std::vector<std::string> pol);
+       const std::vector<std::string> pol, const std::vector<uint_bounds> pixel_i);
 
 /* cutout */
 

data-access/engine/src/common/include/cutout_nljson.hpp

@@ -15,6 +15,8 @@ void to_json(json& j, const cutout_res_s& p);
 void to_json(json& j, const fits_card& p);
 void from_json(const json& j, fits_card& p);
 
+void from_json(const json& j, uint_bounds& p);
+
 void to_json(json& j, const coordinates& p);
 void from_json(const json& j, coordinates& p);
 

data-access/engine/src/common/src/ast_frameset.cpp

@@ -791,12 +791,17 @@ overlap_ranges ast::frameset::overlap_in_wcs(coordinates coord)
    return overlap_ranges{ov_code, pix_ranges };
 }
 #else
-void log_bounds(string prefix, int length, double low[], double up[])
+void ast::frameset::log_bounds(string prefix, int length, double low[], double up[])
 {
 	int ix;
-   LOG_STREAM << prefix << endl;
-   for(ix=0; ix<length; ix++) LOG_STREAM << prefix << low[ix] << " " << up[ix] 
-      << " deg: " << R2D*low[ix] << " " << R2D*up[ix] << endl;
+   double factor;
+   bool is_wcs = (prefix.find("WCS") != std::string::npos);
+	for(ix=0; ix<length; ix++)
+   {
+      factor = (is_wcs && (ix == (m_sky_lon_axis-1) || ix == (m_sky_lat_axis-1))) ? R2D : 1.0;
+		LOG_STREAM << prefix << factor*low[ix] << " " << factor*up[ix] << endl;
+	}
+	//   << " deg: " << R2D*low[ix] << " " << R2D*up[ix] << endl;
 }
 
 
@@ -941,7 +946,7 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 	astGetRegionBounds(pixbox, xlbnd, xubnd);
 	if ( !astOK )
 		throw runtime_error(failed_with_status(__FILE__,__LINE__,"astGetRegionBounds( pixbox )"));
-   log_bounds("XX BOUNDS header_pix: ", naxes, xlbnd, xubnd);
+	log_bounds("BOUNDS header PIX: ", naxes, xlbnd, xubnd);
 	/* DEBUG only */
 
 
@@ -961,11 +966,13 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 	if ( !astOK )
 		throw runtime_error(failed_with_status(__FILE__,__LINE__,"astGetRegionBounds"));
 
-   log_bounds("XX BOUNDS header: ", naxes, low, up);
+	log_bounds("BOUNDS header WCS: ", naxes, low, up);
 
 
-   /* overwrite bounds for sky-axis and spec axis if given by coord input */
+	/* overwrite bounds for sky- spec- time- pol-axis if given by coord */
 
+	if(m_has_skyframe && (coord.skysys != skysystem::NONE))
+	{
 		int ix_lon = m_sky_lon_axis - 1; //astGetI(m_hdr_fs,"LonAxis") - 1;
 		int ix_lat = m_sky_lat_axis - 1; //astGetI(m_hdr_fs,"LatAxis") - 1;
 													//if ( !astOK )
@@ -980,6 +987,7 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 		low[ix_lat] = D2R * (coord.lat_deg - coord.dlat_deg/2.0);
 		up[ix_lon]  = D2R * (coord.lon_deg + coord.dlon_deg/2.0); 
 		up[ix_lat]  = D2R * (coord.lat_deg + coord.dlat_deg/2.0);
+	}
 
 	vector<double_xy> pix_ranges;
 
@@ -1005,8 +1013,8 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 			/* set values only to get correct debug print for client */
 			low[m_spec_axis-1] = coord.vl_kmps;
 			up [m_spec_axis-1] = coord.vu_kmps;
-         log_bounds("XX BOUNDS client: ", naxes, low, up);
-         LOG_STREAM << "XX BOUNDS no overlap in spectrum axis, returning ov_code=1" << endl;
+			log_bounds("BOUNDS client WCS: ", naxes, low, up);
+			LOG_STREAM << "BOUNDS no overlap in spectrum axis, returning ov_code=1" << endl;
 			return overlap_ranges{1, pix_ranges };
 		}
 		else // at least partial overlap -> cut coord to min/max of header values
@@ -1031,7 +1039,7 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 		up [m_stokes_axis-1] = max_pol_state(coord.pol);
 	}
 
-   log_bounds("XX BOUNDS client: ", naxes, low, up);
+	log_bounds("BOUNDS client WCS: ", naxes, low, up);
 
 	/* FIXME ignored coord.shape; add circle later : metters for ovelap-code (but not for cut, which is always rect) */
 	AstRegion * crgn = (AstRegion *)astBox( wcsbox, 1, low, up , (AstRegion*)AST__NULL," ");
@@ -1050,7 +1058,7 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 	if ( !astOK )
 		throw runtime_error(failed_with_status(__FILE__,__LINE__,"astGetRegionBounds"));
 
-   log_bounds("XX BOUNDS client_pix: ", naxes, cllow, clup);
+	log_bounds("BOUNDS client PIX: ", naxes, cllow, clup);
 	/* DBG only */
 
 
@@ -1080,7 +1088,7 @@ overlap_ranges ast::frameset::overlap(coordinates coord)
 		if ( !astOK )
 			throw runtime_error(failed_with_status(__FILE__,__LINE__,"astGetRegionBounds( pixOverlap )"));
 
-      log_bounds("XX BOUNDS overlap_pix: ", m_NAXIS, lbnd, ubnd);
+		log_bounds("BOUNDS overlap PIX: ", m_NAXIS, lbnd, ubnd);
 
 		int ix;
 		for(ix=0; ix<m_NAXIS; ix++)

data-access/engine/src/common/src/ast_frameset.hpp

@@ -45,6 +45,7 @@ class frameset
       std::ostream& serialize(std::ostream& strm) const;
 
    private:
+      void log_bounds(std::string prefix, int length, double low[], double up[]);
       void log_warnings(const AstFitsChan * fchan);
 
       AstRegion * create_header_region(void);

data-access/engine/src/common/src/cutout.cpp

@@ -177,6 +177,7 @@ string axistype2string(unsigned char cc)
       case 'b': return "BAND"; break;
       case 't': return "TIME"; break;
       case 'p': return "POL"; break;
+      case 'x': return "PIXEL_i"; break;
       case ' ': return "UNKNOWN"; break;
       default:
          throw invalid_argument(cc + " is not a valid axis type");
@@ -207,7 +208,7 @@ coordinates parse_coordinates(const string region_string)
    LOG_trace(string(__func__) + " : " + region_string);
 
    json_region reg(region_string);
-   coordinates coord = to_coordinates(reg.get_pos(), reg.get_band(), reg.get_time(), reg.get_pol());
+   coordinates coord = to_coordinates(reg.get_pos(), reg.get_band(), reg.get_time(), reg.get_pol(), reg.get_pixel_i());
 
    LOG_STREAM << "coord parsed: " << coord << endl;
 
@@ -215,7 +216,8 @@ coordinates parse_coordinates(const string region_string)
 }
 
 
-coordinates to_coordinates(const position pos, const band bnd, const time_axis time, const std::vector<std::string> pol)
+coordinates to_coordinates(const position pos, const band bnd, const time_axis time,
+				const std::vector<std::string> pol, const std::vector<uint_bounds> pixel_i)
 {
    coordinates coord;
    coord.skysys = pos.sys;
@@ -274,6 +276,8 @@ coordinates to_coordinates(const position pos, const band bnd, const time_axis t
 
    coord.pol = pol;
 
+   coord.pixel_i = pixel_i;
+
    return coord;
 }
 
@@ -336,7 +340,8 @@ cutout_res_s do_cutout_file(
    const string abs_subimg_pathname = conf_fits_cutpath + "/" + generate_cut_fitsname(fits_pathname, hdunum);
    const string abs_fits_pathname{ conf_fits_path + "/" + fits_pathname };
 
-   coordinates coord = to_coordinates(pos, bnd, time, pol);
+   vector<uint_bounds> pixel_i_none;
+   coordinates coord = to_coordinates(pos, bnd, time, pol, pixel_i_none);
 
    uintmax_t filesize = cutout_file(abs_fits_pathname, hdunum, coord, abs_subimg_pathname, extra_cards);
 

data-access/engine/src/common/src/cutout_nljson.cpp

@@ -119,6 +119,13 @@ void from_json(const json& j, fits_card& p)
 }
 
 
+void from_json(const json& j, uint_bounds& p)
+{
+   if(j.contains("pix1")) j.at("pix1").get_to(p.pix1); else p.pix1 = 0;
+   if(j.contains("pix2")) j.at("pix2").get_to(p.pix2); else p.pix2 = 0;
+   if(j.contains("type")) j.at("type").get_to(p.type); else p.type = ' ';
+}
+
 
 
 // cutout

data-access/engine/src/common/src/cutout_ostream.cpp

@@ -110,15 +110,15 @@ std::ostream& operator<<( std::ostream &out, struct coordinates const& p)
    bool is_poly = (p.shape == area::POLYGON);
 
 
-   out << to_string(p.skysys) << " : (" << p.lon_deg << ", " << p.lat_deg << ") "
+   out << "POS["<< to_string(p.skysys) << "; (" << p.lon_deg << ", " << p.lat_deg << ") "
       << to_string(p.shape) <<  ": ("
       << (is_poly ? poly_lon_str : to_string(p.dlon_deg)) << ", "
-      << (is_poly ? poly_lat_str : to_string(p.dlat_deg)) << ") "
-      << to_string(p.specsys) << " [km/s] : (" << p.vl_kmps << ", " << p.vu_kmps << ") "
+      << (is_poly ? poly_lat_str : to_string(p.dlat_deg)) << ")] "
+      << "BAND[" <<to_string(p.specsys) << "; (" << p.vl_kmps << ", " << p.vu_kmps << ")] "
 //      << "POS(" << p.pos << ") "
 //      << "BAND(" << to_string(p.bandsys) << "; " << p.band_value[0]  << ", " << p.band_value[1] << ") "
-      << "TIME(" << to_string(p.timesys) << "; " << p.time_value[0]  << ", " << p.time_value[1] << ") "
-      << "POL(" << pol_str << ")";
+      << "TIME[" << to_string(p.timesys) << "; " << p.time_value[0]  << ", " << p.time_value[1] << "] "
+      << "POL[" << pol_str << "]";
    return out;
 }
 

data-access/engine/src/common/src/json_region.hpp

@@ -52,16 +52,29 @@ class json_region
 
       std::vector<std::string> get_pol()
       {
-         std::vector<std::string> str;
+         std::vector<std::string> str_vec;
          if(m_jservice.contains("pol"))
          {
             json j = m_jservice.at("pol");
-            str = j.get<std::vector<std::string>>();
+            str_vec = j.get<std::vector<std::string>>();
          }
-         return str;
+         return str_vec;
       }
 
 
+      std::vector<uint_bounds> get_pixel_i()
+      {
+         std::vector<uint_bounds> pixi_vec;
+         if(m_jservice.contains("pixel_i"))
+         {
+            json j = m_jservice.at("pixel_i");
+            pixi_vec = j.get<std::vector<uint_bounds>>();
+         }
+         return pixi_vec;
+      }
+
+
+
    private:
       json m_jservice;
 };

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

@@ -113,36 +113,36 @@ void read_lines(string pathname, vector<string>& lines)
 	}
 }
 
-int header_backup(const string& pathname, const string& extra_cards_pathname, bool backup)
+int header_backup(const string& pathname, int extnum, const string& extra_cards_pathname, bool backup, std::ostream& ostrm)
 {
 	LOG_trace(__func__);
 
+   LOG_STREAM << pathname << " " << extnum << endl;
+
 	vector<string> extra_cards;
 	read_lines(extra_cards_pathname, extra_cards);
 
-	int maxHdu = 1;//FIXME INT_MAX; // read all HDU's
+	int maxHdu = extnum+1;
+	int minHdu = extnum+1;
 	std::vector<fitsfiles::Hdu> allHdus =
-		fitsfiles::fname2hdrstr(pathname, extra_cards, maxHdu);
+		fitsfiles::fname2hdrstr(pathname, extra_cards, maxHdu, minHdu);
 
 	for(unsigned int i=0; i<allHdus.size(); i++)
 	{
-		cerr << "HDU#" << i << endl;
-
 		fitsfiles::Hdu hd = allHdus.at(i);
 
 		if(backup)
 			write_previous(hd.m_header, pathname +"hdr" + ((i>0) ? "#" + to_string(i+1)  : "") );
 		else
 		{
-			unsigned long i = 0;
+			unsigned long ii = 0;
 			unsigned long hdr_len = hd.m_header.length();
-			while((i*80+80) <= hdr_len)
+         LOG_STREAM << "header card count: " << hdr_len/80 << endl;
+			while((ii*80+80) <= hdr_len)
 			{
-				cout << hd.m_header.substr(80*i++, 80) << "<" << endl;
+				ostrm << hd.m_header.substr(80*ii++, 80) << endl;
 			}
 		}
-		// FIXME remove all explicit cout cerr to main.cpp and here use ostream&
-
 	}
 
 	return 0;
@@ -170,6 +170,11 @@ vector<string> split (const string &s, char delim)
 	return result;
 }
 
+void update_with_pixel_i(vector<uint_bounds>& bnds, vector<uint_bounds> pix_vec)
+{
+	for(unsigned int i=0; ( i<pix_vec.size() ) && ( i<bnds.size() ); i++)
+		if(pix_vec[i].type == 'x') bnds[i] = pix_vec[i];
+}
 
 int vlkb_overlap(const string& pathname, const string& region, vector<uint_bounds>& bnds) 
 {
@@ -188,6 +193,7 @@ int vlkb_overlap(const string& pathname, const string& region, vector<uint_bound
 		fitsfiles::Hdu hd = allHdus.at(i);
 		bnds = calc_overlap(hd.m_header, coord, ov_code);
 	}
+   update_with_pixel_i(bnds, coord.pixel_i);
 	return ov_code;
 }
 

data-access/engine/src/vlkb/src/ast.hpp

@@ -5,10 +5,11 @@
 
 #include <string>
 #include <vector>
+#include <iostream>
 
 int vlkb_skyvertices(const std::string& pathname, const std::string& skysys_str);
 int vlkb_listbounds(const std::string& skysys_str, const std::string& specsys_str, const std::string& pathname);
-int header_backup(const std::string& pathname, const std::string& extra_cards_pathname, bool backup = false);
+int header_backup(const std::string& pathname, int extnum, const std::string& extra_cards_pathname, bool backup = false, std::ostream& ostrm=std::cout);
 int vlkb_overlap(const std::string& pathname, const std::string& region, std::vector<uint_bounds>& bnds);
 
 #endif

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

@@ -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

@@ -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\"}}\'"
+         << 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;
 }
@@ -398,7 +404,7 @@ int cmd_header(int argc, char * argv[])
    if (argc < 2)
    {
       std::cerr
-         << "Usage:  header [--backup] [--extra-cards-pathname=<pathname>] <pathname.fits>...\n"
+         << "Usage:  header [--backup] [--extra-cards-pathname=<pathname>] [--extnum=] <pathname.fits>...\n"
          << "\n"
          << "Prints current header (one card per line) or writes the header into a file with the same pathname but 'fitshdr' extension.\n"
          << "Arguments:\n"
@@ -409,6 +415,7 @@ int cmd_header(int argc, char * argv[])
    {
       bool backup = false;
 		string extra_cards_pathname;
+      int extnum=0;
 
       for(int i=1; i<argc; i++)
       {
@@ -419,15 +426,16 @@ int cmd_header(int argc, char * argv[])
          else if(0 == (string(argv[i]).substr(0,2+21)).compare("--extra-cards-pathname="))
          {
             extra_cards_pathname = (string{argv[i]}).substr(2+21);
-				cout << "DBG " << extra_cards_pathname << endl;
+         }
+         else if(0 == (string(argv[i]).substr(0,2+7)).compare("--extnum="))
+         {
+            extnum = stoi( (string{argv[i]}).substr(2+7) );
          }
          else
          {
             string pathname(argv[i]);
-            cout << to_string(i) << " : " << pathname << endl;
 
-            rc = header_backup(pathname, extra_cards_pathname, backup);
-            std::cout << "header_backup rc: " << rc << std::endl;
+            rc = header_backup(pathname, extnum, extra_cards_pathname, backup, cout);
          }
       }
       rc = EXIT_SUCCESS;
@@ -534,7 +542,7 @@ int cmd_overlap(int argc, char * argv[])
          << "Usage:  overlap <filename.fits[ext]> <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";
+         " \'{\"pos\":{\"circle\":{\"lat\":-1.373,\"lon\":21.4458,\"radius\":0.1},\"system\":\"ICRS\"}}\'\n";
       rc = EXIT_FAILURE;
    }
    else

data-access/servlet/pom.xml

@@ -65,7 +65,7 @@
           <dependency>
                   <groupId>vo</groupId>
                   <artifactId>vlkb-volib</artifactId>
-                  <version>0.9.7</version>
+                  <version>0.9.8</version>
           </dependency>
 
           <!-- dependency>

data-access/servlet/src/main/java/common/Coord.java

@@ -7,7 +7,7 @@ class Coord
 
    String skySystem;  // FIXME enum ICRS | GALACTIC
    String shape = "CIRCLE";      // FIXME enum CIRCLE | RECT | POLYGON   FIXME replace RECT -> RANGE
-   String specSystem; // FIXME enum VELO_LSRK | WAVE_Barycentric | NONE
+   String specSystem; // FIXME enum VELO_LSRK | WAVE_Barycentric
 
    Pos  pos;
    Band band;

data-access/servlet/src/main/java/common/Pixeli.java

+
+
+class Pixeli
+{
+	int pix1,pix2;
+   int type;
+   Pixeli(int px1, int px2, char cc) {this.pix1=px1; this.pix2=px2; this.type=cc;}
+}

data-access/servlet/src/main/java/common/json/JsonEncoder.java

@@ -27,7 +27,6 @@ public class JsonEncoder
 
 
    // NOTE: implementation of NULL: do not put into json
-   // (alternatively could put JSON.NULL as "pos" value or use pos.system.NONE)
 
    public void add(Pos pos)
    {
@@ -91,6 +90,24 @@ public class JsonEncoder
       }
    }
 
+   public void add(Pixeli[] pixiArr)
+	{
+		if(pixiArr != null)
+		{
+			JSONArray jarr = new JSONArray();
+			for(Pixeli elem : pixiArr)
+			{
+				JSONObject j = new JSONObject();
+				j.put("pix1", elem.pix1);
+				j.put("pix2", elem.pix2);
+				j.put("type", elem.type);
+				jarr.add(j);
+			}
+			this.obj.put("pixel_i", jarr);
+		}
+	}
+
+
 
 	public void add(FitsCard[] extraCards)
 	{

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

@@ -14,8 +14,14 @@ import vo.parameter.*;
 public interface Soda
 {
 
-   public void doStream(String relPathname, int hdunum,
-         Pos pos, Band band, Time time, Pol pol, String pixels,
+   public int doStream(String relPathname, int hdunum,
+         Pos pos, Band band, Time time, Pol pol, Pixeli[] pixeli,
+         OutputStream outputStream) throws IOException, InterruptedException;
+
+   public int doStream(String relPathname, int hdunum, String pixels,
+         OutputStream outputStream) throws IOException, InterruptedException;
+
+   public int doStreamHeader(String relPathname, int hdunum,
          OutputStream outputStream) throws IOException, InterruptedException;
 
 }

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

@@ -43,237 +43,157 @@ class SodaImpl implements Soda
    }
 
 
-   public void doStream(String relPathname, int hdunum,
-         Pos pos, Band band, Time time, Pol pol, String pixels,
+   public int doStream(String relPathname, int hdunum,
+         Pos pos, Band band, Time time, Pol pol, Pixeli[] pixeli,
          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 = "";
-
-      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);
+		if(outputStream == null)
+			LOGGER.finest("supplied outputStream for cut-file is null");
+			// FIXME throw excpetion here
 
-      if( !pixels_valid )
+      /*/ DBG start
+		Pixeli[] pixeli =
       {
-         ByteArrayOutputStream bos = new ByteArrayOutputStream();
-         if(bos == null)
-            throw new AssertionError("byte output stream for bounds was not created, is null");
+      new Pixeli(0,0,' '),
+      new Pixeli(0,0,' '),
+      new Pixeli(10,20,'x')
+      };
+     // DBG end*/
 
+		boolean has_overlap  = false;
+		String boundsString = "";
 		JsonEncoder jReq = new JsonEncoder();
 		jReq.add(pos);
 		jReq.add(band);
 		jReq.add(time);
 		jReq.add(pol);
+		jReq.add(pixeli);
 		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;
+		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));
 
-         LOGGER.finest(String.join(" ", cmdBounds));
+		StringBuilder errorStrBuilder = new StringBuilder();
 
-         ExecCmd execBounds = new ExecCmd();
-         execBounds.doRun(bos, cmdBounds);
-         LOGGER.finest("execBounds exitValue: " + execBounds.exitValue);
+		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()));
 
-         boolean has_result = (execBounds.exitValue == 0);
-
-         if(has_result)
+		if(rc == 0)
 		{
-            boundsString = new String(bos.toByteArray());
-
-            /* 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());
-
-            if( !has_overlap )
+			return rc; // OK
+		}
+		else if(rc == 1)
+		{
+			return rc; // OK, but no overlap
+		}
+		else
 		{
 			throw new IllegalArgumentException(
-                     "region in file does not overlap with region defined by SODA parameters");
+					"overlap computation could not be completed with the given arguments. "
+					+ errorStrBuilder.toString());
 		}
 	}
-         bos.close();
 
-         Instant boundsDone = Instant.now();
-         LOGGER.finer("EXECTIME boundsDone: " + Duration.between(start, boundsDone));
-      }
 
-      if(has_overlap || pixels_valid)
-      {
-         /* 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));
+	public int doStream(String relPathname, int hdunum,
+			String pixels, OutputStream outputStream)  throws IOException, InterruptedException
+	{
+		Instant start = Instant.now();
+		LOGGER.fine("trace");
 
 		if(outputStream == null)
 			LOGGER.finest("supplied outputStream for cut-file is null");
 
-         ExecCmd execCut = new ExecCmd();
-         execCut.doRun(outputStream, cmdCut);
+		final boolean isDavCall= relPathname.startsWith("http://") || relPathname.startsWith("https://");
+		final boolean isAbsPath= relPathname.startsWith("/");
+		String absPathname = (isDavCall || isAbsPath) ? relPathname
+			: (fitsPaths.surveys() +"/"+ relPathname);
+
+		String[] cmd = new String[5];
+		cmd[0] = "/usr/local/bin/vlkb";
+		cmd[1] = (isDavCall) ? "imcopydav" : "imcopy";
+		cmd[2] = absPathname;
+		cmd[3] = String.valueOf(hdunum);
+		cmd[4] = pixels;
+		LOGGER.finest(String.join(" ", cmd));
 
-         LOGGER.finest("execCut exitValue: " + execCut.exitValue);
+		StringBuilder errorStrBuilder = new StringBuilder();
 
-         boolean cut_successful = (execCut.exitValue == 0);
+		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(!cut_successful)
+		if(rc == 0)
 		{
-            throw new IllegalArgumentException("cut by pixels not completed for pixels : " + pixFilterString);
+			return rc; // OK
 		}
-
-         Instant cutDone = Instant.now();
-         LOGGER.finer("EXECTIME    cutDone: " + Duration.between(start, cutDone));
+		else if(rc == 1)
+		{
+			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)
+	public int doStreamHeader(String relPathname, int hdunum,
+			OutputStream outputStream)  throws IOException, InterruptedException
 	{
+		Instant start = Instant.now();
 		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);
-      }
+		if(outputStream == null)
+			LOGGER.finest("supplied response outputStream is null");
 
-      return region;
-   }
+		final boolean isAbsPath= relPathname.startsWith("/");
+		String absPathname = isAbsPath ? relPathname : (fitsPaths.surveys() +"/"+ relPathname);
 
-/*
-   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);
+		String[] cmd = new String[4];
+		cmd[0] = "/usr/local/bin/vlkb";
+		cmd[1] = "header";
+		cmd[2] = "--extnum=" + String.valueOf(hdunum-1);
+		cmd[3] = absPathname;
+		LOGGER.finest(String.join(" ", cmd));
 
-      // replace in wcsBounds those bounds where pos,band,time or pol has system=GRID
+		StringBuilder errorStrBuilder = new StringBuilder();
 
-      String[] substr = wcsBounds.split("(?=AXES)", 2);
-      for(String ss : substr) LOGGER.finest("boundsResult: " + ss);
+		ExecCmd exec = new ExecCmd();
+		exec.doRun(outputStream, cmd, errorStrBuilder);
+		int rc = exec.exitValue;
+		LOGGER.finest("exec header exitValue: " + rc);
+		LOGGER.finer("EXECTIME    headerDone: " + Duration.between(start, Instant.now()));
 
-      String boundsString = substr[0];
-      boolean noOverlap = ((boundsString != null) && boundsString.trim().isEmpty());
-      if(noOverlap)
+		if(rc == 0)
 		{
-         boundsString = ""; // no overlap
+			return rc; // OK
 		}
 		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);
-         }
+			throw new IllegalArgumentException("header could not be retrieved (rc="
+					+ rc + ") " + errorStrBuilder.toString());
 		}
-      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+");
-   }
-*/
 }