Changeset 33309

Timestamp:

Feb 20, 2012, 6:55:53 AM (14 years ago)

Author:

eugene

Message:

dvo_client with mextract connected to vector IO table now builds

Location:

branches/eam_branches/ipp-20111122/Ohana/src

Files:

• libfits/include/gfitsio.h (modified) (1 diff)
• libfits/table/F_get_column.c (modified) (2 diffs)
• opihi/cmd.data/read_vectors.c (modified) (1 diff)
• opihi/dvo/mextract.c (modified) (3 diffs)
• opihi/dvo/region_list.c (modified) (1 diff)
• opihi/include/dvomath.h (modified) (2 diffs)
• opihi/lib.shell/Makefile (modified) (1 diff)
• opihi/lib.shell/VectorIO.c (added)
• opihi/lib.shell/VectorOps.c (modified) (3 diffs)

branches/eam_branches/ipp-20111122/Ohana/src/libfits/include/gfitsio.h

@@ -184 +184 @@
 int     gfits_get_bintable_column      PROTO((Header *header, FTable *table, char *label, void **data));
 int     gfits_get_bintable_column_type PROTO((Header *header, char *label, char *type, int *Nval));
+int     gfits_get_bintable_column_type_by_N  PROTO((Header *header, int N, char *type, int *Nval));
 void   *gfits_get_bintable_column_data PROTO((Header *header, FTable *table, char *label, char *type, off_t *Nrow, int *Ncol));
 int     gfits_get_table_column         PROTO((Header *header, FTable *table, char *label, void **data));

branches/eam_branches/ipp-20111122/Ohana/src/libfits/table/F_get_column.c

@@ -126 +126 @@
 
 /***********************/
+int gfits_get_bintable_column_type_by_N (Header *header, int N, char *type, int *Nval) {
+
+  int Nbytes;
+  char field[80], format[80];
+
+  assert (N > 0);
+
+  sprintf (field, "TFORM%d", N);
+  if (!gfits_scan (header, field, "%s", 1, format)) return FALSE;
+  if (!gfits_bintable_format (format, type, Nval, &Nbytes)) return (FALSE);
+  return (TRUE);
+}
+
+/***********************/
 int gfits_get_bintable_column_type (Header *header, char *label, char *type, int *Nval) {
 
-  int i, N, Nfields, Nbytes;
-  char tlabel[80], field[80], format[80];
+  int i, N, Nfields;
+  char tlabel[80], field[80];
 
   if (label == (char *) NULL) return (FALSE);
@@ -144 +158 @@
   N = i - 1;
 
-  sprintf (field, "TFORM%d", N);
-  gfits_scan (header, field, "%s", 1, format);
-
-  if (!gfits_bintable_format (format, type, Nval, &Nbytes)) return (FALSE);
+  if (!gfits_get_bintable_column_type_by_N (header, N, type, Nval)) return FALSE;
   return (TRUE);
 }

branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.data/read_vectors.c

@@ -297 +297 @@
   }
 
+  // XXX ReadAll needs: deal with Extnum vs Extname, save vectors, etc
+  // ReadAll = FALSE;
+  // if ((N = get_argument (argc, argv, "-all"))) {
+  //   remove_argument (N, &argc, argv);
+  //   ReadAll = atoi (extname);
+  //   if (argc != 1) ESCAPE ("-all option cannot be mixed with selected field");
+  // }
+
   if (argc < 2) ESCAPE ("USAGE: read -fits extension [-extnum] [-keyword key] name name ...");
 

branches/eam_branches/ipp-20111122/Ohana/src/opihi/dvo/mextract.c

@@ -5 +5 @@
 # define PARALLEL_SERIAL 0
 # define MAX_PATH_LENGTH 1024
+
+int HostTableLaunchJobs (HostTable *table, char *basecmd);
+Vector **MergeVectors (Vector **vec, int *Nvec, Vector **invec, int Ninvec);
 
 int mextract (int argc, char **argv) {
@@ -93 +96 @@
 
     // load fields from file
-    // ReadVectorTables
+    int    Nvec = 0;
+    Vector **vec = NULL;
+    for (i = 0; i < table->Nhosts; i++) {
+      char resultFile[MAX_PATH_LENGTH];
+      snprintf (resultFile, MAX_PATH_LENGTH, "%s/dvo.results.fits", table->hosts[i].pathname);
+        
+      int    Ninvec = 0;
+      Vector **invec = ReadVectorTableFITS (resultFile, "MEXTRACT", &Ninvec);
+
+      vec = MergeVectors (vec, &Nvec, invec, Ninvec);
+      if (vec != invec) {
+        FreeVectorArray (invec, Ninvec);
+      }
+    }
+
+    for (i = 0; i < Nvec; i++) {
+      AssignVector (vec[i], vec[i]->name, ANYVECTOR, TRUE);
+    }
+    free (vec);
+
     return TRUE;
   }
@@ -449 +471 @@
 }
 
+// take two arrays of vectors and merge equal named vectors.
+// for ease, require that the order of the names match & number of vectors match
+Vector **MergeVectors (Vector **vec, int *Nvec, Vector **invec, int Ninvec) {
+
+  int i, j;
+
+  if (vec == NULL) {
+    *Nvec = Ninvec;
+    return invec;
+  }
+
+  myAssert (*Nvec == Ninvec, "programming error (1)");
+
+  for (i = 0; i < Ninvec; i++) {
+    myAssert (!strcmp(vec[i]->name, invec[i]->name), "programming error (2)");
+    myAssert (vec[i]->type == invec[i]->type, "programming error (2)");
+
+    if (vec[i]->type == OPIHI_FLT) {
+      REALLOCATE (vec[i]->elements.Flt, opihi_flt, vec[i]->Nelements + invec[i]->Nelements);
+      for (j = 0; j < invec[i]->Nelements; j++) {
+        vec[i]->elements.Flt[i+j] = vec[i]->elements.Flt[j];
+      }
+    } else {
+      REALLOCATE (vec[i]->elements.Int, opihi_int, vec[i]->Nelements + invec[i]->Nelements);
+      for (j = 0; j < invec[i]->Nelements; j++) {
+        vec[i]->elements.Int[i+j] = vec[i]->elements.Int[j];
+      }
+    }
+    vec[i]->Nelements += invec[i]->Nelements;
+  }
+  return vec;
+}

branches/eam_branches/ipp-20111122/Ohana/src/opihi/dvo/region_list.c

@@ -113 +113 @@
   /* check for Region selection from display */
   if ((N = get_argument (*argc, argv, "-skyregion"))) {
-    if (N + 5 >= *argc) {
+    if (N + 4 >= *argc) {
       gprint (GP_ERR, "USAGE: -skyregion (RA) (RA) (DEC) (DEC)\n");
       FreeSkyRegionSelection (selection);

branches/eam_branches/ipp-20111122/Ohana/src/opihi/include/dvomath.h

@@ -111 +111 @@
 
 /* vector handling */
+void          InitVectors           PROTO((void));
+void          FreeVectors           PROTO((void));
 Vector       *InitVector            PROTO((void));
-void          InitVectors           PROTO((void));
+void          FreeVectorArray       PROTO((Vector **vec, int Nvec));
 int           CopyVector            PROTO((Vector *out, Vector *in));
 int           ResetVector           PROTO((Vector *vec, char type, int Nelements));
@@ -127 +129 @@
 int           ListVectors           PROTO((void));
 Vector       *SelectVector          PROTO((char *name, int mode, int verbose));
+int           AssignVector          PROTO((Vector *vec, char *name, int mode, int verbose));
+
+/* vector IO functions */
 int           WriteVectorTableFITS  PROTO((char *filename, char *extname, Vector **vec, int Nvec, int append, char *format));
+Vector      **ReadVectorTableFITS   PROTO((char *filename, char *extname, int *Nvec));
 
 /* buffer handling */

branches/eam_branches/ipp-20111122/Ohana/src/opihi/lib.shell/Makefile

@@ -24 +24 @@
 $(SDIR)/VariableOps.$(ARCH).o           \
 $(SDIR)/VectorOps.$(ARCH).o             \
+$(SDIR)/VectorIO.$(ARCH).o             \
 $(SDIR)/check_stack.$(ARCH).o           \
 $(SDIR)/command.$(ARCH).o               \

branches/eam_branches/ipp-20111122/Ohana/src/opihi/lib.shell/VectorOps.c

@@ -15 +15 @@
 
 // this function is NOT thread protected : it is only used in startup and/or shutdown
+void FreeVectorArray (Vector **vec, int Nvec) {
+
+  int i;
+
+  if (!vec) return;
+  for (i = 0; i < Nvec; i++) {
+    if (!vec[i]) continue;
+    if (vec[i]->elements.Int) {
+      free (vec[i]->elements.Int);
+    }
+    free (vec[i]);
+  }
+  free (vec);
+}
+
+// this function is NOT thread protected : it is only used in startup and/or shutdown
 void FreeVectors () {
-
-  int i;
-
-  for (i = 0; i < Nvectors; i++) {
-    if (vectors[i][0].elements.Int) {
-      free (vectors[i][0].elements.Int);
-    }
-    free (vectors[i]);
-  }
-  free (vectors);
+  FreeVectorArray (vectors, Nvectors);
 }
 
@@ -93 +100 @@
 }
   
+// Assign the given Vector to the internal array of vectors by name
+int AssignVector (Vector *vec, char *name, int mode, int verbose) {
+
+  int i;
+
+  if (name == NULL) goto error;
+  if (ISNUM(name[0])) goto error;
+  if (IsBuffer(name)) goto error;
+
+  for (i = 0; (i < Nvectors) && (strcmp(vectors[i][0].name, name)); i++);
+  /* is a new vector */
+  if (i == Nvectors) { 
+    if (mode == OLDVECTOR) goto error;
+    pthread_mutex_lock (&mutex);
+    Nvectors ++;
+    REALLOCATE (vectors, Vector *, Nvectors);
+    vectors[i] = vec;
+    pthread_mutex_unlock (&mutex);
+    return TRUE;
+  } 
+  /* is an old vector */
+  if (mode == NEWVECTOR) goto error;
+  vectors[i] = vec;
+  return TRUE;
+
+ error:
+  if (verbose) gprint (GP_ERR, "invalid vector %s\n", name);
+  return FALSE;
+}
+  
 /* delete by pointer */
 int DeleteVector (Vector *vec) {
@@ -287 +324 @@
   return (TRUE);
 }
-  
-// write a set of vectors to a FITS file
-int WriteVectorTableFITS (char *filename, char *extname, Vector **vec, int Nvec, int append, char *format) {
-  
-  char *tformat = NULL;
-  Header header;
-  Matrix matrix;
-  Header theader;
-  FTable ftable;
-
-  int j;
-  FILE *f = NULL;
-
-  /* open file for outuput */
-  if (append) {
-    f = fopen (filename, "a");
-  } else {
-    f = fopen (filename, "w");
-  }
-  if (f == (FILE *) NULL) {
-    gprint (GP_ERR, "can't open file for write\n");
-    return (FALSE);
-  }
-
-  if (!append) {
-    gfits_init_header (&header);
-    header.extend = TRUE;
-    gfits_create_header (&header);
-    gfits_create_matrix (&header, &matrix);
-  }
-
-  gfits_create_table_header (&theader, "BINTABLE", extname);
-
-  ALLOCATE (tformat, char, 2*Nvec);
-  if (format) {
-    // the bintable format string can only define the byte-width of each field.  valid output columns are currently:
-    // B (char), I (16 bit short), J (32 bit int), E (32 bit float), D (64 bit double).
-    // the format string is just the sequence of types, eg: LIIJEED
-    // validate the format string
-    char *ptr = format;
-    for (j = 0; j < Nvec; j++) {
-      while (*ptr && OHANA_WHITESPACE (*ptr)) ptr++;
-      if (*ptr == 0) {
-        gprint (GP_ERR, "error in binary table format %s (insufficient format chars)\n", format);
-        goto escape;
-      }
-      if ((*ptr != 'B') && (*ptr != 'I') && (*ptr != 'J') && (*ptr != 'D') && (*ptr != 'E')) {
-        gprint (GP_ERR, "error in binary table format %s: invalid character %c\n", format, *ptr);
-        goto escape;
-      }
-      tformat[2*j + 0] = *ptr;
-      tformat[2*j + 1] = 0; // a bit sleazy : use a 2xN string to store N 1-byte strings
-      ptr ++;
-    }
-    while (*ptr && OHANA_WHITESPACE (*ptr)) ptr++;
-    if (*ptr) {
-      gprint (GP_ERR, "error in binary table format %s (extra characters in format)\n", format);
-      goto escape;
-    }
-  } else {
-    for (j = 0; j < Nvec; j++) {
-      // if the format is not defined, just use the native byte-widths
-      tformat[2*j + 0] = (vec[j][0].type == OPIHI_FLT) ? 'D' : 'J';
-      tformat[2*j + 1] = 0;
-    }
-  }
-
-  // define the columns of the table.  XXX NOTE: we cannot have duplicate names in
-  // output table (because the data goes to the named column below).  need to enforce
-  // this somehow
-  for (j = 0; j < Nvec; j++) {
-    gfits_define_bintable_column (&theader, &tformat[2*j], vec[j][0].name, NULL, NULL, 1.0, 0.0);
-  }
-  free (tformat);
-
-  // generate the output array that carries the data
-  gfits_create_table (&theader, &ftable);
-
-  // add the vectors to the output array
-  for (j = 0; j < Nvec; j++) {
-    if (vec[j][0].type == OPIHI_FLT) {
-      gfits_set_bintable_column_reformat (&theader, &ftable, vec[j][0].name, "double", vec[j][0].elements.Flt, vec[j][0].Nelements);
-    } else {
-      gfits_set_bintable_column_reformat (&theader, &ftable, vec[j][0].name, "int", vec[j][0].elements.Int, vec[j][0].Nelements);
-    }
-  }
-
-  if (!append) {
-    gfits_fwrite_header  (f, &header);
-    gfits_fwrite_matrix  (f, &matrix);
-    gfits_free_header (&header);
-    gfits_free_matrix (&matrix);
-  }
-  gfits_fwrite_Theader (f, &theader);
-  gfits_fwrite_table  (f, &ftable);
-
-  gfits_free_header (&theader);
-  gfits_free_table (&ftable);
-
-  fclose (f);
-  fflush (f);
-  return (TRUE);
-
- escape:
-  if (!append) {
-    gfits_free_header (&header);
-    gfits_free_matrix (&matrix);
-  }
-  gfits_free_header (&theader);
-  gfits_free_table (&ftable);
-
-  if (tformat) free (tformat);
-  fclose (f);
-  fflush (f);
-  return (FALSE);
-}