Changeset 282

Timestamp:

Feb 19, 2011 11:54:34 AM (14 years ago)

Author:

saunders

Message:

Got read_dataset and write_dataset working for primary and secondary. Need to work on
dim_datasets next.

File:

• hdf5_exchange/idl/trunk/nxexchange.pro (modified) (25 diffs)

hdf5_exchange/idl/trunk/nxexchange.pro ¶

@@ -30 +30 @@
 ;       NXEXCHANGE::CLOSE          closes HDF5 file 
 ;       NXEXCHANGE::WRITE_DATASET  writes out one dataset
+;       NXEXCHANGE::READ_DATASET   reads one dataset
 ;
 ;
 ; EXAMPLE:
-;       ;; Create nxexchange object for writing data.h5 file
-;       nxe = obj_new('nxexchange', version='0.3b')
+;       ;; Create nxexchange object for reading/writing data files
+;       nxe = obj_new('nxexchange')
 ;
 ;       ;; open an HDF5 file for writing
-;       success = nxe->open('data.h5', 'w')
+;       nxe->open, 'data.h5', 'w'
 ;
 ;       ;; make a 3x3 array of ints
@@ -43 +44 @@
 ;
 ;       ;; write it out as primary dataset 
-;       success = nxe->write_dataset('image',['x','y'],'flourescence', idataset)
+;       nxe->write_dataset, 'image',['x','y'],'flourescence', idataset
 ;
 ;       ;; write out a secondary dataset associated with above image
 ;       tdataset = fltarr(5)
-;       success = nxe->write_dataset('temps',['C'],'', tdataset, parent='image')
+;       nxe->write_dataset, 'temps',['C'],'', tdataset, parent='image'
 ;       
 ;       ;; close the file
+;       nxe->close
+;
+;       ;; re-open the file for reading
+;       nxe->open, 'data.h5','r'
+;
+;       ;; read in a primary dataset
+;       idataset = nxe->read_dataset('image')
+;
+;       ;; read in a secondary dataset
+;       tdataset = nxe->read_dataset('temps', parent='image')
+;
+;       ;; close the file again
 ;       nxe->close
 ;
@@ -104 +117 @@
 ;; A simple struct to hold a primary dataset index along with
 ;;   associated HDF5 group ids
-pro datasetentry__define
-  COMPILE_OPT strictarr
-  struct = {datasetentry, $
+pro nxexchangedatasetentry__define
+  COMPILE_OPT strictarr
+  struct = {nxexchangedatasetentry, $
             index: 0L, $
             entry_exchange_gid: 0L, $
@@ -114 +127 @@
 
 ; =============================================================
-;
+; INTRINSIC
 ; METHODNAME:
 ;       NXEXCHANGE::INIT
@@ -129 +142 @@
 ;
 ; RETURNS:
-;       A new nxexchange object.
+;       1 - success in initializing, 0 - failure
 ;
 ; EXAMPLE:
 ;       nxe = obj_new('nxexchange', VERSION='0.3b')
+;       ;; the above indirectly invokes this init function during
+;       ;;   object construction
 ;       
 ;
@@ -138 +153 @@
 
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::init error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
-  endif
   
   if keyword_set(vers) then begin
@@ -181 +190 @@
 ;       none
 ;
-; RETURNS:
-;       1 - success, 0 - failure
-;
 ; EXAMPLE:
-;       nxe->open('data.nxs', 'w')
+;       nxe->open, 'data.h5', 'w'
 ;       
 ;
-function nxexchange::open, filename, mode
-
-  COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::open error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
-  endif
+pro nxexchange::open, filename, mode
+
+  COMPILE_OPT strictarr
 
   if (self.fid ne 0) then begin
-      message, 'a file is already open named: ' + self.filename
+      message, 'a file is already open named: ' + self.filename, /informational
+      return
   endif
 
@@ -211 +212 @@
     self.fid = H5F_CREATE(self.filename)
     ;; build out some initial structure
-    success = self->build_default_structure()
-    if (~success) then begin
-        message, 'unable to build default structure'
-    endif
+    self->build_default_structure
 
   endif else if (self.mode eq 'R') then begin
@@ -223 +221 @@
     if (~success) then begin
         self.fid = 0
-        message, 'this file does not appear to be valid'
+        message, 'this file does not appear to be valid', /informational
+        return
     endif
 
   endif else if (self.mode eq 'A') then begin
     ;; self.fid = H5F_OPEN(self.filename, /WRITE)
-    message, 'the append (A) mode is not supported yet'
+    message, 'the append (A) mode is not supported yet', /informational
+    return
 
   endif else begin
-    message, 'the mode argument must be w or r or a'
+    message, 'the mode argument must be w or r or a', /informational
+    return
   endelse
 
-  return, 1
+  return
 end
 
@@ -255 +256 @@
 ;                 belongs to given parent dataset
 ;
-; RETURNS:
-;       1 - success, 0 - failure
 ;
 ; EXAMPLE:
-;       nxe->write_dataset('data',['ttheta','energy'],'transmission',data)
-;
-;
-function nxexchange::write_dataset, name, axes, data_type, dataset, parent=parent
-  COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::write_dataset error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
+;       nxe->write_dataset, 'data',['ttheta','energy'],'transmission', data
+;
+;
+pro nxexchange::write_dataset, name, axes, data_type, dataset, parent=parent
+  COMPILE_OPT strictarr
+
+  if (self.fid eq 0) then begin
+      message, 'you cannot write a dataset without opening file first', /informational
+      return
   endif
-
-  if (self.fid eq 0) then return, 0
 
   ;; if parent dataset name given, then we are now entering a
@@ -279 +275 @@
       parent_exists = self.primary_dataset_set->iscontained(parent)
       if (~parent_exists) then begin
-          message, 'parent dataset '+parent+' does not exist'
+          message, 'parent dataset '+parent+' does not exist', /informational
+          return
       endif else begin
           primary_dataset = self.primary_dataset_set->get(parent)
@@ -295 +292 @@
   axes_n_elems = n_elements(axes)
   if ((n_dims gt 0) and (n_dims ne axes_n_elems)) then begin
-      message, 'axes must have same number of elements as dimensions of dataset'
+      message, 'axes must have same number of elements as dimensions of dataset', /informational
+      return
   endif
 
@@ -308 +306 @@
   ;; write primary dataset
   if (~secondary) then begin
-      dataset_entry = {datasetentry}
+      dataset_entry = {nxexchangedatasetentry}
       dataset_entry.index = self.primary_dataset_index + 1;
 
@@ -338 +336 @@
           H5A_CLOSE, signal_aid
       endif
-      existing_dataset_path = '/entry/' + name + '/data'
+      exchange_groupname = self->exchange_group_name(self.primary_dataset_index)
+      target_path = '/entry/'+exchange_groupname+'/'+name
       target_aid = H5A_CREATE(dsid, 'target', self.string_dtid, self.simple_dspid)
-      H5A_WRITE, target_aid, existing_dataset_path
+      H5A_WRITE, target_aid, target_path
       H5A_CLOSE, target_aid    
 
@@ -385 +384 @@
   endif 
 
-  return, 1
+  return
 end
 
@@ -404 +403 @@
 ;
 ; RETURNS:
-;       dataset - success, null_ptr - failure
+;       dataset 
 ;
 ; EXAMPLE:
-;       nxe->read_dataset('data')
+;       my_primary_dataset = nxe->read_dataset('image')
+;       my_secondary_dataset = nxe->read_dataset('temps', parent='image')
 ;
 ;
 function nxexchange::read_dataset, name, parent=parent
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::read_dataset error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, ptr_new()
+
+  if (self.fid eq 0) then begin
+      message, 'you cannot read a dataset without opening file first', /informational
+      return, 0
   endif
-
-  if (self.fid eq 0) then return, ptr_new()
 
   ;; if parent dataset name given, then we are reading a
   ;;   secondary dataset
   if keyword_set(parent) then begin  
-      ;; have to iterate exchange groups to find secondary dataset
-;;      n_entry_groups = H5G_GET_NMEMBERS(self.fid, 'entry')
-
-;;      for i=0, n_entry_groups-1 do begin
-;;          obj_name = H5G_GET_MEMBER_NAME(self.fid, 'entry', i)
-;;          s = strpos(obj_name, 'exchange')
-;;          if (s eq 0) then begin
-;;              gid = H5G_OPEN(self.entry_gid, obj_name)
-;;              dsid = H5D_OPEN(gid, parent)
-;;              CATCH, error
-;;              if (error ne 0)
-              
-
-;;          endif
-;;          oid = H5G_OPEN(self.entry_gid, obj_name)
-;;          type_string = H5I_GET_TYPE(oid)
-;;          if (type_string eq 'GROUP') then begin
-              ;; see if group has @NX_class=NXsubentry
-;;              H5A_OPEN_NAME(oid
-              
-;;          endif
-;;      endfor
-
-;; try this a different way...
-      ;; validate that parent group exists
-;;      parent_gid = H5G_OPEN(self.entry_gid,parent)
-;;      link_dest_path = H5G_GET_LINKVAL(parent_gid,'data')
-      ;; slice off end to get group path
-;;      end_pos = strpos(link_dest_path, parent, /REVERSE_SEARCH)
-;;      exchange_path = strpos(link_dest_path, 0, end_pos)
-
-;;      print, '**** exchange_path: ' + exchange_path
+      ;; install temporary exception handler (yuck)
+      CATCH, error
+      if (error ne 0) then begin
+          message, 'given parent dataset ' + parent + ' does not exist in file', /informational
+          return, 0
+      endif
+      ;; attempt to find /entry/'parent' NXdata group
+      parent_gid = H5G_OPEN(self.entry_gid,parent)
+      CATCH, /CANCEL   ;; cancel temporary exception handler
       
-      ;; open dataset
-      dsid = H5D_OPEN(parent_gid, name)
+      ;; open NXdata dataset
+      dsid = H5D_OPEN(parent_gid, 'data')
+      ;; get @target attribute
+      target_aid = H5A_OPEN_NAME(dsid,'target')
+      target_path = H5A_READ(target_aid)
+      H5A_CLOSE, target_aid
+      ;; close out the linked dataset
+      H5D_CLOSE, dsid
+      ;; close out NXdata group
+      H5G_CLOSE, parent_gid
+
+      ;; slice off end of target path to get group path
+      end_pos = strpos(target_path, parent, /REVERSE_SEARCH)
+      exchange_path = strmid(target_path, 0, end_pos)
+      
+      ;; open exchange group
+      parent_gid = H5G_OPEN(self.fid, exchange_path)
+      ;; finally! - read the dataset we are looking for
+      dsid = H5D_OPEN(parent_gid, name);
       dataset = H5D_READ(dsid)
 
@@ -470 +461 @@
   H5D_CLOSE, dsid
 
-  ;; clean up gids
+  ;; clean up gid
   H5G_CLOSE, parent_gid
 
@@ -479 +470 @@
 ; Internal METHOD - builds initial /entry 
 ;
-function nxexchange::build_default_structure
-  COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::build_default_structure error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
-  endif
-
-  if (self.fid eq 0) then begin
-      return, 0
-  endif
+pro nxexchange::build_default_structure
+  COMPILE_OPT strictarr
 
   ;; create /entry group with @NX_class=NXentry
@@ -498 +479 @@
   H5A_CLOSE, nxclass_aid
 
-  return, 1
+  return
 end
 
 ; =============================================================
 ; Internal METHOD - reads in initial file structure and validates
+;    returns 1 - valid, 0 - invalid
 ;
 function nxexchange::read_default_structure
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::read_default_structure error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
-  endif
 
   ;; read /entry group and verify it has @NX_class=NXentry
@@ -529 +505 @@
 ;         index=2 produces /entry/exchange2
 ;   
-;     returns open gid for new group, or 0 if error
+;     returns open gid for new group
 ;
 function nxexchange::build_exchange_group, index
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::build_exchange_group error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
+
+  if (index lt 1) then begin
+      message, 'index must be 1 or greater', /informational
       return, 0
   endif
 
-  if (index lt 1) then begin
-      print, 'NXEXCHANGE::build_exchange_group error: index must be 1 or greater'
-      return, 0
-  endif
-
-  if (index eq 1) then begin
-      groupname = 'exchange'
-  endif else begin
-      groupname = 'exchange'+STRTRIM(STRING(index),1)
-  endelse
-
-    ;; create /entry/exchange(n) group with @NX_class=NXsubentry
+  groupname = self->exchange_group_name(index)
+
+  ;; create /entry/exchange(n) group with @NX_class=NXsubentry
   entry_exchange_gid = H5G_CREATE(self.entry_gid, groupname)
   nxclass_aid = H5A_CREATE(entry_exchange_gid, 'NX_class', self.string_dtid, self.simple_dspid)
@@ -568 +534 @@
 end
 
+function nxexchange::exchange_group_name, index
+  COMPILE_OPT strictarr
+  if (index eq 1) then begin
+      groupname = 'exchange'
+  endif else begin
+      groupname = 'exchange'+STRTRIM(STRING(index),1)
+  endelse
+  return, groupname
+end
+
 ; =============================================================
 ; Internal METHOD - builds a single nxdata group with given name
-;     returns open gid for new group, or 0 if error
+;     returns open gid for new group
 ;
 function nxexchange::build_nxdata_group, name
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::build_nxdata_group error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-      return, 0
-  endif
 
   ;; create /entry/'name' with @NX_class=NXdata
@@ -611 +581 @@
 pro nxexchange::close
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::close error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-  endif
 
   if (self.fid ne 0) then begin
       ;; close out various subgroup gids we have been holding onto
       keys = self.primary_dataset_set->keys()
-      for idx = 0L, N_ELEMENTS(keys)-1 do begin
+      if (keys eq '') then begin 
+          numkeys = 0
+      endif else begin
+          numkeys = n_elements(keys)
+      endelse
+      for idx = 0, numkeys-1 do begin
           key = keys[idx]
           dataset_entry = self.primary_dataset_set->get(key)
@@ -644 +614 @@
 
 ; =============================================================
-;
+; INTRINSIC
 ; METHODNAME:
 ;       NXEXCHANGE::CLEANUP
@@ -660 +630 @@
 ; EXAMPLE:
 ;       OBJ_DESTROY, nxe
+;       ;; the above winds up calling this cleanup procedure
 ;
 ;
 pro nxexchange::cleanup
   COMPILE_OPT strictarr
-  CATCH, error
-  if error ne 0 then begin
-      print, 'NXEXCHANGE::cleanup error: ',error,' ',!ERROR_STATE.MSG
-      CATCH, /CANCEL
-  endif
 
   ;; close out useful types and space definitions
@@ -680 +646 @@
 ; =============================================================
 ; METHODNAME: NXEXCHANGE__DEFINE
-;  internal method: defines nxexchange internal data structures
+;   defines nxexchange class data structure
 ;
 pro nxexchange__define