documentation (for NIAC2014 attributes)

prjemian · Feb 11, 2016 · 01ff715 · 01ff715
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commit 01ff715
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Showing 5 changed files with 26 additions and 16 deletions.
diff --git a/docs/source/eznx.rst b/docs/source/eznx.rst
@@ -20,14 +20,19 @@ Here is a simple example to write a NeXus data file using eznx:
 The output of this code is an HDF5 file (binary).
 It has this structure:
 
-.. code-block:: guess
+.. code-block:: text
     :linenos:
 
 	eznx_example.hdf5:NeXus data file
+     @default = entry
 	  entry:NXentry
 	    @NX_class = NXentry
+       @default = data
 	    data:NXdata
 	      @NX_class = NXdata
+         @signal = counts
+         @axes = two_theta
+         @two_theta_indices = 0
 	      counts --> /entry/instrument/detector/counts
 	      two_theta --> /entry/instrument/detector/two_theta
 	    instrument:NXinstrument
@@ -36,8 +41,6 @@ It has this structure:
 	        @NX_class = NXdetector
 	        counts:NX_FLOAT64[11] = __array
 	          @units = counts
-	          @signal = 1
-	          @axes = two_theta
 	          @target = /entry/instrument/detector/counts
 	          __array = [1037.0, 2857.0, 23819.0, '...', 1321.0]
 	        two_theta:NX_FLOAT64[11] = __array
@@ -52,11 +55,13 @@ The output of this code is an HDF5 file (binary).
 It has this general structure (indentation shows HDF5 groups, 
 @ signs describe attributes of the preceding item):
 
-.. code-block:: guess
+.. code-block:: text
     :linenos:
 
       hdf5_file:NeXus data file
+         @default = S1
          S1:NXentry     (one NXentry for each scan)
+            @default = data
             title = #S
             T or M: #T or #M
             comments: #C for entire scan
@@ -69,11 +74,12 @@ It has this general structure (indentation shows HDF5 groups,
                ...
             data:NXdata
                @description = SPEC scan data (content from #L and data lines)
+               @signal = I0
+               @axes = mr
+               @mr_indices = 0
                Epoch:NX_FLOAT64[]
                I0:NX_FLOAT64[]         (last data column)
                  @spec_name = I0
-                 @signal = 1
-                 @axes = mr
                mr:NX_FLOAT64[]         (first data column)
                ...
             metadata:NXcollection

diff --git a/docs/source/h5toText.rst b/docs/source/h5toText.rst
@@ -50,20 +50,23 @@ Here's an example from a test data file
 (**writer_1_3.h5** from the NeXus documentation [#]_):
 
 
-.. code-block:: guess
+.. code-block:: text
     :linenos:
 
       [linux,512]$ h5toText data/writer_1_3.h5
       data/writer_1_3.h5 : NeXus data file
+        @default = Scan
         Scan:NXentry
           @NX_class = NXentry
+          @default = data
           data:NXdata
             @NX_class = NXdata
+            @signal = counts
+            @axes = two_theta
+            @two_theta_indices = 0
             counts:NX_INT32[31] = __array
               __array = [1037, 1318, 1704, '...', 1321]
               @units = counts
-              @signal = 1
-              @axes = two_theta
             two_theta:NX_FLOAT64[31] = __array
               __array = [17.926079999999999, 17.925909999999998, 17.925750000000001, '...', 17.92108]
               @units = degrees

diff --git a/docs/source/spec2nexus.rst b/docs/source/spec2nexus.rst
@@ -29,7 +29,7 @@ Verify the version of the installed spec2nexus::
 command-line options
 ********************
 
-.. code-block:: guess
+.. code-block:: text
     :linenos:
 
       $ spec2nexus.py -h

diff --git a/src/spec2nexus/eznx.py b/src/spec2nexus/eznx.py
@@ -39,7 +39,7 @@
     In [3]: nxentry = eznx.makeGroup(root, 'entry', 'NXentry')
     In [4]: eznx.write_dataset(nxentry, 'title', 'simple test data', default='data')
     Out[4]: <HDF5 dataset "title": shape (), type "|O8">
-    In [5]: nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata', signal='counts', axes='tth', tth_indices=[0,])
+    In [5]: nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata', signal='counts', axes='tth', tth_indices=0)
     In [6]: eznx.write_dataset(nxdata, 'tth', [10.0, 10.1, 10.2, 10.3], units='degrees')
     Out[6]: <HDF5 dataset "tth": shape (4,), type "<f8">
     In [7]: eznx.write_dataset(nxdata, 'counts', [1, 50, 1000, 5], units='counts')
@@ -61,7 +61,7 @@
           @NX_class = NXdata
           @signal = 'counts'
           @axes = 'tth'
-          @axes_indices = [0,]
+          @axes_indices = 0
           counts:NX_INT64[4] = [1, 50, 1000, 5]
             @units = counts
             @axes = tth

diff --git a/src/spec2nexus/eznx_example.py b/src/spec2nexus/eznx_example.py
@@ -31,16 +31,17 @@
 tthData, countsData = zip(*[map(float,_.split()) for _ in I_v_TTH_DATA.strip().splitlines()])
 
 f = eznx.makeFile(HDF5_FILE)  # create the HDF5 NeXus file
+f.attrs['default'] = 'entry'
 
-nxentry = eznx.makeGroup(f, 'entry', 'NXentry')
+nxentry = eznx.makeGroup(f, 'entry', 'NXentry', default='data')
 nxinstrument = eznx.makeGroup(nxentry, 'instrument', 'NXinstrument')
 nxdetector = eznx.makeGroup(nxinstrument, 'detector', 'NXdetector')
 
 tth = eznx.makeDataset(nxdetector, "two_theta", tthData, units='degrees')
-counts = eznx.makeDataset(nxdetector, "counts", countsData, 
-                   units='counts', signal=1, axes='two_theta')
+counts = eznx.makeDataset(nxdetector, "counts", countsData, units='counts')
 
-nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata')
+nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata', 
+                        signal=1, axes='two_theta', two_theta_indices=0)
 eznx.makeLink(nxdetector, tth, nxdata.name+'/two_theta')
 eznx.makeLink(nxdetector, counts, nxdata.name+'/counts')