diff --git a/manual/source/defs_intro.rst b/manual/source/defs_intro.rst index b55e565efe..3585a8263f 100644 --- a/manual/source/defs_intro.rst +++ b/manual/source/defs_intro.rst @@ -104,7 +104,7 @@ Name must satisfy both :index:`HDF ` and :index:`XML ` :index:`naming `. -.. code-block:: guess +.. code-block:: text :linenos: NameStartChar ::= _ | a..z | A..Z diff --git a/manual/source/design.rst b/manual/source/design.rst index 2c1ec3c6db..51714fc934 100644 --- a/manual/source/design.rst +++ b/manual/source/design.rst @@ -355,7 +355,7 @@ showing an external file link in HDF5: .. rubric:: Example of linking to data in an external HDF5 file - .. code-block:: guess + .. code-block:: text :linenos: EXTERNAL_LINK "data" { diff --git a/manual/source/examples/code_napi.rst b/manual/source/examples/code_napi.rst index 53d277b1ee..f168caec12 100644 --- a/manual/source/examples/code_napi.rst +++ b/manual/source/examples/code_napi.rst @@ -32,7 +32,7 @@ NAPI C Example: write simple NeXus file .. literalinclude:: napi-example.c :tab-width: 4 :linenos: - :language: guess + :language: c NAPI F77 Example: write simple NeXus file +++++++++++++++++++++++++++++++++++++++++ @@ -42,7 +42,7 @@ NAPI F77 Example: write simple NeXus file .. literalinclude:: napi-example.f77 :tab-width: 4 :linenos: - :language: guess + :language: fortran NAPI F90 Example: write simple NeXus file +++++++++++++++++++++++++++++++++++++++++ @@ -54,7 +54,7 @@ NAPI F90 Example: write simple NeXus file .. literalinclude:: napi-example.f90 :tab-width: 4 :linenos: - :language: guess + :language: fortran .. _example.napi.simple.3d.write.python: @@ -75,7 +75,7 @@ NAPI Python Example: write simple NeXus file .. literalinclude:: simple3D.py :tab-width: 4 :linenos: - :language: guess + :language: python View a NeXus HDF5 file using *h5dump* ##################################### @@ -93,7 +93,7 @@ NAPI Python Example: ``h5dump`` output of NeXus HDF5 file .. literalinclude:: simple3D.h5dump.txt :tab-width: 4 :linenos: - :language: guess + :language: text View a NeXus HDF5 file using *h5toText.py* @@ -114,5 +114,5 @@ NAPI Python Example: ``h5toText`` output of NeXus HDF5 file .. literalinclude:: simple3D.xture.txt :tab-width: 4 :linenos: - :language: guess + :language: text diff --git a/manual/source/examples/code_native.rst b/manual/source/examples/code_native.rst index 50dc806c66..554f601ae9 100644 --- a/manual/source/examples/code_native.rst +++ b/manual/source/examples/code_native.rst @@ -26,7 +26,7 @@ Writing a simple NeXus file using native HDF5 commands in C .. literalinclude:: nxh5write.c :tab-width: 4 :linenos: - :language: guess + :language: c .. _code_native.reading: @@ -36,5 +36,5 @@ Reading a simple NeXus file using native HDF5 commands in C .. literalinclude:: nxh5read.c :tab-width: 4 :linenos: - :language: guess + :language: c \ No newline at end of file diff --git a/manual/source/examples/epics/index.rst b/manual/source/examples/epics/index.rst index 6672b2f001..6d805d12af 100644 --- a/manual/source/examples/epics/index.rst +++ b/manual/source/examples/epics/index.rst @@ -67,7 +67,7 @@ default in a *default location*. .. literalinclude:: attributes-reformatted.xml :tab-width: 4 :linenos: - :language: guess + :language: xml If you want to add additional EPICS process variables (PVs) to be written in the HDF5 file, @@ -89,7 +89,7 @@ even if you add PVs (a.k.a. *ndattribute*) to the attributes.xml file. .. literalinclude:: layout.xml :tab-width: 4 :linenos: - :language: guess + :language: xml If you do not specify where in the file to write an *ndattribute* from the attributes file, it will be written within the group that has @@ -220,7 +220,7 @@ This example uses the *h5py* [#]_ package to write the HDF5 file. .. literalinclude:: write_nexus_file.py :tab-width: 4 :linenos: - :language: guess + :language: python The output from that code is given in the @@ -230,7 +230,7 @@ example.h5 file. It has this tree structure: .. literalinclude:: tree_structure.txt :tab-width: 4 :linenos: - :language: guess + :language: text .. note:: Alternatively, the metadata shown in this example might be placed in the ``/entry/instrument/detector`` (*NXdetector*) @@ -252,7 +252,7 @@ using *nexusformat*: .. literalinclude:: write_nexus_file2.py :tab-width: 4 :linenos: - :language: guess + :language: python Visualization diff --git a/manual/source/examples/lrmecs/index.rst b/manual/source/examples/lrmecs/index.rst index 2bba5e9665..19dccef558 100755 --- a/manual/source/examples/lrmecs/index.rst +++ b/manual/source/examples/lrmecs/index.rst @@ -37,7 +37,7 @@ LRMECS ``lrcs3701`` data: ``h5dump`` output .. literalinclude:: dump-histogram1-data.txt :tab-width: 4 :linenos: - :language: guess + :language: text Visualize Using *HDFview* diff --git a/manual/source/examples/matlab/index.rst b/manual/source/examples/matlab/index.rst index 10aede58fc..696d31e383 100644 --- a/manual/source/examples/matlab/index.rst +++ b/manual/source/examples/matlab/index.rst @@ -24,7 +24,7 @@ This is the same data used with :ref:`Example-H5py`. .. literalinclude:: input.dat :tab-width: 4 :linenos: - :language: guess + :language: text writing data ++++++++++++ @@ -38,7 +38,7 @@ writing data .. literalinclude:: basic_writer.m :tab-width: 4 :linenos: - :language: guess + :language: text reading data ++++++++++++ @@ -52,7 +52,7 @@ reading data .. literalinclude:: basic_reader.m :tab-width: 4 :linenos: - :language: guess + :language: text writing data file with links @@ -67,7 +67,7 @@ writing data file with links .. literalinclude:: writer_2_1.m :tab-width: 4 :linenos: - :language: guess + :language: text .. compound:: @@ -78,7 +78,7 @@ writing data file with links .. literalinclude:: h5link.m :tab-width: 4 :linenos: - :language: guess + :language: text Downloads diff --git a/manual/source/fileformat.rst b/manual/source/fileformat.rst index 47ce3605f9..2e144c41f1 100644 --- a/manual/source/fileformat.rst +++ b/manual/source/fileformat.rst @@ -130,7 +130,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/h5dump_group.txt :tab-width: 4 :linenos: - :language: guess + :language: text .. compound:: @@ -141,7 +141,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/h5dump_field.txt :tab-width: 4 :linenos: - :language: guess + :language: text .. compound:: @@ -152,7 +152,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/h5dump_attribute.txt :tab-width: 4 :linenos: - :language: guess + :language: text .. compound:: @@ -163,7 +163,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/h5dump_link.txt :tab-width: 4 :linenos: - :language: guess + :language: text .. XML is no longer a supported backend file format @@ -197,7 +197,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/mapping1.xml.txt :tab-width: 4 :linenos: - :language: guess + :language: xml NeXus data sets are encoded as XML elements with the name of the data. An attribute ``NAPItype`` defines the type and @@ -216,7 +216,7 @@ chapter for examples that use the native HDF5 calls to write NeXus data files. .. literalinclude:: examples/mapping2.xml.txt :tab-width: 4 :linenos: - :language: guess + :language: xml .. index:: attribute; XML diff --git a/manual/source/napi-java.rst b/manual/source/napi-java.rst index e61ca3d4d5..146defbed5 100644 --- a/manual/source/napi-java.rst +++ b/manual/source/napi-java.rst @@ -130,7 +130,7 @@ Here are examples for a UNIX shell and the Windows shell. .. literalinclude:: examples/napi-java-jnexus.sh :tab-width: 4 :linenos: - :language: guess + :language: sh .. compound:: @@ -139,7 +139,7 @@ Here are examples for a UNIX shell and the Windows shell. .. literalinclude:: examples/napi-java-jnexus.bat :tab-width: 4 :linenos: - :language: guess + :language: bat .. _NAPI-java-general-Programming: @@ -173,7 +173,7 @@ to get a feeling for the API: .. literalinclude:: examples/napi-java-prog1.java :tab-width: 4 :linenos: - :language: guess + :language: java Some notes on this little example: @@ -214,7 +214,7 @@ Again a code sample which shows how this looks like: .. literalinclude:: examples/napi-java-datarw1.java :tab-width: 4 :linenos: - :language: guess + :language: java The dataset is created as usual with ``makedata()`` and opened with ``putdata()``. The trick is in ``putdata()``. @@ -240,7 +240,7 @@ converted to and from bytes when reading string data. See a writing example: .. literalinclude:: examples/napi-java-datarw2.java :tab-width: 4 :linenos: - :language: guess + :language: java And reading: @@ -251,7 +251,7 @@ And reading: .. literalinclude:: examples/napi-java-datarw2.java :tab-width: 4 :linenos: - :language: guess + :language: java The aforementioned holds for all strings written as SDS content or as an attribute. SDS or vGroup names do not need this treatment. @@ -271,7 +271,7 @@ Let us compare the C-API and Java-API signatures of the .. literalinclude:: examples/frag-c-api-sig-getinfo.c :tab-width: 4 :linenos: - :language: guess + :language: c .. compound:: @@ -280,7 +280,7 @@ Let us compare the C-API and Java-API signatures of the .. literalinclude:: examples/frag-c-api-sig-getinfo.java :tab-width: 4 :linenos: - :language: guess + :language: java The problem is that Java passes arguments only by value, which means they cannot be modified by the method. Only array arguments can be modified. @@ -300,7 +300,7 @@ stored object for the key. Thus the code for a vGroup search looks like this: .. literalinclude:: examples/napi-java-inquiry1.java :tab-width: 4 :linenos: - :language: guess + :language: java For an attribute search both at global or SDS level the returned Hashtable will hold the name as the key and a little class holding the type and size @@ -313,7 +313,7 @@ information as value. Thus an attribute search looks like this in the Java-API: .. literalinclude:: examples/napi-java-inquiry2.java :tab-width: 4 :linenos: - :language: guess + :language: java For more information about the usage of the API routines see the reference or the NeXus C-API reference pages. Another good source of information is