diff --git a/manual/source/examples/code_napi.rst b/manual/source/examples/code_napi.rst index f168caec12..631853b0eb 100644 --- a/manual/source/examples/code_napi.rst +++ b/manual/source/examples/code_napi.rst @@ -96,20 +96,21 @@ NAPI Python Example: ``h5dump`` output of NeXus HDF5 file :language: text -View a NeXus HDF5 file using *h5toText.py* -########################################## +View a NeXus HDF5 file using *punx tree* +######################################## The output of ``h5dump`` contains a lot of structural information about the HDF5 file that can distract us from the actual content we added to the file. -Next, we show the output from a custom Python tool (``h5toText.py``) built for -this documentation and later moved into the **spec2nexus** package. [#]_ -This tool was developed to show the actual data content of an +Next, we show the output from a custom Python tool (``punx.py tree``) built for +this NeXus data file validation and view. [#]_ +The *tree* option of this tool [#]_ was developed to show the actual data content of an HDF5 file that we create. -.. [#] **spec2nexus** : http://spec2nexus.readthedocs.org +.. [#] **punx** : http://punx.readthedocs.org +.. [#] **punx tree** : https://punx.readthedocs.io/en/latest/source_code/h5tree.html#how-to-use-h5tree -NAPI Python Example: ``h5toText`` output of NeXus HDF5 file -+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +NAPI Python Example: ``punx tree simple3D.h5`` output of NeXus HDF5 file +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. literalinclude:: simple3D.xture.txt :tab-width: 4 diff --git a/manual/source/examples/h5py/create_data.sh b/manual/source/examples/h5py/create_data.sh index e9da0b6490..5d15af5be4 100755 --- a/manual/source/examples/h5py/create_data.sh +++ b/manual/source/examples/h5py/create_data.sh @@ -6,24 +6,22 @@ #python TestReader.py #python TestWriter.py -# h5toText comes from the spec2nexus package - python BasicWriter.py -h5toText prj_test.nexus.hdf5 > prj_test.nexus_structure.txt +punx tree prj_test.nexus.hdf5 > prj_test.nexus_structure.txt h5dump prj_test.nexus.hdf5 > prj_test.nexus_h5dump.txt python externalExample.py -h5toText external_angles.hdf5 > external_angles_structure.txt +punx tree external_angles.hdf5 > external_angles_structure.txt h5dump external_angles.hdf5 > external_angles_h5dump.txt -h5toText external_counts.hdf5 > external_counts_structure.txt +punx tree external_counts.hdf5 > external_counts_structure.txt h5dump external_counts.hdf5 > external_counts_h5dump.txt -h5toText external_master.hdf5 > external_master_structure.txt +punx tree external_master.hdf5 > external_master_structure.txt h5dump external_master.hdf5 > external_master_h5dump.txt python writer_1_3.py -h5toText writer_1_3.hdf5 > writer_1_3_structure.txt +punx tree writer_1_3.hdf5 > writer_1_3_structure.txt h5dump writer_1_3.hdf5 > writer_1_3_h5dump.txt python writer_2_1.py -h5toText writer_2_1.hdf5 > writer_2_1_structure.txt +punx tree writer_2_1.hdf5 > writer_2_1_structure.txt h5dump writer_2_1.hdf5 > writer_2_1_h5dump.txt diff --git a/manual/source/examples/h5py/index.rst b/manual/source/examples/h5py/index.rst index d7dda5e436..974a206c24 100644 --- a/manual/source/examples/h5py/index.rst +++ b/manual/source/examples/h5py/index.rst @@ -351,15 +351,15 @@ file description :download:`BasicWriter.py` python code to write example *prj_test.nexus.hdf5* :download:`external_angles_h5dump.txt` *h5dump* analysis of *external_angles.hdf5* :download:`external_angles.hdf5` HDF5 file written by *externalExample* -:download:`external_angles_structure.txt` *h5toText* analysis of *external_angles.hdf5* +:download:`external_angles_structure.txt` *punx tree* analysis of *external_angles.hdf5* :download:`external_counts_h5dump.txt` *h5dump* analysis of *external_counts.hdf5* :download:`external_counts.hdf5` HDF5 file written by *externalExample* -:download:`external_counts_structure.txt` *h5toText* analysis of *external_counts.hdf5* +:download:`external_counts_structure.txt` *punx tree* analysis of *external_counts.hdf5* :download:`externalExample.py` python code to write external linking examples :download:`external_master_h5dump.txt` *h5dump* analysis of *external_master.hdf5* :download:`external_master.hdf5` NeXus file written by *externalExample* -:download:`external_master_structure.txt` *h5toText* analysis of *external_master.hdf5* +:download:`external_master_structure.txt` *punx tree* analysis of *external_master.hdf5* :download:`prj_test.nexus_h5dump.txt` *h5dump* analysis of the NeXus file :download:`prj_test.nexus.hdf5` NeXus file written by *BasicWriter* -:download:`prj_test.nexus_structure.txt` *h5toText* analysis of the NeXus file +:download:`prj_test.nexus_structure.txt` *punx tree* analysis of the NeXus file =========================================== ============================================= diff --git a/manual/source/examples/h5py/writer_1_3.rst b/manual/source/examples/h5py/writer_1_3.rst index 7f98d9241c..cec0a193b3 100644 --- a/manual/source/examples/h5py/writer_1_3.rst +++ b/manual/source/examples/h5py/writer_1_3.rst @@ -67,7 +67,7 @@ decided by the ``h5py`` support package. :language: text Since the output of ``h5dump`` is verbose (see the *Downloads* section below), -the *h5toText* tool [#]_ was used to +the *punx tree* tool [#]_ was used to print out the structure of HDF5 data files. This tool provides a simplified view of the NeXus file. Here is the output: @@ -77,9 +77,9 @@ of the NeXus file. Here is the output: :language: text As the data files in these examples become more complex, you will appreciate -the information density provided by *h5toText*. +the information density provided by *punx tree*. -.. [#] *h5toText* : http://spec2nexus.readthedocs.org/en/latest/h5toText.html +.. [#] *punx tree* : https://punx.readthedocs.io/en/latest/source_code/h5tree.html#how-to-use-h5tree downloads ********* @@ -92,5 +92,5 @@ file description :download:`writer_1_3.py` python code to write example *writer_1_3* :download:`writer_1_3.hdf5` NeXus file written by this code :download:`writer_1_3_h5dump.txt` *h5dump* analysis of the NeXus file -:download:`writer_1_3_structure.txt` *h5toText* analysis of the NeXus file +:download:`writer_1_3_structure.txt` *punx tree* analysis of the NeXus file ===================================== ============================================= diff --git a/manual/source/examples/h5py/writer_2_1.rst b/manual/source/examples/h5py/writer_2_1.rst index 05427c1edd..80f7729887 100644 --- a/manual/source/examples/h5py/writer_2_1.rst +++ b/manual/source/examples/h5py/writer_2_1.rst @@ -73,7 +73,7 @@ has been made and shows the HDF5 path to the description. NeXus recognizes this behavior of the HDF5 library and adds an additional structure when building hard links, the ``target`` attribute, to preserve the original location of the data. Not that it actually matters. -The ``h5toText.py`` tool knows about the additional NeXus +The ``punx.py tree`` tool knows about the additional NeXus ``target`` attribute and shows the data to appear in its original location, in the ``NXdetector`` group. @@ -93,6 +93,6 @@ file description :download:`writer_2_1.py` python code to write example *writer_2_1* :download:`writer_2_1.hdf5` NeXus file written by this code :download:`writer_2_1_h5dump.txt` *h5dump* analysis of the NeXus file -:download:`writer_2_1_structure.txt` *h5toText* analysis of the NeXus file +:download:`writer_2_1_structure.txt` *punx tree* analysis of the NeXus file ===================================== ============================================= \ No newline at end of file diff --git a/manual/source/faq.rst b/manual/source/faq.rst index 25e2afe782..e1aeb8af03 100644 --- a/manual/source/faq.rst +++ b/manual/source/faq.rst @@ -28,7 +28,7 @@ This is a list of commonly asked questions concerning the NeXus data format. NeXus data files. The easiest graphical tool to use is *HDFview* which can open any HDF file. Other tools such as *PyMCA* and *NeXPy* provide visualization of scientific data while *h5dump* - and *h5toText* provide text renditions of content and structure. + and *punx tree* provide text renditions of content and structure. If you want to try, for example ``nxbrowse`` is a utility provided by the NeXus community that can be very diff --git a/manual/source/utilities.rst b/manual/source/utilities.rst index 76099a6100..e249ac0c73 100644 --- a/manual/source/utilities.rst +++ b/manual/source/utilities.rst @@ -153,7 +153,10 @@ The list is not intended to be a complete list of all available packages. NOTE: project is under initial construction, not yet released for public use, but is useful in its - present form (version 0.0.9). + present form (version 0.2.3). + + **punx** can show the tree structure of any HDF5 file. + The output is more concise than that from *h5dump*. See the program documentation for more details: https://punx.readthedocs.io @@ -283,7 +286,6 @@ as a data format. It is not intended to be a complete list of all available pac **spec2nexus** (http://spec2nexus.readthedocs.io) (Python code) Converts SPEC data files and scans into NeXus HDF5 files. - Provides *h5toText* utility program to inspect HDF5 file content. Provides libraries: * *spec2nexus.spec*: python binding to read SPEC [#]_ data files