From acfc820d69d4fb331d1e4a6b85624d41e925ccbc Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 12:01:59 -0600 Subject: [PATCH 1/6] Update README.md added section for autogenerated files --- README.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/README.md b/README.md index e0ce009..85222d9 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,27 @@ For sure, we need more documentation here. The files *writer_1_3.h5* and *writer_1_3__niac2014.h5* are taken directly from the NeXus online documentation +## Autogenerated examples for all application definitions + +In the `autogenerated_examples/nxdl` directory you will find examples of each +application definition in several forms, hdf5 files and python scripts that will +create hdf5 files which contain the required structure (groups/fields/attributes) +for each application definition. The data used for fields is meant only to show +the type of data required, not actually valid data (spectra or images) for each field, +the hope is that by studying the examples it will make it easier for users to +understand what they need to do in order to create Nexus compliant files for their desired +application definition. + +Directory map of examples found in the `autogenerated_examples/nxdl` directory: + +  `*/applications` Contains hdf5 files for each definition + +  `*/python_scripts/h5py` Contains python scripts to create each definition using **h5py** + +  `*python_scripts/nexusformat` Contains python scripts to create each definition using **nexusformat** + + + ## NeXus compliance of files An automated analysis (via code [*critique.py*](critique.py)) of the files, by directory, From 04d76a74849112c95a728eebc6d343df1dc2aa36 Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 12:14:56 -0600 Subject: [PATCH 2/6] Update README.md added references to validation output for the python scripts --- nxdl/README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nxdl/README.md b/nxdl/README.md index a87ca39..2628e79 100644 --- a/nxdl/README.md +++ b/nxdl/README.md @@ -98,3 +98,8 @@ finished exporting to [G:\tst_nexus\exampledata\nxdl\applications\NXiqproc.hdf5] [nxdl_validate_out](nxdl_validate_out.md) is the output of running **nxvalidate** against each generated file +[ex_h5py_validation_out.md](ex_h5py_validation_out.md) is the output from **nxvalidate** against the files created by the python scripts using **h5py** + +[ex_nexusformat_validation_out.md](ex_nexusformat_validation_out.md) is the output from **nxvalidate** against the files created by the python scripts using **nexusformat** + + From c4948b847e0e32565b0d64fb0720862f2093e26e Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 12:18:29 -0600 Subject: [PATCH 3/6] Update ex_h5py_validation_out.md updated to latest output --- nxdl/ex_h5py_validation_out.md | 78 +++++++++++++++++----------------- 1 file changed, 40 insertions(+), 38 deletions(-) diff --git a/nxdl/ex_h5py_validation_out.md b/nxdl/ex_h5py_validation_out.md index f82c80e..7e24227 100644 --- a/nxdl/ex_h5py_validation_out.md +++ b/nxdl/ex_h5py_validation_out.md @@ -1,40 +1,42 @@ **The following is output from running nxvalidate against the resulting hdf file for each generated ex_h5py_DEFINITION.py script** ``` -h5py_NXarchive.h5 passed validation -h5py_NXarpes.h5 passed validation -definition=NXcanSAS.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXdata sev=error dataPath=/entry dataFile=h5py_NXcanSAS.h5 -1 errors and 9 warnings found when validating h5py_NXcanSAS.h5 -h5py_NXdirecttof.h5 passed validation -h5py_NXfluo.h5 passed validation -h5py_NXindirecttof.h5 passed validation -h5py_NXiqproc.h5 passed validation -h5py_NXlauetof.h5 passed validation -h5py_NXmonopd.h5 passed validation -definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXsample/name sev=error dataPath=/entry/sample/depends_on dataFile=h5py_NXmx.h5 -definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXinstrument/NXdetector sev=error dataPath=/entry/instrument/detector/depends_on dataFile=h5py_NXmx.h5 -2 errors and 16 warnings found when validating h5py_NXmx.h5 -h5py_NXrefscan.h5 passed validation -h5py_NXreftof.h5 passed validation -h5py_NXsas.h5 passed validation -h5py_NXsastof.h5 passed validation -h5py_NXscan.h5 passed validation -h5py_NXspe.h5 passed validation -h5py_NXsqom.h5 passed validation -h5py_NXstxm.h5 passed validation -h5py_NXtas.h5 passed validation -h5py_NXtofnpd.h5 passed validation -h5py_NXtofraw.h5 passed validation -h5py_NXtofsingle.h5 passed validation -h5py_NXtomo.h5 passed validation -h5py_NXtomophase.h5 passed validation -h5py_NXtomoproc.h5 passed validation -h5py_NXxas.h5 passed validation -h5py_NXxasproc.h5 passed validation -h5py_NXxbase.h5 passed validation -h5py_NXxeuler.h5 passed validation -h5py_NXxkappa.h5 passed validation -h5py_NXxlaue.h5 passed validation -h5py_NXxlaueplate.h5 passed validation -h5py_NXxnb.h5 passed validation -h5py_NXxrot.h5 passed validation -``` \ No newline at end of file +NXarchive.h5 passed validation +NXarpes.h5 passed validation +definition=NXcanSAS.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXdata sev=error dataPath=/entry dataFile=NXcanSAS.h5 +1 errors and 9 warnings found when validating NXcanSAS.h5 +NXdirecttof.h5 passed validation +NXfluo.h5 passed validation +NXindirecttof.h5 passed validation +NXiqproc.h5 passed validation +NXlauetof.h5 passed validation +NXmonopd.h5 passed validation +definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXsample/name sev=error dataPath=/entry/sample/depends_on dataFile=NXmx.h5 +definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXinstrument/NXdetector sev=error dataPath=/entry/instrument/detector/depends_on dataFile=NXmx.h5 +2 errors and 16 warnings found when validating NXmx.h5 +NXrefscan.h5 passed validation +NXreftof.h5 passed validation +NXsas.h5 passed validation +NXsastof.h5 passed validation +NXscan.h5 passed validation +NXspe.h5 passed validation +NXsqom.h5 passed validation +NXstxm.h5 passed validation +definition=NXtas.nxdl.xml message="Link target /entry/instrument/analyzer/ef is invalid" nxdlPath=/NXentry/NXdata/ef dataPath=/entry/data/ef sev=error dataFile=NXtas.h5 +1 errors and 18 warnings found when validating NXtas.h5 +NXtofnpd.h5 passed validation +NXtofraw.h5 passed validation +NXtofsingle.h5 passed validation +NXtomo.h5 passed validation +NXtomophase.h5 passed validation +NXtomoproc.h5 passed validation +NXxas.h5 passed validation +NXxasproc.h5 passed validation +NXxbase.h5 passed validation +NXxeuler.h5 passed validation +NXxkappa.h5 passed validation +NXxlaue.h5 passed validation +NXxlaueplate.h5 passed validation +NXxnb.h5 passed validation +NXxrot.h5 passed validation + +``` From ac3b1515aa9c26a36d1575c260e88f67d8fe3ce9 Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 12:19:27 -0600 Subject: [PATCH 4/6] Update ex_nexusformat_validation_out.md updated to latest output --- nxdl/ex_nexusformat_validation_out.md | 77 ++++++++++++++------------- 1 file changed, 39 insertions(+), 38 deletions(-) diff --git a/nxdl/ex_nexusformat_validation_out.md b/nxdl/ex_nexusformat_validation_out.md index ba7cadf..578c93b 100644 --- a/nxdl/ex_nexusformat_validation_out.md +++ b/nxdl/ex_nexusformat_validation_out.md @@ -1,40 +1,41 @@ **The following is output from running nxvalidate against the resulting hdf file for each generated ex_nexusformat_DEFINITION.py script** ``` -nexusformat_NXarchive.h5 passed validation -nexusformat_NXarpes.h5 passed validation -definition=NXcanSAS.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXdata sev=error dataPath=/entry dataFile=nexusformat_NXcanSAS.h5 -1 errors and 10 warnings found when validating nexusformat_NXcanSAS.h5 -nexusformat_NXdirecttof.h5 passed validation -nexusformat_NXfluo.h5 passed validation -nexusformat_NXindirecttof.h5 passed validation -nexusformat_NXiqproc.h5 passed validation -nexusformat_NXlauetof.h5 passed validation -nexusformat_NXmonopd.h5 passed validation -definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXsample/name sev=error dataPath=/entry/sample/depends_on dataFile=nexusformat_NXmx.h5 -definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXinstrument/NXdetector sev=error dataPath=/entry/instrument/detector/depends_on dataFile=nexusformat_NXmx.h5 -2 errors and 16 warnings found when validating nexusformat_NXmx.h5 -nexusformat_NXrefscan.h5 passed validation -nexusformat_NXreftof.h5 passed validation -nexusformat_NXsas.h5 passed validation -nexusformat_NXsastof.h5 passed validation -nexusformat_NXscan.h5 passed validation -nexusformat_NXspe.h5 passed validation -nexusformat_NXsqom.h5 passed validation -nexusformat_NXstxm.h5 passed validation -nexusformat_NXtas.h5 passed validation -nexusformat_NXtofnpd.h5 passed validation -nexusformat_NXtofraw.h5 passed validation -nexusformat_NXtofsingle.h5 passed validation -nexusformat_NXtomo.h5 passed validation -nexusformat_NXtomophase.h5 passed validation -nexusformat_NXtomoproc.h5 passed validation -nexusformat_NXxas.h5 passed validation -nexusformat_NXxasproc.h5 passed validation -nexusformat_NXxbase.h5 passed validation -nexusformat_NXxeuler.h5 passed validation -nexusformat_NXxkappa.h5 passed validation -nexusformat_NXxlaue.h5 passed validation -nexusformat_NXxlaueplate.h5 passed validation -nexusformat_NXxnb.h5 passed validation -nexusformat_NXxrot.h5 passed validation -``` \ No newline at end of file +NXarchive.nxs passed validation +NXarpes.nxs passed validation +definition=NXcanSAS.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXdata sev=error dataPath=/entry dataFile=NXcanSAS.nxs +1 errors and 10 warnings found when validating NXcanSAS.nxs +NXdirecttof.nxs passed validation +NXfluo.nxs passed validation +NXindirecttof.nxs passed validation +NXiqproc.nxs passed validation +NXlauetof.nxs passed validation +NXmonopd.nxs passed validation +definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXsample/name sev=error dataPath=/entry/sample/depends_on dataFile=NXmx.nxs +definition=NXmx.nxdl.xml message="Cannot even find the starting point of the depends_on chain, SAMPLE-CHAR-DATA" nxdlPath=/NXentry/NXinstrument/NXdetector sev=error dataPath=/entry/instrument/detector/depends_on dataFile=NXmx.nxs +2 errors and 16 warnings found when validating NXmx.nxs +NXrefscan.nxs passed validation +NXreftof.nxs passed validation +NXsas.nxs passed validation +NXsastof.nxs passed validation +NXscan.nxs passed validation +NXspe.nxs passed validation +NXsqom.nxs passed validation +NXstxm.nxs passed validation +NXtas.nxs passed validation +NXtofnpd.nxs passed validation +NXtofraw.nxs passed validation +NXtofsingle.nxs passed validation +NXtomo.nxs passed validation +NXtomophase.nxs passed validation +NXtomoproc.nxs passed validation +NXxas.nxs passed validation +NXxasproc.nxs passed validation +NXxbase.nxs passed validation +NXxeuler.nxs passed validation +NXxkappa.nxs passed validation +NXxlaue.nxs passed validation +NXxlaueplate.nxs passed validation +NXxnb.nxs passed validation +NXxrot.nxs passed validation + +``` From 0acb6b03d59bad45e8e9f550230f91372ea45b02 Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 13:55:02 -0600 Subject: [PATCH 5/6] Update README.md reword --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 85222d9..808538b 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ the hope is that by studying the examples it will make it easier for users to understand what they need to do in order to create Nexus compliant files for their desired application definition. -Directory map of examples found in the `autogenerated_examples/nxdl` directory: +Directory contents of examples found in the `autogenerated_examples/nxdl` directory:   `*/applications` Contains hdf5 files for each definition From ef3f16326b54795a472efd7b5c6375af4a3c140f Mon Sep 17 00:00:00 2001 From: RussBerg Date: Thu, 1 Apr 2021 13:56:04 -0600 Subject: [PATCH 6/6] Update README.md add missing dir char --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 808538b..656a9fc 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ Directory contents of examples found in the `autogenerated_examples/nxdl` direct   `*/python_scripts/h5py` Contains python scripts to create each definition using **h5py** -  `*python_scripts/nexusformat` Contains python scripts to create each definition using **nexusformat** +  `*/python_scripts/nexusformat` Contains python scripts to create each definition using **nexusformat**