When trying to get tree structure from an HDF5 prepared by a working version of the NeXus file writer for Bluesky, this error occurs (v0.2.1 of punx):
(base) jemian@otz ~/Documents $ punx tr gov_5.h5
!!!
!!!WARNING: this program is not ready for distribution.
!!!
Traceback (most recent call last):
File "/home/oxygen/JEMIAN/Apps/anaconda/bin/punx", line 11, in <module>
sys.exit(main())
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/main.py", line 456, in main
args.func(args)
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/main.py", line 199, in func_tree
report = mc.report(args.show_attributes)
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 66, in report
tree_string_list = self._renderGroup(f, txt, indentation = "")
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 117, in _renderGroup
s += self._renderGroup(value, itemname, indentation+" ")
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 117, in _renderGroup
s += self._renderGroup(value, itemname, indentation+" ")
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 105, in _renderGroup
s += self._renderDataset(value, itemname, indentation+" ")
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 162, in _renderDataset
s += self._renderAttributes(dset, indentation)
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/h5tree.py", line 126, in _renderAttributes
s.append("%s @%s = %s" % (indentation, name, utils.decode_byte_string(value)))
File "/local/Apps/anaconda/lib/python2.7/site-packages/punx/utils.py", line 44, in decode_byte_string
text = text[0]
IndexError: index 0 is out of bounds for axis 0 with size 0
test file gov_5.h5 will be deposited in the repo
The file passes validation:
(base) jemian@otz ~/Documents $ punx va gov_5.h5
!!!
!!!WARNING: this program is not ready for distribution.
!!!
data file: gov_5.h5
NeXus definitions (release): v2018.5, dated 2018-05-15 16:34:19, sha=a3045fd7ff0029adc811d9ed92f42ad51007f32d
findings
=================================================== ====== ==================================== ========================================================================================
address status test comments
=================================================== ====== ==================================== ========================================================================================
/ TODO NeXus base class NXroot: more validations needed
/ OK known NXDL NXroot: recognized NXDL specification
/ OK NeXus base class NXroot: known NeXus base class
/ OK NeXus default plot found by v3: /gov_5/primary_data@signal
/@HDF5_Version TODO attribute value implement
/@HDF5_Version TODO value of @HDF5_Version TODO: need to validate: @HDF5_Version = 1.8.17
/@HDF5_Version OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/@HDF5_Version OK known attribute known: NXroot@HDF5_Version
/@creator TODO attribute value implement
/@creator TODO value of @creator TODO: need to validate: @creator = https://github.com/NSLS-II/suitcase/suitcase/nexus.py
/@creator OK validItemName strict pattern: [a-z_][a-z0-9_]*
/@creator OK known attribute known: NXroot@creator
/@default TODO attribute value implement
/@default OK validItemName strict pattern: [a-z_][a-z0-9_]*
/@default OK known attribute known: NXroot@default
/@default OK value of @default found: /gov_5
/@file_name TODO attribute value implement
/@file_name TODO value of @file_name TODO: need to validate: @file_name = gov_5.h5
/@file_name OK validItemName strict pattern: [a-z_][a-z0-9_]*
/@file_name OK known attribute known: NXroot@file_name
/@file_time TODO attribute value implement
/@file_time TODO value of @file_time TODO: need to validate: @file_time = 2017-03-28 10:16:54.123762
/@file_time OK validItemName strict pattern: [a-z_][a-z0-9_]*
/@file_time OK known attribute known: NXroot@file_time
/gov_5 TODO NeXus base class NXentry: more validations needed
/gov_5 OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5 OK group in base class not defined: NXroot/gov_5
/gov_5 OK known NXDL NXentry: recognized NXDL specification
/gov_5 OK NeXus base class NXentry: known NeXus base class
/gov_5@NX_class OK validItemName pattern: NX.+
/gov_5@NX_class OK attribute value recognized NXDL base class: NXentry
/gov_5@NX_class OK known attribute known: NXentry@NX_class
/gov_5@_BlueSky__name TODO attribute value implement
/gov_5@_BlueSky__name OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5@_BlueSky__name OK known attribute unknown: NXentry@_BlueSky__name
/gov_5@_BlueSky_start TODO attribute value implement
/gov_5@_BlueSky_start OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5@_BlueSky_start OK known attribute unknown: NXentry@_BlueSky_start
/gov_5@_BlueSky_stop TODO attribute value implement
/gov_5@_BlueSky_stop OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5@_BlueSky_stop OK known attribute unknown: NXentry@_BlueSky_stop
/gov_5@default TODO attribute value implement
/gov_5@default OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5@default OK known attribute known: NXentry@default
/gov_5@default OK value of @default found: /gov_5/primary_data
/gov_5/primary TODO NeXus base class NXlog: more validations needed
/gov_5/primary OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary OK group in base class not defined: NXentry/primary
/gov_5/primary OK known NXDL NXlog: recognized NXDL specification
/gov_5/primary OK NeXus base class NXlog: known NeXus base class
/gov_5/primary OK NXDL field in data file found: /gov_5/primary/time
/gov_5/primary@NX_class OK validItemName pattern: NX.+
/gov_5/primary@NX_class OK attribute value recognized NXDL base class: NXlog
/gov_5/primary@NX_class OK known attribute known: NXlog@NX_class
/gov_5/primary@_BlueSky_configuration TODO attribute value implement
/gov_5/primary@_BlueSky_configuration OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_configuration OK known attribute unknown: NXlog@_BlueSky_configuration
/gov_5/primary@_BlueSky_name TODO attribute value implement
/gov_5/primary@_BlueSky_name OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_name OK known attribute unknown: NXlog@_BlueSky_name
/gov_5/primary@_BlueSky_object_keys TODO attribute value implement
/gov_5/primary@_BlueSky_object_keys OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_object_keys OK known attribute unknown: NXlog@_BlueSky_object_keys
/gov_5/primary@_BlueSky_run_start TODO attribute value implement
/gov_5/primary@_BlueSky_run_start OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_run_start OK known attribute unknown: NXlog@_BlueSky_run_start
/gov_5/primary@_BlueSky_time TODO attribute value implement
/gov_5/primary@_BlueSky_time OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_time OK known attribute unknown: NXlog@_BlueSky_time
/gov_5/primary@_BlueSky_uid TODO attribute value implement
/gov_5/primary@_BlueSky_uid OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary@_BlueSky_uid OK known attribute unknown: NXlog@_BlueSky_uid
/gov_5/primary/noisy OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy OK field in base class not defined: NXlog/noisy
/gov_5/primary/noisy@_BlueSky_dtype TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_dtype OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_lower_ctrl_limit TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_lower_ctrl_limit OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_object_name TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_object_name OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_precision TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_precision OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_shape TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_shape OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_source TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_source OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_units TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_units OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@_BlueSky_upper_ctrl_limit TODO attribute value implement
/gov_5/primary/noisy@_BlueSky_upper_ctrl_limit OK validItemName relaxed pattern: [A-Za-z_][\w_]*
/gov_5/primary/noisy@axes TODO attribute value implement
/gov_5/primary/noisy@axes OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy@key_name TODO attribute value implement
/gov_5/primary/noisy@key_name OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy@target OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy@target OK attribute value found: @target=/gov_5/primary/noisy
/gov_5/primary/noisy_timestamps OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy_timestamps OK field in base class not defined: NXlog/noisy_timestamps
/gov_5/primary/noisy_timestamps@key_name TODO attribute value implement
/gov_5/primary/noisy_timestamps@key_name OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy_timestamps@target OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/noisy_timestamps@target OK attribute value found: @target=/gov_5/primary/noisy_timestamps
/gov_5/primary/time OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/time OK field in base class defined: NXlog/time
/gov_5/primary/time@start TODO attribute value implement
/gov_5/primary/time@start OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary/time@units TODO attribute value implement
/gov_5/primary/time@units OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data TODO NeXus base class NXdata: more validations needed
/gov_5/primary_data OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data OK group in base class not defined: NXentry/primary_data
/gov_5/primary_data OK known NXDL NXdata: recognized NXDL specification
/gov_5/primary_data OK NeXus base class NXdata: known NeXus base class
/gov_5/primary_data@NX_class OK validItemName pattern: NX.+
/gov_5/primary_data@NX_class OK attribute value recognized NXDL base class: NXdata
/gov_5/primary_data@NX_class OK known attribute known: NXdata@NX_class
/gov_5/primary_data@signal OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data@signal OK valid name @signal=noisy strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data@signal OK attribute value found: @signal=noisy
/gov_5/primary_data@signal OK known attribute known: NXdata@signal
/gov_5/primary_data@signal OK value of @signal found: /gov_5/primary_data/noisy
/gov_5/primary_data@signal OK NeXus default plot v3, NXdata@signal correct default plot setup in /NXentry/NXdata
/gov_5/primary_data@signal OK NeXus default plot v3 NIAC2014 default plot setup in /NXentry/NXdata
/gov_5/primary_data/noisy OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data/noisy OK field in base class not defined: NXdata/noisy
/gov_5/primary_data/noisy@_BlueSky_dtype TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_lower_ctrl_limit TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_object_name TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_precision TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_shape TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_source TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_units TODO attribute value implement
/gov_5/primary_data/noisy@_BlueSky_upper_ctrl_limit TODO attribute value implement
/gov_5/primary_data/noisy@axes TODO attribute value implement
/gov_5/primary_data/noisy@key_name TODO attribute value implement
/gov_5/primary_data/noisy@target OK attribute value found: @target=/gov_5/primary/noisy
/gov_5/primary_data/noisy_timestamps OK validItemName strict pattern: [a-z_][a-z0-9_]*
/gov_5/primary_data/noisy_timestamps OK field in base class not defined: NXdata/noisy_timestamps
/gov_5/primary_data/noisy_timestamps@key_name TODO attribute value implement
/gov_5/primary_data/noisy_timestamps@target OK attribute value found: @target=/gov_5/primary/noisy_timestamps
=================================================== ====== ==================================== ========================================================================================
summary statistics
======== ===== =========================================================== =========
status count description (value)
======== ===== =========================================================== =========
OK 93 meets NeXus specification 100
NOTE 0 does not meet NeXus specification, but acceptable 75
WARN 0 does not meet NeXus specification, not generally acceptable 25
ERROR 0 violates NeXus specification -10000000
TODO 47 validation not implemented yet 0
UNUSED 0 optional NeXus item not used in data file 0
COMMENT 0 comment from the punx source code 0
OPTIONAL 49 allowed by NeXus specification, not identified 99
--
TOTAL 189
======== ===== =========================================================== =========
<value>/finding=99.654930 count=142 sum(finding values)=14151.000000
When trying to get tree structure from an HDF5 prepared by a working version of the NeXus file writer for Bluesky, this error occurs (v0.2.1 of punx):
test file
gov_5.h5will be deposited in the repoThe file passes validation: