User interface: subcommand: demo¶
The demo subcommand is useful to demonstrate HDF5 file validation and to verify correct program operation. It uses an example NeXus HDF5 data file supplied with the punx software, the writer_1_3.hdf5 example from the NeXus manual.
command line help
console> punx demo -h
punx demo -h
usage: punx demo [-h]
optional arguments:
-h, --help show this help message and exit
Examples¶
One example of how to use punx is shown in the demo mode. This can be used directly after installing the python package.
Type this command …:
punx demo
… and this output will appear on the console, showing a validation of writer_1_3.hdf5, an example NeXus HDF5 data file from the NeXus documentation.
1C:\Users\Pete\Documents\eclipse\punx\src\punx\main.py
2
3!!! WARNING: this program is not ready for distribution.
4
5
6console> punx validate C:\Users\Pete\Documents\eclipse\punx\src\punx\data\writer_1_3.hdf5
7data file: C:\Users\Pete\Documents\eclipse\punx\src\punx\data\writer_1_3.hdf5
8NeXus definitions (branch): master, dated 2018-05-16 02:07:48, sha=2dc081ee4265eebf80a953080a2ed275c1799a21
9
10findings
11============================ ====== ==================================== =============================================
12address status test comments
13============================ ====== ==================================== =============================================
14/ TODO NeXus base class NXroot: more validations needed
15/ OK known NXDL NXroot: recognized NXDL specification
16/ OK NeXus base class NXroot: known NeXus base class
17/ OK NeXus default plot found by v3: /Scan/data/counts
18/Scan TODO NeXus base class NXentry: more validations needed
19/Scan OK group in base class not defined: NXroot/Scan
20/Scan OK known NXDL NXentry: recognized NXDL specification
21/Scan OK NeXus base class NXentry: known NeXus base class
22/Scan OK NXDL group in data file found: in /Scan/data
23/Scan NOTE validItemName relaxed pattern: [A-Za-z_][\w_]*
24/Scan@NX_class OK validItemName pattern: NX.+
25/Scan@NX_class OK attribute value recognized NXDL base class: NXentry
26/Scan@NX_class OK known attribute known: NXentry@NX_class
27/Scan/data TODO NeXus base class NXdata: more validations needed
28/Scan/data OK validItemName strict pattern: [a-z_][a-z0-9_]*
29/Scan/data OK group in base class defined: NXentry/data
30/Scan/data OK known NXDL NXdata: recognized NXDL specification
31/Scan/data OK NeXus base class NXdata: known NeXus base class
32/Scan/data@NX_class OK validItemName pattern: NX.+
33/Scan/data@NX_class OK attribute value recognized NXDL base class: NXdata
34/Scan/data@NX_class OK known attribute known: NXdata@NX_class
35/Scan/data@axes TODO attribute value implement
36/Scan/data@axes OK validItemName strict pattern: [a-z_][a-z0-9_]*
37/Scan/data@axes OK known attribute known: NXdata@axes
38/Scan/data@signal OK validItemName strict pattern: [a-z_][a-z0-9_]*
39/Scan/data@signal OK valid name @signal=counts strict pattern: [a-z_][a-z0-9_]*
40/Scan/data@signal OK attribute value found: @signal=counts
41/Scan/data@signal OK known attribute known: NXdata@signal
42/Scan/data@signal OK value of @signal found: /Scan/data/counts
43/Scan/data@signal OK NeXus default plot v3, NXdata@signal correct default plot setup in /NXentry/NXdata
44/Scan/data@two_theta_indices TODO attribute value implement
45/Scan/data@two_theta_indices OK validItemName strict pattern: [a-z_][a-z0-9_]*
46/Scan/data@two_theta_indices OK known attribute unknown: NXdata@two_theta_indices
47/Scan/data/counts OK validItemName strict pattern: [a-z_][a-z0-9_]*
48/Scan/data/counts OK field in base class not defined: NXdata/counts
49/Scan/data/counts@units TODO attribute value implement
50/Scan/data/counts@units OK validItemName strict pattern: [a-z_][a-z0-9_]*
51/Scan/data/two_theta OK validItemName strict pattern: [a-z_][a-z0-9_]*
52/Scan/data/two_theta OK field in base class not defined: NXdata/two_theta
53/Scan/data/two_theta@units TODO attribute value implement
54/Scan/data/two_theta@units OK validItemName strict pattern: [a-z_][a-z0-9_]*
55============================ ====== ==================================== =============================================
56
57
58summary statistics
59======== ===== =========================================================== =========
60status count description (value)
61======== ===== =========================================================== =========
62OK 33 meets NeXus specification 100
63NOTE 1 does not meet NeXus specification, but acceptable 75
64WARN 0 does not meet NeXus specification, not generally acceptable 25
65ERROR 0 violates NeXus specification -10000000
66TODO 7 validation not implemented yet 0
67UNUSED 0 optional NeXus item not used in data file 0
68COMMENT 0 comment from the punx source code 0
69OPTIONAL 38 allowed by NeXus specification, not identified 99
70 --
71TOTAL 79
72======== ===== =========================================================== =========
73
74<finding>=99.125000 of 72 items reviewed
75
76console> punx tree C:\Users\Pete\Documents\eclipse\punx\src\punx\data\writer_1_3.hdf5
77C:\Users\Pete\Documents\eclipse\punx\src\punx\data\writer_1_3.hdf5 : NeXus data file
78 Scan:NXentry
79 @NX_class = NXentry
80 data:NXdata
81 @NX_class = NXdata
82 @signal = counts
83 @axes = two_theta
84 @two_theta_indices = 0
85 counts:NX_INT32[31] = [1037, 1318, 1704, '...', 1321]
86 @units = counts
87 two_theta:NX_FLOAT64[31] = [17.92608, 17.92591, 17.92575, '...', 17.92108]
88 @units = degrees
Problems when running the demo¶
Sometimes, problems happen when running the demo. In this section are some common problems encountered and what was done to resolve them.