hdfmap 0.4__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- hdfmap/__init__.py +76 -0
- hdfmap/eval_functions.py +172 -0
- hdfmap/file_functions.py +210 -0
- hdfmap/hdfmap_class.py +656 -0
- hdfmap/logging.py +40 -0
- hdfmap/nexus.py +240 -0
- hdfmap/reloader_class.py +140 -0
- hdfmap-0.4.dist-info/LICENSE +201 -0
- hdfmap-0.4.dist-info/METADATA +476 -0
- hdfmap-0.4.dist-info/RECORD +12 -0
- hdfmap-0.4.dist-info/WHEEL +5 -0
- hdfmap-0.4.dist-info/top_level.txt +1 -0
|
@@ -0,0 +1,476 @@
|
|
|
1
|
+
Metadata-Version: 2.1
|
|
2
|
+
Name: hdfmap
|
|
3
|
+
Version: 0.4
|
|
4
|
+
Summary: Map objects within a HDF file and create a dataset namespace
|
|
5
|
+
Author-email: Dan Porter <dan.porter@diamond.ac.uk>
|
|
6
|
+
Maintainer-email: Dan Porter <dan.porter@diamond.ac.uk>
|
|
7
|
+
License: Apache License
|
|
8
|
+
Version 2.0, January 2004
|
|
9
|
+
http://www.apache.org/licenses/
|
|
10
|
+
|
|
11
|
+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
|
|
12
|
+
|
|
13
|
+
1. Definitions.
|
|
14
|
+
|
|
15
|
+
"License" shall mean the terms and conditions for use, reproduction,
|
|
16
|
+
and distribution as defined by Sections 1 through 9 of this document.
|
|
17
|
+
|
|
18
|
+
"Licensor" shall mean the copyright owner or entity authorized by
|
|
19
|
+
the copyright owner that is granting the License.
|
|
20
|
+
|
|
21
|
+
"Legal Entity" shall mean the union of the acting entity and all
|
|
22
|
+
other entities that control, are controlled by, or are under common
|
|
23
|
+
control with that entity. For the purposes of this definition,
|
|
24
|
+
"control" means (i) the power, direct or indirect, to cause the
|
|
25
|
+
direction or management of such entity, whether by contract or
|
|
26
|
+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
|
|
27
|
+
outstanding shares, or (iii) beneficial ownership of such entity.
|
|
28
|
+
|
|
29
|
+
"You" (or "Your") shall mean an individual or Legal Entity
|
|
30
|
+
exercising permissions granted by this License.
|
|
31
|
+
|
|
32
|
+
"Source" form shall mean the preferred form for making modifications,
|
|
33
|
+
including but not limited to software source code, documentation
|
|
34
|
+
source, and configuration files.
|
|
35
|
+
|
|
36
|
+
"Object" form shall mean any form resulting from mechanical
|
|
37
|
+
transformation or translation of a Source form, including but
|
|
38
|
+
not limited to compiled object code, generated documentation,
|
|
39
|
+
and conversions to other media types.
|
|
40
|
+
|
|
41
|
+
"Work" shall mean the work of authorship, whether in Source or
|
|
42
|
+
Object form, made available under the License, as indicated by a
|
|
43
|
+
copyright notice that is included in or attached to the work
|
|
44
|
+
(an example is provided in the Appendix below).
|
|
45
|
+
|
|
46
|
+
"Derivative Works" shall mean any work, whether in Source or Object
|
|
47
|
+
form, that is based on (or derived from) the Work and for which the
|
|
48
|
+
editorial revisions, annotations, elaborations, or other modifications
|
|
49
|
+
represent, as a whole, an original work of authorship. For the purposes
|
|
50
|
+
of this License, Derivative Works shall not include works that remain
|
|
51
|
+
separable from, or merely link (or bind by name) to the interfaces of,
|
|
52
|
+
the Work and Derivative Works thereof.
|
|
53
|
+
|
|
54
|
+
"Contribution" shall mean any work of authorship, including
|
|
55
|
+
the original version of the Work and any modifications or additions
|
|
56
|
+
to that Work or Derivative Works thereof, that is intentionally
|
|
57
|
+
submitted to Licensor for inclusion in the Work by the copyright owner
|
|
58
|
+
or by an individual or Legal Entity authorized to submit on behalf of
|
|
59
|
+
the copyright owner. For the purposes of this definition, "submitted"
|
|
60
|
+
means any form of electronic, verbal, or written communication sent
|
|
61
|
+
to the Licensor or its representatives, including but not limited to
|
|
62
|
+
communication on electronic mailing lists, source code control systems,
|
|
63
|
+
and issue tracking systems that are managed by, or on behalf of, the
|
|
64
|
+
Licensor for the purpose of discussing and improving the Work, but
|
|
65
|
+
excluding communication that is conspicuously marked or otherwise
|
|
66
|
+
designated in writing by the copyright owner as "Not a Contribution."
|
|
67
|
+
|
|
68
|
+
"Contributor" shall mean Licensor and any individual or Legal Entity
|
|
69
|
+
on behalf of whom a Contribution has been received by Licensor and
|
|
70
|
+
subsequently incorporated within the Work.
|
|
71
|
+
|
|
72
|
+
2. Grant of Copyright License. Subject to the terms and conditions of
|
|
73
|
+
this License, each Contributor hereby grants to You a perpetual,
|
|
74
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
|
75
|
+
copyright license to reproduce, prepare Derivative Works of,
|
|
76
|
+
publicly display, publicly perform, sublicense, and distribute the
|
|
77
|
+
Work and such Derivative Works in Source or Object form.
|
|
78
|
+
|
|
79
|
+
3. Grant of Patent License. Subject to the terms and conditions of
|
|
80
|
+
this License, each Contributor hereby grants to You a perpetual,
|
|
81
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
|
82
|
+
(except as stated in this section) patent license to make, have made,
|
|
83
|
+
use, offer to sell, sell, import, and otherwise transfer the Work,
|
|
84
|
+
where such license applies only to those patent claims licensable
|
|
85
|
+
by such Contributor that are necessarily infringed by their
|
|
86
|
+
Contribution(s) alone or by combination of their Contribution(s)
|
|
87
|
+
with the Work to which such Contribution(s) was submitted. If You
|
|
88
|
+
institute patent litigation against any entity (including a
|
|
89
|
+
cross-claim or counterclaim in a lawsuit) alleging that the Work
|
|
90
|
+
or a Contribution incorporated within the Work constitutes direct
|
|
91
|
+
or contributory patent infringement, then any patent licenses
|
|
92
|
+
granted to You under this License for that Work shall terminate
|
|
93
|
+
as of the date such litigation is filed.
|
|
94
|
+
|
|
95
|
+
4. Redistribution. You may reproduce and distribute copies of the
|
|
96
|
+
Work or Derivative Works thereof in any medium, with or without
|
|
97
|
+
modifications, and in Source or Object form, provided that You
|
|
98
|
+
meet the following conditions:
|
|
99
|
+
|
|
100
|
+
(a) You must give any other recipients of the Work or
|
|
101
|
+
Derivative Works a copy of this License; and
|
|
102
|
+
|
|
103
|
+
(b) You must cause any modified files to carry prominent notices
|
|
104
|
+
stating that You changed the files; and
|
|
105
|
+
|
|
106
|
+
(c) You must retain, in the Source form of any Derivative Works
|
|
107
|
+
that You distribute, all copyright, patent, trademark, and
|
|
108
|
+
attribution notices from the Source form of the Work,
|
|
109
|
+
excluding those notices that do not pertain to any part of
|
|
110
|
+
the Derivative Works; and
|
|
111
|
+
|
|
112
|
+
(d) If the Work includes a "NOTICE" text file as part of its
|
|
113
|
+
distribution, then any Derivative Works that You distribute must
|
|
114
|
+
include a readable copy of the attribution notices contained
|
|
115
|
+
within such NOTICE file, excluding those notices that do not
|
|
116
|
+
pertain to any part of the Derivative Works, in at least one
|
|
117
|
+
of the following places: within a NOTICE text file distributed
|
|
118
|
+
as part of the Derivative Works; within the Source form or
|
|
119
|
+
documentation, if provided along with the Derivative Works; or,
|
|
120
|
+
within a display generated by the Derivative Works, if and
|
|
121
|
+
wherever such third-party notices normally appear. The contents
|
|
122
|
+
of the NOTICE file are for informational purposes only and
|
|
123
|
+
do not modify the License. You may add Your own attribution
|
|
124
|
+
notices within Derivative Works that You distribute, alongside
|
|
125
|
+
or as an addendum to the NOTICE text from the Work, provided
|
|
126
|
+
that such additional attribution notices cannot be construed
|
|
127
|
+
as modifying the License.
|
|
128
|
+
|
|
129
|
+
You may add Your own copyright statement to Your modifications and
|
|
130
|
+
may provide additional or different license terms and conditions
|
|
131
|
+
for use, reproduction, or distribution of Your modifications, or
|
|
132
|
+
for any such Derivative Works as a whole, provided Your use,
|
|
133
|
+
reproduction, and distribution of the Work otherwise complies with
|
|
134
|
+
the conditions stated in this License.
|
|
135
|
+
|
|
136
|
+
5. Submission of Contributions. Unless You explicitly state otherwise,
|
|
137
|
+
any Contribution intentionally submitted for inclusion in the Work
|
|
138
|
+
by You to the Licensor shall be under the terms and conditions of
|
|
139
|
+
this License, without any additional terms or conditions.
|
|
140
|
+
Notwithstanding the above, nothing herein shall supersede or modify
|
|
141
|
+
the terms of any separate license agreement you may have executed
|
|
142
|
+
with Licensor regarding such Contributions.
|
|
143
|
+
|
|
144
|
+
6. Trademarks. This License does not grant permission to use the trade
|
|
145
|
+
names, trademarks, service marks, or product names of the Licensor,
|
|
146
|
+
except as required for reasonable and customary use in describing the
|
|
147
|
+
origin of the Work and reproducing the content of the NOTICE file.
|
|
148
|
+
|
|
149
|
+
7. Disclaimer of Warranty. Unless required by applicable law or
|
|
150
|
+
agreed to in writing, Licensor provides the Work (and each
|
|
151
|
+
Contributor provides its Contributions) on an "AS IS" BASIS,
|
|
152
|
+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
|
|
153
|
+
implied, including, without limitation, any warranties or conditions
|
|
154
|
+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
|
|
155
|
+
PARTICULAR PURPOSE. You are solely responsible for determining the
|
|
156
|
+
appropriateness of using or redistributing the Work and assume any
|
|
157
|
+
risks associated with Your exercise of permissions under this License.
|
|
158
|
+
|
|
159
|
+
8. Limitation of Liability. In no event and under no legal theory,
|
|
160
|
+
whether in tort (including negligence), contract, or otherwise,
|
|
161
|
+
unless required by applicable law (such as deliberate and grossly
|
|
162
|
+
negligent acts) or agreed to in writing, shall any Contributor be
|
|
163
|
+
liable to You for damages, including any direct, indirect, special,
|
|
164
|
+
incidental, or consequential damages of any character arising as a
|
|
165
|
+
result of this License or out of the use or inability to use the
|
|
166
|
+
Work (including but not limited to damages for loss of goodwill,
|
|
167
|
+
work stoppage, computer failure or malfunction, or any and all
|
|
168
|
+
other commercial damages or losses), even if such Contributor
|
|
169
|
+
has been advised of the possibility of such damages.
|
|
170
|
+
|
|
171
|
+
9. Accepting Warranty or Additional Liability. While redistributing
|
|
172
|
+
the Work or Derivative Works thereof, You may choose to offer,
|
|
173
|
+
and charge a fee for, acceptance of support, warranty, indemnity,
|
|
174
|
+
or other liability obligations and/or rights consistent with this
|
|
175
|
+
License. However, in accepting such obligations, You may act only
|
|
176
|
+
on Your own behalf and on Your sole responsibility, not on behalf
|
|
177
|
+
of any other Contributor, and only if You agree to indemnify,
|
|
178
|
+
defend, and hold each Contributor harmless for any liability
|
|
179
|
+
incurred by, or claims asserted against, such Contributor by reason
|
|
180
|
+
of your accepting any such warranty or additional liability.
|
|
181
|
+
|
|
182
|
+
END OF TERMS AND CONDITIONS
|
|
183
|
+
|
|
184
|
+
APPENDIX: How to apply the Apache License to your work.
|
|
185
|
+
|
|
186
|
+
To apply the Apache License to your work, attach the following
|
|
187
|
+
boilerplate notice, with the fields enclosed by brackets "[]"
|
|
188
|
+
replaced with your own identifying information. (Don't include
|
|
189
|
+
the brackets!) The text should be enclosed in the appropriate
|
|
190
|
+
comment syntax for the file format. We also recommend that a
|
|
191
|
+
file or class name and description of purpose be included on the
|
|
192
|
+
same "printed page" as the copyright notice for easier
|
|
193
|
+
identification within third-party archives.
|
|
194
|
+
|
|
195
|
+
Copyright [yyyy] [name of copyright owner]
|
|
196
|
+
|
|
197
|
+
Licensed under the Apache License, Version 2.0 (the "License");
|
|
198
|
+
you may not use this file except in compliance with the License.
|
|
199
|
+
You may obtain a copy of the License at
|
|
200
|
+
|
|
201
|
+
http://www.apache.org/licenses/LICENSE-2.0
|
|
202
|
+
|
|
203
|
+
Unless required by applicable law or agreed to in writing, software
|
|
204
|
+
distributed under the License is distributed on an "AS IS" BASIS,
|
|
205
|
+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
206
|
+
See the License for the specific language governing permissions and
|
|
207
|
+
limitations under the License.
|
|
208
|
+
|
|
209
|
+
Project-URL: Homepage, https://github.com/DanPorter/hdfmap
|
|
210
|
+
Project-URL: Documentation, https://github.com/DanPorter/hdfmap
|
|
211
|
+
Project-URL: Repository, https://github.com/DanPorter/hdfmap
|
|
212
|
+
Project-URL: Bug Tracker, https://github.com/DanPorter/hdfmap
|
|
213
|
+
Project-URL: Changelog, https://github.com/DanPorter/hdfmap/blob/master/README.md
|
|
214
|
+
Keywords: nexus
|
|
215
|
+
Classifier: Programming Language :: Python :: 3.10
|
|
216
|
+
Classifier: Intended Audience :: Science/Research
|
|
217
|
+
Classifier: Topic :: Scientific/Engineering :: Physics
|
|
218
|
+
Classifier: License :: OSI Approved :: Apache Software License
|
|
219
|
+
Classifier: Development Status :: 3 - Alpha
|
|
220
|
+
Requires-Python: >=3.10
|
|
221
|
+
Description-Content-Type: text/markdown
|
|
222
|
+
License-File: LICENSE
|
|
223
|
+
Requires-Dist: numpy
|
|
224
|
+
Requires-Dist: h5py
|
|
225
|
+
Requires-Dist: hdf5plugin
|
|
226
|
+
|
|
227
|
+
# hdfmap
|
|
228
|
+
Map objects within an HDF file and create a dataset namespace.
|
|
229
|
+
|
|
230
|
+
[](https://pypi.org/project/hdfmap)
|
|
231
|
+
[](https://opensource.org/licenses/Apache-2.0)
|
|
232
|
+
[](https://github.com/DiamondLightSource/hdfmap)
|
|
233
|
+
|
|
234
|
+
**Version 0.4**
|
|
235
|
+
|
|
236
|
+
| By Dan Porter |
|
|
237
|
+
|----------------------|
|
|
238
|
+
| Diamond Light Source |
|
|
239
|
+
| 2024 |
|
|
240
|
+
|
|
241
|
+
[](https://diamondlightsource.github.io/hdfmap/)
|
|
242
|
+
|
|
243
|
+
### TL;DR - Usage
|
|
244
|
+
|
|
245
|
+
```python
|
|
246
|
+
from hdfmap import create_nexus_map, load_hdf
|
|
247
|
+
|
|
248
|
+
# HdfMap from NeXus file:
|
|
249
|
+
m = create_nexus_map('file.nxs')
|
|
250
|
+
m['energy'] # >> '/entry/instrument/monochromator/energy'
|
|
251
|
+
m['signal'] # >> '/entry/measurement/sum'
|
|
252
|
+
m['axes'] # >> '/entry/measurement/theta'
|
|
253
|
+
m.get_image_path() # >> '/entry/instrument/pil3_100k/data'
|
|
254
|
+
|
|
255
|
+
with load_hdf('file.nxs') as nxs:
|
|
256
|
+
path = m.get_path('scan_command')
|
|
257
|
+
cmd = nxs[path][()] # returns bytes data direct from file
|
|
258
|
+
cmd = m.get_data(nxs, 'scan_command') # returns converted str output
|
|
259
|
+
string = m.format_hdf(nxs, "the energy is {energy:.2f} keV")
|
|
260
|
+
d = m.get_dataholder(nxs) # classic data table, d.scannable, d.metadata
|
|
261
|
+
|
|
262
|
+
# Shortcuts - single file reloader class
|
|
263
|
+
from hdfmap import NexusLoader
|
|
264
|
+
|
|
265
|
+
scan = NexusLoader('file.hdf')
|
|
266
|
+
[data1, data2] = scan.get_data(['dataset_name_1', 'dataset_name_2'])
|
|
267
|
+
data = scan.eval('dataset_name_1 * 100 + 2')
|
|
268
|
+
string = scan.format('my data is {dataset_name_1:.2f}')
|
|
269
|
+
|
|
270
|
+
# Shortcuts - multifile load data (generate map from first file)
|
|
271
|
+
from hdfmap import hdf_data, hdf_eval, hdf_format, hdf_image
|
|
272
|
+
|
|
273
|
+
all_data = hdf_data([f'file{n}.nxs' for n in range(100)], 'dataset_name')
|
|
274
|
+
normalised_data = hdf_eval(filenames, 'total / Transmission / (rc / 300.)')
|
|
275
|
+
descriptions = hdf_format(filenames, 'Energy: {en:5.3f} keV')
|
|
276
|
+
image_stack = hdf_image(filenames, index=31)
|
|
277
|
+
```
|
|
278
|
+
|
|
279
|
+
### Installation
|
|
280
|
+
*Requires:* Python >=3.10, Numpy, h5py
|
|
281
|
+
```bash
|
|
282
|
+
python -m pip install --upgrade git+https://github.com/DanPorter/hdfmap.git
|
|
283
|
+
```
|
|
284
|
+
|
|
285
|
+
### Description
|
|
286
|
+
Another generic hdf reader but the idea here is to build up a namespace dict of `{'name': 'path'}`
|
|
287
|
+
for every dataset, then group them in hopefully a useful way.
|
|
288
|
+
|
|
289
|
+
Objects within the HDF file are separated into Groups and Datasets. Each object has a
|
|
290
|
+
defined 'path' and 'name' paramater, as well as other attributes
|
|
291
|
+
|
|
292
|
+
- path -> '/entry/measurement/data' -> the location of an object within the file
|
|
293
|
+
- name -> 'data' -> an path expressed as a simple variable name
|
|
294
|
+
|
|
295
|
+
Paths are unique locations within the file but can be used to identify similar objects in other files
|
|
296
|
+
Names may not be unique within a file and are generated from the path.
|
|
297
|
+
|
|
298
|
+
| | **name** | **path** |
|
|
299
|
+
|---------------|------------------------------|--------------------------------------|
|
|
300
|
+
| *Description* | simple identifier of dataset | hdf path built from position in file |
|
|
301
|
+
| *Example* | `'scan_command'` | `'/entry/scan_command'` |
|
|
302
|
+
|
|
303
|
+
Names of different types of datasets are stored for arrays (size > 0) and values (size 0)
|
|
304
|
+
Names for scannables relate to all arrays of a particular size
|
|
305
|
+
A combined list of names is provided where scannables > arrays > values
|
|
306
|
+
|
|
307
|
+
### HdfMap Attributes
|
|
308
|
+
| | |
|
|
309
|
+
|----------------|--------------------------------------------------------|
|
|
310
|
+
| map.groups | stores attributes of each group by path |
|
|
311
|
+
| map.classes | stores list of group paths by nx_class |
|
|
312
|
+
| map.datasets | stores attributes of each dataset by path |
|
|
313
|
+
| map.arrays | stores array dataset paths by name |
|
|
314
|
+
| map.values | stores value dataset paths by name |
|
|
315
|
+
| map.scannables | stores array dataset paths with given size, by name |
|
|
316
|
+
| map.combined | stores array and value paths (arrays overwrite values) |
|
|
317
|
+
| map.image_data | stores dataset paths of image data |
|
|
318
|
+
|
|
319
|
+
#### E.G.
|
|
320
|
+
```python
|
|
321
|
+
map.groups = {'/hdf/group': ('class', 'name', {attrs}, [datasets])}
|
|
322
|
+
map.classes = {'class_name': ['/hdf/group1', '/hdf/group2']}
|
|
323
|
+
map.datasets = {'/hdf/group/dataset': ('name', size, shape, {attrs})}
|
|
324
|
+
map.arrays = {'name': '/hdf/group/dataset'}
|
|
325
|
+
map.values = {'name': '/hdf/group/dataset'}
|
|
326
|
+
map.scannables = {'name': '/hdf/group/dataset'}
|
|
327
|
+
map.image_data = {'name': '/hdf/group/dataset'}
|
|
328
|
+
```
|
|
329
|
+
|
|
330
|
+
|
|
331
|
+
### HdfMap Methods
|
|
332
|
+
| | |
|
|
333
|
+
|---------------------------------------------------|----------------------------------------------------------------|
|
|
334
|
+
| `map.populate(h5py.File)` | populates the dictionaries using the given file |
|
|
335
|
+
| `map.generate_scannables(array_size)` | populates scannables namespace with arrays of same size |
|
|
336
|
+
| `map.most_common_size()` | returns the most common dataset size > 1 |
|
|
337
|
+
| `map.get_size('name_or_path')` | return dataset size |
|
|
338
|
+
| `map.get_shape('name_or_path')` | return dataset size |
|
|
339
|
+
| `map.get_attr('name_or_path', 'attr')` | return value of dataset attribute |
|
|
340
|
+
| `map.get_path('name_or_group_or_class')` | returns path of object with name |
|
|
341
|
+
| `map.get_image_path()` | returns default path of detector dataset (or largest dataset) |
|
|
342
|
+
| `map.get_group_path('name_or_path_or_class')` | return path of group with class |
|
|
343
|
+
| `map.get_group_datasets('name_or_path_or_class')` | return list of dataset paths in class |
|
|
344
|
+
|
|
345
|
+
|
|
346
|
+
### HdfMap File Methods
|
|
347
|
+
| | |
|
|
348
|
+
|------------------------------------------|-------------------------------------------------------|
|
|
349
|
+
| `map.get_metadata(h5py.File)` | returns dict of value datasets |
|
|
350
|
+
| `map.get_scannables(h5py.File)` | returns dict of scannable datasets |
|
|
351
|
+
| `map.get_scannalbes_array(h5py.File)` | returns numpy array of scannable datasets |
|
|
352
|
+
| `map.get_data_block(h5py.File)` | returns dict like object with metadata and scannables |
|
|
353
|
+
| `map.get_image(h5py.File, index)` | returns image data |
|
|
354
|
+
| `map.get_data(h5py.File, 'name')` | returns data from dataset |
|
|
355
|
+
| `map.eval(h5py.File, 'expression')` | returns output of expression using dataset names |
|
|
356
|
+
| `map.format(h5py.File, 'string {name}')` | returns output of str expression |
|
|
357
|
+
|
|
358
|
+
|
|
359
|
+
### NeXus Files
|
|
360
|
+
Files using the [NeXus Format](https://www.nexusformat.org/) can generate special NexusMap objects.
|
|
361
|
+
These work in the same way as the general HdfMaps but contain additional special names in the namespace:
|
|
362
|
+
|
|
363
|
+
| | |
|
|
364
|
+
|----------------|------------------------------------|
|
|
365
|
+
| `'axes'` | returns path of default NXaxes |
|
|
366
|
+
| `'signal'` | returns path of default NXsignal |
|
|
367
|
+
|
|
368
|
+
In addition, the `map.scannables` dict will be populated automatically by the names given in the "scan_fields" dataset
|
|
369
|
+
or by datasets from the first *NXdata* group. The default *image* data will be taken from the first
|
|
370
|
+
*NXdetector* dataset.
|
|
371
|
+
|
|
372
|
+
|
|
373
|
+
## Examples
|
|
374
|
+
### scan data & metadata
|
|
375
|
+
Separate datasets in a NeXus file into Diamond's classic scannables and metadata, similar to what was in the old
|
|
376
|
+
'*.dat' files.
|
|
377
|
+
|
|
378
|
+
```python
|
|
379
|
+
from hdfmap import create_nexus_map, load_hdf
|
|
380
|
+
|
|
381
|
+
# HdfMap from NeXus file:
|
|
382
|
+
hmap = create_nexus_map('file.nxs')
|
|
383
|
+
with load_hdf('file.nxs') as nxs:
|
|
384
|
+
scannables = hmap.get_scannables_array(nxs) # creates 2D numpy array
|
|
385
|
+
labels = scannables.dtype.names
|
|
386
|
+
metadata = hmap.get_metadata(nxs) # {'name': value}
|
|
387
|
+
d = hmap.get_dataholder(nxs) # classic data table, d.scannable, d.metadata
|
|
388
|
+
d.theta == d['theta'] # scannable array 'theta'
|
|
389
|
+
d.metadata.scan_command == d.metadata['scan_command'] # single value 'scan_command'
|
|
390
|
+
|
|
391
|
+
# OR, use the shortcut:
|
|
392
|
+
from hdfmap import nexus_data_block
|
|
393
|
+
|
|
394
|
+
d = nexus_data_block('file.nxs')
|
|
395
|
+
|
|
396
|
+
# The data loader class removes the need to open the files:
|
|
397
|
+
from hdfmap import NexusLoader
|
|
398
|
+
|
|
399
|
+
scan = NexusLoader('file.nxs')
|
|
400
|
+
metadata = scan.get_metadata()
|
|
401
|
+
scannables = scan.get_scannables()
|
|
402
|
+
```
|
|
403
|
+
|
|
404
|
+
### automatic default plot axes
|
|
405
|
+
If defined in the nexus file, 'axes' and 'signal' will be populated automatically
|
|
406
|
+
|
|
407
|
+
```python
|
|
408
|
+
import matplotlib.pyplot as plt
|
|
409
|
+
from hdfmap import create_nexus_map, load_hdf
|
|
410
|
+
|
|
411
|
+
# HdfMap from NeXus file:
|
|
412
|
+
hmap = create_nexus_map('file.nxs')
|
|
413
|
+
with load_hdf('file.nxs') as nxs:
|
|
414
|
+
axes = hmap.get_data(nxs, 'axes')
|
|
415
|
+
signal = hmap.get_data(nxs, 'signal')
|
|
416
|
+
title = hmap.format_hdf(nxs, "{entry_identifier}\n{scan_command}")
|
|
417
|
+
axes_label = hmap.get_path('axes')
|
|
418
|
+
signal_label = hmap.get_path('signal')
|
|
419
|
+
# plot the data (e.g. using matplotlib)
|
|
420
|
+
plt.figure()
|
|
421
|
+
plt.plot(axes, signal)
|
|
422
|
+
plt.xlabel(axes_label)
|
|
423
|
+
plt.ylabel(signal_label)
|
|
424
|
+
plt.title(title)
|
|
425
|
+
|
|
426
|
+
# Or, using NexusLoader:
|
|
427
|
+
from hdfmap import NexusLoader
|
|
428
|
+
|
|
429
|
+
scan = NexusLoader('file.nxs')
|
|
430
|
+
axes, signal = scan('axes, signal')
|
|
431
|
+
axes_label, signal_label = scan('_axes, _signal')
|
|
432
|
+
title = scan.format("{entry_identifier}\n{scan_command}")
|
|
433
|
+
```
|
|
434
|
+
|
|
435
|
+
### Automatic image data
|
|
436
|
+
Get images from the first detector in a NeXus file
|
|
437
|
+
|
|
438
|
+
```python
|
|
439
|
+
from hdfmap import create_nexus_map, load_hdf
|
|
440
|
+
|
|
441
|
+
# HdfMap from NeXus file:
|
|
442
|
+
hmap = create_nexus_map('file.nxs')
|
|
443
|
+
image_location = hmap.get_image_path() # returns the hdf path chosen for the default detector
|
|
444
|
+
with load_hdf('file.nxs') as nxs:
|
|
445
|
+
middle_image = hmap.get_image(nxs) # returns single image from index len(dataset)//2
|
|
446
|
+
first_image = hmap.get_image(nxs, 0) # returns single image from dataset[0, :, :]
|
|
447
|
+
volume = hmap.get_image(nxs, ()) # returns whole volume as array
|
|
448
|
+
roi = hmap.get_image(nxs, (0, slice(5, 10, 1), slice(5, 10, 1))) # returns part of dataset
|
|
449
|
+
|
|
450
|
+
# Or, using NexusLoader:
|
|
451
|
+
from hdfmap import NexusLoader
|
|
452
|
+
|
|
453
|
+
scan = NexusLoader('file.nxs')
|
|
454
|
+
image = scan.get_image(index=0) # using index as defined above
|
|
455
|
+
```
|
|
456
|
+
|
|
457
|
+
### Multi-scan metadata string
|
|
458
|
+
Generate a metadata string from every file in a directory very quickly. The HdfMap is only created for the first file,
|
|
459
|
+
the remaining files are treated as having identical structure.
|
|
460
|
+
```python
|
|
461
|
+
from hdfmap import list_files, hdf_format
|
|
462
|
+
|
|
463
|
+
format_string = "#{entry_identifier}: {start_time} : E={incident_energy:.3f} keV : {scan_command}"
|
|
464
|
+
files = list_files('/directoy/path', extension='.nxs')
|
|
465
|
+
strings_list = hdf_format(files, format_string)
|
|
466
|
+
print('\n'.join(strings_list))
|
|
467
|
+
|
|
468
|
+
# other multi-file readers:
|
|
469
|
+
from hdfmap import hdf_data, hdf_image, hdf_eval
|
|
470
|
+
|
|
471
|
+
data_list = hdf_data(files, 'incident_energy')
|
|
472
|
+
image_list = hdf_image(files, index=0)
|
|
473
|
+
data_list = hdf_eval(files, 'signal / Transmission')
|
|
474
|
+
```
|
|
475
|
+
|
|
476
|
+
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
hdfmap/__init__.py,sha256=K5e-wSQgl7nGdWgiS42WFNQsZZ6AJ5P4PmbL-42-7LY,2461
|
|
2
|
+
hdfmap/eval_functions.py,sha256=v2iYN_bH9jlzXpV6t26tePsj9fyhLoQmEVpeaa6u8Ug,6973
|
|
3
|
+
hdfmap/file_functions.py,sha256=-PVm6JpNYwvU8VPfaZDxNYbk3DVHdN-ORG8ByrNOQXQ,7813
|
|
4
|
+
hdfmap/hdfmap_class.py,sha256=2ZPDcEgjwMpsHNJS5caLi6CaMqfCgIRHxomPoEVufNU,28748
|
|
5
|
+
hdfmap/logging.py,sha256=vyI1HNhi-0cFgcCiiXOfNkymMIX_ZtAt1_UbmrO6iIs,1061
|
|
6
|
+
hdfmap/nexus.py,sha256=KeXw7ZlAkiA90WUiJXKsupJ3uJN7YRo0WQLhM6K92HE,10172
|
|
7
|
+
hdfmap/reloader_class.py,sha256=4BDa9y1ArHpZFSAsOPXNpbAFV-t4Wj-WW48HgfeBRO0,5219
|
|
8
|
+
hdfmap-0.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
|
|
9
|
+
hdfmap-0.4.dist-info/METADATA,sha256=kvtV4ay9l-fHw2TuPzjBq5ONYBHhtFy4fICxL0IFOsY,25194
|
|
10
|
+
hdfmap-0.4.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
|
|
11
|
+
hdfmap-0.4.dist-info/top_level.txt,sha256=JJhkRiuWFLI6ku-5dFtvEA0PbEbeHYyqurPYtWTcWhY,7
|
|
12
|
+
hdfmap-0.4.dist-info/RECORD,,
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
hdfmap
|