1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
|
import nixio as nix
import numpy as np
import os
import unittest
from .tmp import TempDir
VE = nix.validator.ValidationError
VW = nix.validator.ValidationWarning
class TestValidate (unittest.TestCase):
def setUp(self):
# Create completely valid objects and break for each test
self.tmpdir = TempDir("validatetest")
self.testfilename = os.path.join(self.tmpdir.path, "validatetest.nix")
self.file = nix.File.open(self.testfilename, nix.FileMode.Overwrite)
for bidx in range(2):
# Block
blk = self.file.create_block("block-{}".format(bidx),
"validation-test.block")
for gidx in range(2):
# Groups
blk.create_group("group-{}".format(gidx),
"validation-test.group")
# DataArrays + Dimensions
da1d = blk.create_data_array("data-1d",
"validation-test.data_array",
dtype=nix.DataType.Float,
data=np.random.random_sample(5))
rdim = da1d.append_range_dimension(ticks=[0.1, 0.2, 1.5, 2.4, 3.0])
rdim.unit = "ms"
da2d = blk.create_data_array("data-2d",
"validation-test.data_array",
dtype=nix.DataType.Float,
data=np.random.random_sample((2, 10)))
setdim = da2d.append_set_dimension()
setdim.labels = ("A", "B")
da2d.append_sampled_dimension(0.1)
da3d = blk.create_data_array("data-3d",
"validation-test.data_array",
dtype=nix.DataType.Float,
data=np.random.random_sample((4, 2, 10)))
setdim = da3d.append_set_dimension()
setdim.labels = ("1", "2", "3", "4")
da3d.append_set_dimension() # set dim without labels
smpldim = da3d.append_sampled_dimension(0.05)
smpldim.unit = "s"
# Tags + References + Features
tag = blk.create_tag("tag", "validation-test.tag",
position=(1, 1, 1))
tag.extent = (2, 1, 5)
tag.references.append(blk.data_arrays["data-3d"])
tag.units = ("", "", "ms")
pos1d = blk.create_data_array(
"pos-1d", "validation-test.multi_tag.positions",
data=[0, 1, 10, 20]
)
pos1d.append_set_dimension()
tagwf = blk.create_tag("tag-wf", "validation-test.tag",
position=(1, 3))
tag_feat_data = blk.create_data_array(
"feat-1", "validation-test.tag-feature", data=[1]
)
tag_feat_data.append_set_dimension()
tagwf.create_feature(tag_feat_data, nix.LinkType.Untagged)
# MultiTags + References + Features
mtag1d = blk.create_multi_tag(
"mtag1d", "validation-test.multi_tag", positions=pos1d
)
mtag1d.references.append(da1d)
mtag1d.units = ("s",)
pos2d = blk.create_data_array(
"pos-2d", "validation-test.multi_tag.positions",
data=[(10, 2, 100), (20, 5, 101)]
)
pos2d.append_set_dimension()
pos2d.append_set_dimension()
ext2d = blk.create_data_array(
"ext-3d", "validation-test.multi_tag.extents",
data=[(1, 1, 1), (5, 5, 5)]
)
ext2d.append_set_dimension()
ext2d.append_set_dimension()
mtag2d = blk.create_multi_tag(
"mtag2d", "validation-test.multi_tag", positions=pos2d
)
mtag2d.extents = ext2d
mtag2d.references.append(da3d)
mtag2d.units = ("", "", "us")
poswf = blk.create_data_array(
"pos-wf", "validation-test.multi_tag.feature", data=[42]
)
poswf.append_set_dimension()
mtagwf = blk.create_multi_tag(
"mtag-wf", "validation-test.multi_tag.feature",
positions=poswf
)
mtag_feat_data = blk.create_data_array(
"feat-2", "validation-test.tag-feature", data=[4, 2]
)
mtag_feat_data.append_set_dimension()
mtagwf.create_feature(mtag_feat_data, nix.LinkType.Untagged)
# Sources
# Go 3 levels deep (with N = 3:2:1)
typestr = "validation-test.sources"
for idx in range(3):
isrc = blk.create_source("{}:{}".format(blk.name, idx),
typestr)
for jdx in range(2):
jsrc = isrc.create_source("{}:{}".format(isrc.name, jdx),
typestr)
jsrc.create_source("{}:0".format(jsrc.name),
typestr)
# Sections
# Go 3 levels deep (with N = 4:2:2)
# 3 props per Section
def attach_props(section):
section.create_property("intprop", "prop-type", 10).unit = "s"
section.create_property("strprop", "prop-type", 0.1).unit = "mA"
typestr = "validation-test.sections"
for idx in range(4):
isec = self.file.create_section("{}:{}".format(blk.name, idx),
typestr)
attach_props(isec)
for jdx in range(2):
jsec = isec.create_section("{}:{}".format(isec.name, jdx),
typestr)
for kdx in range(2):
jsec.create_section("{}:{}".format(jsec.name, kdx),
typestr)
def tearDown(self):
self.file.close()
self.tmpdir.cleanup()
def test_all_valid(self):
res = self.file.validate()
assert not res["errors"], self.print_all_results(res)
assert not res["warnings"], self.print_all_results(res)
def test_check_file(self):
self.file._root.set_attr("version", tuple())
res = self.file.validate()
assert VW.NoVersion in res["warnings"][self.file]
self.file._root.set_attr("format", "")
res = self.file.validate()
assert VW.NoFormat in res["warnings"][self.file]
self.file._root.set_attr("version", (1, 2, 0)) # needed for ID check
self.file._root.set_attr("id", "")
res = self.file.validate()
assert VW.NoFileID in res["warnings"][self.file]
def test_check_block(self):
block = self.file.blocks[0]
block._h5group.set_attr("name", None)
res = self.file.validate()
assert res["errors"][block] == [VE.NoName]
block._h5group.set_attr("type", None)
res = self.file.validate()
actual = sorted(res["errors"][block])
expected = sorted([VE.NoName, VE.NoType])
assert actual == expected
assert len(res["warnings"]) == 0
def test_check_group(self):
group1 = self.file.blocks[0].groups[0]
group2 = self.file.blocks[1].groups[0]
group1._h5group.set_attr("name", None)
res = self.file.validate()
assert res["errors"][group1] == [VE.NoName]
assert group2 not in res["errors"]
group2._h5group.set_attr("name", None)
res = self.file.validate()
assert res["errors"][group2] == [VE.NoName]
assert group1 not in res["warnings"]
assert group2 not in res["warnings"]
group2._h5group.set_attr("type", None)
res = self.file.validate()
actual = sorted(res["errors"][group2])
expected = sorted([VE.NoName, VE.NoType])
assert actual == expected
assert len(res["warnings"]) == 0
def test_check_data_array_wrong_ticks(self):
expmsg = VE.RangeDimTicksMismatch.format(1)
da = self.file.blocks[0].data_arrays["data-1d"]
rdim = da.dimensions[0]
rdim.ticks = [10]
res = self.file.validate()
assert res["errors"][da] == [expmsg]
def test_check_data_array_wrong_labels(self):
expmsg = VE.SetDimLabelsMismatch.format(1)
da = self.file.blocks[0].data_arrays["data-2d"]
setdim = da.dimensions[0]
setdim.labels = ["-"]
res = self.file.validate()
assert res["errors"][da] == [expmsg]
def test_check_data_array_coefficients(self):
da1 = self.file.blocks[0].data_arrays["data-1d"]
da1.expansion_origin = 0.7
da2 = self.file.blocks[1].data_arrays["data-1d"]
da2.polynom_coefficients = [2, 4]
res = self.file.validate()
warnings = res["warnings"]
assert warnings[da1] == [VW.NoPolynomialCoefficients]
assert warnings[da2] == [VW.NoExpansionOrigin]
def test_check_data_array_bad_dims(self):
da = self.file.blocks[1].data_arrays["data-3d"]
da.append_set_dimension()
res = self.file.validate()
assert res["errors"][da] == [VE.DimensionMismatch]
def test_check_data_array_invalid_unit(self):
da = self.file.blocks[1].data_arrays["data-1d"]
da.unit = "whatevz"
res = self.file.validate()
assert res["warnings"][da] == [VW.InvalidUnit]
def test_incorrect_dim_index(self):
da = self.file.blocks[1].data_arrays["data-1d"]
da.delete_dimensions()
# This wont work if we ever change the internals
nix.SetDimension.create_new(da, "10")
res = self.file.validate()
assert VE.IncorrectDimensionIndex.format(1, 10) in res["errors"][da]
def test_invalid_dim_index(self):
da = self.file.blocks[1].data_arrays["data-1d"]
da.delete_dimensions()
# This wont work if we ever change the internals
nix.SetDimension.create_new(da, "-1")
res = self.file.validate()
assert VE.InvalidDimensionIndex.format(1) in res["errors"][da]
def test_check_tag_no_pos(self):
tag = self.file.blocks[0].tags[0]
tag.position = []
res = self.file.validate()
tagerr = res["errors"][tag]
# will also report mismatch in dimensions with reference
assert "position is not set" in tagerr
def test_check_tag_mismatch_dim(self):
tag = self.file.blocks[0].tags[0]
tag.position = [4, 3, 2, 1]
res = self.file.validate()
tagerr = res["errors"][tag]
assert VE.PositionDimensionMismatch in tagerr
def test_check_tag_invalid_unit(self):
tag = self.file.blocks[0].tags[0]
tag.units = ['abc']
res = self.file.validate()
tagerr = res["errors"][tag]
assert VE.InvalidUnit in tagerr
def test_check_tag_mismatch_units(self):
tag = self.file.blocks[0].tags[0]
tag.units = ("V", "A")
res = self.file.validate()
tagerr = res["errors"][tag]
assert VE.ReferenceUnitsMismatch in tagerr
tag.units = ("V", "A", "L")
res = self.file.validate()
tagerr = res["errors"][tag]
assert VE.ReferenceUnitsIncompatible in tagerr
def test_check_tag_pos_ext_mismatch(self):
tag = self.file.blocks[0].tags[0]
tag.extent = [100]
res = self.file.validate()
tagerr = res["errors"][tag]
assert VE.ExtentDimensionMismatch in tagerr
def test_check_multi_tag_no_pos(self):
blk = self.file.blocks[0]
mtag = blk.multi_tags["mtag1d"]
mtag.positions = blk.create_data_array("empty", "bork", data=[])
res = self.file.validate()
mtagerr = res["errors"][mtag]
# will also report mismatch in dimensions with reference
assert VE.NoPositions in mtagerr
def test_check_multi_tag_mismatch_dim(self):
blk = self.file.blocks[0]
# 2d tag positions on 2d data, with wrong positions length
mtag = blk.multi_tags["mtag2d"]
okpos = mtag.positions
mtag.positions = blk.create_data_array("wrong dim len", "bork",
data=[(1, 1), (2, 2)])
res = self.file.validate()
mtagerr = res["errors"][mtag]
assert VE.PositionsDimensionMismatch in mtagerr
# 1d tag positions on 2d data
mtag.positions = blk.create_data_array("1d v 2d", "bork",
data=[1, 2])
res = self.file.validate()
mtagerr = res["errors"][mtag]
assert VE.PositionsDimensionMismatch in mtagerr
# valid tag positions on 2d data, 1d extents
mtag.positions = okpos
mtag.extents = blk.create_data_array("1d extents", "bork",
data=[1, 2])
res = self.file.validate()
mtagerr = res["errors"][mtag]
assert VE.ExtentsDimensionMismatch in mtagerr
def test_check_multi_tag_invalid_unit(self):
blk = self.file.blocks[0]
mtag = blk.multi_tags["mtag2d"]
mtag.units = ['abc']
res = self.file.validate()
tagerr = res["errors"][mtag]
assert VE.InvalidUnit in tagerr
def test_check_multi_tag_mismatch_units(self):
mtag = self.file.blocks[0].multi_tags["mtag2d"]
mtag.units = ("V", "A")
res = self.file.validate()
tagerr = res["errors"][mtag]
assert VE.ReferenceUnitsMismatch in tagerr
mtag.units = ("V", "A", "L")
res = self.file.validate()
tagerr = res["errors"][mtag]
assert VE.ReferenceUnitsIncompatible in tagerr
def test_check_multi_tag_pos_ext_mismatch(self):
blk = self.file.blocks[0]
mtag = blk.multi_tags["mtag2d"]
mtag.extents = blk.create_data_array("wrong dim", "bork",
data=[(1, 1), (2, 2)])
res = self.file.validate()
mtagerr = res["errors"][mtag]
assert VE.PositionsExtentsMismatch in mtagerr
def test_check_source(self):
# just break one of the deepest Sources
def get_deepest_source(sources):
for source in sources:
if not source.sources:
return source
return get_deepest_source(source.sources)
source = get_deepest_source(self.file.blocks[0].sources)
source._h5group.set_attr("name", None)
source._h5group.set_attr("type", None)
res = self.file.validate()
assert len(res["errors"][source]) == 2
assert len(res["warnings"]) == 0
assert sorted(res["errors"][source]) == sorted([VE.NoName, VE.NoType])
def test_check_section(self):
# just break one of the deepest Sections
def get_deepest_section(sections):
for section in sections:
if not section.sections:
return section
return get_deepest_section(section.sections)
section = get_deepest_section(self.file.sections)
section._h5group.set_attr("name", None)
section._h5group.set_attr("type", None)
res = self.file.validate()
assert len(res["errors"][section]) == 2
assert len(res["warnings"]) == 0
assert sorted(res["errors"][section]) == sorted([VE.NoName, VE.NoType])
def test_check_property(self):
section = self.file.sections[0]
prop = section.props[0]
prop._h5group.set_attr("name", None)
res = self.file.validate()
errmsg = "property 0: {}".format(VE.NoName)
assert res["errors"][section] == [errmsg]
prop = section.props[1]
prop.unit = None
res = self.file.validate()
warnmsg = "property 1: {}".format(VW.NoUnit)
assert res["warnings"][section] == [warnmsg]
def test_check_range_dim_no_ticks(self):
da = self.file.blocks[1].data_arrays["data-1d"]
dim = da.dimensions[0]
dim.ticks = []
res = self.file.validate()
assert VE.NoTicks.format(1) in res["errors"][da]
def test_check_range_dim_invalid_unit(self):
da = self.file.blocks[1].data_arrays["data-1d"]
dim = da.dimensions[0]
dim.unit = "sillyvolts"
res = self.file.validate()
assert VE.InvalidDimensionUnit.format(1) in res["errors"][da]
def test_check_range_dim_unsorted_ticks(self):
da = self.file.blocks[1].data_arrays["data-1d"]
dim = da.dimensions[0]
dim._h5group.write_data("ticks", [10, 3, 1])
res = self.file.validate()
assert VE.UnsortedTicks.format(1) in res["errors"][da]
def test_check_sampled_dim_no_interval(self):
da = self.file.blocks[1].data_arrays["data-2d"]
dim = da.dimensions[1]
dim.sampling_interval = None
res = self.file.validate()
assert VE.NoSamplingInterval.format(2) in res["errors"][da]
def test_check_sampled_dim_bad_interval(self):
da = self.file.blocks[1].data_arrays["data-2d"]
dim = da.dimensions[1]
dim.sampling_interval = -1
res = self.file.validate()
assert VE.InvalidSamplingInterval.format(2) in res["errors"][da]
def test_check_sampled_dim_bad_unit(self):
da = self.file.blocks[1].data_arrays["data-2d"]
dim = da.dimensions[1]
dim.unit = "sillyamps"
res = self.file.validate()
assert VE.InvalidDimensionUnit.format(2) in res["errors"][da]
def test_check_sampled_dim_no_unit(self):
da = self.file.blocks[1].data_arrays["data-2d"]
dim = da.dimensions[1]
dim.unit = None
dim.offset = 10
res = self.file.validate()
assert VW.OffsetNoUnit.format(2) in res["warnings"][da]
@staticmethod
def print_all_results(res):
print("Errors")
for obj, msg in res["errors"].items():
name = obj.name if hasattr(obj, "name") else str(obj)
print(" {}: {}".format(name, msg))
print("Warnings")
for obj, msg in res["warnings"].items():
name = obj.name if hasattr(obj, "name") else str(obj)
print(" {}: {}".format(name, msg))
|
