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
|
# -*- coding: utf-8 -*-
# Copyright © 2014, German Neuroinformatics Node (G-Node)
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted under the terms of the BSD License. See
# LICENSE file in the root of the Project.
import os
import time
import h5py
import unittest
import numpy as np
import nixio as nix
import nixio.file as filepy
from nixio.exceptions import InvalidFile, DuplicateName
from .tmp import TempDir
class TestFile(unittest.TestCase):
def setUp(self):
self.tmpdir = TempDir("filetest")
self.testfilename = os.path.join(self.tmpdir.path, "filetest.nix")
self.file = nix.File.open(self.testfilename, nix.FileMode.Overwrite)
def tearDown(self):
self.file.close()
self.tmpdir.cleanup()
def test_file_format(self):
assert self.file.format == "nix"
assert self.file.version == filepy.HDF_FF_VERSION
def test_file_timestamps(self):
created_at = self.file.created_at
assert created_at > 0
updated_at = self.file.updated_at
assert updated_at > 0
self.file.force_created_at(1403530068)
assert self.file.created_at == 1403530068
def test_file_blocks(self):
assert len(self.file.blocks) == 0
block = self.file.create_block("test block", "recordingsession")
with self.assertRaises(DuplicateName):
self.file.create_block("test block", "recordingsession")
assert len(self.file.blocks) == 1
assert block in self.file.blocks
assert block.id in self.file.blocks
assert "notexist" not in self.file.blocks
assert block.id == self.file.blocks[0].id
assert block.id == self.file.blocks[-1].id
del self.file.blocks[0]
assert len(self.file.blocks) == 0
with self.assertRaises(ValueError):
self.file.create_block()
self.file.create_block(name="a name")
b = self.file.create_block(type_="type_a")
assert b.id == b.name
def test_file_sections(self):
assert len(self.file.sections) == 0
section = self.file.create_section("test section", "recordingsession")
assert len(self.file.sections) == 1
assert section in self.file.sections
assert section.id in self.file.sections
assert "notexist" not in self.file.sections
assert section.id == self.file.sections[0].id
assert section.id == self.file.sections[-1].id
del self.file.sections[0]
assert len(self.file.sections) == 0
def test_file_find_sections(self):
for i in range(2):
self.file.create_section("level1-p0-s" + str(i), "dummy")
for i in range(2):
self.file.sections[0].create_section("level2-p1-s" + str(i),
"dummy")
for i in range(2):
self.file.sections[1].create_section("level2-p2-s" + str(i),
"dummy")
for i in range(2):
self.file.sections[0].sections[0].create_section(
"level3-p1-s" + str(i), "dummy"
)
assert len(self.file.find_sections()) == 8
assert len(self.file.find_sections(limit=1)) == 2
assert(len(self.file.find_sections(filtr=lambda x: "level2-p1-s" in
x.name)) == 2)
assert(len(self.file.find_sections(filtr=lambda x: "level2-p1-s" in
x.name,
limit=1)) == 0)
def test_order_tracking(self):
blknames = []
for idx in range(10):
name = "block_" + str(idx)
self.file.create_block(name, "ordertest")
blknames.append(name)
danames = []
datablockname = blknames[0]
datablock = self.file.blocks[datablockname]
for idx in range(7):
name = "data_" + str(idx)
da = datablock.create_data_array(name, "thedata",
data=np.array([0]))
da.definition = "da definition"
danames.append(name)
self.file.close()
self.file = nix.File.open(self.testfilename, nix.FileMode.ReadOnly)
for idx in range(len(self.file.blocks)):
self.assertEqual(blknames[idx], self.file.blocks[idx].name)
datablock = self.file.blocks[datablockname]
for idx in range(len(datablock.data_arrays)):
self.assertEqual(danames[idx], datablock.data_arrays[idx].name)
def test_context_open(self):
fname = os.path.join(self.tmpdir.path, "contextopen.nix")
with nix.File.open(fname, nix.FileMode.Overwrite) as nf:
nf.create_block("blocky", "test-block")
with nix.File.open(fname, nix.FileMode.ReadOnly) as nf:
self.assertEqual(nf.blocks[0].name, "blocky")
def test_copy_on_file(self):
tar_filename = os.path.join(self.tmpdir.path, "copytarget.nix")
tar_file = nix.File.open(tar_filename, nix.FileMode.Overwrite)
blk1 = self.file.create_block("t111t bk", "testcopy")
blk2 = tar_file.create_block("blk2", "blk")
blk1.create_data_array("da1", 'grp da1', data=[(1, 2, 3)])
da2 = blk2.create_data_array("da2", 'grp da2', data=[(4, 5, 6)])
blk2.create_multi_tag("mt2", "useless", da2)
sec1 = self.file.create_section("test sec", 'test')
sec1.create_section("child sec", "child")
ori_prop = sec1.create_property("prop origin",
values_or_dtype=[1, 2, 3])
tar_file.create_block(copy_from=blk1, keep_copy_id=False)
copied_sec = tar_file.copy_section(sec1, children=False, keep_id=True)
assert tar_file.sections[0].name == sec1.name
assert tar_file.blocks[1].name == blk1.name
assert tar_file.blocks[1].data_arrays[0].name \
== blk1.data_arrays[0].name
assert tar_file.blocks[1].data_arrays[0].id != blk1.data_arrays[0].id
assert tar_file.sections[0] == sec1
assert len(self.file.find_sections()) == 2
assert len(tar_file.find_sections()) == 1
assert copied_sec.props[0] == ori_prop # Properties are still there
assert not copied_sec.sections # children is False
tar_file.close()
# test copying on the same file
self.assertRaises(NameError, self.file.create_block, copy_from=blk1)
self.file.create_block(name="111", copy_from=blk1)
assert self.file.blocks[0] == self.file.blocks[1] # ID stays the same
assert self.file.blocks[0].name != self.file.blocks[1].name
def test_timestamp_autoupdate(self):
# Using Block to test Entity.definition
blk = self.file.create_block("block", "timetest")
blktime = blk.updated_at
time.sleep(1) # wait for time to change
blk.definition = "updated"
# no update
self.assertNotEqual(blk.updated_at, blktime)
rblk = self.file.blocks["block"] # read through container
time.sleep(1) # wait for time to change
rblk.definition = "updated again"
self.assertNotEqual(rblk.updated_at, blktime)
# Using Block to test Entity.type
blktime = blk.updated_at
time.sleep(1) # wait for time to change
blk.type = "updated"
# no update
self.assertNotEqual(blk.updated_at, blktime)
rblk = self.file.blocks["block"] # read through container
time.sleep(1) # wait for time to change
rblk.type = "updated again"
self.assertNotEqual(rblk.updated_at, blktime)
def test_timestamp_noautoupdate(self):
# Using Block to test Entity.definition
blk = self.file.create_block("block", "timetest")
# disable timestamp autoupdating
self.file.auto_update_timestamps = False
blktime = blk.updated_at
time.sleep(1) # wait for time to change
blk.definition = "update"
self.assertEqual(blk.updated_at, blktime)
rblk = self.file.blocks["block"] # read through container
rblktime = rblk.updated_at
time.sleep(1) # wait for time to change
rblk.definition = "time should change"
self.assertEqual(rblk.updated_at, rblktime)
blktime = blk.updated_at
time.sleep(1) # wait for time to change
blk.type = "update"
self.assertEqual(blk.updated_at, blktime)
rblk = self.file.blocks["block"] # read through container
rblktime = rblk.updated_at
time.sleep(1) # wait for time to change
rblk.type = "time should change"
self.assertEqual(rblk.updated_at, rblktime)
class TestFileVer(unittest.TestCase):
backend = "h5py"
filever = filepy.HDF_FF_VERSION
fformat = filepy.FILE_FORMAT
def try_open(self, mode):
nix_file = nix.File.open(self.testfilename, mode)
nix_file.close()
def set_header(self, fformat=None, version=None, fileid=None):
if fformat is None:
fformat = self.fformat
if version is None:
version = self.filever
if fileid is None:
fileid = nix.util.create_id()
self.h5root.attrs["format"] = fformat
self.h5root.attrs["version"] = version
self.h5root.attrs["id"] = fileid
self.h5root.attrs["created_at"] = 0
self.h5root.attrs["updated_at"] = 0
if "data" not in self.h5root:
self.h5root.create_group("data")
self.h5root.create_group("metadata")
def setUp(self):
self.tmpdir = TempDir("vertest")
self.testfilename = os.path.join(self.tmpdir.path, "vertest.nix")
self.h5file = h5py.File(self.testfilename, mode="w")
self.h5root = self.h5file["/"]
def tearDown(self):
self.h5file.close()
self.tmpdir.cleanup()
def test_read_write(self):
self.set_header()
self.try_open(nix.FileMode.ReadWrite)
def test_read_only(self):
ver_x, ver_y, ver_z = self.filever
roversion = (ver_x, ver_y, ver_z+2)
self.set_header(version=roversion)
self.try_open(nix.FileMode.ReadOnly)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadWrite)
def test_no_open(self):
ver_x, ver_y, ver_z = self.filever
noversion = (ver_x, ver_y+3, ver_z+2)
self.set_header(version=noversion)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadWrite)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
noversion = (ver_x, ver_y+1, ver_z)
self.set_header(version=noversion)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadWrite)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
noversion = (ver_x+1, ver_y, ver_z)
self.set_header(version=noversion)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadWrite)
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
def test_bad_tuple(self):
self.set_header(version=(-1, -1, -1))
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
self.set_header(version=(1, 2))
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
def test_bad_format(self):
self.set_header(fformat="NOT_A_NIX_FILE")
with self.assertRaises(InvalidFile):
self.try_open(nix.FileMode.ReadOnly)
def test_bad_id(self):
self.set_header(fileid="")
with self.assertRaises(RuntimeError):
self.try_open(nix.FileMode.ReadOnly)
# empty file ID OK for versions older than 1.2.0
self.set_header(version=(1, 1, 1), fileid="")
self.try_open(nix.FileMode.ReadOnly)
self.set_header(version=(1, 1, 0), fileid="")
self.try_open(nix.FileMode.ReadOnly)
self.set_header(version=(1, 0, 0), fileid="")
self.try_open(nix.FileMode.ReadOnly)
|
