def test_HDF5RemoveAttributes(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/ExampleGroup")
data1 = np.random.rand(50)
F.writeDataset("/Data", "ExampleData1", data1)
attr = {"attr1": "hello world", "attr2": np.array(["foo"])}
F.addAttributes("/Data", attr, overwrite=False)
self.assertTrue("attr1" in F.fileObj["/Data"].attrs.keys())
self.assertTrue("attr2" in F.fileObj["/Data"].attrs.keys())
attr = {"attr1": "goodbye world", "attr2": np.random.rand(5)}
F.addAttributes("/Data/ExampleData1", attr, overwrite=False)
# Test removing attributes
F.rmAttributes("/Data", attributes=None)
self.assertFalse("attr1" in F.fileObj["/Data"].attrs.keys())
self.assertFalse("attr2" in F.fileObj["/Data"].attrs.keys())
F.rmAttributes("/Data/ExampleData1", attributes=["attr1"])
self.assertFalse(
"attr1" in F.fileObj["/Data/ExampleData1"].attrs.keys())
self.assertTrue(
"attr2" in F.fileObj["/Data/ExampleData1"].attrs.keys())
F.close()
F = HDF5(self.tmpfile, 'r')
with self.assertRaises(IOError):
F.rmAttributes("/Data/ExampleData1", attributes=["attr1"])
F.close()
return
def test_HDF5WriteDatasets(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/ExampleGroup")
# Test writing dataset to root
data1 = np.random.rand(50)
F.writeDataset("/Data", "ExampleData1", data1)
self.assertTrue("ExampleData1" in F.fileObj["/Data"].keys())
self.assertTrue(F.datasetExists("/Data", "ExampleData1"))
diff = np.fabs(data1 - np.array(F.fileObj["/Data/ExampleData1"]))
[self.assertEqual(d, 0.0) for d in diff]
# Test writing dataset to subgroup
data2 = np.random.rand(50)
F.writeDataset("/Data/ExampleGroup", "ExampleData2", data2)
self.assertTrue(
"ExampleData2" in F.fileObj["/Data/ExampleGroup"].keys())
self.assertTrue(F.datasetExists("/Data/ExampleGroup", "ExampleData2"))
diff = np.fabs(data2 -
np.array(F.fileObj["/Data/ExampleGroup/ExampleData2"]))
[self.assertEqual(d, 0.0) for d in diff]
# Test overwriting option
with warnings.catch_warnings():
warnings.filterwarnings("ignore")
F.writeDataset("/Data", "ExampleData1", data2, overwrite=False)
diff = np.fabs(data1 - np.array(F.fileObj["/Data/ExampleData1"]))
[self.assertEqual(d, 0.0) for d in diff]
F.writeDataset("/Data", "ExampleData1", data2, overwrite=True)
diff = np.fabs(data2 - np.array(F.fileObj["/Data/ExampleData1"]))
[self.assertEqual(d, 0.0) for d in diff]
# Testing appending datasets
data3 = np.random.rand(50)
F.appendDataset("/Data", "ExampleData1", data3)
self.assertEqual(F.fileObj["/Data/ExampleData1"].size, 100)
diff = np.fabs(
np.append(data2, data3) -
np.array(F.fileObj["/Data/ExampleData1"]))
[self.assertEqual(d, 0.0) for d in diff]
with self.assertRaises(KeyError):
F.appendDataset("/Data",
"ExampleData3",
data3,
exit_if_missing=True)
F.close()
# Testing writing to file opened in read-only mode
F = HDF5(self.tmpfile, 'r')
with self.assertRaises(IOError):
F.writeDataset("/Data", "ExampleData1", data1)
F.close()
return
def test_HDF5ReadAttributes(self):
F = HDF5(self.examplefile, 'r')
attr = F.readAttributes("/Data")
self.assertEqual(len(attr.keys()), 1)
self.assertTrue("greeting" in attr.keys())
self.assertTrue(attr["greeting"], "hello world")
attr = F.readAttributes("/Data/ExampleGroup/ExampleIntData2")
self.assertEqual(len(attr.keys()), 2)
self.assertTrue("value" in attr.keys())
self.assertTrue(attr["value"], 50)
self.assertTrue("array" in attr.keys())
[
self.assertEqual(a, b)
for a, b in zip(np.arange(5, dtype=float), attr["array"])
]
attr = F.readAttributes("/Data/ExampleGroup/ExampleIntData2",
required=["value"])
self.assertEqual(len(attr.keys()), 1)
self.assertTrue("value" in attr.keys())
self.assertTrue(attr["value"], 50)
self.assertFalse("array" in attr.keys())
with self.assertRaises(KeyError):
F.readAttributes("/Data/Example")
F.close()
return
def test_HDF5RemoveGroups(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/SubGroup")
grps0 = F.fileObj["/"].keys()
self.assertTrue("Header" in grps0)
self.assertTrue("Data" in grps0)
F.rmGroup("/Header")
grps0 = F.fileObj["/"].keys()
self.assertFalse("Header" in grps0)
self.assertTrue("Data" in grps0)
F.rmGroup("/Data")
self.assertFalse("Data" in F.fileObj["/"].keys())
F.close()
F = HDF5(self.tmpfile, 'r')
with self.assertRaises(IOError):
F.rmGroup("/Header")
F.close()
return
def test_HDF5CreateGroups(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/SubGroup")
grps0 = F.fileObj["/"].keys()
self.assertTrue("Header" in grps0)
self.assertTrue("Data" in grps0)
grps1 = F.fileObj["/Data"].keys()
self.assertTrue("SubGroup" in grps1)
F.close()
return
def test_HDF5AddAttributes(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/ExampleGroup")
data1 = np.random.rand(50)
F.writeDataset("/Data", "ExampleData1", data1)
attr = {"attr1": "hello world"}
F.addAttributes("/Data", attr, overwrite=False)
self.assertEqual(F.fileObj["/Data"].attrs["attr1"], b"hello world")
F.addAttributes("/Data/ExampleData1", {"value": 1}, overwrite=False)
self.assertEqual(F.fileObj["/Data/ExampleData1"].attrs["value"], 1)
F.addAttributes("/Data/ExampleData1", {"value": 2}, overwrite=True)
self.assertEqual(F.fileObj["/Data/ExampleData1"].attrs["value"], 2)
F.close()
# Test attempting to write in read-only mode
F = HDF5(self.tmpfile, 'r')
with self.assertRaises(IOError):
F.addAttributes("/Data", attr, overwrite=False)
F.close()
return
def test_HDF5RemoveDatasets(self):
F = HDF5(self.tmpfile, 'w')
F.mkGroup("/Header")
F.mkGroup("/Data/ExampleGroup")
data1 = np.random.rand(50)
F.writeDataset("/Data", "ExampleData1", data1)
self.assertTrue("ExampleData1" in F.fileObj["/Data"].keys())
F.rmDataset("/Data", "ExampleData1")
self.assertFalse("ExampleData1" in F.fileObj["/Data"].keys())
data2 = np.random.rand(50)
F.writeDataset("/Data/ExampleGroup", "ExampleData2", data2)
self.assertTrue(
"ExampleData2" in F.fileObj["/Data/ExampleGroup"].keys())
F.rmDataset("/Data/ExampleGroup", "ExampleData2")
self.assertFalse(
"ExampleData2" in F.fileObj["/Data/ExampleGroup"].keys())
F.close()
F = HDF5(self.tmpfile, 'r')
with self.assertRaises(IOError):
F.rmDataset("/Data/ExampleGroup", "ExampleData2")
F.close()
return
def test_HDF5ListDatasets(self):
F = HDF5(self.examplefile, 'r')
self.assertEqual(F.lsDatasets("/", recursive=False), [])
dsets = F.lsDatasets("/", recursive=True)
keys = ['/Data/ExampleFloatData','/Data/ExampleGroup/ExampleFloatData2',\
'/Data/ExampleGroup/ExampleIntData2','/Data/ExampleIntData']
self.assertEqual(len(dsets), len(keys))
[self.assertTrue(key in dsets) for key in keys]
dsets = F.lsDatasets("/Data", recursive=False)
keys = ['ExampleFloatData', 'ExampleIntData']
self.assertEqual(len(dsets), len(keys))
[self.assertTrue(key in dsets) for key in keys]
F.close()
return
def testHDF5ListObjects(self):
F = HDF5(self.examplefile, 'r')
objs = F.lsObjects("/", recursive=False)
self.assertEqual(len(objs), 2)
keys = ["Header", "Data"]
[self.assertTrue(key in objs) for key in keys]
objs = F.lsObjects("/", recursive=True)
self.assertEqual(len(objs), 7)
keys = ['/Data','/Data/ExampleFloatData','/Data/ExampleGroup',\
'/Data/ExampleGroup/ExampleFloatData2',\
'/Data/ExampleGroup/ExampleIntData2',\
'/Data/ExampleIntData','/Header']
[self.assertTrue(key in objs) for key in keys]
F.close()
return
def test_HDF5ListGroups(self):
F = HDF5(self.examplefile, 'r')
grps0 = list(F.fileObj["/"].keys())
grps = F.lsGroups("/", recursive=False)
self.assertTrue(grps == grps0)
self.assertTrue("Header" in grps)
self.assertTrue("Data" in grps)
grps = F.lsGroups("/", recursive=True)
self.assertEqual(len(grps), 3)
self.assertTrue("/Header" in grps)
self.assertTrue("/Data" in grps)
self.assertTrue("/Data/ExampleGroup" in grps)
grps = F.lsGroups("/Data", recursive=True)
self.assertEqual(len(grps), 1)
self.assertTrue("/Data/ExampleGroup" in grps)
grps = F.lsGroups("/Data", recursive=False)
self.assertEqual(len(grps), 1)
self.assertTrue("ExampleGroup" in grps)
F.close()
return
def test_HDF5ReadDatasets(self):
F = HDF5(self.examplefile, 'r')
dset = F.readDataset("/Data/ExampleFloatData", exit_if_missing=False)
[
self.assertEqual(a, b)
for a, b in zip(dset, np.arange(100, dtype=float))
]
dset = F.readDataset("/Data/ExampleIntData", exit_if_missing=False)
[
self.assertEqual(a, b)
for a, b in zip(dset, np.arange(100, dtype=int))
]
self.assertIsNone(
F.readDataset("/Data/ExampleData", exit_if_missing=False))
with self.assertRaises(KeyError):
F.readDataset("/Data/ExampleData", exit_if_missing=True)
dset = F.readDataset("/Data/ExampleGroup/ExampleFloatData2",
exit_if_missing=False)
[
self.assertEqual(a, b)
for a, b in zip(dset, np.arange(10, dtype=float))
]
dset = F.readDataset("/Data/ExampleGroup/ExampleIntData2",
exit_if_missing=False)
[
self.assertEqual(a, b)
for a, b in zip(dset, np.arange(100, dtype=int))
]
self.assertIsNone(
F.readDataset("/Data/ExampleGroup/ExampleData",
exit_if_missing=False))
with self.assertRaises(KeyError):
F.readDataset("/Data/ExampleGroup/ExampleData",
exit_if_missing=True)
F.readDataset("/Data/ExampleGroup1/ExampleFloatData2",
exit_if_missing=False)
F.readDataset("/Data/ExampleGroup1/ExampleFloatData2",
exit_if_missing=True)
F.close()
return