class TestVisit(TestCase):
"""
Feature: The .visit and .visititems methods allow iterative access to
group and subgroup members
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = [
'grp1', 'grp1/sg1', 'grp1/sg2', 'grp2', 'grp2/sg1', 'grp2/sg1/ssg1'
]
for x in self.groups:
self.f.create_group(x)
def tearDown(self):
self.f.close()
def test_visit(self):
""" All subgroups are visited """
l = []
self.f.visit(l.append)
self.assertSameElements(l, self.groups)
def test_visititems(self):
""" All subgroups and contents are visited """
l = []
comp = [(x, self.f[x]) for x in self.groups]
self.f.visititems(lambda x, y: l.append((x, y)))
self.assertSameElements(comp, l)
def test_bailout(self):
""" Returning a non-None value immediately aborts iteration """
x = self.f.visit(lambda x: x)
self.assertEqual(x, self.groups[0])
x = self.f.visititems(lambda x, y: (x, y))
self.assertEqual(x, (self.groups[0], self.f[self.groups[0]]))
def test_visit(self):
fname = self.mktemp()
fid = File(fname, 'w')
fid.create_dataset('foo', (100, ), dtype='uint8')
with pytest.raises(TestException, match='throwing exception'):
fid.visititems(throwing)
fid.close()
def get_dataset(h5file: File, path: DatasetPath) -> Dataset:
res = None
if isinstance(path, DatasetPathContains):
res = h5file.visititems(partial(_v_item, path.path))
elif isinstance(path, DatasetPathWithAttribute):
res = h5file.visititems(partial(_v_attrs, path.attribute, path.value))
return res
def get_dataset(h5file: File, path: DatasetPath) -> Dataset:
res = None
if isinstance(path, DatasetPathContains):
res = h5file.visititems(partial(_v_item, path.path))
elif isinstance(path, DatasetPathWithAttribute):
res = h5file.visititems(partial(_v_attrs,
path.attribute, path.value))
return res
def hdf5_keys(dataset: h5py.File):
keys = []
def visitor(key, value):
if isinstance(value, h5py.Dataset):
keys.append(key)
dataset.visititems(visitor)
return keys
def find_virtual_datasets(file: h5py.File):
"""Return a list of 2-tuples: (path in file, dataset)"""
res = []
def visit(path, obj):
if isinstance(obj, h5py.Dataset) and obj.is_virtual:
res.append((path, obj))
file.visititems(visit)
return sorted(res)
def axf2dict(axf: h5py.File) -> Dict:
megaobject = NestedDict()
def itemsvisitor(k, v):
print(k, type(v), v)
keys = k.split("/")
if type(v) is Dataset:
d: Dataset = v
print(d.shape)
if d.shape == ():
print(d.dtype, d.value)
if str(d.dtype).startswith('|S'):
megaobject[keys] = str(d.value)
elif d.dtype == np.float32:
megaobject[keys] = float(d.value)
elif d.dtype == np.int32:
megaobject[keys] = int(d.value)
elif d.dtype == np.uint8:
megaobject[keys] = int(d.value)
elif d.dtype == np.uint32:
megaobject[keys] = int(d.value)
else:
megaobject[keys] = d.value
elif len(d.shape) == 1:
print(d.dtype, type(d[0]), np.array(d))
if isinstance(d[0], bytes):
megaobject[keys] = list(map(lambda x: str(x), d))
elif isinstance(d[0], np.float32):
megaobject[keys] = list(map(lambda x: float(x), d))
elif isinstance(d[0], np.int32):
megaobject[keys] = list(map(lambda x: int(x), d))
else:
megaobject[keys] = list(d)
json.dumps(megaobject[keys])
else:
x = reduce(lambda a, b: a * b, d.shape)
if x < 100:
ll = np.array(d).tolist()
megaobject[keys] = ll
else:
megaobject[keys] = f'BIG{d.shape}'
json.dumps(megaobject[keys])
elif type(v) is Group:
print('group')
megaobject[keys] = {}
else:
raise Exception(f"unhandled type {type(v)} {k}")
axf.visititems(itemsvisitor)
return megaobject.dict
class TestVisit(TestCase):
"""
Feature: The .visit and .visititems methods allow iterative access to
group and subgroup members
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = [
'grp1', 'grp1/sg1', 'grp1/sg2', 'grp2', 'grp2/sg1', 'grp2/sg1/ssg1'
]
for x in self.groups:
self.f.create_group(x)
def tearDown(self):
self.f.close()
def test_visit(self):
""" All subgroups are visited """
l = []
self.f.visit(l.append)
self.assertSameElements(l, self.groups)
def test_visititems(self):
""" All subgroups and contents are visited """
l = []
comp = [(x, self.f[x]) for x in self.groups]
self.f.visititems(lambda x, y: l.append((x,y)))
self.assertSameElements(comp, l)
def test_bailout(self):
""" Returning a non-None value immediately aborts iteration """
x = self.f.visit(lambda x: x)
self.assertEqual(x, self.groups[0])
x = self.f.visititems(lambda x, y: (x,y))
self.assertEqual(x, (self.groups[0], self.f[self.groups[0]]))
