def test_Put_Data():
"""The datasetType can put its own data and datasetIDs.
"""
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
dsIDs['acqID'] = 1
ds = Localizations(datasetIDs=dsIDs)
ds.data = pd.DataFrame({'A': [1, 2], 'B': [3, 4]})
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path('test_db.h5'))):
remove(str(pathToDB / Path('test_db.h5')))
with db.HDFDatastore(pathToDB / Path('test_db.h5')) as myDB:
myDB.put(ds)
key = 'test_prefix/test_prefix_1/Localizations'
with h5py.File(str(pathToDB / Path('test_db.h5')), 'r') as hdf:
assert_equal(hdf[key].attrs['SMLM_datasetType'], 'Localizations')
df = pd.read_hdf(str(pathToDB / Path('test_db.h5')), key=key)
assert_equal(df.loc[0, 'A'], 1)
assert_equal(df.loc[1, 'A'], 2)
assert_equal(df.loc[0, 'B'], 3)
assert_equal(df.loc[1, 'B'], 4)
finally:
# Remove the test datastore
remove(str(pathToDB / Path('test_db.h5')))
def test_Put_Data():
"""The datasetType can put its own data and datasetIDs.
"""
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
dsIDs['acqID'] = 1
ds = Localizations(datasetIDs = dsIDs)
ds.data = pd.DataFrame({'A' : [1,2], 'B' : [3,4]})
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path('test_db.h5'))):
remove(str(pathToDB / Path('test_db.h5')))
myDB = db.HDFDatastore(pathToDB / Path('test_db.h5'))
myDB.put(ds)
key = 'test_prefix/test_prefix_1/Localizations'
with h5py.File(str(pathToDB / Path('test_db.h5')), 'r') as hdf:
assert_equal(hdf[key].attrs['SMLM_datasetType'], 'Localizations')
df = pd.read_hdf(str(pathToDB / Path('test_db.h5')), key = key)
assert_equal(df.loc[0, 'A'], 1)
assert_equal(df.loc[1, 'A'], 2)
assert_equal(df.loc[0, 'B'], 3)
assert_equal(df.loc[1, 'B'], 4)
finally:
# Remove the test datastore
remove(str(pathToDB / Path('test_db.h5')))
def test__repr__():
"""DatasetType generates the correct __repr__ string.
"""
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
ds = Localizations(datasetIDs=dsIDs)
assert_equal(ds.__repr__(), 'Localizations: {\'prefix\': \'test_prefix\'}')
del (ds.datasetIDs['prefix'])
assert_equal(ds.__repr__(), 'Localizations: {}')
def test__repr__():
"""DatasetType generates the correct __repr__ string.
"""
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
ds = Localizations(datasetIDs = dsIDs)
assert_equal(ds.__repr__(), 'Localizations: {\'prefix\': \'test_prefix\'}')
del(ds.datasetIDs['prefix'])
assert_equal(ds.__repr__(), 'Localizations: {}')
def test_Instantiation():
"""The datasetType is properly instantiated.
"""
# Make up some dataset IDs
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
dsIDs['acqID'] = 1
Localizations(datasetIDs=dsIDs)
def test_Get_Data():
"""The datasetType can get its own data and datasetIDs.
"""
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs["prefix"] = "test_prefix"
dsIDs["acqID"] = 1
ds = Localizations(datasetIDs=dsIDs)
ds.data = pd.DataFrame({"A": [1, 2], "B": [3, 4]})
# Make up the attribute DatasetType
dsAttr = LocMetadata(datasetIDs=dsIDs)
dsAttr.data = {"A": 2, "B": "hello"}
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path("test_db.h5"))):
remove(str(pathToDB / Path("test_db.h5")))
myDB = db.HDFDatastore(pathToDB / Path("test_db.h5"))
myDB.put(ds)
myDB.put(dsAttr)
# Test the get() function now.
myNewDSID = myDB.dsID("test_prefix", 1, "LocMetadata", "Localizations", None, None, None, None)
myNewDS = myDB.get(myNewDSID)
ids = myNewDS.datasetIDs
assert_equal(ids["prefix"], "test_prefix")
assert_equal(ids["acqID"], 1)
assert_equal(ids["channelID"], None)
assert_equal(ids["dateID"], None)
assert_equal(ids["posID"], None)
assert_equal(ids["sliceID"], None)
assert_equal(myNewDS.datasetType, "LocMetadata")
assert_equal(myNewDS.data["A"], 2)
assert_equal(myNewDS.data["B"], "hello")
finally:
# Remove the test datastore
# remove(str(pathToDB / Path('test_db.h5')))
pass
def test_Get_Data():
"""The datasetType can get its own data and datasetIDs.
"""
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
dsIDs['acqID'] = 1
ds = Localizations(datasetIDs=dsIDs)
ds.data = pd.DataFrame({'A': [1, 2], 'B': [3, 4]})
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path('test_db.h5'))):
remove(str(pathToDB / Path('test_db.h5')))
with db.HDFDatastore(pathToDB / Path('test_db.h5')) as myDB:
myDB.put(ds)
# Create a new dataset containing only IDs to test getting of the data
myNewDSID = db.DatasetID('test_prefix', 1, 'Localizations', None, None,
None, None, None, None)
myNewDS = myDB.get(myNewDSID)
ids = myNewDS.datasetIDs
assert_equal(ids['prefix'], 'test_prefix')
assert_equal(ids['acqID'], 1)
assert_equal(myNewDS.datasetType, 'Localizations')
assert_equal(ids['channelID'], None)
assert_equal(ids['dateID'], None)
assert_equal(ids['posID'], None)
assert_equal(ids['sliceID'], None)
assert_equal(ids['replicateID'], None)
assert_equal(myNewDS.data.loc[0, 'A'], 1)
assert_equal(myNewDS.data.loc[1, 'A'], 2)
assert_equal(myNewDS.data.loc[0, 'B'], 3)
assert_equal(myNewDS.data.loc[1, 'B'], 4)
finally:
# Remove the test datastore
remove(str(pathToDB / Path('test_db.h5')))
def test_Put_Data():
"""The datasetType can put its own data and datasetIDs.
"""
mdPrefix = config.__HDF_Metadata_Prefix__
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs["prefix"] = "test_prefix"
dsIDs["acqID"] = 1
ds = Localizations(datasetIDs=dsIDs)
ds.data = pd.DataFrame({"A": [1, 2], "B": [3, 4]})
# Make up the attribute DatasetType
dsAttr = LocMetadata(datasetIDs=dsIDs)
dsAttr.data = {"A": 2, "B": "hello"}
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path("test_db.h5"))):
remove(str(pathToDB / Path("test_db.h5")))
myDB = db.HDFDatastore(pathToDB / Path("test_db.h5"))
myDB.put(ds)
myDB.put(dsAttr)
key = "test_prefix/test_prefix_1/Localizations"
with h5py.File(str(pathToDB / Path("test_db.h5")), "r") as hdf:
assert_equal(hdf[key].attrs["SMLM_datasetType"], "Localizations")
assert_equal(hdf[key].attrs[mdPrefix + "A"], "2")
assert_equal(hdf[key].attrs[mdPrefix + "B"], '"hello"')
df = pd.read_hdf(str(pathToDB / Path("test_db.h5")), key=key)
assert_equal(df.loc[0, "A"], 1)
assert_equal(df.loc[1, "A"], 2)
assert_equal(df.loc[0, "B"], 3)
assert_equal(df.loc[1, "B"], 4)
finally:
# Remove the test datastore
remove(str(pathToDB / Path("test_db.h5")))
def test_Get_Data():
"""The datasetType can get its own data and datasetIDs.
"""
try:
# Make up some dataset IDs and a dataset
dsIDs = {}
dsIDs['prefix'] = 'test_prefix'
dsIDs['acqID'] = 1
ds = Localizations(datasetIDs = dsIDs)
ds.data = pd.DataFrame({'A' : [1,2], 'B' : [3,4]})
pathToDB = testDataRoot
# Remove datastore if it exists
if exists(str(pathToDB / Path('test_db.h5'))):
remove(str(pathToDB / Path('test_db.h5')))
myDB = db.HDFDatastore(pathToDB / Path('test_db.h5'))
myDB.put(ds)
# Create a new dataset containing only IDs to test getting of the data
myNewDSID = myDB.dsID('test_prefix', 1, 'Localizations', None,
None, None, None, None)
myNewDS = myDB.get(myNewDSID)
ids = myNewDS.datasetIDs
assert_equal(ids['prefix'], 'test_prefix')
assert_equal(ids['acqID'], 1)
assert_equal(myNewDS.datasetType, 'Localizations')
assert_equal(ids['channelID'], None)
assert_equal(ids['dateID'], None)
assert_equal(ids['posID'], None)
assert_equal(ids['sliceID'], None)
assert_equal(myNewDS.data.loc[0, 'A'], 1)
assert_equal(myNewDS.data.loc[1, 'A'], 2)
assert_equal(myNewDS.data.loc[0, 'B'], 3)
assert_equal(myNewDS.data.loc[1, 'B'], 4)
finally:
# Remove the test datastore
remove(str(pathToDB / Path('test_db.h5')))
