def test_MMParser_Dataset():
"""MMParser returns the correct Dataset.
"""
f = 'HeLa_Control_A750_1_MMStack_Pos0_locMetadata.json'
inputFile = testDataRoot / Path('parsers_test_files') / Path(f)
datasetType = 'LocMetadata'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFile, datasetType)
ds = mmParser.dataset
ok_(isinstance(ds, database.Dataset))
assert_equal(ds.datasetIDs['acqID'], 1)
assert_equal(ds.datasetIDs['channelID'], 'A750')
assert_equal(ds.datasetIDs['posID'], (0, ))
assert_equal(ds.datasetIDs['prefix'], 'HeLa_Control')
assert_equal(ds.datasetIDs['sliceID'], None)
assert_equal(ds.datasetType, 'LocMetadata')
# Test a few metadata entries
ds.data = ds.readFromFile(inputFile)
assert_equal(ds.data['Slices'], 1)
assert_equal(ds.data['InitialPositionList'], None)
assert_equal(ds.data['PixelType'], 'GRAY8')
assert_equal(ds.data['Positions'], 1)
def test_MMParser_Widefield_NoChannel():
"""Will MMParser properly extract widefield info w/o a channel?
"""
f = [
'HeLa_Control_WF13_MMStack_Pos0.ome.tif',
'HeLa_WF13_Control_MMStack_Pos0.ome.tif',
'WF13_HeLa_Control_MMStack_Pos0.ome.tif',
'HeLa_Control_WF13__MMStack_Pos0.ome.tif',
'_WF13_HeLa_Control_MMStack_Pos0.ome.tif',
'_WF13_HeLa_Control_MMStack_Pos0.ome.tif',
'HeLa_Control_WF13_MMStack_Pos0.ome.tif',
'HeLa_Control_WF_13_MMStack_Pos0.ome.tif',
'HeLa_WF__13_Control_MMStack_Pos0.ome.tif'
]
mmParser = leb.MMParser()
for filename in f:
mmParser.parseFilename(filename, 'WidefieldImage')
assert_equal(mmParser.dataset.datasetIDs['acqID'], 13)
assert_equal(mmParser.dataset.datasetIDs['channelID'], None)
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'HeLa_Control')
assert_equal(mmParser.dataset.datasetIDs['sliceID'], None)
assert_equal(mmParser.dataset.datasetType, 'WidefieldImage')
def test_MMParser_ParseFailure():
"""MMParser raises a ParseFilenameFailure error when the filename is bad.
"""
f = 'blablabla 214'
parser = leb.MMParser()
parser.parseFilename(f, 'TestType')
def test_MMParser_UnregisteredType_WillNot_Parse():
"""Unregistered datasetTypes should raise an error if parsed.
"""
inputFilename = 'Cos7_Microtubules_A647_3_MMStack_Pos0_locResults.dat'
datasetType = 'Localizations_Cool'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFilename, datasetType)
def test_MMParser_Attributes_NoChannel():
"""Will MMParser extract the acquisition info w/o a channel identifier?
"""
inputFilename = 'Cos7_Microtubules_12_MMStack_Pos1_locResults.dat'
datasetType = 'TestType'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFilename, datasetType)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 12)
assert_equal(mmParser.dataset.datasetIDs['posID'], (1, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'Cos7_Microtubules')
assert_equal(mmParser.dataset.datasetType, 'TestType')
assert_equal(mmParser.dataset.datasetIDs['channelID'], None)
def test_MMParser_ParseGenericFile():
"""Will MMParser properly extract the acquisition information?
"""
inputFilename = 'Cos7_Microtubules_A647_3_MMStack_Pos0_locResults.dat'
datasetType = 'TestType'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFilename, datasetType)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 3)
assert_equal(mmParser.dataset.datasetIDs['channelID'], 'A647')
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'Cos7_Microtubules')
assert_equal(mmParser.dataset.datasetType, 'TestType')
def test_MMParser_Uninitialized_After_Use():
"""Will MMParser throw an error if dataset is accessed after uninit'ing?
"""
f = 'HeLa_Control_A750_1_MMStack_Pos0_locMetadata.json'
inputFile = testDataRoot / Path('parsers_test_files') / Path(f)
datasetType = 'LocMetadata'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFile, datasetType)
mmParser.dataset
mmParser.initialized = False
mmParser.dataset
def test_MMParser_Widefield_Bizarre_Underscores():
"""Will MMParser correctly parse this name with bizarre underscores?
"""
filename = '__HeLa_Control__FISH___WF__173_MMStack_Pos0.ome.tif'
mmParser = leb.MMParser()
mmParser.parseFilename(filename, 'WidefieldImage')
assert_equal(mmParser.dataset.datasetIDs['acqID'], 173)
assert_equal(mmParser.dataset.datasetIDs['channelID'], None)
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'HeLa_Control_FISH')
assert_equal(mmParser.dataset.datasetIDs['sliceID'], None)
assert_equal(mmParser.dataset.datasetType, 'WidefieldImage')
def test_MMParser_Attributes_MultipleXY():
"""Will MMParser extract multiple xy positions?
"""
inputFilename = 'HeLa_Actin_4_MMStack_1-Pos_012_003_locResults.dat'
datasetType = 'TestType'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFilename, datasetType)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 4)
assert_equal(mmParser.dataset.datasetIDs['channelID'], None)
assert_equal(mmParser.dataset.datasetIDs['posID'], (12, 3))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'HeLa_Actin')
assert_equal(mmParser.dataset.datasetIDs['sliceID'], None)
assert_equal(mmParser.dataset.datasetType, 'TestType')
def test_MMParser_ConvertsSpacesToUnderscores():
"""The MMParser will convert spaces in the prefix to underscores.
"""
# Note the space in prefix!
f = 'my dataset_A647_1_MMStack_Pos0_locResults.dat'
parser = leb.MMParser()
parser.parseFilename(f, 'TestType')
assert_equal(parser.dataset.datasetIDs['acqID'], 1)
assert_equal(parser.dataset.datasetIDs['channelID'], 'A647')
assert_equal(parser.dataset.datasetIDs['posID'], (0, ))
# The space should now be an underscore
assert_equal(parser.dataset.datasetIDs['prefix'], 'my_dataset')
assert_equal(parser.dataset.datasetType, 'TestType')
def test_MMParser_Widefield_Data():
"""MMParser correctly loads widefield image data.
"""
f = 'Cos7_A647_WF1_MMStack_Pos0.ome.tif'
inputFile = testDataRoot / Path('parsers_test_files') \
/ Path('Cos7_A647_WF1/') / Path(f)
datasetType = 'WidefieldImage'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFile, datasetType)
ds = mmParser.dataset
ds.data = ds.readFromFile(inputFile)
assert_equal(ds.data.shape, (512, 512))
def test_MMParser_Path_Input():
"""Will MMParser properly convert Path inputs to strings?
"""
inputFile = \
Path('results/Cos7_Microtubules_A750_3_MMStack_Pos0_locResults.dat')
datasetType = 'TestType'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFile, datasetType)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 3)
assert_equal(mmParser.dataset.datasetIDs['channelID'], 'A750')
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'Cos7_Microtubules')
assert_equal(mmParser.dataset.datasetIDs['sliceID'], None)
assert_equal(mmParser.dataset.datasetType, 'TestType')
def test_MMParser_Do_Not_Read_Data():
"""Filenames can be parsed without reading data from the file.
"""
inputFilename = 'HeLa_Actin_4_MMStack_1_Pos0_Localizations.csv'
datasetType = 'Localizations'
mmParser = leb.MMParser()
mmParser.parseFilename(inputFilename, datasetType, readData=False)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 4)
assert_equal(mmParser.dataset.datasetIDs['channelID'], None)
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'], 'HeLa_Actin')
assert_equal(mmParser.dataset.datasetIDs['sliceID'], None)
assert_equal(mmParser.dataset.datasetType, 'Localizations')
assert (mmParser.dataset.data is None)
def test_MMParser_Channel_Underscores():
"""Will MMParser extract the prefix and channel with weird underscores?
"""
inputFilename = [
'Cos7_Microtubules_Cy5_3_MMStack_Pos0_locResults.dat',
'_Cy5_Cos7_Microtubules_3_MMStack_Pos0_locResults.dat',
'Cy5_Cos7_Microtubules_3_MMStack_Pos0_locResults.dat',
'Cos7_Cy5_Microtubules_3_MMStack_Pos0_locResults.dat',
'Cos7_MicrotubulesCy5_3_MMStack_Pos0_locResults.dat',
'Cos7_Microtubules__Cy5_3_MMStack_Pos0_locResults.dat',
'Cos7___Microtubules__Cy5_3_MMStack_Pos0_locResults.dat'
]
datasetType = 'TestType'
mmParser = leb.MMParser()
for currFilename in inputFilename:
mmParser.parseFilename(currFilename, datasetType)
assert_equal(mmParser.dataset.datasetIDs['acqID'], 3)
assert_equal(mmParser.dataset.datasetIDs['channelID'], 'Cy5')
assert_equal(mmParser.dataset.datasetIDs['posID'], (0, ))
assert_equal(mmParser.dataset.datasetIDs['prefix'],
'Cos7_Microtubules')
assert_equal(mmParser.dataset.datasetType, 'TestType')
def test_MMParser_Uninitialized():
"""Will MMParser throw an error when prematurely accessing the dataset?
"""
mmParser = leb.MMParser()
mmParser.dataset
