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feat: add channel_labels #323

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merged 6 commits into from
Nov 9, 2020
Merged

feat: add channel_labels #323

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1de20df
feat: add channel_labels
abawchen Mar 9, 2020
a4a2982
Added channel_labels description on FCSData docstring.
castillohair Jun 13, 2020
eb81322
Added channel_labels to TestFCSDataPickle.
castillohair Jun 13, 2020
68cea40
test: add TestFCSAttributesChannelLabels
abawchen Oct 26, 2020
2b7028a
docs: docstrings for test case
abawchen Oct 26, 2020
9454d02
Correct naming convention in docstring comment.
JS3xton Oct 29, 2020
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57 changes: 57 additions & 0 deletions FlowCal/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -960,6 +960,7 @@ def __repr__(self):
'amplification_type',
'detector_voltage',
'amplifier_gain',
'channel_labels',
'range',
'resolution'])

Expand Down Expand Up @@ -1015,6 +1016,8 @@ class FCSData(np.ndarray):
Get the detector voltage used for the specified channel(s).
amplifier_gain
Get the amplifier gain used for the specified channel(s).
channel_labels
Get the label of the specified channel(s).
range
Get the range of the specified channel(s).
resolution
Expand Down Expand Up @@ -1331,6 +1334,42 @@ def amplifier_gain(self, channels=None):
else:
return self._amplifier_gain[channels]

def channel_labels(self, channels=None):
"""
Get the label of the specified channel(s).

The label for channel "n" is extracted from the $PnS
parameter, if available.

Parameters
----------
channels : int, str, list of int, list of str
Channel(s) for which to get the label. If None,
return a list with the label of all channels, in the
order of ``FCSData.channels``.

Return
------
str or list of str
The label of the specified channel(s). If no
information about the label is found for a channel,
return None.

"""
# Check default
if channels is None:
channels = self._channels

# Get numerical indices of channels
channels = self._name_to_index(channels)

# Get the label of the specified channels
if hasattr(channels, '__iter__') \
and not isinstance(channels, six.string_types):
return [self._channel_labels[ch] for ch in channels]
else:
return self._channel_labels[channels]

def range(self, channels=None):
"""
Get the range of the specified channel(s).
Expand Down Expand Up @@ -1708,6 +1747,13 @@ def __new__(cls, infile):
amplifier_gain.append(channel_amp_gain)
amplifier_gain = tuple(amplifier_gain)

# Channel label: Stored in the keyword parameter $PnS for channel n.
channel_labels = []
for i in range(1, num_channels + 1):
channel_label = fcs_file.text.get('$P{}S'.format(i), None)
channel_labels.append(channel_label)
channel_labels = tuple(channel_labels)

# Get data from fcs_file object, and change writeable flag.
data = fcs_file.data
data.flags.writeable = True
Expand All @@ -1729,6 +1775,7 @@ def __new__(cls, infile):
obj._amplification_type = amplification_type
obj._detector_voltage = detector_voltage
obj._amplifier_gain = amplifier_gain
obj._channel_labels = channel_labels
obj._range = data_range
obj._resolution = resolution

Expand Down Expand Up @@ -1771,6 +1818,8 @@ def __array_finalize__(self, obj):
self._detector_voltage = copy.deepcopy(obj._detector_voltage)
if hasattr(obj, '_amplifier_gain'):
self._amplifier_gain = copy.deepcopy(obj._amplifier_gain)
if hasattr(obj, '_channel_labels'):
self._channel_labels = copy.deepcopy(obj._channel_labels)
if hasattr(obj, '_range'):
self._range = copy.deepcopy(obj._range)
if hasattr(obj, '_resolution'):
Expand Down Expand Up @@ -1824,6 +1873,7 @@ def __reduce__(self):
amplification_type = self._amplification_type,
detector_voltage = self._detector_voltage,
amplifier_gain = self._amplifier_gain,
channel_labels = self._channel_labels,
range = self._range,
resolution = self._resolution)

Expand Down Expand Up @@ -1885,6 +1935,7 @@ def __setstate__(self, state):
self._amplification_type = fcsdata_state.amplification_type
self._detector_voltage = fcsdata_state.detector_voltage
self._amplifier_gain = fcsdata_state.amplifier_gain
self._channel_labels = fcsdata_state.channel_labels
self._range = fcsdata_state.range
self._resolution = fcsdata_state.resolution

Expand Down Expand Up @@ -2105,6 +2156,8 @@ def __getitem__(self, key):
[new_arr._detector_voltage[kc] for kc in key_channel])
new_arr._amplifier_gain = tuple(
[new_arr._amplifier_gain[kc] for kc in key_channel])
new_arr._channel_labels = tuple(
[new_arr._channel_labels[kc] for kc in key_channel])
new_arr._range = \
[new_arr._range[kc] for kc in key_channel]
new_arr._resolution = tuple(\
Expand All @@ -2117,6 +2170,8 @@ def __getitem__(self, key):
new_arr._detector_voltage[key_channel]
new_arr._amplifier_gain = \
new_arr._amplifier_gain[key_channel]
new_arr._channel_labels = \
new_arr._channel_labels[key_channel]
new_arr._range = \
new_arr._range[key_channel]
new_arr._resolution = \
Expand All @@ -2129,6 +2184,8 @@ def __getitem__(self, key):
tuple([new_arr._detector_voltage[key_channel]])
new_arr._amplifier_gain = \
tuple([new_arr._amplifier_gain[key_channel]])
new_arr._channel_labels = \
tuple([new_arr._channel_labels[key_channel]])
new_arr._range = \
[new_arr._range[key_channel]]
new_arr._resolution = \
Expand Down
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162 changes: 158 additions & 4 deletions test/test_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,13 @@
- Data003.fcs: FCS 3.0 from FlowJo Collectors Edition 7.5 /
BD FACScan Flow Cytometer
- Data004.fcs: FCS 3.0 including floating-point data
- Data005.fcs: FCS 3.0 including $PnS value
"""
filenames = ['test/Data001.fcs',
'test/Data002.fcs',
'test/Data003.fcs',
'test/Data004.fcs',
'test/Data005.fcs',
]

class TestFCSDataLoading(unittest.TestCase):
Expand Down Expand Up @@ -2301,6 +2303,146 @@ def test_nondefault_nbins_many_5(self):
scale='linear'),
[bins1, np.arange(262145) - 0.5, bins2])

class TestFCSAttributesChannelLabels(unittest.TestCase):
"""
Test correct extraction, functioning, and slicing of channel label.

We have previously looked at the contents of the $PnS attribute for
the test files and identified the correct label(marker):
- Data001.fcs: [None, None, None, None, None, None]
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The last element of this list should be 'Time (204.80 sec.)'. This is what you have later in the test_attribute() function.

- Data002.fcs: [None, None, None, None, None, None, None, None, None]
- Data003.fcs: [None, None, None, None, None, None, None, None]
- Data004.fcs: [None, None, None, None, None, None, None,
None, None, None, None, None, None, None]
- Data005.fcs: ['209Bi_CD11b', '140Ce', '142Ce', 'Center', '161Dy_CD56',
'162Dy_gdTCR', '163Dy_CRTH2', '164Dy_CLEC12A', '166Er_CD25',
'167Er_CCR7', '168Er_CD3', '170Er_CD38', '151Eu_CD123',
'153Eu_PD-1', 'Event_length', '155Gd_CD27', '156Gd_CCR5',
'157Gd', '158Gd_CD117', '160Gd_CD14', '165Ho_CCR6', '127I',
'113In_CD57', '115In_CD11c', '191Ir', '193Ir', '175Lu', '176Lu',
'93Nb', '142Nd_CD19', '143Nd_CD45RA', '144Nd_CD141', '145Nd_CD4',
'146Nd_CD8', '148Nd_CD16', '150Nd_CD1c', 'Offset', '192Os',
'206Pb', '102Pd', '104Pd', '105Pd', '106Pd', '108Pd', '110Pd',
'141Pr_CD33', '194Pt', '195Pt', '196Pt', '198Pt', 'Residual',
'103Rh', '147Sm_CD20', '149Sm_CD127', '152Sm_CD66b', '154Sm_CD86',
'181Ta', '159Tb_CD24', '169Tm_CX3CR1', '131Xe', '89Y_CD45',
'171Yb_CD161', '172Yb_CD209', '173Yb_CXCR3', '174Yb_HLADR',
'176Yb_CCR4', None, None, 'Time'])

"""
def setUp(self):
self.d = [FlowCal.io.FCSData(filenames[i]) for i in range(5)]


def test_attribute(self):
"""
Testing correct reporting of channel_labels.

"""
self.assertListEqual(
self.d[0].channel_labels(),
[None, None, None, None, None, 'Time (204.80 sec.)'])
self.assertListEqual(
self.d[1].channel_labels(),
[None, None, None, None, None, None, None, None, None])
self.assertListEqual(
self.d[2].channel_labels(),
[None, None, None, None, None, None, None, None])
self.assertListEqual(
self.d[3].channel_labels(),
[None, None, None, None, None, None, None,
None, None, None, None, None, None, None])
self.assertListEqual(
self.d[4].channel_labels(),
['209Bi_CD11b', '140Ce', '142Ce', 'Center', '161Dy_CD56',
'162Dy_gdTCR', '163Dy_CRTH2', '164Dy_CLEC12A', '166Er_CD25',
'167Er_CCR7', '168Er_CD3', '170Er_CD38', '151Eu_CD123',
'153Eu_PD-1', 'Event_length', '155Gd_CD27', '156Gd_CCR5',
'157Gd', '158Gd_CD117', '160Gd_CD14', '165Ho_CCR6', '127I',
'113In_CD57', '115In_CD11c', '191Ir', '193Ir', '175Lu', '176Lu',
'93Nb', '142Nd_CD19', '143Nd_CD45RA', '144Nd_CD141', '145Nd_CD4',
'146Nd_CD8', '148Nd_CD16', '150Nd_CD1c', 'Offset', '192Os',
'206Pb', '102Pd', '104Pd', '105Pd', '106Pd', '108Pd', '110Pd',
'141Pr_CD33', '194Pt', '195Pt', '196Pt', '198Pt', 'Residual',
'103Rh', '147Sm_CD20', '149Sm_CD127', '152Sm_CD66b', '154Sm_CD86',
'181Ta', '159Tb_CD24', '169Tm_CX3CR1', '131Xe', '89Y_CD45',
'171Yb_CD161', '172Yb_CD209', '173Yb_CXCR3', '174Yb_HLADR',
'176Yb_CCR4', None, None, 'Time'])

def test_attribute_single(self):
"""
Testing correct reporting of label_channels for a single channel.

"""
self.assertEqual(self.d[0].channel_labels('FSC-H'), None)
self.assertEqual(self.d[1].channel_labels('FITC-A'), None)
self.assertEqual(self.d[2].channel_labels('SSC'), None)
self.assertEqual(self.d[3].channel_labels('GFP-A'), None)
self.assertEqual(self.d[4].channel_labels('Bi209Di'), '209Bi_CD11b')

def test_attribute_many(self):
"""
Testing correct reporting of channel_labels for many channels.

"""
self.assertListEqual(
self.d[0].channel_labels(['SSC-H', 'FL2-H', 'FL3-H']),
[None, None, None])
self.assertListEqual(
self.d[1].channel_labels(['FITC-A', 'PE-A', 'PE-Cy7-A']),
[None, None, None])
self.assertListEqual(
self.d[2].channel_labels(['FSC', 'SSC', 'TIME']),
[None, None, None])
self.assertListEqual(
self.d[3].channel_labels(['FSC PMT-A', 'FSC PMT-H', 'FSC PMT-W']),
[None, None, None])
self.assertListEqual(
self.d[4].channel_labels(['Bi209Di', 'Ce140Di', 'Ce142Di']),
['209Bi_CD11b', '140Ce', '142Ce'])

def test_slice_single_str(self):
"""
Testing correct reporting of channel_labels after slicing.

"""
self.assertListEqual(
self.d[0][:, 'FSC-H'].channel_labels(),
[None,])
self.assertListEqual(
self.d[1][:, 'FITC-A'].channel_labels(),
[None,])
self.assertListEqual(
self.d[2][:, 'SSC'].channel_labels(),
[None,])
self.assertListEqual(
self.d[3][:, 'GFP-A'].channel_labels(),
[None,])
self.assertListEqual(
self.d[4][:, 'Bi209Di'].channel_labels(),
['209Bi_CD11b',])

def test_slice_many_str(self):
"""
Testing correct reporting of channel_labels after slicing.

"""
self.assertListEqual(
self.d[0][:, ['SSC-H', 'FL2-H', 'FL3-H']].channel_labels(),
[None, None, None])
self.assertListEqual(
self.d[1][:, ['FITC-A', 'PE-A', 'PE-Cy7-A']].channel_labels(),
[None, None, None])
self.assertListEqual(
self.d[2][:, ['FSC', 'SSC', 'TIME']].channel_labels(),
[None, None, None])
self.assertListEqual(
self.d[3][:,['FSC PMT-A', 'FSC PMT-H', 'FSC PMT-W']].channel_labels(),
[None, None, None])
self.assertListEqual(
self.d[4][:,['Bi209Di', 'Ce140Di', 'Ce142Di']].channel_labels(),
['209Bi_CD11b', '140Ce', '142Ce'])

class TestFCSAttributes(unittest.TestCase):
def setUp(self):
self.d = FlowCal.io.FCSData(filenames[0])
Expand Down Expand Up @@ -2789,10 +2931,21 @@ def test_pickle_unpickle(self):
loaded_attrs = set(dir(test_fcs))
self.assertEqual(attrs, loaded_attrs)
# Check contents of attrs affected by pickling
pickle_sensitive_attrs = ['_resolution', '_range', '_amplifier_gain',
'_detector_voltage', '_amplification_type', '_channels',
'_acquisition_end_time', '_acquisition_start_time', '_time_step',
'_data_type', '_analysis', '_text', '_infile']
pickle_sensitive_attrs = [
'_resolution',
'_range',
'_amplifier_gain',
'_channel_labels',
'_detector_voltage',
'_amplification_type',
'_channels',
'_acquisition_end_time',
'_acquisition_start_time',
'_time_step',
'_data_type',
'_analysis',
'_text',
'_infile']
# Also test computed (property) attrs
computed_attrs = [
'infile',
Expand All @@ -2810,6 +2963,7 @@ def test_pickle_unpickle(self):
'amplification_type',
'detector_voltage',
'amplifier_gain',
'channel_labels',
'range',
'resolution',
'hist_bins',
Expand Down