def decode_per_hyb_max(self,
intensities: IntensityTable) -> IntensityTable:
"""decode each feature by selecting the per-hybridization round max-valued channel
Notes
-----
If no code matches the per-channel max of a feature, it will be assigned np.nan instead
of a gene value
Parameters
----------
intensities : IntensityTable
features to be decoded
Returns
-------
IntensityTable :
intensity table containing additional data variables for gene assignments
"""
def _view_row_as_element(array: np.ndarray) -> np.ndarray:
"""view an entire code as a single element
This view allows vectors (codes) to be compared for equality without need for multiple
comparisons by casting the data in each code to a structured dtype that registers as
a single value
Parameters
----------
array : np.ndarray
2-dimensional numpy array of shape (n_observations, (n_ch * n_hyb)) where
observations may be either features or codes.
Returns
-------
np.ndarray :
1-dimensional vector of shape n_observations
"""
nrows, ncols = array.shape
dtype = {
'names': ['f{}'.format(i) for i in range(ncols)],
'formats': ncols * [array.dtype]
}
return array.view(dtype)
max_channels = intensities.argmax(Indices.CH.value)
codes = self.argmax(Indices.CH.value)
a = _view_row_as_element(codes.values.reshape(self.shape[0], -1))
b = _view_row_as_element(
max_channels.values.reshape(intensities.shape[0], -1))
genes = np.empty(intensities.shape[0], dtype=object)
genes.fill(np.nan)
for i in np.arange(a.shape[0]):
genes[np.where(a[i] == b)[0]] = codes['gene_name'][i]
gene_index = pd.Index(genes.astype('U'))
intensities[IntensityTable.Constants.GENE.value] = (
IntensityTable.Constants.FEATURES.value, gene_index)
return intensities
def decode_per_round_max(self,
intensities: IntensityTable) -> IntensityTable:
"""decode each feature by selecting the per-imaging-round max-valued channel
Notes
-----
- If no code matches the per-round maximum for a feature, it will be assigned 'nan' instead
of a target value
- Numpy's argmax breaks ties by picking the first channel -- this can lead to
unexpected results where some features with "tied" channels will decode, but others will
be assigned 'nan'.
Parameters
----------
intensities : IntensityTable
features to be decoded
Returns
-------
IntensityTable :
intensity table containing additional data variables for target assignments
"""
def _view_row_as_element(array: np.ndarray) -> np.ndarray:
"""view an entire code as a single element
This view allows vectors (codes) to be compared for equality without need for multiple
comparisons by casting the data in each code to a structured dtype that registers as
a single value
Parameters
----------
array : np.ndarray
2-dimensional numpy array of shape (n_observations, (n_ch * n_round)) where
observations may be either features or codes.
Returns
-------
np.ndarray :
1-dimensional vector of shape n_observations
"""
nrows, ncols = array.shape
dtype = {
'names': ['f{}'.format(i) for i in range(ncols)],
'formats': ncols * [array.dtype]
}
return array.view(dtype)
self._validate_decode_intensity_input_matches_codebook_shape(
intensities)
max_channels = intensities.argmax(Indices.CH.value)
codes = self.argmax(Indices.CH.value)
# TODO ambrosejcarr, dganguli: explore this quality score further
# calculate distance scores by evaluating the fraction of signal in each round that is
# found in the non-maximal channels.
max_intensities = intensities.max(Indices.CH.value)
round_intensities = intensities.sum(Indices.CH.value)
distance = 1 - (max_intensities / round_intensities).mean(
Indices.ROUND.value)
a = _view_row_as_element(codes.values.reshape(self.shape[0], -1))
b = _view_row_as_element(
max_channels.values.reshape(intensities.shape[0], -1))
targets = np.full(intensities.shape[0],
fill_value=np.nan,
dtype=object)
# decode the intensities
for i in np.arange(codes.shape[0]):
targets[np.where(a[i] == b)[0]] = codes[Features.TARGET][i]
# a code passes filters if it decodes successfully
passes_filters = ~pd.isnull(targets)
intensities[Features.TARGET] = (Features.AXIS, targets.astype('U'))
intensities[Features.DISTANCE] = (Features.AXIS, distance)
intensities[Features.PASSES_THRESHOLDS] = (Features.AXIS,
passes_filters)
return intensities