postprocessor.chainer.Chainer¶
- class Chainer(*args, **kwargs)[source]¶
Bases:
Signal
Extend Signal by applying post-processes and allowing composite signals that combine basic signals. It “chains” multiple processes upon fetching a dataset to produce the desired datasets.
Instead of reading processes previously applied, it executes them when called.
- Attributes
- available
Get data sets available in h5 file.
- cell_tree
channels
Get channels as an array of strings.
datasets
Print data sets available in h5 file.
- max_span
- merges
Get merges.
meta_h5
Return metadata, defining it if necessary.
- n_merges
Get number of merges.
- nstages
- ntimepoints
Find the number of time points for one position, or one h5 file.
ntps
Get number of time points from the metadata.
- p_available
Print data sets available in h5 file.
- picks
Get picks.
stages
Get the contents of the pump with highest flow rate at each stage.
stages_span
Get consecutive stages and their corresponding number of time points.
- stages_span_tp
stem
Get name of h5 file.
- switch_times
- tinterval
Find the interval between time points (minutes).
Methods
add_name
(df, name)Add column of identical strings to a dataframe.
apply_chain
(input_data, chain, **kwargs)Apply a series of processes to a data set.
apply_prepost
(data[, merges, picks])Apply modifier operations (picker or merger) to a dataframe.
close
()Close the h5 file.
dataset_to_df
(f, path)Get data from h5 file as a dataframe.
get
(dataset[, chain, in_minutes, stages, retain])Load data from an h5 file.
get_consecutives
(tree, nstepsback)Receives a sorted tree and returns the keys of consecutive elements.
get_info_tree
([fields])Return traps, time points and labels for this position in the form of a tree in the hierarchy determined by the argument fields.
get_merged
(dataset)Run preprocessing for merges.
Get merge events going up to the first level.
get_picks
([names, path])Get the relevant picks based on names.
get_raw
(dataset[, in_minutes, lineage])Load data from a h5 file and return as a dataframe.
get_retained
(df, cutoff)Return a fraction of the df, one without later time points.
lineage
([lineage_location, merged])Get lineage data from a given location in the h5 file.
retained
(signal[, cutoff])Load data (via decorator) and reduce the resulting dataframe.
store_signal_path
(fullname, node)Store the name of a signal if it is a leaf node (a group with no more groups inside) and if it starts with extraction.
cols_in_mins
get_npairs
get_npairs_over_time
Define index_names for dataframes, candidate fluorescence channels, and composite statistics.
- Attributes
- available
Get data sets available in h5 file.
- cell_tree
channels
Get channels as an array of strings.
datasets
Print data sets available in h5 file.
- max_span
- merges
Get merges.
meta_h5
Return metadata, defining it if necessary.
- n_merges
Get number of merges.
- nstages
- ntimepoints
Find the number of time points for one position, or one h5 file.
ntps
Get number of time points from the metadata.
- p_available
Print data sets available in h5 file.
- picks
Get picks.
stages
Get the contents of the pump with highest flow rate at each stage.
stages_span
Get consecutive stages and their corresponding number of time points.
- stages_span_tp
stem
Get name of h5 file.
- switch_times
- tinterval
Find the interval between time points (minutes).
Methods
add_name
(df, name)Add column of identical strings to a dataframe.
apply_chain
(input_data, chain, **kwargs)Apply a series of processes to a data set.
apply_prepost
(data[, merges, picks])Apply modifier operations (picker or merger) to a dataframe.
close
()Close the h5 file.
dataset_to_df
(f, path)Get data from h5 file as a dataframe.
get
(dataset[, chain, in_minutes, stages, retain])Load data from an h5 file.
get_consecutives
(tree, nstepsback)Receives a sorted tree and returns the keys of consecutive elements.
get_info_tree
([fields])Return traps, time points and labels for this position in the form of a tree in the hierarchy determined by the argument fields.
get_merged
(dataset)Run preprocessing for merges.
Get merge events going up to the first level.
get_picks
([names, path])Get the relevant picks based on names.
get_raw
(dataset[, in_minutes, lineage])Load data from a h5 file and return as a dataframe.
get_retained
(df, cutoff)Return a fraction of the df, one without later time points.
lineage
([lineage_location, merged])Get lineage data from a given location in the h5 file.
retained
(signal[, cutoff])Load data (via decorator) and reduce the resulting dataframe.
store_signal_path
(fullname, node)Store the name of a signal if it is a leaf node (a group with no more groups inside) and if it starts with extraction.
cols_in_mins
get_npairs
get_npairs_over_time
- __init__(*args, **kwargs)[source]¶
Define index_names for dataframes, candidate fluorescence channels, and composite statistics.
Methods
__init__
(*args, **kwargs)Define index_names for dataframes, candidate fluorescence channels, and composite statistics.
add_name
(df, name)Add column of identical strings to a dataframe.
apply_chain
(input_data, chain, **kwargs)Apply a series of processes to a data set.
apply_prepost
(data[, merges, picks])Apply modifier operations (picker or merger) to a dataframe.
close
()Close the h5 file.
cols_in_mins
(df)dataset_to_df
(f, path)Get data from h5 file as a dataframe.
get
(dataset[, chain, in_minutes, stages, retain])Load data from an h5 file.
get_consecutives
(tree, nstepsback)Receives a sorted tree and returns the keys of consecutive elements.
get_info_tree
([fields])Return traps, time points and labels for this position in the form of a tree in the hierarchy determined by the argument fields.
get_merged
(dataset)Run preprocessing for merges.
Get merge events going up to the first level.
get_npairs
([nstepsback, tree])get_npairs_over_time
([nstepsback])get_picks
([names, path])Get the relevant picks based on names.
get_raw
(dataset[, in_minutes, lineage])Load data from a h5 file and return as a dataframe.
get_retained
(df, cutoff)Return a fraction of the df, one without later time points.
lineage
([lineage_location, merged])Get lineage data from a given location in the h5 file.
retained
(signal[, cutoff])Load data (via decorator) and reduce the resulting dataframe.
store_signal_path
(fullname, node)Store the name of a signal if it is a leaf node (a group with no more groups inside) and if it starts with extraction.
Attributes
Get data sets available in h5 file.
cell_tree
Get channels as an array of strings.
Print data sets available in h5 file.
max_span
- rtype
int
Get merges.
Return metadata, defining it if necessary.
Get number of merges.
nstages
- rtype
int
Find the number of time points for one position, or one h5 file.
Get number of time points from the metadata.
Print data sets available in h5 file.
Get picks.
Get the contents of the pump with highest flow rate at each stage.
Get consecutive stages and their corresponding number of time points.
stages_span_tp
- rtype
Tuple
[Tuple
[str
,int
],...
]
Get name of h5 file.
switch_times
- rtype
List
[int
]
Find the interval between time points (minutes).
- static add_name(df, name)¶
Add column of identical strings to a dataframe.
- apply_chain(input_data, chain, **kwargs)[source]¶
Apply a series of processes to a data set.
Like postprocessing, Chainer consecutively applies processes.
Parameters can be passed as kwargs.
Chainer does not support applying the same process multiple times with different parameters.
- Parameters
- input_datapd.DataFrame
Input data to process.
- chaint.Tuple[str, …]
Tuple of strings with the names of the processes
- **kwargskwargs
Arguments passed on to Process.as_function() method to modify the parameters.
Examples
FIXME: Add docs.
- apply_prepost(data, merges=True, picks=True)¶
Apply modifier operations (picker or merger) to a dataframe.
- Parameters
- datat.Union[str, pd.DataFrame]
DataFrame or path to one.
- mergest.Union[np.ndarray, bool]
(optional) 2-D array with three columns: the tile id, the mother label, and the daughter id. If True, fetch merges from file.
- pickst.Union[np.ndarray, bool]
(optional) 2-D array with two columns: the tiles and the cell labels. If True, fetch picks from file.
Examples
FIXME: Add docs.
- property available¶
Get data sets available in h5 file.
- property channels: Collection[str]¶
Get channels as an array of strings.
- Return type
Collection
[str
]
- close()¶
Close the h5 file.
- dataset_to_df(f, path)¶
Get data from h5 file as a dataframe.
- Return type
DataFrame
- property datasets¶
Print data sets available in h5 file.
- get(dataset, chain=('standard', 'interpolate', 'savgol'), in_minutes=True, stages=True, retain=None, **kwargs)[source]¶
Load data from an h5 file.
- static get_consecutives(tree, nstepsback)¶
Receives a sorted tree and returns the keys of consecutive elements.
- get_info_tree(fields=('trap', 'timepoint', 'cell_label'))¶
Return traps, time points and labels for this position in the form of a tree in the hierarchy determined by the argument fields.
Note that it is compressed to non-empty elements and timepoints.
Default hierarchy is: - trap - time point - cell label
This function currently produces trees of depth 3, but it can easily be extended for deeper trees if needed (e.g. considering groups, chambers and/or positions).
- Parameters
- fields: list of strs
Fields to fetch from ‘cell_info’ inside the h5 file.
- Returns
- Nested dictionary where keys (or branches) are the upper levels and the leaves are the last element of :fields:.
- get_merged(dataset)¶
Run preprocessing for merges.
- get_merges()¶
Get merge events going up to the first level.
- get_picks(names=('trap', 'cell_label'), path='modifiers/picks/')¶
Get the relevant picks based on names.
- Return type
Set
[Tuple
[int
,str
]]
- get_raw(dataset, in_minutes=True, lineage=False)¶
Load data from a h5 file and return as a dataframe.
- Parameters
- dataset: str or list of strs
The name of the h5 file or a list of h5 file names
- in_minutes: boolean
If True,
- lineage: boolean
- :rtype: :py:class:`~pandas.core.frame.DataFrame`
- static get_retained(df, cutoff)¶
Return a fraction of the df, one without later time points.
- lineage(lineage_location=None, merged=False)¶
Get lineage data from a given location in the h5 file.
Returns an array with three columns: the tile id, the mother label, and the daughter label.
- Return type
ndarray
- property merges: ndarray¶
Get merges.
- property meta_h5: Dict[str, Any]¶
Return metadata, defining it if necessary.
- Return type
Dict
[str
,Any
]
- property n_merges¶
Get number of merges.
- property ntimepoints¶
Find the number of time points for one position, or one h5 file.
- property ntps: int¶
Get number of time points from the metadata.
- Return type
int
- property p_available¶
Print data sets available in h5 file.
- property picks: ndarray¶
Get picks.
- retained(signal, cutoff=0.8)¶
Load data (via decorator) and reduce the resulting dataframe.
Load data for a signal or a list of signals and reduce the resulting dataframes to a fraction of their original size, losing late time points.
- property stages: List[str]¶
Get the contents of the pump with highest flow rate at each stage.
- Return type
List
[str
]
- property stages_span: Tuple[Tuple[str, int], ...]¶
Get consecutive stages and their corresponding number of time points.
- Return type
Tuple
[Tuple
[str
,int
],...
]
- property stem¶
Get name of h5 file.
- store_signal_path(fullname, node)¶
Store the name of a signal if it is a leaf node (a group with no more groups inside) and if it starts with extraction.
- property tinterval: int¶
Find the interval between time points (minutes).