Ts group
pynapple.core.ts_group
The class TsGroup
helps group objects with different timestamps (i.e. timestamps of spikes of a population of neurons).
TsGroup
Bases: UserDict
The TsGroup is a dictionnary-like object to hold multiple Ts
or Tsd
objects with different time index.
Attributes:
Name | Type | Description |
---|---|---|
time_support |
IntervalSet
|
The time support of the TsGroup |
rates |
Series
|
The rate of each element of the TsGroup |
Source code in pynapple/core/ts_group.py
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__init__
TsGroup Initializer.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data |
dict
|
Dictionary containing Ts/Tsd objects, keys should contain integer values or should be convertible to integer. |
required |
time_support |
IntervalSet
|
The time support of the TsGroup. Ts/Tsd objects will be restricted to the time support if passed. If no time support is specified, TsGroup will merge time supports from all the Ts/Tsd objects in data. |
None
|
time_units |
str
|
Time units if data does not contain Ts/Tsd objects ('us', 'ms', 's' [default]). |
's'
|
bypass_check |
To avoid checking that each element is within time_support. Useful to speed up initialization of TsGroup when Ts/Tsd objects have already been restricted beforehand |
False
|
|
**kwargs |
Meta-info about the Ts/Tsd objects. Can be either pandas.Series, numpy.ndarray, list or tuple Note that the index should match the index of the input dictionary if pandas Series |
{}
|
Raises:
Type | Description |
---|---|
RuntimeError
|
Raise error if the union of time support of Ts/Tsd object is empty. |
ValueError
|
|
Source code in pynapple/core/ts_group.py
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__getattr__
Allows dynamic access to metadata columns as properties.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
The name of the metadata column to access. |
required |
Returns:
Type | Description |
---|---|
Series
|
The series of values for the requested metadata column. |
Raises:
Type | Description |
---|---|
AttributeError
|
If the requested attribute is not a metadata column. |
Source code in pynapple/core/ts_group.py
keys
items
values
Return a list of all the Ts/Tsd objects in the TsGroup
Returns:
Type | Description |
---|---|
list
|
List of Ts/Tsd objects |
set_info
Add metadata information about the TsGroup. Metadata are saved as a DataFrame.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
*args |
pandas.Dataframe or list of pandas.DataFrame |
()
|
|
**kwargs |
Can be either pandas.Series, numpy.ndarray, list or tuple |
{}
|
Raises:
Type | Description |
---|---|
RuntimeError
|
Raise an error if no column labels are found when passing simple arguments, indexes are not equals for a pandas series,+ not the same length when passing numpy array. |
TypeError
|
If some of the provided metadata could not be set. |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp)
To add metadata with a pandas.DataFrame:
>>> import pandas as pd
>>> structs = pd.DataFrame(index = [0,1,2], data=['pfc','pfc','ca1'], columns=['struct'])
>>> tsgroup.set_info(structs)
>>> tsgroup
Index Freq. (Hz) struct
------- ------------ --------
0 1 pfc
1 2 pfc
2 4 ca1
To add metadata with a pd.Series, numpy.ndarray, list or tuple:
>>> hd = pd.Series(index = [0,1,2], data = [0,1,1])
>>> tsgroup.set_info(hd=hd)
>>> tsgroup
Index Freq. (Hz) struct hd
------- ------------ -------- ----
0 1 pfc 0
1 2 pfc 1
2 4 ca1 1
Source code in pynapple/core/ts_group.py
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get_info
Returns the metainfo located in one column. The key for the column frequency is "rate".
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key |
str
|
One of the metainfo columns name |
required |
Returns:
Type | Description |
---|---|
Series
|
The metainfo |
Source code in pynapple/core/ts_group.py
restrict
Restricts a TsGroup object to a set of time intervals delimited by an IntervalSet object
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ep |
IntervalSet
|
the IntervalSet object |
required |
Returns:
Type | Description |
---|---|
TsGroup
|
TsGroup object restricted to ep |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp)
>>> ep = nap.IntervalSet(start=0, end=100, time_units='s')
>>> newtsgroup = tsgroup.restrict(ep)
All objects within the TsGroup automatically inherit the epochs defined by ep.
>>> newtsgroup.time_support
start end
0 0.0 100.0
>>> newtsgroup[0].time_support
start end
0 0.0 100.0
Source code in pynapple/core/ts_group.py
value_from
Replace the value of each Ts/Tsd object within the Ts group with the closest value from tsd argument
Parameters:
Name | Type | Description | Default |
---|---|---|---|
tsd |
Tsd
|
The Tsd object holding the values to replace |
required |
ep |
IntervalSet
|
The IntervalSet object to restrict the operation. If None, the time support of the tsd input object is used. |
None
|
Returns:
Type | Description |
---|---|
TsGroup
|
TsGroup object with the new values |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp)
>>> ep = nap.IntervalSet(start=0, end=100, time_units='s')
The variable tsd is a time series object containing the values to assign, for example the tracking data:
>>> tsd = nap.Tsd(t=np.arange(0,100), d=np.random.rand(100), time_units='s')
>>> ep = nap.IntervalSet(start = 0, end = 100, time_units = 's')
>>> newtsgroup = tsgroup.value_from(tsd, ep)
Source code in pynapple/core/ts_group.py
count
Count occurences of events within bin_size or within a set of bins defined as an IntervalSet. You can call this function in multiple ways :
-
tsgroup.count(bin_size=1, time_units = 'ms') -> Count occurence of events within a 1 ms bin defined on the time support of the object.
-
tsgroup.count(1, ep=my_epochs) -> Count occurent of events within a 1 second bin defined on the IntervalSet my_epochs.
-
tsgroup.count(ep=my_bins) -> Count occurent of events within each epoch of the intervalSet object my_bins
-
tsgroup.count() -> Count occurent of events within each epoch of the time support.
bin_size should be seconds unless specified. If bin_size is used and no epochs is passed, the data will be binned based on the time support of the object.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
bin_size |
None or float
|
The bin size (default is second) |
required |
ep |
None or IntervalSet
|
IntervalSet to restrict the operation |
required |
time_units |
str
|
Time units of bin size ('us', 'ms', 's' [default]) |
required |
Returns:
Name | Type | Description |
---|---|---|
out |
TsdFrame
|
A TsdFrame with the columns being the index of each item in the TsGroup. |
Examples:
This example shows how to count events within bins of 0.1 second for the first 100 seconds.
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp)
>>> ep = nap.IntervalSet(start=0, end=100, time_units='s')
>>> bincount = tsgroup.count(0.1, ep)
>>> bincount
0 1 2
Time (s)
0.05 0 0 0
0.15 0 0 0
0.25 0 0 1
0.35 0 0 0
0.45 0 0 0
... .. .. ..
99.55 0 1 1
99.65 0 0 0
99.75 0 0 1
99.85 0 0 0
99.95 1 1 1
[1000 rows x 3 columns]
Source code in pynapple/core/ts_group.py
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to_tsd
Convert TsGroup to a Tsd. The timestamps of the TsGroup are merged together and sorted.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
*args |
string, list, numpy.ndarray or pandas.Series |
()
|
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tsgroup = nap.TsGroup({0:nap.Ts(t=np.array([0, 1])), 5:nap.Ts(t=np.array([2, 3]))})
Index rate
------- ------
0 1
5 1
By default, the values of the Tsd is the index of the timestamp in the TsGroup:
Values can be inherited from the metadata of the TsGroup by giving the key of the corresponding columns.
>>> tsgroup.set_info( phase=np.array([np.pi, 2*np.pi]) ) # assigning a phase to my 2 elements of the TsGroup
>>> tsgroup.to_tsd("phase")
Time (s)
0.0 3.141593
1.0 3.141593
2.0 6.283185
3.0 6.283185
dtype: float64
Values can also be passed directly to the function from a list, numpy.ndarray or pandas.Series of values as long as the length matches :
The reverse operation can be done with the Tsd.to_tsgroup function :
>>> my_tsd
Time (s)
0.0 0.0
1.0 0.0
2.0 5.0
3.0 5.0
dtype: float64
>>> my_tsd.to_tsgroup()
Index rate
------- ------
0 1
5 1
Returns:
Type | Description |
---|---|
Tsd
|
|
Raises:
Type | Description |
---|---|
RuntimeError
|
"Index are not equals" : if pandas.Series indexes don't match the TsGroup indexes "Values is not the same length" : if numpy.ndarray/list object is not the same size as the TsGroup object "Key not in metadata of TsGroup" : if string argument does not match any column names of the metadata, "Unknown argument format" ; if argument is not a string, list, numpy.ndarray or pandas.Series |
Source code in pynapple/core/ts_group.py
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get
Slice the TsGroup
object from start
to end
such that all the timestamps within the group satisfy start<=t<=end
.
If end
is None, only the timepoint closest to start
is returned.
By default, the time support doesn't change. If you want to change the time support, use the restrict
function.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
start |
float or int
|
The start (or closest time point if |
required |
end |
float or int or None
|
The end |
None
|
Source code in pynapple/core/ts_group.py
getby_threshold
Return a TsGroup with all Ts/Tsd objects with values above threshold for metainfo under key.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key |
str
|
One of the metainfo columns name |
required |
thr |
float
|
THe value for thresholding |
required |
op |
str
|
The type of operation. Possibilities are '>', '<', '>=' or '<='. |
'>'
|
Returns:
Type | Description |
---|---|
TsGroup
|
The new TsGroup |
Raises:
Type | Description |
---|---|
RuntimeError
|
Raise eror is operation is not recognized. |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp)
Index Freq. (Hz)
------- ------------
0 1
1 2
2 4
This exemple shows how to get a new TsGroup with all elements for which the metainfo frequency is above 1.
>>> newtsgroup = tsgroup.getby_threshold('freq', 1, op = '>')
Index Freq. (Hz)
------- ------------
1 2
2 4
Source code in pynapple/core/ts_group.py
getby_intervals
Return a list of TsGroup binned.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key |
str
|
One of the metainfo columns name |
required |
bins |
ndarray or list
|
The bin intervals |
required |
Returns:
Type | Description |
---|---|
list
|
A list of TsGroup |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp, alpha = np.arange(3))
Index Freq. (Hz) alpha
------- ------------ -------
0 1 0
1 2 1
2 4 2
This exemple shows how to bin the TsGroup according to one metainfo key.
>>> newtsgroup, bincenter = tsgroup.getby_intervals('alpha', [0, 1, 2])
>>> newtsgroup
[ Index Freq. (Hz) alpha
------- ------------ -------
0 1 0,
Index Freq. (Hz) alpha
------- ------------ -------
1 2 1]
By default, the function returns the center of the bins.
Source code in pynapple/core/ts_group.py
getby_category
Return a list of TsGroup grouped by category.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key |
str
|
One of the metainfo columns name |
required |
Returns:
Type | Description |
---|---|
dict
|
A dictionnary of TsGroup |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tmp = { 0:nap.Ts(t=np.arange(0,200), time_units='s'),
1:nap.Ts(t=np.arange(0,200,0.5), time_units='s'),
2:nap.Ts(t=np.arange(0,300,0.25), time_units='s'),
}
>>> tsgroup = nap.TsGroup(tmp, group = [0,1,1])
Index Freq. (Hz) group
------- ------------ -------
0 1 0
1 2 1
2 4 1
This exemple shows how to group the TsGroup according to one metainfo key.
>>> newtsgroup = tsgroup.getby_category('group')
>>> newtsgroup
{0: Index Freq. (Hz) group
------- ------------ -------
0 1 0,
1: Index Freq. (Hz) group
------- ------------ -------
1 2 1
2 4 1}
Source code in pynapple/core/ts_group.py
save
Save TsGroup object in npz format. The file will contain the timestamps, the data (if group of Tsd), group index, the time support and the metadata
The main purpose of this function is to save small/medium sized TsGroup objects.
The function will "flatten" the TsGroup by sorting all the timestamps and assigning to each the corresponding index. Typically, a TsGroup like this :
will be saved as npz with the following keys:
{
't' : [0, 1, 2, 4, 5],
'd' : [1, 5, 2, 3, 5],
'index' : [0, 1, 0, 0, 1],
'start' : [0],
'end' : [5],
'keys' : [0, 1],
'type' : 'TsGroup'
}
Metadata are saved by columns with the column name as the npz key. To avoid potential conflicts, make sure the columns name of the metadata are different from ['t', 'd', 'start', 'end', 'index', 'keys']
You can load the object with nap.load_file
. Default keys are 't', 'd'(optional),
'start', 'end', 'index', 'keys' and 'type'.
See the example below.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
filename |
str
|
The filename |
required |
Examples:
>>> import pynapple as nap
>>> import numpy as np
>>> tsgroup = nap.TsGroup({
0 : nap.Ts(t=np.array([0.0, 2.0, 4.0])),
6 : nap.Ts(t=np.array([1.0, 5.0]))
},
group = np.array([0, 1]),
location = np.array(['right foot', 'left foot'])
)
>>> tsgroup
Index rate group location
------- ------ ------- ----------
0 0.6 0 right foot
6 0.4 1 left foot
>>> tsgroup.save("my_tsgroup.npz")
To get back to pynapple, you can use the nap.load_file
function :
>>> tsgroup = nap.load_file("my_tsgroup.npz")
>>> tsgroup
Index rate group location
------- ------ ------- ----------
0 0.6 0 right foot
6 0.4 1 left foot
Raises:
Type | Description |
---|---|
RuntimeError
|
If filename is not str, path does not exist or filename is a directory. |
Source code in pynapple/core/ts_group.py
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