repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 | partition stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|
kwikteam/phy | phy/cluster/clustering.py | _extend_spikes | def _extend_spikes(spike_ids, spike_clusters):
"""Return all spikes belonging to the clusters containing the specified
spikes."""
# We find the spikes belonging to modified clusters.
# What are the old clusters that are modified by the assignment?
old_spike_clusters = spike_clusters[spike_ids]
u... | python | def _extend_spikes(spike_ids, spike_clusters):
"""Return all spikes belonging to the clusters containing the specified
spikes."""
# We find the spikes belonging to modified clusters.
# What are the old clusters that are modified by the assignment?
old_spike_clusters = spike_clusters[spike_ids]
u... | [
"def",
"_extend_spikes",
"(",
"spike_ids",
",",
"spike_clusters",
")",
":",
"# We find the spikes belonging to modified clusters.",
"# What are the old clusters that are modified by the assignment?",
"old_spike_clusters",
"=",
"spike_clusters",
"[",
"spike_ids",
"]",
"unique_clusters... | Return all spikes belonging to the clusters containing the specified
spikes. | [
"Return",
"all",
"spikes",
"belonging",
"to",
"the",
"clusters",
"containing",
"the",
"specified",
"spikes",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L29-L41 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering.reset | def reset(self):
"""Reset the clustering to the original clustering.
All changes are lost.
"""
self._undo_stack.clear()
self._spike_clusters = self._spike_clusters_base
self._new_cluster_id = self._new_cluster_id_0 | python | def reset(self):
"""Reset the clustering to the original clustering.
All changes are lost.
"""
self._undo_stack.clear()
self._spike_clusters = self._spike_clusters_base
self._new_cluster_id = self._new_cluster_id_0 | [
"def",
"reset",
"(",
"self",
")",
":",
"self",
".",
"_undo_stack",
".",
"clear",
"(",
")",
"self",
".",
"_spike_clusters",
"=",
"self",
".",
"_spike_clusters_base",
"self",
".",
"_new_cluster_id",
"=",
"self",
".",
"_new_cluster_id_0"
] | Reset the clustering to the original clustering.
All changes are lost. | [
"Reset",
"the",
"clustering",
"to",
"the",
"original",
"clustering",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L178-L186 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering._do_assign | def _do_assign(self, spike_ids, new_spike_clusters):
"""Make spike-cluster assignments after the spike selection has
been extended to full clusters."""
# Ensure spike_clusters has the right shape.
spike_ids = _as_array(spike_ids)
if len(new_spike_clusters) == 1 and len(spike_ids... | python | def _do_assign(self, spike_ids, new_spike_clusters):
"""Make spike-cluster assignments after the spike selection has
been extended to full clusters."""
# Ensure spike_clusters has the right shape.
spike_ids = _as_array(spike_ids)
if len(new_spike_clusters) == 1 and len(spike_ids... | [
"def",
"_do_assign",
"(",
"self",
",",
"spike_ids",
",",
"new_spike_clusters",
")",
":",
"# Ensure spike_clusters has the right shape.",
"spike_ids",
"=",
"_as_array",
"(",
"spike_ids",
")",
"if",
"len",
"(",
"new_spike_clusters",
")",
"==",
"1",
"and",
"len",
"("... | Make spike-cluster assignments after the spike selection has
been extended to full clusters. | [
"Make",
"spike",
"-",
"cluster",
"assignments",
"after",
"the",
"spike",
"selection",
"has",
"been",
"extended",
"to",
"full",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L258-L296 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering.merge | def merge(self, cluster_ids, to=None):
"""Merge several clusters to a new cluster.
Parameters
----------
cluster_ids : array-like
List of clusters to merge.
to : integer or None
The id of the new cluster. By default, this is `new_cluster_id()`.
... | python | def merge(self, cluster_ids, to=None):
"""Merge several clusters to a new cluster.
Parameters
----------
cluster_ids : array-like
List of clusters to merge.
to : integer or None
The id of the new cluster. By default, this is `new_cluster_id()`.
... | [
"def",
"merge",
"(",
"self",
",",
"cluster_ids",
",",
"to",
"=",
"None",
")",
":",
"if",
"not",
"_is_array_like",
"(",
"cluster_ids",
")",
":",
"raise",
"ValueError",
"(",
"\"The first argument should be a list or \"",
"\"an array.\"",
")",
"cluster_ids",
"=",
"... | Merge several clusters to a new cluster.
Parameters
----------
cluster_ids : array-like
List of clusters to merge.
to : integer or None
The id of the new cluster. By default, this is `new_cluster_id()`.
Returns
-------
up : UpdateInfo i... | [
"Merge",
"several",
"clusters",
"to",
"a",
"new",
"cluster",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L320-L368 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering.assign | def assign(self, spike_ids, spike_clusters_rel=0):
"""Make new spike cluster assignments.
Parameters
----------
spike_ids : array-like
List of spike ids.
spike_clusters_rel : array-like
Relative cluster ids of the spikes in `spike_ids`. This
... | python | def assign(self, spike_ids, spike_clusters_rel=0):
"""Make new spike cluster assignments.
Parameters
----------
spike_ids : array-like
List of spike ids.
spike_clusters_rel : array-like
Relative cluster ids of the spikes in `spike_ids`. This
... | [
"def",
"assign",
"(",
"self",
",",
"spike_ids",
",",
"spike_clusters_rel",
"=",
"0",
")",
":",
"assert",
"not",
"isinstance",
"(",
"spike_ids",
",",
"slice",
")",
"# Ensure `spike_clusters_rel` is an array-like.",
"if",
"not",
"hasattr",
"(",
"spike_clusters_rel",
... | Make new spike cluster assignments.
Parameters
----------
spike_ids : array-like
List of spike ids.
spike_clusters_rel : array-like
Relative cluster ids of the spikes in `spike_ids`. This
must have the same size as `spike_ids`.
Returns
... | [
"Make",
"new",
"spike",
"cluster",
"assignments",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L370-L446 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering.undo | def undo(self):
"""Undo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation.
"""
_, _, undo_state = self._undo_stack.back()
# Retrieve the initial spike_cluster structure.
spike_clusters... | python | def undo(self):
"""Undo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation.
"""
_, _, undo_state = self._undo_stack.back()
# Retrieve the initial spike_cluster structure.
spike_clusters... | [
"def",
"undo",
"(",
"self",
")",
":",
"_",
",",
"_",
",",
"undo_state",
"=",
"self",
".",
"_undo_stack",
".",
"back",
"(",
")",
"# Retrieve the initial spike_cluster structure.",
"spike_clusters_new",
"=",
"self",
".",
"_spike_clusters_base",
".",
"copy",
"(",
... | Undo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation. | [
"Undo",
"the",
"last",
"cluster",
"assignment",
"operation",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L477-L508 | train |
kwikteam/phy | phy/cluster/clustering.py | Clustering.redo | def redo(self):
"""Redo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation.
"""
# Go forward in the stack, and retrieve the new assignment.
item = self._undo_stack.forward()
if item is N... | python | def redo(self):
"""Redo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation.
"""
# Go forward in the stack, and retrieve the new assignment.
item = self._undo_stack.forward()
if item is N... | [
"def",
"redo",
"(",
"self",
")",
":",
"# Go forward in the stack, and retrieve the new assignment.",
"item",
"=",
"self",
".",
"_undo_stack",
".",
"forward",
"(",
")",
"if",
"item",
"is",
"None",
":",
"# No redo has been performed: abort.",
"return",
"# NOTE: the undo_s... | Redo the last cluster assignment operation.
Returns
-------
up : UpdateInfo instance of the changes done by this operation. | [
"Redo",
"the",
"last",
"cluster",
"assignment",
"operation",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/clustering.py#L510-L537 | train |
kwikteam/phy | phy/stats/ccg.py | _increment | def _increment(arr, indices):
"""Increment some indices in a 1D vector of non-negative integers.
Repeated indices are taken into account."""
arr = _as_array(arr)
indices = _as_array(indices)
bbins = np.bincount(indices)
arr[:len(bbins)] += bbins
return arr | python | def _increment(arr, indices):
"""Increment some indices in a 1D vector of non-negative integers.
Repeated indices are taken into account."""
arr = _as_array(arr)
indices = _as_array(indices)
bbins = np.bincount(indices)
arr[:len(bbins)] += bbins
return arr | [
"def",
"_increment",
"(",
"arr",
",",
"indices",
")",
":",
"arr",
"=",
"_as_array",
"(",
"arr",
")",
"indices",
"=",
"_as_array",
"(",
"indices",
")",
"bbins",
"=",
"np",
".",
"bincount",
"(",
"indices",
")",
"arr",
"[",
":",
"len",
"(",
"bbins",
"... | Increment some indices in a 1D vector of non-negative integers.
Repeated indices are taken into account. | [
"Increment",
"some",
"indices",
"in",
"a",
"1D",
"vector",
"of",
"non",
"-",
"negative",
"integers",
".",
"Repeated",
"indices",
"are",
"taken",
"into",
"account",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/stats/ccg.py#L19-L26 | train |
kwikteam/phy | phy/stats/ccg.py | _symmetrize_correlograms | def _symmetrize_correlograms(correlograms):
"""Return the symmetrized version of the CCG arrays."""
n_clusters, _, n_bins = correlograms.shape
assert n_clusters == _
# We symmetrize c[i, j, 0].
# This is necessary because the algorithm in correlograms()
# is sensitive to the order of identical... | python | def _symmetrize_correlograms(correlograms):
"""Return the symmetrized version of the CCG arrays."""
n_clusters, _, n_bins = correlograms.shape
assert n_clusters == _
# We symmetrize c[i, j, 0].
# This is necessary because the algorithm in correlograms()
# is sensitive to the order of identical... | [
"def",
"_symmetrize_correlograms",
"(",
"correlograms",
")",
":",
"n_clusters",
",",
"_",
",",
"n_bins",
"=",
"correlograms",
".",
"shape",
"assert",
"n_clusters",
"==",
"_",
"# We symmetrize c[i, j, 0].",
"# This is necessary because the algorithm in correlograms()",
"# is... | Return the symmetrized version of the CCG arrays. | [
"Return",
"the",
"symmetrized",
"version",
"of",
"the",
"CCG",
"arrays",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/stats/ccg.py#L39-L54 | train |
kwikteam/phy | phy/stats/ccg.py | correlograms | def correlograms(spike_times,
spike_clusters,
cluster_ids=None,
sample_rate=1.,
bin_size=None,
window_size=None,
symmetrize=True,
):
"""Compute all pairwise cross-correlograms among the clusters ap... | python | def correlograms(spike_times,
spike_clusters,
cluster_ids=None,
sample_rate=1.,
bin_size=None,
window_size=None,
symmetrize=True,
):
"""Compute all pairwise cross-correlograms among the clusters ap... | [
"def",
"correlograms",
"(",
"spike_times",
",",
"spike_clusters",
",",
"cluster_ids",
"=",
"None",
",",
"sample_rate",
"=",
"1.",
",",
"bin_size",
"=",
"None",
",",
"window_size",
"=",
"None",
",",
"symmetrize",
"=",
"True",
",",
")",
":",
"assert",
"sampl... | Compute all pairwise cross-correlograms among the clusters appearing
in `spike_clusters`.
Parameters
----------
spike_times : array-like
Spike times in seconds.
spike_clusters : array-like
Spike-cluster mapping.
cluster_ids : array-like
The list of unique clusters, in a... | [
"Compute",
"all",
"pairwise",
"cross",
"-",
"correlograms",
"among",
"the",
"clusters",
"appearing",
"in",
"spike_clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/stats/ccg.py#L57-L177 | train |
kwikteam/phy | phy/cluster/views/correlogram.py | CorrelogramView.set_bin_window | def set_bin_window(self, bin_size=None, window_size=None):
"""Set the bin and window sizes."""
bin_size = bin_size or self.bin_size
window_size = window_size or self.window_size
assert 1e-6 < bin_size < 1e3
assert 1e-6 < window_size < 1e3
assert bin_size < window_size
... | python | def set_bin_window(self, bin_size=None, window_size=None):
"""Set the bin and window sizes."""
bin_size = bin_size or self.bin_size
window_size = window_size or self.window_size
assert 1e-6 < bin_size < 1e3
assert 1e-6 < window_size < 1e3
assert bin_size < window_size
... | [
"def",
"set_bin_window",
"(",
"self",
",",
"bin_size",
"=",
"None",
",",
"window_size",
"=",
"None",
")",
":",
"bin_size",
"=",
"bin_size",
"or",
"self",
".",
"bin_size",
"window_size",
"=",
"window_size",
"or",
"self",
".",
"window_size",
"assert",
"1e-6",
... | Set the bin and window sizes. | [
"Set",
"the",
"bin",
"and",
"window",
"sizes",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/views/correlogram.py#L56-L67 | train |
kwikteam/phy | phy/io/datasets.py | _md5 | def _md5(path, blocksize=2 ** 20):
"""Compute the checksum of a file."""
m = hashlib.md5()
with open(path, 'rb') as f:
while True:
buf = f.read(blocksize)
if not buf:
break
m.update(buf)
return m.hexdigest() | python | def _md5(path, blocksize=2 ** 20):
"""Compute the checksum of a file."""
m = hashlib.md5()
with open(path, 'rb') as f:
while True:
buf = f.read(blocksize)
if not buf:
break
m.update(buf)
return m.hexdigest() | [
"def",
"_md5",
"(",
"path",
",",
"blocksize",
"=",
"2",
"**",
"20",
")",
":",
"m",
"=",
"hashlib",
".",
"md5",
"(",
")",
"with",
"open",
"(",
"path",
",",
"'rb'",
")",
"as",
"f",
":",
"while",
"True",
":",
"buf",
"=",
"f",
".",
"read",
"(",
... | Compute the checksum of a file. | [
"Compute",
"the",
"checksum",
"of",
"a",
"file",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/datasets.py#L66-L75 | train |
kwikteam/phy | phy/io/datasets.py | download_file | def download_file(url, output_path):
"""Download a binary file from an URL.
The checksum will be downloaded from `URL + .md5`. If this download
succeeds, the file's MD5 will be compared to the expected checksum.
Parameters
----------
url : str
The file's URL.
output_path : str
... | python | def download_file(url, output_path):
"""Download a binary file from an URL.
The checksum will be downloaded from `URL + .md5`. If this download
succeeds, the file's MD5 will be compared to the expected checksum.
Parameters
----------
url : str
The file's URL.
output_path : str
... | [
"def",
"download_file",
"(",
"url",
",",
"output_path",
")",
":",
"output_path",
"=",
"op",
".",
"realpath",
"(",
"output_path",
")",
"assert",
"output_path",
"is",
"not",
"None",
"if",
"op",
".",
"exists",
"(",
"output_path",
")",
":",
"checked",
"=",
"... | Download a binary file from an URL.
The checksum will be downloaded from `URL + .md5`. If this download
succeeds, the file's MD5 will be compared to the expected checksum.
Parameters
----------
url : str
The file's URL.
output_path : str
The path where the file is to be saved. | [
"Download",
"a",
"binary",
"file",
"from",
"an",
"URL",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/datasets.py#L103-L138 | train |
kwikteam/phy | phy/plot/plot.py | _make_class | def _make_class(cls, **kwargs):
"""Return a custom Visual class with given parameters."""
kwargs = {k: (v if v is not None else getattr(cls, k, None))
for k, v in kwargs.items()}
# The class name contains a hash of the custom parameters.
name = cls.__name__ + '_' + _hash(kwargs)
if nam... | python | def _make_class(cls, **kwargs):
"""Return a custom Visual class with given parameters."""
kwargs = {k: (v if v is not None else getattr(cls, k, None))
for k, v in kwargs.items()}
# The class name contains a hash of the custom parameters.
name = cls.__name__ + '_' + _hash(kwargs)
if nam... | [
"def",
"_make_class",
"(",
"cls",
",",
"*",
"*",
"kwargs",
")",
":",
"kwargs",
"=",
"{",
"k",
":",
"(",
"v",
"if",
"v",
"is",
"not",
"None",
"else",
"getattr",
"(",
"cls",
",",
"k",
",",
"None",
")",
")",
"for",
"k",
",",
"v",
"in",
"kwargs",... | Return a custom Visual class with given parameters. | [
"Return",
"a",
"custom",
"Visual",
"class",
"with",
"given",
"parameters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/plot.py#L46-L56 | train |
kwikteam/phy | phy/plot/plot.py | View._add_item | def _add_item(self, cls, *args, **kwargs):
"""Add a plot item."""
box_index = kwargs.pop('box_index', self._default_box_index)
data = cls.validate(*args, **kwargs)
n = cls.vertex_count(**data)
if not isinstance(box_index, np.ndarray):
k = len(self._default_box_index... | python | def _add_item(self, cls, *args, **kwargs):
"""Add a plot item."""
box_index = kwargs.pop('box_index', self._default_box_index)
data = cls.validate(*args, **kwargs)
n = cls.vertex_count(**data)
if not isinstance(box_index, np.ndarray):
k = len(self._default_box_index... | [
"def",
"_add_item",
"(",
"self",
",",
"cls",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"box_index",
"=",
"kwargs",
".",
"pop",
"(",
"'box_index'",
",",
"self",
".",
"_default_box_index",
")",
"data",
"=",
"cls",
".",
"validate",
"(",
"*",
... | Add a plot item. | [
"Add",
"a",
"plot",
"item",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/plot.py#L118-L133 | train |
kwikteam/phy | phy/plot/plot.py | View.scatter | def scatter(self, *args, **kwargs):
"""Add a scatter plot."""
cls = _make_class(ScatterVisual,
_default_marker=kwargs.pop('marker', None),
)
return self._add_item(cls, *args, **kwargs) | python | def scatter(self, *args, **kwargs):
"""Add a scatter plot."""
cls = _make_class(ScatterVisual,
_default_marker=kwargs.pop('marker', None),
)
return self._add_item(cls, *args, **kwargs) | [
"def",
"scatter",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"cls",
"=",
"_make_class",
"(",
"ScatterVisual",
",",
"_default_marker",
"=",
"kwargs",
".",
"pop",
"(",
"'marker'",
",",
"None",
")",
",",
")",
"return",
"self",
"."... | Add a scatter plot. | [
"Add",
"a",
"scatter",
"plot",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/plot.py#L153-L158 | train |
kwikteam/phy | phy/plot/plot.py | View.build | def build(self):
"""Build all added items.
Visuals are created, added, and built. The `set_data()` methods can
be called afterwards.
"""
for cls, data_list in self._items.items():
# Some variables are not concatenated. They are specified
# in `allow_list... | python | def build(self):
"""Build all added items.
Visuals are created, added, and built. The `set_data()` methods can
be called afterwards.
"""
for cls, data_list in self._items.items():
# Some variables are not concatenated. They are specified
# in `allow_list... | [
"def",
"build",
"(",
"self",
")",
":",
"for",
"cls",
",",
"data_list",
"in",
"self",
".",
"_items",
".",
"items",
"(",
")",
":",
"# Some variables are not concatenated. They are specified",
"# in `allow_list`.",
"data",
"=",
"_accumulate",
"(",
"data_list",
",",
... | Build all added items.
Visuals are created, added, and built. The `set_data()` methods can
be called afterwards. | [
"Build",
"all",
"added",
"items",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/plot.py#L176-L200 | train |
kwikteam/phy | phy/io/array.py | _range_from_slice | def _range_from_slice(myslice, start=None, stop=None, step=None, length=None):
"""Convert a slice to an array of integers."""
assert isinstance(myslice, slice)
# Find 'step'.
step = myslice.step if myslice.step is not None else step
if step is None:
step = 1
# Find 'start'.
start = m... | python | def _range_from_slice(myslice, start=None, stop=None, step=None, length=None):
"""Convert a slice to an array of integers."""
assert isinstance(myslice, slice)
# Find 'step'.
step = myslice.step if myslice.step is not None else step
if step is None:
step = 1
# Find 'start'.
start = m... | [
"def",
"_range_from_slice",
"(",
"myslice",
",",
"start",
"=",
"None",
",",
"stop",
"=",
"None",
",",
"step",
"=",
"None",
",",
"length",
"=",
"None",
")",
":",
"assert",
"isinstance",
"(",
"myslice",
",",
"slice",
")",
"# Find 'step'.",
"step",
"=",
"... | Convert a slice to an array of integers. | [
"Convert",
"a",
"slice",
"to",
"an",
"array",
"of",
"integers",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L28-L54 | train |
kwikteam/phy | phy/io/array.py | _index_of | def _index_of(arr, lookup):
"""Replace scalars in an array by their indices in a lookup table.
Implicitely assume that:
* All elements of arr and lookup are non-negative integers.
* All elements or arr belong to lookup.
This is not checked for performance reasons.
"""
# Equivalent of np.... | python | def _index_of(arr, lookup):
"""Replace scalars in an array by their indices in a lookup table.
Implicitely assume that:
* All elements of arr and lookup are non-negative integers.
* All elements or arr belong to lookup.
This is not checked for performance reasons.
"""
# Equivalent of np.... | [
"def",
"_index_of",
"(",
"arr",
",",
"lookup",
")",
":",
"# Equivalent of np.digitize(arr, lookup) - 1, but much faster.",
"# TODO: assertions to disable in production for performance reasons.",
"# TODO: np.searchsorted(lookup, arr) is faster on small arrays with large",
"# values",
"lookup"... | Replace scalars in an array by their indices in a lookup table.
Implicitely assume that:
* All elements of arr and lookup are non-negative integers.
* All elements or arr belong to lookup.
This is not checked for performance reasons. | [
"Replace",
"scalars",
"in",
"an",
"array",
"by",
"their",
"indices",
"in",
"a",
"lookup",
"table",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L99-L121 | train |
kwikteam/phy | phy/io/array.py | _pad | def _pad(arr, n, dir='right'):
"""Pad an array with zeros along the first axis.
Parameters
----------
n : int
Size of the returned array in the first axis.
dir : str
Direction of the padding. Must be one 'left' or 'right'.
"""
assert dir in ('left', 'right')
if n < 0:
... | python | def _pad(arr, n, dir='right'):
"""Pad an array with zeros along the first axis.
Parameters
----------
n : int
Size of the returned array in the first axis.
dir : str
Direction of the padding. Must be one 'left' or 'right'.
"""
assert dir in ('left', 'right')
if n < 0:
... | [
"def",
"_pad",
"(",
"arr",
",",
"n",
",",
"dir",
"=",
"'right'",
")",
":",
"assert",
"dir",
"in",
"(",
"'left'",
",",
"'right'",
")",
"if",
"n",
"<",
"0",
":",
"raise",
"ValueError",
"(",
"\"'n' must be positive: {0}.\"",
".",
"format",
"(",
"n",
")"... | Pad an array with zeros along the first axis.
Parameters
----------
n : int
Size of the returned array in the first axis.
dir : str
Direction of the padding. Must be one 'left' or 'right'. | [
"Pad",
"an",
"array",
"with",
"zeros",
"along",
"the",
"first",
"axis",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L124-L160 | train |
kwikteam/phy | phy/io/array.py | _in_polygon | def _in_polygon(points, polygon):
"""Return the points that are inside a polygon."""
from matplotlib.path import Path
points = _as_array(points)
polygon = _as_array(polygon)
assert points.ndim == 2
assert polygon.ndim == 2
if len(polygon):
polygon = np.vstack((polygon, polygon[0]))
... | python | def _in_polygon(points, polygon):
"""Return the points that are inside a polygon."""
from matplotlib.path import Path
points = _as_array(points)
polygon = _as_array(polygon)
assert points.ndim == 2
assert polygon.ndim == 2
if len(polygon):
polygon = np.vstack((polygon, polygon[0]))
... | [
"def",
"_in_polygon",
"(",
"points",
",",
"polygon",
")",
":",
"from",
"matplotlib",
".",
"path",
"import",
"Path",
"points",
"=",
"_as_array",
"(",
"points",
")",
"polygon",
"=",
"_as_array",
"(",
"polygon",
")",
"assert",
"points",
".",
"ndim",
"==",
"... | Return the points that are inside a polygon. | [
"Return",
"the",
"points",
"that",
"are",
"inside",
"a",
"polygon",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L183-L193 | train |
kwikteam/phy | phy/io/array.py | read_array | def read_array(path, mmap_mode=None):
"""Read a .npy array."""
file_ext = op.splitext(path)[1]
if file_ext == '.npy':
return np.load(path, mmap_mode=mmap_mode)
raise NotImplementedError("The file extension `{}` ".format(file_ext) +
"is not currently supported.") | python | def read_array(path, mmap_mode=None):
"""Read a .npy array."""
file_ext = op.splitext(path)[1]
if file_ext == '.npy':
return np.load(path, mmap_mode=mmap_mode)
raise NotImplementedError("The file extension `{}` ".format(file_ext) +
"is not currently supported.") | [
"def",
"read_array",
"(",
"path",
",",
"mmap_mode",
"=",
"None",
")",
":",
"file_ext",
"=",
"op",
".",
"splitext",
"(",
"path",
")",
"[",
"1",
"]",
"if",
"file_ext",
"==",
"'.npy'",
":",
"return",
"np",
".",
"load",
"(",
"path",
",",
"mmap_mode",
"... | Read a .npy array. | [
"Read",
"a",
".",
"npy",
"array",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L219-L225 | train |
kwikteam/phy | phy/io/array.py | write_array | def write_array(path, arr):
"""Write an array to a .npy file."""
file_ext = op.splitext(path)[1]
if file_ext == '.npy':
return np.save(path, arr)
raise NotImplementedError("The file extension `{}` ".format(file_ext) +
"is not currently supported.") | python | def write_array(path, arr):
"""Write an array to a .npy file."""
file_ext = op.splitext(path)[1]
if file_ext == '.npy':
return np.save(path, arr)
raise NotImplementedError("The file extension `{}` ".format(file_ext) +
"is not currently supported.") | [
"def",
"write_array",
"(",
"path",
",",
"arr",
")",
":",
"file_ext",
"=",
"op",
".",
"splitext",
"(",
"path",
")",
"[",
"1",
"]",
"if",
"file_ext",
"==",
"'.npy'",
":",
"return",
"np",
".",
"save",
"(",
"path",
",",
"arr",
")",
"raise",
"NotImpleme... | Write an array to a .npy file. | [
"Write",
"an",
"array",
"to",
"a",
".",
"npy",
"file",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L228-L234 | train |
kwikteam/phy | phy/io/array.py | _concatenate_virtual_arrays | def _concatenate_virtual_arrays(arrs, cols=None, scaling=None):
"""Return a virtual concatenate of several NumPy arrays."""
return None if not len(arrs) else ConcatenatedArrays(arrs, cols,
scaling=scaling) | python | def _concatenate_virtual_arrays(arrs, cols=None, scaling=None):
"""Return a virtual concatenate of several NumPy arrays."""
return None if not len(arrs) else ConcatenatedArrays(arrs, cols,
scaling=scaling) | [
"def",
"_concatenate_virtual_arrays",
"(",
"arrs",
",",
"cols",
"=",
"None",
",",
"scaling",
"=",
"None",
")",
":",
"return",
"None",
"if",
"not",
"len",
"(",
"arrs",
")",
"else",
"ConcatenatedArrays",
"(",
"arrs",
",",
"cols",
",",
"scaling",
"=",
"scal... | Return a virtual concatenate of several NumPy arrays. | [
"Return",
"a",
"virtual",
"concatenate",
"of",
"several",
"NumPy",
"arrays",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L359-L362 | train |
kwikteam/phy | phy/io/array.py | _excerpt_step | def _excerpt_step(n_samples, n_excerpts=None, excerpt_size=None):
"""Compute the step of an excerpt set as a function of the number
of excerpts or their sizes."""
assert n_excerpts >= 2
step = max((n_samples - excerpt_size) // (n_excerpts - 1),
excerpt_size)
return step | python | def _excerpt_step(n_samples, n_excerpts=None, excerpt_size=None):
"""Compute the step of an excerpt set as a function of the number
of excerpts or their sizes."""
assert n_excerpts >= 2
step = max((n_samples - excerpt_size) // (n_excerpts - 1),
excerpt_size)
return step | [
"def",
"_excerpt_step",
"(",
"n_samples",
",",
"n_excerpts",
"=",
"None",
",",
"excerpt_size",
"=",
"None",
")",
":",
"assert",
"n_excerpts",
">=",
"2",
"step",
"=",
"max",
"(",
"(",
"n_samples",
"-",
"excerpt_size",
")",
"//",
"(",
"n_excerpts",
"-",
"1... | Compute the step of an excerpt set as a function of the number
of excerpts or their sizes. | [
"Compute",
"the",
"step",
"of",
"an",
"excerpt",
"set",
"as",
"a",
"function",
"of",
"the",
"number",
"of",
"excerpts",
"or",
"their",
"sizes",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L369-L375 | train |
kwikteam/phy | phy/io/array.py | chunk_bounds | def chunk_bounds(n_samples, chunk_size, overlap=0):
"""Return chunk bounds.
Chunks have the form:
[ overlap/2 | chunk_size-overlap | overlap/2 ]
s_start keep_start keep_end s_end
Except for the first and last chunks which do not have a left/right
overlap.
This gen... | python | def chunk_bounds(n_samples, chunk_size, overlap=0):
"""Return chunk bounds.
Chunks have the form:
[ overlap/2 | chunk_size-overlap | overlap/2 ]
s_start keep_start keep_end s_end
Except for the first and last chunks which do not have a left/right
overlap.
This gen... | [
"def",
"chunk_bounds",
"(",
"n_samples",
",",
"chunk_size",
",",
"overlap",
"=",
"0",
")",
":",
"s_start",
"=",
"0",
"s_end",
"=",
"chunk_size",
"keep_start",
"=",
"s_start",
"keep_end",
"=",
"s_end",
"-",
"overlap",
"//",
"2",
"yield",
"s_start",
",",
"... | Return chunk bounds.
Chunks have the form:
[ overlap/2 | chunk_size-overlap | overlap/2 ]
s_start keep_start keep_end s_end
Except for the first and last chunks which do not have a left/right
overlap.
This generator yields (s_start, s_end, keep_start, keep_end). | [
"Return",
"chunk",
"bounds",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L378-L411 | train |
kwikteam/phy | phy/io/array.py | data_chunk | def data_chunk(data, chunk, with_overlap=False):
"""Get a data chunk."""
assert isinstance(chunk, tuple)
if len(chunk) == 2:
i, j = chunk
elif len(chunk) == 4:
if with_overlap:
i, j = chunk[:2]
else:
i, j = chunk[2:]
else:
raise ValueError("'ch... | python | def data_chunk(data, chunk, with_overlap=False):
"""Get a data chunk."""
assert isinstance(chunk, tuple)
if len(chunk) == 2:
i, j = chunk
elif len(chunk) == 4:
if with_overlap:
i, j = chunk[:2]
else:
i, j = chunk[2:]
else:
raise ValueError("'ch... | [
"def",
"data_chunk",
"(",
"data",
",",
"chunk",
",",
"with_overlap",
"=",
"False",
")",
":",
"assert",
"isinstance",
"(",
"chunk",
",",
"tuple",
")",
"if",
"len",
"(",
"chunk",
")",
"==",
"2",
":",
"i",
",",
"j",
"=",
"chunk",
"elif",
"len",
"(",
... | Get a data chunk. | [
"Get",
"a",
"data",
"chunk",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L428-L441 | train |
kwikteam/phy | phy/io/array.py | _spikes_in_clusters | def _spikes_in_clusters(spike_clusters, clusters):
"""Return the ids of all spikes belonging to the specified clusters."""
if len(spike_clusters) == 0 or len(clusters) == 0:
return np.array([], dtype=np.int)
return np.nonzero(np.in1d(spike_clusters, clusters))[0] | python | def _spikes_in_clusters(spike_clusters, clusters):
"""Return the ids of all spikes belonging to the specified clusters."""
if len(spike_clusters) == 0 or len(clusters) == 0:
return np.array([], dtype=np.int)
return np.nonzero(np.in1d(spike_clusters, clusters))[0] | [
"def",
"_spikes_in_clusters",
"(",
"spike_clusters",
",",
"clusters",
")",
":",
"if",
"len",
"(",
"spike_clusters",
")",
"==",
"0",
"or",
"len",
"(",
"clusters",
")",
"==",
"0",
":",
"return",
"np",
".",
"array",
"(",
"[",
"]",
",",
"dtype",
"=",
"np... | Return the ids of all spikes belonging to the specified clusters. | [
"Return",
"the",
"ids",
"of",
"all",
"spikes",
"belonging",
"to",
"the",
"specified",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L465-L469 | train |
kwikteam/phy | phy/io/array.py | grouped_mean | def grouped_mean(arr, spike_clusters):
"""Compute the mean of a spike-dependent quantity for every cluster.
The two arguments should be 1D array with `n_spikes` elements.
The output is a 1D array with `n_clusters` elements. The clusters are
sorted in increasing order.
"""
arr = np.asarray(arr... | python | def grouped_mean(arr, spike_clusters):
"""Compute the mean of a spike-dependent quantity for every cluster.
The two arguments should be 1D array with `n_spikes` elements.
The output is a 1D array with `n_clusters` elements. The clusters are
sorted in increasing order.
"""
arr = np.asarray(arr... | [
"def",
"grouped_mean",
"(",
"arr",
",",
"spike_clusters",
")",
":",
"arr",
"=",
"np",
".",
"asarray",
"(",
"arr",
")",
"spike_clusters",
"=",
"np",
".",
"asarray",
"(",
"spike_clusters",
")",
"assert",
"arr",
".",
"ndim",
"==",
"1",
"assert",
"arr",
".... | Compute the mean of a spike-dependent quantity for every cluster.
The two arguments should be 1D array with `n_spikes` elements.
The output is a 1D array with `n_clusters` elements. The clusters are
sorted in increasing order. | [
"Compute",
"the",
"mean",
"of",
"a",
"spike",
"-",
"dependent",
"quantity",
"for",
"every",
"cluster",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L506-L526 | train |
kwikteam/phy | phy/io/array.py | regular_subset | def regular_subset(spikes, n_spikes_max=None, offset=0):
"""Prune the current selection to get at most n_spikes_max spikes."""
assert spikes is not None
# Nothing to do if the selection already satisfies n_spikes_max.
if n_spikes_max is None or len(spikes) <= n_spikes_max: # pragma: no cover
re... | python | def regular_subset(spikes, n_spikes_max=None, offset=0):
"""Prune the current selection to get at most n_spikes_max spikes."""
assert spikes is not None
# Nothing to do if the selection already satisfies n_spikes_max.
if n_spikes_max is None or len(spikes) <= n_spikes_max: # pragma: no cover
re... | [
"def",
"regular_subset",
"(",
"spikes",
",",
"n_spikes_max",
"=",
"None",
",",
"offset",
"=",
"0",
")",
":",
"assert",
"spikes",
"is",
"not",
"None",
"# Nothing to do if the selection already satisfies n_spikes_max.",
"if",
"n_spikes_max",
"is",
"None",
"or",
"len",... | Prune the current selection to get at most n_spikes_max spikes. | [
"Prune",
"the",
"current",
"selection",
"to",
"get",
"at",
"most",
"n_spikes_max",
"spikes",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L529-L542 | train |
kwikteam/phy | phy/io/array.py | select_spikes | def select_spikes(cluster_ids=None,
max_n_spikes_per_cluster=None,
spikes_per_cluster=None,
batch_size=None,
subset=None,
):
"""Return a selection of spikes belonging to the specified clusters."""
subset = subset or 'regul... | python | def select_spikes(cluster_ids=None,
max_n_spikes_per_cluster=None,
spikes_per_cluster=None,
batch_size=None,
subset=None,
):
"""Return a selection of spikes belonging to the specified clusters."""
subset = subset or 'regul... | [
"def",
"select_spikes",
"(",
"cluster_ids",
"=",
"None",
",",
"max_n_spikes_per_cluster",
"=",
"None",
",",
"spikes_per_cluster",
"=",
"None",
",",
"batch_size",
"=",
"None",
",",
"subset",
"=",
"None",
",",
")",
":",
"subset",
"=",
"subset",
"or",
"'regular... | Return a selection of spikes belonging to the specified clusters. | [
"Return",
"a",
"selection",
"of",
"spikes",
"belonging",
"to",
"the",
"specified",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L545-L582 | train |
kwikteam/phy | phy/io/array.py | ConcatenatedArrays._get_recording | def _get_recording(self, index):
"""Return the recording that contains a given index."""
assert index >= 0
recs = np.nonzero((index - self.offsets[:-1]) >= 0)[0]
if len(recs) == 0: # pragma: no cover
# If the index is greater than the total size,
# return the las... | python | def _get_recording(self, index):
"""Return the recording that contains a given index."""
assert index >= 0
recs = np.nonzero((index - self.offsets[:-1]) >= 0)[0]
if len(recs) == 0: # pragma: no cover
# If the index is greater than the total size,
# return the las... | [
"def",
"_get_recording",
"(",
"self",
",",
"index",
")",
":",
"assert",
"index",
">=",
"0",
"recs",
"=",
"np",
".",
"nonzero",
"(",
"(",
"index",
"-",
"self",
".",
"offsets",
"[",
":",
"-",
"1",
"]",
")",
">=",
"0",
")",
"[",
"0",
"]",
"if",
... | Return the recording that contains a given index. | [
"Return",
"the",
"recording",
"that",
"contains",
"a",
"given",
"index",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/io/array.py#L297-L307 | train |
kwikteam/phy | phy/traces/filter.py | bandpass_filter | def bandpass_filter(rate=None, low=None, high=None, order=None):
"""Butterworth bandpass filter."""
assert low < high
assert order >= 1
return signal.butter(order,
(low / (rate / 2.), high / (rate / 2.)),
'pass') | python | def bandpass_filter(rate=None, low=None, high=None, order=None):
"""Butterworth bandpass filter."""
assert low < high
assert order >= 1
return signal.butter(order,
(low / (rate / 2.), high / (rate / 2.)),
'pass') | [
"def",
"bandpass_filter",
"(",
"rate",
"=",
"None",
",",
"low",
"=",
"None",
",",
"high",
"=",
"None",
",",
"order",
"=",
"None",
")",
":",
"assert",
"low",
"<",
"high",
"assert",
"order",
">=",
"1",
"return",
"signal",
".",
"butter",
"(",
"order",
... | Butterworth bandpass filter. | [
"Butterworth",
"bandpass",
"filter",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/traces/filter.py#L19-L25 | train |
kwikteam/phy | phy/traces/filter.py | apply_filter | def apply_filter(x, filter=None, axis=0):
"""Apply a filter to an array."""
x = _as_array(x)
if x.shape[axis] == 0:
return x
b, a = filter
return signal.filtfilt(b, a, x, axis=axis) | python | def apply_filter(x, filter=None, axis=0):
"""Apply a filter to an array."""
x = _as_array(x)
if x.shape[axis] == 0:
return x
b, a = filter
return signal.filtfilt(b, a, x, axis=axis) | [
"def",
"apply_filter",
"(",
"x",
",",
"filter",
"=",
"None",
",",
"axis",
"=",
"0",
")",
":",
"x",
"=",
"_as_array",
"(",
"x",
")",
"if",
"x",
".",
"shape",
"[",
"axis",
"]",
"==",
"0",
":",
"return",
"x",
"b",
",",
"a",
"=",
"filter",
"retur... | Apply a filter to an array. | [
"Apply",
"a",
"filter",
"to",
"an",
"array",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/traces/filter.py#L28-L34 | train |
kwikteam/phy | phy/traces/filter.py | Whitening.fit | def fit(self, x, fudge=1e-18):
"""Compute the whitening matrix.
Parameters
----------
x : array
An `(n_samples, n_channels)` array.
"""
assert x.ndim == 2
ns, nc = x.shape
x_cov = np.cov(x, rowvar=0)
assert x_cov.shape == (nc, nc)
... | python | def fit(self, x, fudge=1e-18):
"""Compute the whitening matrix.
Parameters
----------
x : array
An `(n_samples, n_channels)` array.
"""
assert x.ndim == 2
ns, nc = x.shape
x_cov = np.cov(x, rowvar=0)
assert x_cov.shape == (nc, nc)
... | [
"def",
"fit",
"(",
"self",
",",
"x",
",",
"fudge",
"=",
"1e-18",
")",
":",
"assert",
"x",
".",
"ndim",
"==",
"2",
"ns",
",",
"nc",
"=",
"x",
".",
"shape",
"x_cov",
"=",
"np",
".",
"cov",
"(",
"x",
",",
"rowvar",
"=",
"0",
")",
"assert",
"x_... | Compute the whitening matrix.
Parameters
----------
x : array
An `(n_samples, n_channels)` array. | [
"Compute",
"the",
"whitening",
"matrix",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/traces/filter.py#L72-L92 | train |
kwikteam/phy | phy/cluster/_history.py | History.current_item | def current_item(self):
"""Return the current element."""
if self._history and self._index >= 0:
self._check_index()
return self._history[self._index] | python | def current_item(self):
"""Return the current element."""
if self._history and self._index >= 0:
self._check_index()
return self._history[self._index] | [
"def",
"current_item",
"(",
"self",
")",
":",
"if",
"self",
".",
"_history",
"and",
"self",
".",
"_index",
">=",
"0",
":",
"self",
".",
"_check_index",
"(",
")",
"return",
"self",
".",
"_history",
"[",
"self",
".",
"_index",
"]"
] | Return the current element. | [
"Return",
"the",
"current",
"element",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L28-L32 | train |
kwikteam/phy | phy/cluster/_history.py | History._check_index | def _check_index(self):
"""Check that the index is without the bounds of _history."""
assert 0 <= self._index <= len(self._history) - 1
# There should always be the base item at least.
assert len(self._history) >= 1 | python | def _check_index(self):
"""Check that the index is without the bounds of _history."""
assert 0 <= self._index <= len(self._history) - 1
# There should always be the base item at least.
assert len(self._history) >= 1 | [
"def",
"_check_index",
"(",
"self",
")",
":",
"assert",
"0",
"<=",
"self",
".",
"_index",
"<=",
"len",
"(",
"self",
".",
"_history",
")",
"-",
"1",
"# There should always be the base item at least.",
"assert",
"len",
"(",
"self",
".",
"_history",
")",
">=",
... | Check that the index is without the bounds of _history. | [
"Check",
"that",
"the",
"index",
"is",
"without",
"the",
"bounds",
"of",
"_history",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L39-L43 | train |
kwikteam/phy | phy/cluster/_history.py | History.iter | def iter(self, start=0, end=None):
"""Iterate through successive history items.
Parameters
----------
end : int
Index of the last item to loop through + 1.
start : int
Initial index for the loop (0 by default).
"""
if end is None:
... | python | def iter(self, start=0, end=None):
"""Iterate through successive history items.
Parameters
----------
end : int
Index of the last item to loop through + 1.
start : int
Initial index for the loop (0 by default).
"""
if end is None:
... | [
"def",
"iter",
"(",
"self",
",",
"start",
"=",
"0",
",",
"end",
"=",
"None",
")",
":",
"if",
"end",
"is",
"None",
":",
"end",
"=",
"self",
".",
"_index",
"+",
"1",
"elif",
"end",
"==",
"0",
":",
"raise",
"StopIteration",
"(",
")",
"if",
"start"... | Iterate through successive history items.
Parameters
----------
end : int
Index of the last item to loop through + 1.
start : int
Initial index for the loop (0 by default). | [
"Iterate",
"through",
"successive",
"history",
"items",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L51-L73 | train |
kwikteam/phy | phy/cluster/_history.py | History.add | def add(self, item):
"""Add an item in the history."""
self._check_index()
# Possibly truncate the history up to the current point.
self._history = self._history[:self._index + 1]
# Append the item
self._history.append(item)
# Increment the index.
self._in... | python | def add(self, item):
"""Add an item in the history."""
self._check_index()
# Possibly truncate the history up to the current point.
self._history = self._history[:self._index + 1]
# Append the item
self._history.append(item)
# Increment the index.
self._in... | [
"def",
"add",
"(",
"self",
",",
"item",
")",
":",
"self",
".",
"_check_index",
"(",
")",
"# Possibly truncate the history up to the current point.",
"self",
".",
"_history",
"=",
"self",
".",
"_history",
"[",
":",
"self",
".",
"_index",
"+",
"1",
"]",
"# App... | Add an item in the history. | [
"Add",
"an",
"item",
"in",
"the",
"history",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L81-L92 | train |
kwikteam/phy | phy/cluster/_history.py | History.back | def back(self):
"""Go back in history if possible.
Return the undone item.
"""
if self._index <= 0:
return None
undone = self.current_item
self._index -= 1
self._check_index()
return undone | python | def back(self):
"""Go back in history if possible.
Return the undone item.
"""
if self._index <= 0:
return None
undone = self.current_item
self._index -= 1
self._check_index()
return undone | [
"def",
"back",
"(",
"self",
")",
":",
"if",
"self",
".",
"_index",
"<=",
"0",
":",
"return",
"None",
"undone",
"=",
"self",
".",
"current_item",
"self",
".",
"_index",
"-=",
"1",
"self",
".",
"_check_index",
"(",
")",
"return",
"undone"
] | Go back in history if possible.
Return the undone item. | [
"Go",
"back",
"in",
"history",
"if",
"possible",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L94-L105 | train |
kwikteam/phy | phy/cluster/_history.py | History.forward | def forward(self):
"""Go forward in history if possible.
Return the current item after going forward.
"""
if self._index >= len(self._history) - 1:
return None
self._index += 1
self._check_index()
return self.current_item | python | def forward(self):
"""Go forward in history if possible.
Return the current item after going forward.
"""
if self._index >= len(self._history) - 1:
return None
self._index += 1
self._check_index()
return self.current_item | [
"def",
"forward",
"(",
"self",
")",
":",
"if",
"self",
".",
"_index",
">=",
"len",
"(",
"self",
".",
"_history",
")",
"-",
"1",
":",
"return",
"None",
"self",
".",
"_index",
"+=",
"1",
"self",
".",
"_check_index",
"(",
")",
"return",
"self",
".",
... | Go forward in history if possible.
Return the current item after going forward. | [
"Go",
"forward",
"in",
"history",
"if",
"possible",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L110-L120 | train |
kwikteam/phy | phy/cluster/_history.py | GlobalHistory.add_to_current_action | def add_to_current_action(self, controller):
"""Add a controller to the current action."""
item = self.current_item
self._history[self._index] = item + (controller,) | python | def add_to_current_action(self, controller):
"""Add a controller to the current action."""
item = self.current_item
self._history[self._index] = item + (controller,) | [
"def",
"add_to_current_action",
"(",
"self",
",",
"controller",
")",
":",
"item",
"=",
"self",
".",
"current_item",
"self",
".",
"_history",
"[",
"self",
".",
"_index",
"]",
"=",
"item",
"+",
"(",
"controller",
",",
")"
] | Add a controller to the current action. | [
"Add",
"a",
"controller",
"to",
"the",
"current",
"action",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L137-L140 | train |
kwikteam/phy | phy/cluster/_history.py | GlobalHistory.redo | def redo(self):
"""Redo the last action.
This will call `redo()` on all controllers involved in this action.
"""
controllers = self.forward()
if controllers is None:
ups = ()
else:
ups = tuple([controller.redo() for
contr... | python | def redo(self):
"""Redo the last action.
This will call `redo()` on all controllers involved in this action.
"""
controllers = self.forward()
if controllers is None:
ups = ()
else:
ups = tuple([controller.redo() for
contr... | [
"def",
"redo",
"(",
"self",
")",
":",
"controllers",
"=",
"self",
".",
"forward",
"(",
")",
"if",
"controllers",
"is",
"None",
":",
"ups",
"=",
"(",
")",
"else",
":",
"ups",
"=",
"tuple",
"(",
"[",
"controller",
".",
"redo",
"(",
")",
"for",
"con... | Redo the last action.
This will call `redo()` on all controllers involved in this action. | [
"Redo",
"the",
"last",
"action",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_history.py#L159-L174 | train |
kwikteam/phy | phy/plot/base.py | _insert_glsl | def _insert_glsl(vertex, fragment, to_insert):
"""Insert snippets in a shader.
to_insert is a dict `{(shader_type, location): snippet}`.
Snippets can contain `{{ var }}` placeholders for the transformed variable
name.
"""
# Find the place where to insert the GLSL snippet.
# This is "gl_Po... | python | def _insert_glsl(vertex, fragment, to_insert):
"""Insert snippets in a shader.
to_insert is a dict `{(shader_type, location): snippet}`.
Snippets can contain `{{ var }}` placeholders for the transformed variable
name.
"""
# Find the place where to insert the GLSL snippet.
# This is "gl_Po... | [
"def",
"_insert_glsl",
"(",
"vertex",
",",
"fragment",
",",
"to_insert",
")",
":",
"# Find the place where to insert the GLSL snippet.",
"# This is \"gl_Position = transform(data_var_name);\" where",
"# data_var_name is typically an attribute.",
"vs_regex",
"=",
"re",
".",
"compile... | Insert snippets in a shader.
to_insert is a dict `{(shader_type, location): snippet}`.
Snippets can contain `{{ var }}` placeholders for the transformed variable
name. | [
"Insert",
"snippets",
"in",
"a",
"shader",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L117-L165 | train |
kwikteam/phy | phy/plot/base.py | BaseVisual.on_draw | def on_draw(self):
"""Draw the visual."""
# Skip the drawing if the program hasn't been built yet.
# The program is built by the interact.
if self.program:
# Draw the program.
self.program.draw(self.gl_primitive_type)
else: # pragma: no cover
... | python | def on_draw(self):
"""Draw the visual."""
# Skip the drawing if the program hasn't been built yet.
# The program is built by the interact.
if self.program:
# Draw the program.
self.program.draw(self.gl_primitive_type)
else: # pragma: no cover
... | [
"def",
"on_draw",
"(",
"self",
")",
":",
"# Skip the drawing if the program hasn't been built yet.",
"# The program is built by the interact.",
"if",
"self",
".",
"program",
":",
"# Draw the program.",
"self",
".",
"program",
".",
"draw",
"(",
"self",
".",
"gl_primitive_t... | Draw the visual. | [
"Draw",
"the",
"visual",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L67-L76 | train |
kwikteam/phy | phy/plot/base.py | GLSLInserter.add_transform_chain | def add_transform_chain(self, tc):
"""Insert the GLSL snippets of a transform chain."""
# Generate the transforms snippet.
for t in tc.gpu_transforms:
if isinstance(t, Clip):
# Set the varying value in the vertex shader.
self.insert_vert('v_temp_pos_tr... | python | def add_transform_chain(self, tc):
"""Insert the GLSL snippets of a transform chain."""
# Generate the transforms snippet.
for t in tc.gpu_transforms:
if isinstance(t, Clip):
# Set the varying value in the vertex shader.
self.insert_vert('v_temp_pos_tr... | [
"def",
"add_transform_chain",
"(",
"self",
",",
"tc",
")",
":",
"# Generate the transforms snippet.",
"for",
"t",
"in",
"tc",
".",
"gpu_transforms",
":",
"if",
"isinstance",
"(",
"t",
",",
"Clip",
")",
":",
"# Set the varying value in the vertex shader.",
"self",
... | Insert the GLSL snippets of a transform chain. | [
"Insert",
"the",
"GLSL",
"snippets",
"of",
"a",
"transform",
"chain",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L207-L219 | train |
kwikteam/phy | phy/plot/base.py | GLSLInserter.insert_into_shaders | def insert_into_shaders(self, vertex, fragment):
"""Apply the insertions to shader code."""
to_insert = defaultdict(str)
to_insert.update({key: '\n'.join(self._to_insert[key]) + '\n'
for key in self._to_insert})
return _insert_glsl(vertex, fragment, to_insert) | python | def insert_into_shaders(self, vertex, fragment):
"""Apply the insertions to shader code."""
to_insert = defaultdict(str)
to_insert.update({key: '\n'.join(self._to_insert[key]) + '\n'
for key in self._to_insert})
return _insert_glsl(vertex, fragment, to_insert) | [
"def",
"insert_into_shaders",
"(",
"self",
",",
"vertex",
",",
"fragment",
")",
":",
"to_insert",
"=",
"defaultdict",
"(",
"str",
")",
"to_insert",
".",
"update",
"(",
"{",
"key",
":",
"'\\n'",
".",
"join",
"(",
"self",
".",
"_to_insert",
"[",
"key",
"... | Apply the insertions to shader code. | [
"Apply",
"the",
"insertions",
"to",
"shader",
"code",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L221-L226 | train |
kwikteam/phy | phy/plot/base.py | BaseCanvas.add_visual | def add_visual(self, visual):
"""Add a visual to the canvas, and build its program by the same
occasion.
We can't build the visual's program before, because we need the canvas'
transforms first.
"""
# Retrieve the visual's GLSL inserter.
inserter = visual.insert... | python | def add_visual(self, visual):
"""Add a visual to the canvas, and build its program by the same
occasion.
We can't build the visual's program before, because we need the canvas'
transforms first.
"""
# Retrieve the visual's GLSL inserter.
inserter = visual.insert... | [
"def",
"add_visual",
"(",
"self",
",",
"visual",
")",
":",
"# Retrieve the visual's GLSL inserter.",
"inserter",
"=",
"visual",
".",
"inserter",
"# Add the visual's transforms.",
"inserter",
".",
"add_transform_chain",
"(",
"visual",
".",
"transforms",
")",
"# Then, add... | Add a visual to the canvas, and build its program by the same
occasion.
We can't build the visual's program before, because we need the canvas'
transforms first. | [
"Add",
"a",
"visual",
"to",
"the",
"canvas",
"and",
"build",
"its",
"program",
"by",
"the",
"same",
"occasion",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L258-L286 | train |
kwikteam/phy | phy/plot/base.py | BaseCanvas.on_resize | def on_resize(self, event):
"""Resize the OpenGL context."""
self.context.set_viewport(0, 0, event.size[0], event.size[1])
for visual in self.visuals:
visual.on_resize(event.size)
self.update() | python | def on_resize(self, event):
"""Resize the OpenGL context."""
self.context.set_viewport(0, 0, event.size[0], event.size[1])
for visual in self.visuals:
visual.on_resize(event.size)
self.update() | [
"def",
"on_resize",
"(",
"self",
",",
"event",
")",
":",
"self",
".",
"context",
".",
"set_viewport",
"(",
"0",
",",
"0",
",",
"event",
".",
"size",
"[",
"0",
"]",
",",
"event",
".",
"size",
"[",
"1",
"]",
")",
"for",
"visual",
"in",
"self",
".... | Resize the OpenGL context. | [
"Resize",
"the",
"OpenGL",
"context",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L288-L293 | train |
kwikteam/phy | phy/plot/base.py | BaseCanvas.on_draw | def on_draw(self, e):
"""Draw all visuals."""
gloo.clear()
for visual in self.visuals:
logger.log(5, "Draw visual `%s`.", visual)
visual.on_draw() | python | def on_draw(self, e):
"""Draw all visuals."""
gloo.clear()
for visual in self.visuals:
logger.log(5, "Draw visual `%s`.", visual)
visual.on_draw() | [
"def",
"on_draw",
"(",
"self",
",",
"e",
")",
":",
"gloo",
".",
"clear",
"(",
")",
"for",
"visual",
"in",
"self",
".",
"visuals",
":",
"logger",
".",
"log",
"(",
"5",
",",
"\"Draw visual `%s`.\"",
",",
"visual",
")",
"visual",
".",
"on_draw",
"(",
... | Draw all visuals. | [
"Draw",
"all",
"visuals",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L295-L300 | train |
kwikteam/phy | phy/plot/base.py | BaseInteract.update | def update(self):
"""Update all visuals in the attached canvas."""
if not self.canvas:
return
for visual in self.canvas.visuals:
self.update_program(visual.program)
self.canvas.update() | python | def update(self):
"""Update all visuals in the attached canvas."""
if not self.canvas:
return
for visual in self.canvas.visuals:
self.update_program(visual.program)
self.canvas.update() | [
"def",
"update",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"canvas",
":",
"return",
"for",
"visual",
"in",
"self",
".",
"canvas",
".",
"visuals",
":",
"self",
".",
"update_program",
"(",
"visual",
".",
"program",
")",
"self",
".",
"canvas",
".... | Update all visuals in the attached canvas. | [
"Update",
"all",
"visuals",
"in",
"the",
"attached",
"canvas",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/base.py#L324-L330 | train |
kwikteam/phy | phy/utils/cli.py | _add_log_file | def _add_log_file(filename):
"""Create a `phy.log` log file with DEBUG level in the
current directory."""
handler = logging.FileHandler(filename)
handler.setLevel(logging.DEBUG)
formatter = _Formatter(fmt=_logger_fmt,
datefmt='%Y-%m-%d %H:%M:%S')
handler.setFormatter(... | python | def _add_log_file(filename):
"""Create a `phy.log` log file with DEBUG level in the
current directory."""
handler = logging.FileHandler(filename)
handler.setLevel(logging.DEBUG)
formatter = _Formatter(fmt=_logger_fmt,
datefmt='%Y-%m-%d %H:%M:%S')
handler.setFormatter(... | [
"def",
"_add_log_file",
"(",
"filename",
")",
":",
"handler",
"=",
"logging",
".",
"FileHandler",
"(",
"filename",
")",
"handler",
".",
"setLevel",
"(",
"logging",
".",
"DEBUG",
")",
"formatter",
"=",
"_Formatter",
"(",
"fmt",
"=",
"_logger_fmt",
",",
"dat... | Create a `phy.log` log file with DEBUG level in the
current directory. | [
"Create",
"a",
"phy",
".",
"log",
"log",
"file",
"with",
"DEBUG",
"level",
"in",
"the",
"current",
"directory",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/cli.py#L46-L55 | train |
kwikteam/phy | phy/utils/cli.py | _run_cmd | def _run_cmd(cmd, ctx, glob, loc): # pragma: no cover
"""Run a command with optionally a debugger, IPython, or profiling."""
if PDB:
_enable_pdb()
if IPYTHON:
from IPython import start_ipython
args_ipy = ['-i', '--gui=qt']
ns = glob.copy()
ns.update(loc)
retu... | python | def _run_cmd(cmd, ctx, glob, loc): # pragma: no cover
"""Run a command with optionally a debugger, IPython, or profiling."""
if PDB:
_enable_pdb()
if IPYTHON:
from IPython import start_ipython
args_ipy = ['-i', '--gui=qt']
ns = glob.copy()
ns.update(loc)
retu... | [
"def",
"_run_cmd",
"(",
"cmd",
",",
"ctx",
",",
"glob",
",",
"loc",
")",
":",
"# pragma: no cover",
"if",
"PDB",
":",
"_enable_pdb",
"(",
")",
"if",
"IPYTHON",
":",
"from",
"IPython",
"import",
"start_ipython",
"args_ipy",
"=",
"[",
"'-i'",
",",
"'--gui=... | Run a command with optionally a debugger, IPython, or profiling. | [
"Run",
"a",
"command",
"with",
"optionally",
"a",
"debugger",
"IPython",
"or",
"profiling",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/cli.py#L58-L73 | train |
kwikteam/phy | phy/utils/cli.py | load_cli_plugins | def load_cli_plugins(cli, config_dir=None):
"""Load all plugins and attach them to a CLI object."""
from .config import load_master_config
config = load_master_config(config_dir=config_dir)
plugins = discover_plugins(config.Plugins.dirs)
for plugin in plugins:
if not hasattr(plugin, 'attac... | python | def load_cli_plugins(cli, config_dir=None):
"""Load all plugins and attach them to a CLI object."""
from .config import load_master_config
config = load_master_config(config_dir=config_dir)
plugins = discover_plugins(config.Plugins.dirs)
for plugin in plugins:
if not hasattr(plugin, 'attac... | [
"def",
"load_cli_plugins",
"(",
"cli",
",",
"config_dir",
"=",
"None",
")",
":",
"from",
".",
"config",
"import",
"load_master_config",
"config",
"=",
"load_master_config",
"(",
"config_dir",
"=",
"config_dir",
")",
"plugins",
"=",
"discover_plugins",
"(",
"conf... | Load all plugins and attach them to a CLI object. | [
"Load",
"all",
"plugins",
"and",
"attach",
"them",
"to",
"a",
"CLI",
"object",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/cli.py#L94-L109 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.get_mouse_pos | def get_mouse_pos(self, pos):
"""Return the mouse coordinates in NDC, taking panzoom into account."""
position = np.asarray(self._normalize(pos))
zoom = np.asarray(self._zoom_aspect())
pan = np.asarray(self.pan)
mouse_pos = ((position / zoom) - pan)
return mouse_pos | python | def get_mouse_pos(self, pos):
"""Return the mouse coordinates in NDC, taking panzoom into account."""
position = np.asarray(self._normalize(pos))
zoom = np.asarray(self._zoom_aspect())
pan = np.asarray(self.pan)
mouse_pos = ((position / zoom) - pan)
return mouse_pos | [
"def",
"get_mouse_pos",
"(",
"self",
",",
"pos",
")",
":",
"position",
"=",
"np",
".",
"asarray",
"(",
"self",
".",
"_normalize",
"(",
"pos",
")",
")",
"zoom",
"=",
"np",
".",
"asarray",
"(",
"self",
".",
"_zoom_aspect",
"(",
")",
")",
"pan",
"=",
... | Return the mouse coordinates in NDC, taking panzoom into account. | [
"Return",
"the",
"mouse",
"coordinates",
"in",
"NDC",
"taking",
"panzoom",
"into",
"account",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L228-L234 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.pan | def pan(self, value):
"""Pan translation."""
assert len(value) == 2
self._pan[:] = value
self._constrain_pan()
self.update() | python | def pan(self, value):
"""Pan translation."""
assert len(value) == 2
self._pan[:] = value
self._constrain_pan()
self.update() | [
"def",
"pan",
"(",
"self",
",",
"value",
")",
":",
"assert",
"len",
"(",
"value",
")",
"==",
"2",
"self",
".",
"_pan",
"[",
":",
"]",
"=",
"value",
"self",
".",
"_constrain_pan",
"(",
")",
"self",
".",
"update",
"(",
")"
] | Pan translation. | [
"Pan",
"translation",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L245-L250 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.zoom | def zoom(self, value):
"""Zoom level."""
if isinstance(value, (int, float)):
value = (value, value)
assert len(value) == 2
self._zoom = np.clip(value, self._zmin, self._zmax)
# Constrain bounding box.
self._constrain_pan()
self._constrain_zoom()
... | python | def zoom(self, value):
"""Zoom level."""
if isinstance(value, (int, float)):
value = (value, value)
assert len(value) == 2
self._zoom = np.clip(value, self._zmin, self._zmax)
# Constrain bounding box.
self._constrain_pan()
self._constrain_zoom()
... | [
"def",
"zoom",
"(",
"self",
",",
"value",
")",
":",
"if",
"isinstance",
"(",
"value",
",",
"(",
"int",
",",
"float",
")",
")",
":",
"value",
"=",
"(",
"value",
",",
"value",
")",
"assert",
"len",
"(",
"value",
")",
"==",
"2",
"self",
".",
"_zoo... | Zoom level. | [
"Zoom",
"level",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L258-L269 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.pan_delta | def pan_delta(self, d):
"""Pan the view by a given amount."""
dx, dy = d
pan_x, pan_y = self.pan
zoom_x, zoom_y = self._zoom_aspect(self._zoom)
self.pan = (pan_x + dx / zoom_x, pan_y + dy / zoom_y)
self.update() | python | def pan_delta(self, d):
"""Pan the view by a given amount."""
dx, dy = d
pan_x, pan_y = self.pan
zoom_x, zoom_y = self._zoom_aspect(self._zoom)
self.pan = (pan_x + dx / zoom_x, pan_y + dy / zoom_y)
self.update() | [
"def",
"pan_delta",
"(",
"self",
",",
"d",
")",
":",
"dx",
",",
"dy",
"=",
"d",
"pan_x",
",",
"pan_y",
"=",
"self",
".",
"pan",
"zoom_x",
",",
"zoom_y",
"=",
"self",
".",
"_zoom_aspect",
"(",
"self",
".",
"_zoom",
")",
"self",
".",
"pan",
"=",
... | Pan the view by a given amount. | [
"Pan",
"the",
"view",
"by",
"a",
"given",
"amount",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L271-L279 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.zoom_delta | def zoom_delta(self, d, p=(0., 0.), c=1.):
"""Zoom the view by a given amount."""
dx, dy = d
x0, y0 = p
pan_x, pan_y = self._pan
zoom_x, zoom_y = self._zoom
zoom_x_new, zoom_y_new = (zoom_x * math.exp(c * self._zoom_coeff * dx),
zoom_y *... | python | def zoom_delta(self, d, p=(0., 0.), c=1.):
"""Zoom the view by a given amount."""
dx, dy = d
x0, y0 = p
pan_x, pan_y = self._pan
zoom_x, zoom_y = self._zoom
zoom_x_new, zoom_y_new = (zoom_x * math.exp(c * self._zoom_coeff * dx),
zoom_y *... | [
"def",
"zoom_delta",
"(",
"self",
",",
"d",
",",
"p",
"=",
"(",
"0.",
",",
"0.",
")",
",",
"c",
"=",
"1.",
")",
":",
"dx",
",",
"dy",
"=",
"d",
"x0",
",",
"y0",
"=",
"p",
"pan_x",
",",
"pan_y",
"=",
"self",
".",
"_pan",
"zoom_x",
",",
"zo... | Zoom the view by a given amount. | [
"Zoom",
"the",
"view",
"by",
"a",
"given",
"amount",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L281-L305 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.set_range | def set_range(self, bounds, keep_aspect=False):
"""Zoom to fit a box."""
# a * (v0 + t) = -1
# a * (v1 + t) = +1
# =>
# a * (v1 - v0) = 2
bounds = np.asarray(bounds, dtype=np.float64)
v0 = bounds[:2]
v1 = bounds[2:]
pan = -.5 * (v0 + v1)
zo... | python | def set_range(self, bounds, keep_aspect=False):
"""Zoom to fit a box."""
# a * (v0 + t) = -1
# a * (v1 + t) = +1
# =>
# a * (v1 - v0) = 2
bounds = np.asarray(bounds, dtype=np.float64)
v0 = bounds[:2]
v1 = bounds[2:]
pan = -.5 * (v0 + v1)
zo... | [
"def",
"set_range",
"(",
"self",
",",
"bounds",
",",
"keep_aspect",
"=",
"False",
")",
":",
"# a * (v0 + t) = -1",
"# a * (v1 + t) = +1",
"# =>",
"# a * (v1 - v0) = 2",
"bounds",
"=",
"np",
".",
"asarray",
"(",
"bounds",
",",
"dtype",
"=",
"np",
".",
"float64"... | Zoom to fit a box. | [
"Zoom",
"to",
"fit",
"a",
"box",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L317-L330 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.get_range | def get_range(self):
"""Return the bounds currently visible."""
p, z = np.asarray(self.pan), np.asarray(self.zoom)
x0, y0 = -1. / z - p
x1, y1 = +1. / z - p
return (x0, y0, x1, y1) | python | def get_range(self):
"""Return the bounds currently visible."""
p, z = np.asarray(self.pan), np.asarray(self.zoom)
x0, y0 = -1. / z - p
x1, y1 = +1. / z - p
return (x0, y0, x1, y1) | [
"def",
"get_range",
"(",
"self",
")",
":",
"p",
",",
"z",
"=",
"np",
".",
"asarray",
"(",
"self",
".",
"pan",
")",
",",
"np",
".",
"asarray",
"(",
"self",
".",
"zoom",
")",
"x0",
",",
"y0",
"=",
"-",
"1.",
"/",
"z",
"-",
"p",
"x1",
",",
"... | Return the bounds currently visible. | [
"Return",
"the",
"bounds",
"currently",
"visible",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L332-L337 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.on_mouse_move | def on_mouse_move(self, event):
"""Pan and zoom with the mouse."""
if event.modifiers:
return
if event.is_dragging:
x0, y0 = self._normalize(event.press_event.pos)
x1, y1 = self._normalize(event.last_event.pos)
x, y = self._normalize(event.pos)
... | python | def on_mouse_move(self, event):
"""Pan and zoom with the mouse."""
if event.modifiers:
return
if event.is_dragging:
x0, y0 = self._normalize(event.press_event.pos)
x1, y1 = self._normalize(event.last_event.pos)
x, y = self._normalize(event.pos)
... | [
"def",
"on_mouse_move",
"(",
"self",
",",
"event",
")",
":",
"if",
"event",
".",
"modifiers",
":",
"return",
"if",
"event",
".",
"is_dragging",
":",
"x0",
",",
"y0",
"=",
"self",
".",
"_normalize",
"(",
"event",
".",
"press_event",
".",
"pos",
")",
"... | Pan and zoom with the mouse. | [
"Pan",
"and",
"zoom",
"with",
"the",
"mouse",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L386-L399 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.on_mouse_wheel | def on_mouse_wheel(self, event):
"""Zoom with the mouse wheel."""
# NOTE: not called on OS X because of touchpad
if event.modifiers:
return
dx = np.sign(event.delta[1]) * self._wheel_coeff
# Zoom toward the mouse pointer.
x0, y0 = self._normalize(event.pos)
... | python | def on_mouse_wheel(self, event):
"""Zoom with the mouse wheel."""
# NOTE: not called on OS X because of touchpad
if event.modifiers:
return
dx = np.sign(event.delta[1]) * self._wheel_coeff
# Zoom toward the mouse pointer.
x0, y0 = self._normalize(event.pos)
... | [
"def",
"on_mouse_wheel",
"(",
"self",
",",
"event",
")",
":",
"# NOTE: not called on OS X because of touchpad",
"if",
"event",
".",
"modifiers",
":",
"return",
"dx",
"=",
"np",
".",
"sign",
"(",
"event",
".",
"delta",
"[",
"1",
"]",
")",
"*",
"self",
".",
... | Zoom with the mouse wheel. | [
"Zoom",
"with",
"the",
"mouse",
"wheel",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L425-L433 | train |
kwikteam/phy | phy/plot/panzoom.py | PanZoom.on_key_press | def on_key_press(self, event):
"""Pan and zoom with the keyboard."""
# Zooming with the keyboard.
key = event.key
if event.modifiers:
return
# Pan.
if self.enable_keyboard_pan and key in self._arrows:
self._pan_keyboard(key)
# Zoom.
... | python | def on_key_press(self, event):
"""Pan and zoom with the keyboard."""
# Zooming with the keyboard.
key = event.key
if event.modifiers:
return
# Pan.
if self.enable_keyboard_pan and key in self._arrows:
self._pan_keyboard(key)
# Zoom.
... | [
"def",
"on_key_press",
"(",
"self",
",",
"event",
")",
":",
"# Zooming with the keyboard.",
"key",
"=",
"event",
".",
"key",
"if",
"event",
".",
"modifiers",
":",
"return",
"# Pan.",
"if",
"self",
".",
"enable_keyboard_pan",
"and",
"key",
"in",
"self",
".",
... | Pan and zoom with the keyboard. | [
"Pan",
"and",
"zoom",
"with",
"the",
"keyboard",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/panzoom.py#L435-L452 | train |
kwikteam/phy | tools/api.py | _replace_docstring_header | def _replace_docstring_header(paragraph):
"""Process NumPy-like function docstrings."""
# Replace Markdown headers in docstrings with light headers in bold.
paragraph = re.sub(_docstring_header_pattern,
r'*\1*',
paragraph,
)
paragrap... | python | def _replace_docstring_header(paragraph):
"""Process NumPy-like function docstrings."""
# Replace Markdown headers in docstrings with light headers in bold.
paragraph = re.sub(_docstring_header_pattern,
r'*\1*',
paragraph,
)
paragrap... | [
"def",
"_replace_docstring_header",
"(",
"paragraph",
")",
":",
"# Replace Markdown headers in docstrings with light headers in bold.",
"paragraph",
"=",
"re",
".",
"sub",
"(",
"_docstring_header_pattern",
",",
"r'*\\1*'",
",",
"paragraph",
",",
")",
"paragraph",
"=",
"re... | Process NumPy-like function docstrings. | [
"Process",
"NumPy",
"-",
"like",
"function",
"docstrings",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L47-L61 | train |
kwikteam/phy | tools/api.py | _iter_vars | def _iter_vars(mod):
"""Iterate through a list of variables define in a module's
public namespace."""
vars = sorted(var for var in dir(mod) if _is_public(var))
for var in vars:
yield getattr(mod, var) | python | def _iter_vars(mod):
"""Iterate through a list of variables define in a module's
public namespace."""
vars = sorted(var for var in dir(mod) if _is_public(var))
for var in vars:
yield getattr(mod, var) | [
"def",
"_iter_vars",
"(",
"mod",
")",
":",
"vars",
"=",
"sorted",
"(",
"var",
"for",
"var",
"in",
"dir",
"(",
"mod",
")",
"if",
"_is_public",
"(",
"var",
")",
")",
"for",
"var",
"in",
"vars",
":",
"yield",
"getattr",
"(",
"mod",
",",
"var",
")"
] | Iterate through a list of variables define in a module's
public namespace. | [
"Iterate",
"through",
"a",
"list",
"of",
"variables",
"define",
"in",
"a",
"module",
"s",
"public",
"namespace",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L145-L150 | train |
kwikteam/phy | tools/api.py | _function_header | def _function_header(subpackage, func):
"""Generate the docstring of a function."""
args = inspect.formatargspec(*inspect.getfullargspec(func))
return "{name}{args}".format(name=_full_name(subpackage, func),
args=args,
) | python | def _function_header(subpackage, func):
"""Generate the docstring of a function."""
args = inspect.formatargspec(*inspect.getfullargspec(func))
return "{name}{args}".format(name=_full_name(subpackage, func),
args=args,
) | [
"def",
"_function_header",
"(",
"subpackage",
",",
"func",
")",
":",
"args",
"=",
"inspect",
".",
"formatargspec",
"(",
"*",
"inspect",
".",
"getfullargspec",
"(",
"func",
")",
")",
"return",
"\"{name}{args}\"",
".",
"format",
"(",
"name",
"=",
"_full_name",... | Generate the docstring of a function. | [
"Generate",
"the",
"docstring",
"of",
"a",
"function",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L185-L190 | train |
kwikteam/phy | tools/api.py | _doc_method | def _doc_method(klass, func):
"""Generate the docstring of a method."""
argspec = inspect.getfullargspec(func)
# Remove first 'self' argument.
if argspec.args and argspec.args[0] == 'self':
del argspec.args[0]
args = inspect.formatargspec(*argspec)
header = "{klass}.{name}{args}".format(... | python | def _doc_method(klass, func):
"""Generate the docstring of a method."""
argspec = inspect.getfullargspec(func)
# Remove first 'self' argument.
if argspec.args and argspec.args[0] == 'self':
del argspec.args[0]
args = inspect.formatargspec(*argspec)
header = "{klass}.{name}{args}".format(... | [
"def",
"_doc_method",
"(",
"klass",
",",
"func",
")",
":",
"argspec",
"=",
"inspect",
".",
"getfullargspec",
"(",
"func",
")",
"# Remove first 'self' argument.",
"if",
"argspec",
".",
"args",
"and",
"argspec",
".",
"args",
"[",
"0",
"]",
"==",
"'self'",
":... | Generate the docstring of a method. | [
"Generate",
"the",
"docstring",
"of",
"a",
"method",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L199-L211 | train |
kwikteam/phy | tools/api.py | _doc_property | def _doc_property(klass, prop):
"""Generate the docstring of a property."""
header = "{klass}.{name}".format(klass=klass.__name__,
name=_name(prop),
)
docstring = _doc(prop)
return _concat(header, docstring) | python | def _doc_property(klass, prop):
"""Generate the docstring of a property."""
header = "{klass}.{name}".format(klass=klass.__name__,
name=_name(prop),
)
docstring = _doc(prop)
return _concat(header, docstring) | [
"def",
"_doc_property",
"(",
"klass",
",",
"prop",
")",
":",
"header",
"=",
"\"{klass}.{name}\"",
".",
"format",
"(",
"klass",
"=",
"klass",
".",
"__name__",
",",
"name",
"=",
"_name",
"(",
"prop",
")",
",",
")",
"docstring",
"=",
"_doc",
"(",
"prop",
... | Generate the docstring of a property. | [
"Generate",
"the",
"docstring",
"of",
"a",
"property",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L214-L220 | train |
kwikteam/phy | tools/api.py | _generate_paragraphs | def _generate_paragraphs(package, subpackages):
"""Generate the paragraphs of the API documentation."""
# API doc of each module.
for subpackage in _iter_subpackages(package, subpackages):
subpackage_name = subpackage.__name__
yield "## {}".format(subpackage_name)
# Subpackage doc... | python | def _generate_paragraphs(package, subpackages):
"""Generate the paragraphs of the API documentation."""
# API doc of each module.
for subpackage in _iter_subpackages(package, subpackages):
subpackage_name = subpackage.__name__
yield "## {}".format(subpackage_name)
# Subpackage doc... | [
"def",
"_generate_paragraphs",
"(",
"package",
",",
"subpackages",
")",
":",
"# API doc of each module.",
"for",
"subpackage",
"in",
"_iter_subpackages",
"(",
"package",
",",
"subpackages",
")",
":",
"subpackage_name",
"=",
"subpackage",
".",
"__name__",
"yield",
"\... | Generate the paragraphs of the API documentation. | [
"Generate",
"the",
"paragraphs",
"of",
"the",
"API",
"documentation",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/tools/api.py#L260-L289 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor._add_field_column | def _add_field_column(self, field): # pragma: no cover
"""Add a column for a given label field."""
@self.add_column(name=field)
def get_my_label(cluster_id):
return self.cluster_meta.get(field, cluster_id) | python | def _add_field_column(self, field): # pragma: no cover
"""Add a column for a given label field."""
@self.add_column(name=field)
def get_my_label(cluster_id):
return self.cluster_meta.get(field, cluster_id) | [
"def",
"_add_field_column",
"(",
"self",
",",
"field",
")",
":",
"# pragma: no cover",
"@",
"self",
".",
"add_column",
"(",
"name",
"=",
"field",
")",
"def",
"get_my_label",
"(",
"cluster_id",
")",
":",
"return",
"self",
".",
"cluster_meta",
".",
"get",
"(... | Add a column for a given label field. | [
"Add",
"a",
"column",
"for",
"a",
"given",
"label",
"field",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L234-L238 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor._emit_select | def _emit_select(self, cluster_ids, **kwargs):
"""Choose spikes from the specified clusters and emit the
`select` event on the GUI."""
# Remove non-existing clusters from the selection.
cluster_ids = self._keep_existing_clusters(cluster_ids)
logger.debug("Select cluster(s): %s.",... | python | def _emit_select(self, cluster_ids, **kwargs):
"""Choose spikes from the specified clusters and emit the
`select` event on the GUI."""
# Remove non-existing clusters from the selection.
cluster_ids = self._keep_existing_clusters(cluster_ids)
logger.debug("Select cluster(s): %s.",... | [
"def",
"_emit_select",
"(",
"self",
",",
"cluster_ids",
",",
"*",
"*",
"kwargs",
")",
":",
"# Remove non-existing clusters from the selection.",
"cluster_ids",
"=",
"self",
".",
"_keep_existing_clusters",
"(",
"cluster_ids",
")",
"logger",
".",
"debug",
"(",
"\"Sele... | Choose spikes from the specified clusters and emit the
`select` event on the GUI. | [
"Choose",
"spikes",
"from",
"the",
"specified",
"clusters",
"and",
"emit",
"the",
"select",
"event",
"on",
"the",
"GUI",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L336-L343 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor._update_cluster_view | def _update_cluster_view(self):
"""Initialize the cluster view with cluster data."""
logger.log(5, "Update the cluster view.")
cluster_ids = [int(c) for c in self.clustering.cluster_ids]
self.cluster_view.set_rows(cluster_ids) | python | def _update_cluster_view(self):
"""Initialize the cluster view with cluster data."""
logger.log(5, "Update the cluster view.")
cluster_ids = [int(c) for c in self.clustering.cluster_ids]
self.cluster_view.set_rows(cluster_ids) | [
"def",
"_update_cluster_view",
"(",
"self",
")",
":",
"logger",
".",
"log",
"(",
"5",
",",
"\"Update the cluster view.\"",
")",
"cluster_ids",
"=",
"[",
"int",
"(",
"c",
")",
"for",
"c",
"in",
"self",
".",
"clustering",
".",
"cluster_ids",
"]",
"self",
"... | Initialize the cluster view with cluster data. | [
"Initialize",
"the",
"cluster",
"view",
"with",
"cluster",
"data",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L379-L383 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor._update_similarity_view | def _update_similarity_view(self):
"""Update the similarity view with matches for the specified
clusters."""
if not self.similarity:
return
selection = self.cluster_view.selected
if not len(selection):
return
cluster_id = selection[0]
clust... | python | def _update_similarity_view(self):
"""Update the similarity view with matches for the specified
clusters."""
if not self.similarity:
return
selection = self.cluster_view.selected
if not len(selection):
return
cluster_id = selection[0]
clust... | [
"def",
"_update_similarity_view",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"similarity",
":",
"return",
"selection",
"=",
"self",
".",
"cluster_view",
".",
"selected",
"if",
"not",
"len",
"(",
"selection",
")",
":",
"return",
"cluster_id",
"=",
"se... | Update the similarity view with matches for the specified
clusters. | [
"Update",
"the",
"similarity",
"view",
"with",
"matches",
"for",
"the",
"specified",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L385-L412 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.on_cluster | def on_cluster(self, up):
"""Update the cluster views after clustering actions."""
similar = self.similarity_view.selected
# Reinitialize the cluster view if clusters have changed.
if up.added:
self._update_cluster_view()
# Select all new clusters in view 1.
... | python | def on_cluster(self, up):
"""Update the cluster views after clustering actions."""
similar = self.similarity_view.selected
# Reinitialize the cluster view if clusters have changed.
if up.added:
self._update_cluster_view()
# Select all new clusters in view 1.
... | [
"def",
"on_cluster",
"(",
"self",
",",
"up",
")",
":",
"similar",
"=",
"self",
".",
"similarity_view",
".",
"selected",
"# Reinitialize the cluster view if clusters have changed.",
"if",
"up",
".",
"added",
":",
"self",
".",
"_update_cluster_view",
"(",
")",
"# Se... | Update the cluster views after clustering actions. | [
"Update",
"the",
"cluster",
"views",
"after",
"clustering",
"actions",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L438-L488 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.select | def select(self, *cluster_ids):
"""Select a list of clusters."""
# HACK: allow for `select(1, 2, 3)` in addition to `select([1, 2, 3])`
# This makes it more convenient to select multiple clusters with
# the snippet: `:c 1 2 3` instead of `:c 1,2,3`.
if cluster_ids and isinstance(... | python | def select(self, *cluster_ids):
"""Select a list of clusters."""
# HACK: allow for `select(1, 2, 3)` in addition to `select([1, 2, 3])`
# This makes it more convenient to select multiple clusters with
# the snippet: `:c 1 2 3` instead of `:c 1,2,3`.
if cluster_ids and isinstance(... | [
"def",
"select",
"(",
"self",
",",
"*",
"cluster_ids",
")",
":",
"# HACK: allow for `select(1, 2, 3)` in addition to `select([1, 2, 3])`",
"# This makes it more convenient to select multiple clusters with",
"# the snippet: `:c 1 2 3` instead of `:c 1,2,3`.",
"if",
"cluster_ids",
"and",
... | Select a list of clusters. | [
"Select",
"a",
"list",
"of",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L556-L566 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.merge | def merge(self, cluster_ids=None, to=None):
"""Merge the selected clusters."""
if cluster_ids is None:
cluster_ids = self.selected
if len(cluster_ids or []) <= 1:
return
self.clustering.merge(cluster_ids, to=to)
self._global_history.action(self.clustering) | python | def merge(self, cluster_ids=None, to=None):
"""Merge the selected clusters."""
if cluster_ids is None:
cluster_ids = self.selected
if len(cluster_ids or []) <= 1:
return
self.clustering.merge(cluster_ids, to=to)
self._global_history.action(self.clustering) | [
"def",
"merge",
"(",
"self",
",",
"cluster_ids",
"=",
"None",
",",
"to",
"=",
"None",
")",
":",
"if",
"cluster_ids",
"is",
"None",
":",
"cluster_ids",
"=",
"self",
".",
"selected",
"if",
"len",
"(",
"cluster_ids",
"or",
"[",
"]",
")",
"<=",
"1",
":... | Merge the selected clusters. | [
"Merge",
"the",
"selected",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L575-L582 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.split | def split(self, spike_ids=None, spike_clusters_rel=0):
"""Split the selected spikes."""
if spike_ids is None:
spike_ids = self.emit('request_split', single=True)
spike_ids = np.asarray(spike_ids, dtype=np.int64)
assert spike_ids.dtype == np.int64
assert sp... | python | def split(self, spike_ids=None, spike_clusters_rel=0):
"""Split the selected spikes."""
if spike_ids is None:
spike_ids = self.emit('request_split', single=True)
spike_ids = np.asarray(spike_ids, dtype=np.int64)
assert spike_ids.dtype == np.int64
assert sp... | [
"def",
"split",
"(",
"self",
",",
"spike_ids",
"=",
"None",
",",
"spike_clusters_rel",
"=",
"0",
")",
":",
"if",
"spike_ids",
"is",
"None",
":",
"spike_ids",
"=",
"self",
".",
"emit",
"(",
"'request_split'",
",",
"single",
"=",
"True",
")",
"spike_ids",
... | Split the selected spikes. | [
"Split",
"the",
"selected",
"spikes",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L584-L599 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.get_labels | def get_labels(self, field):
"""Return the labels of all clusters, for a given field."""
return {c: self.cluster_meta.get(field, c)
for c in self.clustering.cluster_ids} | python | def get_labels(self, field):
"""Return the labels of all clusters, for a given field."""
return {c: self.cluster_meta.get(field, c)
for c in self.clustering.cluster_ids} | [
"def",
"get_labels",
"(",
"self",
",",
"field",
")",
":",
"return",
"{",
"c",
":",
"self",
".",
"cluster_meta",
".",
"get",
"(",
"field",
",",
"c",
")",
"for",
"c",
"in",
"self",
".",
"clustering",
".",
"cluster_ids",
"}"
] | Return the labels of all clusters, for a given field. | [
"Return",
"the",
"labels",
"of",
"all",
"clusters",
"for",
"a",
"given",
"field",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L610-L613 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.label | def label(self, name, value, cluster_ids=None):
"""Assign a label to clusters.
Example: `quality 3`
"""
if cluster_ids is None:
cluster_ids = self.cluster_view.selected
if not hasattr(cluster_ids, '__len__'):
cluster_ids = [cluster_ids]
if len(cl... | python | def label(self, name, value, cluster_ids=None):
"""Assign a label to clusters.
Example: `quality 3`
"""
if cluster_ids is None:
cluster_ids = self.cluster_view.selected
if not hasattr(cluster_ids, '__len__'):
cluster_ids = [cluster_ids]
if len(cl... | [
"def",
"label",
"(",
"self",
",",
"name",
",",
"value",
",",
"cluster_ids",
"=",
"None",
")",
":",
"if",
"cluster_ids",
"is",
"None",
":",
"cluster_ids",
"=",
"self",
".",
"cluster_view",
".",
"selected",
"if",
"not",
"hasattr",
"(",
"cluster_ids",
",",
... | Assign a label to clusters.
Example: `quality 3` | [
"Assign",
"a",
"label",
"to",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L615-L628 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.move | def move(self, group, cluster_ids=None):
"""Assign a group to some clusters.
Example: `good`
"""
if isinstance(cluster_ids, string_types):
logger.warn("The list of clusters should be a list of integers, "
"not a string.")
return
s... | python | def move(self, group, cluster_ids=None):
"""Assign a group to some clusters.
Example: `good`
"""
if isinstance(cluster_ids, string_types):
logger.warn("The list of clusters should be a list of integers, "
"not a string.")
return
s... | [
"def",
"move",
"(",
"self",
",",
"group",
",",
"cluster_ids",
"=",
"None",
")",
":",
"if",
"isinstance",
"(",
"cluster_ids",
",",
"string_types",
")",
":",
"logger",
".",
"warn",
"(",
"\"The list of clusters should be a list of integers, \"",
"\"not a string.\"",
... | Assign a group to some clusters.
Example: `good` | [
"Assign",
"a",
"group",
"to",
"some",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L630-L640 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.next | def next(self):
"""Select the next cluster."""
if not self.selected:
self.cluster_view.next()
else:
self.similarity_view.next() | python | def next(self):
"""Select the next cluster."""
if not self.selected:
self.cluster_view.next()
else:
self.similarity_view.next() | [
"def",
"next",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"selected",
":",
"self",
".",
"cluster_view",
".",
"next",
"(",
")",
"else",
":",
"self",
".",
"similarity_view",
".",
"next",
"(",
")"
] | Select the next cluster. | [
"Select",
"the",
"next",
"cluster",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L670-L675 | train |
kwikteam/phy | phy/cluster/supervisor.py | Supervisor.save | def save(self):
"""Save the manual clustering back to disk."""
spike_clusters = self.clustering.spike_clusters
groups = {c: self.cluster_meta.get('group', c) or 'unsorted'
for c in self.clustering.cluster_ids}
# List of tuples (field_name, dictionary).
labels = ... | python | def save(self):
"""Save the manual clustering back to disk."""
spike_clusters = self.clustering.spike_clusters
groups = {c: self.cluster_meta.get('group', c) or 'unsorted'
for c in self.clustering.cluster_ids}
# List of tuples (field_name, dictionary).
labels = ... | [
"def",
"save",
"(",
"self",
")",
":",
"spike_clusters",
"=",
"self",
".",
"clustering",
".",
"spike_clusters",
"groups",
"=",
"{",
"c",
":",
"self",
".",
"cluster_meta",
".",
"get",
"(",
"'group'",
",",
"c",
")",
"or",
"'unsorted'",
"for",
"c",
"in",
... | Save the manual clustering back to disk. | [
"Save",
"the",
"manual",
"clustering",
"back",
"to",
"disk",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/supervisor.py#L692-L704 | train |
kwikteam/phy | phy/cluster/_utils.py | create_cluster_meta | def create_cluster_meta(cluster_groups):
"""Return a ClusterMeta instance with cluster group support."""
meta = ClusterMeta()
meta.add_field('group')
cluster_groups = cluster_groups or {}
data = {c: {'group': v} for c, v in cluster_groups.items()}
meta.from_dict(data)
return meta | python | def create_cluster_meta(cluster_groups):
"""Return a ClusterMeta instance with cluster group support."""
meta = ClusterMeta()
meta.add_field('group')
cluster_groups = cluster_groups or {}
data = {c: {'group': v} for c, v in cluster_groups.items()}
meta.from_dict(data)
return meta | [
"def",
"create_cluster_meta",
"(",
"cluster_groups",
")",
":",
"meta",
"=",
"ClusterMeta",
"(",
")",
"meta",
".",
"add_field",
"(",
"'group'",
")",
"cluster_groups",
"=",
"cluster_groups",
"or",
"{",
"}",
"data",
"=",
"{",
"c",
":",
"{",
"'group'",
":",
... | Return a ClusterMeta instance with cluster group support. | [
"Return",
"a",
"ClusterMeta",
"instance",
"with",
"cluster",
"group",
"support",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L35-L44 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.add_field | def add_field(self, name, default_value=None):
"""Add a field with an optional default value."""
self._fields[name] = default_value
def func(cluster):
return self.get(name, cluster)
setattr(self, name, func) | python | def add_field(self, name, default_value=None):
"""Add a field with an optional default value."""
self._fields[name] = default_value
def func(cluster):
return self.get(name, cluster)
setattr(self, name, func) | [
"def",
"add_field",
"(",
"self",
",",
"name",
",",
"default_value",
"=",
"None",
")",
":",
"self",
".",
"_fields",
"[",
"name",
"]",
"=",
"default_value",
"def",
"func",
"(",
"cluster",
")",
":",
"return",
"self",
".",
"get",
"(",
"name",
",",
"clust... | Add a field with an optional default value. | [
"Add",
"a",
"field",
"with",
"an",
"optional",
"default",
"value",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L116-L123 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.set | def set(self, field, clusters, value, add_to_stack=True):
"""Set the value of one of several clusters."""
# Add the field if it doesn't exist.
if field not in self._fields:
self.add_field(field)
assert field in self._fields
clusters = _as_list(clusters)
for c... | python | def set(self, field, clusters, value, add_to_stack=True):
"""Set the value of one of several clusters."""
# Add the field if it doesn't exist.
if field not in self._fields:
self.add_field(field)
assert field in self._fields
clusters = _as_list(clusters)
for c... | [
"def",
"set",
"(",
"self",
",",
"field",
",",
"clusters",
",",
"value",
",",
"add_to_stack",
"=",
"True",
")",
":",
"# Add the field if it doesn't exist.",
"if",
"field",
"not",
"in",
"self",
".",
"_fields",
":",
"self",
".",
"add_field",
"(",
"field",
")"... | Set the value of one of several clusters. | [
"Set",
"the",
"value",
"of",
"one",
"of",
"several",
"clusters",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L140-L163 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.get | def get(self, field, cluster):
"""Retrieve the value of one cluster."""
if _is_list(cluster):
return [self.get(field, c) for c in cluster]
assert field in self._fields
default = self._fields[field]
return self._data.get(cluster, {}).get(field, default) | python | def get(self, field, cluster):
"""Retrieve the value of one cluster."""
if _is_list(cluster):
return [self.get(field, c) for c in cluster]
assert field in self._fields
default = self._fields[field]
return self._data.get(cluster, {}).get(field, default) | [
"def",
"get",
"(",
"self",
",",
"field",
",",
"cluster",
")",
":",
"if",
"_is_list",
"(",
"cluster",
")",
":",
"return",
"[",
"self",
".",
"get",
"(",
"field",
",",
"c",
")",
"for",
"c",
"in",
"cluster",
"]",
"assert",
"field",
"in",
"self",
".",... | Retrieve the value of one cluster. | [
"Retrieve",
"the",
"value",
"of",
"one",
"cluster",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L165-L171 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.set_from_descendants | def set_from_descendants(self, descendants):
"""Update metadata of some clusters given the metadata of their
ascendants."""
for field in self.fields:
# This gives a set of metadata values of all the parents
# of any new cluster.
candidates = defaultdict(set)
... | python | def set_from_descendants(self, descendants):
"""Update metadata of some clusters given the metadata of their
ascendants."""
for field in self.fields:
# This gives a set of metadata values of all the parents
# of any new cluster.
candidates = defaultdict(set)
... | [
"def",
"set_from_descendants",
"(",
"self",
",",
"descendants",
")",
":",
"for",
"field",
"in",
"self",
".",
"fields",
":",
"# This gives a set of metadata values of all the parents",
"# of any new cluster.",
"candidates",
"=",
"defaultdict",
"(",
"set",
")",
"for",
"... | Update metadata of some clusters given the metadata of their
ascendants. | [
"Update",
"metadata",
"of",
"some",
"clusters",
"given",
"the",
"metadata",
"of",
"their",
"ascendants",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L173-L191 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.undo | def undo(self):
"""Undo the last metadata change.
Returns
-------
up : UpdateInfo instance
"""
args = self._undo_stack.back()
if args is None:
return
self._data = deepcopy(self._data_base)
for clusters, field, value, up, undo_state i... | python | def undo(self):
"""Undo the last metadata change.
Returns
-------
up : UpdateInfo instance
"""
args = self._undo_stack.back()
if args is None:
return
self._data = deepcopy(self._data_base)
for clusters, field, value, up, undo_state i... | [
"def",
"undo",
"(",
"self",
")",
":",
"args",
"=",
"self",
".",
"_undo_stack",
".",
"back",
"(",
")",
"if",
"args",
"is",
"None",
":",
"return",
"self",
".",
"_data",
"=",
"deepcopy",
"(",
"self",
".",
"_data_base",
")",
"for",
"clusters",
",",
"fi... | Undo the last metadata change.
Returns
-------
up : UpdateInfo instance | [
"Undo",
"the",
"last",
"metadata",
"change",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L194-L217 | train |
kwikteam/phy | phy/cluster/_utils.py | ClusterMeta.redo | def redo(self):
"""Redo the next metadata change.
Returns
-------
up : UpdateInfo instance
"""
args = self._undo_stack.forward()
if args is None:
return
clusters, field, value, up, undo_state = args
self.set(field, clusters, value, ad... | python | def redo(self):
"""Redo the next metadata change.
Returns
-------
up : UpdateInfo instance
"""
args = self._undo_stack.forward()
if args is None:
return
clusters, field, value, up, undo_state = args
self.set(field, clusters, value, ad... | [
"def",
"redo",
"(",
"self",
")",
":",
"args",
"=",
"self",
".",
"_undo_stack",
".",
"forward",
"(",
")",
"if",
"args",
"is",
"None",
":",
"return",
"clusters",
",",
"field",
",",
"value",
",",
"up",
",",
"undo_state",
"=",
"args",
"self",
".",
"set... | Redo the next metadata change.
Returns
-------
up : UpdateInfo instance | [
"Redo",
"the",
"next",
"metadata",
"change",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/cluster/_utils.py#L219-L237 | train |
kwikteam/phy | phy/plot/utils.py | _get_boxes | def _get_boxes(pos, size=None, margin=0, keep_aspect_ratio=True):
"""Generate non-overlapping boxes in NDC from a set of positions."""
# Get x, y.
pos = np.asarray(pos, dtype=np.float64)
x, y = pos.T
x = x[:, np.newaxis]
y = y[:, np.newaxis]
w, h = size if size is not None else _get_box_si... | python | def _get_boxes(pos, size=None, margin=0, keep_aspect_ratio=True):
"""Generate non-overlapping boxes in NDC from a set of positions."""
# Get x, y.
pos = np.asarray(pos, dtype=np.float64)
x, y = pos.T
x = x[:, np.newaxis]
y = y[:, np.newaxis]
w, h = size if size is not None else _get_box_si... | [
"def",
"_get_boxes",
"(",
"pos",
",",
"size",
"=",
"None",
",",
"margin",
"=",
"0",
",",
"keep_aspect_ratio",
"=",
"True",
")",
":",
"# Get x, y.",
"pos",
"=",
"np",
".",
"asarray",
"(",
"pos",
",",
"dtype",
"=",
"np",
".",
"float64",
")",
"x",
","... | Generate non-overlapping boxes in NDC from a set of positions. | [
"Generate",
"non",
"-",
"overlapping",
"boxes",
"in",
"NDC",
"from",
"a",
"set",
"of",
"positions",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/utils.py#L76-L105 | train |
kwikteam/phy | phy/plot/utils.py | _get_texture | def _get_texture(arr, default, n_items, from_bounds):
"""Prepare data to be uploaded as a texture.
The from_bounds must be specified.
"""
if not hasattr(default, '__len__'): # pragma: no cover
default = [default]
n_cols = len(default)
if arr is None: # pragma: no cover
arr = ... | python | def _get_texture(arr, default, n_items, from_bounds):
"""Prepare data to be uploaded as a texture.
The from_bounds must be specified.
"""
if not hasattr(default, '__len__'): # pragma: no cover
default = [default]
n_cols = len(default)
if arr is None: # pragma: no cover
arr = ... | [
"def",
"_get_texture",
"(",
"arr",
",",
"default",
",",
"n_items",
",",
"from_bounds",
")",
":",
"if",
"not",
"hasattr",
"(",
"default",
",",
"'__len__'",
")",
":",
"# pragma: no cover",
"default",
"=",
"[",
"default",
"]",
"n_cols",
"=",
"len",
"(",
"de... | Prepare data to be uploaded as a texture.
The from_bounds must be specified. | [
"Prepare",
"data",
"to",
"be",
"uploaded",
"as",
"a",
"texture",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/utils.py#L122-L147 | train |
kwikteam/phy | phy/plot/utils.py | _get_array | def _get_array(val, shape, default=None, dtype=np.float64):
"""Ensure an object is an array with the specified shape."""
assert val is not None or default is not None
if hasattr(val, '__len__') and len(val) == 0: # pragma: no cover
val = None
# Do nothing if the array is already correct.
if... | python | def _get_array(val, shape, default=None, dtype=np.float64):
"""Ensure an object is an array with the specified shape."""
assert val is not None or default is not None
if hasattr(val, '__len__') and len(val) == 0: # pragma: no cover
val = None
# Do nothing if the array is already correct.
if... | [
"def",
"_get_array",
"(",
"val",
",",
"shape",
",",
"default",
"=",
"None",
",",
"dtype",
"=",
"np",
".",
"float64",
")",
":",
"assert",
"val",
"is",
"not",
"None",
"or",
"default",
"is",
"not",
"None",
"if",
"hasattr",
"(",
"val",
",",
"'__len__'",
... | Ensure an object is an array with the specified shape. | [
"Ensure",
"an",
"object",
"is",
"an",
"array",
"with",
"the",
"specified",
"shape",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/utils.py#L150-L168 | train |
kwikteam/phy | phy/plot/utils.py | _get_index | def _get_index(n_items, item_size, n):
"""Prepare an index attribute for GPU uploading."""
index = np.arange(n_items)
index = np.repeat(index, item_size)
index = index.astype(np.float64)
assert index.shape == (n,)
return index | python | def _get_index(n_items, item_size, n):
"""Prepare an index attribute for GPU uploading."""
index = np.arange(n_items)
index = np.repeat(index, item_size)
index = index.astype(np.float64)
assert index.shape == (n,)
return index | [
"def",
"_get_index",
"(",
"n_items",
",",
"item_size",
",",
"n",
")",
":",
"index",
"=",
"np",
".",
"arange",
"(",
"n_items",
")",
"index",
"=",
"np",
".",
"repeat",
"(",
"index",
",",
"item_size",
")",
"index",
"=",
"index",
".",
"astype",
"(",
"n... | Prepare an index attribute for GPU uploading. | [
"Prepare",
"an",
"index",
"attribute",
"for",
"GPU",
"uploading",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/utils.py#L225-L231 | train |
kwikteam/phy | phy/plot/utils.py | _load_shader | def _load_shader(filename):
"""Load a shader file."""
curdir = op.dirname(op.realpath(__file__))
glsl_path = op.join(curdir, 'glsl')
path = op.join(glsl_path, filename)
with open(path, 'r') as f:
return f.read() | python | def _load_shader(filename):
"""Load a shader file."""
curdir = op.dirname(op.realpath(__file__))
glsl_path = op.join(curdir, 'glsl')
path = op.join(glsl_path, filename)
with open(path, 'r') as f:
return f.read() | [
"def",
"_load_shader",
"(",
"filename",
")",
":",
"curdir",
"=",
"op",
".",
"dirname",
"(",
"op",
".",
"realpath",
"(",
"__file__",
")",
")",
"glsl_path",
"=",
"op",
".",
"join",
"(",
"curdir",
",",
"'glsl'",
")",
"path",
"=",
"op",
".",
"join",
"(... | Load a shader file. | [
"Load",
"a",
"shader",
"file",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/plot/utils.py#L242-L248 | train |
kwikteam/phy | phy/utils/_color.py | _random_color | def _random_color(h_range=(0., 1.),
s_range=(.5, 1.),
v_range=(.5, 1.),
):
"""Generate a random RGB color."""
h, s, v = uniform(*h_range), uniform(*s_range), uniform(*v_range)
r, g, b = hsv_to_rgb(np.array([[[h, s, v]]])).flat
return r, g, b | python | def _random_color(h_range=(0., 1.),
s_range=(.5, 1.),
v_range=(.5, 1.),
):
"""Generate a random RGB color."""
h, s, v = uniform(*h_range), uniform(*s_range), uniform(*v_range)
r, g, b = hsv_to_rgb(np.array([[[h, s, v]]])).flat
return r, g, b | [
"def",
"_random_color",
"(",
"h_range",
"=",
"(",
"0.",
",",
"1.",
")",
",",
"s_range",
"=",
"(",
".5",
",",
"1.",
")",
",",
"v_range",
"=",
"(",
".5",
",",
"1.",
")",
",",
")",
":",
"h",
",",
"s",
",",
"v",
"=",
"uniform",
"(",
"*",
"h_ran... | Generate a random RGB color. | [
"Generate",
"a",
"random",
"RGB",
"color",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/_color.py#L18-L25 | train |
kwikteam/phy | phy/utils/_color.py | _is_bright | def _is_bright(rgb):
"""Return whether a RGB color is bright or not."""
r, g, b = rgb
gray = 0.299 * r + 0.587 * g + 0.114 * b
return gray >= .5 | python | def _is_bright(rgb):
"""Return whether a RGB color is bright or not."""
r, g, b = rgb
gray = 0.299 * r + 0.587 * g + 0.114 * b
return gray >= .5 | [
"def",
"_is_bright",
"(",
"rgb",
")",
":",
"r",
",",
"g",
",",
"b",
"=",
"rgb",
"gray",
"=",
"0.299",
"*",
"r",
"+",
"0.587",
"*",
"g",
"+",
"0.114",
"*",
"b",
"return",
"gray",
">=",
".5"
] | Return whether a RGB color is bright or not. | [
"Return",
"whether",
"a",
"RGB",
"color",
"is",
"bright",
"or",
"not",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/_color.py#L28-L32 | train |
kwikteam/phy | phy/utils/_types.py | _bunchify | def _bunchify(b):
"""Ensure all dict elements are Bunch."""
assert isinstance(b, dict)
b = Bunch(b)
for k in b:
if isinstance(b[k], dict):
b[k] = Bunch(b[k])
return b | python | def _bunchify(b):
"""Ensure all dict elements are Bunch."""
assert isinstance(b, dict)
b = Bunch(b)
for k in b:
if isinstance(b[k], dict):
b[k] = Bunch(b[k])
return b | [
"def",
"_bunchify",
"(",
"b",
")",
":",
"assert",
"isinstance",
"(",
"b",
",",
"dict",
")",
"b",
"=",
"Bunch",
"(",
"b",
")",
"for",
"k",
"in",
"b",
":",
"if",
"isinstance",
"(",
"b",
"[",
"k",
"]",
",",
"dict",
")",
":",
"b",
"[",
"k",
"]"... | Ensure all dict elements are Bunch. | [
"Ensure",
"all",
"dict",
"elements",
"are",
"Bunch",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/_types.py#L34-L41 | train |
kwikteam/phy | phy/utils/_types.py | _as_list | def _as_list(obj):
"""Ensure an object is a list."""
if obj is None:
return None
elif isinstance(obj, string_types):
return [obj]
elif isinstance(obj, tuple):
return list(obj)
elif not hasattr(obj, '__len__'):
return [obj]
else:
return obj | python | def _as_list(obj):
"""Ensure an object is a list."""
if obj is None:
return None
elif isinstance(obj, string_types):
return [obj]
elif isinstance(obj, tuple):
return list(obj)
elif not hasattr(obj, '__len__'):
return [obj]
else:
return obj | [
"def",
"_as_list",
"(",
"obj",
")",
":",
"if",
"obj",
"is",
"None",
":",
"return",
"None",
"elif",
"isinstance",
"(",
"obj",
",",
"string_types",
")",
":",
"return",
"[",
"obj",
"]",
"elif",
"isinstance",
"(",
"obj",
",",
"tuple",
")",
":",
"return",... | Ensure an object is a list. | [
"Ensure",
"an",
"object",
"is",
"a",
"list",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/_types.py#L67-L78 | train |
kwikteam/phy | phy/utils/_types.py | _as_array | def _as_array(arr, dtype=None):
"""Convert an object to a numerical NumPy array.
Avoid a copy if possible.
"""
if arr is None:
return None
if isinstance(arr, np.ndarray) and dtype is None:
return arr
if isinstance(arr, integer_types + (float,)):
arr = [arr]
out = np... | python | def _as_array(arr, dtype=None):
"""Convert an object to a numerical NumPy array.
Avoid a copy if possible.
"""
if arr is None:
return None
if isinstance(arr, np.ndarray) and dtype is None:
return arr
if isinstance(arr, integer_types + (float,)):
arr = [arr]
out = np... | [
"def",
"_as_array",
"(",
"arr",
",",
"dtype",
"=",
"None",
")",
":",
"if",
"arr",
"is",
"None",
":",
"return",
"None",
"if",
"isinstance",
"(",
"arr",
",",
"np",
".",
"ndarray",
")",
"and",
"dtype",
"is",
"None",
":",
"return",
"arr",
"if",
"isinst... | Convert an object to a numerical NumPy array.
Avoid a copy if possible. | [
"Convert",
"an",
"object",
"to",
"a",
"numerical",
"NumPy",
"array",
"."
] | 7e9313dc364304b7d2bd03b92938347343703003 | https://github.com/kwikteam/phy/blob/7e9313dc364304b7d2bd03b92938347343703003/phy/utils/_types.py#L85-L104 | train |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.