statebuilder.helpers

Functions:

• make_connectivity_state_map –

  Create a Neuroglancer state with input and output synapses.

• make_line_state –

  Generate a state builder that puts line segments from two columns with a linked segmentaton id

• make_neuron_neuroglancer_link –

  Create a Neuroglancer state with a neuron and optionally its inputs and outputs.

• make_point_state –

  Generate a state builder that puts points on a single column with a linked segmentaton id

• sort_dataframe_by_root_id –

  Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.

make_connectivity_state_map(client, show_inputs=True, show_outputs=True, point_column='ctr_pt_position', input_root_id_col='pre_pt_root_id', output_root_id_col='post_pt_root_id', dataframe_resolution_input=None, dataframe_resolution_output=None, input_layer_name='syns_in', output_layer_name='syns_out', input_layer_color=DEFAULT_POSTSYN_COLOR, output_layer_color=DEFAULT_PRESYN_COLOR, input_shader=True, output_shader=True, selected_alpha=None, alpha_3d=None, mesh_silhouette=None)

Create a Neuroglancer state with input and output synapses.

Parameters:

• client (CAVEclient) –

  CAVEclient configured for the datastack desired

• show_inputs (bool, default: True ) –

  Whether to show input synapses, by default True

• show_outputs (bool, default: True ) –

  Whether to show output synapses, by default True

• point_column (str, default: 'ctr_pt_position' ) –

  Column in the dataframe to use for point positions, by default "ctr_pt_position"

• input_root_id_col (str, default: 'pre_pt_root_id' ) –

  Column in the dataframe to use for input synapse root ids, by default "pre_pt_root_id"

• output_root_id_col (str, default: 'post_pt_root_id' ) –

  Column in the dataframe to use for output synapse root ids, by default "post_pt_root_id"

• dataframe_resolution_input (Optional[list], default: None ) –

  Resolution of the input dataframe, by default None

• dataframe_resolution_output (Optional[list], default: None ) –

  Resolution of the output dataframe, by default None

• input_layer_name (str, default: 'syns_in' ) –

  Name of the input layer, by default "syns_in"

• output_layer_name (str, default: 'syns_out' ) –

  Name of the output layer, by default "syns_out"

• input_layer_color (Union[tuple, str], default: DEFAULT_POSTSYN_COLOR ) –

  Color of the input layer, by default "turquoise"

• output_layer_color (Union[tuple, str], default: DEFAULT_PRESYN_COLOR ) –

  Color of the output layer, by default "tomato"

• input_shader (Optional[Union[bool, str]], default: True ) –

  Shader to use for input synapses, by default None.

• output_shader (Optional[Union[bool, str]], default: True ) –

  Shader to use for output synapses, by default None (uses default shader)

• selected_alpha (Optional[float], default: None ) –

  Alpha value for selected segments in the 2d view, by default None (uses default value)

• alpha_3d (Optional[float], default: None ) –

  Alpha value for meshes, by default None (uses default value)

• mesh_silhouette (Optional[float], default: None ) –

  Mesh silhouette value, by default None (uses default value)

Returns:

• ViewerState –

  A Neuroglancer ViewerState with input and output synapses configured.

make_line_state(client, data=None, point_a_column='pre_pt_position', point_b_column='post_pt_position', segment_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, tags=None, layer_name='lines', shader=True, selected_alpha=None, alpha_3d=None, mesh_silhouette=None)

Generate a state builder that puts line segments from two columns with a linked segmentaton id

Parameters:

• client (CAVEclient) –

  CAVEclient configured for the datastack desired

• data (Optional[DataFrame], default: None ) –

  Dataframe to use for points, by default None. If None, a simple DataMap will be used with no key. Fill in the resulting state with viewer.map(df).

• point_a_column (str, default: 'pre_pt_position' ) –

  Column in the dataframe to use for line start positions, by default "pre_pt_position"

• point_b_column (str, default: 'post_pt_position' ) –

  Column in the dataframe to use for line end, by default "post_pt_position"

• segment_column (str, default: 'pt_root_id' ) –

  Column in the dataframe to use for segment ids, by default "pt_root_id"

• description_column (Optional[str], default: None ) –

  Column in the dataframe to use for point descriptions, by default None

• tag_column (Optional[str], default: None ) –

  Column in the dataframe to use for tags, by default None

• data_resolution (Optional[list], default: None ) –

  Resolution of the data, by default None

• tags (Optional[list], default: None ) –

  List of tags to apply to the points, by default None

• layer_name (str, default: 'lines' ) –

  Name of the layer to create, by default "Points"

• shader (Optional[Union[bool, str]], default: True ) –

  Shader to use for the points, by default True (uses default shader)

• selected_alpha (Optional[float], default: None ) –

  Alpha value for selected segments in the 2D view, by default None (uses default value)

• alpha_3d (Optional[float], default: None ) –

  Alpha value for meshes, by default None (uses default value)

• mesh_silhouette (Optional[float], default: None ) –

  Mesh silhouette value, by default None (uses default value)

Returns:

• ViewerState ( ViewerState ) –

  A viewerstate to make points with linked segmentations

make_neuron_neuroglancer_link(client, root_ids, return_as='link', shorten='if_long', show_inputs=True, show_outputs=True, point_column='ctr_pt_position', target_url=None, target_site=None, timestamp=None, infer_coordinates=True)

Create a Neuroglancer state with a neuron and optionally its inputs and outputs.

Parameters:

• client (CAVEclient) –

  CAVEclient configured for the datastack desired

• root_ids (Union[int, list[int]]) –

  Root IDs of the neuron to visualize. Can be a single ID or a list of IDs.

• return_as (Literal['link', 'dict', 'json', 'url'], default: 'link' ) –

  Format to return the Neuroglancer state, by default "link". Options are "link", "dict", "json", or "url".

• shorten (Literal['never', 'always', 'if_long'], default: 'if_long' ) –

  Whether to shorten the URL if it is long, by default "if_long". Options are "never", "always", or "if_long".

• show_inputs (bool, default: True ) –

  Whether to show input synapses, by default True

• show_outputs (bool, default: True ) –

  Whether to show output synapses, by default True

• point_column (str, default: 'ctr_pt_position' ) –

  Column in the dataframe to use for point positions, by default "ctr_pt_position"

• target_url (Optional[str], default: None ) –

  Target URL to use for the Neuroglancer link, by default None. If None, the default CAVEclient URL will be used.

• target_site (Optional[str], default: None ) –

  Target site to use for the Neuroglancer link, by default None. If None, the default CAVEclient site will be used.

• timestamp (Optional[datetime], default: None ) –

  Timestamp to use for the query, by default None. If None, the current time will be used.

• infer_coordinates (bool, default: True ) –

  Whether to infer coordinates from the data, by default True.

Returns:

• Neuroglancer state in the specified format. –

make_point_state(client, data=None, point_column='pt_position', segment_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, tags=None, layer_name='Points', shader=True, selected_alpha=None, alpha_3d=None, mesh_silhouette=None)

Generate a state builder that puts points on a single column with a linked segmentaton id

Parameters:

• client (CAVEclient) –

  CAVEclient configured for the datastack desired

• data (Optional[DataFrame], default: None ) –

  Dataframe to use for points, by default None. If None, a simple DataMap will be used with no key. Fill in the resulting state with viewer.map(df).

• point_column (str, default: 'pt_position' ) –

  Column in the dataframe to use for point positions, by default "pt_position"

• segment_column (str, default: 'pt_root_id' ) –

  Column in the dataframe to use for segment ids, by default "pt_root_id"

• description_column (Optional[str], default: None ) –

  Column in the dataframe to use for point descriptions, by default None

• tag_column (Optional[str], default: None ) –

  Column in the dataframe to use for tags, by default None

• data_resolution (Optional[list], default: None ) –

  Resolution of the data, by default None

• tags (Optional[list], default: None ) –

  List of tags to apply to the points, by default None

• layer_name (str, default: 'Points' ) –

  Name of the layer to create, by default "Points"

• shader (Optional[Union[bool, str]], default: True ) –

  Shader to use for the points, by default True (uses default shader)

• selected_alpha (Optional[float], default: None ) –

  Alpha value for selected segments in the 2D view, by default None (uses default value)

• alpha_3d (Optional[float], default: None ) –

  Alpha value for meshes, by default None (uses default value)

• mesh_silhouette (Optional[float], default: None ) –

  Mesh silhouette value, by default None (uses default value)

Returns:

• ViewerState ( ViewerState ) –

  A viewerstate to make points with linked segmentations

sort_dataframe_by_root_id(df, root_id_column, ascending=False, num_column='n_times', drop=False)

Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.

Parameters:

• df (DataFrame) –

  dataframe to sort

• root_id_column (str) –

  Column name to use for sorting root ids

• ascending (bool, default: False ) –

  Whether to sort ascending (lowest count to highest) or not, by default False

• num_column (str, default: 'n_times' ) –

  Temporary column name to use for count information, by default 'n_times'

• drop (bool, default: False ) –

  If True, drop the additional column when returning.

Returns:

• DataFrame –