vis_tools.SpatialReports module

SpatialReports.py

This class is a collection class that keeps track of all the SpatialReport_* files in a given directory. It is used by VisSet.

Usage:

reports = SpatialReports("output/")
print reports

class vis_tools.SpatialReports.SpatialReports(spatial_dir='', verbose=False)

Bases: object

Collection class for a set of spatial reports.

The class is constructed with the directory in which SpatialReport_* files reside. Thereafter the public data members described below, and the various accessor functions, can be used to get access to the list.

Additionally, since SpatialReports implements __len__, __iter__, and

__getitem__, the SpatialReports object can be treated as a list:, e.g.:

spatial_reports = SpatialReports("/output")
path = spatial_reports[0]

Public members:

source_dir (str): The source directory used to construct the SpatialReports object.

paths (array): Array of strings with paths to the SpatialReport_* files.

properties (dict): Dictionary<friendlyName, dict<key,value>> of additional properties to associate with each SpatialBinary file path. Currently these are unused, but will be used in an upcoming version.

k_spatial_filename_glob = 'SpatialReport*_*.bin'

k_spatial_leaf_re = '^SpatialReport[^_]*_(.*)'

get(index)

Returns detailed information on spatial binary by index.

Returns:

An object containing the name, friendly name, and path (url) to the spatial binary at the provided index.

Return type:

obj

Parameters:

index (int) – Index, 0-based, into path list.

add(report_path)

Manually add a spatial binary to the list.

This method can be used to manually add a spatial binary to the list even if it is not in the source_dir where spatial_binaries normally live. This is useful for adding a programmatically-generated spatial binary to the list. Such generated spatial binaries are generally located in the preprocessing script’s products directory.

Example:

reports = SpatialReports("output/")
reports.add(path.join(k_products_dir,
    'SpatialReport_Infectious_Vector_Count'))

Returns:

None.

Parameters:

• report_path (str) – The path to the spatial binary. Note that this

• source_dir. (path need not be within) –

emit_object()

Emits an object used by VisSet to represent spatial binary channels.

Result:

object: A Dictionary<friendly_name, file_path> for the spatial binaries found in the target directory.

Parameters:

None. –

emit_object_json()

Emits the JSON for the object from emit_object.

Result:

str: JSON representation of the emit_object() result.

Parameters:

None. –

remove(friendly_name)

Removes a spatial binary from the list by friendly name.

Returns:

None.

Parameters:

• friendly_name (str) – The friendly name of the spatial binary path

• E.g. (to remove.) –

• SpatialReport_Adult_Vectors (for) –

• friendly (the) –

• Vectors". (name is "Adult) –