MeasurePointList#

Measurements on a subset of points in large arrays.

Paralllel measuremnts at specified points of the data only. Useful to speed up processing in large arrays and only a smaller number of measurement points.

See also

ClearMap.Analysis.Measurements

find_smaller_than_fraction(source, points, search, fraction, sink=None, processes=None, verbose=False)[source]#

Find index in local search indices with a voxel with value smaller than a fraction of the value of the center voxel for a list of points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
fractionfloat: Search for first voxel in local area with value smaller than this fraction of the center value.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the first search index with voxel below the fraction of the center value.

find_smaller_than_value(source, points, search, value, sink=None, processes=None, verbose=False)[source]#

Find index in local search indices with a voxel with value smaller than a specified value for a list of points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
valuefloat: Search for first voxel in local area with value smaller than this value.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the first search index with voxel below value.

find_smaller_than_values(source, points, search, values, sink=None, processes=None, verbose=False)[source]#

Find index in local search indices with a voxel with value smaller than a fraction of the value of the center voxel for a list of points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
fractionfloat: Search for first voxel in local area with value smaller than this fraction of the center value.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the first search index with voxel below the fraction of the center value.

measure_max(source, points, search, max_search_indices, sink=None, processes=None, verbose=False)[source]#

Find local maximum in a large array for a list of center points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
max_search_indicesarray: The maximal index in the search array for each point to use.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the local maxima.

measure_mean(source, points, search, max_search_indices, sink=None, processes=None, verbose=False)[source]#

Find local mean in a large array for a list of center points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
max_search_indicesarray: The maximal index in the search array for each point to use.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the local mean.

measure_min(source, points, search, max_search_indices, sink=None, processes=None, verbose=False)[source]#

Find local minimum in a large array for a list of center points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
max_search_indicesarray: The maximal index in the search array for each point to use.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the local minima.

measure_sum(source, points, search, max_search_indices, sink=None, processes=None, verbose=False)[source]#

Find local mean in a large array for a list of center points.

Arguments

sourcearray: Data source.
pointsarray: List of linear indices of center points.
searcharray: List of linear indices to add to the center index defining the local search area.
max_search_indicesarray: The maximal index in the search array for each point to use.
sinkarray or None: Optional sink for result indices.
processesint or None: Number of processes to use.
verbosebool: If True, print progress info.

Returns

sinkarray: Linear array with length of points containing the local mean.

test()[source]#