topostats

Topostats.

Subpackages

• topostats.logs
  • topostats.logs.logs
• topostats.tracing
  • topostats.tracing.dnacurvature
  • topostats.tracing.dnatracing
  • topostats.tracing.skeletonize
  • topostats.tracing.tracingfuncs

Submodules

• topostats.__main__
• topostats.entry_point
• topostats.filters
• topostats.grains
• topostats.grainstats
• topostats.io
• topostats.plotting
• topostats.plottingfuncs
• topostats.processing
• topostats.run_topostats
• topostats.scars
• topostats.statistics
• topostats.theme
• topostats.thresholds
• topostats.utils
• topostats.validation

Package Contents

Classes

Colormap

Class for setting the Colormap.

Functions

setup_logger(→ logging.Logger)

Logger setup.

Attributes

LOGGER
release
__version__

topostats.setup_logger(log_name: str = LOGGER_NAME) → logging.Logger

Logger setup.

The logger for the module is initialised when the module is loaded (as this functions is called from __init__.py). This creates two stream handlers, one for general output and one for errors which are formatted differently (there is greater information in the error formatter). To use in modules import the ‘LOGGER_NAME’ and create a logger as shown in the Examples, it will inherit the formatting and direction of messages to the correct stream.

Parameters:

log_name (str) – Name under which logging information occurs.

Returns:

Logger object.

Return type:

logging.Logger

Examples

To use the logger in (sub-)modules have the following.

import logging from topostats.logs.logs import LOGGER_NAME

LOGGER = logging.getLogger(LOGGER_NAME)

LOGGER.info(‘This is a log message.’)

class topostats.Colormap(name: str = 'nanoscope')

Class for setting the Colormap.

Parameters:

name (str) – Name of colormap to use.

__str__() → str

Return string representation of object.

Returns:

String detailing the colormap.

Return type:

str

set_cmap(name: str) → None

Set the ColorMap.

Parameters:

name (str) – Name of the colormap to return.

get_cmap() → matplotlib.cm

Return the matplotlib.cm colormap object.

Returns:

Matplotlib Color map object.

Return type:

matplotlib.cm

static nanoscope() → matplotlib.colors.LinearSegmentedColormap

Matplotlib compatible colormap that replicates the Bruker Nanoscope colorscale.

The colormap is implemented in Gwyddion’s GwyGradient via ‘Nanoscope.txt’.

Returns:

MatplotLib LinearSegmentedColourmap that replicates Bruker Nanoscope colorscale.

Return type:

LinearSegmentedColormap

static gwyddion() → matplotlib.colors.LinearSegmentedColormap

Set RGBA colour map for the Gwyddion.net colour gradient.

Returns:

The ‘gwyddion’ colormap.

Return type:

LinearSegmentedColormap

static blu() → matplotlib.colors.ListedColormap

Set RGBA colour map of just the colour blue.

Returns:

The ‘blu’ colormap.

Return type:

ListedColormap

topostats.LOGGER

topostats.release

topostats.__version__