topostats#
Topostats.
Submodules#
- topostats.entry_point
- topostats.filters
- topostats.grains
- topostats.grainstats
- topostats.io
- topostats.logs
- topostats.plotting
- topostats.plottingfuncs
- topostats.processing
- topostats.run_modules
- topostats.scars
- topostats.statistics
- topostats.theme
- topostats.thresholds
- topostats.tracing
- topostats.unet_masking
- topostats.utils
- topostats.validation
Attributes#
Classes#
Dataclass for storing the crops of grains in an image. |
|
Class for setting the Colormap. |
|
Class for storing TopoStats objects. |
Functions#
|
Logger setup. |
Package Contents#
- class topostats.ImageGrainCrops[source]#
Dataclass for storing the crops of grains in an image.
- above#
Grains in the above direction.
- Type:
GrainCropDirection | None
- below#
Grains in the below direction.
- Type:
GrainCropDirection | None
- above: GrainCropsDirection | None#
- below: GrainCropsDirection | None#
- __eq__(other: object) bool [source]#
Check if two ImageGrainCrops objects are equal.
- Parameters:
other (object) – Object to compare to.
- Returns:
True if the objects are equal, False otherwise.
- Return type:
bool
- topostats.setup_logger(log_name: str = LOGGER_NAME) logging.Logger [source]#
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')[source]#
Class for setting the Colormap.
- Parameters:
name (str) – Name of colormap to use.
- name = 'nanoscope'#
- cmap = None#
- __str__() str [source]#
Return string representation of object.
- Returns:
String detailing the colormap.
- Return type:
str
- set_cmap(name: str) None [source]#
Set the ColorMap.
- Parameters:
name (str) – Name of the colormap to return.
- get_cmap() matplotlib.cm [source]#
Return the matplotlib.cm colormap object.
- Returns:
Matplotlib Color map object.
- Return type:
matplotlib.cm
- static nanoscope() matplotlib.colors.LinearSegmentedColormap [source]#
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 [source]#
Set RGBA colour map for the Gwyddion.net colour gradient.
- Returns:
The ‘gwyddion’ colormap.
- Return type:
LinearSegmentedColormap
- topostats.LOGGER#
- topostats.__version__#
- topostats.__release__ = ''#
- class topostats.TopoStats[source]#
Class for storing TopoStats objects.
- image_grain_crops#
ImageGrainCrops of processed image.
- Type:
ImageGrainCrops | None
- filename#
Filename.
- Type:
str | None
- pixel_to_nm_scaling#
Pixel to nanometre scaling.
- Type:
str | None
- img_path#
Original path to image.
- Type:
str | None
- image#
Flattened image (post ‘’Filter()’’).
- Type:
npt.NDArray | None
- image_original#
Original image.
- Type:
npt.NDArray | None
- topostats_version#
TopoStats version.
- Type:
str | None
- property image_grain_crops: grains.ImageGrainCrops#
Getter for the Image Grain Crops.
- Returns:
Image Grain Crops.
- Return type:
- property filename: str#
Getter for the ‘’filename’’ attribute.
- Returns:
Image filename.
- Return type:
str
- property pixel_to_nm_scaling: str#
Getter for the ‘’pixel_to_nm_scaling’’ attribute.
- Returns:
Image ‘’pixel_to_nm_scaling’’.
- Return type:
str
- property img_path: pathlib.Path#
Getter for the ‘’img_path’’ attribute.
- Returns:
Path to original image on disk.
- Return type:
Path
- property image: str#
Getter for the ‘’image’’ attribute, post filtering.
- Returns:
Image image.
- Return type:
str
- property image_original: str#
Getter for the ‘’image_original’’ attribute.
- Returns:
Original image.
- Return type:
str
- property topostats_version: str#
Getter for the ‘’topostats_version’’ attribute, post filtering.
- Returns:
Version of TopoStats the class was created with.
- Return type:
str
- __eq__(other: object) bool [source]#
Check if two TopoStats objects are equal.
- Parameters:
other (object) – Object to compare to.
- Returns:
True if the objects are equal, False otherwise.
- Return type:
bool
- topostats_to_dict() dict[str, str | grains.ImageGrainCrops | numpy.typing.NDArray] [source]#
Convert ‘’TopoStats’’ object to dictionary.
- Returns:
Dictionary of ‘’TopoStats’’ object.
- Return type:
dict[str, str | ImageGrainCrops | npt.NDArray]