# coding: utf-8 # /*########################################################################## # Copyright (C) 2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # # ############################################################################*/ """ This module provides implementations based on marching squares algorithms. The main implementation is done by :class:`MarchingSquaresMergeImpl`. It was designed to speed up the computation of iso surface using Cython and OpenMP. It also provides features like support of mask, and cache of min/max per tiles which is very efficient to find many iso contours from image gradient. Utilitary functions are provided as facade for simple use. :meth:`find_contours` to find iso contours from an image and using the same main signature as `find_contours` from `skimage`, but supporting mask. And :meth:`find_pixels` which returns a set of pixel coords containing the points of the iso contours. """ __authors__ = ["V. Valls"] __license__ = "MIT" __date__ = "02/07/2018" from ._mergeimpl import MarchingSquaresMergeImpl def _factory(engine, image, mask): """Factory to create the marching square implementation from the engine name""" if engine == "merge": return MarchingSquaresMergeImpl(image, mask) elif engine == "skimage": from _skimage import MarchingSquaresSciKitImage return MarchingSquaresSciKitImage(image, mask) else: raise ValueError("Engine '%s' is not supported ('merge' or 'skimage' expected).") def find_pixels(image, level, mask=None): """ Find the pixels following the iso contours at the given `level`. These pixels are localized by the bound of the segment generated by the iso contour algorithm. The result is returned as a numpy array storing a list of coordinates y/x. .. code-block:: python # Example using a mask shape = 100, 100 image = numpy.random.random(shape) mask = numpy.random.random(shape) < 0.01 pixels = silx.image.marchingsquares.find_pixels(image, 0.5, mask=mask) :param numpy.ndarray image: Image to process :param float level: Level of the requested iso contours. :param numpy.ndarray mask: An optional mask (a non-zero value invalidate the pixels of the image) :returns: An array of coordinates in y/x :rtype: numpy.ndarray """ assert(image is not None) if mask is not None: assert(image.shape == mask.shape) engine = "merge" impl = _factory(engine, image, mask) return impl.find_pixels(level) def find_contours(image, level, mask=None): """ Find the iso contours at the given `level`. The result is returned as a list of polygons. .. code-block:: python # Example using a mask shape = 100, 100 image = numpy.random.random(shape) mask = numpy.random.random(shape) < 0.01 polygons = silx.image.marchingsquares.find_contours(image, 0.5, mask=mask) :param numpy.ndarray image: Image to process :param float level: Level of the requested iso contours. :param numpy.ndarray mask: An optional mask (a non-zero value invalidate the pixels of the image) :returns: A list of array containing y-x coordinates of points :rtype: List[numpy.ndarray] """ assert(image is not None) if mask is not None: assert(image.shape == mask.shape) engine = "merge" impl = _factory(engine, image, mask) return impl.find_contours(level)