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+# 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.
+#
+# ############################################################################*/
+
+__authors__ = ["V. Valls"]
+__license__ = "MIT"
+__date__ = "05/04/2018"
+
+
+import numpy
+import skimage.measure
+
+
+class MarchingSquaresSciKitImage(object):
+ """Reference implementation of a marching squares using sci-kit image.
+
+ It uses `skimage.measure.find_contours` to find iso contours taking care of
+ an optional mask. As result the computation is not accurate but can be used
+ as reference for benchmark or for testing the API without compiling the
+ cython part of silx.
+
+ :param numpy.ndarray image: 2d-image containing the values
+ :param numpy.ndarray mask: Optional 2d-image containing mask to cancel
+ mask on part of the image. A `0` means the pixel at this location is
+ valid, else the pixel from the image will not be used.
+ """
+
+ def __init__(self, image, mask=None):
+ self._image = image
+ self._mask = mask
+
+ _deltas = [(0.0, 0.0), (0.99, 0.0), (0.0, 0.99), (0.99, 0.99)]
+
+ def _flag_coord_over_mask(self, coord):
+ """Flag coord over the mask as NaN"""
+ for dx, dy in self._deltas:
+ if self._mask[int(coord[0] + dx), int(coord[1] + dy)] != 0:
+ return float("nan"), float("nan")
+ return coord
+
+ def find_pixels(self, level):
+ """
+ Compute the pixels from the image over the requested iso contours
+ at this `level`.
+
+ This implementation have to use `skimage.measure.find_contours` then
+ it is not accurate nor efficient.
+
+ :param float level: Level of the requested iso contours.
+ :returns: An array of y-x coordinates.
+ :rtype: numpy.ndarray
+ """
+ polylines = skimage.measure.find_contours(self._image, level=level)
+ size = 0
+ for polyline in polylines:
+ size += len(polyline)
+ result = numpy.empty((size, 2), dtype=numpy.int32)
+ size = 0
+ delta = numpy.array([0.5, 0.5])
+ for polyline in polylines:
+ if len(polyline) == 0:
+ continue
+ integer_polyline = numpy.floor(polyline + delta)
+ result[size:size + len(polyline)] = integer_polyline
+ size += len(polyline)
+
+ if len(result) == 0:
+ return result
+
+ if self._mask is not None:
+ # filter out pixels over the mask
+ x_dim = self._image.shape[1]
+ indexes = result[:, 0] * x_dim + result[:, 1]
+ indexes = indexes.ravel()
+ mask = self._mask.ravel()
+ indexes = numpy.unique(indexes)
+ indexes = indexes[mask[indexes] == 0]
+ pixels = numpy.concatenate((indexes // x_dim, indexes % x_dim))
+ pixels.shape = 2, -1
+ pixels = pixels.T
+ result = pixels
+ else:
+ # Note: Cound be done using a single line numpy.unique(result, axis=0)
+ # But here it supports Debian 8
+ x_dim = self._image.shape[1]
+ indexes = result[:, 0] * x_dim + result[:, 1]
+ indexes = indexes.ravel()
+ indexes = numpy.unique(indexes)
+ pixels = numpy.concatenate((indexes // x_dim, indexes % x_dim))
+ pixels.shape = 2, -1
+ pixels = pixels.T
+ result = pixels
+ return result
+
+ def find_contours(self, level):
+ """
+ Compute the list of polygons of the iso contours at this `level`.
+
+ If no mask is involved, the result is the same as
+ `skimage.measure.find_contours`.
+
+ If the result have to be filtered with a mask, the result is not
+ accurate nor efficient. Polygons are not splited, but only points are
+ filtered out using NaN coordinates. This could create artefacts.
+
+ :param float level: Level of the requested iso contours.
+ :returns: A list of array containg y-x coordinates of points
+ :rtype: List[numpy.ndarray]
+ """
+ polylines = skimage.measure.find_contours(self._image, level=level)
+ if self._mask is None:
+ return polylines
+ result = []
+ for polyline in polylines:
+ polyline = map(self._flag_coord_over_mask, polyline)
+ polyline = list(polyline)
+ polyline = numpy.array(polyline)
+ result.append(polyline)
+ return result