diff --git a/jwst/skymatch/region.py b/jwst/skymatch/region.py deleted file mode 100755 index 6e7a596ef0..0000000000 --- a/jwst/skymatch/region.py +++ /dev/null @@ -1,433 +0,0 @@ -""" -Polygon filling algorithm. - -""" -# Original author: Nadezhda Dencheva -# -# modifications by Mihai Cara: removed functionality not needed for the -# skymatch algorithm and modified the code to be able to work with polygons -# that have vertices with negative coordinates. Polygon vertices are now -# *internally* (to region.py) rounded to integers so that Polygon will not -# crash when input vertices are floats. Fixed a bug in _construct_ordered_GET -# that was causing varying polygon filling for different ordering of the -# vertices. Finally, modified the algorithm to fill the right-most pixels -# as well as top-most row of the polygon. -# -# NOTE: Algorithm description can be found, e.g., here: -# http://www.cs.rit.edu/~icss571/filling/how_to.html -# http://www.cs.uic.edu/~jbell/CourseNotes/ComputerGraphics/PolygonFilling.html -# -from collections import OrderedDict -import numpy as np - -__all__ = ['Region', 'Edge', 'Polygon'] -__taskname__ = 'region' -__author__ = 'Nadezhda Dencheva, Mihai Cara' - - -class ValidationError(Exception): - def __init__(self, message): - self._message = message - - def __str__(self): - return self._message - - -class Region(): - """ - Base class for regions. - - Parameters - ------------- - rid : int or string - region ID - coordinate_system : astropy.wcs.CoordinateSystem instance or a string - in the context of WCS this would be an instance of wcs.CoordinateSysem - """ - - def __init__(self, rid, coordinate_system): - self._coordinate_system = coordinate_system - self._rid = rid - - def __contains__(self, x, y): - """ - Determines if a pixel is within a region. - - Parameters - ---------- - x, y : float - x , y values of a pixel - - Returns - ------- - True or False - - Subclasses must define this method. - """ - raise NotImplementedError("__contains__") - - def scan(self, mask): - """ - Sets mask values to region id for all pixels within the region. - Subclasses must define this method. - - Parameters - ---------- - mask : ndarray - a byte array with the shape of the observation to be used as a mask - - Returns - ------- - mask : array where the value of the elements is the region ID or 0 (for - pixels which are not included in any region). - """ - raise NotImplementedError("scan") - - -class Polygon(Region): - """ - Represents a 2D polygon region with multiple vertices - - Parameters - ---------- - rid : string - polygon id - vertices : list of (x,y) tuples or lists - The list is ordered in such a way that when traversed in a - counterclockwise direction, the enclosed area is the polygon. - The last vertex must coincide with the first vertex, minimum - 4 vertices are needed to define a triangle - coord_system : string - coordinate system - - """ - - def __init__(self, rid, vertices, coord_system="Cartesian"): - assert len(vertices) >= 4, ("Expected vertices to be " - "a list of minimum 4 tuples (x,y)") - super(Polygon, self).__init__(rid, coord_system) - - # self._shiftx & self._shifty are introduced to shift the bottom-left - # corner of the polygon's bounding box to (0,0) as a (hopefully - # temporary) workaround to a limitation of the original code that the - # polygon must be completely contained in the image. It seems that the - # code works fine if we make sure that the bottom-left corner of the - # polygon's bounding box has non-negative coordinates. - self._shiftx = 0 - self._shifty = 0 - for vertex in vertices: - x, y = vertex - if x < self._shiftx: - self._shiftx = x - if y < self._shifty: - self._shifty = y - v = [(i - self._shiftx, j - self._shifty) for i, j in vertices] - - # convert to integer coordinates: - self._vertices = np.asarray(list(map(_round_vertex, v))) - self._shiftx = int(round(self._shiftx)) - self._shifty = int(round(self._shifty)) - - self._bbox = self._get_bounding_box() - self._scan_line_range = \ - list(range(self._bbox[1], self._bbox[3] + self._bbox[1] + 1)) - # constructs a Global Edge Table (GET) in bbox coordinates - self._GET = self._construct_ordered_GET() - - def _get_bounding_box(self): - x = self._vertices[:, 0].min() - y = self._vertices[:, 1].min() - w = self._vertices[:, 0].max() - x - h = self._vertices[:, 1].max() - y - return x, y, w, h - - def _construct_ordered_GET(self): - """ - Construct a Global Edge Table (GET) - - The GET is an OrderedDict. Keys are scan line numbers, - ordered from bbox.ymin to bbox.ymax, where bbox is the - bounding box of the polygon. - Values are lists of edges for which edge.ymin==scan_line_number. - - Returns - ------- - GET: OrderedDict - {scan_line: [edge1, edge2]} - """ - # edges is a list of Edge objects which define a polygon - # with these vertices - edges = self.get_edges() - GET = OrderedDict.fromkeys(self._scan_line_range) - ymin = np.asarray([e._ymin for e in edges]) - for i in self._scan_line_range: - ymin_ind = (ymin == i).nonzero()[0] - # a hack for incomplete filling .any() fails if 0 is in ymin_ind - # if ymin_ind.any(): - yminindlen, = ymin_ind.shape - if yminindlen: - GET[i] = [edges[ymin_ind[0]]] - for j in ymin_ind[1:]: - GET[i].append(edges[j]) - return GET - - def get_edges(self): - """ - Create a list of Edge objects from vertices - """ - edges = [] - for i in range(1, len(self._vertices)): - name = 'E' + str(i - 1) - edges.append( - Edge( - name=name, - start=self._vertices[i - 1], - stop=self._vertices[i] - ) - ) - return edges - - def scan(self, data): - """ - This is the main function which scans the polygon and creates the mask - - Parameters - ---------- - data : array - the mask array - it has all zeros initially, elements within a region are set to - the region's ID - - Algorithm: - - Set the Global Edge Table (GET) - - Set y to be the smallest y coordinate that has an entry in GET - - Initialize the Active Edge Table (AET) to be empty - - For each scan line: - 1. Add edges from GET to AET for which ymin==y - 2. Remove edges from AET fro which ymax==y - 3. Compute the intersection of the current scan line with all edges - in the AET - 4. Sort on X of intersection point - 5. Set elements between pairs of X in the AET to the Edge's ID - - """ - # TODO: - # 1. This algorithm does not mark pixels in the top row and left - # most column. Pad the initial pixel description on top and left - # with 1 px to prevent this. - # 2. Currently it uses intersection of the scan line with edges. - # If this is too slow it should use the 1/m increment - # (replace 3 above) (or the increment should be removed from - # the GET entry). - - # see comments in the __init__ function for the reason of introducing - # polygon shifts (self._shiftx & self._shifty). Here we need to shift - # it back. - - (ny, nx) = data.shape - - y = np.min(list(self._GET.keys())) - - AET = [] - scline = self._scan_line_range[-1] - - while y <= scline: - - if y < scline: - AET = self.update_AET(y, AET) - - if self._bbox[2] <= 0: - y += 1 - continue - - scan_line = Edge('scan_line', start=[self._bbox[0], y], - stop=[self._bbox[0] + self._bbox[2], y]) - x = [ - int(np.ceil(e.compute_AET_entry(scan_line)[1])) - for e in AET if e is not None - ] - xnew = np.sort(x) - ysh = y + self._shifty - - if ysh < 0 or ysh >= ny: - y += 1 - continue - - for i, j in zip(xnew[::2], xnew[1::2]): - xstart = max(0, i + self._shiftx) - xend = min(j + self._shiftx, nx - 1) - data[ysh][xstart:xend + 1] = self._rid - - y += 1 - - return data - - def update_AET(self, y, AET): - """ - Update the Active Edge Table (AET) - - Add edges from GET to AET for which ymin of the edge is - equal to the y of the scan line. - Remove edges from AET for which ymax of the edge is - equal to y of the scan line. - - """ - edge_cont = self._GET[y] - if edge_cont is not None: - for edge in edge_cont: - if edge._start[1] != edge._stop[1] and edge._ymin == y: - AET.append(edge) - for edge in AET[::-1]: - if edge is not None: - if edge._ymax == y: - AET.remove(edge) - return AET - - def __contains__(self, px): - """even-odd algorithm or smth else better should be used""" - # minx = self._vertices[:,0].min() - # maxx = self._vertices[:,0].max() - # miny = self._vertices[:,1].min() - # maxy = self._vertices[:,1].max() - return ( - px[0] >= self._bbox[0] and - px[0] <= self._bbox[0] + self._bbox[2] and - px[1] >= self._bbox[1] and - px[1] <= self._bbox[1] + self._bbox[3] - ) - - -class Edge(): - """ - Edge representation - - An edge has a "start" and "stop" (x,y) vertices and an entry in the - GET table of a polygon. The GET entry is a list of these values: - - [ymax, x_at_ymin, delta_x/delta_y] - - """ - - def __init__(self, name=None, start=None, stop=None, next=None): - self._start = None - if start is not None: - self._start = np.asarray(start) - self._name = name - self._stop = stop - if stop is not None: - self._stop = np.asarray(stop) - self._next = next - - if self._stop is not None and self._start is not None: - if self._start[1] < self._stop[1]: - self._ymin = self._start[1] - self._yminx = self._start[0] - else: - self._ymin = self._stop[1] - self._yminx = self._stop[0] - self._ymax = max(self._start[1], self._stop[1]) - self._xmin = min(self._start[0], self._stop[0]) - self._xmax = max(self._start[0], self._stop[1]) - else: - self._ymin = None - self._yminx = None - self._ymax = None - self._xmin = None - self._xmax = None - self.GET_entry = self.compute_GET_entry() - - @property - def ymin(self): - return self._ymin - - @property - def start(self): - return self._start - - @property - def stop(self): - return self._stop - - @property - def ymax(self): - return self._ymax - - def compute_GET_entry(self): - """ - Compute the entry in the Global Edge Table - - [ymax, x@ymin, 1/m] - - """ - if self._start is None: - entry = None - else: - earr = np.asarray([self._start, self._stop]) - if np.diff(earr[:, 1]).item() == 0: - return None - else: - entry = [ - self._ymax, - self._yminx, - (np.diff(earr[:, 0]) / np.diff(earr[:, 1])).item(), - None - ] - return entry - - def compute_AET_entry(self, edge): - """ - Compute the entry for an edge in the current Active Edge Table - - [ymax, x_intersect, 1/m] - note: currently 1/m is not used - """ - x = self.intersection(edge)[0] - return [self._ymax, x, self.GET_entry[2]] - - def __repr__(self): - fmt = "" - if self._name is not None: - fmt += self._name - next = self.next - while next is not None: - fmt += "-->" - fmt += next._name - next = next.next - return fmt - - @property - def next(self): - return self._next - - @next.setter - def next(self, edge): - if self._name is None: - self._name = edge._name - self._stop = edge._stop - self._start = edge._start - self._next = edge.next - else: - self._next = edge - - def intersection(self, edge): - u = self._stop - self._start - v = edge._stop - edge._start - w = self._start - edge._start - D = np.cross(u, v) - - if np.allclose(np.cross(u, v), 0, rtol=0, - atol=1e2 * np.finfo(float).eps): - return np.array(self._start) - - return np.cross(v, w) / D * u + self._start - - def is_parallel(self, edge): - u = self._stop - self._start - v = edge._stop - edge._start - return np.allclose(np.cross(u, v), 0, rtol=0, - atol=1e2 * np.finfo(float).eps) - - -def _round_vertex(v): - x, y = v - return int(round(x)), int(round(y)) diff --git a/jwst/skymatch/skyimage.py b/jwst/skymatch/skyimage.py deleted file mode 100644 index 65bc943bec..0000000000 --- a/jwst/skymatch/skyimage.py +++ /dev/null @@ -1,1025 +0,0 @@ -""" -The ``skyimage`` module contains algorithms that are used by -``skymatch`` to manage all of the information for footprints (image outlines) -on the sky as well as perform useful operations on these outlines such as -computing intersections and statistics in the overlap regions. - -:Authors: Mihai Cara (contact: help@stsci.edu) - - -""" - -# STDLIB -import abc -import tempfile - -# THIRD-PARTY -import numpy as np -from spherical_geometry.polygon import SphericalPolygon - -# LOCAL -from . skystatistics import SkyStats -from . import region - - -__all__ = ['SkyImage', 'SkyGroup', 'DataAccessor', 'NDArrayInMemoryAccessor', - 'NDArrayMappedAccessor'] - - -class DataAccessor(abc.ABC): - """ Base class for all data accessors. Provides a common interface to - access data. - """ - @abc.abstractmethod - def get_data(self): # pragma: no cover - pass - - @abc.abstractmethod - def set_data(self, data): # pragma: no cover - """ Sets data. - - Parameters - ---------- - data : numpy.ndarray - Data array to be set. - - """ - pass - - @abc.abstractmethod - def get_data_shape(self): # pragma: no cover - pass - - -class NDArrayInMemoryAccessor(DataAccessor): - """ Acessor for in-memory `numpy.ndarray` data. """ - def __init__(self, data): - super().__init__() - self._data = data - - def get_data(self): - return self._data - - def set_data(self, data): - self._data = data - - def get_data_shape(self): - return np.shape(self._data) - - -class NDArrayMappedAccessor(DataAccessor): - """ Data accessor for arrays stored in temporary files. """ - def __init__(self, data, tmpfile=None, prefix='tmp_skymatch_', - suffix='.npy', tmpdir=''): - super().__init__() - if tmpfile is None: - self._close = True - self._tmp = tempfile.NamedTemporaryFile( - prefix=prefix, - suffix=suffix, - dir=tmpdir - ) - if not self._tmp: - raise RuntimeError("Unable to create temporary file.") - else: - # temp file managed by the caller - self._close = False - self._tmp = tmpfile - - self.set_data(data) - - def get_data(self): - self._tmp.seek(0) - return np.load(self._tmp) - - def set_data(self, data): - data = np.asanyarray(data) - self._data_shape = data.shape - self._tmp.seek(0) - np.save(self._tmp, data) - - def __del__(self): - if self._close: - self._tmp.close() - - def get_data_shape(self): - return self._data_shape - - -class SkyImage: - """ - Container that holds information about properties of a *single* - image such as: - - * image data; - * WCS of the chip image; - * bounding spherical polygon; - * id; - * pixel area; - * sky background value; - * sky statistics parameters; - * mask associated image data indicating "good" (1) data. - - """ - - def __init__(self, image, wcs_fwd, wcs_inv, pix_area=1.0, convf=1.0, - mask=None, id=None, skystat=None, stepsize=None, meta=None, - reduce_memory_usage=True): - """ Initializes the SkyImage object. - - Parameters - ---------- - image : numpy.ndarray, NDArrayDataAccessor - A 2D array of image data or a `NDArrayDataAccessor`. - - wcs_fwd : function - "forward" pixel-to-world transformation function. - - wcs_inv : function - "inverse" world-to-pixel transformation function. - - pix_area : float, optional - Average pixel's sky area. - - convf : float, optional - Conversion factor that when multiplied to `image` data converts - the data to "uniform" (across multiple images) surface - brightness units. - - .. note:: - - The functionality to support this conversion is not yet - implemented and at this moment `convf` is ignored. - - mask : numpy.ndarray, NDArrayDataAccessor - A 2D array or `NDArrayDataAccessor` of a 2D array that indicates - which pixels in the input `image` should be used for sky - computations (``1``) and which pixels should **not** be used - for sky computations (``0``). - - id : anything - The value of this parameter is simple stored within the `SkyImage` - object. While it can be of any type, it is preferable that `id` be - of a type with nice string representation. - - skystat : callable, None, optional - A callable object that takes a either a 2D image (2D - `numpy.ndarray`) or a list of pixel values (a Nx1 array) and - returns a tuple of two values: some statistics (e.g., mean, - median, etc.) and number of pixels/values from the input image - used in computing that statistics. - - When `skystat` is not set, `SkyImage` will use - :py:class:`~jwst_pipeline.skymatch.skystatistics.SkyStats` object - to perform sky statistics on image data. - - stepsize : int, None, optional - Spacing between vertices of the image's bounding polygon. Default - value of `None` creates bounding polygons with four vertices - corresponding to the corners of the image. - - meta : dict, None, optional - A dictionary of various items to be stored within the `SkyImage` - object. - - reduce_memory_usage : bool, optional - Indicates whether to attempt to minimize memory usage by attaching - input ``image`` and/or ``mask`` `numpy.ndarray` arrays to - file-mapped accessor. This has no effect when input parameters - ``image`` and/or ``mask`` are already of `NDArrayDataAccessor` - objects. - - """ - self._image = None - self._mask = None - self._image_shape = None - self._mask_shape = None - self._reduce_memory_usage = reduce_memory_usage - - self.image = image - - self.convf = convf - self.meta = meta - self._id = id - self._pix_area = pix_area - - # WCS - self.wcs_fwd = wcs_fwd - self.wcs_inv = wcs_inv - - # initial sky value: - self._sky = 0.0 - self._sky_is_valid = False - - self.mask = mask - - # create spherical polygon bounding the image - if image is None or wcs_fwd is None or wcs_inv is None: - self._radec = [(np.array([]), np.array([]))] - self._polygon = SphericalPolygon([]) - self._poly_area = 0.0 - - else: - self.calc_bounding_polygon(stepsize) - - # set sky statistics function (NOTE: it must return statistics and - # the number of pixels used after clipping) - if skystat is None: - self.set_builtin_skystat() - else: - self.skystat = skystat - - @property - def mask(self): - """ Set or get `SkyImage`'s ``mask`` data array or `None`. """ - if self._mask is None: - return None - else: - return self._mask.get_data() - - @mask.setter - def mask(self, mask): - if mask is None: - self._mask = None - self._mask_shape = None - - elif isinstance(mask, DataAccessor): - if self._image is None: - raise ValueError("'mask' must be None when 'image' is None") - - self._mask = mask - self._mask_shape = mask.get_data_shape() - - # check that mask has the same shape as image: - if self._mask_shape != self.image_shape: - raise ValueError("'mask' must have the same shape as 'image'.") - - else: - if self._image is None: - raise ValueError("'mask' must be None when 'image' is None") - - mask = np.asanyarray(mask, dtype=bool) - self._mask_shape = mask.shape - - # check that mask has the same shape as image: - if self._mask_shape != self.image_shape: - raise ValueError("'mask' must have the same shape as 'image'.") - - if self._mask is None: - if self._reduce_memory_usage: - self._mask = NDArrayMappedAccessor( - mask, - prefix='tmp_skymatch_mask_' - ) - else: - self._mask = NDArrayInMemoryAccessor(mask) - else: - self._mask.set_data(mask) - - @property - def image(self): - """ Set or get `SkyImage`'s ``image`` data array. """ - if self._image is None: - return None - else: - return self._image.get_data() - - @image.setter - def image(self, image): - if image is None: - self._image = None - self._image_shape = None - self.mask = None - - if isinstance(image, DataAccessor): - self._image = image - self._image_shape = image.get_data_shape() - - else: - image = np.asanyarray(image) - self._image_shape = image.shape - if self._image is None: - if self._reduce_memory_usage: - self._image = NDArrayMappedAccessor( - image, - prefix='tmp_skymatch_image_' - ) - else: - self._image = NDArrayInMemoryAccessor(image) - else: - self._image.set_data(image) - - @property - def image_shape(self): - """ Get `SkyImage`'s ``image`` data shape. """ - if self._image_shape is None and self._image is not None: - self._image_shape = self._image.get_data_shape() - return self._image_shape - - @property - def id(self): - """ Set or get `SkyImage`'s `id`. - - While `id` can be of any type, it is preferable that `id` be - of a type with nice string representation. - - """ - return self._id - - @id.setter - def id(self, id): - self._id = id - - @property - def pix_area(self): - """ Set or get mean pixel area. - """ - return self._pix_area - - @pix_area.setter - def pix_area(self, pix_area): - self._pix_area = pix_area - - @property - def poly_area(self): - """ Get bounding polygon area in srad units. - """ - return self._poly_area - - @property - def sky(self): - """ Sky background value. See `calc_sky` for more details. - """ - return self._sky - - @sky.setter - def sky(self, sky): - self._sky = sky - - @property - def is_sky_valid(self): - """ - Indicates whether sky value was successfully computed. - Must be set externally. - """ - return self._sky_is_valid - - @is_sky_valid.setter - def is_sky_valid(self, valid): - self._sky_is_valid = valid - - @property - def radec(self): - """ - Get RA and DEC of the vertices of the bounding polygon as a - `~numpy.ndarray` of shape (N, 2) where N is the number of vertices + 1. - """ - return self._radec - - @property - def polygon(self): - """ Get image's bounding polygon. - """ - return self._polygon - - def intersection(self, skyimage): - """ - Compute intersection of this `SkyImage` object and another - `SkyImage`, `SkyGroup`, or - :py:class:`~spherical_geometry.polygon.SphericalPolygon` - object. - - Parameters - ---------- - skyimage : SkyImage, SkyGroup, SphericalPolygon - Another object that should be intersected with this `SkyImage`. - - Returns - ------- - polygon : SphericalPolygon - A :py:class:`~spherical_geometry.polygon.SphericalPolygon` that is - the intersection of this `SkyImage` and `skyimage`. - - """ - if isinstance(skyimage, (SkyImage, SkyGroup)): - other = skyimage.polygon - else: - other = skyimage - - pts1 = np.sort(list(self._polygon.points)[0], axis=0) - pts2 = np.sort(list(other.points)[0], axis=0) - if np.allclose(pts1, pts2, rtol=0, atol=5e-9): - intersect_poly = self._polygon.copy() - else: - intersect_poly = self._polygon.intersection(other) - return intersect_poly - - def calc_bounding_polygon(self, stepsize=None): - """ Compute image's bounding polygon. - - Parameters - ---------- - stepsize : int, None, optional - Indicates the maximum separation between two adjacent vertices - of the bounding polygon along each side of the image. Corners - of the image are included automatically. If `stepsize` is `None`, - bounding polygon will contain only vertices of the image. - - """ - ny, nx = self.image_shape - - if stepsize is None: - nintx = 2 - ninty = 2 - else: - nintx = max(2, int(np.ceil((nx + 1.0) / stepsize))) - ninty = max(2, int(np.ceil((ny + 1.0) / stepsize))) - - xs = np.linspace(-0.5, nx - 0.5, nintx, dtype=float) - ys = np.linspace(-0.5, ny - 0.5, ninty, dtype=float)[1:-1] - nptx = xs.size - npty = ys.size - - npts = 2 * (nptx + npty) - - borderx = np.empty((npts + 1,), dtype=float) - bordery = np.empty((npts + 1,), dtype=float) - - # "bottom" points: - borderx[:nptx] = xs - bordery[:nptx] = -0.5 - # "right" - sl = np.s_[nptx:nptx + npty] - borderx[sl] = nx - 0.5 - bordery[sl] = ys - # "top" - sl = np.s_[nptx + npty:2 * nptx + npty] - borderx[sl] = xs[::-1] - bordery[sl] = ny - 0.5 - # "left" - sl = np.s_[2 * nptx + npty:-1] - borderx[sl] = -0.5 - bordery[sl] = ys[::-1] - - # close polygon: - borderx[-1] = borderx[0] - bordery[-1] = bordery[0] - - ra, dec = self.wcs_fwd(borderx, bordery, with_bounding_box=False) - # TODO: for strange reasons, occasionally ra[0] != ra[-1] and/or - # dec[0] != dec[-1] (even though we close the polygon in the - # previous two lines). Then SphericalPolygon fails because - # points are not closed. Therefore we force it to be closed: - ra[-1] = ra[0] - dec[-1] = dec[0] - - self._radec = [(ra, dec)] - self._polygon = SphericalPolygon.from_radec(ra, dec) - self._poly_area = np.fabs(self._polygon.area()) - - @property - def skystat(self): - """ Stores/retrieves a callable object that takes a either a 2D image - (2D `numpy.ndarray`) or a list of pixel values (a Nx1 array) and - returns a tuple of two values: some statistics - (e.g., mean, median, etc.) and number of pixels/values from the input - image used in computing that statistics. - - When `skystat` is not set, `SkyImage` will use - :py:class:`~jwst_pipeline.skymatch.skystatistics.SkyStats` object - to perform sky statistics on image data. - - """ - return self._skystat - - @skystat.setter - def skystat(self, skystat): - self._skystat = skystat - - def set_builtin_skystat(self, skystat='median', lower=None, upper=None, - nclip=5, lsigma=4.0, usigma=4.0, binwidth=0.1): - """ - Replace already set `skystat` with a "built-in" version of a - statistics callable object used to measure sky background. - - See :py:class:`~jwst_pipeline.skymatch.skystatistics.SkyStats` for the - parameter description. - - """ - self._skystat = SkyStats( - skystat=skystat, - lower=lower, - upper=upper, - nclip=nclip, - lsig=lsigma, - usig=usigma, - binwidth=binwidth - ) - - # TODO: due to a bug in the sphere package, see - # https://github.com/spacetelescope/sphere/issues/74 - # intersections with polygons formed as union does not work. - # For this reason I re-implement 'calc_sky' below with - # a workaround for the bug. - # The original implementation (now called ``_calc_sky_orig`` - # should replace current 'calc_sky' once the bug is fixed. - # - def calc_sky(self, overlap=None, delta=True): - """ - Compute sky background value. - - Parameters - ---------- - overlap : SkyImage, SkyGroup, SphericalPolygon, list of tuples, \ -None, optional - Another `SkyImage`, `SkyGroup`, - :py:class:`spherical_geometry.polygons.SphericalPolygon`, or - a list of tuples of (RA, DEC) of vertices of a spherical - polygon. This parameter is used to indicate that sky statistics - should computed only in the region of intersection of *this* - image with the polygon indicated by `overlap`. When `overlap` is - `None`, sky statistics will be computed over the entire image. - - delta : bool, optional - Should this function return absolute sky value or the difference - between the computed value and the value of the sky stored in the - `sky` property. - - Returns - ------- - skyval : float, None - Computed sky value (absolute or relative to the `sky` attribute). - If there are no valid data to perform this computations (e.g., - because this image does not overlap with the image indicated by - `overlap`), `skyval` will be set to `None`. - - npix : int - Number of pixels used to compute sky statistics. - - polyarea : float - Area (in srad) of the polygon that bounds data used to compute - sky statistics. - - """ - if overlap is None: - - if self._mask is None: - data = self.image - else: - data = self.image[self._mask.get_data()] - - polyarea = self.poly_area - - else: - fill_mask = np.zeros(self.image_shape, dtype=bool) - - if isinstance(overlap, SkyImage): - intersection = self.intersection(overlap) - polyarea = np.fabs(intersection.area()) - radec = list(intersection.to_radec()) - - elif isinstance(overlap, SkyGroup): - radec = [] - polyarea = 0.0 - for im in overlap: - intersection = self.intersection(im) - polyarea1 = np.fabs(intersection.area()) - if polyarea1 == 0.0: - continue - polyarea += polyarea1 - radec += list(intersection.to_radec()) - - elif isinstance(overlap, SphericalPolygon): - radec = [] - polyarea = 0.0 - for p in overlap._polygons: - intersection = self.intersection(SphericalPolygon([p])) - polyarea1 = np.fabs(intersection.area()) - if polyarea1 == 0.0: - continue - polyarea += polyarea1 - radec += list(intersection.to_radec()) - - else: # assume a list of (ra, dec) tuples: - radec = [] - polyarea = 0.0 - for r, d in overlap: - poly = SphericalPolygon.from_radec(r, d) - polyarea1 = np.fabs(poly.area()) - if polyarea1 == 0.0 or len(r) < 4: - continue - polyarea += polyarea1 - radec.append(self.intersection(poly).to_radec()) - - if polyarea == 0.0: - return None, 0, 0.0 - - for ra, dec in radec: - if len(ra) < 4: - continue - - # set pixels in 'fill_mask' that are inside a polygon to True: - x, y = self.wcs_inv(ra, dec) - poly_vert = list(zip(*[x, y])) - - polygon = region.Polygon(True, poly_vert) - fill_mask = polygon.scan(fill_mask) - - if self._mask is not None: - fill_mask &= self._mask.get_data() - - data = self.image[fill_mask] - - if data.size < 1: - return None, 0, 0.0 - - # Calculate sky - try: - skyval, npix = self._skystat(data) - except ValueError: - return None, 0, 0.0 - - if not np.isfinite(skyval): - return None, 0, 0.0 - - if delta: - skyval -= self._sky - - return skyval, npix, polyarea - -# def _calc_sky_orig(self, overlap=None, delta=True): -# """ -# Compute sky background value. -# -# Parameters -# ---------- -# overlap : SkyImage, SkyGroup, SphericalPolygon, list of tuples, \ -# None, optional -# Another `SkyImage`, `SkyGroup`, -# :py:class:`spherical_geometry.polygons.SphericalPolygon`, or -# a list of tuples of (RA, DEC) of vertices of a spherical -# polygon. This parameter is used to indicate that sky statistics -# should computed only in the region of intersection of *this* -# image with the polygon indicated by `overlap`. When `overlap` is -# `None`, sky statistics will be computed over the entire image. -# -# delta : bool, optional -# Should this function return absolute sky value or the difference -# between the computed value and the value of the sky stored in the -# `sky` property. -# -# Returns -# ------- -# skyval : float, None -# Computed sky value (absolute or relative to the `sky` attribute). -# If there are no valid data to perform this computations (e.g., -# because this image does not overlap with the image indicated by -# `overlap`), `skyval` will be set to `None`. -# -# npix : int -# Number of pixels used to compute sky statistics. -# -# polyarea : float -# Area (in srad) of the polygon that bounds data used to compute -# sky statistics. -# -# """ -# -# if overlap is None: -# -# if self._mask is None: -# data = self.image -# else: -# data = self.image[self._mask.get_data()] -# -# polyarea = self.poly_area -# -# else: -# fill_mask = np.zeros(self.image_shape, dtype=bool) -# -# if isinstance(overlap, (SkyImage, SkyGroup, SphericalPolygon)): -# intersection = self.intersection(overlap) -# polyarea = np.fabs(intersection.area()) -# radec = intersection.to_radec() -# -# else: # assume a list of (ra, dec) tuples: -# radec = [] -# polyarea = 0.0 -# for r, d in overlap: -# poly = SphericalPolygon.from_radec(r, d) -# polyarea1 = np.fabs(poly.area()) -# if polyarea1 == 0.0 or len(r) < 4: -# continue -# polyarea += polyarea1 -# radec.append(self.intersection(poly).to_radec()) -# -# if polyarea == 0.0: -# return None, 0, 0.0 -# -# for ra, dec in radec: -# if len(ra) < 4: -# continue -# -# # set pixels in 'fill_mask' that are inside a polygon -# # to True: -# x, y = self.wcs_inv(ra, dec) -# poly_vert = list(zip(*[x, y])) -# -# polygon = region.Polygon(True, poly_vert) -# fill_mask = polygon.scan(fill_mask) -# -# if self._mask is not None: -# fill_mask &= self._mask.get_data() -# -# data = self.image[fill_mask] -# -# if data.size < 1: -# return None, 0, 0.0 -# -# # Calculate sky -# try: -# -# skyval, npix = self._skystat(data) -# -# except ValueError: -# -# return None, 0, 0.0 -# -# if delta: -# skyval -= self._sky -# -# return skyval, npix, polyarea - - def copy(self): - """ - Return a shallow copy of the `SkyImage` object. - """ - si = SkyImage( - image=None, - wcs_fwd=self.wcs_fwd, - wcs_inv=self.wcs_inv, - pix_area=self.pix_area, - convf=self.convf, - mask=None, - id=self.id, - stepsize=None, - meta=self.meta - ) - - si._image = self._image - si._mask = self._mask - si._image_shape = self._image_shape - si._mask_shape = self._mask_shape - si._reduce_memory_usage = self._reduce_memory_usage - - si._radec = self._radec - si._polygon = self._polygon - si._poly_area = self._poly_area - si.sky = self.sky - return si - - -class SkyGroup: - """ - Holds multiple :py:class:`SkyImage` objects whose sky background values - must be adjusted together. - - `SkyGroup` provides methods for obtaining bounding polygon of the group - of :py:class:`SkyImage` objects and to compute sky value of the group. - - """ - - def __init__(self, images, id=None, sky=0.0): - - if isinstance(images, SkyImage): - self._images = [images] - - elif hasattr(images, '__iter__'): - self._images = [] - for im in images: - if not isinstance(im, SkyImage): - raise TypeError("Each element of the 'images' parameter " - "must be an 'SkyImage' object.") - self._images.append(im) - - else: - raise TypeError( - "Parameter 'images' must be either a single 'SkyImage' object " - "or a list of 'SkyImage' objects" - ) - - self._id = id - self._update_bounding_polygon() - self._sky = sky - for im in self._images: - im.sky += sky - - @property - def id(self): - """ Set or get `SkyImage`'s `id`. - - While `id` can be of any type, it is preferable that `id` be - of a type with nice string representation. - - """ - return self._id - - @id.setter - def id(self, id): - self._id = id - - @property - def sky(self): - """ Sky background value. See `calc_sky` for more details. - """ - return self._sky - - @sky.setter - def sky(self, sky): - delta_sky = sky - self._sky - self._sky = sky - for im in self._images: - im.sky += delta_sky - - @property - def radec(self): - """ - Get RA and DEC of the vertices of the bounding polygon as a - `~numpy.ndarray` of shape (N, 2) where N is the number of vertices + 1. - - """ - return self._radec - - @property - def polygon(self): - """ Get image's bounding polygon. - """ - return self._polygon - - def intersection(self, skyimage): - """ - Compute intersection of this `SkyImage` object and another - `SkyImage`, `SkyGroup`, or - :py:class:`~spherical_geometry.polygon.SphericalPolygon` - object. - - Parameters - ---------- - skyimage : SkyImage, SkyGroup, SphericalPolygon - Another object that should be intersected with this `SkyImage`. - - Returns - ------- - intersect_poly : SphericalPolygon - A :py:class:`~spherical_geometry.polygon.SphericalPolygon` that is - the intersection of this `SkyImage` and `skyimage`. - - """ - if isinstance(skyimage, (SkyImage, SkyGroup)): - other = skyimage.polygon - else: - other = skyimage - - pts1 = np.sort(list(self._polygon.points)[0], axis=0) - pts2 = np.sort(list(other.points)[0], axis=0) - if np.allclose(pts1, pts2, rtol=0, atol=1e-8): - intersect_poly = self._polygon.copy() - else: - intersect_poly = self._polygon.intersection(other) - return intersect_poly - - def _update_bounding_polygon(self): - polygons = [im.polygon for im in self._images] - if len(polygons) == 0: - self._polygon = SphericalPolygon([]) - self._radec = [] - else: - self._polygon = SphericalPolygon.multi_union(polygons) - self._radec = list(self._polygon.to_radec()) - - def __len__(self): - return len(self._images) - - def __getitem__(self, idx): - return self._images[idx] - - def __setitem__(self, idx, value): - if not isinstance(value, SkyImage): - raise TypeError("Item must be of 'SkyImage' type") - value.sky += self._sky - self._images[idx] = value - self._update_bounding_polygon() - - def __delitem__(self, idx): - del self._images[idx] - if len(self._images) == 0: - self._sky = 0.0 - self._id = None - self._update_bounding_polygon() - - def __iter__(self): - for image in self._images: - yield image - - def insert(self, idx, value): - """Inserts a `SkyImage` into the group. - """ - if not isinstance(value, SkyImage): - raise TypeError("Item must be of 'SkyImage' type") - value.sky += self._sky - self._images.insert(idx, value) - self._update_bounding_polygon() - - def append(self, value): - """Appends a `SkyImage` to the group. - """ - if not isinstance(value, SkyImage): - raise TypeError("Item must be of 'SkyImage' type") - value.sky += self._sky - self._images.append(value) - self._update_bounding_polygon() - - def calc_sky(self, overlap=None, delta=True): - """ - Compute sky background value. - - Parameters - ---------- - overlap : SkyImage, SkyGroup, SphericalPolygon, list of tuples, \ -None, optional - Another `SkyImage`, `SkyGroup`, - :py:class:`spherical_geometry.polygons.SphericalPolygon`, or - a list of tuples of (RA, DEC) of vertices of a spherical - polygon. This parameter is used to indicate that sky statistics - should computed only in the region of intersection of *this* - image with the polygon indicated by `overlap`. When `overlap` is - `None`, sky statistics will be computed over the entire image. - - delta : bool, optional - Should this function return absolute sky value or the difference - between the computed value and the value of the sky stored in the - `sky` property. - - Returns - ------- - skyval : float, None - Computed sky value (absolute or relative to the `sky` attribute). - If there are no valid data to perform this computations (e.g., - because this image does not overlap with the image indicated by - `overlap`), `skyval` will be set to `None`. - - npix : int - Number of pixels used to compute sky statistics. - - polyarea : float - Area (in srad) of the polygon that bounds data used to compute - sky statistics. - - """ - - if len(self._images) == 0: - return None, 0, 0.0 - - wght = 0 - area = 0.0 - - if overlap is None: - # compute minimum sky across all images in the group: - wsky = None - - for image in self._images: - # make sure all images have the same background: - image.background = self._sky - - sky, npix, imarea = image.calc_sky(overlap=None, delta=delta) - - if sky is None: - continue - - if wsky is None or wsky > sky: - wsky = sky - wght = npix - area = imarea - - return wsky, wght, area - - # compute weighted sky in various overlaps: - wsky = 0.0 - - for image in self._images: - # make sure all images have the same background: - image.background = self._sky - - sky, npix, area1 = image.calc_sky(overlap=overlap, delta=delta) - - area += area1 - - if sky is not None and npix > 0: - pix_area = npix * image.pix_area - wsky += sky * pix_area - wght += pix_area - - if wght == 0.0 or area == 0.0: - return None, wght, area - else: - return wsky / wght, wght, area diff --git a/jwst/skymatch/skymatch.py b/jwst/skymatch/skymatch.py deleted file mode 100644 index ff649598c2..0000000000 --- a/jwst/skymatch/skymatch.py +++ /dev/null @@ -1,565 +0,0 @@ -""" -A module that provides functions for matching sky in overlapping images. - -:Authors: Mihai Cara - -""" -import logging -from datetime import datetime -import numpy as np - -# LOCAL -from . skyimage import SkyImage, SkyGroup - - -__all__ = ['match'] - - -__author__ = 'Mihai Cara' - - -# DEBUG -__local_debug__ = True - -log = logging.getLogger(__name__) -log.setLevel(logging.DEBUG) - - -def match(images, skymethod='global+match', match_down=True, subtract=False): - """ - A function to compute and/or "equalize" sky background in input images. - - .. note:: - Sky matching ("equalization") is possible only for **overlapping** - images. - - Parameters - ---------- - - images : list of SkyImage or SkyGroup - A list of of :py:class:`~jwst.skymatch.skyimage.SkyImage` or - :py:class:`~jwst.skymatch.skyimage.SkyGroup` objects. - - skymethod : {'local', 'global+match', 'global', 'match'}, optional - Select the algorithm for sky computation: - - * **'local'** : compute sky background values of each input image or - group of images (members of the same "exposure"). A single sky value - is computed for each group of images. - - .. note:: - This setting is recommended when regions of overlap between images - are dominated by "pure" sky (as opposed to extended, diffuse - sources). - - * **'global'** : compute a common sky value for all input images and - groups of images. With this setting `local` will compute - sky values for each input image/group, find the minimum sky value, - and then it will set (and/or subtract) the sky value of each input - image to this minimum value. This method *may* be - useful when the input images have been already matched. - - * **'match'** : compute differences in sky values between images - and/or groups in (pair-wise) common sky regions. In this case - the computed sky values will be relative (delta) to the sky computed - in one of the input images whose sky value will be set to - (reported to be) 0. This setting will "equalize" sky values between - the images in large mosaics. However, this method is not recommended - when used in conjunction with - `astrodrizzle `_ - because it computes relative sky values while `astrodrizzle` needs - "absolute" sky values for median image generation and CR rejection. - - * **'global+match'** : first use the **'match'** method to - equalize sky values between images and then find a minimum - "global" sky value amongst all input images. - - .. note:: - This is the *recommended* setting for images - containing diffuse sources (e.g., galaxies, nebulae) - covering significant parts of the image. - - match_down : bool, optional - Specifies whether the sky *differences* should be subtracted from - images with higher sky values (`match_down` = `True`) to match the - image with the lowest sky or sky differences should be added to the - images with lower sky values to match the sky of the image with the - highest sky value (`match_down` = `False`). - - .. note:: - This setting applies *only* when the `skymethod` parameter is - either `'match'` or `'global+match'`. - - subtract : bool (Default = False) - Subtract computed sky value from image data. - - - Raises - ------ - - TypeError - The `images` argument must be a Python list of - :py:class:`~jwst.skymatch.skyimage.SkyImage` and/or - :py:class:`~jwst.skymatch.skyimage.SkyGroup` objects. - - - Notes - ----- - - :py:func:`match` provides new algorithms for sky value computations - and enhances previously available algorithms used by, e.g., - `astrodrizzle `_. - - Two new methods of sky subtraction have been introduced (compared to the - standard ``'local'``): ``'global'`` and ``'match'``, as well as a - combination of the two -- ``'global+match'``. - - - The ``'global'`` method computes the minimum sky value across *all* - input images and/or groups. That sky value is then considered to be - the background in all input images. - - - The ``'match'`` algorithm is somewhat similar to the traditional sky - subtraction method (`skymethod` = `'local'`) in the sense that it - measures the sky independently in input images (or groups). The major - differences are that, unlike the traditional method, - - #. ``'match'`` algorithm computes *relative* (delta) sky values with - regard to the sky in a reference image chosen from the input list - of images; *and* - - #. Sky statistics are computed only in the part of the image - that intersects other images. - - This makes the ``'match'`` sky computation algorithm particularly useful - for "equalizing" sky values in large mosaics in which one may have - only (at least) pair-wise intersection of images without having - a common intersection region (on the sky) in all images. - - The `'match'` method works in the following way: for each pair - of intersecting images, an equation is written that - requires that average surface brightness in the overlapping part of - the sky be equal in both images. The final system of equations is then - solved for unknown background levels. - - .. warning:: - - The current algorithm is not capable of detecting cases where some - subsets of intersecting images (from the input list of images) do not - intersect at all with other subsets of intersecting images (except for - the simple case when *single* images do not intersect any other - images). In these cases the algorithm will find equalizing sky values - for each intersecting subset of images and/or groups of images. - However since these subsets of images do not intersect each other, - sky will be matched only within each subset and the "inter-subset" - sky mismatch could be significant. - - Users are responsible for detecting such cases and adjusting processing - accordingly. - - - The ``'global+match'`` algorithm combines the ``'match'`` and - ``'global'`` methods in order to overcome the limitation of the - ``'match'`` method described in the note above: it uses the ``'global'`` - algorithm to find a baseline sky value common to all input images - and the ``'match'`` algorithm to "equalize" sky values in the mosaic. - Thus, the sky value of the "reference" image will be equal to the - baseline sky value (instead of 0 in ``'match'`` algorithm alone). - - **Remarks:** - * :py:func:`match` works directly on *geometrically distorted* - flat-fielded images thus avoiding the need to perform distortion - correction on the input images. - - Initially, the footprint of a chip in an image is approximated by a - 2D planar rectangle representing the borders of chip's distorted - image. After applying distortion model to this rectangle and - projecting it onto the celestial sphere, it is approximated by - spherical polygons. Footprints of exposures and mosaics are - computed as unions of such spherical polygons while overlaps - of image pairs are found by intersecting these spherical polygons. - - **Limitations and Discussions:** - Primary reason for introducing "sky match" algorithm was to try to - equalize the sky in large mosaics in which computation of the - "absolute" sky is difficult due to the presence of large diffuse - sources in the image. As discussed above, :py:func:`match` - accomplishes this by comparing "sky values" in a pair of images in the - overlap region (that is common to both images). Quite obviously the - quality of sky "matching" will depend on how well these "sky values" - can be estimated. We use quotation marks around *sky values* because - for some image "true" background may not be present at all and the - measured sky may be the surface brightness of large galaxy, nebula, etc. - - In the discussion below we will refer to parameter names in - :py:class:`~jwst.skymatch.skystatistics.SkyStats` and these - parameter names may differ from the parameters of the actual `skystat` - object passed to initializer of the - :py:class:`~jwst.skymatch.skyimage.SkyImage`. - - Here is a brief list of possible limitations/factors that can affect - the outcome of the matching (sky subtraction in general) algorithm: - - * Since sky subtraction is performed on *flat-fielded* but - *not distortion corrected* images, it is important to keep in mind - that flat-fielding is performed to obtain uniform surface brightness - and not flux. This distinction is important for images that have - not been distortion corrected. As a consequence, it is advisable that - point-like sources be masked through the user-supplied mask files. - Values different from zero in user-supplied masks indicate "good" data - pixels. Alternatively, one can use `upper` parameter to limit the use - of bright objects in sky computations. - - * Normally, distorted flat-fielded images contain cosmic rays. This - algorithm does not perform CR cleaning. A possible way of minimizing - the effect of the cosmic rays on sky computations is to use - clipping (`nclip` > 0) and/or set `upper` parameter to a value - larger than most of the sky background (or extended source) but - lower than the values of most CR pixels. - - * In general, clipping is a good way of eliminating "bad" pixels: - pixels affected by CR, hot/dead pixels, etc. However, for - images with complicated backgrounds (extended galaxies, nebulae, - etc.), affected by CR and noise, clipping process may mask different - pixels in different images. If variations in the background are - too strong, clipping may converge to different sky values in - different images even when factoring in the "true" difference - in the sky background between the two images. - - * In general images can have different "true" background values - (we could measure it if images were not affected by large diffuse - sources). However, arguments such as `lower` and `upper` will - apply to all images regardless of the intrinsic differences - in sky levels. - - """ - function_name = match.__name__ - - # Time it - runtime_begin = datetime.now() - - log.info(" ") - log.info("***** {:s}.{:s}() started on {}" - .format(__name__, function_name, runtime_begin)) - log.info(" ") - - # check sky method: - skymethod = skymethod.lower() - if skymethod not in ['local', 'global', 'match', 'global+match']: - raise ValueError("Unsupported 'skymethod'. Valid values are: " - "'local', 'global', 'match', or 'global+match'") - do_match = 'match' in skymethod - do_global = 'global' in skymethod - show_old = subtract - - log.info("Sky computation method: '{}'".format(skymethod)) - if do_match: - log.info("Sky matching direction: {:s}" - .format("DOWN" if match_down else "UP")) - - log.info("Sky subtraction from image data: {:s}" - .format("ON" if subtract else "OFF")) - - # check that input file name is a list of either SkyImage or SkyGroup: - nimages = 0 - for img in images: - if isinstance(img, SkyImage): - nimages += 1 - elif isinstance(img, SkyGroup): - nimages += len(img) - else: - raise TypeError("Each element of the 'images' must be either a " - "'SkyImage' or a 'SkyGroup'") - - if nimages == 0: - raise ValueError("Argument 'images' must contain at least one image") - - log.debug( - "Total number of images to be sky-subtracted and/or matched: {:d}" - .format(nimages) - ) - - # Print conversion factors - log.debug(" ") - log.debug("---- Image data conversion factors:") - - for img in images: - img_type = 'Image' if isinstance(img, SkyImage) else 'Group' - - if img_type == 'Group': - log.debug(" * Group ID={}. Conversion factors:".format(img.id)) - for im in img: - log.debug(" - Image ID={}. Conversion factor = {:G}" - .format(im.id, im.convf)) - else: - log.debug(" * Image ID={}. Conversion factor = {:G}" - .format(img.id, img.convf)) - - # 1. Method: "match" (or "global+match"). - # Find sky "deltas" that will match sky across all - # (intersecting) images. - if do_match: - - log.info(" ") - log.info("---- Computing differences in sky values in " - "overlapping regions.") - - # find "optimum" sky changes: - sky_deltas = _find_optimum_sky_deltas(images, apply_sky=not subtract) - sky_good = np.isfinite(sky_deltas) - - if np.any(sky_good): - # match sky "Up" or "Down": - if match_down: - refsky = np.amin(sky_deltas[sky_good]) - else: - refsky = np.amax(sky_deltas[sky_good]) - sky_deltas[sky_good] -= refsky - - # convert to Python list and replace numpy.nan with None - sky_deltas = [ - float(skd) if np.isfinite(skd) else None for skd in sky_deltas - ] - - _apply_sky(images, sky_deltas, False, subtract, show_old) - show_old = True - - # 2. Method: "local". Compute the minimum sky background - # value in each sky group/image. - # This is an improved (use of masks) replacement - # for the classical 'subtract' used by astrodrizzle. - # - # NOTE: incompatible with "match"-containing - # 'skymethod' modes. - # - # 3. Method: "global". Compute the minimum sky background - # value *across* *all* sky line members. - if do_global or not do_match: - - log.info(" ") - if do_global: - minsky = None - log.info("---- Computing \"global\" sky - smallest sky value " - "across *all* input images.") - else: - log.info("---- Sky values computed per image and/or image " - "groups.") - - sky_deltas = [] - for img in images: - sky = img.calc_sky(delta=not subtract)[0] - sky_deltas.append(sky) - if do_global and (minsky is None or sky < minsky): - minsky = sky - - if do_global: - log.info(" ") - if minsky is None: - log.warning(" Unable to compute \"global\" sky value") - sky_deltas = len(sky_deltas) * [minsky] - log.info(" \"Global\" sky value correction: {} " - "[not converted]".format(minsky)) - - if do_match: - log.info(" ") - log.info("---- Final (match+global) sky for:") - - _apply_sky(images, sky_deltas, do_global, subtract, show_old) - - # log running time: - runtime_end = datetime.now() - log.info(" ") - log.info("***** {:s}.{:s}() ended on {}" - .format(__name__, function_name, runtime_end)) - log.info("***** {:s}.{:s}() TOTAL RUN TIME: {}" - .format(__name__, function_name, runtime_end - runtime_begin)) - log.info(" ") - - -def _apply_sky(images, sky_deltas, do_global, do_skysub, show_old): - for img, sky in zip(images, sky_deltas): - is_group = not isinstance(img, SkyImage) - - if do_global: - if sky is None: - valid = img[0].is_sky_valid if is_group else img.is_sky_valid - sky = 0.0 - else: - valid = True - - else: - valid = sky is not None - if not valid: - log.warning(" * {:s} ID={}: Unable to compute sky value" - .format('Group' if is_group else 'Image', img.id)) - sky = 0.0 - - if is_group: - # apply sky change: - old_img_sky = [im.sky for im in img] - if do_skysub: - for im in img: - im._image.set_data(im._image.get_data() - sky) - img.sky += sky - new_img_sky = [im.sky for im in img] - - # log sky values: - log.info(" * Group ID={}. Sky background of " - "component images:".format(img.id)) - - for im, old_sky, new_sky in zip(img, old_img_sky, new_img_sky): - c = 1.0 / im.convf - if show_old: - log.info(" - Image ID={}. Sky background: {:G} " - "(old={:G}, delta={:G})" - .format(im.id, c * new_sky, c * old_sky, c * sky)) - else: - log.info(" - Image ID={}. Sky background: {:G}" - .format(im.id, c * new_sky)) - - im.is_sky_valid = valid - - else: - # apply sky change: - old_sky = img.sky - if do_skysub: - img._image.set_data(img._image.get_data() - sky) - img.sky += sky - new_sky = img.sky - - # log sky values: - c = 1.0 / img.convf - if show_old: - log.info(" * Image ID={}. Sky background: {:G} " - "(old={:G}, delta={:G})" - .format(img.id, c * new_sky, c * old_sky, c * sky)) - else: - log.info(" * Image ID={}. Sky background: {:G}" - .format(img.id, c * new_sky)) - - img.is_sky_valid = valid - - -# TODO: due to a bug in the sphere package, see -# https://github.com/spacetelescope/sphere/issues/74 -# intersections with polygons formed as union does not work. -# For this reason I re-implement '_overlap_matrix' below with -# a workaround for the bug. -# The original implementation should be uncommented once the bug -# is fixed. -# - -# Original version: -# def _overlap_matrix(images, apply_sky=True): -# # TODO: to improve performance, the nested loops could be parallelized -# # since _calc_sky() here can be called independently from previous steps. -# ns = len(images) -# A = np.zeros((ns, ns), dtype=float) -# W = np.zeros((ns, ns), dtype=float) -# for i in range(ns): -# for j in range(i+1, ns): -# overlap = images[i].intersection(images[j]) -# s1, w1, area1 = images[i].calc_sky( -# overlap=overlap, -# delta=apply_sky -# ) -# s2, w2, area2 = images[j].calc_sky( -# overlap=overlap, -# delta=apply_sky -# ) -# if area1 == 0.0 or area2 == 0.0 or s1 is None or s2 is None: -# continue -# A[j,i] = s1 -# W[j,i] = w1 -# A[i,j] = s2 -# W[i,j] = w2 -# return A, W - -# bug workaround version: -def _overlap_matrix(images, apply_sky=True): - # TODO: to improve performance, the nested loops could be parallelized - # since _calc_sky() here can be called independently from previous steps. - ns = len(images) - A = np.zeros((ns, ns), dtype=float) - W = np.zeros((ns, ns), dtype=float) - - for i in range(ns): - for j in range(i + 1, ns): - s1, w1, area1 = images[i].calc_sky( - overlap=images[j], delta=apply_sky - ) - - s2, w2, area2 = images[j].calc_sky( - overlap=images[i], delta=apply_sky - ) - - if area1 == 0.0 or area2 == 0.0 or s1 is None or s2 is None: - continue - - A[j, i] = s1 - W[j, i] = w1 - A[i, j] = s2 - W[i, j] = w2 - - return A, W - - -def _find_optimum_sky_deltas(images, apply_sky=True): - ns = len(images) - A, W = _overlap_matrix(images, apply_sky=apply_sky) - - def is_valid(i, j): - return W[i, j] > 0 and W[j, i] > 0 - - # We need to know how many "non-trivial" (at least for now... - we will - # compute rank later) equations can be built so that we know the - # shape of the arrays that need to be created... - # NOTE: for now use only pairs that *both* have weights > 0 (but a - # different scenario when only one image has a valid weight can be - # considered): - neq = 0 - for i in range(ns): - for j in range(i + 1, ns): - if is_valid(i, j): - neq += 1 - - # average weights: - Wm = 0.5 * (W + W.T) - - # create arrays for coefficients and free terms: - K = np.zeros((neq, ns), dtype=float) - F = np.zeros(neq, dtype=float) - invalid = (ns) * [True] - - # now process intersections between the rest of the images: - ieq = 0 - for i in range(0, ns): - for j in range(i + 1, ns): - if is_valid(i, j): - K[ieq, i] = Wm[i, j] - K[ieq, j] = -Wm[i, j] - F[ieq] = Wm[i, j] * (A[j, i] - A[i, j]) - invalid[i] = False - invalid[j] = False - ieq += 1 - - try: - rank = np.linalg.matrix_rank(K, 1.0e-12) - except np.linalg.LinAlgError: - log.warning("Unable to compute sky: No valid data in common " - "image areas") - deltas = np.full(ns, np.nan, dtype=float) - return deltas - - if rank < ns - 1: - log.warning("There are more unknown sky values ({}) to be solved for" - .format(ns)) - log.warning("than there are independent equations available " - "(matrix rank={}).".format(rank)) - log.warning("Sky matching (delta) values will be computed only for") - log.warning("a subset (or more independent subsets) of input images.") - invK = np.linalg.pinv(K, rcond=1.0e-12) - - deltas = np.dot(invK, F) - deltas[np.asarray(invalid, dtype=bool)] = np.nan - return deltas diff --git a/jwst/skymatch/skymatch_step.py b/jwst/skymatch/skymatch_step.py index 9762a72048..bdbef2bd54 100644 --- a/jwst/skymatch/skymatch_step.py +++ b/jwst/skymatch/skymatch_step.py @@ -17,17 +17,15 @@ interpret_bit_flags, ) +from stcal.skymatch.skymatch import match +from stcal.skymatch.skyimage import SkyImage, SkyGroup +from stcal.skymatch.skystatistics import SkyStats from stdatamodels.jwst.datamodels.dqflags import pixel from jwst.datamodels import ModelLibrary from ..stpipe import Step -# LOCAL: -from .skymatch import match -from .skyimage import SkyImage, SkyGroup -from .skystatistics import SkyStats - __all__ = ['SkyMatchStep'] diff --git a/jwst/skymatch/skystatistics.py b/jwst/skymatch/skystatistics.py deleted file mode 100644 index 982d85777b..0000000000 --- a/jwst/skymatch/skystatistics.py +++ /dev/null @@ -1,131 +0,0 @@ -""" -`skystatistics` module provides statistics computation class used by -:py:func:`~jwst.skymatch.skymatch.match` -and :py:class:`~jwst.skymatch.skyimage.SkyImage`. - -:Authors: Mihai Cara (contact: help@stsci.edu) - - -""" -# THIRD PARTY -from stsci.imagestats import ImageStats -from copy import deepcopy - -__all__ = ['SkyStats'] -__taskname__ = 'skystatistics' -__author__ = 'Mihai Cara' - - -class SkyStats(): - """ - This is a superclass build on top of - :py:class:`stsci.imagestats.ImageStats`. Compared to - :py:class:`stsci.imagestats.ImageStats`, `SkyStats` has - "persistent settings" in the sense that object's parameters need to be - set once and these settings will be applied to all subsequent - computations on different data. - - """ - - def __init__(self, skystat='mean', lower=None, upper=None, - nclip=5, lsig=4.0, usig=4.0, binwidth=0.1, **kwargs): - """Initializes the SkyStats object. - - Parameters - ----------- - skystat : {'mode', 'median', 'mode', 'midpt'}, optional - Sets the statistics that will be returned by `~SkyStats.calc_sky`. - The following statistics are supported: 'mean', 'mode', 'midpt', - and 'median'. First three statistics have the same meaning as in - `stsdas.toolbox.imgtools.gstatistics `_ - while 'median' will compute the median of the distribution. - - lower : float, None, optional - Lower limit of usable pixel values for computing the sky. - This value should be specified in the units of the input image(s). - - upper : float, None, optional - Upper limit of usable pixel values for computing the sky. - This value should be specified in the units of the input image(s). - - nclip : int, optional - A non-negative number of clipping iterations to use when computing - the sky value. - - lsig : float, optional - Lower clipping limit, in sigma, used when computing the sky value. - - usig : float, optional - Upper clipping limit, in sigma, used when computing the sky value. - - binwidth : float, optional - Bin width, in sigma, used to sample the distribution of pixel - brightness values in order to compute the sky background - statistics. - - kwargs : dict - A dictionary of optional arguments to be passed to `ImageStats`. - - """ - self.npix = None - self.skyval = None - - self._fields = ','.join(['npix', skystat]) - - self._kwargs = deepcopy(kwargs) - if 'fields' in self._kwargs: - del self._kwargs['fields'] - if 'image' in self._kwargs: - del self._kwargs['image'] - self._kwargs['lower'] = lower - self._kwargs['upper'] = upper - self._kwargs['nclip'] = nclip - self._kwargs['lsig'] = lsig - self._kwargs['usig'] = usig - self._kwargs['binwidth'] = binwidth - - self._skystat = {'mean': self._extract_mean, - 'mode': self._extract_mode, - 'median': self._extract_median, - 'midpt': self._extract_midpt - }[skystat] - - def _extract_mean(self, imstat): - return imstat.mean - - def _extract_median(self, imstat): - return imstat.median - - def _extract_mode(self, imstat): - return imstat.mode - - def _extract_midpt(self, imstat): - return imstat.midpt - - def calc_sky(self, data): - """ Computes statistics on data. - - Parameters - ----------- - data : numpy.ndarray - A numpy array of values for which the statistics needs to be - computed. - - Returns - -------- - statistics : tuple - A tuple of two values: (`skyvalue`, `npix`), where `skyvalue` is - the statistics specified by the `skystat` parameter during the - initialization of the `SkyStats` object and `npix` is the number - of pixels used in computing the statistics reported in `skyvalue`. - - """ - imstat = ImageStats(image=data, fields=self._fields, - **(self._kwargs)) - self.skyval = self._skystat(imstat) - self.npix = imstat.npix - return self.skyval, self.npix - - def __call__(self, data): - return self.calc_sky(data)