def __init__(self, fig, ax, labels_and_handlers):
self.fig = fig
self.ax = ax
self.labels_and_handlers = labels_and_handlers
self.car_box = Box(-self.LENGHT/2.0, -self.WIDHT/2.0, self.LENGHT/2.0, self.WIDHT/2.0)
centerx, centery = 0, 0
radius = self.FOV_DISTANCE
start_angle, end_angle = -self.FOV_WIDE/2.0, +self.FOV_WIDE/2.0 # In degrees
# We do not really need that many, do we?
numsegments = 10
# The coordinates of the arc
theta = np.radians(np.linspace(start_angle, end_angle, numsegments))
x = centerx + radius * np.cos(theta)
x = np.insert(x, 0, 0.0)
y = centery + radius * np.sin(theta)
y = np.insert(y, 0, 0.0)
arc = LineString(np.column_stack([x, y]))
self.fov = Polygon(list(arc.coords))
def clipped_voronoi(points, bbox):
vor = scipy.spatial.Voronoi(points)
regions, vertices = voronoi_finite_polygons_2d(vor)
clip = Box(*bbox)
clipped = [clip.intersection(poly) for poly in
(Polygon(p) for p in (vertices[region] for region in regions))]
regions = [np.array(polygon.exterior.coords) for polygon in clipped]
vor.clipped_vertices = vertices
vor.clipped_regions = regions
return vor
def compare_tile_segment(coordinates, tile, image_dir, tile_images_directory):
"""
Compares whether the box bounded by the tile's original coordinates intersects the tumor
segment indicated in the xml file. Saves all tiles images.
Arguments:
coordinates: a list of tumor segments coordinates from xml annotations
tile: the tile being investigated
image_dir: directory of original WSI files
tile_images_directory: directory to which images of tiles will be saved
Returns:
Depending on the positivity of the tile:
- if positive tumor: returns the coordinates on that tile image of the tumor region(s)
- if negative: returns None, None values
"""
box = Box(tile.o_c_s, tile.o_r_s, tile.o_c_e, tile.o_r_e)
for i in range(len(coordinates)):
# We disregard coordinates with less than 2 xy values
if len(coordinates[i]) < 3:
continue
if not os.path.exists(tile_images_directory + tile.file_title + "_" + str(tile.tile_num) + '.png'):
save_tile_image(tile, image_dir, tile_images_directory)
print(tile.file_title + "_", str(tile.tile_num) + ".png image saved")
segment = Polygon(coordinates[i])
if segment.intersects(box):
segment = transform(reflection(1), segment)
box = transform(reflection(1), box)
try:
overlap = segment.intersection(box)
except:
print("Error in ", tile.file_title, " num: ", tile.tile_num, " coord index: ", i)
continue
if isinstance(overlap, MultiPolygon):
x_overlap_shifted_list = []
y_overlap_shifted_list = []
for element in overlap:
x_overlap_shifted, y_overlap_shifted = get_xy(tile, element)
x_overlap_shifted_list.append(x_overlap_shifted)
y_overlap_shifted_list.append(y_overlap_shifted)
return x_overlap_shifted_list, y_overlap_shifted_list
else:
x_overlap_shifted, y_overlap_shifted = get_xy(tile, overlap)
return x_overlap_shifted, y_overlap_shifted
else:
continue
return None, None
def main(req: func.HttpRequest) -> func.HttpResponse:
try:
trace = parse_trace(req)
db = CountryDatabase.load()
result = ({
"name": country["name"],
"continent": country["continent"]
} for country in db.query_by_box(trace.bounds)
if country["shape"].intersects(Box(*trace.bounds)))
return func.HttpResponse(json.dumps(list(result)))
except ParseException as e:
return func.HttpResponse(e.message, status_code=400)
def intersect_disks_on_globe(xs, ys, rads):
"""Return the intersection of many DiskOnGlobe objects, constructed
from three arrays of longitudes (xs), latitudes (ys), and radii (rads).
"""
assert len(xs) == len(ys) == len(rads)
result = Box(-180, -90, 180, 90)
for x, y, rad in zip(xs, ys, rads):
d = DiskOnGlobe(x, y, rad)
result = result.intersection(d)
return result
def area(self):
"""Weighted area of the nonzero region of the probability matrix."""
if self._area is None:
# Notionally, each grid point should be treated as a
# rectangle of parallels and meridians _centered_ on the
# point. The area of such a rectangle, however, only
# depends on its latitude and its breadth; the actual
# longitude values don't matter. Since the grid is
# equally spaced, we can use [0],[1] always, and then we
# do not have to worry about crossing the discontinuity at ±180.
west = self.longitudes[0]
east = self.longitudes[1]
# For latitude, the actual values do matter, but the map
# never goes all the way to the poles, and the grid is
# equally spaced, so we can precompute the north-south
# delta from any pair of latitudes and not have to worry
# about running off the ends of the array.
d_lat = (self.latitudes[1] - self.latitudes[0]) / 2
# We don't need X, so throw it away immediately. (We
# don't use iter_csr_nonzero here because we need to
# modify V.)
X, Y, V = sparse.find(self.probability)
X = None
# The value vector is supposed to be normalized, but make
# sure it is, and then adjust from 1-overall to 1-per-cell
# normalization.
assert len(V.shape) == 1
S = V.sum()
if S == 0:
return 0
if S != 1:
V /= S
V *= V.shape[0]
area = 0
for y, v in zip(Y, V):
north = self.latitudes[y] + d_lat
south = self.latitudes[y] - d_lat
if not (-90 <= south < north <= 90):
raise AssertionError(
"expected -90 <= {} < {} <= 90".format(south, north))
tile = sh_transform(wgs_to_cea, Box(west, south, east, north))
area += v * tile.area
self._area = area
return self._area
def _extract_polygons(self, data):
# This method should return a dictionary with key-value pairs of
# polygon_center : shapely polygon
for i in range(data.shape[0]):
north, east, alt, d_north, d_east, d_alt = data[i, :]
# Extract the min & max extents of the obstacle and create a box shaped
# polygon
p = Box(north - d_north, east - d_east, north + d_north,
east + d_east)
# Compute the height of the polygon
height = alt + d_alt
center = (north, east)
self._poly_dict[center] = (p, height)
self._poly_center.append(center)
def __init__(self, mapfile):
with tables.open_file(mapfile, 'r') as f:
M = f.root.baseline
if M.shape[0] == len(M.attrs.longitudes):
baseline = sparse.csr_matrix(M)
elif M.shape[1] == len(M.attrs.longitudes):
baseline = sparse.csr_matrix(M).T
else:
raise RuntimeError(
"mapfile matrix shape {!r} is inconsistent with "
"lon/lat vectors ({},{})".format(M.shape,
len(M.attrs.longitudes),
len(M.attrs.latitudes)))
# The probabilities stored in the file are not normalized.
s = baseline.sum()
assert s > 0
baseline /= s
# Note: this bound may not be tight, but it should be
# good enough. It's not obvious to me how to extract
# a tight bounding rectangle from a scipy sparse matrix.
bounds = Box(M.attrs.west, M.attrs.south, M.attrs.east,
M.attrs.north)
if not bounds.is_valid:
bounds = bounds.buffer(0)
assert bounds.is_valid
Location.__init__(self,
resolution=M.attrs.resolution,
fuzz=M.attrs.fuzz,
north=M.attrs.north,
south=M.attrs.south,
east=M.attrs.east,
west=M.attrs.west,
lon_spacing=M.attrs.lon_spacing,
lat_spacing=M.attrs.lat_spacing,
longitudes=M.attrs.longitudes,
latitudes=M.attrs.latitudes,
probability=baseline,
vacuity=False,
bounds=bounds)
def _lazy_load_pmatrix(self):
assert self._loaded_from is not None
with tables.open_file(self._loaded_from, "r") as f:
t = f.root.location
M = sparse.dok_matrix((t.attrs.lon_count, t.attrs.lat_count),
dtype=np.float32)
vacuous = True
negative_warning = False
for row in t.iterrows():
pmass = row['prob_mass']
# The occasional zero is normal, but negative numbers
# should never occur.
if pmass > 0:
M[row['grid_x'], row['grid_y']] = pmass
vacuous = False
elif pmass < 0:
if not negative_warning:
sys.stderr.write(fname + ": warning: negative pmass\n")
negative_warning = True
M = M.tocsr()
if vacuous:
wb = 0
eb = 0
sb = 0
nb = 0
else:
i, j = M.nonzero()
wb = self.longitudes[i.min()]
eb = self.longitudes[i.max()]
sb = self.latitudes[j.min()]
nb = self.latitudes[j.max()]
self._probability = M
self._vacuous = vacuous
self._bounds = Box(wb, sb, eb, nb)
def extract_patches(image, polygons, shape, stride=None, threshold=0.5):
"""Extract patches from a geocoded image
Args:
image: Filename of geocoded image or rasterio.Dataset
polygons: GeoDataFrame with labelled polygons.
shape: Desired shape of the extracted patches. Is also used to
calculate the number of extracted patches.
stride:
threshold: How many points of the extracted rectangle should be covered
by the labelled polygon? Must be a float be 0 and 1.
Yields:
A tuple of two elements: the index of the polygon and the corresponding
patch.
"""
if stride is None:
stride = shape
image_bounds = Box(*image.bounds)
BoundingBox = namedtuple(
'BoundingBox',
['col_start', 'col_end', 'row_start', 'row_end', 'height', 'width'])
# We want to extract as many rectangles from the labelled polygons as possible.
# We are working with two coordinate systems: the index system (row, column) to
# extract the pixel values from the image matrix and the geo-referenced
# coordinates (x,y) to find the patches corresponding to the labelled polygons.
for idx, polygon in polygons.iterrows():
if not polygon.geometry.is_valid:
print('Polygon {} is not valid!'.format(idx))
continue
if not polygon.geometry.intersects(image_bounds):
continue
# Extract the bounding box of the polygon, so we can divide it easily
# into sub-rectangles:
row1, col1 = image.index(polygon.geometry.bounds[0],
polygon.geometry.bounds[1])
row2, col2 = image.index(polygon.geometry.bounds[2],
polygon.geometry.bounds[3])
polygon_bbox = BoundingBox(col_start=min([col1, col2]),
col_end=max([col1, col2]),
row_start=min([row1, row2]),
row_end=max([row1, row2]),
height=abs(row2 - row1),
width=abs(col2 - col1))
for column in range((polygon_bbox.width // stride[0]) + 1):
for row in range((polygon_bbox.height // stride[1]) + 1):
# Transform the patch bounding box indices to coordinates to
# calculate the percentage that is covered by the labelled
# polygon:
x1, y1 = image.xy(polygon_bbox.row_start + row * stride[1],
polygon_bbox.col_start + column * stride[0])
x2, y2 = image.xy(
polygon_bbox.row_start + row * stride[1] + shape[1],
polygon_bbox.col_start + column * stride[0] + shape[1])
patch_bounds = Box(x1, y1, x2, y2)
# We check first whether the threshold condition is fullfilled
# and then we extract the patch from the image:
overlapping_area = \
polygon.geometry.intersection(patch_bounds).area
if overlapping_area / patch_bounds.area < threshold:
# The labelled polygon covers less than $threshold$ of the
# whole patch, i.e. we reject it:
continue
# rasterio returns data in CxHxW format, so we have to transpose
# it:
patch = image.read(
window=Window(polygon_bbox.col_start +
column * stride[0], polygon_bbox.row_start +
row * stride[1], shape[1], shape[0])).T
# The fourth channel shows the alpha (transparency) value. We do not
# allow patch with transparent pixels:
if not patch.size or (patch.shape[-1] == 4
and 0 in patch[..., 3]):
continue
yield idx, patch
def DiskOnGlobe(x, y, radius):
"""Return a shapely polygon which is a circle centered at longitude X,
latitude Y, with radius RADIUS (meters), projected onto the
surface of the Earth.
"""
# Make sure the radius is at least 1km to prevent underflow.
radius = max(radius, 1000)
# If the radius is too close to half the circumference of the
# Earth, the projection operation below will produce an invalid
# polygon. We don't get much use out of a region that includes
# the whole planet but for a tiny disk (which will probably be
# somewhere in the ocean anyway) so just give up and say that the
# region is the entire planet.
if radius > 19975000:
return Box(-180, -90, 180, 90)
# To find all points on the Earth within a certain distance of
# a reference latitude and longitude, back-project onto the
# Earth from an azimuthal-equidistant map with its zero point
# at the reference latitude and longitude.
aeqd = pyproj.Proj(proj='aeqd', ellps='WGS84', datum='WGS84', lat_0=y, lon_0=x)
disk = sh_transform(
functools.partial(pyproj.transform, aeqd, wgs_proj),
Point(0, 0).buffer(radius, resolution=64))
# Two special cases must be manually dealt with. First, if any
# side of the "disk" (really a many-sided polygon) crosses the
# coordinate singularity at longitude ±180, we must replace that
# side with a diversion to either the north or south pole
# (whichever is closer) to ensure the diskstill encloses all of
# the area it should.
boundary = np.array(disk.boundary)
i = 0
while i < boundary.shape[0] - 1:
if abs(boundary[i+1,0] - boundary[i,0]) > 180:
pole = -90 if boundary[i,1] < 0 else 90
west = -180 if boundary[i,0] < 0 else 180
east = 180 if boundary[i,0] < 0 else -180
boundary = np.insert(boundary, i+1, [
[west, boundary[i,1]],
[west, pole],
[east, pole],
[east, boundary[i+1,1]]
], axis=0)
i += 5
else:
i += 1
# If there were two sides that crossed the singularity and they
# were both on the same side of the equator, the excursions will
# coincide and shapely will be unhappy. buffer(0) corrects this.
disk = Polygon(boundary).buffer(0)
# Second, if the radius is very large, the projected disk might
# enclose the complement of the region that it ought to enclose.
# If it doesn't contain the reference point, we must subtract it
# from the entire map.
origin = Point(x, y)
if not disk.contains(origin):
disk = Box(-180, -90, 180, 90).difference(disk)
assert disk.is_valid
assert disk.contains(origin)
return disk
def tx_geojson(responses):
from itertools import takewhile
from shapely.geometry import Point, GeometryCollection, Polygon, box as Box
transformed = []
xs = []
ys = []
labels = []
arr3d = []
polygons = []
colors = ["royalblue", "crimson", "lightseagreen", "orange"]
my_traces = []
buffer = 0.05
for i, obj in enumerate(responses):
color = colors[i % len(colors)]
label = f"Name: {obj['display_name']}<br>Centroid: {obj['lat']},{obj['lon']}"
points = []
geojson = obj["geojson"]
points = []
print(json.dumps(obj))
if geojson["type"] == "Polygon":
for shape in geojson["coordinates"]:
print(f"shape: {shape}")
for point in shape:
print(f"Point: {point}")
points.append(point)
poly = Polygon([point for point in points])
buffered = poly.buffer(buffer)
elif geojson["type"] == "Point":
x1, x2, y1, y2 = [float(x) for x in obj["boundingbox"]]
xy = sorted([x1, x2]) + sorted([y1, y2])
minx, maxx, miny, maxy = xy
box = Box(minx, miny, maxx, maxy)
buffered = box.buffer(buffer)
else:
print(geojson)
print(f"Weird type: {geojson['type']}")
continue
hull = list(buffered.convex_hull.exterior.coords)
simplex = []
for g in grouper(4, hull, fillvalue=hull[-1]):
print(f"Next group is: {g}")
print(f"Appending {g[0]}")
simplex.append(list(reversed(g[0])))
poly = Polygon(simplex)
polygons.append(poly)
coords = list(poly.exterior.coords)
center = list(poly.centroid.coords)
print(f"Coords are: {coords}")
arr2d = []
_xs = []
_ys = []
_lab = []
for x, y in coords:
x, y = list(sorted([x, y]))
print(f"x:{x}, y:{y}")
arr2d.append([x, y])
_xs.append(x)
_ys.append(y)
_lab.append(label)
arr3d.append(arr2d)
labels.extend(_lab + [None])
xs.extend(_xs + [None])
ys.extend(_ys + [None])
_tx = copy(obj)
_tx["geojson"] = {"type": "Polygon", "coordinates": [arr2d]}
trace = {
"fill": "toself",
"hoverinfo": "all",
"mode": "lines+text",
"text": _lab,
"lon": _xs,
"lat": _ys,
"selected": {
"marker": {
"opacity": 1 / (len(responses) + 1) * i
}
},
"name": obj["display_name"],
"marker": {
"size": 10,
"color": color
},
}
print(json.dumps(trace))
transformed.append(_tx)
my_traces.append(trace)
print(my_traces)
arr2d = list(flatten_list(arr3d))
polygons = GeometryCollection(polygons)
# area = {}
# for trace, poly in zip(my_traces, polygons):
# area[trace['name']] = poly.area
# my_traces = list(sorted(my_traces, key=lambda trace: area[trace['name']]))
centroids = sorted(list(polygons.centroid.coords))
centroid = (
sum([x for x, y in centroids]) / (1 + len(centroids)),
sum([y for x, y in centroids]) / (1 + len(centroids)),
)
for trace in my_traces:
print(json.dumps(trace, indent=4))
out = {
"traces": my_traces,
"centroids": centroid,
"centroid": centroid,
"lats": xs,
"longs": ys,
"geom": polygons,
"labels": labels,
"points": arr2d,
"polygons": arr3d,
"data": transformed,
}
return Munch(out)
def plotproj(plotdef, data, outdir):
'''
Plot map.
'''
axes = plt.axes()
box = Box(
plotdef['lonmin'], plotdef['latmin'],
plotdef['lonmax'], plotdef['latmax'])
for feat in data["features"]:
geom = shape(feat["geometry"])
if not geom.intersects(box):
continue
temp_pol = geom.intersection(box)
if plotdef['type'] == 'poly':
if isinstance(temp_pol, MultiPolygon):
polys = [resample_polygon(polygon) for polygon in temp_pol.geoms]
pol = MultiPolygon(polys)
else:
pol = resample_polygon(temp_pol)
else:
pol = temp_pol
trans = functools.partial(project_xy, proj_string=plotdef['projstring'])
proj_geom = transform(trans, pol)
if plotdef['type'] == 'poly':
try:
patch = PolygonPatch(proj_geom, fc=COLOR_LAND, zorder=0)
axes.add_patch(patch)
except TypeError:
pass
else:
x, y = proj_geom.xy
axes.plot(x, y, color=COLOR_COAST, linewidth=0.5)
# Plot frame
frame = [
parallel(plotdef['latmin'], plotdef['lonmin'], plotdef['lonmax']),
parallel(plotdef['latmax'], plotdef['lonmin'], plotdef['lonmax']),
]
for line in frame:
line = project(line, plotdef['projstring'])
x = line[:, 0]
y = line[:, 1]
axes.plot(x, y, '-k')
graticule = build_graticule(
plotdef['lonmin'],
plotdef['lonmax'],
plotdef['latmin'],
plotdef['latmax'],
)
# Plot graticule
for feature in graticule:
feature = project(feature, plotdef['projstring'])
x = feature[:, 0]
y = feature[:, 1]
axes.plot(x, y, color=COLOR_GRAT, linewidth=0.4)
# Switch off the axis lines...
plt.axis('off')
# ... and additionally switch off the visibility of the axis lines and
# labels so they can be removed by "bbox_inches='tight'" when saving
axes.get_xaxis().set_visible(False)
axes.get_yaxis().set_visible(False)
font = {
'family': 'serif',
'color': 'black',
'style': 'italic',
'size': 12
}
# Make sure the plot is not stretched
axes.set_aspect('equal')
outdir = Path(outdir)
if not outdir.exists():
outdir.mkdir(parents=True)
if not outdir.is_dir():
raise OSError("outdir is not a directory")
plt.savefig(outdir / plotdef['filename'],
dpi=400,
bbox_inches='tight')
# Clean up
axes = None
del axes
plt.close()
def to_box(box: typ.Tuple[int, int, int, int]) -> Box:
"""Converts box [top, left, right, bottom] to shapely.Box"""
x, y, w, h = box
return Box(x, y, x + w, y + h)
def compute_bounding_region_now(self):
if self._bounds is not None: return
distance_bound = self.range_fn.distance_bound()
# If the distance bound is too close to half the circumference
# of the Earth, the projection operation below will produce an
# invalid polygon. We don't get much use out of a bounding
# region that includes the whole planet but for a tiny disk
# (which will probably be somewhere in the ocean anyway) so
# just give up and say that the bound is the entire planet.
# Similarly, if the distance bound is zero, give up.
if distance_bound > 19975000 or distance_bound == 0:
self._bounds = Box(self.west, self.south, self.east, self.north)
return
# To find all points on the Earth within a certain distance of
# a reference latitude and longitude, back-project onto the
# Earth from an azimuthal-equidistant map with its zero point
# at the reference latitude and longitude.
aeqd = pyproj.Proj(proj='aeqd',
ellps='WGS84',
datum='WGS84',
lat_0=self.ref_lat,
lon_0=self.ref_lon)
try:
disk = sh_transform(
functools.partial(pyproj.transform, aeqd, wgs_proj),
Disk(0, 0, distance_bound))
# Two special cases must be manually dealt with. First, if
# any side of the "circle" (really a many-sided polygon)
# crosses the coordinate singularity at longitude ±180, we
# must replace it with a diversion to either the north or
# south pole (whichever is closer) to ensure that it still
# encloses all of the area it should.
boundary = np.array(disk.boundary)
i = 0
while i < boundary.shape[0] - 1:
if abs(boundary[i + 1, 0] - boundary[i, 0]) > 180:
pole = self.south if boundary[i, 1] < 0 else self.north
west = self.west if boundary[i, 0] < 0 else self.east
east = self.east if boundary[i, 0] < 0 else self.west
boundary = np.insert(
boundary,
i + 1, [[west, boundary[i, 1]], [west, pole],
[east, pole], [east, boundary[i + 1, 1]]],
axis=0)
i += 5
else:
i += 1
# If there were two edges that crossed the singularity and they
# were both on the same side of the equator, the excursions will
# coincide and shapely will be unhappy. buffer(0) corrects this.
disk = Polygon(boundary).buffer(0)
# Second, if the disk is very large, the projected disk might
# enclose the complement of the region that it ought to enclose.
# If it doesn't contain the reference point, we must subtract it
# from the entire map.
origin = Point(self.ref_lon, self.ref_lat)
if not disk.contains(origin):
disk = (Box(self.west, self.south, self.east,
self.north).difference(disk))
assert disk.is_valid
assert disk.contains(origin)
self._bounds = disk
except Exception as e:
setattr(e, 'offending_disk', disk)
setattr(e, 'offending_obs', self)
raise