def selectArea(self, ptlist, latlon=False, reduced=None):
"""Select an area of the grid.
Parameters
----------
ptlist : list
latlon : bool
reduced : int
The amount by which the index array should be short (i.e., 1 for
basic difference, 2 for center difference).
"""
ptlist = np.asarray(ptlist)
if latlon:
ptlist[:,0], ptlist[:,1] = self.basemap(ptlist[:,0], ptlist[:,1])
# create the polygon
path = Path(ptlist)
if reduced is not None:
X, Y = np.meshgrid(self.x[:-reduced], self.y[:-reduced])
areaind = path.contains_points(zip(X.flatten(), Y.flatten()))
areaind = areaind.reshape((self.shape[0]-reduced,
self.shape[1]-reduced))
else:
X, Y = np.meshgrid(self.x, self.y)
areaind = path.contains_points(zip(X.flatten(), Y.flatten()))
areaind = areaind.reshape(self.shape)
# return array indices
return areaind
def reverse_geocode(tweet):
# print index
# latlong = json.load(tweets)[index]['coordinates']
latlong = tweet["coordinates"]
if latlong == [0.0, 0.0]:
return False
# latlong.reverse()
with open('world-countries.json.txt', 'r') as countries_json:
found_country = None
countries = json.load(countries_json)['features']
for country in countries:
country_name = country['properties']['name']
if country['geometry']['type'] == 'Polygon':
country_vertices = country['geometry']['coordinates'][0]
country_path = Path(country_vertices)
if country_path.contains_point(latlong):
found_country = country_name
break
if country['geometry']['type'] == 'MultiPolygon':
country_polygons = country['geometry']['coordinates']
for polygon in country_polygons:
country_vertices = polygon[0]
country_path = Path(country_vertices)
if country_path.contains_point(latlong):
found_country = country_name
break
if not found_country:
found_country = False
return found_country
# with open('Ferguson_tweets.txt', 'r') as tweets:
# print reverse_geocode(tweets, 0)
def processPolygon(polygon, rows, columns, mode):
"""
Finds the points within a particular polygon
"""
length = len(polygon)
polygon.append((0.0, 0.0))
codes = [Path.MOVETO]
for index in range(length - 1):
codes.append(Path.LINETO)
codes.append(Path.CLOSEPOLY)
path = Path(polygon, codes)
points = []
if mode == 'V':
for index in range(rows):
row = [(x, index) for x in range(columns)]
check = path.contains_points(row)
temp_points = ([row[i] for i, j in enumerate(check) if j == True and not contains(row[i], polygon)])
if (len(temp_points) > 0):
points.append(temp_points)
else:
for index in range(columns):
col = [(index, x) for x in range(rows)]
check = path.contains_points(col)
temp_points = ([col[i] for i, j in enumerate(check) if j == True and not contains(col[i], polygon)])
if (len(temp_points) > 0):
points.append(temp_points)
return points
def __init__(self, shape, scale=1):
"""
Initalize a Warper with a reference shape with coordinates in the
numpy array 'shape'
"""
xy = shape.copy() * scale
self.scale = scale
xy = self.shape_to_xy(xy)
xy = xy - np.min(xy,axis=0)
dt = scipy.spatial.Delaunay(xy)
# Define a grid
cols = int(np.ceil(np.max(xy[:,0])))
rows = int(np.ceil(np.max(xy[:,1])))
xx, yy = np.meshgrid(range(cols),range(rows))
xy_grid = np.vstack((xx.flatten(),yy.flatten())).T
# Define a mask
mask = Path(xy).contains_points(xy_grid)
self.mask = mask.reshape(xx.shape)
xy_grid = xy_grid[mask==True,:] # Remove pts not inside mask
# Calculate barycentric coordinates for all points inside mask
simplex_ids = dt.find_simplex(xy_grid)
bary_coords = points_to_bary(dt,simplex_ids,xy_grid)
self.tri = dt.simplices
self.warp_template = np.hstack((simplex_ids[:,np.newaxis],bary_coords))
def transform_path_non_affine(self, path):
# Adaptive interpolation:
# we keep adding control points, till all control points
# have an error of less than 0.01 (about 1%)
# or if the number of control points is > 80.
ra0 = self.ra0
path = path.cleaned(curves=False)
v = path.vertices
diff = v[:, 0] - v[0, 0]
v00 = v[0][0] - ra0
while v00 > 180: v00 -= 360
while v00 < -180: v00 += 360
v00 += ra0
v[:, 0] = v00 + diff
nonstop = path.codes > 0
path = Path(v[nonstop], path.codes[nonstop])
isteps = path._interpolation_steps * 2
while True:
ipath = path.interpolated(isteps)
tiv = self.transform(ipath.vertices)
itv = Path(self.transform(path.vertices)).interpolated(isteps).vertices
if np.mean(np.abs(tiv - itv)) < 0.01:
break
if isteps > 20:
break
isteps = isteps * 2
return Path(tiv, ipath.codes)
def make_venn3_region_patch(region):
'''
Given a venn3 region (as returned from compute_venn3_regions) produces a Patch object,
depicting the region as a curve.
>>> centers, radii = solve_venn3_circles((1, 1, 1, 1, 1, 1, 1))
>>> regions = compute_venn3_regions(centers, radii)
>>> patches = [make_venn3_region_patch(r) for r in regions]
'''
if region is None or len(region[0]) == 0:
return None
if region[0] == "CIRCLE":
return Circle(region[1][0], region[1][1])
pts, arcs, label_pos = region
path = [pts[0]]
for i in range(len(pts)):
j = (i + 1) % len(pts)
(center, radius, direction) = arcs[i]
fromangle = vector_angle_in_degrees(pts[i] - center)
toangle = vector_angle_in_degrees(pts[j] - center)
if direction:
vertices = Path.arc(fromangle, toangle).vertices
else:
vertices = Path.arc(toangle, fromangle).vertices
vertices = vertices[np.arange(len(vertices) - 1, -1, -1)]
vertices = vertices * radius + center
path = path + list(vertices[1:])
codes = [1] + [4] * (len(path) - 1)
return PathPatch(Path(path, codes))
def _gating(self,DF_array_data,x_ax,y_ax,coords):
#np.ones(DF_array_data.shape[0],dtype=bool)
gate=Path(coords,closed=True)
projection=np.array(DF_array_data[[x_ax,y_ax]])
index=gate.contains_points(projection)
return index
def estimate_mean_extinction(self, poly):
"""Estimate the mean extinction Av in within a footprint.
Parameters
----------
poly : ndarray
The RA,Dec polygon (a rectangle) defining the footprint.
"""
sigma_dust = self._f[0].data
ny, nx = sigma_dust.shape
# Make a coordinate grid out of RA, Dec across the dust map
y_image, x_image = np.mgrid[0:ny, 0:nx]
y = y_image.reshape(nx * ny)
x = x_image.reshape(nx * ny)
ra, dec = self._wcs.all_pix2world(x, y, 0)
points = np.vstack((ra, dec)).T
# Find all pixels in the footprint
path = Path(poly, closed=False)
in_poly = path.contains_points(points)
s = np.where(in_poly)[0]
dust_pixels = sigma_dust[y[s], x[s]]
mean = np.nanmean(dust_pixels)
# Estimate Av from the Lewis et al attenuation law
return 10. ** (-5.4) * mean
def contained_in(lat, lng, bound_coords):
"""
Returns true if (lat, lng) is contained within the polygon formed by the
points in bound_coords.
"""
bound_path = Path(np.array(bound_coords))
return bound_path.contains_point((lat, lng))
def path_contains_points(verts, points):
p = Path(verts, closed=True)
result = num.zeros(points.shape[0], dtype=num.bool)
for i in range(result.size):
result[i] = p.contains_point(points[i, :])
return result
def get_path( img, verts ):
#verts=array( verts, int)
path1 = Path(verts)
print path1
dx,dy=img.shape
data = zeros( [dx,dy,2])
data[:,:,0]= range(dx)
for i in range(dy):
data[i,:,1] = i
#print data
data=data.reshape( [dx*dy,2])
#print data.shape
#print path1,data
index = path1.contains_points(data)
print index.shape, len(where(index)[0])
#print data[index, :2]
#plot(data[:,0],data[:,1], 'b.')
fig, ax = plt.subplots(nrows=1)
vmin=img.min();vmax=img.max()
ax.imshow( img,cmap=plt.get_cmap('winter'), vmin=vmin,vmax=vmax )
#ax.set_xlim(0,dx-1)
#ax.set_ylim(0,dy-1)
patch = patches.PathPatch(path1, facecolor='orange', lw=2)
gca().add_patch(patch)
plot(data[index,0], data[index,1], 'r.')
show()
def Ablate_outside_area(n_pixels, contour_coords):
''' Function takes points from contour and returns list of coordinates
lying outside of the contour - to be used to ablate image '''
#Search points outside and black them out:
all_points = []
for i in range(n_pixels):
for j in range(n_pixels):
all_points.append([i,j])
all_points = np.array(all_points)
vertixes = np.array(contour_coords)
vertixes_path = Path(vertixes)
mask = vertixes_path.contains_points(all_points)
ablate_coords=[]
counter=0
for i in range(n_pixels):
for j in range(n_pixels):
if mask[counter] == False:
#images_processed[100][i][j]=0
ablate_coords.append([i,j])
counter+=1
return ablate_coords
def _filter_block(vertices, block_origin, block_shape):
"""
Keyword arguments:
vertices --
block_origin_list --
block_shape --
Return values
-- True/False vertices contain block
"""
# check arguments
# create path object
path = Path(vertices, closed=True)
# create path for the block
x0 = block_origin[0]
y0 = block_origin[1]
w = block_shape[0]
h = block_shape[1]
box_vertices = np.asarray([[x0, y0], [x0 + w, y0], [x0 + w, y0 + h], [x0, y0 + h]])
box = Path(box_vertices, closed=True)
# determine if points inside the specified path
# Note: there appears to be an error in contains_points(). For
# example, reversing the direction of the vertices requires raidus=-0.01
# to be specified. See the e-mails in the link below
# http://matplotlib.1069221.n5.nabble.com/How-to-properly-use-path-Path-contains-point-tc40718.html#none
return path.contains_path(box)
def number_of_images(self, sourceposition):
rc=self.radial_caustic()
tc=self.tangential_caustic()
if usePath:
# New Matplotlib:
rc=Path(rc)
tc=Path(tc)
if rc.contains_points(np.atleast_2d(sourceposition))[0]:
if tc.contains_points(np.atleast_2d(sourceposition))[0]:
return 4
return 2
if tc.contains_points(np.atleast_2d(sourceposition))[0]:
return 3
else:
# Old Matplotlib:
if nxutils.points_inside_poly(np.atleast_2d(sourceposition),rc)[0]:
if nxutils.points_inside_poly(np.atleast_2d(sourceposition),tc)[0]:
return 4
return 2
if nxutils.points_inside_poly(np.atleast_2d(sourceposition),tc)[0]:
return 3
return 1
def distribute_pixels(self, edges, length, width):
corners = self.get_corners()
reg_path = Path(corners)
# Get region boundaries.
bounds = reg_path.get_extents().get_points()
[[x_min_bound, y_min_bound], [x_max_bound, y_max_bound]] = bounds
# For cases when the boundary pixels are not integers:
x_min_bound = floor(x_min_bound)
y_min_bound = floor(y_min_bound)
x_max_bound = ceil(x_max_bound)
y_max_bound = ceil(y_max_bound)
pixels_in_bins = []
for x in range(max(0, x_min_bound), min(x_max_bound+1, width)):
for y in range(max(0, y_min_bound), min(y_max_bound+1, length)):
if reg_path.contains_point((x, y)):
x_nonrotated, y_nonrotated = rotate_point(self.x0, self.y0,
x - self.x0,
y - self.y0,
-self.angle)
dist_from_box_bottom = self.height/2. - \
(self.y0 - y_nonrotated)
for i, edge in enumerate(edges[1:]):
if edge > dist_from_box_bottom:
pixels_in_bins.append((y, x, i))
break
return pixels_in_bins
def test_start_with_moveto():
# Should be entirely clipped away to a single MOVETO
data = b"""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"""
verts = np.frombuffer(base64.decodebytes(data), dtype='<i4')
verts = verts.reshape((len(verts) // 2, 2))
path = Path(verts)
segs = path.iter_segments(transforms.IdentityTransform(),
clip=(0.0, 0.0, 100.0, 100.0))
segs = list(segs)
assert len(segs) == 1
assert segs[0][1] == Path.MOVETO
def onselect(self, verts):
path = Path(verts)
self.ind = np.nonzero([path.contains_point(xy) for xy in self.xys])[0]
self.fc[:, -1] = self.alpha_other
self.fc[self.ind, -1] = 1
self.collection.set_facecolors(self.fc)
self.canvas.draw_idle()
def test_path_no_doubled_point_in_to_polygon():
hand = np.array(
[[1.64516129, 1.16145833],
[1.64516129, 1.59375],
[1.35080645, 1.921875],
[1.375, 2.18229167],
[1.68548387, 1.9375],
[1.60887097, 2.55208333],
[1.68548387, 2.69791667],
[1.76209677, 2.56770833],
[1.83064516, 1.97395833],
[1.89516129, 2.75],
[1.9516129, 2.84895833],
[2.01209677, 2.76041667],
[1.99193548, 1.99479167],
[2.11290323, 2.63020833],
[2.2016129, 2.734375],
[2.25403226, 2.60416667],
[2.14919355, 1.953125],
[2.30645161, 2.36979167],
[2.39112903, 2.36979167],
[2.41532258, 2.1875],
[2.1733871, 1.703125],
[2.07782258, 1.16666667]])
(r0, c0, r1, c1) = (1.0, 1.5, 2.1, 2.5)
poly = Path(np.vstack((hand[:, 1], hand[:, 0])).T, closed=True)
clip_rect = transforms.Bbox([[r0, c0], [r1, c1]])
poly_clipped = poly.clip_to_bbox(clip_rect).to_polygons()[0]
assert np.all(poly_clipped[-2] != poly_clipped[-1])
assert np.all(poly_clipped[-1] == poly_clipped[0])
def test_point_in_path_nan():
box = np.array([[0, 0], [1, 0], [1, 1], [0, 1], [0, 0]])
p = Path(box)
test = np.array([[np.nan, 0.5]])
contains = p.contains_points(test)
assert len(contains) == 1
assert not contains[0]
def _endGate(self, event):
#draw gate rectangle
start_x = self.start_x if self.start_x < event.xdata else event.xdata
start_y = self.start_y if self.start_y < event.ydata else event.ydata
width = np.absolute(event.xdata-self.start_x)
height = np.absolute(event.ydata-self.start_y)
rect = Rectangle((start_x, start_y), width, height,
fill=False, ec='black', alpha=1, lw=2)
self.ax.add_patch(rect)
self.canvas.draw()
#disable mouse events
self.canvas.mpl_disconnect(self.buttonPress)
self.canvas.mpl_disconnect(self.buttonRelease)
self.canvas.get_tk_widget().config(cursor='arrow')
#save cell gate
gate = Path([[start_x, start_y],
[start_x + width, start_y],
[start_x + width, start_y + height],
[start_x, start_y + height],
[start_x, start_y]])
gated_cells = self.scdata.tsne.index[gate.contains_points(self.scdata.tsne)]
self.gates[self.gateName.get()] = gated_cells
#replot tSNE w gate colored
self.fig.clf()
plt.scatter(self.scdata.tsne['x'], self.scdata.tsne['y'], s=10, edgecolors='none', color='lightgrey')
plt.scatter(self.scdata.tsne.ix[gated_cells, 'x'], self.scdata.tsne.ix[gated_cells, 'y'], s=10, edgecolors='none')
self.canvas.draw()
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
def pca_var(sub_dims):
data = np.array([df[d] for d in sub_dims]).T
try: pca = PCA(data, standardize=True)
except: return 0,1,0,1,None,None,None,sub_dims
classed_points = zip(classes, pca.Y)
pos = [(it[0], it[1]) for c, it in classed_points if c]
neg = [(it[0], it[1]) for c, it in classed_points if not c]
P_hull = [pos[i] for i in ConvexHull(pos).vertices]; P_hull.append(P_hull[0])
N_hull = [neg[i] for i in ConvexHull(neg).vertices]; N_hull.append(N_hull[0])
P_hull = np.array(P_hull)
N_hull = np.array(N_hull)
P_path = Path(P_hull)
N_path = Path(N_hull)
N_sep = 0
for it in neg:
if not P_path.contains_point(it):
N_sep += 1
P_sep = 0
for it in pos:
if not N_path.contains_point(it):
P_sep += 1
return N_sep, float(len(neg)), P_sep, float(len(pos)), P_hull, N_hull, pca, sub_dims
def paths_in_shape(paths):
shape = shape_(shape_path)
minx, miny, maxx, maxy = shape.bounds
#print minx; print miny; print maxx; print maxy
#bounding_box = geometry.box(minx, miny, maxx, maxy)
#generate random points within bounding box!
sf = shapefile.Reader(shape_path)
shape = sf.shapes()[0]
#find polygon nodes lat lons
verticies = shape.points
#convert to a matplotlib path class!
polygon = Path(verticies)
points_in_shape = polygon.contains_points(paths)
points_in_shape = paths[points_in_shape == True]
return points_in_shape
def get_mask_img(transform, target_bin, camera_model):
"""
:param point: point that is going to be transformed
:type point: PointStamped
:param transform: camera_frame -> bbox_frame
:type transform: Transform
"""
# check frame_id of a point and transform just in case
assert camera_model.tf_frame == transform.header.frame_id
assert target_bin.bbox.header.frame_id == transform.child_frame_id
transformed_list = [
do_transform_point(corner, transform)
for corner in target_bin.corners]
projected_points = project_points(transformed_list, camera_model)
# generate an polygon that covers the region
path = Path(projected_points)
x, y = np.meshgrid(
np.arange(camera_model.width),
np.arange(camera_model.height))
x, y = x.flatten(), y.flatten()
points = np.vstack((x, y)).T
mask_img = path.contains_points(
points).reshape(
camera_model.height, camera_model.width
).astype('bool')
return mask_img
def subsample(self, vertices):
xiyi = np.vstack((self.traj_lon[0,:], self.traj_lat[0,:])).T
mpath = MplPath( vertices )
outside_area = ~mpath.contains_points(xiyi)
self.init_x, self.init_y, self.init_z, self.init_s, \
self.traj_lon, self.traj_lat, self.traj_depth, self.traj_time, self.final_z = \
[x.compress(outside_area,axis=-1) for x in (self.init_x, self.init_y, self.init_z, self.init_s,
self.traj_lon, self.traj_lat, self.traj_depth, self.traj_time, self.final_z)]
def check_paths(path):
for other_path in a:
res = 'no cross'
chck = Path(other_path)
if chck.contains_path(path) == 1:
res = 'cross'
break
return res
def __init__(self):
self.inner_path = Path(inner)
self.outer_path = Path(outer)
self.lines = list()
for arr in (inner, outer):
for i in range(len(arr)-1):
self.lines.append(self.get_line_from_two_points(arr[i], arr[i+1]))
def test_point_in_path():
# Test #1787
verts2 = [(0, 0), (0, 1), (1, 1), (1, 0), (0, 0)]
path = Path(verts2, closed=True)
points = [(0.5, 0.5), (1.5, 0.5)]
assert np.all(path.contains_points(points) == [True, False])
def draw_star(ax, x, y, color, scale=0.1):
path = Path(unit_star.vertices * scale, unit_star.codes)
trans = matplotlib.transforms.Affine2D().translate(x, y)
t_path = path.transformed(trans)
patch = patches.PathPatch(t_path, facecolor=color.value, lw=line_weight, zorder=2)
a = ax.add_patch(patch)
ma = MonosaccharidePatch(saccharide_shape=(a,))
return ma
def segments_in_polygon(segments, poly_verts):
"""Go to the centroid of each segment, see if it is in the polygon
"""
segments = np.array(segments, dtype=float)
pt1 = segments[:, 0]
pt2 = segments[:, 1]
centroids = (pt1 + pt2) / 2.
p = Path(poly_verts)
return p.contains_points(centroids)
def test_point_in_path():
# Test #1787
verts2 = [(0, 0), (0, 1), (1, 1), (1, 0), (0, 0)]
path = Path(verts2, closed=True)
points = [(0.5, 0.5), (1.5, 0.5)]
ret = path.contains_points(points)
assert ret.dtype == 'bool'
assert np.all(ret == [True, False])
def onselect(self, verts):
path = Path(verts)
self.poly_mask = poly2mask(self.x, self.y, path)
self.canvas.draw_idle()
c1x_left, c1y_left, c1x_right, c1y_right = \
get_normal_points(c1x, c1y, cos_t1, sin_t1, width*w1)
c3x_left, c3y_left, c3x_right, c3y_right = \
get_normal_points(c3x, c3y, cos_t2, sin_t2, width*w2)
# find c12, c23 and c123 which are middle points of c1-cm, cm-c3 and c12-c23
c12x, c12y = (c1x + cmx) * .5, (c1y + cmy) * .5
c23x, c23y = (cmx + c3x) * .5, (cmy + c3y) * .5
c123x, c123y = (c12x + c23x) * .5, (c12y + c23y) * .5
# tangential angle of c123 (angle between c12 and c23)
cos_t123, sin_t123 = get_cos_sin(c12x, c12y, c23x, c23y)
c123x_left, c123y_left, c123x_right, c123y_right = \
get_normal_points(c123x, c123y, cos_t123, sin_t123, width*wm)
path_left = find_control_points(c1x_left, c1y_left, c123x_left, c123y_left,
c3x_left, c3y_left)
path_right = find_control_points(c1x_right, c1y_right, c123x_right,
c123y_right, c3x_right, c3y_right)
return path_left, path_right
if 0:
path = Path([(0, 0), (1, 0), (2, 2)],
[Path.MOVETO, Path.CURVE3, Path.CURVE3])
left, right = divide_path_inout(path, inside)
clf()
ax = gca()
class Ticks(AttributeCopier, Line2D):
"""
Ticks are derived from Line2D, and note that ticks themselves
are markers. Thus, you should use set_mec, set_mew, etc.
To change the tick size (length), you need to use
set_ticksize. To change the direction of the ticks (ticks are
in opposite direction of ticklabels by default), use
set_tick_out(False).
"""
def __init__(self, ticksize, tick_out=False, *, axis=None, **kwargs):
self._ticksize = ticksize
self.locs_angles_labels = []
self.set_tick_out(tick_out)
self._axis = axis
if self._axis is not None:
if "color" not in kwargs:
kwargs["color"] = "auto"
if "mew" not in kwargs and "markeredgewidth" not in kwargs:
kwargs["markeredgewidth"] = "auto"
Line2D.__init__(self, [0.], [0.], **kwargs)
self.set_snap(True)
def get_ref_artist(self):
# docstring inherited
return self._axis.majorTicks[0].tick1line
def get_color(self):
return self.get_attribute_from_ref_artist("color")
def get_markeredgecolor(self):
return self.get_attribute_from_ref_artist("markeredgecolor")
def get_markeredgewidth(self):
return self.get_attribute_from_ref_artist("markeredgewidth")
def set_tick_out(self, b):
"""Set whether ticks are drawn inside or outside the axes."""
self._tick_out = b
def get_tick_out(self):
"""Return whether ticks are drawn inside or outside the axes."""
return self._tick_out
def set_ticksize(self, ticksize):
"""Set length of the ticks in points."""
self._ticksize = ticksize
def get_ticksize(self):
"""Return length of the ticks in points."""
return self._ticksize
def set_locs_angles(self, locs_angles):
self.locs_angles = locs_angles
_tickvert_path = Path([[0., 0.], [1., 0.]])
def draw(self, renderer):
if not self.get_visible():
return
gc = renderer.new_gc()
gc.set_foreground(self.get_markeredgecolor())
gc.set_linewidth(self.get_markeredgewidth())
gc.set_alpha(self._alpha)
path_trans = self.get_transform()
marker_transform = (Affine2D().scale(
renderer.points_to_pixels(self._ticksize)))
if self.get_tick_out():
marker_transform.rotate_deg(180)
for loc, angle in self.locs_angles:
locs = path_trans.transform_non_affine(np.array([loc]))
if self.axes and not self.axes.viewLim.contains(*locs[0]):
continue
renderer.draw_markers(
gc, self._tickvert_path,
marker_transform + Affine2D().rotate_deg(angle), Path(locs),
path_trans.get_affine())
gc.restore()
def _points_inside_poly(points, verts):
poly = Path(verts)
return [ind for ind, p in enumerate(points) if poly.contains_point(p)]
def getAlertMasks(map_group):
_, graphics = map_group
# mask will have shape defined by the image map extent divided
# into 0.1 degree grid
res = 0.1
# lon_min, lon_max, lat_min, lat_max = [round(x, 1) for x in extent_MAP_IMG]
# nx, ny = np.array([lon_max - lon_min, lat_max - lat_min])/res
# img_shape = (round(nx), round(ny), 3)
lon_min, lon_max, lat_min, lat_max = extent_MAP_IMG
x = np.arange(lon_min, lon_max, res) # [round(x,1) for x in x]
y = np.arange(lat_min, lat_max, res) # [round(y,1) for y in y]
xx, yy = np.meshgrid(x, y)
xy = np.vstack((xx.ravel(), yy.ravel())).T
# Create transformation matrix
tm = np.array([res, 0, 0, res, lon_min, lat_min])
m = np.hstack((tm.reshape(3,2), np.array([[0],[0],[1]])))
try:
m_inv = LA.inv(m)
except LinAlgError:
sys.exit("Could not invert transformation matrix")
mask_list = []
for i in range(len(graphics)):
col = graphics[i]['path']['colour']
print(col)
if col['stroke'] is not None and col['stroke'].count(col['stroke'][0]) != 3:
# got a contour with RGB colour
alert_val = 0
r, g, b = col
if col == (0.0, 0.0, 0.0):
print("colour: black")
elif col == (1.0, 1.0, 0.0):
print("colour: yellow")
alert_val = 1
elif g > 0.33 and g < 0.66:
# (0.89, 0.424, 0.0392)
# (0.969, 0.588, 0.275)
print("colour: orange")
alert_val = 2
elif g < 0.33:
print("colour: red")
alert_val = 3
else:
print("colour: other")
#img = np.zeros(img_shape, dtype = np.double)
img2 = np.array([alert_val]*xx.size).reshape(xx.shape)
img = np.zeros(xx.shape, dtype = np.double)
# nodes_new = []
# for curve in graphics[i]['path']['contour']:
# # transform curve to grid coords
# nodes = curve.nodes
# for i in range(len(nodes.T)):
# # Multiply node by transformation matrix m to
# # get grid coordinates
# v = np.matmul(np.append(nodes.T[i], 1), m_inv)
# nodes_new.append(v[:-1])
# nodes = np.array([node.round() for node in nodes_new])
# mask = skimage.draw.polygon2mask(img_shape[:-1], nodes)
# img[mask] = col
#mask_list.append(img)
## alternative approach
vv = np.vstack([curve.nodes.T for curve in graphics[i]['path']['contour']])
# construct a Path from the vertices
pth = Path(vv, closed=False)
# test which pixels fall within the path
mask = pth.contains_points(xy)
# reshape to the same size as the grid
mask = mask.reshape(xx.shape)
# create a masked array
masked = np.ma.masked_array(img2, ~mask)
# or simply set values for masked pixels
img[mask] = alert_val
# combine with coords...
am = np.stack((xx, yy, img))
mask_list.append(am)
return mask_list
from py_eddy_tracker.dataset.grid import RegularGridDataset
from py_eddy_tracker.data import get_path
from matplotlib.path import Path
from pytest import approx
G = RegularGridDataset(get_path("mask_1_60.nc"), "lon", "lat")
X = 0.025
contour = Path(((-X, 0), (X, 0), (X, X), (-X, X), (-X, 0),))
# contour
def test_contour_lon():
assert (contour.lon == (-X, X, X, -X, -X)).all()
def test_contour_lat():
assert (contour.lat == (0, 0, X, X, 0)).all()
def test_contour_mean():
assert (contour.mean_coordinates == (0, X / 2)).all()
def test_contour_fit_circle():
x, y, r, err = contour.fit_circle()
assert x == approx(0)
assert y == approx(X / 2)
assert r == approx(3108, rel=1e-1)
assert err == approx(49.1, rel=1e-1)
df = pd.read_csv('Columbus_TVData_GradeB_SepDis.csv')
cols_to_use = df.columns
cols_to_use = []
for degree in range(1, 360, 2):
cols_to_use.append("Latitude." + str(degree))
cols_to_use.append("Longitude." + str(degree))
dfa = df[cols_to_use]
fr = dfa
fr.values.shape
poly_overall = fr.values.reshape((len(dfa), 180, 2))
path_overall = []
for row in range(0, len(dfa)):
temp = dfa.ix[row]
path_individual_row = [m(t[1], t[0]) for t in poly_overall[row]]
path_overall.append(Path(path_individual_row))
chan_NA = []
chan_NA_co = []
chan_NA_adj = []
chan_NA_SET = []
Num_chan_avl = []
chan_avl = []
CELL_MAX = len(center) #Total number of cells in the area
out_channels = {}
for cell in range(0, CELL_MAX):
CHAN_CNT_USE = []
center_ext = []
print 'Cell no is'
print cell
TV_loc = []
TV_ERP = []
def triplot(ax, *args, **kwargs):
"""
Draw a unstructured triangular grid as lines and/or markers to
the :class:`~matplotlib.axes.Axes`.
The triangulation to plot can be specified in one of two ways;
either::
triplot(triangulation, ...)
where triangulation is a :class:`~matplotlib.tri.Triangulation`
object, or
::
triplot(x, y, ...)
triplot(x, y, triangles, ...)
triplot(x, y, triangles=triangles, ...)
triplot(x, y, mask, ...)
triplot(x, y, mask=mask, ...)
triplot(x, y, triangles, mask, ...)
triplot(x, y, triangles, mask=mask, ...)
in which case a Triangulation object will be created. See
:class:`~matplotlib.tri.Triangulation` for a explanation of these
possibilities.
The remaining args and kwargs are the same as for
:meth:`~matplotlib.axes.Axes.plot`.
**Example:**
.. plot:: mpl_examples/pylab_examples/triplot_demo.py
"""
import matplotlib.axes
tri, args, kwargs = Triangulation.get_from_args_and_kwargs(*args, **kwargs)
x = tri.x
y = tri.y
edges = tri.edges
# If draw both lines and markers at the same time, e.g.
# ax.plot(x[edges].T, y[edges].T, *args, **kwargs)
# then the markers are drawn more than once which is incorrect if alpha<1.
# Hence draw lines and markers separately.
# Decode plot format string, e.g. 'ro-'
fmt = ''
if len(args) > 0:
fmt = args[0]
linestyle, marker, color = matplotlib.axes._process_plot_format(fmt)
# Draw lines without markers, if lines are required.
if linestyle is not None and linestyle is not 'None':
kw = kwargs.copy()
kw.pop('marker', None) # Ignore marker if set.
kw['linestyle'] = ls_mapper[linestyle]
kw['edgecolor'] = color
kw['facecolor'] = None
vertices = np.column_stack((x[edges].flatten(), y[edges].flatten()))
codes = ([Path.MOVETO] + [Path.LINETO])*len(edges)
path = Path(vertices, codes)
pathpatch = PathPatch(path, **kw)
ax.add_patch(pathpatch)
# Draw markers without lines.
# Should avoid drawing markers for points that are not in any triangle?
kwargs['linestyle'] = ''
ax.plot(x, y, *args, **kwargs)
def test_path_to_polygons():
data = [[10, 10], [20, 20]]
p = Path(data)
assert_array_equal(p.to_polygons(width=40, height=40), [])
assert_array_equal(p.to_polygons(width=40, height=40, closed_only=False),
[data])
assert_array_equal(p.to_polygons(), [])
assert_array_equal(p.to_polygons(closed_only=False), [data])
data = [[10, 10], [20, 20], [30, 30]]
closed_data = [[10, 10], [20, 20], [30, 30], [10, 10]]
p = Path(data)
assert_array_equal(p.to_polygons(width=40, height=40), [closed_data])
assert_array_equal(p.to_polygons(width=40, height=40, closed_only=False),
[data])
assert_array_equal(p.to_polygons(), [closed_data])
assert_array_equal(p.to_polygons(closed_only=False), [data])
def test_make_compound_path_empty():
# We should be able to make a compound path with no arguments.
# This makes it easier to write generic path based code.
r = Path.make_compound_path()
assert r.vertices.shape == (0, 2)
def get_markers_per_structure(self):
"""Sort markers into ROIs.
The markers in the hdf5 file will be sorted into each identified
ROI and a table with counts per ROI is returned.
Returns
-------
pandas.Series
A pandas table with ROI name and cell counts
"""
ontology = Ontology()
sorted_markers = pd.DataFrame(index=np.arange(self.nmarkers))
for roi_name, roi_xy in self.rois.items():
path = Path(roi_xy)
sorted_markers[roi_name] = path.contains_points(
self.markers)
# Raise an error if a marker is not assigned to at least one
# ROI.
if not np.all(sorted_markers.sum(axis=1) > 0):
msg = "There are markers with no ROI ({})".format(
os.path.split(self.fname)[-1])
raise ValueError(msg)
# Remove the structures without markers from analysis.
sorted_markers = sorted_markers[
sorted_markers.columns[sorted_markers.sum(0) > 0]]
# Verify that all structure names in the set do exist as
# acronyms in the Allen ontology.
structs = [ontology(name) for name in
sorted_markers.columns.values]
if None in structs:
indices = np.where(structs)
iswrong = np.ones(sorted_markers.columns.size, bool)
iswrong[indices] = False
iswrong = sorted_markers.columns.values[iswrong]
msg = '{}: invalid acronym(s) {}'.format(
self.fname, iswrong)
self.ISW = iswrong
raise ValueError(msg)
# Some markers may fall inside more than one structure. In
# those cases the sum per row (i.e. sum of True values per
# marker) will be more than one: sorted_mrk[sorted_mrk.sum(1)
# > 1]. We must decide which structure to assign the marker to
# on a case-by-case basis. Each series in the following
# iteration is a marker with boolean values of the structure it
# falls into.
is_repeated = sorted_markers.sum(1) > 1
for indx, ser in sorted_markers[is_repeated].iterrows():
# Use only the True values in the series.
ser = ser[ser]
# Create a list of structures that all contain the same
# marker.
isin = [ontology[key] for key in list(ser.keys())]
# 'None' will be returned from ontology if the key is not
# in it, ie if the acronym does not exist in the ontology
# database (as would happen when typing wrong
# capitalisation, not naming roi, etc).
if None in isin:
msg = 'File {}: {} is not a valid acronym'.format(
self.fname, ser.index.values)
raise ValueError(msg)
# I have not decided how to deal with cases where the
# marker falls inside more that 2 structures.
msg = 'One marker in more than one structure {}'.format(
isin)
assert len(isin) == 2, msg
# Sort list of structures. The order will increase with
# depth in the ontology tree, so we expect the last
# structure in the list to be within the first one.
isin.sort()
if isin[-1] not in isin[0]:
msg = 'Structure {} is not part of structure {}'.format(
isin[-1], isin[0])
raise ValueError(msg)
# If the above assumptions are true (ie that, compared to
# the first structure, the second structure in the list is
# deeper in the ontology and it is its subset), then we can
# set the membership of the marker to the topmost structure
# to false. That is, of the two structures, the marker is
# assigned to the deeper one.
sorted_markers.loc[indx][isin[0].acronym] = False
# Confirm that now each marker belongs to only one structure.
assert np.all(sorted_markers.sum(axis=1) == 1)
# Finally, quantify and return the number of markers per
# structure.
return sorted_markers.sum(axis=0)
def _get_transformed_clip_path(self):
x, y, width, height = self.state.clipping_path
rect = ((x, y), (x + width, y), (x + width, y + height), (x,
y + height))
transform = Affine2D.from_values(*affine.affine_params(self.get_ctm()))
return TransformedPath(Path(rect), transform)
lim = -5.8, 5.7
ax.set(xlim=lim, ylim=lim)
print(mpl.__file__)
marker_obj = m.MarkerStyle('$?$')
path = marker_obj.get_path().transformed(marker_obj.get_transform())
path._vertices = np.array(path._vertices) * 8 #To make it larger
path._vertices[4] = [0, 0] #This is where the vertices close
full_codes = path.codes
full_vertices = path._vertices
mark_vertices = full_vertices[5:]
mark_codes = full_codes[5:]
circ_path = Path.unit_circle()
circ_verts = circ_path._vertices * 0.65 + [0.1, -3]
circ_codes = circ_path.codes
##print(circ_verts)
##print(circ_codes)
new_vertices = np.append(circ_verts, mark_vertices, axis=0) - [0, 0.5]
new_codes = np.append(circ_codes, mark_codes, axis=0)
"""All this stuff that is commented out was used to make this path.
when ? was used to create the path. The little dot under the ? was
shown as a square, not a circle. So I had to modify the geometric
descriptors of the patch to make it look better. DO NOT ATTEMPT
THIS ON IMPORTANT FILES"""
##print(new_vertices)
code_map = {
'M': (Path.MOVETO, 1),
'C': (Path.CURVE4, 3),
'L': (Path.LINETO, 1)
}
while i < len(parts):
code = parts[i]
path_code, npoints = code_map[code]
codes.extend([path_code] * npoints)
vertices.extend([[float(x) for x in y.split(',')]
for y in parts[i + 1:i + npoints + 1]])
i += npoints + 1
vertices = np.array(vertices, np.float)
vertices[:, 1] -= 160
dolphin_path = Path(vertices, codes)
dolphin_patch = PathPatch(dolphin_path,
facecolor=(0.6, 0.6, 0.6),
edgecolor=(0.0, 0.0, 0.0))
ax.add_patch(dolphin_patch)
vertices = Affine2D().rotate_deg(60).transform(vertices)
dolphin_path2 = Path(vertices, codes)
dolphin_patch2 = PathPatch(dolphin_path2,
facecolor=(0.5, 0.5, 0.5),
edgecolor=(0.0, 0.0, 0.0))
ax.add_patch(dolphin_patch2)
plt.show()
plt.connect('button_press_event', cnv.update_path_mouse)
plt.connect('motion_notify_event', cnv.set_location)
plt.connect('key_press_event', cnv.update_path_key)
if args.keepROI:
print "Keep points inside ROI"
else:
print "Throw away points inside ROI"
plt.show()
myVerts = cnv.vert
eigvec.attrs['/outlierROI'] = myVerts
print "myVerts: ", myVerts
path1 = Path(myVerts)
index = path1.contains_points(eigvec[:, np.array([eigs[0], eigs[1]])])
if args.keepROI:
myRejects = np.sort(np.asarray(
np.where(index == 0)[0])) # reject indices outside ROI
myKeeps = np.asarray(
np.where(index == 1)[0]) # keep indices inside ROI
else:
myRejects = np.sort(np.asarray(
np.where(index == 1)[0])) # reject indices inside ROI
myKeeps = np.asarray(
np.where(index == 0)[0]) # keep indices outside ROI
numRejects = len(myRejects)
print "myRejects: ", numRejects
def __init__(self,
llcrnrlon,
llcrnrlat,
urcrnrlon,
urcrnrlat,
resolution='i',
projection='merc',
rasterize=True,
rasterize_resolution=500):
logging.debug('Creating Basemap...')
if projection == 'cyl': # TODO: should be fixed
raise ValueError(
'Cyl projection not supported, as rasterisation needs units of m'
)
# Generate Basemap instane
self.map = Basemap(llcrnrlon,
llcrnrlat,
urcrnrlon,
urcrnrlat,
area_thresh=0,
resolution=resolution,
projection=projection)
# Store proj4 string
self.proj4 = self.map.proj4string
# Run constructor of parent Reader class
super(Reader, self).__init__()
# Depth
self.z = None
# Time
self.start_time = None
self.end_time = None
self.time_step = None
# Read and store min, max and step of x and y
self.xmin, self.ymin = self.lonlat2xy(llcrnrlon, llcrnrlat)
self.xmax, self.ymax = self.lonlat2xy(urcrnrlon, urcrnrlat)
self.delta_x = None
self.delta_y = None
# Extract polygons for faster checking of stranding
if has_nxutils is True:
self.polygons = [p.boundary for p in self.map.landpolygons]
else:
self.polygons = [Path(p.boundary) for p in self.map.landpolygons]
# Generate rasterized version of polygons for faster checking of stranding
# (if enabled)
if (rasterize == True):
if (len(self.map.landpolygons) == 0):
logging.debug('No land polygons to rasterize...')
self.bmap_raster = None
else:
logging.debug('Creating rasterized Basemap...')
try:
self.bmap_raster = self.gen_land_bitmap(
self.map, rasterize_resolution)
except Exception as e:
logging.warning(
'Rasterizing Basemap failed! Continuing without rasterized version. Received "'
+ e.message + '"')
self.bmap_raster = None
else:
self.bmap_raster = None
# Calculate aspect ratio, to minimise whitespace on figures
# Drawback is that empty figure is created in interactive mode
meanlat = (llcrnrlat + urcrnrlat) / 2
aspect_ratio = np.float(urcrnrlat - llcrnrlat) / \
(np.float(urcrnrlon-llcrnrlon))
if projection != 'cyl':
aspect_ratio = aspect_ratio / np.cos(np.radians(meanlat))
if aspect_ratio > 1:
self.figsize = (10. / aspect_ratio, 10.)
plt.figure(0, figsize=(10. / aspect_ratio, 10.))
else:
self.figsize = (11., 11. * aspect_ratio)
plt.figure(0, figsize=(11., 11. * aspect_ratio))
ax = plt.axes([.05, .05, .85, .9])
def action_method(parentwidget):
from matplotlib.patches import FancyArrowPatch,PathPatch
from matplotlib.path import Path
import dev_tools.hierarchy
plt.ion()
operations = parentwidget.design.operations
ids = [operation.id for operation in operations]
children = {}
for item in ids:
children[item] = []
# labels = dict([(operation.id,str(operation)) for operation in operations])
# links = []
for child in operations:
# parentrefs = child.parentrefs()
for parentref in child.parentrefs():
# links.append([parentref,child.id])
children[parentref].append(child.id)
# edges = [(item[0],item[1]) for item in links]
connections = dev_tools.hierarchy.create_sorted_connections(ids,lambda item:children[item])
# num_levels = dev_tools.hierarchy.num_levels(connections)
arrow_points = {}
arrow_points2 = {}
# codes = [Path.MOVETO,Path.CURVE3,Path.CURVE3]
codes = []
codes.append(Path.MOVETO)
codes.append(Path.LINETO)
# codes.append(Path.CURVE3)
# codes.append(Path.CURVE3)
# codes.append(Path.LINETO)
# codes.append(Path.CURVE3)
# codes.append(Path.CURVE3)
# codes.append(Path.LINETO)
codes.append(Path.CURVE4)
codes.append(Path.CURVE4)
codes.append(Path.CURVE4)
codes.append(Path.LINETO)
for c in connections:
vertices = []
vertices.append((0,-c.ii))
vertices.append((.25,-c.ii))
# vertices.append((c.level+.75,c.ii))
vertices.append((c.level+1,-c.ii))
# vertices.append((c.level+1,c.ii+.25))
# vertices.append((c.level+1,c.jj-.25))
vertices.append((c.level+1,-c.jj))
# vertices.append((c.level+.75,c.jj))
vertices.append((.25,-c.jj))
vertices.append((0,-c.jj))
arrow_points[c]=Path(vertices,codes)
arrow_points2[c]=Path([(.25,-c.jj),(0,-c.jj),(0,-c.jj)],[Path.MOVETO,Path.CURVE3,Path.CURVE3])
# y = numpy.r_[spacing*len(ids):0:-1*spacing]
# xy = numpy.c_[y*0,y]
# pos = dict([(item,pos) for item,pos in zip(ids,xy)])
w = GraphView(parentwidget)
w.axes.autoscale(True)
# labelpos = dict((key,value+[-0.1,0]) for key,value in pos.items())
w.clear()
# for link,(x,y) in labelpos.items():
# w.text(x, y,labels[link],**text_style)
for ii,operation in enumerate(operations):
w.text(0,-ii,str(operation),**text_style)
# for edge in edges:
for c in connections:
w.add_patch(PathPatch(path=arrow_points[c],facecolor='none', lw=2))
w.add_patch(FancyArrowPatch(path=arrow_points2[c],**arrow_style))
# circlepos = numpy.array([(0,-item) for item in range(len(operations))])
# w.scatter(circlepos[:,0],circlepos[:,1],**circle_style)
w.axes.axis('equal')
w.axes.axis('off')
w.draw()
return w
def print_multiplepath(x,y,stations_coord,h=20,l=20, Dlab = 10, Slab = 20, name = 0):
# plot
verts_x = []
for st in x: # take the best path and plot
try:
verts_x.append(stations_coord[st])
except Exception as e:
print(e)
codes_x = [Path.MOVETO]*len(verts_x)
path_x = Path(verts_x, codes_x)
verts_y = []
for st in y: # take the best path and plot
try:
verts_y.append(stations_coord[st])
except Exception as e:
print(e)
codes_y = [Path.MOVETO]*len(verts_y)
path_y = Path(verts_y, codes_y)
fig = plt.figure(figsize=(h,l))
#ax1 = fig.add_subplot(111)
ax1 = plt.axes()
plt.grid()
#fig, ax = plt.subplots()
patch_x = patches.PathPatch(path_x, facecolor='none', lw=2)
ax1.add_patch(patch_x)
x_xs, x_ys = zip(*verts_x)
patch_y = patches.PathPatch(path_y, facecolor='none', lw=2)
ax1.add_patch(patch_y)
y_xs, y_ys = zip(*verts_y)
# settings of plto
ax1.plot(x_xs, x_ys, lw=4, color='blue', ms=10,alpha = 0.3, label='x')
ax1.plot(y_xs, y_ys, lw=4, color='red', ms=10,alpha = 0.5, label='y')
#plot ticks
ax1.set_xticks(np.arange(min(x_xs)-1, max(x_xs)+1,max(x_xs)/10))
ax1.set_yticks(np.arange(min(x_ys)-1, max(x_ys)+1,max(x_ys)/10))
for i,txt in enumerate(labels_stations):
if i != len(labels_stations)-1:
dx,dy = get_labels_distances(x_xs[i],x_ys[i],d=Dlab)
plt.annotate(txt,
(x_xs[i], x_ys[i]),
textcoords="offset points", # how to position the text
xytext=(dx,dy), # distance from text to points (x,y)
ha='center', # horizontal alignment can be left, right or center
size = Slab
)
#plot the nodes
ax1.scatter(x_xs,x_ys, s=10, c='b', marker="s", alpha = 0.3)
ax1.scatter(y_xs,y_ys, s=10, c='r', marker="o", alpha = 0.5)
#plot legend and title
plt.legend(loc='upper left');
if name != 0:
plotlabel = "%s" %name
plt.title (plotlabel , size=20)
plt.show()
def createGriddedData(map_groups, alert_data, file_path=None):
# container for gridded data layers
vars = {}
# data will have shape defined by the image map extent divided
# into 0.1 degree grid
res = 0.1
lon_min, lon_max, lat_min, lat_max = extent_MAP_IMG
x = np.arange(lon_min, lon_max, res) # [round(x,1) for x in x]
y = np.arange(lat_min, lat_max, res) # [round(y,1) for y in y]
xx, yy = np.meshgrid(x, y)
xy = np.vstack((xx.ravel(), yy.ravel())).T
# Create transformation matrix
tm = np.array([res, 0, 0, res, lon_min, lat_min])
m = np.hstack((tm.reshape(3,2), np.array([[0],[0],[1]])))
try:
m_inv = LA.inv(m)
except LinAlgError:
sys.exit("Could not invert transformation matrix")
for i, mg in enumerate(map_groups):
_, graphics = mg
print(i)
# count arrays added for this group
n = 0
for j, gfx in enumerate(graphics):
colour = gfx['path']['colour']
print(colour)
col = None
if colour['stroke'] is not None and len(colour['stroke']) == 3:
col = colour['stroke']
elif colour['fill'] is not None and len(colour['fill']) == 3:
col = colour['fill']
if col is not None:
# got a contour with associated RGB colour
print(col)
alert_val = 0
r, g, b = col
if col == (0.0, 0.0, 0.0):
print("colour: black")
elif col == (1.0, 1.0, 0.0):
print("colour: yellow")
alert_val = 1
elif col == (1.0, 0.0, 0.0):
print("colour: red")
alert_val = 3
elif g > 0.25 and g < 0.66:
# (0.89, 0.424, 0.0392)
# (0.969, 0.588, 0.275)
# (0.596, 0.282, 0.0275)
print("colour: orange")
alert_val = 2
elif r > 0.9 and g < 0.25:
print("colour: red")
alert_val = 3
else:
print("colour: other")
img = np.zeros(xx.shape, dtype = np.double)
# get nodes for the alert area
vv = np.vstack([curve.nodes.T for curve in gfx['path']['contour']])
# construct a Path from the vertices
pth = Path(vv, closed=False)
# test which pixels fall within the path
mask = pth.contains_points(xy)
# reshape to the same size as the grid
mask = mask.reshape(xx.shape)
# set values for masked pixels
img[mask] = alert_val
da = xr.DataArray(data=img, dims=["lat", "lon"], coords=[y, x])
da.attrs = {
'issue_date': alert_data.loc[i,'issue_date'],
'alert_date': alert_data.loc[i,'date'],
'alert_day': alert_data.loc[i,'day'],
'alert_weekday': alert_data.loc[i,'weekday'],
'alert_id': n+1,
'alert_type': '',
'alert_text': alert_data.loc[i,'alert_text'],
}
var_name = '_'.join(['alert', 'day'+str(da.attrs['alert_day']),
str(da.attrs['alert_id'])])
vars[var_name] = da
n += 1
# combine data arrays into data set
issue_date = alert_data.loc[0, 'issue_date']
ds = xr.Dataset(data_vars=vars,
attrs={
'title': 'TMA weather warnings for ' + issue_date,
'issue_date': issue_date,
})
if file_path is None:
file_path = 'TMA_weather_warning_'+issue_date+'.nc'
ds.to_netcdf(file_path)
def print_path(current_path,stations_coord,test,h=30,l=30, Dlab = 10, Slab = 20, name = 0):
# plot
if test != None:
verts = []
#best_path = optimized_paths[len(optimized_paths)-1]
best_path = current_path
for st in best_path: # take the best path and plot
try:
verts.append(stations_coord[st])
except Exception as e:
print(e)
codes = [Path.MOVETO]*len(verts)
#print (best_path)
#print (len(verts))
#print ((len(codes)))
path = Path(verts, codes)
fig = plt.figure(figsize=(h,l))
ax = plt.axes()
plt.grid()
#fig, ax = plt.subplots()
patch = patches.PathPatch(path, facecolor='none', lw=2)
ax.add_patch(patch)
xs, ys = zip(*verts)
# settings of plto
ax.plot(xs, ys, lw=2, color='red', ms=10)
x_axis = np.arange(min(xs)-1, max(xs)+1,max(xs)/10)
ax.set_xticks(x_axis)
xlabels = ["%.2f"%x for x in x_axis]
ax.set_xticklabels(xlabels, rotation=90)
ax.set_yticks(np.arange(min(ys)-1, max(ys)+1,max(ys)/10))
if this_type == ("ex_circular" or "circular"):
for i,txt in enumerate(labels_stations):
if i < len(current_path):
dx,dy = get_labels_distances(xs[i],ys[i],d=Dlab)
plt.annotate(txt,
(xs[i], ys[i]),
textcoords="offset points", # how to position the text
xytext=(dx,dy), # distance from text to points (x,y)
ha='center', # horizontal alignment can be left, right or center
size = Slab
)
else:
for i,txt in enumerate(labels_stations):
if i < len(current_path):
plt.annotate(txt,
(xs[i], ys[i]),
size = Slab
)
plt.scatter(xs, ys)
#ax.set_xlim(-0.1, 200)
#ax.set_ylim(-0.1, 200)
if name != 0:
plotlabel = "%s" %name
plt.title (plotlabel , size=20)
plt.show()
img = cv2.imread(img_path)
rois = read_roi_zip(img_path.replace(".tif", ".zip"))
height_o, width_o, channel = img.shape
finished_image = np.zeros((height_o, width_o), np.uint8)
h = height_o
w = width_o
rois_len = len(rois)
for iter, roi in enumerate(rois):
x = rois[roi]['x']
y = rois[roi]['y']
n = len(x)
i = 0
ListOfCorners = []
for i in range(i, n):
ListOfCorners.append((int((y[i])), int((x[i]))))
poly_path = Path(ListOfCorners)
Nx, Ny = np.mgrid[:h, :w]
coordinates = np.hstack((Nx.reshape(-1, 1), Ny.reshape(-1, 1)))
mask = poly_path.contains_points(coordinates)
mask = mask.reshape(h, w)
mask = np.array(mask, dtype=bool)
mask = np.array(mask, dtype='uint8')
# EROSION
eroded_image = cv2.erode(mask, kernel_one, iterations=1)
eroded_image = cv2.erode(eroded_image, kernel_two, iterations=1)
border_erosion = mask - eroded_image
# DILATION
dilation = cv2.dilate(mask, kernel_two, iterations=1)
border_dilatation = dilation - mask
end_result = cv2.add(border_erosion, border_dilatation)
def draw_graph(obstacles, grownobstacles, edges, sp, bb):
fig, ax = plt.subplots()
#DRAW GROWN OBSTACLES
for vertices in grownobstacles:
codes = [Path.MOVETO]
for vertex in range(0, len(vertices) - 2):
codes.append(Path.LINETO)
codes.append(Path.CLOSEPOLY)
newvertices = []
for vertex in vertices:
newvertices.append((vertex[0], vertex[1]))
path = Path(newvertices, codes)
ax = fig.add_subplot(111)
patch = patches.PathPatch(path, facecolor='#BEDB39', lw=0, alpha=0.3)
ax.add_patch(patch)
#DRAW SMALL OBSTACLES
for vertices in obstacles:
codes = [Path.MOVETO]
for vertex in range(0, len(vertices) - 2):
codes.append(Path.LINETO)
codes.append(Path.CLOSEPOLY)
newvertices = []
for vertex in vertices:
newvertices.append((vertex[0], vertex[1]))
path = Path(newvertices, codes)
ax = fig.add_subplot(111)
patch = patches.PathPatch(path, facecolor='#BEDB39', lw=0)
ax.add_patch(patch)
# DRAW ALL POSSIBLE LINES IN VISIBILITY GRAPH
lines = []
for edge in edges:
lines.append([(edge[0][0], edge[0][1]), (edge[1][0], edge[1][1])])
c = np.array(['#077EA8'])
lc = mc.LineCollection(lines, colors=c, linewidths=2)
ax.add_collection(lc)
# DRAW SHORTEST PATH
to_highlight = []
for i in range(0, len(sp) - 1):
to_highlight.append([sp[i], sp[i + 1]])
c = np.array(['#FD7400'])
lc = mc.LineCollection(to_highlight, colors=c, linewidths=3)
ax.add_collection(lc)
# DRAW BOUNDING BOX
bounding = []
for i in range(0, len(bb) - 1):
bounding.append([bb[i], bb[i + 1]])
c = np.array(['#BEDB39'])
lc = mc.LineCollection(bounding, colors=c, linewidths=2)
ax.add_collection(lc)
ax.autoscale()
ax.margins(0.1)
plt.show()
def sankey(ax,
outputs=[100.],
outlabels=None,
inputs=[100.],
inlabels='',
dx=40,
dy=10,
outangle=45,
w=3,
inangle=30,
offset=2,
**kwargs):
"""Draw a Sankey diagram.
outputs: array of outputs, should sum up to 100%
outlabels: output labels (same length as outputs),
or None (use default labels) or '' (no labels)
inputs and inlabels: similar for inputs
dx: horizontal elongation
dy: vertical elongation
outangle: output arrow angle [deg]
w: output arrow shoulder
inangle: input dip angle
offset: text offset
**kwargs: propagated to Patch (e.g. fill=False)
Return (patch,[intexts,outtexts]).
"""
import matplotlib.patches as mpatches
from matplotlib.path import Path
outs = np.absolute(outputs)
outsigns = np.sign(outputs)
outsigns[-1] = 0 # Last output
ins = np.absolute(inputs)
insigns = np.sign(inputs)
insigns[0] = 0 # First input
assert sum(outs) == 100, "Outputs don't sum up to 100%"
assert sum(ins) == 100, "Inputs don't sum up to 100%"
def add_output(path, loss, sign=1):
h = (loss / 2 + w) * np.tan(
outangle / 180. * np.pi) # Arrow tip height
move, (x, y) = path[-1] # Use last point as reference
if sign == 0: # Final loss (horizontal)
path.extend([
(Path.LINETO, [x + dx, y]),
(Path.LINETO, [x + dx, y + w]),
(Path.LINETO, [x + dx + h, y - loss / 2]), # Tip
(Path.LINETO, [x + dx, y - loss - w]),
(Path.LINETO, [x + dx, y - loss])
])
outtips.append((sign, path[-3][1]))
else: # Intermediate loss (vertical)
path.extend([
(Path.CURVE4, [x + dx / 2, y]),
(Path.CURVE4, [x + dx, y]),
(Path.CURVE4, [x + dx, y + sign * dy]),
(Path.LINETO, [x + dx - w, y + sign * dy]),
(Path.LINETO, [x + dx + loss / 2, y + sign * (dy + h)]), # Tip
(Path.LINETO, [x + dx + loss + w, y + sign * dy]),
(Path.LINETO, [x + dx + loss, y + sign * dy]),
(Path.CURVE3, [x + dx + loss, y - sign * loss]),
(Path.CURVE3, [x + dx / 2 + loss, y - sign * loss])
])
outtips.append((sign, path[-5][1]))
def add_input(path, gain, sign=1):
h = (gain / 2) * np.tan(inangle / 180. * np.pi) # Dip depth
move, (x, y) = path[-1] # Use last point as reference
if sign == 0: # First gain (horizontal)
path.extend([
(Path.LINETO, [x - dx, y]),
(Path.LINETO, [x - dx + h, y + gain / 2]), # Dip
(Path.LINETO, [x - dx, y + gain])
])
xd, yd = path[-2][1] # Dip position
indips.append((sign, [xd - h, yd]))
else: # Intermediate gain (vertical)
path.extend([
(Path.CURVE4, [x - dx / 2, y]),
(Path.CURVE4, [x - dx, y]),
(Path.CURVE4, [x - dx, y + sign * dy]),
(Path.LINETO, [x - dx - gain / 2, y + sign * (dy - h)]), # Dip
(Path.LINETO, [x - dx - gain, y + sign * dy]),
(Path.CURVE3, [x - dx - gain, y - sign * gain]),
(Path.CURVE3, [x - dx / 2 - gain, y - sign * gain])
])
xd, yd = path[-4][1] # Dip position
indips.append((sign, [xd, yd + sign * h]))
outtips = [] # Output arrow tip dir. and positions
urpath = [(Path.MOVETO, [0, 100])] # 1st point of upper right path
lrpath = [(Path.LINETO, [0, 0])] # 1st point of lower right path
for loss, sign in zip(outs, outsigns):
add_output(sign >= 0 and urpath or lrpath, loss, sign=sign)
indips = [] # Input arrow tip dir. and positions
llpath = [(Path.LINETO, [0, 0])] # 1st point of lower left path
ulpath = [(Path.MOVETO, [0, 100])] # 1st point of upper left path
for gain, sign in reversed(list(zip(ins, insigns))):
add_input(sign <= 0 and llpath or ulpath, gain, sign=sign)
def revert(path):
"""A path is not just revertable by path[::-1] because of Bezier
curves."""
rpath = []
nextmove = Path.LINETO
for move, pos in path[::-1]:
rpath.append((nextmove, pos))
nextmove = move
return rpath
# Concatenate subpathes in correct order
path = urpath + revert(lrpath) + llpath + revert(ulpath)
codes, verts = zip(*path)
verts = np.array(verts)
# Path patch
path = Path(verts, codes)
patch = mpatches.PathPatch(path, **kwargs)
ax.add_patch(patch)
if False: # DEBUG
print("urpath", urpath)
print("lrpath", revert(lrpath))
print("llpath", llpath)
print("ulpath", revert(ulpath))
xs, ys = zip(*verts)
ax.plot(xs, ys, 'go-')
# Labels
def set_labels(labels, values):
"""Set or check labels according to values."""
if labels == '': # No labels
return labels
elif labels is None: # Default labels
return ['%2d%%' % val for val in values]
else:
assert len(labels) == len(values)
return labels
def put_labels(labels, positions, output=True):
"""Put labels to positions."""
texts = []
lbls = output and labels or labels[::-1]
for i, label in enumerate(lbls):
s, (x, y) = positions[i] # Label direction and position
if s == 0:
t = ax.text(x + offset,
y,
label,
ha=output and 'left' or 'right',
va='center')
elif s > 0:
t = ax.text(x, y + offset, label, ha='center', va='bottom')
else:
t = ax.text(x, y - offset, label, ha='center', va='top')
texts.append(t)
return texts
outlabels = set_labels(outlabels, outs)
outtexts = put_labels(outlabels, outtips, output=True)
inlabels = set_labels(inlabels, ins)
intexts = put_labels(inlabels, indips, output=False)
# Axes management
ax.set_xlim(verts[:, 0].min() - dx, verts[:, 0].max() + dx)
ax.set_ylim(verts[:, 1].min() - dy, verts[:, 1].max() + dy)
ax.set_aspect('equal', adjustable='datalim')
return patch, [intexts, outtexts]
verts = [
(ymin, xmin), # left, bottom
(ymin, xmax), # left, top
(ymax, xmax), # right, top
(ymax, xmin), # right, bottom
(0., 0.), # ignored
]
codes = [
Path.MOVETO,
Path.LINETO,
Path.LINETO,
Path.LINETO,
Path.CLOSEPOLY,
]
path = Path(verts, codes)
y0 = median(xx)
x0 = median(yy)
# rgb2 = rgb[:, :, 1]
loop += 1
sio.savemat('rgb' + str(loop) + '.mat', {'rgb': rgb})
sio.savemat('depth' + str(loop) + '.mat', {'depth': depth})
#
######################################################################
## Plotting depth image
######################################################################
# fig = plt.figure(1)
ax0 = fig.add_subplot(121)
# ax0.image_depth.set_data(depth)
def split_path_inout(path, inside, tolerence=0.01, reorder_inout=False):
""" divide a path into two segment at the point where inside(x, y)
becomes False.
"""
path_iter = path.iter_segments()
ctl_points, command = path_iter.next()
begin_inside = inside(ctl_points[-2:]) # true if begin point is inside
bezier_path = None
ctl_points_old = ctl_points
concat = np.concatenate
iold = 0
i = 1
for ctl_points, command in path_iter:
iold = i
i += len(ctl_points) / 2
if inside(ctl_points[-2:]) != begin_inside:
bezier_path = concat([ctl_points_old[-2:], ctl_points])
break
ctl_points_old = ctl_points
if bezier_path is None:
raise ValueError("The path does not seem to intersect with the patch")
bp = zip(bezier_path[::2], bezier_path[1::2])
left, right = split_bezier_intersecting_with_closedpath(
bp, inside, tolerence)
if len(left) == 2:
codes_left = [Path.LINETO]
codes_right = [Path.MOVETO, Path.LINETO]
elif len(left) == 3:
codes_left = [Path.CURVE3, Path.CURVE3]
codes_right = [Path.MOVETO, Path.CURVE3, Path.CURVE3]
elif len(left) == 4:
codes_left = [Path.CURVE4, Path.CURVE4, Path.CURVE4]
codes_right = [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]
else:
raise ValueError()
verts_left = left[1:]
verts_right = right[:]
#i += 1
if path.codes is None:
path_in = Path(concat([path.vertices[:i], verts_left]))
path_out = Path(concat([verts_right, path.vertices[i:]]))
else:
path_in = Path(concat([path.vertices[:iold], verts_left]),
concat([path.codes[:iold], codes_left]))
path_out = Path(concat([verts_right, path.vertices[i:]]),
concat([codes_right, path.codes[i:]]))
if reorder_inout and begin_inside == False:
path_in, path_out = path_out, path_in
return path_in, path_out
def add(self,
patchlabel='',
flows=np.array([1.0, -1.0]),
orientations=[0, 0],
labels='',
trunklength=1.0,
pathlengths=0.25,
prior=None,
connect=(0, 0),
rotation=0,
**kwargs):
"""
call signature::
add(patchlabel='', flows=np.array([1.0,-1.0]), orientations=[0,0],
labels='', trunklength=1.0, pathlengths=0.25, prior=None,
connect=(0,0), rotation=0, **kwargs)
Add a simple Sankey diagram with flows at the same hierarchical level.
Return value is the instance of :class:`Sankey`.
Optional keyword arguments:
=============== ==========================================
Keyword Description
=============== ==========================================
*patchlabel* label to be placed at the center of the diagram
Note: *label* (not *patchlabel*) will be passed to
the patch through **kwargs and can be used to create
an entry in the legend.
*flows* array of flow values
By convention, inputs are positive and outputs are
negative.
*orientations* list of orientations of the paths
Valid values are 1 (from/to the top), 0 (from/to the
left or right), or -1 (from/to the bottom). If
*orientations* == 0, inputs will break in from the
left and outputs will break away to the right.
*labels* list of specifications of the labels for the flows
Each value may be None (no labels), '' (just label
the quantities), or a labeling string. If a single
value is provided, it will be applied to all flows.
If an entry is a non-empty string, then the quantity
for the corresponding flow will be shown below the
string. However, if the *unit* of the main diagram
is None, then quantities are never shown, regardless
of the value of this argument.
*trunklength* length between the bases of the input and output
groups
*pathlengths* list of lengths of the arrows before break-in or
after break-away
If a single value is given, then it will be applied
to the first (inside) paths on the top and bottom,
and the length of all other arrows will be justified
accordingly. The *pathlengths* are not applied to
the horizontal inputs and outputs.
*prior* index of the prior diagram to which this diagram
should be connected
*connect* a (prior, this) tuple indexing the flow of the prior
diagram and the flow of this diagram which should be
connected
If this is the first diagram or *prior* is None,
*connect* will be ignored.
*rotation* angle of rotation of the diagram [deg]
*rotation* is ignored if this diagram is connected
to an existing one (using *prior* and *connect*).
The interpretation of the *orientations* argument
will be rotated accordingly (e.g., if *rotation*
== 90, an *orientations* entry of 1 means to/from
the left).
=============== ==========================================
Valid kwargs are :meth:`~matplotlib.patches.PathPatch` arguments:
%(PathPatch)s
As examples, *fill*=False and *label*="A legend entry". By default,
*facecolor*='#bfd1d4' (light blue) and *lineweight*=0.5.
The indexing parameters (*prior* and *connect*) are zero-based.
The flows are placed along the top of the diagram from the inside out in
order of their index within the *flows* list or array. They are placed
along the sides of the diagram from the top down and along the bottom
from the outside in.
If the the sum of the inputs and outputs is nonzero, the discrepancy
will appear as a cubic Bezier curve along the top and bottom edges of
the trunk.
.. seealso::
:meth:`finish`
"""
# Check and preprocess the arguments.
flows = np.array(flows)
n = flows.shape[0] # Number of flows
if rotation == None:
rotation = 0
else:
rotation /= 90.0 # In the code below, angles are expressed in deg/90
assert len(orientations) == n, (
"orientations and flows must have the "
"same length.\norientations has length "
"%d, but flows has length %d." % len(orientations), n)
if getattr(labels, '__iter__', False):
# iterable() isn't used because it would give True if labels is a string
assert len(labels) == n, ("If labels is a list, then labels and "
"flows must have the same length.\n"
"labels has length %d, but flows has "
"length %d." % len(labels), n)
else:
labels = [labels] * n
assert trunklength >= 0, ("trunklength is negative.\nThis isn't "
"allowed, because it would cause poor "
"layout.")
if np.absolute(np.sum(flows)) > self.tolerance:
verbose.report(
"The sum of the flows is nonzero (%f).\nIs the "
"system not at steady state?" % np.sum(flows), 'helpful')
scaled_flows = self.scale * flows
gain = sum(max(flow, 0) for flow in scaled_flows)
loss = sum(min(flow, 0) for flow in scaled_flows)
if not (0.5 <= gain <= 2.0):
verbose.report(
"The scaled sum of the inputs is %f.\nThis may "
"cause poor layout.\nConsider changing the scale so "
"that the scaled sum is approximately 1.0." % gain, 'helpful')
if not (-2.0 <= loss <= -0.5):
verbose.report(
"The scaled sum of the outputs is %f.\nThis may "
"cause poor layout.\nConsider changing the scale so "
"that the scaled sum is approximately 1.0." % gain, 'helpful')
if prior is not None:
assert prior >= 0, "The index of the prior diagram is negative."
assert min(connect) >= 0, (
"At least one of the connection indices "
"is negative.")
assert prior < len(self.diagrams), ("The index of the prior "
"diagram is %d, but there are "
"only %d other diagrams.\nThe "
"index is zero-based." % prior,
len(self.diagrams))
assert connect[0] < len(self.diagrams[prior].flows), \
("The connection index to the source diagram is %d, but "
"that diagram has only %d flows.\nThe index is zero-based."
% connect[0], len(self.diagrams[prior].flows))
assert connect[1] < n, ("The connection index to this diagram is "
"%d, but this diagram has only %d flows.\n"
"The index is zero-based." % connect[1], n)
assert self.diagrams[prior].angles[connect[0]] is not None, \
("The connection cannot be made. Check that the magnitude "
"of flow %d of diagram %d is greater than or equal to the "
"specified tolerance." % connect[0], prior)
flow_error = self.diagrams[prior].flows[connect[0]] \
+ flows[connect[1]]
assert abs(flow_error) < self.tolerance, \
("The scaled sum of the connected flows is %f, which is not "
"within the tolerance (%f)." % flow_error, self.tolerance)
# Determine if the flows are inputs.
are_inputs = [None] * n
for i, flow in enumerate(flows):
if flow >= self.tolerance:
are_inputs[i] = True
elif flow <= -self.tolerance:
are_inputs[i] = False
else:
verbose.report(
"The magnitude of flow %d (%f) is below the "
"tolerance (%f).\nIt will not be shown, and it "
"cannot be used in a connection." %
(i, flow, self.tolerance), 'helpful')
# Determine the angles of the arrows (before rotation).
angles = [None] * n
for i, (orient, is_input) in enumerate(zip(orientations, are_inputs)):
if orient == 1:
if is_input:
angles[i] = DOWN
elif is_input == False: # Be specific since is_input can be None.
angles[i] = UP
elif orient == 0:
if is_input is not None:
angles[i] = RIGHT
else:
assert orient == -1, ("The value of orientations[%d] is %d, "
"but it must be -1, 0, or 1." % i,
orient)
if is_input:
angles[i] = UP
elif is_input == False:
angles[i] = DOWN
# Justify the lengths of the paths.
if iterable(pathlengths):
assert len(pathlengths) == n, (
"If pathlengths is a list, then "
"pathlengths and flows must have "
"the same length.\npathlengths has "
"length %d, but flows has length %d." % len(pathlengths), n)
else: # Make pathlengths into a list.
urlength = pathlengths
ullength = pathlengths
lrlength = pathlengths
lllength = pathlengths
d = dict(RIGHT=pathlengths)
pathlengths = [d.get(angle, 0) for angle in angles]
# Determine the lengths of the top-side arrows
# from the middle outwards.
for i, (angle, is_input, flow) \
in enumerate(zip(angles, are_inputs, scaled_flows)):
if angle == DOWN and is_input:
pathlengths[i] = ullength
ullength += flow
elif angle == UP and not is_input:
pathlengths[i] = urlength
urlength -= flow # Flow is negative for outputs.
# Determine the lengths of the bottom-side arrows
# from the middle outwards.
for i, (angle, is_input, flow) \
in enumerate(zip(angles, are_inputs, scaled_flows)[::-1]):
if angle == UP and is_input:
pathlengths[n - i - 1] = lllength
lllength += flow
elif angle == DOWN and not is_input:
pathlengths[n - i - 1] = lrlength
lrlength -= flow
# Determine the lengths of the left-side arrows
# from the bottom upwards.
has_left_input = False
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs, zip(scaled_flows,
pathlengths))[::-1]):
if angle == RIGHT:
if is_input:
if has_left_input:
pathlengths[n - i - 1] = 0
else:
has_left_input = True
# Determine the lengths of the right-side arrows
# from the top downwards.
has_right_output = False
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs, zip(scaled_flows,
pathlengths))):
if angle == RIGHT:
if not is_input:
if has_right_output:
pathlengths[i] = 0
else:
has_right_output = True
# Begin the subpaths, and smooth the transition if the sum of the flows
# is nonzero.
urpath = [
(
Path.MOVETO,
[
(self.gap - trunklength / 2.0), # Upper right
gain / 2.0
]),
(Path.LINETO, [(self.gap - trunklength / 2.0) / 2.0, gain / 2.0]),
(Path.CURVE4, [(self.gap - trunklength / 2.0) / 8.0, gain / 2.0]),
(Path.CURVE4, [(trunklength / 2.0 - self.gap) / 8.0, -loss / 2.0]),
(Path.LINETO, [(trunklength / 2.0 - self.gap) / 2.0, -loss / 2.0]),
(Path.LINETO, [(trunklength / 2.0 - self.gap), -loss / 2.0])
]
llpath = [
(
Path.LINETO,
[
(trunklength / 2.0 - self.gap), # Lower left
loss / 2.0
]),
(Path.LINETO, [(trunklength / 2.0 - self.gap) / 2.0, loss / 2.0]),
(Path.CURVE4, [(trunklength / 2.0 - self.gap) / 8.0, loss / 2.0]),
(Path.CURVE4, [(self.gap - trunklength / 2.0) / 8.0, -gain / 2.0]),
(Path.LINETO, [(self.gap - trunklength / 2.0) / 2.0, -gain / 2.0]),
(Path.LINETO, [(self.gap - trunklength / 2.0), -gain / 2.0])
]
lrpath = [(
Path.LINETO,
[
(trunklength / 2.0 - self.gap), # Lower right
loss / 2.0
])]
ulpath = [(
Path.LINETO,
[
self.gap - trunklength / 2.0, # Upper left
gain / 2.0
])]
# Add the subpaths and assign the locations of the tips and labels.
tips = np.zeros((n, 2))
label_locations = np.zeros((n, 2))
# Add the top-side inputs and outputs from the middle outwards.
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs,
zip(scaled_flows, pathlengths))):
if angle == DOWN and is_input:
tips[i, :], label_locations[i, :] = self._add_input(
ulpath, angle, *spec)
elif angle == UP and not is_input:
tips[i, :], label_locations[i, :] = self._add_output(
urpath, angle, *spec)
# Add the bottom-side inputs and outputs from the middle outwards.
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs,
zip(scaled_flows, pathlengths))[::-1]):
if angle == UP and is_input:
(tips[n - i - 1, :],
label_locations[n - i - 1, :]) = self._add_input(
llpath, angle, *spec)
elif angle == DOWN and not is_input:
(tips[n - i - 1, :],
label_locations[n - i - 1, :]) = self._add_output(
lrpath, angle, *spec)
# Add the left-side inputs from the bottom upwards.
has_left_input = False
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs,
zip(scaled_flows, pathlengths))[::-1]):
if angle == RIGHT and is_input:
if not has_left_input:
# Make sure the lower path extends
# at least as far as the upper one.
if llpath[-1][1][0] > ulpath[-1][1][0]:
llpath.append(
(Path.LINETO, [ulpath[-1][1][0],
llpath[-1][1][1]]))
has_left_input = True
(tips[n - i - 1, :],
label_locations[n - i - 1, :]) = self._add_input(
llpath, angle, *spec)
# Add the right-side outputs from the top downwards.
has_right_output = False
for i, (angle, is_input, spec) \
in enumerate(zip(angles, are_inputs,
zip(scaled_flows, pathlengths))):
if angle == RIGHT and not is_input:
if not has_right_output:
# Make sure the upper path extends
# at least as far as the lower one.
if urpath[-1][1][0] < lrpath[-1][1][0]:
urpath.append(
(Path.LINETO, [lrpath[-1][1][0],
urpath[-1][1][1]]))
has_right_output = True
(tips[i, :], label_locations[i, :]) = self._add_output(
urpath, angle, *spec)
# Trim any hanging vertices.
if not has_left_input:
ulpath.pop()
llpath.pop()
if not has_right_output:
lrpath.pop()
urpath.pop()
# Concatenate the subpaths in the correct order (clockwise from top).
path = (urpath + self._revert(lrpath) + llpath + self._revert(ulpath) +
[(Path.CLOSEPOLY, urpath[0][1])])
# Create a patch with the Sankey outline.
codes, vertices = zip(*path)
vertices = np.array(vertices)
def _get_angle(a, r):
if a is None: return None
else: return a + r
if prior is None:
if rotation != 0: # By default, none of this is needed.
angles = [_get_angle(angle, rotation) for angle in angles]
rotate = Affine2D().rotate_deg(rotation * 90).transform_point
tips = rotate(tips)
label_locations = rotate(label_locations)
vertices = rotate(vertices)
text = self.ax.text(0, 0, s=patchlabel, ha='center', va='center')
else:
rotation = (self.diagrams[prior].angles[connect[0]] -
angles[connect[1]])
angles = [_get_angle(angle, rotation) for angle in angles]
rotate = Affine2D().rotate_deg(rotation * 90).transform_point
tips = rotate(tips)
offset = self.diagrams[prior].tips[connect[0]] - tips[connect[1]]
translate = Affine2D().translate(*offset).transform_point
tips = translate(tips)
label_locations = translate(rotate(label_locations))
vertices = translate(rotate(vertices))
kwds = dict(s=patchlabel, ha='center', va='center')
text = self.ax.text(*offset, **kwds)
if False: # Debug
print "llpath\n", llpath
print "ulpath\n", self._revert(ulpath)
print "urpath\n", urpath
print "lrpath\n", self._revert(lrpath)
xs, ys = zip(*vertices)
self.ax.plot(xs, ys, 'go-')
patch = PathPatch(
Path(vertices, codes),
fc=kwargs.pop('fc', kwargs.pop('facecolor',
'#bfd1d4')), # Custom defaults
lw=kwargs.pop('lw', kwargs.pop('linewidth', '0.5')),
**kwargs)
self.ax.add_patch(patch)
# Add the path labels.
for i, (number, angle) in enumerate(zip(flows, angles)):
if labels[i] is None or angle is None:
labels[i] = ''
elif self.unit is not None:
quantity = self.format % abs(number) + self.unit
if labels[i] != '':
labels[i] += "\n"
labels[i] += quantity
texts = []
for i, (label, location) in enumerate(zip(labels, label_locations)):
if label: s = label
else: s = ''
texts.append(
self.ax.text(x=location[0],
y=location[1],
s=s,
ha='center',
va='center'))
# Text objects are placed even they are empty (as long as the magnitude
# of the corresponding flow is larger than the tolerance) in case the
# user wants to provide labels later.
# Expand the size of the diagram if necessary.
self.extent = (min(np.min(vertices[:, 0]),
np.min(label_locations[:, 0]), self.extent[0]),
max(np.max(vertices[:, 0]),
np.max(label_locations[:, 0]), self.extent[1]),
min(np.min(vertices[:, 1]),
np.min(label_locations[:, 1]), self.extent[2]),
max(np.max(vertices[:, 1]),
np.max(label_locations[:, 1]), self.extent[3]))
# Include both vertices _and_ label locations in the extents; there are
# where either could determine the margins (e.g., arrow shoulders).
# Add this diagram as a subdiagram.
self.diagrams.append(
Bunch(patch=patch,
flows=flows,
angles=angles,
tips=tips,
text=text,
texts=texts))
# Allow a daisy-chained call structure (see docstring for the class).
return self
def plot(
trj: TrajaDataFrame,
n_coords: Optional[int] = None,
show_time: bool = False,
accessor: Optional[traja.TrajaAccessor] = None,
ax=None,
**kwargs,
) -> matplotlib.collections.PathCollection:
"""Plot trajectory for single animal over period.
Args:
trj (:class:`traja.TrajaDataFrame`): trajectory
n_coords (int, optional): Number of coordinates to plot
show_time (bool): Show colormap as time
accessor (:class:`~traja.accessor.TrajaAccessor`, optional): TrajaAccessor instance
ax (:class:`~matplotlib.axes.Axes`): axes for plotting
interactive (bool): show plot immediately
**kwargs: additional keyword arguments to :meth:`matplotlib.axes.Axes.scatter`
Returns:
collection (:class:`~matplotlib.collections.PathCollection`): collection that was plotted
"""
import matplotlib.patches as patches
from matplotlib.path import Path
after_plot_args, kwargs = _get_after_plot_args(**kwargs)
GRAY = "#999999"
xlim = kwargs.pop("xlim", None)
ylim = kwargs.pop("ylim", None)
if not xlim or not ylim:
xlim, ylim = traja.trajectory._get_xylim(trj)
title = kwargs.pop("title", None)
time_units = kwargs.pop("time_units", "s")
fps = kwargs.pop("fps", None)
figsize = kwargs.pop("figsize", None)
coords = trj[["x", "y"]]
time_col = traja.trajectory._get_time_col(trj)
if time_col == "index":
is_datetime = True
else:
is_datetime = is_datetime64_any_dtype(
trj[time_col]) if time_col else False
if n_coords is None:
# Plot all coords
start, end = 0, len(coords)
verts = coords.iloc[start:end].values
else:
# Plot first `n_coords`
verts = coords.iloc[:n_coords].values
n_coords = len(verts)
codes = [Path.MOVETO] + [Path.LINETO] * (len(verts) - 1)
path = Path(verts, codes)
if not ax:
fig, ax = plt.subplots(figsize=figsize)
fig.canvas.draw()
patch = patches.PathPatch(path,
edgecolor=GRAY,
facecolor="none",
lw=3,
alpha=0.3)
ax.add_patch(patch)
xs, ys = zip(*verts)
if time_col == "index":
# DatetimeIndex determines color
colors = [ind for ind, x in enumerate(trj.index[:n_coords])]
elif time_col and time_col != "index":
# `time_col` determines color
colors = [ind for ind, x in enumerate(trj[time_col].iloc[:n_coords])]
else:
# Frame count determines color
colors = trj.index[:n_coords]
if time_col:
# TODO: Calculate fps if not in datetime
vmin = min(colors)
vmax = max(colors)
if is_datetime:
# Show timestamps without units
time_units = ""
else:
# Index/frame count is our only reference
vmin = trj.index[0]
vmax = trj.index[n_coords - 1]
if not show_time:
time_units = ""
label = f"Time ({time_units})" if time_units else ""
collection = ax.scatter(
xs,
ys,
c=colors,
s=kwargs.pop("s", 1),
cmap=plt.cm.viridis,
alpha=0.7,
vmin=vmin,
vmax=vmax,
**kwargs,
)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
if kwargs.pop("invert_yaxis", None):
plt.gca().invert_yaxis()
_label_axes(trj, ax)
ax.set_title(title)
ax.set_aspect("equal")
# Number of color bar ticks
CBAR_TICKS = 10 if n_coords > 20 else n_coords
indices = np.linspace(0,
n_coords - 1,
CBAR_TICKS,
endpoint=True,
dtype=int)
cbar = plt.colorbar(collection,
fraction=0.046,
pad=0.04,
orientation="vertical",
label=label)
# Get colorbar labels from time
if time_col == "index":
if is_datetime64_any_dtype(trj.index):
cbar_labels = (trj.index[indices].strftime(
"%Y-%m-%d %H:%M:%S").values.astype(str))
elif is_timedelta64_dtype(trj.index):
if time_units in ("s", "", None):
cbar_labels = [
round(x, 2) for x in trj.index[indices].total_seconds()
]
else:
logger.error(
"Time unit {} not yet implemented".format(time_units))
else:
raise NotImplementedError(
"Indexing on {} is not yet implemented".format(type(
trj.index)))
elif time_col and is_timedelta64_dtype(trj[time_col]):
cbar_labels = trj[time_col].iloc[indices].dt.total_seconds().values
cbar_labels = ["%.2f" % number for number in cbar_labels]
elif time_col and is_datetime:
cbar_labels = (trj[time_col].iloc[indices].dt.strftime(
"%Y-%m-%d %H:%M:%S").values.astype(str))
else:
# Convert frames to time
if time_col:
cbar_labels = trj[time_col][indices].values
else:
cbar_labels = trj.index[indices].values
cbar_labels = np.round(cbar_labels, 6)
if fps is not None and fps > 0 and fps is not 1 and show_time:
cbar_labels = cbar_labels / fps
cbar.set_ticks(indices)
cbar.set_ticklabels(cbar_labels)
plt.tight_layout()
_process_after_plot_args(**after_plot_args)
return collection
def transform_path_non_affine(self, path):
vertices = path.vertices
ipath = path.interpolated(self._resolution)
return Path(self.transform(ipath.vertices), ipath.codes)
def draw_labels(fig,
ax,
out_value,
features,
feature_type,
offset_text,
total_effect=0,
min_perc=0.05):
start_text = out_value
pre_val = out_value
# Define variables specific to positive and negative effect features
if feature_type == 'positive':
colors = ['#FF0D57', '#FFC3D5']
alignement = 'right'
sign = 1
else:
colors = ['#1E88E5', '#D1E6FA']
alignement = 'left'
sign = -1
# Draw initial line
if feature_type == 'positive':
x, y = np.array([[pre_val, pre_val], [0, -0.18]])
line = lines.Line2D(x, y, lw=1., alpha=0.5, color=colors[0])
line.set_clip_on(False)
ax.add_line(line)
start_text = pre_val
box_end = out_value
val = out_value
for feature in features:
# Exclude all labels that do not contribute at least 10% to the total
feature_contribution = np.abs(float(feature[0]) -
pre_val) / np.abs(total_effect)
if feature_contribution < min_perc:
break
# Compute value for current feature
val = float(feature[0])
# Draw labels.
if feature[1] == "":
text = feature[2]
else:
text = feature[2] + ' = ' + feature[1]
text_out_val = plt.text(start_text - sign * offset_text,
-0.15,
text,
fontsize=12,
color=colors[0],
horizontalalignment=alignement)
text_out_val.set_bbox(dict(facecolor='none', edgecolor='none'))
# We need to draw the plot to be able to get the size of the
# text box
fig.canvas.draw()
box_size = text_out_val.get_bbox_patch().get_extents()\
.transformed(ax.transData.inverted())
if feature_type == 'positive':
box_end_ = box_size.get_points()[0][0]
else:
box_end_ = box_size.get_points()[1][0]
# If the feature goes over the side of the plot, we remove that label
# and stop drawing labels
if box_end_ > ax.get_xlim()[1]:
text_out_val.remove()
break
# Create end line
if (sign * box_end_) > (sign * val):
x, y = np.array([[val, val], [0, -0.18]])
line = lines.Line2D(x, y, lw=1., alpha=0.5, color=colors[0])
line.set_clip_on(False)
ax.add_line(line)
start_text = val
box_end = val
else:
box_end = box_end_ - sign * offset_text
x, y = np.array([[val, box_end, box_end], [0, -0.08, -0.18]])
line = lines.Line2D(x, y, lw=1., alpha=0.5, color=colors[0])
line.set_clip_on(False)
ax.add_line(line)
start_text = box_end
# Update previous value
pre_val = float(feature[0])
# Create line for labels
extent_shading = [out_value, box_end, 0, -0.31]
path = [[out_value, 0], [pre_val, 0], [box_end, -0.08], [box_end, -0.2],
[out_value, -0.2], [out_value, 0]]
path = Path(path)
patch = PathPatch(path, facecolor='none', edgecolor='none')
ax.add_patch(patch)
# Extend axis if needed
lower_lim, upper_lim = ax.get_xlim()
if (box_end < lower_lim):
ax.set_xlim(box_end, upper_lim)
if (box_end > upper_lim):
ax.set_xlim(lower_lim, box_end)
# Create shading
if feature_type == 'positive':
colors = np.array([(255, 13, 87), (255, 255, 255)]) / 255.
else:
colors = np.array([(30, 136, 229), (255, 255, 255)]) / 255.
cm = matplotlib.colors.LinearSegmentedColormap.from_list('cm', colors)
Z, Z2 = np.meshgrid(np.linspace(0, 10), np.linspace(-10, 10))
im = plt.imshow(Z2,
interpolation='quadric',
cmap=cm,
vmax=0.01,
alpha=0.3,
origin='lower',
extent=extent_shading,
clip_path=patch,
clip_on=True,
aspect='auto')
im.set_clip_path(patch)
return fig, ax
def pressure_design(
capsule_material='copper',
pressure_medium_material='BaCO$_3$',
sleeve_material='pyrophyllite',
buffer_material='H$_2$O, Ni,\nNiO, SC ol.,\nSC enst.',
lid_shape='bevel', # or flat or suaged
h_graphite_button=1.5,
h_pressure_medium=33.35,
h_graphite_cylinder=33.35,
h_sleeve=11.5,
h_sleeve_bottom=1.,
h_capsule=9.7,
h_lid=1., # total
h_MgO_base=10.6,
h_MgO_wafer=1.5,
h_MgO_top=10.6,
od_pressure_medium=18.9,
od_graphite_cylinder=11.5,
id_graphite_cylinder=10.0,
id_sleeve=8.7,
id_capsule=6.7,
legend_on=True,
figsize=(3., 3),
):
"""Creates and returns figure and axis
showing experimental setup for a high pressure
experiment used to hydrate olivine and potentially
other nominally anhydrous minerals in the green 4-post piston cylinder
at Lamont. All dimensions are input in mm. h=height, d=diameter,
od=outer diameter, id=inner diameter
"""
# reset all style labels to None for legend
style_capsule['color'] = None
style_buffer['label'] = buffer_material
for style in [style_graphite, style_MgO, style_capsule]:
style['label'] = None
d_graphite_button = od_pressure_medium
od_MgO_base = id_graphite_cylinder
od_sleeve = id_graphite_cylinder
fig = plt.figure(figsize=figsize)
ax = fig.add_subplot(111)
ax.set_xlim(0, od_pressure_medium)
ax.set_xlabel('(mm)')
ax.set_ylabel('(mm)')
h_guts = h_MgO_base + h_sleeve + h_MgO_wafer + h_MgO_top
highest_point = max(h_pressure_medium, h_graphite_cylinder, h_guts)
ax.set_ylim(0., h_graphite_button + highest_point + 2.)
plt.tick_params(axis='x', top='off')
ax.spines['top'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.spines['right'].set_visible(False)
th_gc = (od_graphite_cylinder - id_graphite_cylinder) / 2.
xgc = (od_pressure_medium - od_graphite_cylinder) / 2.
style_pressure_medium['label'] = pressure_medium_material
pressure_medium = patches.Rectangle(
(0., h_graphite_button), # (x,y)
od_pressure_medium, # width
h_pressure_medium, # height
**style_pressure_medium)
graphite_button = patches.Rectangle((0., 0.), d_graphite_button,
h_graphite_button, **style_graphite)
style_graphite['label'] = 'graphite'
graphite_cylinder = patches.Rectangle(
(xgc, h_graphite_button), od_graphite_cylinder, h_graphite_cylinder,
**style_graphite)
the_guts = patches.Rectangle((xgc + th_gc, h_graphite_button),
id_graphite_cylinder,
h_graphite_cylinder,
facecolor='w')
MgO_base = patches.Rectangle((xgc + th_gc, h_graphite_button), od_MgO_base,
h_MgO_base, **style_MgO)
def make_capsule_shape(x, y, height, outerD, innerD, shape='regular'):
thick = (outerD - innerD) / 2.
if shape == 'regular':
verts = [(x + thick * 2 + innerD, y), (x, y), (x, y + height),
(x + thick, y + height), (x + thick, y + innerD / 2.),
(x + thick + innerD / 2., y + thick),
(x + thick + innerD, y + innerD / 2.),
(x + thick + innerD, y + height),
(x + thick * 2 + innerD, y + height), (0., 0.)]
codes = [Path.MOVETO] + ([Path.LINETO] * 8) + [Path.CLOSEPOLY]
elif shape == 'suaged':
th_flap = thick / 2.
verts = [(x + thick * 2 + innerD, y), (x, y),
(x, y + height + th_flap),
(x + thick + innerD / 2., y + height + th_flap),
(x + thick + innerD / 2., y + height),
(x + thick, y + height), (x + thick, y + thick),
(x + thick + innerD, y + thick),
(x + thick + innerD, y + height),
(x + thick + innerD / 2., y + height),
(x + thick + innerD / 2., y + height + th_flap),
(x + thick * 2 + innerD, y + height + th_flap),
(x + thick * 2 + innerD, y + height - th_flap), (0., 0.)]
codes = [Path.MOVETO] + ([Path.LINETO] *
(len(verts) - 2)) + [Path.CLOSEPOLY]
path = Path(verts, codes)
return path
# sleeve around capsule
sleeve_path = make_capsule_shape(x=xgc + th_gc,
y=h_graphite_button + h_MgO_base,
height=h_sleeve,
outerD=od_sleeve,
innerD=id_sleeve)
if sleeve_material == 'MgO':
style_sleeve = style_MgO.copy()
elif sleeve_material == 'pyrophyllite':
style_sleeve = style_pyrophyllite.copy()
style_sleeve['label'] = 'pyrophyllite'
else:
print 'unknown sleeve material. Assuming pyrophyllite'
style_sleeve = style_pyrophyllite.copy()
style_sleeve['label'] = 'pyrophyllite'
sleeve = patches.PathPatch(sleeve_path, **style_sleeve)
# capsule
th_sleeve = (od_sleeve - id_sleeve) / 2.
if (lid_shape == 'bevel') or (lid_shape == 'flat'):
capsule_path = make_capsule_shape(x=xgc + th_gc + th_sleeve,
y=h_graphite_button + h_MgO_base +
h_sleeve_bottom,
height=h_capsule,
outerD=id_sleeve,
innerD=id_capsule)
elif lid_shape == 'suaged':
capsule_path = make_capsule_shape(x=xgc + th_gc + th_sleeve,
y=h_graphite_button + h_MgO_base +
h_sleeve_bottom,
height=h_capsule,
outerD=id_sleeve,
innerD=id_capsule,
shape='suaged')
else:
print 'valid entries for lid_shape are flat, bevel, and suaged'
capsule_path = make_capsule_shape(x=xgc + th_gc + th_sleeve,
y=h_graphite_button + h_MgO_base +
h_sleeve_bottom,
height=h_capsule,
outerD=id_sleeve,
innerD=id_capsule)
if capsule_material == 'copper':
style_capsule['label'] = 'copper'
style_capsule['facecolor'] = 'orange'
elif capsule_material == 'silver':
style_capsule['label'] = 'silver'
style_capsule['facecolor'] = 'silver'
elif capsule_material == 'gold':
style_capsule['label'] = 'gold'
style_capsule['facecolor'] = 'gold'
elif capsule_material == 'platinum':
style_capsule['label'] = 'platinum'
style_capsule['facecolor'] = 'lightblue'
elif capsule_material == 'nickel':
style_capsule['label'] = 'nickel'
style_capsule['facecolor'] = 'lightsage'
else:
print 'unknown capsule material'
style_capsule['label'] = 'capsule'
capsule = patches.PathPatch(capsule_path, **style_capsule)
# MgO on top
MgO_wafer = patches.Rectangle(
(xgc + th_gc, h_graphite_button + h_MgO_base + h_sleeve), od_MgO_base,
h_MgO_wafer, **style_MgO)
style_MgO['label'] = 'MgO'
MgO_top = patches.Rectangle(
(xgc + th_gc, h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer),
od_MgO_base, h_MgO_top, **style_MgO)
thermocouple = patches.Rectangle(
(od_pressure_medium / 2. - 0.5,
h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer),
1.,
h_MgO_top,
facecolor='w')
ax.plot([od_pressure_medium / 2 - 0.15, od_pressure_medium / 2. - 0.15], [
h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer + h_MgO_top +
2., h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer
],
color='r',
linewidth=1)
ax.plot([od_pressure_medium / 2 + 0.15, od_pressure_medium / 2. + 0.15], [
h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer + h_MgO_top +
2., h_graphite_button + h_MgO_base + h_sleeve + h_MgO_wafer
],
color='b',
linewidth=1)
# buffer
th_capsule = (id_sleeve - id_capsule) / 2.
buffer_inside = patches.Rectangle(
(xgc + th_gc + th_sleeve + th_capsule,
h_graphite_button + h_MgO_base + h_sleeve_bottom + th_capsule),
id_capsule, h_capsule - th_capsule, **style_buffer)
# capsule lid
del style_capsule['label'] # so it doesn't appear twice in the legend
if lid_shape == 'flat':
lid = patches.Rectangle(
(xgc + th_gc + th_sleeve,
h_graphite_button + h_MgO_base + h_sleeve_bottom + h_capsule),
id_sleeve, h_lid, **style_capsule)
elif lid_shape == 'bevel':
x = xgc + th_gc + th_sleeve
y = h_graphite_button + h_MgO_base + h_sleeve_bottom + h_capsule
th_lid = h_lid / 2.
th_capsule = (id_sleeve - id_capsule) / 2.
lid_verts = [(x + th_capsule, y), (x, y), (x, y + th_lid),
(x + id_sleeve, y + th_lid), (x + id_sleeve, y),
(x + id_sleeve - th_capsule, y),
(x + id_sleeve - th_capsule, y - th_lid),
(x + th_capsule, y - th_lid), (0., 0.)]
lid_codes = [Path.MOVETO] + ([Path.LINETO] * 7) + [Path.CLOSEPOLY]
lid_path = Path(lid_verts, lid_codes)
lid = patches.PathPatch(lid_path, **style_capsule)
elif lid_shape == 'suaged':
th_flap = th_capsule / 2.
x = xgc + th_gc + th_sleeve + th_flap
ystart = h_graphite_button + h_MgO_base + h_sleeve_bottom
y = ystart + h_capsule - th_flap * 2
th_lid = h_lid / 2.
th_capsule = (id_sleeve - id_capsule) / 2.
lid_verts = [(x + th_capsule - th_flap, y), (x, y), (x, y + th_lid),
(x + id_sleeve - th_capsule, y + th_lid),
(x + id_sleeve - th_capsule, y),
(x + id_sleeve - th_capsule - th_flap, y),
(x + id_sleeve - th_capsule - th_flap, y - th_lid),
(x + th_capsule - th_flap, y - th_lid), (0., 0.)]
lid_codes = [Path.MOVETO] + ([Path.LINETO] * 7) + [Path.CLOSEPOLY]
lid_path = Path(lid_verts, lid_codes)
lid = patches.PathPatch(lid_path, **style_capsule)
else:
print 'valid entries for lid_shape are flat, bevel, and suaged'
lid = patches.Rectangle(
(xgc + th_gc + th_sleeve,
h_graphite_button + h_MgO_base + th_sleeve + h_capsule),
id_sleeve, h_lid, **style_capsule)
ax.add_patch(pressure_medium)
ax.add_patch(graphite_button)
ax.add_patch(graphite_cylinder)
ax.add_patch(the_guts)
ax.add_patch(MgO_base)
ax.add_patch(sleeve)
ax.add_patch(buffer_inside)
ax.add_patch(MgO_wafer)
ax.add_patch(MgO_top)
ax.add_patch(thermocouple)
ax.add_patch(capsule)
ax.add_patch(lid)
fig.tight_layout()
if legend_on is True:
plt.subplots_adjust(right=0.55, left=0.17, bottom=0.15, top=0.9)
ax.legend(bbox_to_anchor=(2.25, 0.8), frameon=False)
else:
plt.subplots_adjust(right=0.9, left=0.17, bottom=0.15, top=0.9)
return fig, ax