def animate(p):
global count, centers, angles, coords, skip, colors, histogram, success, angle_histogram
mc()
density = histogram/leny/dx/count
xnew, density = make_square(xcoords, density)
line.set_ydata(density)
ang_vals = angle_histogram/count/pi
ax3.collections = []
angplot = ax3.pcolormesh(x, theta, ang_vals, vmin=0, vmax=.01, edgecolors='face', cmap=cm.hot_r)
#angplot = ax3.contourf(x, theta, ang_vals, levels=arange(0, .0105, .001), extend="max", rasterized=True)
cbar_ax.collections = []
cs = fig.colorbar(angplot, cax=cbar_ax, ticks=[])
cs.cmap.set_over('k')
cs.set_clim([0, .01])
ax2.set_ylim(0, 0.8)
for i in xrange(n):
coords[i] = verts(centers[i], angles[i])
coll = PolyCollection(coords)
colors = zeros(n) + cdefault
colors[0] = cspecial
coll.set_color([cm.jet(val) for val in colors])
ax.collections=[]
ax.add_collection(coll)
ax.set_title("Attempted: %6i, Successful: %6i" %(count*n, success))
#fig.tight_layout()
print p
return line, ax2, ax3
def poly3d(df, elev=0, azim=0, **pltkwds):
''' Written by evelyn, updated by Adam 12/1/12.'''
xlabel, ylabel, title, pltkwds=pu.smart_label(df, pltkwds)
zlabel_def=''
zlabel=pltkwds.pop('zlabel', zlabel_def)
zs=df.columns
verts=[zip(df.index, df[col]) for col in df] #don't have to say df.columns
fig = plt.figure()
ax = fig.gca(projection='3d')
### Convert verts(type:list) to poly(type:mpl_toolkits.mplot3d.art3d.Poly3DCollection)
### poly used in plotting function ax.add_collection3d to do polygon plot
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.6)
poly = PolyCollection((verts), facecolors = [cc('b'), cc('g'), cc('r'),
cc('y'),cc('m'), cc('c'), cc('b'),cc('g'),cc('r'), cc('y')])
poly.set_alpha(0.2)
### zdir is the direction used to plot,here we use time so y axis
ax.add_collection3d(poly, zs=zs, zdir='x')
ax.set_xlabel(xlabel)
ax.set_ylabel(ylabel) #Y
ax.set_zlabel(zlabel) #data
ax.set_title(title)
ax.set_ylim3d(min(df.index), max(df.index))
ax.set_xlim3d(min(df.columns), max(df.columns)) #x
ax.set_zlim3d(min(df.min()), max(df.max())) #How to get absolute min/max of df values
ax.view_init(elev, azim)
return ax
def index_bar(ax, vals,
facecolor='b', edgecolor='l',
width=4, alpha=1.0, ):
"""
Add a bar collection graph with height vals (-1 is missing).
ax : an Axes instance to plot to
width : the bar width in points
alpha : bar transparency
"""
facecolors = (colorConverter.to_rgba(facecolor, alpha),)
edgecolors = (colorConverter.to_rgba(edgecolor, alpha),)
right = width/2.0
left = -width/2.0
bars = [ ( (left, 0), (left, v), (right, v), (right, 0)) for v in vals if v != -1 ]
sx = ax.figure.dpi * (1.0/72.0) # scale for points
sy = ax.bbox.height / ax.viewLim.height
barTransform = Affine2D().scale(sx,sy)
offsetsBars = [ (i, 0) for i,v in enumerate(vals) if v != -1 ]
barCollection = PolyCollection(bars,
facecolors = facecolors,
edgecolors = edgecolors,
antialiaseds = (0,),
linewidths = (0.5,),
offsets = offsetsBars,
transOffset = ax.transData,
)
barCollection.set_transform(barTransform)
minpy, maxx = (0, len(offsetsBars))
miny = 0
maxy = max([v for v in vals if v!=-1])
corners = (minpy, miny), (maxx, maxy)
ax.update_datalim(corners)
ax.autoscale_view()
ax.add_collection(barCollection)
return barCollection
def funDisplayDifferenceCurveIn3D(vecDigitLevel, inputData_x, dataToDisplay_y, xLabelText, yLabelText, zLabelText, titleText, figureName):
'''
Exactly the same as the function above, but in 3D, yes in 3D, it is the future here.
'''
fig = plt.figure()
ax = fig.gca(projection='3d')
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.2)
xs = inputData_x
verts = []
tabColor = []
zs = vecDigitLevel
for ii in np.arange(0,np.size(vecDigitLevel)):
ys = dataToDisplay_y[ii,:]
ys[0], ys[-1] = 0, 0
verts.append(list(zip(xs, ys)))
tabColor.append(list(cc(repr(vecDigitLevel[ii]/255.))))
poly = PolyCollection(verts, facecolors = tabColor)
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlabel(xLabelText)#'level search')
ax.set_xlim3d(0, 255)
ax.set_ylabel(yLabelText)#'level tested')
ax.set_ylim3d(-1, 256)
ax.set_zlabel(zLabelText)#L difference')
ax.set_zlim3d(0, 1)
plt.title(titleText)#'Various difference curves in 3D')
plt.draw()
plt.savefig(figureName)# dirToSaveResults+prefixName+'_c1_2.png')
def __init__(self, ax, *args, **kw):
self.ax = ax
X, Y, U, V, C = self._parse_args(*args)
self.X = X
self.Y = Y
self.N = len(X)
self.scale = kw.pop('scale', None)
self.headwidth = kw.pop('headwidth', 3)
self.headlength = float(kw.pop('headlength', 5))
self.headaxislength = kw.pop('headaxislength', 4.5)
self.minshaft = kw.pop('minshaft', 1)
self.minlength = kw.pop('minlength', 1)
self.units = kw.pop('units', 'width')
self.width = kw.pop('width', None)
self.color = kw.pop('color', 'k')
self.pivot = kw.pop('pivot', 'tail')
kw.setdefault('facecolors', self.color)
kw.setdefault('linewidths', (0,))
PolyCollection.__init__(self, None, offsets=zip(X, Y),
transOffset=ax.transData, **kw)
self.polykw = kw
self.set_UVC(U, V, C)
self._initialized = False
self.keyvec = None
self.keytext = None
def make_image(x):
''' x wil be a matrix data structure. '''
fig = plt.figure()
ax = fig.gca(projection='3d')
#
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.6)
#
xs = np.arange(0, 10, 0.4)
verts = x.get_verts('freq')
for i in xrange(17):
print verts[0][i],'\n'
for i in xrange(17):
print verts[1][i],'\n'
zs = [0.0, 1.0, 2.0, 3.0]
# for z in zs:
# ys = np.random.rand(len(xs))
# ys[0], ys[-1] = 0, 0
# verts.append(list(zip(xs, ys)))
# poly = PolyCollection(verts, facecolors = [cc('r'), cc('g'), cc('b'),cc('y')])
poly = PolyCollection(verts)
poly.set_alpha(0.3)
# ax.add_collection3d(poly, zs=zs, zdir='y')
ax.add_collection3d(poly, zs=zs, zdir='y')
#
ax.set_xlabel('X')
ax.set_xlim3d(0, 123456)
ax.set_ylabel('Y')
ax.set_ylim3d(0, 65536)
ax.set_zlabel('Z')
ax.set_zlim3d(0, 1000)
#
plt.show()
def plotPolyArrayFunction(self,result):
interval = ((self.endValue - self.startValue) / (self.polyNumber - 1))
self.rr.reset()
fig = plt.figure()
ax = fig.gca(projection='3d')
if self.startValue is None:
self.startValue = self.rr.model[self.value]
columnNumber = self.polyNumber + 1
lastPoint = [self.endTime]
firstPoint = [self.startTime]
for i in range(int(columnNumber) - 1):
lastPoint.append(0)
firstPoint.append(0)
lastPoint = np.array(lastPoint)
firstPoint = np.array(firstPoint)
zresult = np.vstack((result, lastPoint))
zresult = np.vstack((firstPoint, zresult))
zs = []
result = []
for i in range(int(columnNumber) - 1):
zs.append(i)
result.append(zip(zresult[:, 0], zresult[:, (i + 1)]))
if self.color is None:
poly = PolyCollection(result)
else:
if len(self.color) != self.polyNumber:
self.color = self.colorCycle()
poly = PolyCollection(result, facecolors=self.color, closed=False)
poly.set_alpha(self.alpha)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlim3d(0, self.endTime)
ax.set_ylim3d(0, (columnNumber - 1))
ax.set_zlim3d(0, (self.endValue + interval))
if self.xlabel == 'toSet':
ax.set_xlabel('Time')
elif self.xlabel:
ax.set_xlabel(self.xlabel)
if self.ylabel == 'toSet':
ax.set_ylabel('Trial Number')
elif self.ylabel:
ax.set_ylabel(self.ylabel)
if self.zlabel == 'toSet':
ax.set_zlabel(self.value)
elif self.zlabel:
ax.set_zlabel(self.zlabel)
# ax.set_xlabel('Time') if self.xlabel is None else ax.set_xlabel(self.xlabel)
# ax.set_ylabel('Trial Number') if self.ylabel is None else ax.set_ylabel(self.ylabel)
# ax.set_zlabel(self.value) if self.zlabel is None else ax.set_zlabel(self.zlabel)
if self.title is not None:
ax.set_title(self.title)
if not IPYTHON:
plt.show()
else:
FILENAME = str(uuid.uuid4()) + ".png"
plt.savefig(FILENAME)
plt.close()
imag = mpimg.imread(FILENAME)
return(imag)
def draw(self, renderer):
self._init()
if self._new_UV:
verts = self._make_verts(self.U, self.V)
self.set_verts(verts)
self._new_UV = False
PolyCollection.draw(self, renderer)
def visualizeHealPixMap(theMap, nest=True, title="map", norm=None, vmin=None, vmax=None, cmap=plt.cm.hot_r):
from matplotlib.collections import PolyCollection
from matplotlib.colors import Normalize
nside = hp.npix2nside(theMap.size)
mapValue = theMap[theMap != hp.UNSEEN]
indices = np.arange(theMap.size)
seenInds = indices[theMap != hp.UNSEEN]
print "Building polygons from HEALPixel map."
vertices = np.zeros( (seenInds.size, 4, 2) )
print "Building polygons for "+str(seenInds.size)+" HEALPixels."
for HPixel,i in zip(seenInds,xrange(seenInds.size)):
corners = hp.vec2ang( np.transpose(hp.boundaries(nside,HPixel,nest=nest) ) )
# HEALPix insists on using theta/phi; we in astronomy like to use ra/dec.
vertices[i,:,0] = corners[1] *180./np.pi
vertices[i,:,1] = 90.0 - corners[0] * 180/np.pi
fig, ax = plt.subplots(figsize=(12,12))
#coll = PolyCollection(vertices, array = mapValue, cmap = plt.cm.seismic, edgecolors='none')
coll = PolyCollection(vertices, array=mapValue, cmap=cmap, edgecolors='none')
coll.set_clim(vmin=vmin, vmax=vmax)
ax.add_collection(coll)
ax.set_title(title)
ax.autoscale_view()
fig.colorbar(coll,ax=ax)
#ax.set_ylim([-60.2, -43])
print "Writing to file: "+title+".png"
fig.savefig(title+".png",format="png")
def __init__(self, start_ls, end_ls, y=0, width=0.001, x_offset=0, is_arrow=True, length_includes_head=True, \ head_width=None, head_length=None, shape='full', overhang=0, \ head_starts_at_zero=False,**kwargs): if head_width is None: head_width = 2 * width if head_length is None: head_length = 1/(2.0 * abs(end_ls[0]-start_ls[0])) distance = abs(end_ls[-1]-start_ls[0]) if length_includes_head: length=distance else: length=distance+head_length no_of_blocks = len(start_ls) if not distance: verts_ls = [] #display nothing if empty else: """ start by drawing horizontal arrow, point (tip of the arrow) at (0,0). the whole arrow sticks on the x-axis (<=0 part) Notice: the XY -coordination is not the usual math coordination system. it's canvas coordination. (0,0) is top left. horizontal is y-axis. vertical is x-axis. start from the last block, reversely to the 1st block """ verts_ls = [] for i in range(no_of_blocks): block_start = start_ls[i] block_end = end_ls[i] verts = [[block_start, width/2.0+y], [block_start, -width/2.0+y], [block_end, -width/2.0+y], [block_end, width/2.0+y]] verts_ls.append(verts) PolyCollection.__init__(self, verts_ls, **kwargs)
def plot_series(time, variable, series, ylabel='Y', zlabel='Z', fromzero=False):
figure = plt.figure()
ax = figure.gca(projection='3d')
globalmin = np.min(map(lambda trial: np.min(trial), series))
globalmax = np.max(map(lambda trial: np.max(trial), series))
def stub(trial):
if not fromzero:
trial = map(lambda x: x - globalmin, np.array(trial))
trial[0] = 0
trial[-1] = 0
return np.array(trial)
verts = map(lambda trial: zip(time, stub(trial)), series)
poly = PolyCollection(np.array(verts), facecolors=map(lambda n: cm.jet(n), np.linspace(0, 1, len(series))))
poly.set_alpha(0.7)
if not fromzero:
globalmax -= globalmin
globalmin -= globalmin
ax.add_collection3d(poly, zs=variable, zdir='y')
ax.set_xlim3d(time[0], time[-1])
ax.set_ylim3d(min(variable), max(variable))
ax.set_zlim3d(globalmin, globalmax)
ax.set_xlabel('Time (ms)')
ax.set_ylabel(ylabel)
ax.set_zlabel(zlabel)
def plot4MainDir(degVector):
fourDirVector = allDeg24Directions(degVector['Value'])
pHours = 24 # periodo considerado
sampling = 60 # 10min de amostragem
base = pHours*60/sampling
totDays = len(fourDirVector)/base # Dias multiplo de 5, para graficos poly 3d
days = np.arange(totDays)+1
hours = np.arange(0,pHours*60,sampling)
meshTime, indices = np.meshgrid(hours, days)
meshProfile = np.zeros(meshTime.shape)
profileList = []
ii = 1
for i in range(totDays):
dataPeriod = fourDirVector[i*base:ii*base]
profileList.append( dataPeriod )
ii +=1
profileMatrix = np.array(profileList)
for i in range( indices.shape[0] ):
for j in range( indices.shape[1] ):
meshProfile[(i,j)] = profileMatrix[(i,j)]
fig = plt.figure()
ax = fig.gca(projection='3d')
X = meshTime
Y = indices
Z = meshProfile
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap='coolwarm', alpha=0.8) # ou a linha abaixo
ax.set_xlabel('minutos')
ax.set_ylabel('dia')
ax.set_zlabel(r'$^oC$')
# Visao apenas dos perfis
fig2 = plt.figure()
ax2 = fig2.gca(projection='3d')
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.6)
verts = []
cs = [cc('r'), cc('g'), cc('b'), cc('y'), cc('c')]*(totDays/5)
k = 0
for d in days:
verts.append(list(zip(hours, meshProfile[k])))
k += 1
poly = PolyCollection(verts, facecolors = cs)
poly.set_alpha(0.7)
ax2.add_collection3d(poly, zs=days, zdir='y')
""" OK! Mostra grafico de barras
cs = ['r', 'g', 'b', 'y','c']*(totDays/5)
k = 0
for c, d in zip(cs, days):
cc = [c]*len(hours)
ax2.bar(hours, meshProfile[k], zs=d, zdir='y', color=cc, alpha=0.5)
k += 1
"""
ax2.set_xlabel('minutos')
ax2.set_xlim3d(0, hours[-1])
ax2.set_ylabel('dia')
ax2.set_ylim3d(0, days[-1])
ax2.set_zlabel('Dir')
ax2.set_zlim3d(0, 360)
plt.show()
def test_something(self):
fig = plt.figure()
ax = fig.gca(projection='3d')
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.6)
xs = np.arange(0, 10, 0.4)
verts = []
zs = [0.0, 1.0, 2.0, 3.0]
for z in zs:
ys = np.random.rand(len(xs))
ys[0], ys[-1] = 0, 0
verts.append(list(zip(xs, ys)))
poly = PolyCollection(verts, facecolors = [cc('r'), cc('g'), cc('b'),
cc('y')])
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlabel('Coordinate')
ax.set_xlim3d(0, 10)
ax.set_ylabel('hypothesis#')
ax.set_ylim3d(-1, 4)
ax.set_zlabel('Concentration')
ax.set_zlim3d(0, 1)
plt.show()
def init(self, view):
cube_points = np.arange(0, 10, 0.4)
verts = []
# number of polygons
figures_num = [0.0, 1.0, 2.0, 3.0]
for z in figures_num:
ys = np.random.rand(len(cube_points))
ys[0], ys[-1] = 0, 0
verts.append(list(zip(cube_points, ys)))
poly = PolyCollection(verts, facecolors=[self.convert_color('r'), self.convert_color('g'), self.convert_color('b'),
self.convert_color('y')])
poly.set_alpha(0.7)
self.ax.add_collection3d(poly, zs=figures_num, zdir='y')
self.ax.set_xlabel('X')
self.ax.set_xlim3d(0, 10)
self.ax.set_ylabel('Y')
self.ax.set_ylim3d(-1, 4)
self.ax.set_zlabel('Z')
self.ax.set_zlim3d(0, 1)
if view == "image":
savefig('polygon.png')
print "Image saved on tredify folder"
else:
plt.show()
def do_3d_projection(self, renderer):
"""
Perform the 3D projection for this object.
"""
# FIXME: This may no longer be needed?
if self._A is not None:
self.update_scalarmappable()
self._facecolors3d = self._facecolors
txs, tys, tzs = proj3d.proj_transform_vec(self._vec, renderer.M)
xyzlist = [(txs[si:ei], tys[si:ei], tzs[si:ei])
for si, ei in self._segis]
# This extra fuss is to re-order face / edge colors
cface = self._facecolors3d
cedge = self._edgecolors3d
if len(cface) != len(xyzlist):
cface = cface.repeat(len(xyzlist), axis=0)
if len(cedge) != len(xyzlist):
if len(cedge) == 0:
cedge = cface
else:
cedge = cedge.repeat(len(xyzlist), axis=0)
# if required sort by depth (furthest drawn first)
if self._zsort:
z_segments_2d = sorted(
((self._zsortfunc(zs), np.column_stack([xs, ys]), fc, ec, idx)
for idx, ((xs, ys, zs), fc, ec)
in enumerate(zip(xyzlist, cface, cedge))),
key=lambda x: x[0], reverse=True)
else:
raise ValueError("whoops")
segments_2d = [s for z, s, fc, ec, idx in z_segments_2d]
if self._codes3d is not None:
codes = [self._codes3d[idx] for z, s, fc, ec, idx in z_segments_2d]
PolyCollection.set_verts_and_codes(self, segments_2d, codes)
else:
PolyCollection.set_verts(self, segments_2d, self._closed)
self._facecolors2d = [fc for z, s, fc, ec, idx in z_segments_2d]
if len(self._edgecolors3d) == len(cface):
self._edgecolors2d = [ec for z, s, fc, ec, idx in z_segments_2d]
else:
self._edgecolors2d = self._edgecolors3d
# Return zorder value
if self._sort_zpos is not None:
zvec = np.array([[0], [0], [self._sort_zpos], [1]])
ztrans = proj3d.proj_transform_vec(zvec, renderer.M)
return ztrans[2][0]
elif tzs.size > 0 :
# FIXME: Some results still don't look quite right.
# In particular, examine contourf3d_demo2.py
# with az = -54 and elev = -45.
return np.min(tzs)
else :
return np.nan
def set_3d_properties(self):
# Force the collection to initialize the face and edgecolors
# just in case it is a scalarmappable with a colormap.
self.update_scalarmappable()
self._sort_zpos = None
self.set_zsort(True)
self._facecolors3d = PolyCollection.get_facecolors(self)
self._edgecolors3d = PolyCollection.get_edgecolors(self)
def multidraw(courbesA,courbesB):
fig = plt.figure()
ax = fig.gca(projection='3d')
verts = []
facecolor=[]
for lacourbe in courbesA:
xs=[]
closepoly=[]
for idx,X in enumerate(lacourbe):
xs.append(idx)
closepoly.append(0)
xs.append(idx)
closepoly.append(X)
xs.append(idx+.3)
closepoly.append(X)
xs.append(idx+.3)
closepoly.append(0)
xs.append(0)
closepoly.append(0)
verts.append(list(zip(xs, closepoly)))
facecolor.append(cc('b'))
for lacourbe in courbesB:
xs=[]
closepoly=[]
for idx,X in enumerate(lacourbe):
xs.append(idx)
closepoly.append(0)
xs.append(idx)
closepoly.append(X)
xs.append(idx+.3)
closepoly.append(X)
xs.append(idx+.3)
closepoly.append(0)
xs.append(0)
closepoly.append(0)
verts.append(list(zip(xs, closepoly)))
facecolor.append(cc('y'))
print len(facecolor) ,len(verts)
poly = PolyCollection(verts, facecolors=facecolor)
zs = range(0,len(facecolor))
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlabel('X')
ax.set_xlim3d(0,5)
ax.set_ylabel('Y')
ax.set_ylim3d(-1, len(verts))
ax.set_zlabel('Z')
ax.set_zlim3d(-3, 3)
plt.show()
def set_data(self, zname, zdata, zcolor):
if zdata!=None:
if zname not in self.clts: #plottables['plotted']:#self.pd.list_data():
clt=PolyCollection(zdata, alpha=0.5, antialiased=True)#, rasterized=False, antialiased=False)
clt.set_color(colorConverter.to_rgba(zcolor))
self.clts[zname]=clt
self.axe.add_collection(self.clts[zname], autolim=True)
else:
self.clts[zname].set_verts(zdata)
def poly_plot(self, zname, zdata, zcolor=None):
if zname not in self.clts:
clt=PolyCollection(zdata, alpha=0.5, antialiased=True)
if zcolor is not None:
clt.set_color(zcolor) #colorConverter.to_rgba(zcolor))
self.clts[zname]=clt
self.axe.add_collection(self.clts[zname])
else:
self.clts[zname].set_verts(zdata)
def plotPolyArray(self):
"""Plots results as individual graphs parallel to each other in 3D space using results
from graduatedSim().
p.plotPolyArray()"""
result = self.graduatedSim()
interval = (self.endValue - self.startValue) / (self.polyNumber - 1)
self.rr.reset()
fig = plt.figure()
ax = fig.gca(projection="3d")
if self.startValue is None:
self.startValue = self.rr.model[self.value]
columnNumber = self.polyNumber + 1
lastPoint = [self.endTime]
firstPoint = [self.startTime]
for i in range(int(columnNumber) - 1):
lastPoint.append(0)
firstPoint.append(0)
lastPoint = np.array(lastPoint)
firstPoint = np.array(firstPoint)
zresult = np.vstack((result, lastPoint))
zresult = np.vstack((firstPoint, zresult))
zs = []
result = []
for i in range(int(columnNumber) - 1):
zs.append(i)
result.append(zip(zresult[:, 0], zresult[:, (i + 1)]))
if self.color is None:
poly = PolyCollection(result)
else:
if len(self.color) != self.polyNumber:
self.color = self.colorCycle()
poly = PolyCollection(result, facecolors=self.color, closed=False)
poly.set_alpha(self.alpha)
ax.add_collection3d(poly, zs=zs, zdir="y")
ax.set_xlim3d(0, self.endTime)
ax.set_ylim3d(0, (columnNumber - 1))
ax.set_zlim3d(0, (self.endValue + interval))
if self.xlabel == "toSet":
ax.set_xlabel("Time")
elif self.xlabel:
ax.set_xlabel(self.xlabel)
if self.ylabel == "toSet":
ax.set_ylabel("Trial Number")
elif self.ylabel:
ax.set_ylabel(self.ylabel)
if self.zlabel == "toSet":
ax.set_zlabel(self.value)
elif self.zlabel:
ax.set_zlabel(self.zlabel)
# ax.set_xlabel('Time') if self.xlabel is None else ax.set_xlabel(self.xlabel)
# ax.set_ylabel('Trial Number') if self.ylabel is None else ax.set_ylabel(self.ylabel)
# ax.set_zlabel(self.value) if self.zlabel is None else ax.set_zlabel(self.zlabel)
if self.title is not None:
ax.set_title(self.title)
plt.show()
def __init__(self, verts, *args, **kwargs):
'''
Create a Poly3DCollection.
*verts* should contain 3D coordinates.
Note that this class does a bit of magic with the _facecolors
and _edgecolors properties.
'''
PolyCollection.__init__(self, verts, *args, **kwargs)
self._zsort = 1
self._sort_zpos = None
def map_poly_shp(shp, which='all', bbox=None):
'''
Create a map object from a polygon shape
...
Arguments
---------
shp : iterable
PySAL polygon iterable (e.g.
shape object from `ps.open` a poly shapefile) If it does
not contain the attribute `bbox`, it must be passed
separately in `bbox`.
which : str/list
List of booleans for which polygons of the shapefile to
be included (True) or excluded (False)
bbox : None/list
[Optional. Default=None] List with bounding box as in a
PySAL object. If nothing is passed, it tries to obtain
it as an attribute from `shp`.
Returns
-------
map : PatchCollection
Map object with the polygons from the shape
This includes the attribute `shp2dbf_row` with the
cardinality of every polygon to its row in the dbf
(zero-offset)
'''
if not bbox:
bbox = shp.bbox
patches = []
rows = []
i = 0
if which == 'all':
for shape in shp:
for ring in shape.parts:
xy = np.array(ring)
patches.append(xy)
rows.append(i)
i += 1
else:
for inwhich, shape in zip(which, shp):
if inwhich:
for ring in shape.parts:
xy = np.array(ring)
patches.append(xy)
rows.append(i)
i += 1
pc = PolyCollection(patches)
_ = _add_axes2col(pc, bbox)
pc.shp2dbf_row = rows
return pc
def volume_overlay(ax, opens, closes, volumes, colorup="k", colordown="r", width=4, alpha=1.0):
"""
Add a volume overlay to the current axes. The opens and closes
are used to determine the color of the bar. -1 is missing. If a
value is missing on one it must be missing on all
ax : an Axes instance to plot to
width : the bar width in points
colorup : the color of the lines where close >= open
colordown : the color of the lines where close < open
alpha : bar transparency
"""
r, g, b = colorConverter.to_rgb(colorup)
colorup = r, g, b, alpha
r, g, b = colorConverter.to_rgb(colordown)
colordown = r, g, b, alpha
colord = {True: colorup, False: colordown}
colors = [colord[open < close] for open, close in zip(opens, closes) if open != -1 and close != -1]
right = width / 2.0
left = -width / 2.0
bars = [((left, 0), (left, v), (right, v), (right, 0)) for v in volumes if v != -1]
sx = ax.figure.dpi * (1.0 / 72.0) # scale for points
sy = (ax.bbox.ur().y() - ax.bbox.ll().y()) / (ax.viewLim.ur().y() - ax.viewLim.ll().y())
barTransform = Affine2D().scaled(sx, sy)
offsetsBars = [(i, 0) for i, v in enumerate(volumes) if v != -1]
barCollection = PolyCollection(
bars,
facecolors=colors,
edgecolors=((0, 0, 0, 1),),
antialiaseds=(0,),
linewidths=(0.5,),
offsets=offsetsBars,
transOffset=ax.transData,
)
barCollection.set_transform(barTransform)
minpy, maxx = (0, len(offsetsBars))
miny = 0
maxy = max([v for v in volumes if v != -1])
corners = (minpy, miny), (maxx, maxy)
ax.update_datalim(corners)
ax.autoscale_view()
# add these last
return barCollection
def do_3d_projection(self, renderer):
'''
Perform the 3D projection for this object.
'''
# FIXME: This may no longer be needed?
if self._A is not None:
self.update_scalarmappable()
self._facecolors3d = self._facecolors
txs, tys, tzs = proj3d.proj_transform_vec(self._vec, renderer.M)
xyzlist = [(txs[si:ei], tys[si:ei], tzs[si:ei]) \
for si, ei in self._segis]
# This extra fuss is to re-order face / edge colors
cface = self._facecolors3d
cedge = self._edgecolors3d
if len(cface) != len(xyzlist):
cface = cface.repeat(len(xyzlist), axis=0)
if len(cedge) != len(xyzlist):
if len(cedge) == 0:
cedge = cface
cedge = cedge.repeat(len(xyzlist), axis=0)
# if required sort by depth (furthest drawn first)
if self._zsort:
z_segments_2d = [(self._zsortfunc(zs), zip(xs, ys), fc, ec) for
(xs, ys, zs), fc, ec in zip(xyzlist, cface, cedge)]
z_segments_2d.sort(cmp=lambda x, y: cmp(y[0], x[0]))
else:
raise ValueError, "whoops"
segments_2d = [s for z, s, fc, ec in z_segments_2d]
PolyCollection.set_verts(self, segments_2d)
self._facecolors2d = [fc for z, s, fc, ec in z_segments_2d]
if len(self._edgecolors3d) == len(cface):
self._edgecolors2d = [ec for z, s, fc, ec in z_segments_2d]
else:
self._edgecolors2d = self._edgecolors3d
# Return zorder value
if self._sort_zpos is not None:
zvec = np.array([[0], [0], [self._sort_zpos], [1]])
ztrans = proj3d.proj_transform_vec(zvec, renderer.M)
return ztrans[2][0]
elif tzs.size > 0 :
# FIXME: Some results still don't look quite right.
# In particular, examine contourf3d_demo2.py
# with az = -54 and elev = -45.
return np.min(tzs)
else :
return np.nan
def plot():
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
col = PolyCollection(
[], facecolors="none", edgecolors="red", linestyle="--", linewidth=1.2
)
col.set_zorder(1)
axis.add_collection(col)
axis.set_xlim(0.5, 2.5)
axis.set_ylim(0.5, 2.5)
axis.collections[0].set_verts([[[1, 1], [1, 2], [2, 2], [2, 1]]])
return fig
def plot_energy_3d(name, key_steps=50, filename=None):
data = np.loadtxt('%s_energy.ndt' % name)
if data.ndim == 1:
data.shape = (1, -1)
fig = plt.figure()
ax = fig.gca(projection='3d')
# image index
xs = range(1, data.shape[1])
steps = data[:, 0]
each_n_step = int(len(steps) / key_steps)
if each_n_step < 1:
each_n_step = 1
cc = lambda arg: colorConverter.to_rgba(arg, alpha=0.6)
colors = [cc('r'), cc('g'), cc('b'), cc('y')]
facecolors = []
line_data = []
energy_min = np.min(data[:, 1:])
zs = []
index = 0
for i in range(0, len(steps), each_n_step):
line_data.append(list(zip(xs, data[i, 1:] - energy_min)))
facecolors.append(colors[index % 4])
zs.append(data[i, 0])
index += 1
poly = PolyCollection(line_data, facecolors=facecolors, closed=False)
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=zs, zdir='x')
ax.set_xlabel('Steps')
ax.set_ylabel('images')
ax.set_zlabel('Energy (J)')
ax.set_ylim3d(0, len(xs) + 1)
ax.set_xlim3d(0, int(data[-1, 0]) + 1)
ax.set_zlim3d(0, np.max(data[:, 1:] - energy_min))
if filename is None:
filename = '%s_energy_3d.pdf' % name
fig.savefig(filename)
def redraw(self):
self._canvas.axes.grid(True, color='gray')
# Set axis bounds
ymin = ymax = None
xmax = 0
xmin = sys.maxint
for curve in self._curves.values():
data_x, _, _, range_y, c = curve
if len(data_x) == 0:
continue
xmax = max(xmax, data_x[-1])
xmin = min(xmin, data_x[0])
if ymin is None:
ymin = range_y[0]
ymax = range_y[1]
else:
ymin = min(range_y[0], ymin)
ymax = max(range_y[1], ymax)
# pad the min/max
# delta = max(ymax - ymin, 0.1)
# ymin -= .05 * delta
# ymax += .05 * delta
if self._autoscroll and ymin is not None:
self._canvas.axes.set_xbound(lower=xmin, upper=xmax)
self._canvas.axes.set_zbound(lower=ymin, upper=ymax)
self._canvas.axes.set_ybound(lower=0,
upper=len(self._curves.keys()))
# create poly object
verts = []
colors = []
for curve_id in self._curves_verts.keys():
(data_x, data_y) = self._curves_verts[curve_id]
colors.append(self._curves[curve_id][4])
if self._use_poly:
verts.append([(xmin, ymin)] + list(zip(data_x, data_y))
+ [(xmax, ymin)])
else:
verts.append(zip(data_x, data_y))
line_num = len(self._curves.keys())
if self._use_poly:
poly = PolyCollection(verts, facecolors=colors, closed=False)
else:
poly = LineCollection(verts, colors=colors)
poly.set_alpha(0.7)
self._canvas.axes.cla()
self._canvas.axes.add_collection3d(poly,
zs=range(line_num), zdir='y')
self._update_legend()
self._canvas.draw()
def plot_triangles(p, adjustLowerLeft=False, values=None, values_cmap=matplotlib.cm.jet, edgecolors='k'):
""" Add mesh triangles to a pyplot plot
@param p = object holding sww vertex information (from util.get_output)
@param adjustLowerLeft = if TRUE, use spatial coordinates, otherwise use ANUGA internal coordinates
@param values = list or array of length(p.vols), or None. All triangles are assigned this value (for face plotting colors).
@param values_cmap = colormap for faces [e.g. values_cmap = matplotlib.cm.get_cmap('spectral')]
@param edgecolors = edge color for polygons (using matplotlib.colors notation). Use 'none' for no color
"""
import matplotlib
from matplotlib import pyplot as pyplot
from matplotlib.collections import PolyCollection
x0=p.xllcorner
y0=p.yllcorner
# Make vertices for PolyCollection Object
vertices = []
for i in range(len(p.vols)):
k1=p.vols[i][0]
k2=p.vols[i][1]
k3=p.vols[i][2]
tri_coords = numpy.array([ [p.x[k1], p.y[k1]], [p.x[k2], p.y[k2]], [p.x[k3], p.y[k3]] ])
if adjustLowerLeft:
tri_coords[:,0] = tri_coords[:,0] + x0
tri_coords[:,1] = tri_coords[:,1] + y0
vertices.append(tri_coords)
# Make PolyCollection
if values is None:
all_poly = PolyCollection( vertices, array = numpy.zeros(len(vertices)),
edgecolors=edgecolors)
all_poly.set_facecolor('none')
else:
try:
lv = len(values)
except:
values = numpy.array(len(p.vols)*[values])
lv = len(values)
msg = 'len(values) must be the same as len(p.vols) (or values can be a constant)'
assert lv==len(p.vols), msg
all_poly = PolyCollection( vertices, array = values, cmap = values_cmap,
edgecolors=edgecolors)
# Add to plot
# FIXME: To see the triangles, this might require that the user does
# something else to the plot?
pyplot.gca().add_collection(all_poly)
def _waveform_3d(self, fig_type, zmin, zmax, alpha, cmap):
fig = plt.figure(figsize=(10, 10))
ax = fig.gca(projection='3d')
num_times = self._inspector.num_times
num_samples = self._inspector.num_samples
if fig_type == 'surf':
x = np.arange(0, num_samples)
y = np.arange(0, num_times)
x, y = np.meshgrid(x, y)
z = self._inspector.waveform
surf = ax.plot_surface(x, y, z, rstride=3, cstride=3, cmap=cmap, shade=True,
linewidth=0, antialiased=False)
# ax.zaxis.set_major_locator(LinearLocator(10))
# ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
fig.colorbar(surf, shrink=0.5, aspect=5)
else:
waveforms = []
for y_index in range(num_times):
waveform = np.ndarray(shape=(num_samples, 2), dtype=np.float64)
waveform[:, 0] = np.arange(0, num_samples)
waveform[:, 1] = self._inspector.waveform[y_index]
waveforms.append(waveform)
line_widths = [0.5] * num_times
# TODO (forman, 20160725): check why cmap is not recognized
if fig_type == 'poly':
edge_colors = ((0.2, 0.2, 1., 0.7),) * num_times
face_colors = ((1., 1., 1., 0.5),) * num_times
collection = PolyCollection(waveforms, cmap=cmap,
linewidths=line_widths,
edgecolors=edge_colors,
facecolors=face_colors)
else:
colors = ((0.2, 0.2, 1., 0.7),) * num_times
collection = LineCollection(waveforms, cmap=cmap,
linewidths=line_widths, colors=colors)
collection.set_alpha(alpha)
ax.add_collection3d(collection, zs=np.arange(0, num_times), zdir='y')
wf_min, wf_max = self._inspector.waveform_range
ax.set_xlabel('Echo Sample Index')
ax.set_xlim3d(0, num_samples - 1)
ax.set_ylabel('Time Index')
ax.set_ylim3d(0, num_times - 1)
ax.set_zlabel('Waveform')
ax.set_zlim3d(zmin if zmin is not None else wf_min, zmax if zmax is not None else wf_max)
if self._interactive:
plt.show()
else:
self.savefig("fig-waveform-3d-%s.png" % fig_type)
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
(X, Y, I) = (0, 1, 2)
shapes = [self.shapes, self.rshapes][rotated]
trans = TransformScalePart(g.combined_transform)
artists = []
for (motif, cvalues, offsets) in self.per_shape_values:
shape = shapes[motif]
a = PolyCollection([shape], closed=True,
facecolors=cvalues, edgecolors=cvalues, offsets=offsets,
transOffset=g.combined_transform)
g.add(a)
a.set_transform(trans)
return g
def __init__(self,
vars,
title=None,
limits={},
cmap=None,
colorbar='vertical',
axes=None,
figaspect='auto',
**kwlimits):
"""Creates a `Matplotlib2DViewer`.
:Parameters:
vars
a `CellVariable` object.
title
displayed at the top of the `Viewer` window
limits : dict
a (deprecated) alternative to limit keyword arguments
cmap
the colormap. Defaults to `matplotlib.cm.jet`
xmin, xmax, ymin, ymax, datamin, datamax
displayed range of data. Any limit set to
a (default) value of `None` will autoscale.
colorbar
plot a colorbar in specified orientation if not `None`
axes
if not `None`, `vars` will be plotted into this Matplotlib `Axes` object
figaspect
desired aspect ratio of figure. If arg is a number, use that aspect
ratio. If arg is 'auto', the aspect ratio will be determined from
the Variable's mesh.
"""
kwlimits.update(limits)
AbstractMatplotlib2DViewer.__init__(self,
vars=vars,
title=title,
figaspect=figaspect,
cmap=cmap,
colorbar=colorbar,
axes=axes,
**kwlimits)
self.mesh = self.vars[0].mesh
vertexIDs = self.mesh._orderedCellVertexIDs
vertexCoords = self.mesh.vertexCoords
xCoords = numerix.take(vertexCoords[0], vertexIDs)
yCoords = numerix.take(vertexCoords[1], vertexIDs)
polys = []
for x, y in zip(xCoords.swapaxes(0, 1), yCoords.swapaxes(0, 1)):
if hasattr(x, 'mask'):
x = x.compressed()
if hasattr(y, 'mask'):
y = y.compressed()
polys.append(zip(x, y))
from matplotlib.collections import PolyCollection
self.collection = PolyCollection(polys)
self.collection.set_linewidth(0.5)
try:
self.axes.add_patch(self.collection)
except:
# PolyCollection not child of PatchCollection in matplotlib 0.98
self.axes.add_collection(self.collection)
xmin = self._getLimit('xmin', default=xCoords.min())
xmax = self._getLimit('xmax', default=xCoords.max())
ymin = self._getLimit('ymin', default=yCoords.min())
ymax = self._getLimit('ymax', default=yCoords.max())
self.axes.set_xlim(xmin=xmin, xmax=xmax)
self.axes.set_ylim(ymin=ymin, ymax=ymax)
self._plot()
project = AggregationAPI(348, public_panoptes_connection=True)
subject_image = project.__image_setup__(subject_id)
for minimum_users in [8]:
print minimum_users
fig, ax = plt.subplots()
image_file = cbook.get_sample_data(subject_image)
image = plt.imread(image_file)
# fig, ax = plt.subplots()
im = ax.imshow(image)
all_vertices = []
with open("/tmp/348/4_ComplexAMOS/vegetation_polygons_heatmap.csv",
"rb") as f:
polygon_reader = csv.reader(f)
next(polygon_reader, None)
for row in polygon_reader:
if int(row[1]) == minimum_users:
vertices = json.loads(row[2])
all_vertices.append(vertices)
all_vertices = np.asarray(all_vertices)
coll = PolyCollection(all_vertices, alpha=0.3)
ax.add_collection(coll)
ax.autoscale_view()
plt.show()
def volume_overlay(ax, opens, closes, volumes,
colorup='k', colordown='r',
width=4, alpha=1.0):
"""Add a volume overlay to the current axes. The opens and closes
are used to determine the color of the bar. -1 is missing. If a
value is missing on one it must be missing on all
Parameters
----------
ax : `Axes`
an Axes instance to plot to
opens : sequence
a sequence of opens
closes : sequence
a sequence of closes
volumes : sequence
a sequence of volumes
width : int
the bar width in points
colorup : color
the color of the lines where close >= open
colordown : color
the color of the lines where close < open
alpha : float
bar transparency
Returns
-------
ret : `barCollection`
The `barrCollection` added to the axes
"""
r, g, b = colorConverter.to_rgb(colorup)
colorup = r, g, b, alpha
r, g, b = colorConverter.to_rgb(colordown)
colordown = r, g, b, alpha
colord = {True: colorup,
False: colordown,
}
colors = [colord[open < close]
for open, close in zip(opens, closes)
if open != -1 and close != -1]
delta = width / 2.
bars = [((i - delta, 0), (i - delta, v), (i + delta, v), (i + delta, 0))
for i, v in enumerate(volumes)
if v != -1]
barCollection = PolyCollection(bars,
facecolors=colors,
edgecolors=((0, 0, 0, 1), ),
antialiaseds=(0,),
linewidths=(0.5,),
)
ax.add_collection(barCollection)
corners = (0, 0), (len(bars), max(volumes))
ax.update_datalim(corners)
ax.autoscale_view()
# add these last
return barCollection
continue
values = line.split()
if not values:
continue
if values[0] == 'v':
V.append([float(x) for x in values[1:4]])
elif values[0] == 'f':
F.append([int(x) for x in values[1:4]])
V, F = np.array(V), np.array(F) - 1
V = (V - (V.max(0) + V.min(0)) / 2) / max(V.max(0) - V.min(0))
V = np.c_[V, np.ones(len(V))] @ perspective(25, 1, 1, 100).T
V /= V[:, 3].reshape(-1, 1)
T = V[F][..., :2]
# Rendering
fig = plt.figure(figsize=(6, 6))
ax = fig.add_axes([0, 0, 1, 1],
xlim=[-1, +1],
ylim=[-1, +1],
aspect=1,
frameon=False)
collection = PolyCollection(T,
closed=True,
linewidth=0.1,
facecolor="None",
edgecolor="black")
ax.add_collection(collection)
plt.savefig("bunny-2.png", dpi=300)
plt.show()
def plot_probe(probe, ax=None, contacts_colors=None,
with_channel_index=False, with_contact_id=False,
with_device_index=False, text_on_contact=None,
first_index='auto',
contacts_values=None, cmap='viridis',
title=True, contacts_kargs={}, probe_shape_kwargs={},
xlims=None, ylims=None, zlims=None,
show_channel_on_click=False):
"""Plot a Probe object.
Generates a 2D or 3D axis, depending on Probe.ndim
Parameters
----------
probe : Probe
The probe object
ax : matplotlib.axis, optional
The axis to plot the probe on. If None, an axis is created, by default None
contacts_colors : matplotlib color, optional
The color of the contacts, by default None
with_channel_index : bool, optional
If True, channel indices are displayed on top of the channels, by default False
with_contact_id : bool, optional
If True, channel ids are displayed on top of the channels, by default False
with_device_index : bool, optional
If True, device channel indices are displayed on top of the channels, by default False
text_on_contact: None or list or numpy.array
Addintional text to plot on each contact
first_index : str, optional
The first index of the contacts, by default 'auto' (taken from channel ids)
contacts_values : np.array, optional
Values to color the contacts with, by default None
cmap : str, optional
[description], by default 'viridis'
title : bool, optional
If True, the axis title is set to the probe name, by default True
contacts_kargs : dict, optional
Dict with kwargs for contacts (e.g. alpha, edgecolor, lw), by default {}
probe_shape_kwargs : dict, optional
Dict with kwargs for probe shape (e.g. alpha, edgecolor, lw), by default {}
xlims : tuple, optional
Limits for x dimension, by default None
ylims : tuple, optional
Limits for y dimension, by default None
zlims : tuple, optional
Limits for z dimension, by default None
show_channel_on_click : bool, optional
If True, the channel information is shown upon click, by default False
Returns
-------
poly : PolyCollection
The polygon collection for contacts
poly_contour : PolyCollection
The polygon collection for the probe shape
"""
import matplotlib.pyplot as plt
if probe.ndim == 2:
from matplotlib.collections import PolyCollection
elif probe.ndim == 3:
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
if ax is None:
if probe.ndim == 2:
fig, ax = plt.subplots()
ax.set_aspect('equal')
else:
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1, projection='3d')
else:
fig = ax.get_figure()
if first_index == 'auto':
if 'first_index' in probe.annotations:
first_index = probe.annotations['first_index']
elif probe.annotations.get('manufacturer', None) == 'neuronexus':
# neuronexus is one based indexing
first_index = 1
else:
first_index = 0
assert first_index in (0, 1)
_probe_shape_kwargs = dict(
facecolor='green', edgecolor='k', lw=0.5, alpha=0.3)
_probe_shape_kwargs.update(probe_shape_kwargs)
_contacts_kargs = dict(alpha=0.7, edgecolor=[0.3, 0.3, 0.3], lw=0.5)
_contacts_kargs.update(contacts_kargs)
n = probe.get_contact_count()
if contacts_colors is None and contacts_values is None:
contacts_colors = ['orange'] * n
elif contacts_colors is not None:
contacts_colors = contacts_colors
elif contacts_values is not None:
contacts_colors = None
vertices = probe.get_contact_vertices()
if probe.ndim == 2:
poly = PolyCollection(
vertices, color=contacts_colors, **_contacts_kargs)
ax.add_collection(poly)
elif probe.ndim == 3:
poly = Poly3DCollection(
vertices, color=contacts_colors, **_contacts_kargs)
ax.add_collection3d(poly)
if contacts_values is not None:
poly.set_array(contacts_values)
poly.set_cmap(cmap)
if show_channel_on_click:
assert probe.ndim == 2, 'show_channel_on_click works only for ndim=2'
def on_press(event): return _on_press(probe, event)
fig.canvas.mpl_connect('button_press_event', on_press)
fig.canvas.mpl_connect('button_release_event', on_release)
# probe shape
planar_contour = probe.probe_planar_contour
if planar_contour is not None:
if probe.ndim == 2:
poly_contour = PolyCollection(
[planar_contour], **_probe_shape_kwargs)
ax.add_collection(poly_contour)
elif probe.ndim == 3:
poly_contour = Poly3DCollection(
[planar_contour], **_probe_shape_kwargs)
ax.add_collection3d(poly_contour)
else:
poly_contour = None
if text_on_contact is not None:
text_on_contact = np.asarray(text_on_contact)
assert text_on_contact.size == probe.get_contact_count()
if with_channel_index or with_contact_id or with_device_index or text_on_contact is not None:
if probe.ndim == 3:
raise NotImplementedError('Channel index is 2d only')
for i in range(n):
txt = []
if with_channel_index:
txt.append(f'{i + first_index}')
if with_contact_id and probe.contact_ids is not None:
contact_id = probe.contact_ids[i]
txt.append(f'id{contact_id}')
if with_device_index and probe.device_channel_indices is not None:
chan_ind = probe.device_channel_indices[i]
txt.append(f'dev{chan_ind}')
if text_on_contact is not None:
txt.append(f'{text_on_contact[i]}')
txt = '\n'.join(txt)
x, y = probe.contact_positions[i]
ax.text(x, y, txt, ha='center', va='center', clip_on=True)
if xlims is None or ylims is None or (zlims is None and probe.ndim == 3):
xlims, ylims, zlims = get_auto_lims(probe)
ax.set_xlim(*xlims)
ax.set_ylim(*ylims)
if probe.si_units == "um":
unit_str = "($\mu m$)"
else:
unit_str = f"({probe.si_units})"
ax.set_xlabel(f'x {unit_str}', fontsize=15)
ax.set_ylabel(f'y {unit_str}', fontsize=15)
if probe.ndim == 3:
ax.set_zlim(zlims)
ax.set_zlabel('z')
if probe.ndim == 2:
ax.set_aspect('equal')
if title:
ax.set_title(probe.get_title())
return poly, poly_contour
def show_mesh_2d(axes,
mesh,
nodecolor='k',
edgecolor='k',
cellcolor='grey',
aspect='equal',
linewidths=1,
markersize=20,
showaxis=False,
showcolorbar=False,
cmap='gnuplot2',
box=None):
try:
axes.set_aspect(aspect)
except NotImplementedError:
pass
if showaxis == False:
axes.set_axis_off()
else:
axes.set_axis_on()
if (type(nodecolor) is np.ndarray) & np.isreal(nodecolor[0]):
cmax = nodecolor.max()
cmin = nodecolor.min()
norm = colors.Normalize(vmin=cmin, vmax=cmax)
mapper = cm.ScalarMappable(norm=norm, cmap=cmap)
nodecolor = mapper.to_rgba(nodecolor)
if (type(cellcolor) is np.ndarray) & np.isreal(cellcolor[0]):
cmax = cellcolor.max()
cmin = cellcolor.min()
norm = colors.Normalize(vmin=cmin, vmax=cmax)
mapper = cm.ScalarMappable(norm=norm, cmap=cmap)
mapper.set_array(cellcolor)
cellcolor = mapper.to_rgba(cellcolor)
if showcolorbar:
f = axes.get_figure()
f.colorbar(mapper, shrink=0.5, ax=axes)
node = mesh.entity('node')
cell = mesh.entity('cell')
if mesh.meshtype not in {'polygon', 'hepolygon', 'halfedge', 'halfedge2d'}:
if mesh.geo_dimension() == 2:
poly = PolyCollection(node[cell[:, mesh.ds.ccw], :])
else:
poly = a3.art3d.Poly3DCollection(node[cell, :])
else:
cell, cellLocation = cell
NC = mesh.number_of_cells()
patches = [
Polygon(node[cell[cellLocation[i]:cellLocation[i + 1]], :], True)
for i in range(NC)
]
poly = PatchCollection(patches)
poly.set_edgecolor(edgecolor)
poly.set_linewidth(linewidths)
poly.set_facecolors(cellcolor)
if box is None:
if mesh.geo_dimension() == 2:
box = np.zeros(4, dtype=np.float)
else:
box = np.zeros(6, dtype=np.float)
box[0::2] = np.min(node, axis=0)
box[1::2] = np.max(node, axis=0)
axes.set_xlim(box[0:2])
axes.set_ylim(box[2:4])
if mesh.geo_dimension() == 3:
axes.set_zlim(box[4:6])
return axes.add_collection(poly)
B_wass[:, i] = ot.bregman.barycenter(A, M, reg, weights)
#%% plot interpolation
pl.figure(3)
cmap = pl.cm.get_cmap('viridis')
verts = []
zs = alpha_list
for i, z in enumerate(zs):
ys = B_l2[:, i]
verts.append(list(zip(x, ys)))
ax = pl.gcf().gca(projection='3d')
poly = PolyCollection(verts, facecolors=[cmap(a) for a in alpha_list])
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlabel('x')
ax.set_xlim3d(0, n)
ax.set_ylabel('$\\alpha$')
ax.set_ylim3d(0, 1)
ax.set_zlabel('')
ax.set_zlim3d(0, B_l2.max() * 1.01)
pl.title('Barycenter interpolation with l2')
pl.tight_layout()
pl.figure(4)
cmap = pl.cm.get_cmap('viridis')
verts = []
zs = alpha_list
def overlayFan(myData,
myMap,
myFig,
param,
coords='geo',
gsct=0,
site=None,
fov=None,
gs_flg=[],
fill=True,
velscl=1000.,
dist=1000.,
cmap=None,
norm=None,
alpha=1):
"""A function of overlay radar scan data on a map
Parameters
----------
myData : pydarn.sdio.radDataTypes.scanData or
pydarn.sdio.radDataTypes.beamData or
list of pydarn.sdio.radDataTypes.beamData objects
A radar beam object, a radar scanData object, or simply a list of
radar beams
myMap :
The map we are plotting on
myFig :
Figure object that we are plotting to
coords : Optional[str]
The coordinates we are plotting in. Default: geo
param : Optional[str]
The parameter to be plotted, valid inputs are 'velocity', 'power',
'width', 'elevation', 'phi0'. default = 'velocity
gsct : Optional[boolean]
A flag indicating whether we are distinguishing ground scatter.
default = 0
intensities : Optional[ ]
A list of intensities (used for colorbar)
fov : Optional[pydarn.radar.radFov.fov]
A radar fov object
gs_flg : Optional[ ]
A list of gs flags, 1 per range gate
fill : Optional[boolean]
A flag indicating whether to plot filled or point RB cells.
default = True
velscl : Optional[float]
The velocity to use as baseline for velocity vector length, only
applicable if fill = 0. default = 1000
lines : Optional[ ]
An array to have the endpoints of velocity vectors. only applicable if
fill = 0. default = []
dist : Optional [float]
The length in map projection coords of a velscl length velocity vector.
default = 1000. km
Returns
-------
intensities
pcoll
lcoll
Example
-------
overlayFan(aBeam,myMap,param,coords,gsct=gsct,site=sites[i],fov=fovs[i],
verts=verts,intensities=intensities,gs_flg=gs_flg)
"""
from davitpy import pydarn
if (site is None):
site = pydarn.radar.site(radId=myData[0].stid, dt=myData[0].time)
if (fov is None):
fov = pydarn.radar.radFov.fov(site=site,
rsep=myData[0].prm.rsep,
ngates=myData[0].prm.nrang + 1,
nbeams=site.maxbeam,
coords=coords,
date_time=myData[0].time)
if (isinstance(myData, pydarn.sdio.beamData)): myData = [myData]
gs_flg, lines = [], []
if fill: verts, intensities = [], []
else: verts, intensities = [[], []], [[], []]
# loop through gates with scatter
for myBeam in myData:
for k in range(0, len(myBeam.fit.slist)):
if myBeam.fit.slist[k] not in fov.gates: continue
r = myBeam.fit.slist[k]
if fill:
x1, y1 = myMap(fov.lonFull[myBeam.bmnum, r],
fov.latFull[myBeam.bmnum, r])
x2, y2 = myMap(fov.lonFull[myBeam.bmnum, r + 1],
fov.latFull[myBeam.bmnum, r + 1])
x3, y3 = myMap(fov.lonFull[myBeam.bmnum + 1, r + 1],
fov.latFull[myBeam.bmnum + 1, r + 1])
x4, y4 = myMap(fov.lonFull[myBeam.bmnum + 1, r],
fov.latFull[myBeam.bmnum + 1, r])
# save the polygon vertices
verts.append(
((x1, y1), (x2, y2), (x3, y3), (x4, y4), (x1, y1)))
# save the param to use as a color scale
if (param == 'velocity'):
intensities.append(myBeam.fit.v[k])
elif (param == 'power'):
intensities.append(myBeam.fit.p_l[k])
elif (param == 'width'):
intensities.append(myBeam.fit.w_l[k])
elif (param == 'elevation' and myBeam.prm.xcf):
intensities.append(myBeam.fit.elv[k])
elif (param == 'phi0' and myBeam.prm.xcf):
intensities.append(myBeam.fit.phi0[k])
else:
x1, y1 = myMap(fov.lonCenter[myBeam.bmnum, r],
fov.latCenter[myBeam.bmnum, r])
verts[0].append(x1)
verts[1].append(y1)
x2, y2 = myMap(fov.lonCenter[myBeam.bmnum, r + 1],
fov.latCenter[myBeam.bmnum, r + 1])
theta = math.atan2(y2 - y1, x2 - x1)
x2, y2 = x1 + myBeam.fit.v[k] / velscl * (-1.0) * \
math.cos(theta) * dist, y1 + myBeam.fit.v[k] / velscl * \
(-1.0) * math.sin(theta) * dist
lines.append(((x1, y1), (x2, y2)))
# save the param to use as a color scale
if (param == 'velocity'):
intensities[0].append(myBeam.fit.v[k])
elif (param == 'power'):
intensities[0].append(myBeam.fit.p_l[k])
elif (param == 'width'):
intensities[0].append(myBeam.fit.w_l[k])
elif (param == 'elevation' and myBeam.prm.xcf):
intensities[0].append(myBeam.fit.elv[k])
elif (param == 'phi0' and myBeam.prm.xcf):
intensities[0].append(myBeam.fit.phi0[k])
if (myBeam.fit.p_l[k] > 0):
intensities[1].append(myBeam.fit.p_l[k])
else:
intensities[1].append(0.)
if (gsct):
gs_flg.append(myBeam.fit.gflg[k])
# do the actual overlay
if (fill):
# if we have data
if (verts != []):
if (gsct == 0):
inx = numpy.arange(len(verts))
else:
inx = numpy.where(numpy.array(gs_flg) == 0)
x = PolyCollection(
numpy.array(verts)[numpy.where(numpy.array(gs_flg) == 1)],
facecolors='.3',
linewidths=0,
zorder=5,
alpha=alpha)
myFig.gca().add_collection(x, autolim=True)
pcoll = PolyCollection(numpy.array(verts)[inx],
edgecolors='face',
linewidths=0,
closed=False,
zorder=4,
alpha=alpha,
cmap=cmap,
norm=norm)
# set color array to intensities
pcoll.set_array(numpy.array(intensities)[inx])
myFig.gca().add_collection(pcoll, autolim=True)
return intensities, pcoll
else:
# if we have data
if (verts != [[], []]):
if (gsct == 0):
inx = numpy.arange(len(verts[0]))
else:
inx = numpy.where(numpy.array(gs_flg) == 0)
# plot the ground scatter as open circles
x = myFig.scatter(
numpy.array(
verts[0])[numpy.where(numpy.array(gs_flg) == 1)],
numpy.array(
verts[1])[numpy.where(numpy.array(gs_flg) == 1)],
s=.1 * numpy.array(
intensities[1])[numpy.where(numpy.array(gs_flg) == 1)],
zorder=5,
marker='o',
linewidths=.5,
facecolors='w',
edgecolors='k')
myFig.gca().add_collection(x, autolim=True)
# plot the i-s as filled circles
ccoll = myFig.gca().scatter(numpy.array(verts[0])[inx],
numpy.array(verts[1])[inx],
s=.1 *
numpy.array(intensities[1])[inx],
zorder=10,
marker='o',
linewidths=.5,
edgecolors='face',
cmap=cmap,
norm=norm)
# set color array to intensities
ccoll.set_array(numpy.array(intensities[0])[inx])
myFig.gca().add_collection(ccoll)
# plot the velocity vectors
lcoll = LineCollection(numpy.array(lines)[inx],
linewidths=.5,
zorder=12,
cmap=cmap,
norm=norm)
lcoll.set_array(numpy.array(intensities[0])[inx])
myFig.gca().add_collection(lcoll)
return intensities, lcoll
def swhglobl(swhs,
nvrts,
ncels,
svrts,
scels,
colrs,
config,
mdlname='SMC',
datx='2018010106',
psfile='output.ps',
paprtyp='a3'):
"""
## Draw global swh plot with given polycollections and cell
## array. Output as A3 ps file. JGLi28Feb2019
##
"""
# Degree to radian conversion parameter.
d2rad = np.pi / 180.0
# Global plot configuration parameters.
rdpols = config[0]
sztpxy = config[1]
rngsxy = config[2]
clrbxy = config[3]
ncabgm = config[4]
# Maximum mapping radius.
radius = rdpols[0]
pangle = rdpols[1]
plon = rdpols[2]
plat = rdpols[3]
# Outline circle at equator
ciran = np.arange(1081) * d2rad / 3.0
xcirc = radius * np.cos(ciran)
ycirc = radius * np.sin(ciran)
# Set up wave height scale and marks with colrs.N.
# colrs.N returns colrs' total number of colors 256.
waveht, factor, residu, marks, ncstr, nclrm = scale_swh(nclrm=colrs.N)
resmn1 = residu - 1.0
nswh0 = ncstr + int(factor * np.log(-resmn1 + residu))
#print (' factor, residu, resmn1, nswh0 = {} {} {} {: d}'
#.format(factor, residu, resmn1, nswh0) )
# Some constant variables for plots.
xprop = {'xlim': rngsxy[0:2], 'xlabel': ''}
yprop = {'ylim': rngsxy[2:4], 'ylabel': ''}
if True:
# Work out max and min values, excluding missing data (-999.0)
cmax = swhs.max()
cmin = swhs[swhs > -999.0].min()
print(' swh range %f, %f' % (cmin, cmax))
cmxs = 'SWHmx = %6.2f m' % cmax
cmns = 'SWHmn = %10.3E' % cmin
# Reset missing values (-999.0) to be -resmn1
swhs[swhs < -resmn1] = -resmn1
# Trim large values into plot range if any
swhs[swhs > 32.0] = 32.0
# Convert swhs with logarithm scale.
icnf = np.rint(factor * np.log(swhs + residu))
nswh = np.array(icnf, dtype=np.int)
print(" Drawing " + psfile)
# Set up first subplot and axis for northern hemisphere
fig = plt.figure(figsize=sztpxy[0:2])
ax1 = fig.add_subplot(1, 2, 1)
ax1.set_aspect('equal')
ax1.set_autoscale_on(False)
ax1.set_axis_off()
plt.subplots_adjust(left=0.02, bottom=0.02, right=0.98, top=0.95)
plt.subplots_adjust(wspace=0.02, hspace=0.01)
ax1.set(**xprop)
ax1.set(**yprop)
ax1.plot(xcirc, ycirc, 'b-')
# Use loaded verts to setup PolyCollection.
polynorth = PolyCollection(nvrts)
# Create color array for this plot
pcface = []
pcedge = []
for i in ncels:
if (nswh[i] == nswh0):
pcface.append(colrs(255))
pcedge.append(colrs(0))
else:
pcface.append(colrs(nswh[i]))
pcedge.append(colrs(nswh[i]))
#smcpoly.set_color(pcolr) ## This line defines both edge and face color.
polynorth.set_facecolor(pcface)
polynorth.set_edgecolor(pcedge)
polynorth.set_linewidth(0.2)
ax1.add_collection(polynorth)
# Draw colorbar for ax1.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks)
ax1.add_collection(clrply)
for i in range(len(waveht)):
m = marks[i]
plt.text(xkeys[m],
ykeys[0] + 1.18 * (ykeys[1] - ykeys[0]),
str(waveht[i]),
horizontalalignment='center',
fontsize=11,
color='b')
#rotation=-90,verticalalignment='center', fontsize=11, color='b' )
plt.text(xkeys[marks[0]],
ykeys[0] + 2.2 * (ykeys[1] - ykeys[0]),
'SWH m',
horizontalalignment='left',
fontsize=15,
color='k')
#rotation=-90,verticalalignment='center', fontsize=15, color='k' )
# Southern hemisphere subplot.
ax2 = fig.add_subplot(1, 2, 2)
ax2.set_aspect('equal')
ax2.axis('off')
plt.subplots_adjust(left=0.02, bottom=0.02, right=0.98, top=0.95)
plt.subplots_adjust(wspace=0.02, hspace=0.01)
ax2.set(**xprop)
ax2.set(**yprop)
ax2.plot(xcirc, ycirc, 'b-')
# Use loaded verts to set up PolyCollection.
polysouth = PolyCollection(svrts)
# Create color array for this plot
pcface = []
pcedge = []
for i in scels:
if (nswh[i] == nswh0):
pcface.append(colrs(255))
pcedge.append(colrs(0))
else:
pcface.append(colrs(nswh[i]))
pcedge.append(colrs(nswh[i]))
# smcpoly.set_color(pcolr) ## This line defines both edge and face color.
polysouth.set_facecolor(pcface)
polysouth.set_edgecolor(pcedge)
polysouth.set_linewidth(0.2)
ax2.add_collection(polysouth)
# Put statistic information inside subplot ax2
tpx = sztpxy[2]
tpy = sztpxy[3]
dpy = 0.6
plt.text(tpx,
9.0,
mdlname + ' SWH',
horizontalalignment='center',
fontsize=19,
color='r')
plt.text(tpx,
tpy + dpy * 1.0,
cmns,
horizontalalignment='center',
fontsize=15,
color='b')
plt.text(tpx,
tpy + dpy * 2.0,
cmxs,
horizontalalignment='center',
fontsize=15,
color='r')
plt.text(tpx,
tpy + dpy * 3.0,
datx,
horizontalalignment='center',
fontsize=17,
color='k')
# Draw colorbar for ax2.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks)
ax2.add_collection(clrply)
for i in range(len(waveht)):
m = marks[i]
plt.text(xkeys[m],
ykeys[0] + 1.18 * (ykeys[1] - ykeys[0]),
str(waveht[i]),
horizontalalignment='center',
fontsize=13,
color='b')
#rotation=-90,verticalalignment='center', fontsize=11, color='b' )
plt.text(xkeys[marks[-1]],
ykeys[0] + 2.2 * (ykeys[1] - ykeys[0]),
'SWH m',
horizontalalignment='right',
fontsize=15,
color='k')
#rotation=-90,verticalalignment='center', fontsize=15, color='k' )
# Refresh subplots and save them.
plt.subplots_adjust(wspace=0.02, hspace=0.01)
plt.savefig(psfile,
dpi=None,
facecolor='w',
edgecolor='w',
orientation='landscape',
papertype=paprtyp,
format='ps')
plt.close()
def _gen2d3d(*args, **pltkwargs):
# UPDATE
""" Abstract layout for 2d plot.
For convienence, a few special labels, colorbar and background keywords
have been implemented. If these are not adequate, it one can add
custom colorbars, linelabels background images etc... easily just by
using respecitve calls to plot (plt.colorbar(), plt.imshow(),
plt.clabel() ); my implementations are only for convienences and
some predefined, cool styles.
countours: Number of desired contours from output.
label: Predefined label types. For now, only integer values 1,2. Use plt.clabel to add a custom label.
background: Integers 1,2 will add gray or autumn colormap under contour plot. Use plt.imgshow() to generate
custom background, or pass a PIL-opened image (note, proper image scaling not yet implemented).
c_iso, r_iso: These control how man column and row iso lines will be projected onto the 3d plot.
For example, if c_iso=10, then 10 isolines will be plotted as columns, despite the actual length of the
columns. Alternatively, one can pass in c_stride directly, which is a column step size rather than
an absolute number, and c_iso will be disregarded.
fill: bool (False)
Fill between contour lines.
**pltkwargs: Will be passed directly to plt.contour().
Returns
-------
tuple: (Axes, SurfaceFunction)
Returns axes object and the surface function (e.g. contours for
contour plot. Surface for surface plot.
"""
# Use a label mapper to allow for datetimes in any plot x/y axis
_x_dti = _ = _y_dti = False
# Passed Spectra
if len(args) == 1:
ts = args[0]
try:
index = np.array([dates.date2num(x) for x in ts.index])
_x_dti = True
except AttributeError:
index = ts.index.values #VALUES NECESSARY FOR POLY CMAP
try:
cols = np.array([dates.date2num(x) for x in ts.columns])
_y_dti = True
except AttributeError:
cols = ts.columns.values #VALUES NECESSARY FOR POLY CMAP
yy, xx = np.meshgrid(cols, index)
# Passed xx, yy, ts/zz
elif len(args) == 3:
xx, yy, ts = args
cols, index = ts.columns.values, ts.index.values
else:
raise PlotError(
"Please pass a single spectra, or xx, yy, zz. Got %s args" %
len(args))
# Boilerplate from basic_plots._genplot(); could refactor as decorator
xlabel = pltkwargs.pop('xlabel', '')
ylabel = pltkwargs.pop('ylabel', '')
zlabel = pltkwargs.pop('zlabel', '')
title = pltkwargs.pop('title', '')
# Choose plot kind
kind = pltkwargs.pop('kind', 'contour')
grid = pltkwargs.pop('grid', '')
# pltkwargs.setdefault('legend', False) #(any purpose in 2d?)
# LEGEND FOR 2D PLOT: http://stackoverflow.com/questions/10490302/how-do-you-create-a-legend-for-a-contour-plot-in-matplotlib
pltkwargs.setdefault('linewidth', 1)
cbar = pltkwargs.pop('cbar', False)
fig = pltkwargs.pop('fig', None)
ax = pltkwargs.pop('ax', None)
fill = pltkwargs.pop('fill', False)
xlim = pltkwargs.pop('xlim', None)
ylim = pltkwargs.pop('ylim', None)
zlim = pltkwargs.pop('zlim', None)
#Private attributes
_modifyax = pltkwargs.pop('_modifyax', True)
contours = pltkwargs.pop('contours', 6)
label = pltkwargs.pop('label', None)
projection = None
if kind in PLOTPARSER.plots_3d:
projection = '3d'
elev = pltkwargs.pop('elev', 35)
azim = pltkwargs.pop('azim', -135)
view = pltkwargs.pop('view', None)
if view:
if view == 1:
elev, azim = 35, -135
elif view == 2:
elev, azim = 35, -45
elif view == 3:
elev, azim = 20, -10 # Side view
elif view == 4:
elev, azim = 20, -170
elif view == 5:
elev, azim = 0, -90
elif view == 6:
elev, azim = 65, -90
else:
raise PlotError('View must be between 1 and 6; otherwise set'
' "elev" and "azim" keywords.')
# Orientation of zlabel (doesn't work...)
_zlabel_rotation = 0.0
if azim < 0:
_zlabel_rotation = 90.0
c_iso = pltkwargs.pop('c_iso', 10)
r_iso = pltkwargs.pop('r_iso', 10)
if c_iso > ts.shape[1] or c_iso < 0:
raise PlotError('"c_iso" must be between 0 and %s, got "%s"' %
(ts.shape[1], c_iso))
if r_iso > ts.shape[0] or r_iso < 0:
raise PlotError('"r_iso" must be between 0 and %s, got "%s"' %
(ts.shape[0], r_iso))
if c_iso == 0:
cstride = 0
else:
cstride = _ir(ts.shape[1] / float(c_iso))
if r_iso == 0:
rstride = 0
else:
rstride = _ir(ts.shape[0] / float(r_iso))
pltkwargs.setdefault('cstride', cstride)
pltkwargs.setdefault('rstride', rstride)
elif kind == 'contour':
pass
else:
raise PlotError('_gen2d3d invalid kind: "%s". '
'Choose from %s' % (kind, PLOTPARSER.plots_2d_3d))
# Is this the best logic for 2d/3d fig?
if not ax:
f = plt.figure()
# ax = f.gca(projection=projection)
ax = f.add_subplot(111, projection=projection)
if not fig:
fig = f
labelsize = pltkwargs.pop('labelsize', 'medium') #Can also be ints
titlesize = pltkwargs.pop('titlesize', 'large')
ticksize = pltkwargs.pop('ticksize',
'') #Put in default and remove bool gate
# PLT.CONTOUR() doesn't take 'color'; rather, takes 'colors' for now
if 'color' in pltkwargs:
if kind == 'contour':
pltkwargs['colors'] = pltkwargs.pop('color')
# Convienence method to pass in string colors
if 'colormap' in pltkwargs:
pltkwargs['cmap'] = pltkwargs.pop('colormap')
if 'cmap' in pltkwargs:
if isinstance(pltkwargs['cmap'], basestring):
pltkwargs['cmap'] = pu.cmget(pltkwargs['cmap'])
# Contour Plots
# -------------
# Broken background image
### More here http://matplotlib.org/examples/pylab_examples/image_demo3.html ###
# Refactored with xx, yy instead of df.columns/index UNTESTED
#if background:
#xmin, xmax, ymin, ymax = xx.min(), xx.max(), yy.min(), yy.max()
## Could try rescaling contour rather than image:
##http://stackoverflow.com/questions/10850882/pyqt-matplotlib-plot-contour-data-on-top-of-picture-scaling-issue
#if background==1:
#im = ax.imshow(ts, interpolation='bilinear', origin='lower',
#cmap=cm.gray, extent=(xmin, xmax, ymin, ymax))
#### This will take a custom image opened in PIL or it will take plt.imshow() returned from somewhere else
#else:
#try:
#im = ax.imshow(background)
#### Perhaps image was not correctly opened
#except Exception:
#raise badvalue_error(background, 'integer 1,2 or a PIL-opened image')
# Note this overwrites the 'contours' variable from an int to array
if kind == 'contour' or kind == 'contour3d':
if fill:
mappable = ax.contourf(xx, yy, ts, contours,
**pltkwargs) #linewidths is a pltkwargs arg
else:
mappable = ax.contour(xx, yy, ts, contours, **pltkwargs)
### Pick a few label styles to choose from.
if label:
if label == 1:
ax.clabel(inline=1, fontsize=10)
elif label == 2:
ax.clabel(levels[1::2], inline=1,
fontsize=10) #label every second line
else:
raise PlotError(label, 'integer of value 1 or 2')
elif kind == 'surf':
mappable = ax.plot_surface(xx, yy, ts, **pltkwargs)
# pltkwargs.pop('edgecolors')
wires = overload_plot_wireframe(ax, xx, yy, ts, **pltkwargs)
# print np.shape(wires._segments3d)
wires = wire_cmap(wires, ax, cmap='jet')
elif kind == 'wire':
pltkwargs.setdefault('color', 'black')
mappable = overload_plot_wireframe(ax, xx, yy, ts, **pltkwargs)
elif kind == 'waterfall':
edgecolors = pltkwargs.setdefault('edgecolors', None)
pltkwargs.setdefault('closed', False)
alpha = pltkwargs.setdefault('alpha', None)
# Need to handle cmap/colors a bit differently for PolyCollection API
if 'color' in pltkwargs:
pltkwargs['facecolors'] = pltkwargs.pop('color')
cmap = pltkwargs.setdefault('cmap', None)
if alpha is None: #as opposed to 0
alpha = 0.6 * (13.0 / ts.shape[1])
if alpha > 0.6:
alpha = 0.6
#Delete stride keywords
for key in ['cstride', 'rstride']:
try:
del pltkwargs[key]
except KeyError:
pass
# Verts are index dotted with data
verts = []
for col in ts.columns:
values = ts[col]
values[0], values[-1] = values.min().min(), values.min().min()
verts.append(list(zip(ts.index, values)))
mappable = PolyCollection(verts, **pltkwargs)
if cmap:
mappable.set_array(
cols) #If set array in __init__, autogens a cmap!
mappable.set_cmap(pltkwargs['cmap'])
mappable.set_alpha(alpha)
#zdir is the direction used to plot; dont' fully understand
ax.add_collection3d(mappable, zs=cols, zdir='x')
# custom limits/labels polygon plot (reverse x,y)
if not ylim:
ylim = (max(index), min(index)) #REVERSE AXIS FOR VIEWING PURPOSES
if not xlim:
xlim = (min(cols), max(cols)) #x
if not zlim:
zlim = (min(ts.min()), max(ts.max())
) #How to get absolute min/max of ts values
# Reverse labels/DTI call for correct orientaion HACK HACK HACK
xlabel, ylabel = ylabel, xlabel
_x_dti, _y_dti = _y_dti, _x_dti
azim = -1 * azim
# General Features
# ----------------
# Some applications (like add_projection) shouldn't alther axes features
if not _modifyax:
return (ax, mappable)
if cbar:
# Do I want colorbar outside of fig? Wouldn't be better on axes?
try:
fig.colorbar(mappable, ax=ax)
except Exception:
raise PlotError("Colorbar failed; did you pass a colormap?")
if grid:
ax.grid()
# Format datetime axis
# -------------------
if _x_dti:
ax.xaxis.set_major_formatter(mplticker.FuncFormatter(format_date))
# Uncomment for custom 3d timestamp orientation
# if projection:
# for t1 in ax.yaxis.get_ticklabels():
# t1.set_ha('right')
# t1.set_rotation(30)
# ax.yaxis._axinfo['label']['space_factor'] = _TIMESTAMPPADDING
if _y_dti:
ax.yaxis.set_major_formatter(mplticker.FuncFormatter(format_date))
# Uncomment for custom 3d timestamp orientation
# if projection:
# for t1 in ax.yaxis.get_ticklabels():
# t1.set_ha('right')
# t1.set_rotation(30)
# ax.yaxis._axinfo['label']['space_factor'] = _TIMESTAMPPADDING
if xlim:
ax.set_xlim3d(xlim)
if ylim:
ax.set_ylim3d(ylim)
if zlim:
ax.set_zlim3d(zlim)
# Set elevation/azimuth for 3d plots
if projection:
ax.view_init(elev, azim)
ax.set_zlabel(zlabel, fontsize=labelsize, rotation=_zlabel_rotation)
ax.set_xlabel(xlabel, fontsize=labelsize)
ax.set_ylabel(ylabel, fontsize=labelsize)
ax.set_title(title, fontsize=titlesize)
# Return Ax, contours/surface/polygons etc...
return (ax, mappable)
def triplot(mesh, axes=None, interior_kw={}, boundary_kw={}):
r"""Plot a mesh with a different color for each boundary segment
The interior and boundary keyword arguments can be any keyword argument for
:class:`LineCollection <matplotlib.collections.LinecCollection>` and
related types.
:arg mesh: mesh to be plotted
:arg axes: matplotlib :class:`Axes <matplotlib.axes.Axes>` object on which to plot mesh
:arg interior_kw: keyword arguments to apply when plotting the mesh interior
:arg boundary_kw: keyword arguments to apply when plotting the mesh boundary
:return: list of matplotlib :class:`Collection <matplotlib.collections.Collection>` objects
"""
gdim = mesh.geometric_dimension()
tdim = mesh.topological_dimension()
BoundaryCollection, InteriorCollection = _get_collection_types(gdim, tdim)
quad = mesh.ufl_cell().cellname() == "quadrilateral"
if axes is None:
figure = plt.figure()
if gdim == 3:
axes = figure.add_subplot(111, projection='3d')
else:
axes = figure.add_subplot(111)
coordinates = mesh.coordinates
element = coordinates.function_space().ufl_element()
if element.degree() != 1:
# Interpolate to piecewise linear.
V = VectorFunctionSpace(mesh, element.family(), 1)
coordinates = interpolate(coordinates, V)
coords = coordinates.dat.data_ro
result = []
interior_kw = dict(interior_kw)
# If the domain isn't a 3D volume, draw the interior.
if tdim <= 2:
cell_node_map = coordinates.cell_node_map().values
idx = (tuple(range(tdim + 1)) if not quad else (0, 1, 3, 2)) + (0, )
vertices = coords[cell_node_map[:, idx]]
interior_kw["edgecolors"] = interior_kw.get("edgecolors", "k")
interior_kw["linewidths"] = interior_kw.get("linewidths", 1.0)
if gdim == 2:
interior_kw["facecolors"] = interior_kw.get("facecolors", "none")
interior_collection = InteriorCollection(vertices, **interior_kw)
axes.add_collection(interior_collection)
result.append(interior_collection)
# Add colored lines/polygons for the boundary facets
facets = mesh.exterior_facets
local_facet_ids = facets.local_facet_dat.data_ro
exterior_facet_node_map = coordinates.exterior_facet_node_map().values
topology = coordinates.function_space().finat_element.cell.get_topology()
mask = np.zeros(exterior_facet_node_map.shape, dtype=bool)
for facet_index, local_facet_index in enumerate(local_facet_ids):
mask[facet_index, topology[tdim - 1][local_facet_index]] = True
faces = exterior_facet_node_map[mask].reshape(-1, tdim)
markers = facets.unique_markers
color_key = "colors" if tdim <= 2 else "facecolors"
boundary_colors = boundary_kw.pop(color_key, None)
if boundary_colors is None:
cmap = matplotlib.cm.get_cmap("Dark2")
num_markers = len(markers)
colors = cmap([k / num_markers for k in range(num_markers)])
else:
colors = matplotlib.colors.to_rgba_array(boundary_colors)
boundary_kw = dict(boundary_kw)
if tdim == 3:
boundary_kw["edgecolors"] = boundary_kw.get("edgecolors", "k")
boundary_kw["linewidths"] = boundary_kw.get("linewidths", 1.0)
for marker, color in zip(markers, colors):
face_indices = facets.subset(int(marker)).indices
marker_faces = faces[face_indices, :]
vertices = coords[marker_faces]
_boundary_kw = dict(**{
color_key: color,
"label": marker
}, **boundary_kw)
marker_collection = BoundaryCollection(vertices, **_boundary_kw)
axes.add_collection(marker_collection)
result.append(marker_collection)
# Dirty hack to enable legends for 3D volume plots. See the function
# `Poly3DCollection.set_3d_properties`.
for collection in result:
if isinstance(collection, Poly3DCollection):
collection._facecolors2d = PolyCollection.get_facecolor(collection)
collection._edgecolors2d = PolyCollection.get_edgecolor(collection)
_autoscale_view(axes, coords)
return result
ax = fig.gca(projection='3d')
fig.set_tight_layout(True)
fig.tight_layout(pad=10.4, w_pad=10.5, h_pad=11.0)
def cc(arg):
return mcolors.to_rgba(arg, alpha=0.6)
xs = wl
verts = []
zs = [0.0, 1.0, 2.0, 3.0, 4.0]
for z in zs:
ys = dict_for_dyn[dyn_conc][int(z)][1:1500]
ys[0], ys[-1] = 0, 0
verts.append(list(zip(xs, ys)))
poly = PolyCollection(verts, facecolors=[cc('r'), cc('g'), cc('b'),
cc('y'), cc('r')])
poly.set_alpha(0.4)
ax.add_collection3d(poly, zs=zs, zdir='y')
ax.set_xlabel('Wavelength, nm',labelpad=20)
ax.set_xlim3d(200, 900)
ax.set_ylabel('T',labelpad=20)
ax.set_ylim3d(0, 4)
ax.set_zlabel('I, Relative units',labelpad=20)
ax.set_zlim3d(0, max(ys))
if do_save == 1:
fig.savefig(sna+'_Dynamic'+dyn_conc+'.jpg',transparent=False,dpi=300,bbox_inches="tight")
plt.show()
def index_bar(ax, vals,
facecolor='b', edgecolor='l',
width=4, alpha=1.0, ):
"""Add a bar collection graph with height vals (-1 is missing).
Parameters
----------
ax : `Axes`
an Axes instance to plot to
vals : sequence
a sequence of values
facecolor : color
the color of the bar face
edgecolor : color
the color of the bar edges
width : int
the bar width in points
alpha : float
bar transparency
Returns
-------
ret : `barCollection`
The `barrCollection` added to the axes
"""
facecolors = (colorConverter.to_rgba(facecolor, alpha),)
edgecolors = (colorConverter.to_rgba(edgecolor, alpha),)
right = width / 2.0
left = -width / 2.0
bars = [((left, 0), (left, v), (right, v), (right, 0))
for v in vals if v != -1]
sx = ax.figure.dpi * (1.0 / 72.0) # scale for points
sy = ax.bbox.height / ax.viewLim.height
barTransform = Affine2D().scale(sx, sy)
offsetsBars = [(i, 0) for i, v in enumerate(vals) if v != -1]
barCollection = PolyCollection(bars,
facecolors=facecolors,
edgecolors=edgecolors,
antialiaseds=(0,),
linewidths=(0.5,),
offsets=offsetsBars,
transOffset=ax.transData,
)
barCollection.set_transform(barTransform)
minpy, maxx = (0, len(offsetsBars))
miny = 0
maxy = max([v for v in vals if v != -1])
corners = (minpy, miny), (maxx, maxy)
ax.update_datalim(corners)
ax.autoscale_view()
# add these last
ax.add_collection(barCollection)
return barCollection
def volume_overlay3(ax, quotes,
colorup='k', colordown='r',
width=4, alpha=1.0):
"""Add a volume overlay to the current axes. quotes is a list of (d,
open, high, low, close, volume) and close-open is used to
determine the color of the bar
Parameters
----------
ax : `Axes`
an Axes instance to plot to
quotes : sequence of (time, open, high, low, close, ...) sequences
data to plot. time must be in float date format - see date2num
width : int
the bar width in points
colorup : color
the color of the lines where close1 >= close0
colordown : color
the color of the lines where close1 < close0
alpha : float
bar transparency
Returns
-------
ret : `barCollection`
The `barrCollection` added to the axes
"""
r, g, b = colorConverter.to_rgb(colorup)
colorup = r, g, b, alpha
r, g, b = colorConverter.to_rgb(colordown)
colordown = r, g, b, alpha
colord = {True: colorup,
False: colordown,
}
dates, opens, highs, lows, closes, volumes = list(zip(*quotes))
colors = [colord[close1 >= close0]
for close0, close1 in zip(closes[:-1], closes[1:])
if close0 != -1 and close1 != -1]
colors.insert(0, colord[closes[0] >= opens[0]])
right = width / 2.0
left = -width / 2.0
bars = [((left, 0), (left, volume), (right, volume), (right, 0))
for d, open, high, low, close, volume in quotes]
sx = ax.figure.dpi * (1.0 / 72.0) # scale for points
sy = ax.bbox.height / ax.viewLim.height
barTransform = Affine2D().scale(sx, sy)
dates = [d for d, open, high, low, close, volume in quotes]
offsetsBars = [(d, 0) for d in dates]
useAA = 0, # use tuple here
lw = 0.5, # and here
barCollection = PolyCollection(bars,
facecolors=colors,
edgecolors=((0, 0, 0, 1),),
antialiaseds=useAA,
linewidths=lw,
offsets=offsetsBars,
transOffset=ax.transData,
)
barCollection.set_transform(barTransform)
minpy, maxx = (min(dates), max(dates))
miny = 0
maxy = max([volume for d, open, high, low, close, volume in quotes])
corners = (minpy, miny), (maxx, maxy)
ax.update_datalim(corners)
#print 'datalim', ax.dataLim.bounds
#print 'viewlim', ax.viewLim.bounds
ax.add_collection(barCollection)
ax.autoscale_view()
return barCollection
def set_verts(self, verts, closed=True):
'''Set 3D vertices.'''
self.get_vector(verts)
# 2D verts will be updated at draw time
PolyCollection.set_verts(self, [], closed)
def genPlot(self, ax=None, filled=False, plot_var=None, cax_kws=None,
cb_kws=None, txtloc=None, center=False, dotsize=0.008, mapext=None,
vmin=None, vmax=None, vint=None, txtSize=7, cbtxtSize=None,
linewidth=0.1):
"""
Generate plot for plot_var on SMC grid
Args:
ax (object): axis object
filled (bool): fill cells or not
plot_var (str): the parameter need to be plotted, of which valules
determine the filled color
cax_kws (dict): kws for colorbar location
cb_kwds (dict): kws for colobar
txtloc (str): loc of necessary text info. (x, y)
center (bool): draw dots in each cell
dotsize (int): the radius of Circles (for cell center dots)
mapext (list): map bbox to zoom in the cartopy map
vmin/vmax/vint (float): colorbar range/tick
"""
if not hasattr(self, 'poly'):
self._genPoly()
# -- plot setting
if plot_var.lower() == 'depth':
norm = mpl.colors.LogNorm(vmin=1, vmax=10000, clip=False)
cmap = cmocean.cm.deep
cbtl = 'Depth [m]'
cticks = [1, 10, 100, 1000, 10000]
elif plot_var.lower() == 'swh':
if vmin is None: vmin = 0.
if vmax is None: vmax = 6.
if vint is None: vint = 1.
norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax, clip=False)
cmap = plt.get_cmap('viridis')
cbtl = 'SWH [m]'
cticks = np.arange(vmin, vmax+.1*vint, vint)
elif plot_var.lower() == 'sx' or plot_var.lower() == 'sy':
filled = True
norm = mpl.colors.Normalize(vmin=0., vmax=100., clip=False)
cmap = plt.get_cmap('viridis')
cbtl = 'Obs. in {:s} dirc. [%]'.format(plot_var.lower()[1])
cticks = np.arange(0, 101, 20)
elif plot_var.lower() == 'wspd':
vmax = vmax if vmax else 40
vmin = vmin if vmin else 0.
vint = vint if vint else 10.
cmap = plt.get_cmap('plasma')
norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax, clip=False)
cbtl = 'Wind [m/s]'
cticks = np.arange(vmin, vmax+.1*vint, vint)
else:
pass
facecolor = None if filled else 'none'
# -- cells
if self.proj is not None:
polyc = PolyCollection(self.poly, cmap=cmap, norm=norm,
linewidth=linewidth, facecolor=facecolor)
else:
polyc = PolyCollection(self.poly, cmap=cmap, norm=norm,
linewidth=linewidth, facecolor=facecolor,
transform=ccrs.PlateCarree())
polyc.set_edgecolor('face')
polyc.set_array(ma.masked_equal(getattr(self, plot_var), -999999))
ax.add_collection(polyc)
# -- center dot of each cell
# -- use 'o' or 's' to replace '.'
if center: # use very small size for scatter/marker
ax.scatter(self.clon, self.clat, s=dotsize, c=getattr(self,
plot_var), marker='o', norm=norm, cmap=cmap,
transform=ccrs.PlateCarree())
# circlec = PatchCollection([Circle((x, y), radius=radius)
# for x, y in np.c_[self.clon, self.clat]],
# edgecolor='none', cmap=cmap, norm=norm,
# transform=ccrs.PlateCarree())
# circlec.set_array(getattr(self, plot_var))
# ax.add_collection(circlec)
# -- lim axis
ax.autoscale_view() # !!! Very important
if mapext is not None:
ax.set_extent(mapext, crs=ccrs.PlateCarree())
# -- colorbar
if cax_kws is None: cax_kws = dict()
btr = None if cax_kws.get('bbox_to_anchor') is None else ax.transAxes
cax = inset_axes(ax,
width=cax_kws.get('width', '40%'),
height=cax_kws.get('height', '3%'),
loc=cax_kws.get('loc', 2), # upper right
bbox_to_anchor=cax_kws.get('bbox_to_anchor', None),
bbox_transform=btr,
borderpad=cax_kws.get('borderpad', None)) # units: fontsize
#borderpad=cax_kws.get('borderpad', 2.)) # units: fontsize
# This is causing a crash for some reason...
if cb_kws is None: cb_kws=dict()
cb = plt.colorbar(polyc, cax=cax, format='%d',
orientation=cb_kws.get('orientation', 'horizontal'))
cb.set_label(cbtl, size=txtSize)
cb.set_ticks(cticks)
if cbtxtSize is None: cbtxtSize = txtSize - 1
cb.ax.tick_params(labelsize=cbtxtSize)
# -- cell info.
if plot_var in ['depth', 'sx', 'sy']:
info = ('{:s}\n'
r'$\longmapsto$'
'\n NL = {:d}\n N1 = {:d}\n N2 = {:d}\n N4 = {:d}').format(
self.gid, self.NL, self.N1, self.N2, self.N4)
if plot_var in ['swh', 'wspd']:
try:
timeStr = self.time.strftime('%Y-%m-%d %HZ')
except:
timeStr = str(self.time)
info = '{:s}\n Max: {:.1f}\n Min: {:.1f}'.format(
timeStr, getattr(self, plot_var).max(), getattr(self, plot_var).min())
if txtloc is None: txtloc = (0.1, 0.85)
ax.text(txtloc[0], txtloc[1], info, ha='left',
va='top', multialignment='left', transform=ax.transAxes,
fontsize=txtSize, color='k')
def __init__(self, map, mask, nest=False, **kwargs):
nside = healpix.npix2nside(len(mask))
self.v = pix2quad(nside, mask.nonzero()[0], nest)
PolyCollection.__init__(self, self.v, array=map[mask], **kwargs)
def colrboxy(cboxy, colrmap, marks, ncstr=0, nclrm=256):
"""
Generate a colour bar polycollection with given key box
cboxy=[x, y, dx, dy] and colormap, plus marks.
The colour index arrays will generated out of given colormap.
JGLi01Mar2019
"""
## Input variables include x, y as Numpy Arrays or lists for the
## colorbar locations, the colormap to be plotted, integer list
## or Numpy Array marks for key scale ticks as enlarged polygon.
## Tick labels should be added outside this program when the
## colorbar PolyCollection is drawn in a corresponding plot.
## Workout color bar orientaion by x and y sizes
## and generate poly verts and colors.
x0 = cboxy[0]
y0 = cboxy[1]
bx = cboxy[2]
by = cboxy[3]
verts = []
pcolr = []
ic = ncstr
if (bx > by): ## Horizontal color bar
dx = bx / nclrm
xkeys = np.arange(nclrm) * dx + x0
ykeys = np.array([y0, y0 + by])
syc = [y0, y0, y0 + by, y0 + by]
for xi in xkeys:
sxc = [xi, xi + dx, xi + dx, xi]
verts.append(list(zip(sxc, syc)))
pcolr.append(colrmap(ic))
ic += 1
dm = 1.1 * by
sym = [y0, y0, y0 + dm, y0 + dm]
for i in marks:
xi = xkeys[i]
sxc = [xi, xi + dx, xi + dx, xi]
verts.append(list(zip(sxc, sym)))
pcolr.append(colrmap(i))
else: ## Vertical color bar
dy = by / nclrm
xkeys = np.array([x0, x0 + bx])
ykeys = np.arange(nclrm) * dy + y0
sxc = [x0, x0 + bx, x0 + bx, x0]
for yj in ykeys:
syc = [yj, yj, yj + dy, yj + dy]
verts.append(list(zip(sxc, syc)))
pcolr.append(colrmap(ic))
ic += 1
dm = 1.1 * bx
sxm = [x0, x0 + dm, x0 + dm, x0]
for j in marks:
yj = ykeys[j]
syc = [yj, yj, yj + dy, yj + dy]
verts.append(list(zip(sxm, syc)))
pcolr.append(colrmap(j))
## Generate PolyCollection
cbarpoly = PolyCollection(verts)
cbarpoly.set_color(pcolr)
return (xkeys, ykeys, cbarpoly)
class Matplotlib2DViewer(AbstractMatplotlib2DViewer):
"""
Displays a contour plot of a 2D `CellVariable` object.
The `Matplotlib2DViewer` plots a 2D `CellVariable` using Matplotlib_.
.. _Matplotlib: http://matplotlib.sourceforge.net/
"""
__doc__ += AbstractMatplotlib2DViewer._test2Dirregular(
viewer="Matplotlib2DViewer")
def __init__(self,
vars,
title=None,
limits={},
cmap=None,
colorbar='vertical',
axes=None,
figaspect='auto',
**kwlimits):
"""Creates a `Matplotlib2DViewer`.
:Parameters:
vars
a `CellVariable` object.
title
displayed at the top of the `Viewer` window
limits : dict
a (deprecated) alternative to limit keyword arguments
cmap
the colormap. Defaults to `matplotlib.cm.jet`
xmin, xmax, ymin, ymax, datamin, datamax
displayed range of data. Any limit set to
a (default) value of `None` will autoscale.
colorbar
plot a colorbar in specified orientation if not `None`
axes
if not `None`, `vars` will be plotted into this Matplotlib `Axes` object
figaspect
desired aspect ratio of figure. If arg is a number, use that aspect
ratio. If arg is 'auto', the aspect ratio will be determined from
the Variable's mesh.
"""
kwlimits.update(limits)
AbstractMatplotlib2DViewer.__init__(self,
vars=vars,
title=title,
figaspect=figaspect,
cmap=cmap,
colorbar=colorbar,
axes=axes,
**kwlimits)
self.mesh = self.vars[0].mesh
vertexIDs = self.mesh._orderedCellVertexIDs
vertexCoords = self.mesh.vertexCoords
xCoords = numerix.take(vertexCoords[0], vertexIDs)
yCoords = numerix.take(vertexCoords[1], vertexIDs)
polys = []
for x, y in zip(xCoords.swapaxes(0, 1), yCoords.swapaxes(0, 1)):
if hasattr(x, 'mask'):
x = x.compressed()
if hasattr(y, 'mask'):
y = y.compressed()
polys.append(zip(x, y))
from matplotlib.collections import PolyCollection
self.collection = PolyCollection(polys)
self.collection.set_linewidth(0.5)
try:
self.axes.add_patch(self.collection)
except:
# PolyCollection not child of PatchCollection in matplotlib 0.98
self.axes.add_collection(self.collection)
xmin = self._getLimit('xmin', default=xCoords.min())
xmax = self._getLimit('xmax', default=xCoords.max())
ymin = self._getLimit('ymin', default=yCoords.min())
ymax = self._getLimit('ymax', default=yCoords.max())
self.axes.set_xlim(xmin=xmin, xmax=xmax)
self.axes.set_ylim(ymin=ymin, ymax=ymax)
self._plot()
def _getSuitableVars(self, vars):
from fipy.meshes.mesh2D import Mesh2D
from fipy.variables.cellVariable import CellVariable
vars = [var for var in AbstractMatplotlib2DViewer._getSuitableVars(self, vars) \
if ((var.mesh.dim == 2 and isinstance(var, CellVariable))
and var.rank == 0)]
if len(vars) == 0:
from fipy.viewers import MeshDimensionError
raise MeshDimensionError, "Matplotlib2DViewer can only display a rank-0, 2D CellVariable"
# this viewer can only display one variable
return [vars[0]]
def _plot(self):
## pylab.clf()
## ## Added garbage collection since matplotlib objects seem to hang
## ## around and accumulate.
## import gc
## gc.collect()
Z = self.vars[0].value
self.norm.vmin = self._getLimit(('datamin', 'zmin'))
self.norm.vmax = self._getLimit(('datamax', 'zmax'))
rgba = self.cmap(self.norm(Z))
self.collection.set_facecolors(rgba)
self.collection.set_edgecolors(rgba)
if self.colorbar is not None:
self.colorbar.plot() #vmin=zmin, vmax=zmax)
def swhlocal(swhs,
verts,
ncels,
colrs,
config,
mdlname='SMC',
datx='2018',
psfile='output.ps',
paprorn='portrait',
paprtyp='a3'):
"""
## Draw local swh plot with given polycollections and cell
## array. Output as A3 ps file. JGLi28Feb2019
"""
# Degree to radian conversion parameter.
d2rad = np.pi / 180.0
# Local plot configuration parameters
rdpols = config[0]
sztpxy = config[1]
rngsxy = config[2]
clrbxy = config[3]
# Maximum mapping radius.
radius = rdpols[0]
# Set up wave height scale and marks with colrs.N.
# colrs.N returns colrs' total number of colors 256.
waveht, factor, residu, marks, ncstr, nclrm = scale_swh(nclrm=colrs.N)
resmn1 = residu - 1.0
nswh0 = ncstr + int(factor * np.log(-resmn1 + residu))
#print ' nswh0 and marks = ', nswh0, marks
#print ' factor, residu, resmn1 = %f, %f, %f' % (factor, residu, resmn1)
# Some constant variables for plots.
xprop = {'xlim': rngsxy[0:2], 'xlabel': ''}
yprop = {'ylim': rngsxy[2:4], 'ylabel': ''}
# Use ijk to count how many times to draw.
ijk = 0
if True:
# Work out max and min values, excluding missing data (-999.0)
cmax = swhs.max()
cmin = swhs[swhs > -999.0].min()
print(' swh range %f, %f' % (cmin, cmax))
cmxs = 'SWHmx = %6.2f m' % cmax
cmns = 'SWHmn = %10.3E' % cmin
# Reset missing values (-999.0) to be -resmn1
swhs[swhs < -resmn1] = -resmn1
# Trim large values into plot range if any
swhs[swhs > 32.0] = 32.0
# Convert swhs with logarithm scale.
icnf = ncstr + np.rint(factor * np.log(swhs + residu))
nswh = np.array(icnf, dtype=np.int16)
print(" Drawing " + psfile)
# Set up first subplot and axis for northern hemisphere
fig = plt.figure(figsize=sztpxy[0:2])
ax = fig.add_subplot(1, 1, 1)
ax.set(**xprop)
ax.set(**yprop)
ax.set_aspect('equal')
ax.set_autoscale_on(False)
ax.set_axis_off()
plt.subplots_adjust(left=0.0, bottom=0.0, right=1.0, top=1.0)
# Prepare PolyCollection for this plot.
polynorth = PolyCollection(verts)
# Create color array for this plot
pcface = []
pcedge = []
for i in ncels:
if (nswh[i] != nswh0):
pcface.append(colrs(nswh[i]))
pcedge.append(colrs(nswh[i]))
else:
pcface.append(colrs(255))
pcedge.append(colrs(0))
#smcpoly.set_color(pcolr) # This line defines both edge and face color.
polynorth.set_facecolor(pcface)
polynorth.set_edgecolor(pcedge)
polynorth.set_linewidth(0.2)
#print (" Drawing north hemisphere cells ... ")
ax.add_collection(polynorth)
# Draw colorbar inside plot.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks)
ax.add_collection(clrply)
dkx = clrbxy[2]
dky = clrbxy[3]
for i in range(len(waveht)):
m = marks[i]
if (dkx < dky):
plt.text(xkeys[0] + 1.15 * dkx,
ykeys[m],
str(waveht[i]),
verticalalignment='center',
fontsize=11,
color='b')
else:
plt.text(xkeys[m],
ykeys[0] + 1.15 * dky,
str(waveht[i]),
horizontalalignment='center',
fontsize=11,
color='b')
if (dkx < dky):
plt.text(xkeys[0] + 2.0 * dkx,
ykeys[marks[3]],
'SWH m',
rotation=90,
verticalalignment='center',
fontsize=15,
color='k')
else:
plt.text(xkeys[marks[3]],
ykeys[0] + 2.0 * dky,
'SWH m',
rotation=0,
horizontalalignment='center',
fontsize=15,
color='k')
# Put cell information inside plot
tpx = sztpxy[2]
tpy = sztpxy[3]
plt.text(tpx,
tpy - 1.0,
mdlname,
horizontalalignment='center',
fontsize=17,
color='g')
plt.text(tpx,
tpy - 1.6,
datx,
horizontalalignment='center',
fontsize=15,
color='k')
plt.text(tpx,
tpy - 2.1,
cmxs,
horizontalalignment='center',
fontsize=13,
color='r')
plt.text(tpx,
tpy - 2.6,
cmns,
horizontalalignment='center',
fontsize=13,
color='b')
# Refresh subplots and save them.
plt.savefig(psfile,
dpi=None,
facecolor='w',
edgecolor='w',
orientation=paprorn,
papertype=paprtyp)
plt.close()
# print 'in update'
depth = slider1.val
mDot[0].set_data([.5, -.2])
mDot[0].set_3d_properties(depth, zdir='y')
# plt.show()
plt.pause(.001)
slider1.on_changed(update1)
# Back plane
verts3D = np.array([[-1, -1, 1], [1, -1, 1], [1, 1, 1], [-1, 1, 1],
[-1, -1, 1]])
vertsXY = [verts3D[:, :2]]
vertsZ = verts3D[:, 2]
poly1 = PolyCollection(vertsXY)
poly1.set_alpha(0.7)
poly1.set_color('w')
poly1.set_edgecolor('k')
ax.add_collection3d(poly1, zs=vertsZ, zdir='y')
# Front plane
verts3D = np.array([[-1, -1, -1], [1, -1, -1], [1, 1, -1], [-1, 1, -1],
[-1, -1, -1]])
vertsXY = [verts3D[:, :2]]
vertsZ = verts3D[:, 2]
poly2 = PolyCollection(vertsXY)
poly2.set_alpha(0.7)
poly2.set_color('w')
poly2.set_edgecolor('k')
ax.add_collection3d(poly2, zs=vertsZ, zdir='y')
def set_edgecolor(self, colors):
PolyCollection.set_edgecolor(self, colors)
self._edgecolor3d = PolyCollection.get_edgecolor(self)
def gen_land_bitmap(bmap, resolution_meters):
#Get land polygons and bbox of polygons
polys = []
xmin = np.finfo(np.float64).max
xmax = -np.finfo(np.float64).max
ymin = xmin
ymax = xmax
logging.debug('Rasterizing Basemap, number of land polys: ' +
str(len(bmap.landpolygons)))
# If no polys: return a zero map
if (len(bmap.landpolygons) == 0):
raise Exception('Basemap contains no land polys to rasterize')
for polygon in bmap.landpolygons:
coords = polygon.get_coords()
xmin = min(xmin, np.min(coords[:, 0]))
xmax = max(xmax, np.max(coords[:, 0]))
ymin = min(ymin, np.min(coords[:, 1]))
ymax = max(ymax, np.max(coords[:, 1]))
polys.append(coords)
xmin = np.floor(xmin / resolution_meters) * resolution_meters
xmax = np.ceil(xmax / resolution_meters) * resolution_meters
ymin = np.floor(ymin / resolution_meters) * resolution_meters
ymax = np.ceil(ymax / resolution_meters) * resolution_meters
# For debugging
logging.debug('Rasterizing Basemap, bounding box: ' +
str([xmin, xmax, ymin, ymax]))
# Switch backend to prevent creating an empty figure in notebook
orig_backend = plt.get_backend()
plt.switch_backend('agg')
# Create figure to help rasterize
fig = plt.figure(frameon=False)
ax = plt.Axes(fig, [0., 0., 1., 1.])
ax.set_axis_off()
fig.add_axes(ax)
ax.set_xlim(xmin, xmax)
ax.set_ylim(ymin, ymax)
# Set aspect and resolution
# Aspect gives 1 in high plot
aspect = (xmax - xmin) / (ymax - ymin)
resolution_dpi = (ymax - ymin) / resolution_meters
fig.set_dpi(resolution_dpi)
fig.set_size_inches(aspect, 1)
# Add polygons
lc = PolyCollection(polys, facecolor='k', lw=0)
ax.add_collection(lc)
# Create canvas and rasterize
canvas = FigureCanvasAgg(fig)
try:
canvas.draw()
width, height = canvas.get_width_height()
rgb_data = np.fromstring(canvas.tostring_rgb(),
dtype='uint8').reshape(height, width, 3)
data = rgb_data[:, :, 1]
plt.close(
fig
) #comment this for debugging purposes and replace with plt.show()
logging.debug('Rasterized size: ' + str([width, height]))
except MemoryError:
gc.collect()
raise Exception('Basemap rasterized size too large: ' +
str(aspect * resolution_dpi) + '*' +
str(resolution_dpi) + ' cells')
finally:
# Reset backend
plt.switch_backend(orig_backend)
return RasterizedBasemap(xmin, xmax, ymin, ymax, resolution_meters,
data)
def plot_driver_states(self, driver_id, trip_count=50, start_time=0, fig_size=(30, 2), legend_size=6,
xtick_size=10):
driver_data = self.driver_actions.xs(driver_id, level=1).copy()
driver_data.sort_values(by='assigned_time', inplace=True)
trip_times = []
for i in driver_data[['assigned_time', 'driver_action', 'pickup_time', 'travel_time']].values:
if i[1] == 1:
assign_time = i[0]
pickup_time = assign_time + i[2]
drop_time = pickup_time + i[3]
points = [assign_time, pickup_time, drop_time]
trip_times.append(points)
states = {'idle': 1, 'pick_up': 1, 'in_trip': 1}
color_mapping = {"idle": "C0", "pick_up": "C1", "in_trip": "C2"}
state_mapping = {0: "pick_up", 1: 'in_trip'}
vertices = []
colors = []
end_time = start_time
for t in trip_times[:trip_count]:
if t[2] < end_time:
continue
v = [
(end_time, states['idle'] - 0.4),
(end_time, states['idle'] + 0.4),
(t[0], states['idle'] + 0.4),
(t[0], states['idle'] - 0.4),
(end_time, states['idle'] - 0.4),
]
vertices.append(v)
colors.append(color_mapping['idle'])
for k in range(2):
state = states[state_mapping[k]]
v = [
(t[k], state - 0.4),
(t[k], state + 0.4),
(t[k + 1], state + 0.4),
(t[k + 1], state - 0.4),
(t[k], state - 0.4),
]
vertices.append(v)
colors.append(color_mapping[state_mapping[k]])
end_time = t[2]
bars = PolyCollection(vertices, facecolors=colors)
fig, ax = plt.subplots(figsize=fig_size)
ax.add_collection(bars)
ax.get_yaxis().set_visible(False)
ax.autoscale()
ax.tick_params(axis='x', which='major', labelsize=xtick_size)
ax.tick_params(axis='x', which='minor', labelsize=xtick_size)
idle = mpatches.Patch(color='C0', label='Idle time')
pick_up = mpatches.Patch(color='C1', label='Pick up time')
in_trip = mpatches.Patch(color='C2', label='Trip time')
plt.legend(handles=[idle, pick_up, in_trip], bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0.,
prop={'size': legend_size})
plt.show()
ax.set_xlabel('Month')
ax.set_xticks(np.arange(1, 13))
ax.set_ylabel('Year')
ax.set_yticks(np.arange(2016, 2020))
ax.set_zlabel('Precipitation')
# 绘制3D多边形
ax = fig.add_subplot(1, 2, 2, projection='3d')
precipitation = []
for year in years:
value = np.random.rand(len(month)) * 300
value[0], value[-1] = 0, 0
precipitation.append(list(zip(month, value)))
poly = PolyCollection(precipitation, facecolors=['b', 'c', 'r', 'm'])
poly.set_alpha(0.7)
ax.add_collection3d(poly, zs=years, zdir='y')
ax.set_xlabel('Month')
ax.set_xlim3d(0, 12)
ax.set_ylabel('Year')
ax.set_ylim3d(2015, 2020)
ax.set_zlabel('Precipitation')
ax.set_zlim3d(0, 300)
plt.show()
# ### Axes3D
# API：https://matplotlib.org/api/_as_gen/mpl_toolkits.mplot3d.axes3d.Axes3D.html
# 本文涉及的绘制3D图形函数都位于此接口；
def set_facecolor(self, colors):
PolyCollection.set_facecolor(self, colors)
self._facecolors3d = PolyCollection.get_facecolor(self)
def set_verts(self, verts, closed=True):
"""Set 3D vertices."""
self.get_vector(verts)
# 2D verts will be updated at draw time
PolyCollection.set_verts(self, [], False)
self._closed = closed
def smcglobl(cel,
nvrts,
ncels,
svrts,
scels,
colrs,
config,
Arctic=None,
mdlname='SMC',
buoys=None,
psfile='output.ps',
paprtyp='a3'):
"""
## The smcglobl function plots a global view of a given smc grid.
## cel is the full cell array in shape(nc, 5).
## JGLi04Mar2019
"""
## Degree to radian conversion parameter.
d2rad = np.pi / 180.0
## Global plot configuration parameters.
rdpols = config[0]
sztpxy = config[1]
rngsxy = config[2]
clrbxy = config[3]
if (Arctic is not None): ncabgm = config[4]
## Maximum mapping radius.
radius = rdpols[0]
pangle = rdpols[1]
plon = rdpols[2]
plat = rdpols[3]
## Outline circle at equator
ciran = np.arange(1081) * d2rad / 3.0
xcirc = radius * np.cos(ciran)
ycirc = radius * np.sin(ciran)
## Define depth to color index conversion parameters and marks.
## Use only first 131 colors in colrs(0:255).
depth, factr, cstar, marks, ncstr, nclrm = scale_depth(nclrm=131)
## Cell color is decided by its depth value, dry cells use default 0 color.
nc = cel.shape[0]
ndeps = np.zeros((nc), dtype=np.int)
for j in range(nc):
if (cel[j, 4] > 0):
ndeps[j] = ncstr + np.rint(
(cstar - np.log10(cel[j, 4])) * factr).astype(np.int)
#ndeps = ncstr + np.rint( (cstar-np.log10(cel[:,4]))*factr ).astype(np.int)
if (Arctic is not None):
na = int(ncabgm[1])
nb = int(ncabgm[2])
jm = int(ncabgm[3])
## Set up first subplot and axis for northern hemisphere
print(" Drawing north hemisphere cells ... ")
fig = plt.figure(figsize=sztpxy[0:2])
ax1 = fig.add_subplot(1, 2, 1)
ax1.set_aspect('equal')
ax1.set_autoscale_on(False)
ax1.set_axis_off()
plt.subplots_adjust(left=0.02, bottom=0.02, right=0.98, top=0.95)
plt.subplots_adjust(wspace=0.02, hspace=0.01)
xprop = {'xlim': rngsxy[0:2], 'xlabel': 'Nothing'}
yprop = {'ylim': rngsxy[2:4], 'ylabel': 'Nothing'}
ax1.set(**xprop)
ax1.set(**yprop)
ax1.plot(xcirc, ycirc, 'b-')
## Select cells for one subplot and create verts and pcolr.
pcface = []
pcedge = []
for i in ncels:
if (Arctic is not None) and (cel[i, 1] == Arctic):
# Mark the arctic map-east reference region by first ring of its boundary cells
pcface.append(colrs(246))
pcedge.append(colrs(246))
#elif( Arctic is not None ) and ( cel[i,1] == jm ):
# # Mark the arctic cells
# pcface.append(colrs(168))
# pcedge.append(colrs(168))
else:
pcface.append(colrs(255))
pcedge.append(colrs(ndeps[i]))
## Draw this hemisphere cells
smcpoly = PolyCollection(nvrts)
smcpoly.set_facecolor(pcface)
smcpoly.set_edgecolor(pcedge)
smcpoly.set_linewidth(0.2)
ax1.add_collection(smcpoly)
## Draw colorbar for ax1.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks, nclrm=nclrm)
ax1.add_collection(clrply)
for i in range(len(depth)):
m = marks[i]
plt.text(xkeys[m],
ykeys[0] + 1.15 * (ykeys[1] - ykeys[0]),
str(depth[i]),
horizontalalignment='center',
fontsize=11,
color='b')
#rotation=-90,verticalalignment='center', fontsize=11, color='b' )
plt.text(xkeys[marks[0]],
ykeys[0] + 2.2 * (ykeys[1] - ykeys[0]),
'Depth m',
horizontalalignment='left',
fontsize=15,
color='k')
#rotation=-90,verticalalignment='center', fontsize=15, color='k' )
# Overlay buoy sites on grid map if buoy file is provided.
if (buoys is not None):
hdr, buoyll = readtext(buoys)
nmbu = long(hdr[0])
buoyids = buoyll[:, 0].astype(str)
buoylat = buoyll[:, 1].astype(np.float)
buoylon = buoyll[:, 2].astype(np.float)
#; Convert slat slon to elat elon with given new pole
elat, elon, sxc, syc = steromap(buoylat,
buoylon,
plat,
plon,
Pangl=pangle)
#; Mark buoy position on map
print(' Selected buoys on north hemisphere ...')
for i in range(nmbu):
if ((elat[i] >= 0.0) and (rngsxy[0] < sxc[i] < rngsxy[1])
and (rngsxy[2] < syc[i] < rngsxy[3])):
print(' {:6} {:8.3f} {:8.3f}'.format(buoyids[i], buoylat[i],
buoylon[i]))
txtsz = int(abs(np.sin(elat[i] * d2rad) * 12.0))
plt.text(sxc[i],
syc[i],
'r',
fontsize=txtsz,
horizontalalignment='center',
color='r')
plt.text(sxc[i],
syc[i],
'.',
fontsize=txtsz * 2,
horizontalalignment='center',
color='r')
## Southern hemisphere
print(" Drawing south hemisphere cells ... ")
ax2 = fig.add_subplot(1, 2, 2)
ax2.set_aspect('equal')
ax2.axis('off')
plt.subplots_adjust(left=0.02, bottom=0.02, right=0.98, top=0.95)
plt.subplots_adjust(wspace=0.02, hspace=0.01)
ax2.set(**xprop)
ax2.set(**yprop)
ax2.plot(xcirc, ycirc, 'b-')
## Select cells for one subplot and create verts and pcolr.
pcface = []
pcedge = []
for i in scels:
pcface.append(colrs(255))
pcedge.append(colrs(ndeps[i]))
## Generate polygon collections for southern hemisphere
smcpoly = PolyCollection(svrts)
smcpoly.set_facecolor(pcface)
smcpoly.set_edgecolor(pcedge)
smcpoly.set_linewidth(0.2)
ax2.add_collection(smcpoly)
## Put cell information inside plot
tpx = sztpxy[2]
tpy = sztpxy[3]
dpy = 0.6
plt.text(tpx,
tpy + dpy * 0.5,
mdlname + ' Grid',
horizontalalignment='center',
fontsize=15,
color='k')
plt.text(tpx,
tpy + dpy * 2.0,
'NC=' + str(nc),
horizontalalignment='center',
fontsize=13,
color='r')
if (Arctic is not None):
plt.text(tpx,
tpy + dpy * 3.0,
'NA=' + str(na),
horizontalalignment='center',
fontsize=13,
color='r')
plt.text(tpx,
tpy + dpy * 4.0,
'NB=' + str(nb),
horizontalalignment='center',
fontsize=13,
color='r')
## Draw colorbar for ax2.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks, nclrm=nclrm)
ax2.add_collection(clrply)
for i in range(len(depth)):
m = marks[i]
plt.text(xkeys[m],
ykeys[0] + 1.18 * (ykeys[1] - ykeys[0]),
str(depth[i]),
horizontalalignment='center',
fontsize=11,
color='b')
#verticalalignment='center', fontsize=11, color='b' )
#rotation=-90,verticalalignment='center', fontsize=11, color='b' )
plt.text(xkeys[marks[-1]],
ykeys[0] + 2.2 * (ykeys[1] - ykeys[0]),
'Depth m',
horizontalalignment='right',
fontsize=15,
color='k')
#rotation=-90,verticalalignment='center', fontsize=15, color='k' )
# Overlay buoy sites on grid map if buoy file is provided.
if (buoys is not None):
#; Mark buoy position on map
print(' Selected buoys on south hemisphere ...')
for i in range(nmbu):
if ((elat[i] < 0.0) and (rngsxy[0] < -sxc[i] < rngsxy[1])
and (rngsxy[2] < syc[i] < rngsxy[3])):
print(' {:6} {:8.3f} {:8.3f}'.format(buoyids[i], buoylat[i],
buoylon[i]))
txtsz = int(abs(np.sin(elat[i] * d2rad) * 12.0))
plt.text(-sxc[i],
syc[i],
'r',
fontsize=txtsz,
horizontalalignment='center',
color='r')
plt.text(-sxc[i],
syc[i],
'.',
fontsize=txtsz * 2,
horizontalalignment='center',
color='r')
## Refresh subplots and save them.
plt.subplots_adjust(wspace=0.02, hspace=0.01)
plt.savefig(psfile, dpi=None,facecolor='w',edgecolor='w', \
orientation='landscape',papertype=paprtyp,format='ps')
def candlestick2_ohlc(ax, opens, highs, lows, closes, width=4,
colorup='k', colordown='r',
alpha=0.75,
):
"""Represent the open, close as a bar line and high low range as a
vertical line.
NOTE: this code assumes if any value open, low, high, close is
missing they all are missing
Parameters
----------
ax : `Axes`
an Axes instance to plot to
opens : sequence
sequence of opening values
highs : sequence
sequence of high values
lows : sequence
sequence of low values
closes : sequence
sequence of closing values
ticksize : int
size of open and close ticks in points
colorup : color
the color of the lines where close >= open
colordown : color
the color of the lines where close < open
alpha : float
bar transparency
Returns
-------
ret : tuple
(lineCollection, barCollection)
"""
_check_input(opens, highs, lows, closes)
delta = width / 2.
barVerts = [((i - delta, open),
(i - delta, close),
(i + delta, close),
(i + delta, open))
for i, open, close in zip(xrange(len(opens)), opens, closes)
if open != -1 and close != -1]
rangeSegments = [((i, low), (i, high))
for i, low, high in zip(xrange(len(lows)), lows, highs)
if low != -1]
r, g, b = colorConverter.to_rgb(colorup)
colorup = r, g, b, alpha
r, g, b = colorConverter.to_rgb(colordown)
colordown = r, g, b, alpha
colord = {True: colorup,
False: colordown,
}
colors = [colord[open < close]
for open, close in zip(opens, closes)
if open != -1 and close != -1]
useAA = 0, # use tuple here
lw = 0.5, # and here
rangeCollection = LineCollection(rangeSegments,
colors=((0, 0, 0, 1), ),
linewidths=lw,
antialiaseds=useAA,
)
barCollection = PolyCollection(barVerts,
facecolors=colors,
edgecolors=((0, 0, 0, 1), ),
antialiaseds=useAA,
linewidths=lw,
)
minx, maxx = 0, len(rangeSegments)
miny = min([low for low in lows if low != -1])
maxy = max([high for high in highs if high != -1])
corners = (minx, miny), (maxx, maxy)
ax.update_datalim(corners)
ax.autoscale_view()
# add these last
ax.add_collection(rangeCollection)
ax.add_collection(barCollection)
return rangeCollection, barCollection
def smclocal(cel,
verts,
ncels,
colrs,
config,
Arctic=None,
mdlname='SMC',
buoys=None,
psfile='output.ps',
paprorn='portrait',
paprtyp='a3'):
"""
## The smclocal function plots a local region of a given smc grid.
## cel is the full cell array in shape(nc, 5).
## JGLi04Mar2019
"""
# Degree to radian conversion parameter.
d2rad = np.pi / 180.0
# Local plot configuration parameters
rdpols = config[0]
sztpxy = config[1]
rngsxy = config[2]
clrbxy = config[3]
if (Arctic): ncabgm = config[4]
# Maximum mapping radius.
radius = rdpols[0]
pangle = rdpols[1]
plon = rdpols[2]
plat = rdpols[3]
# Define depth to color index conversion parameters and marks.
# Use only first 131 colors in colrs(0:255).
depth, factr, cstar, marks, ncstr, nclrm = scale_depth(nclrm=136)
# Cell color is decided by its depth value.
nc = cel.shape[0]
ndeps = np.zeros((nc), dtype=np.int)
for j in range(nc):
if (cel[j, 4] > -11):
ndeps[j] = ncstr + np.rint(
(cstar - np.log10(cel[j, 4] + 11)) * factr).astype(np.int)
#ndeps = ncstr + np.rint( (cstar-np.log10(cel[:,4]))*factr ).astype(np.int)
if (Arctic is not None):
na = int(ncabgm[1])
nb = int(ncabgm[2])
jm = int(ncabgm[3])
# Workout output file format from its extension
#for i in np.arange(len(psfile))[::-1]:
# if( psfile[i] == '.' ):
# psfmt = psfile[i+1:]
# break
#print " Output file format will be "+psfmt
# Python plt.savefig will do this automatically.
# Use selected cells to draw the plot.
fig = plt.figure(figsize=sztpxy[0:2])
ax = fig.add_subplot(1, 1, 1)
yprop = {'ylim': rngsxy[2:4], 'ylabel': ''}
xprop = {'xlim': rngsxy[0:2], 'xlabel': ''}
ax.set(**xprop)
ax.set(**yprop)
ax.set_aspect('equal')
ax.set_autoscale_on(False)
ax.set_axis_off()
plt.subplots_adjust(left=0.0, bottom=0.0, right=1.0, top=1.0)
# Create color array for this plot
pcface = []
pcedge = []
for i in ncels:
if (Arctic is not None) and (cel[i, 1] == Arctic):
# Mark the arctic map-east reference region by first ring of its boundary cells
pcface.append(colrs(246))
pcedge.append(colrs(246))
#elif( Arctic is not None ) and ( cel[i,1] == jm ):
# # Mark the arctic cells
# pcface.append(colrs(168))
# pcedge.append(colrs(168))
else:
pcedge.append(colrs(ndeps[i] + 10))
pcface.append(colrs(ndeps[i]))
#pcface.append(colrs(255))
#pcedge.append(colrs(ndeps[i]))
# Create PolyCollection from selected verts and define edge and face color.
polynorth = PolyCollection(verts)
polynorth.set_facecolor(pcface)
polynorth.set_edgecolor(pcedge)
polynorth.set_linewidth(0.2)
# Draw the selected cells as colored polygons.
ax.add_collection(polynorth)
# Draw colorbar inside plot.
xkeys, ykeys, clrply = colrboxy(clrbxy, colrs, marks, nclrm=nclrm)
ax.add_collection(clrply)
dkx = clrbxy[2]
dky = clrbxy[3]
for i in range(len(depth)):
m = marks[i]
if (dkx < dky):
plt.text(xkeys[0] + 1.15 * dkx,
ykeys[m],
str(depth[i]),
verticalalignment='center',
fontsize=11,
color='b')
else:
plt.text(xkeys[m],
ykeys[0] + 1.15 * dky,
str(depth[i]),
horizontalalignment='center',
fontsize=11,
color='b')
if (dkx < dky):
plt.text(xkeys[0] + 1.9 * dkx,
ykeys[marks[2]],
'Depth m',
rotation=-90,
verticalalignment='center',
fontsize=15,
color='k')
else:
plt.text(xkeys[marks[2]],
ykeys[0] + 1.9 * dky,
'Depth m',
rotation=0,
horizontalalignment='center',
fontsize=15,
color='k')
# Put cell information inside plot
tpx = sztpxy[2]
tpy = sztpxy[3]
dpy = -0.6
plt.text(tpx,
tpy + dpy * 1,
mdlname + ' Grid',
horizontalalignment='center',
fontsize=15,
color='k')
plt.text(tpx,
tpy + dpy * 2,
'NC=' + str(nc),
horizontalalignment='center',
fontsize=13,
color='r')
if (Arctic is not None):
plt.text(tpx,
tpy + dpy * 3,
'NA=' + str(na),
horizontalalignment='center',
fontsize=13,
color='r')
plt.text(tpx,
tpy + dpy * 4,
'NB=' + str(nb),
horizontalalignment='center',
fontsize=13,
color='r')
# Overlay buoy sits on grid map if buoy file is provided.
if (buoys is not None):
hdr, buoyll = readtext(buoys)
nmbu = int(hdr[0])
buoyids = buoyll[:, 0].astype(str)
buoylat = buoyll[:, 1].astype(np.float)
buoylon = buoyll[:, 2].astype(np.float)
# Convert slat slon to elat elon with given new pole
elat, elon, sxc, syc = steromap(buoylat,
buoylon,
plat,
plon,
Pangl=pangle)
# Mark buoy position on map
print(' Selected buoys in this plot:')
for i in range(nmbu):
if ((elat[i] >= 25.0) and (rngsxy[0] < sxc[i] < rngsxy[1])
and (rngsxy[2] < syc[i] < rngsxy[3])):
print(' {:6} {:8.3f} {:8.3f}'.format(buoyids[i], buoylat[i],
buoylon[i]))
txtsz = int(abs(np.sin(elat[i] * d2rad) * 12.0))
plt.text(sxc[i],
syc[i],
'r',
fontsize=txtsz,
horizontalalignment='center',
color='r')
plt.text(sxc[i],
syc[i],
'.',
fontsize=txtsz * 2,
horizontalalignment='center',
color='r')
# Save plot as ps file
print(" Save the smc grid local plot ... ")
plt.savefig(psfile, dpi=None,facecolor='w',edgecolor='w', \
orientation=paprorn,papertype=paprtyp,format='ps')
