def test_embed():
p3.clear()
x, y, z = np.random.random((3, 100))
p3.scatter(x, y, z)
p3.save("tmp/ipyolume_scatter_online.html", offline=False)
assert os.path.getsize("tmp/ipyolume_scatter_online.html") > 0
p3.save("tmp/ipyolume_scatter_offline.html",
offline=True,
scripts_path='js/subdir')
assert os.path.getsize("tmp/ipyolume_scatter_offline.html") > 0
def plot(self,
width=800,
height=600,
voxel_count_offset=0,
voxel_limit=None,
use_centroids_instead=False,
ipyvol_fig=None,
scaling=1,
**kwargs):
"""
This method needs better documentation.
:param **kwargs: Is used in ipyvolume.pylab.scatter() or ipyvolume.pylab.plot() depending on whether use_centroids_instead
is set to true or not.
"""
if ipyvol_fig is None:
p3.figure(width=width, height=height)
else:
p3.figure(ipyvol_fig)
voxels_length = len(self)
if voxel_count_offset >= voxels_length:
raise ValueError(
"voxel_count_offset is greater than the number of voxels!")
else:
if voxel_limit is None:
n_voxels_to_plot = len(self)
else:
n_voxels_to_plot = voxel_count_offset + voxel_limit
if n_voxels_to_plot > voxels_length:
n_voxels_to_plot = len(self)
if use_centroids_instead:
if 'marker' not in kwargs:
kwargs['marker'] = 'sphere'
if 'color' not in kwargs:
kwargs['color'] = 'blue'
if 'size' not in kwargs:
kwargs['size'] = 0.5
p3.scatter(
*self.centroids[voxel_count_offset:n_voxels_to_plot].T *
scaling, **kwargs)
else:
voxel_count_offset *= 18
n_voxels_to_plot *= 18
drawable_bboxes = self.drawable_bboxes[
voxel_count_offset:n_voxels_to_plot]
p3.plot(*drawable_bboxes.T * scaling, **kwargs)
p3.squarelim()
p3.show()
def test_bokeh():
from bokeh.io import output_notebook, show
from bokeh.plotting import figure
import ipyvolume.bokeh
x, y, z = np.random.random((3, 100))
p3.figure()
scatter = p3.scatter(x, y, z)
tools = "wheel_zoom,box_zoom,box_select,lasso_select,help,reset,"
p = figure(title="E Lz space",
tools=tools,
webgl=True,
width=500,
height=500)
r = p.circle(x, y, color="navy", alpha=0.2)
ipyvolume.bokeh.link_data_source_selection_to_widget(
r.data_source, scatter, 'selected')
from bokeh.resources import CDN
from bokeh.embed import components
script, div = components(p)
ipyvolume.embed.embed_html(
"tmp/bokeh.html", [p3.gcc(), ipyvolume.bokeh.wmh],
all=True,
extra_script_head=script + CDN.render_js() + CDN.render_css(),
body_pre="<h2>Do selections in 2d (bokeh)<h2>" + div +
"<h2>And see the selection in ipyvolume<h2>")
def _scalar_handler(self, change):
import ipyvolume.pylab as p3
array_name = change['owner'].owner
pa_widgets = self._widgets.particles[array_name]
new = change['new']
old = change['old']
if old == 'None' and new == 'None':
pass
elif old != 'None' and new == 'None':
self.scatters[array_name].visible = False
elif old != 'None' and new != 'None':
colormap = getattr(mpl.cm, pa_widgets.scalar_cmap.value)
data = self.get_frame(self._widgets.frame.value)['arrays']
c = colormap(getattr(data[array_name], pa_widgets.scalar.value))
self.scatters[array_name].color = c
else:
colormap = getattr(mpl.cm, pa_widgets.scalar_cmap.value)
data = self.get_frame(self._widgets.frame.value)['arrays']
c = colormap(getattr(data[array_name], pa_widgets.scalar.value))
self.scatters[array_name] = p3.scatter(
data[array_name].x,
data[array_name].y,
data[array_name].z,
color=c,
size=pa_widgets.scalar_size.value,
)
self._legend_handler(None)
def show_spatial_series(node: SpatialSeries, **kwargs):
data, unit = get_timeseries_in_units(node)
tt = get_timeseries_tt(node)
if len(data.shape) == 1:
fig, ax = plt.subplots()
ax.plot(tt, data, **kwargs)
ax.set_xlabel('t (sec)')
if unit:
ax.set_xlabel('x ({})'.format(unit))
else:
ax.set_xlabel('x')
ax.set_ylabel('x')
elif data.shape[1] == 2:
fig, ax = plt.subplots()
ax.plot(data[:, 0], data[:, 1], **kwargs)
if unit:
ax.set_xlabel('x ({})'.format(unit))
ax.set_ylabel('y ({})'.format(unit))
else:
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.axis('equal')
elif data.shape[1] == 3:
import ipyvolume.pylab as p3
fig = p3.figure()
p3.scatter(data[:, 0], data[:, 1], data[:, 2], **kwargs)
p3.xlim(np.min(data[:, 0]), np.max(data[:, 0]))
p3.ylim(np.min(data[:, 1]), np.max(data[:, 1]))
p3.zlim(np.min(data[:, 2]), np.max(data[:, 2]))
else:
raise NotImplementedError
return fig
def init_vector(show=True):
#This function initializes a figure with basis vectors in world frame - requires import ipyvolume.pylab as p3 outside scope
#p3.clear()
origin = np.array([0.0, 0.0, 0.0])
x = origin + np.array([1.0, 0.0, 0.0])
y = origin + np.array([0.0, 1.0, 0.0])
z = origin + np.array([0.0, 0.0, 1.0])
u = np.array([1.0, 0.0, 0.0])
v = np.array([0.0, 1.0, 0.0])
w = np.array([0.0, 0.0, 1.0])
quiver = p3.quiver(x,
y,
z,
u,
v,
w,
size=10,
marker='arrow',
color=np.array([[1, 0, 0], [0, 1, 0],
[0, 0, 1]])) #ipv.show()
scatter = p3.scatter(np.array([origin[0]]),
np.array([origin[0]]),
np.array([origin[0]]),
size=5,
marker='sphere',
color='red')
line1 = p3.plot(np.array([origin[0], x[0]]),
np.array([origin[0], x[1]]),
np.array([origin[0], x[2]]),
color='red')
line2 = p3.plot(np.array([origin[0], y[0]]),
np.array([origin[0], y[1]]),
np.array([origin[0], y[2]]),
color='green')
line3 = p3.plot(np.array([origin[0], z[0]]),
np.array([origin[0], z[1]]),
np.array([origin[0], z[2]]),
color='blue')
#scatter = p3.scatter(x,y,z,size=2,marker = 'sphere',color='red') # the origin
if show:
p3.show()
p3.style.box_off()
handle = {
'origin': scatter,
'arrows': quiver,
'linex': line1,
'liney': line2,
'linez': line3
}
#p3.style.axes_off()
return handle
def test_widgets_state(performance):
try:
_remove_buffers = None
try:
from ipywidgets.widgets.widget import _remove_buffers
except:
pass
ipyvolume.serialize.performance = performance
x, y, z = np.random.random((3, 100))
p3.figure()
scatter = p3.scatter(x, y, z)
state = scatter.get_state()
if _remove_buffers:
_remove_buffers(state)
else:
scatter._split_state_buffers(state)
finally:
ipyvolume.serialize.performance = 0
def interactive_plot(self):
import ipyvolume.pylab as p3
self._create_widgets()
self.scatters = {}
self.vectors = {}
self.legend = widgets.Output()
with self.legend:
self.pltfigure = plt.figure(figsize=(8, 8))
# creating a dummy figure, so that 'self.pltfigure.clf()'
# in self._legend_handler() does not throw an error
# during initialization
p3.clear()
data = self.get_frame(self._widgets.frame.value)['arrays']
for array_name in self._widgets.particles.keys():
pa_widgets = self._widgets.particles[array_name]
if pa_widgets.scalar.value != 'None':
colormap = getattr(mpl.cm, pa_widgets.scalar_cmap.value)
c = colormap(getattr(data[array_name],
pa_widgets.scalar.value))
self.scatters[array_name] = p3.scatter(
data[array_name].x,
data[array_name].y,
data[array_name].z,
color=c,
size=pa_widgets.scalar_size.value,
)
self.plot_container = p3.gcc()
self.plot = p3.gcf() # used in 'self._save_figure_handler()'
self._legend_handler(None)
display(
widgets.HBox(
[widgets.VBox([self.plot]),
widgets.VBox([self.legend])]))
# HBox does not allow custom layout, therefore using an HBox
# of two VBoxes to place 'plot' and 'legend' next to each other
display(self._widgets._create_vbox())
def interactive_plot(self):
self._create_widgets()
self.scatters = {}
display(self._widgets._create_vbox())
self.vectors = {}
self.legend = widgets.Output()
import ipyvolume.pylab as p3
p3.clear()
data = self.get_frame(self._widgets.frame.value)['arrays']
for array_name in self._widgets.particles.keys():
pa_widgets = self._widgets.particles[array_name]
colormap = getattr(mpl.cm, pa_widgets.scalar_cmap.value)
c = colormap(getattr(data[array_name], pa_widgets.scalar.value))
self.scatters[array_name] = p3.scatter(
data[array_name].x,
data[array_name].y,
data[array_name].z,
color=c,
size=pa_widgets.scalar_size.value,
)
self._legend_handler(None)
display(widgets.VBox((p3.gcc(), self.legend)))
def quickscatter(x, y, z, **kwargs):
import ipyvolume.pylab as p3
p3.figure()
p3.scatter(x, y, z, **kwargs)
return p3.current.container
def test_scatter():
x, y, z = np.random.random((3, 100))
p3.scatter(x, y, z)
p3.save("tmp/ipyolume_scatter.html")
def process_the_lidar(filename):
# Get today's date, used for Nearmap data imagery. This way, the API will pull the latest image
todays_date = datetime.datetime.today().strftime('%Y%m%d')
trees = gpd.read_file(las_shapefile)
# Name the output as the RBG plant id number
lidarextension = filename.split('/')[-1].split('.')[0][-2:]
lidarnumber = str(trees['RBGno'].loc[trees['LASfile'] == 'merged_0000' +
str(lidarextension)].values[0])
if os.path.isfile(
os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + 'meta.csv')):
print(lidarnumber, '- Already has been run, skipping')
else:
df = import_lidar(filename)
df = df.loc[df['tree_potential']]
print(lidarnumber, "- Amount of tree points in dataframe:", len(df))
lep = local_max(
df.loc[df['tree_potential'],
['X', 'Y', 'Z', 'HeightAboveGround', 'X_0', 'Y_0', 'Z_0']],
radius=3,
density_threshold=15)
treetop_spheres = p3.scatter(lep['Y'],
lep['Z'],
lep['X'],
color='black',
size=.5,
marker='sphere')
# Cluster the trees. We're using KDTree method here. But something better could be used
kdtree = scipy.spatial.kdtree.KDTree(lep[['X', 'Y', 'Z']])
dist, idx = kdtree.query(df.loc[df['tree_potential'],
['X', 'Y', 'Z']].values)
df.loc[df['tree_potential'], 'tree_idx'] = idx
# DBSCAN clustering alternative. This takes up too much memory when multiprocessing -- Python doesn't seem
# garbage collect the lidar data and exceeds 32gb of RAM when using this. Although, will be ok when running
# small LAS files individually. If used, comment out the last 3 lines and uncomment the next two.
#dbscan = DBSCAN(eps=0.9, min_samples=7).fit(df.loc[df['tree_potential'],['X','Y','Z']].values)
#df.loc[df['tree_potential'], 'tree_idx'] = dbscan.labels_
# Define centroid of XYZ plane
centroid = df['Y'].mean(), df['Z'].mean(), df['X'].mean()
# Calculate distance of tree top points to centroid, add their distance to lep
tree_distances = []
for tree in lep.values.tolist():
tree_distances.append(
euclid_dist(tree[0], tree[1], centroid[0], centroid[1]))
lep['distance'] = tree_distances
# Pull out tree top with the shorted distance to centroid. The index will be the tree id
closest_treetop = lep[lep['distance'] == lep['distance'].min()]
# Builds an entire dataframe which corresponds to the tree that matched in the closest_treetop search
centre_tree_df = df.loc[df['tree_idx'] == df.loc[
closest_treetop.index[0]]['tree_idx']]
# Get CRS of project from the shapefile of trees (caution: not the lidar)
project_crs = trees.crs['init']
nearmap_crs = 'epsg:4326'
# Reproject coordinate of tree to one suitable for Nearmap's API (WGS84/EPSG:4326)
inProj = Proj(init=project_crs)
outProj = Proj(init=nearmap_crs)
x1, y1 = closest_treetop[['X_0',
'Y_0']].values[0][0], closest_treetop[[
'X_0', 'Y_0'
]].values[0][1]
x2, y2 = transform(inProj, outProj, x1, y1)
# Tree's coordinates in WGS84
tree_coords_wgs84 = (x2, y2)
tree_coords_wgs84utm = (x1, y1)
print(
lidarnumber, "- WGS84 UTM coordinates are:\t",
str(tree_coords_wgs84utm[1]) + ',' + str(tree_coords_wgs84utm[0]))
print(lidarnumber, "- WGS84 long coordinates are:\t",
str(tree_coords_wgs84[1]) + ',' + str(tree_coords_wgs84[0]))
if not os.path.isdir(os.path.join('.', output_folder)):
os.makedirs(os.path.join('.', output_folder))
print(lidarnumber, "- Created folder",
os.path.join('.', output_folder))
if not os.path.isdir(os.path.join('.', output_folder, 'lidar')):
os.makedirs(os.path.join('.', output_folder, 'lidar'))
print(lidarnumber, "- Created folder",
os.path.join('.', output_folder, 'lidar'))
# Volume and height of tree cloud (in cubic metres, expecting coordinate system is metres - UTM WGS84 in this case)
tree_volume = round(
scipy.spatial.ConvexHull(centre_tree_df[['X', 'Y', 'Z']]).volume,
2)
tree_height = round(closest_treetop['HeightAboveGround'].values[0], 2)
print(lidarnumber, "- Dimensions of the tree are:\t Volume:",
str(tree_volume) + "m^3", "Height:",
str(tree_height) + "m")
# Save lidar 3D plot
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.dist = 8
ax.scatter(centre_tree_df['X'].values,
centre_tree_df['Y'].values,
centre_tree_df['Z'].values,
zdir="z",
s=1,
marker='^')
ax.view_init(elev=10., azim=0)
fig.savefig(os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + '_plot0deg.jpg'),
dpi=400)
print(
lidarnumber, "- Saved 0° plot to:\t\t",
os.path.join('.', output_folder, 'lidar',
lidarnumber + '_plot0deg.jpg'))
ax.view_init(elev=10., azim=45)
fig.savefig(os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + '_plot45deg.jpg'),
dpi=400)
print(
lidarnumber, "- Saved 45° plot to:\t\t",
os.path.join('.', output_folder, 'lidar',
lidarnumber + '_plot45deg.jpg'))
ax.view_init(elev=10., azim=90)
fig.savefig(os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + '_plot90deg.jpg'),
dpi=400)
print(
lidarnumber, "- Saved 90° plot to:\t\t",
os.path.join('.', output_folder, 'lidar',
lidarnumber + '_plot45deg.jpg'))
plt.close()
# Obtain nearmap imagery
nearmap_url = "http://au0.nearmap.com/staticmap?center=" + str(
tree_coords_wgs84[1]
) + "," + str(
tree_coords_wgs84[0]
) + "&size=3000x3000&zoom=22&date=" + todays_date + "&httpauth=false&apikey=" + NEARMAP_API_KEY
fn, _ = urllib.request.urlretrieve(
nearmap_url,
os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + '_aerial.jpg'))
print(
lidarnumber, "- Saved Nearmap imagery to:\t",
os.path.join('.', output_folder, 'lidar',
lidarnumber + '_aerial.jpg'))
import csv
with open(
os.path.join(os.getcwd(), output_folder, 'lidar',
lidarnumber + 'meta.csv'), 'w') as csvfile:
lidar_metawriter = csv.writer(csvfile, delimiter=',')
lidar_metawriter.writerow([
'treenumber', 'long', 'lat', 'utm_x', 'utm_y', 'height',
'tree_volume'
])
lidar_metawriter.writerow([
lidarnumber, tree_coords_wgs84[0], tree_coords_wgs84[1],
tree_coords_wgs84utm[0], tree_coords_wgs84utm[1], tree_height,
tree_volume
])
print(
lidarnumber, "- Written csv file: ./" + output_folder + "/lidar/" +
lidarnumber + "meta.csv")
def create_ivol(vstruct,
width=500,
height=400,
ssize=5,
min_voxels=None,
max_voxels=None,
**volargs):
"""
Parameters
----------
vstruct: dict
width: int
height: int
ssize: int
min_voxels : int
minimum number of voxels in density cube
max_voxels : int
maximum number of voxels in density cube
volargs: dict
Returns
-------
Examples
--------
>>> from jsonextended import edict
>>> dstruct = {
... 'type': 'repeat_density',
... 'dtype': 'charge',
... 'name': '',
... 'dcube':np.ones((3,3,3)),
... 'centre':[0,0,0],
... 'cell_vectors':{
... 'a':[2.,0,0],
... 'b':[0,2.,0],
... 'c':[0,0,2.]},
... 'color_bbox': 'black',
... 'transforms': []
... }
>>> cstruct = {
... 'type': 'repeat_cell',
... 'name': '',
... 'centre':[0,0,0],
... 'cell_vectors':{
... 'a':[2.,0,0],
... 'b':[0,2.,0],
... 'c':[0,0,2.]},
... 'color_bbox': 'black',
... 'sites': [{
... 'label': "Fe",
... 'ccoord': [1,1,1],
... 'color_fill': "red",
... 'color_outline': None,
... 'transparency': 1,
... 'radius': 1,
... }],
... 'bonds': [],
... 'transforms': []
... }
>>> vstruct = {"elements": [dstruct, cstruct], "transforms": []}
>>> new_struct, fig, controls = create_ivol(vstruct)
>>> print(edict.apply(edict.filter_keys(new_struct, ["ivol"], list_of_dicts=True),
... "ivol", lambda x: [v.__class__.__name__ for v in x], list_of_dicts=True))
{'elements': [{'ivol': ['Figure', 'Mesh']}, {'ivol': ['Mesh', 'Scatter']}]}
"""
new_struct = apply_transforms(vstruct)
bonds = compute_bonds(
new_struct
) #edict.filter_keyvals(vstruct, {"type": "repeat_cell"}, keep_siblings=True))
# ivolume currently only allows one volume rendering per plot
# voltypes = edict.filter_keyvals(vstructs,[('type','repeat_density')])
vol_index = [
i for i, el in enumerate(vstruct['elements'])
if el['type'] == 'repeat_density'
]
assert len(
vol_index) <= 1, "ipyvolume only allows one volume rendering per scene"
p3.clear()
fig = p3.figure(width=width, height=height, controls=True)
fig.screen_capture_enabled = True
# the volume rendering must be created first,
# for appropriately scaled axis
if vol_index:
volstruct = new_struct['elements'][vol_index[0]]
a = volstruct['cell_vectors']['a']
b = volstruct['cell_vectors']['b']
c = volstruct['cell_vectors']['c']
centre = volstruct['centre']
#print(centre)
# convert dcube to cartesian
out = cube_frac2cart(volstruct['dcube'],
a,
b,
c,
centre,
max_voxels=max_voxels,
min_voxels=min_voxels,
make_cubic=True)
new_density, (xmin, ymin, zmin), (xmax, ymax, zmax) = out
vol = p3.volshow(new_density, **volargs)
if volstruct["color_bbox"] is not None:
a = np.asarray(a)
b = np.asarray(b)
c = np.asarray(c)
o = np.asarray(centre) - 0.5 * (a + b + c)
mesh = _create_mesh([
o, o + a, o + b, o + c, o + a + b, o + a + c, o + c + b,
o + a + b + c
],
color=volstruct["color_bbox"],
line_indices=[[0, 1], [0, 2], [0, 3], [2, 4],
[2, 6], [1, 4], [1, 5], [3, 5],
[3, 6], [7, 6], [7, 4], [7, 5]])
vol = [vol, mesh]
# todo better way of storing ivol components?
volstruct['ivol'] = vol
# appropriately scale axis
p3.xlim(xmin, xmax)
p3.ylim(ymin, ymax)
p3.zlim(zmin, zmax)
for element in new_struct['elements']:
if element['type'] == 'repeat_density':
continue
elif element['type'] == 'repeat_cell':
scatters = []
if element["color_bbox"] is not None:
a = np.asarray(element['cell_vectors']['a'])
b = np.asarray(element['cell_vectors']['b'])
c = np.asarray(element['cell_vectors']['c'])
centre = element['centre']
o = np.asarray(centre) - 0.5 * (a + b + c)
mesh = _create_mesh([
o, o + a, o + b, o + c, o + a + b, o + a + c, o + c + b,
o + a + b + c
],
color=element["color_bbox"],
line_indices=[[0, 1], [0, 2], [0,
3], [2, 4],
[2, 6], [1, 4], [1,
5], [3, 5],
[3, 6], [7, 6], [7, 4],
[7, 5]])
scatters.append(mesh)
for color, radius in set([(s['color_fill'], s['radius'])
for s in element["sites"]]):
scatter = edict.filter_keyvals(element, {
"color_fill": color,
"radius": radius
},
"AND",
keep_siblings=True,
list_of_dicts=True)
scatter = edict.combine_lists(scatter, ["sites"],
deepcopy=False)
scatter = edict.remove_keys(scatter, ["sites"], deepcopy=False)
x, y, z = np.array(scatter['ccoord']).T
s = p3.scatter(x,
y,
z,
marker='sphere',
size=ssize * radius,
color=color)
scatters.append(s)
element['ivol'] = scatters
elif element['type'] == 'repeat_poly':
polys = []
for poly in element['polys']:
mesh = _create_mesh(poly, element['color'], element['solid'])
polys.append(mesh)
element['ivol'] = polys
else:
raise ValueError("unknown element type: {}".format(
element['type']))
for bond in bonds:
p1, p2, c1, c2, radius = bond
meshes = _create_bond(p1, p2, c1, c2, radius)
# split up controls
if vol_index:
(level_ctrls, figbox, extractrl1, extractrl2) = p3.gcc().children
controls = OrderedDict([('transfer function', [level_ctrls]),
('lighting', [extractrl1, extractrl2])])
else:
# figbox = p3.gcc().children
controls = {}
return new_struct, fig, controls
