def test_slicer_init():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
# Need a valid volume
with raises(TypeError):
VolumeSlicer(app, [3, 4, 5])
with raises(TypeError):
VolumeSlicer(app, vol[0])
# Need a valid axis
with raises(ValueError):
VolumeSlicer(app, vol, axis=4)
# Need a valide thumbnail
with raises(ValueError):
VolumeSlicer(app, vol, thumbnail=20.2)
# This works
s = VolumeSlicer(app, vol)
# Check properties
assert isinstance(s.graph, dcc.Graph)
assert isinstance(s.slider, dcc.Slider)
assert isinstance(s.stores, list)
assert all(
isinstance(store, (dcc.Store, dcc.Interval)) for store in s.stores)
def test_slicer_thumbnail():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
_ = VolumeSlicer(app, vol)
# Test for name pattern of server-side callback when thumbnails are used
assert any(["server-data.data" in key for key in app.callback_map])
app = dash.Dash()
_ = VolumeSlicer(app, vol, thumbnail=False)
# No server-side callbacks when no thumbnails are used
assert not any(["server-data.data" in key for key in app.callback_map])
def test_scene_id_and_context_id():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
s1 = VolumeSlicer(app, vol, axis=0)
s2 = VolumeSlicer(app, vol, axis=0)
s3 = VolumeSlicer(app, vol, axis=1)
# The scene id's are equal, so indicators will match up
assert s1.scene_id == s2.scene_id and s1.scene_id == s3.scene_id
# Context id's must be unique
assert s1._context_id != s2._context_id and s1._context_id != s3._context_id
def test_clim():
app = dash.Dash()
vol = np.random.uniform(0, 255, (10, 10, 10)).astype(np.uint8)
mi, ma = vol.min(), vol.max()
s = VolumeSlicer(app, vol)
assert s._initial_clim == (mi, ma)
s = VolumeSlicer(app, vol, clim=None)
assert s._initial_clim == (mi, ma)
s = VolumeSlicer(app, vol, clim=(10, 12))
assert s._initial_clim == (10, 12)
# Fails
with raises(TypeError):
VolumeSlicer(app, vol, clim=10)
with raises(TypeError):
VolumeSlicer(app, vol, clim=(10, 12, 14))
def test_slice():
app = dash.Dash()
vol = np.random.uniform(0, 255, (10, 20, 30)).astype(np.uint8)
s = VolumeSlicer(app, vol, axis=0)
im = s._slice(1, (0, 100))
assert im.dtype == np.uint8
assert im.shape == (20, 30)
s = VolumeSlicer(app, vol, axis=1)
im = s._slice(1, (0, 100))
assert im.dtype == np.uint8
assert im.shape == (10, 30)
s = VolumeSlicer(app, vol, axis=2)
im = s._slice(1, (0, 100))
assert im.dtype == np.uint8
assert im.shape == (10, 20)
def test_slicer_thumbnail():
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
app = dash.Dash()
_ = VolumeSlicer(app, vol)
# Test for name pattern of server-side callback when thumbnails are used
assert any(["server-data.data" in key for key in app.callback_map])
app = dash.Dash()
_ = VolumeSlicer(app, vol, thumbnail=False)
# No server-side callbacks when no thumbnails are used
assert not any(["server-data.data" in key for key in app.callback_map])
# Default thumbnail size
s = VolumeSlicer(app, vol)
assert s._slice_info["thumbnail_size"] == (32, 32)
# Custom size
s = VolumeSlicer(app, vol, thumbnail=20)
assert s._slice_info["thumbnail_size"] == (20, 20)
s = VolumeSlicer(app, vol, thumbnail=50)
assert s._slice_info["thumbnail_size"] == (50, 50)
# Custom but too big
s = VolumeSlicer(app, vol, thumbnail=102)
assert s._slice_info["thumbnail_size"] == (100, 100)
# Disable
s = VolumeSlicer(app, vol, thumbnail=False)
assert s._slice_info["thumbnail_size"] == (100, 100)
s = VolumeSlicer(app, vol, thumbnail=0)
assert s._slice_info["thumbnail_size"] == (100, 100)
s = VolumeSlicer(app, vol, thumbnail=-1)
assert s._slice_info["thumbnail_size"] == (100, 100)
# None is simply not allowed - removes ambiguity about
# whether None means no-thumbnails, or the default size
with raises(TypeError):
VolumeSlicer(app, vol, thumbnail=None)
def test_slicer_init():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
# Need a dash app
with raises(TypeError):
VolumeSlicer("not a dash app", vol)
# Need a valid volume
with raises(TypeError):
VolumeSlicer(app, [3, 4, 5])
with raises(TypeError):
VolumeSlicer(app, vol[0])
# Need a valid axis
with raises(ValueError):
VolumeSlicer(app, vol, axis=4)
# Need a valide thumbnail
with raises(TypeError):
VolumeSlicer(app, vol, thumbnail=20.2)
# Need a valide scene id
with raises(TypeError):
VolumeSlicer(app, vol, scene_id=20)
# This works
s = VolumeSlicer(app, vol)
# Check properties
assert s.axis == 0
assert isinstance(s.graph, dcc.Graph)
assert isinstance(s.slider, dcc.Slider)
assert isinstance(s.stores, list)
assert all(
isinstance(store, (dcc.Store, dcc.Interval)) for store in s.stores)
for store in [s.clim, s.state, s.extra_traces, s.overlay_data]:
assert isinstance(store, dcc.Store)
def test_create_overlay_data():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
s = VolumeSlicer(app, vol)
# Bool overlay
overlay = s.create_overlay_data(vol > 10)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(isinstance(x, str) for x in overlay)
# Reset
overlay = s.create_overlay_data(None)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(x is None for x in overlay)
# Reset by zero mask
overlay = s.create_overlay_data(vol > 300)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(x is None for x in overlay)
# Wrong
with raises(ValueError):
s.create_overlay_data(vol[:-1]) # wrong shape
import dash
import dash_html_components as html
from dash_slicer import VolumeSlicer
import imageio
app = dash.Dash(__name__, update_title=None)
vol1 = imageio.volread("imageio:stent.npz")
vol2 = vol1[::3, ::2, :]
spacing = 3, 2, 1
ori = 1000, 2000, 3000
slicer1 = VolumeSlicer(app,
vol1,
axis=1,
origin=ori,
scene_id="scene1",
color="red")
slicer2 = VolumeSlicer(app,
vol1,
axis=0,
origin=ori,
scene_id="scene1",
color="green")
slicer3 = VolumeSlicer(app,
vol2,
axis=0,
origin=ori,
spacing=spacing,
scene_id="scene1",
color="blue")
import plotly
import dash
import dash_html_components as html
import dash_core_components as dcc
from dash.dependencies import Input, Output
from dash_slicer import VolumeSlicer
import imageio
from skimage import measure
app = dash.Dash(__name__, update_title=None)
server = app.server
vol = imageio.volread("imageio:stent.npz")
mi, ma = vol.min(), vol.max()
slicer = VolumeSlicer(app, vol)
app.layout = html.Div([
slicer.graph,
slicer.slider,
dcc.Slider(
id="level-slider",
min=mi,
max=ma,
step=1,
value=mi + 0.2 * (ma - mi),
),
*slicer.stores,
])
spacing = abs(mat[2, 2]), abs(mat[1, 1]), abs(mat[0, 0])
# Create smoothed image and histogram
med_img = filters.median(img, selem=np.ones((1, 3, 3), dtype=np.bool))
hi = exposure.histogram(med_img)
# Create mesh
verts, faces, _, _ = measure.marching_cubes(med_img, 200, step_size=5)
x, y, z = verts.T
i, j, k = faces.T
fig_mesh = go.Figure()
fig_mesh.add_trace(go.Mesh3d(x=z, y=y, z=x, opacity=0.2, i=k, j=j, k=i))
# Create slicers
slicer1 = VolumeSlicer(app, img, axis=0, spacing=spacing, thumbnail=False)
slicer1.graph.figure.update_layout(
dragmode="drawclosedpath", newshape_line_color="cyan"
)
slicer1.graph.config.update(
modeBarButtonsToAdd=["drawclosedpath", "eraseshape",]
)
slicer2 = VolumeSlicer(app, img, axis=1, spacing=spacing, thumbnail=False)
slicer2.graph.figure.update_layout(dragmode="drawrect", newshape_line_color="cyan")
slicer2.graph.config.update(
modeBarButtonsToAdd=["drawrect", "eraseshape",]
)
def path_to_coords(path):
# Load the initial data
(table, description, reference, conn_mat,
parcellation) = get_atlas(atlas_keys[0])
region_labels = table["Region Name"]
vol = template_img.get_fdata().squeeze()
parcellation_colormap = px.colors.qualitative.Alphabet
connectivity_colormap = [[
val,
px.colors.label_rgb(
plt.cm.plasma(val, alpha=1 if not val == 0 else 0, bytes=True)),
] for val in np.linspace(0, 1, 100)]
sagittal_slicer = VolumeSlicer(app,
vol,
axis=0,
scene_id="brain",
color="white")
coronal_slicer = VolumeSlicer(app,
vol,
axis=1,
scene_id="brain",
color="white")
axial_slicer = VolumeSlicer(app, vol, axis=2, scene_id="brain", color="white")
# Update all slicers in order
slicer_list = []
for slicer_idx, slicer in enumerate(
[sagittal_slicer, coronal_slicer, axial_slicer]):
slicer.graph.figure.update_layout(dragmode=False,
plot_bgcolor="rgb(0, 0, 0)")
import plotly.graph_objects as go
import dash
import dash_html_components as html
import dash_core_components as dcc
from dash_slicer import VolumeSlicer
from dash.dependencies import Input, Output, State, ALL
from skimage.measure import marching_cubes
import imageio
app = dash.Dash(__name__, update_title=None)
server = app.server
# Read volumes and create slicer objects
vol = imageio.volread("imageio:stent.npz")
slicer0 = VolumeSlicer(app, vol, clim=(0, 800), axis=0)
slicer1 = VolumeSlicer(app, vol, clim=(0, 800), axis=1)
slicer2 = VolumeSlicer(app, vol, clim=(0, 800), axis=2)
# Calculate isosurface and create a figure with a mesh object
verts, faces, _, _ = marching_cubes(vol, 300, step_size=4)
x, y, z = verts.T
i, j, k = faces.T
mesh = go.Mesh3d(x=z, y=y, z=x, opacity=0.2, i=k, j=j, k=i)
fig = go.Figure(data=[mesh])
fig.update_layout(uirevision="anything") # prevent orientation reset on update
# Put everything together in a 2x2 grid
app.layout = html.Div(
style={
def test_create_overlay_data():
app = dash.Dash()
vol = np.random.uniform(0, 255, (100, 100, 100)).astype(np.uint8)
s = VolumeSlicer(app, vol)
# Bool overlay
overlay = s.create_overlay_data(vol > 10)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(isinstance(x, str) for x in overlay)
# Bool overlay - with color
overlay = s.create_overlay_data(vol > 10, "#ff0000")
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(isinstance(x, str) for x in overlay)
# Uint8 overlay - with colormap
overlay = s.create_overlay_data(vol.astype(np.uint8),
["#ff0000", "#00ff00"])
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(isinstance(x, str) for x in overlay)
# Reset
overlay = s.create_overlay_data(None)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(x is None for x in overlay)
# Reset by zero mask
overlay = s.create_overlay_data(vol > 300)
assert isinstance(overlay, list) and len(overlay) == s.nslices
assert all(x is None for x in overlay)
# Wrong
with raises(TypeError):
s.create_overlay_data("not a valid mask")
with raises(ValueError):
s.create_overlay_data(vol.astype(np.float32)) # wrong dtype
with raises(ValueError):
s.create_overlay_data(vol[:-1]) # wrong shape
import imageio
from skimage import measure
app = dash.Dash(__name__, update_title=None)
server = app.server
# Read volume
vol = imageio.volread("imageio:stent.npz")
vol = vol[::3, :, :]
spacing = 3, 1, 1
ori = 1000, 2000, 3000
# Create slicer objects
slicer0 = VolumeSlicer(app,
vol,
spacing=spacing,
origin=ori,
axis=0,
thumbnail=False)
slicer1 = VolumeSlicer(app,
vol,
spacing=spacing,
origin=ori,
axis=1,
thumbnail=8,
reverse_y=False)
slicer2 = VolumeSlicer(app,
vol,
spacing=spacing,
origin=ori,
axis=2,
color="#00ff99")
"""
This is an example that shows how the slicer position can be both read from and written to
by listening to the "drag_value" of the default slider with an auxiliary slider
"""
import dash
import dash_html_components as html
from dash_slicer import VolumeSlicer
import dash_core_components as dcc
from dash.dependencies import Input, Output
import imageio
app = dash.Dash(__name__, update_title=None)
vol = imageio.volread("imageio:stent.npz")
slicer0 = VolumeSlicer(app, vol, axis=0, scene_id="brain")
slicer1 = VolumeSlicer(app, vol, axis=1, scene_id="brain")
slicer2 = VolumeSlicer(app, vol, axis=2, scene_id="brain")
setpos_store = dcc.Store(id={
"context": "app",
"scene": slicer0.scene_id,
"name": "setpos"
})
# Here we create an auxiliary slider for each slicer and encapsulate it inside a Div
# to be added to the app layout
slicer_list = [setpos_store]
for sidx, slicer in enumerate([slicer0, slicer1, slicer2]):
slider = dcc.Slider(id=f"slider-{sidx}", max=slicer.nslices)
slicer_list.append(
import dash
import dash_html_components as html
import imageio
from dash_slicer import VolumeSlicer
from apps.imagens.dash_app.utilidades.import_imagem import seleciona_lista_arquivos, import_file
app = dash.Dash(__name__, update_title=None)
list_imagens = seleciona_lista_arquivos(38)
im = import_file(list_imagens)
slicer = VolumeSlicer(app, im)
app.layout = html.Div([slicer.graph, slicer.slider, *slicer.stores])
if __name__ == "__main__":
app.run_server(debug=True, dev_tools_props_check=False)
import dash
import dash_html_components as html
import imageio
from dash_slicer import VolumeSlicer
app = dash.Dash(__name__, update_title=None)
vol = imageio.volread("imageio:stent.npz")
slicer0 = VolumeSlicer(app, vol, axis=0)
slicer1 = VolumeSlicer(app, vol, axis=1)
slicer2 = VolumeSlicer(app, vol, axis=2)
slicer0.graph.config["scrollZoom"] = False
slicer1.graph.config["scrollZoom"] = False
slicer2.graph.config["scrollZoom"] = False
app.layout = html.Div(
style={
"display": "grid",
"gridTemplateColumns": "33% 33% 33%",
},
children=[
html.Div([slicer0.graph, html.Br(), slicer0.slider, *slicer0.stores]),
html.Div([slicer1.graph, html.Br(), slicer1.slider, *slicer1.stores]),
html.Div([slicer2.graph, html.Br(), slicer2.slider, *slicer2.stores]),
],
)
if __name__ == "__main__":
"""
import dash
import dash_html_components as html
import dash_core_components as dcc
from dash.dependencies import Input, Output
from dash_slicer import VolumeSlicer
import numpy as np
import imageio
app = dash.Dash(__name__, update_title=None)
server = app.server
vol = imageio.volread("imageio:stent.npz")
mi, ma = vol.min(), vol.max()
slicer = VolumeSlicer(app, vol, clim=(0, 800))
app.layout = html.Div([
slicer.graph,
slicer.slider,
dcc.RangeSlider(
id="level-slider",
min=vol.min(),
max=vol.max(),
step=1,
value=[mi + 0.1 * (ma - mi), mi + 0.3 * (ma - mi)],
),
*slicer.stores,
])
# Define colormap to make the lower threshold shown in yellow, and higher in red
import dash
import dash_html_components as html
import imageio
from dash_slicer import VolumeSlicer
app = dash.Dash(__name__, update_title=None)
vol = imageio.volread("imageio:stent.npz")
vol = vol[::3,:,:]
spacing = 3, 1, 1
slicer0 = VolumeSlicer(app, vol, spacing=spacing, axis=0)
slicer1 = VolumeSlicer(app, vol, spacing=spacing, axis=1)
slicer0.graph.config["scrollZoom"] = False
slicer1.graph.config["scrollZoom"] = False
app.layout = html.Div(
style={
"display": "grid",
"gridTemplateColumns": "33% 33%",
},
children=[
html.Div([slicer0.graph, html.Br(), slicer0.slider, *slicer0.stores]),
html.Div([slicer1.graph, html.Br(), slicer1.slider, *slicer1.stores]),
],
)
if __name__ == "__main__":
