我尝试按照"Visualizing MRI Volume Slices"示例进行绘图，但是在离线模式下。我运行的代码与示例中的代码相同，但我做了一些更改以避免使用网格，因为这些代码仅适用于在线图。每当我运行脚本时，我都会得到一个带滑块和所有内容的交互式网格，但是图表是空的（没有MRI切片或任何东西）。我已经验证MRI数据正在被正确下载和格式化。这是我的完整源代码：
import plotly
import plotly.plotly as py
from plotly.grid_objs import Grid, Column
import numpy as np
from skimage import io
import time
vol = io.imread("https://s3.amazonaws.com/assets.datacamp.com/blog_assets/attention-mri.tif")
volume = vol.T
r, c = volume[0].shape
# Set the color scale
pl_bone = [
[0.0, 'rgb(0, 0, 0)'],
[0.05, 'rgb(10, 10, 14)'],
[0.1, 'rgb(21, 21, 30)'],
[0.15, 'rgb(33, 33, 46)'],
[0.2, 'rgb(44, 44, 62)'],
[0.25, 'rgb(56, 55, 77)'],
[0.3, 'rgb(66, 66, 92)'],
[0.35, 'rgb(77, 77, 108)'],
[0.4, 'rgb(89, 92, 121)'],
[0.45, 'rgb(100, 107, 132)'],
[0.5, 'rgb(112, 123, 143)'],
[0.55, 'rgb(122, 137, 154)'],
[0.6, 'rgb(133, 153, 165)'],
[0.65, 'rgb(145, 169, 177)'],
[0.7, 'rgb(156, 184, 188)'],
[0.75, 'rgb(168, 199, 199)'],
[0.8, 'rgb(185, 210, 210)'],
[0.85, 'rgb(203, 221, 221)'],
[0.9, 'rgb(220, 233, 233)'],
[0.95, 'rgb(238, 244, 244)'],
[1.0, 'rgb(255, 255, 255)']
]
# Create the grid
my_columns = []
z_source = []
surface_color_source = []
nr_frames = 68
for k in range(nr_frames):
z_source.append((6.7 - k * 0.1) * np.ones((r, c)))
surface_color_source.append(np.flipud(volume[67 - k]))
# Create the chart
data=[
dict(
type='surface',
zsrc=z_source[0],
surfacecolorsrc=surface_color_source[0],
colorscale=pl_bone,
colorbar=dict(thickness=20, ticklen=4)
)
]
frames=[]
for k in range(nr_frames):
frames.append(
dict(
data=[dict(zsrc=z_source[k], surfacecolorsrc=surface_color_source[k])],
name='frame{}'.format(k + 1)
)
)
sliders=[
dict(
steps=[dict(method='animate',
args= [['frame{}'.format(k + 1)],
dict(mode='immediate',
frame= dict(duration=70, redraw= False),
transition=dict(duration=0))],
label='{:d}'.format(k+1)) for k in range(68)],
transition= dict(duration=0),
x=0,
y=0,
currentvalue=dict(font=dict(size=12),
prefix='slice: ',
visible=True,
xanchor='center'
),
len=1.0
)
]
axis3d = dict(
showbackground=True,
backgroundcolor="rgb(230, 230,230)",
gridcolor="rgb(255, 255, 255)",
zerolinecolor="rgb(255, 255, 255)",
)
layout3d = dict(
title='Slices in volumetric data',
font=dict(family='Balto'),
width=600,
height=600,
scene=dict(xaxis=(axis3d),
yaxis=(axis3d),
zaxis=dict(axis3d, **dict(range=[-0.1, 6.8], autorange=False)),
aspectratio=dict(x=1, y=1, z=1),
),
updatemenus=[
dict(type='buttons',
showactive=False,
y=1,
x=1.3,
xanchor='right',
yanchor='top',
pad=dict(t=0, r=10),
buttons=[dict(label='Play',
method='animate',
args=[
None,
dict(frame=dict(duration=70, redraw=False),
transition=dict(duration=0),
fromcurrent=True,
mode='immediate')
])])
],
sliders=sliders
)
fig=dict(data=data, layout=layout3d, frames=frames)
plotly.offline.plot(fig)
答案 0 :(得分：0)
我简化了您的代码以显示可能的错误：
import os
import pickle
import plotly
import numpy as np
from skimage import io
filename = 'data.pickle'
url = ('https://s3.amazonaws.com/assets.datacamp.com/blog_assets/'
'attention-mri.tif')
if not os.path.exists(filename):
vol = io.imread(url)
with open(filename, 'wb') as f:
pickle.dump(vol, f)
else:
with open(filename, 'rb') as f:
vol = pickle.load(f)
volume = vol.T
r, c = volume[0].shape
# Set the color scale
pl_bone = [
[0.0, 'rgb(0, 0, 0)'],
[0.05, 'rgb(10, 10, 14)'],
[0.1, 'rgb(21, 21, 30)'],
[0.15, 'rgb(33, 33, 46)'],
[0.2, 'rgb(44, 44, 62)'],
[0.25, 'rgb(56, 55, 77)'],
[0.3, 'rgb(66, 66, 92)'],
[0.35, 'rgb(77, 77, 108)'],
[0.4, 'rgb(89, 92, 121)'],
[0.45, 'rgb(100, 107, 132)'],
[0.5, 'rgb(112, 123, 143)'],
[0.55, 'rgb(122, 137, 154)'],
[0.6, 'rgb(133, 153, 165)'],
[0.65, 'rgb(145, 169, 177)'],
[0.7, 'rgb(156, 184, 188)'],
[0.75, 'rgb(168, 199, 199)'],
[0.8, 'rgb(185, 210, 210)'],
[0.85, 'rgb(203, 221, 221)'],
[0.9, 'rgb(220, 233, 233)'],
[0.95, 'rgb(238, 244, 244)'],
[1.0, 'rgb(255, 255, 255)']
]
# Create the grid
my_columns = []
z_source = []
surface_color_source = []
nr_frames = 68
for k in range(nr_frames):
z_source.append((6.7 - k * 0.1) * np.ones((r, c)))
surface_color_source.append(np.flipud(volume[67 - k]))
# Create the chart
data=[
dict(
type='surface',
zsrc=z_source[0],
surfacecolorsrc=surface_color_source[0],
colorscale=pl_bone,
colorbar=dict(thickness=20, ticklen=4)
)
]
fig=dict(data=data)
plotly.offline.plot(fig)
这将导致以下错误：
plotly.offline.plot(fig)
PlotlyError: Invalid 'figure_or_data' argument. Plotly will not be able to properly parse the resulting JSON. If you want to send this 'figure_or_data' to Plotly anyway (not recommended), you can set 'validate=False' as a plot option.
Here's why you're seeing this error:
zsrc does not have an `id` property. [[6.7 6.7 6.7 ... 6.7 6.7 6.7]
[6.7 6.7 6.7 ... 6.7 6.7 6.7]
[6.7 6.7 6.7 ... 6.7 6.7 6.7]
...
[6.7 6.7 6.7 ... 6.7 6.7 6.7]
[6.7 6.7 6.7 ... 6.7 6.7 6.7]
[6.7 6.7 6.7 ... 6.7 6.7 6.7]] needs to be assigned to either an object with an `id` (like a plotly.grid_objs.Column) or a string. The `id` is a unique identifier assigned by the Plotly webserver to this grid column.
也许在消化fig=dict(data=data, layout=layout3d, frames=frames)时阴谋认为它是'validate = False'情况，因此什么也没画。