Use Image trace and add low-res slices#3

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Merged
almarklein merged 4 commits into from
Nov 3, 2020
Merged

Use Image trace and add low-res slices #3

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26508fe
wip low-res data
almarklein Oct 30, 2020
4f5e653
use Image trace instead of layout images.
almarklein Nov 2, 2020
0b27f23
tweaks
almarklein Nov 3, 2020
31eaf64
cleanup
almarklein Nov 3, 2020
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56 changes: 28 additions & 28 deletions dash_3d_viewer/slicer.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
self._id = id

# Get the slice size (width, height), and max index
arr_shape = list(volume.shape)
arr_shape.pop(self._axis)
slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
self._max_index = self._volume.shape[self._axis] - 1

# Prep low-res slices
thumbnails = [
img_array_to_uri(self._slice(i), (32, 32))
for i in range(self._max_index + 1)
]

# Create a placeholder trace
# todo: can add "%{z[0]}", but that would be the scaled value ...
trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
# Create the figure object
fig = Figure()
fig = Figure(data=[trace])
fig.update_layout(
template=None,
margin=dict(l=0, r=0, b=0, t=0, pad=4),
)
fig.update_xaxes(
# range=(0, slice_size[0]),
showgrid=False,
range=(0, slice_size[0]),
showticklabels=False,
zeroline=False,
)
fig.update_yaxes(
# range=(slice_size[1], 0), # todo: allow flipping x or y
showgrid=False,
scaleanchor="x",
range=(slice_size[1], 0), # todo: allow flipping x or y
showticklabels=False,
zeroline=False,
)
# Add an empty layout image that we can populate from JS.
fig.add_layout_image(
dict(
source="",
xref="x",
yref="y",
x=0,
y=0,
sizex=slice_size[0],
sizey=slice_size[1],
sizing="contain",
layer="below",
)
)
# Wrap the figure in a graph
# todo: or should the user provide this?
self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
Store(id=self._subid("_requested-slice-index"), data=0),
Store(id=self._subid("_slice-data"), data=""),
Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
]

self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
"""Sample a slice from the volume."""
indices = [slice(None), slice(None), slice(None)]
indices[self._axis] = index
return self._volume[tuple(indices)]
im = self._volume[tuple(indices)]
return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

def _create_server_callbacks(self, app):
"""Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
)
def upload_requested_slice(slice_index):
slice = self._slice(slice_index)
slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
return [slice_index, img_array_to_uri(slice)]

def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

app.clientside_callback(
"""
function handle_incoming_slice(index, index_and_data, ori_figure) {
function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
let new_index = index_and_data[0];
let new_data = index_and_data[1];
// Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
slice_cache[new_index] = new_data;
// Get the data we need *now*
let data = slice_cache[index];
//slice_cache[new_index] = undefined; // todo: disabled cache for now!
// Maybe we do not need an update
if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
}
if (data == ori_figure.layout.images[0].source) {
if (data == ori_figure.data[0].source) {
return window.dash_clientside.no_update;
}
// Otherwise, perform update
console.log("updating figure");
let figure = {...ori_figure};
figure.layout.images[0].source = data;
figure.data[0].source = data;
return figure;
}
""".replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
Input(self._subid("slice-index"), "data"),
Input(self._subid("_slice-data"), "data"),
],
[State(self._subid("graph"), "figure")],
[
State(self._subid("graph"), "figure"),
State(self._subid("_slice-data-lowres"), "data"),
],
)
14 changes: 10 additions & 4 deletions dash_3d_viewer/utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
img_array = skimage.util.img_as_ubyte(img_array)
# todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
# from plotly.express._imshow import _array_to_b64str
# return _array_to_b64str(img_array)
img_pil = PIL.Image.fromarray(img_array)
uri = ImageUriValidator.pil_image_to_uri(img_pil)
return uri
if new_size:
img_pil.thumbnail(new_size)
# The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
f = io.BytesIO()
img_pil.save(f, format="PNG")
base64_str = base64.b64encode(f.getvalue()).decode()
return "data:image/png;base64," + base64_str
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Use Image trace and add low-res slices#3

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
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26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use Image trace and add low-res slices#3

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
Show file tree
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Commits

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4 commits


Select commit
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26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

File filter

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Use Image trace and add low-res slices#3

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 Merged

almarklein
merged 4 commits into

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Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
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26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Use Image trace and add low-res slices#3

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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Already on GitHub?
Sign in
to your account

 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
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26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use Image trace and add low-res slices#3

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
Show file tree
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4 commits


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Hold shift + click to select a range
26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

File filter

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Filter by extension
Conversations

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Use Image trace and add low-res slices#3

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 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
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26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Use Image trace and add low-res slices#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

almarklein
merged 4 commits into

from

Nov 3, 2020
 Merged


Use Image trace and add low-res slices
#3
Show file tree
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Commits

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4 commits


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Hold shift + click to select a range
26508fe

wip low-res data


almarklein Oct 30, 2020
4f5e653

use Image trace instead of layout images.


almarklein Nov 2, 2020
0b27f23

tweaks


almarklein Nov 3, 2020
31eaf64

cleanup


almarklein Nov 3, 2020

File filter

Filter by extension
Filter by extension
Conversations

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56 changes: 28 additions & 28 deletions
dash_3d_viewer/slicer.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
import numpy as np
from plotly.graph_objects import Figure
from plotly.graph_objects import Figure, Image
from dash import Dash
from dash.dependencies import Input, Output, State
from dash_core_components import Graph, Slider, Store
Expand DownExpand Up@@ -29,44 +29,39 @@ def __init__(self, app, volume, axis=0, id=None):
 self._id = id

 # Get the slice size (width, height), and max index
 arr_shape = list(volume.shape)
 arr_shape.pop(self._axis)
 slice_size = list(reversed(arr_shape))
# arr_shape = list(volume.shape)
# arr_shape.pop(self._axis)
# slice_size = list(reversed(arr_shape))
 self._max_index = self._volume.shape[self._axis] - 1

 # Prep low-res slices
 thumbnails = [
 img_array_to_uri(self._slice(i), (32, 32))
 for i in range(self._max_index + 1)
 ]

 # Create a placeholder trace
 # todo: can add "%{z[0]}", but that would be the scaled value ...
 trace = Image(source="", hovertemplate="(%{x}, %{y})<extra></extra>")
 # Create the figure object
 fig = Figure()
 fig = Figure(data=[trace])
 fig.update_layout(
 template=None,
 margin=dict(l=0, r=0, b=0, t=0, pad=4),
 )
 fig.update_xaxes(
 # range=(0, slice_size[0]),
 showgrid=False,
 range=(0, slice_size[0]),
 showticklabels=False,
 zeroline=False,
 )
 fig.update_yaxes(
 # range=(slice_size[1], 0), # todo: allow flipping x or y
 showgrid=False,
 scaleanchor="x",
 range=(slice_size[1], 0), # todo: allow flipping x or y
 showticklabels=False,
 zeroline=False,
 )
 # Add an empty layout image that we can populate from JS.
 fig.add_layout_image(
 dict(
 source="",
 xref="x",
 yref="y",
 x=0,
 y=0,
 sizex=slice_size[0],
 sizey=slice_size[1],
 sizing="contain",
 layer="below",
 )
 )
 # Wrap the figure in a graph
 # todo: or should the user provide this?
 self.graph = Graph(
Expand All@@ -88,6 +83,7 @@ def __init__(self, app, volume, axis=0, id=None):
 Store(id=self._subid("slice-index"), data=volume.shape[self._axis] // 2),
 Store(id=self._subid("_requested-slice-index"), data=0),
 Store(id=self._subid("_slice-data"), data=""),
 Store(id=self._subid("_slice-data-lowres"), data=thumbnails),
 ]

 self._create_server_callbacks(app)
Expand All@@ -101,7 +97,8 @@ def _slice(self, index):
 """Sample a slice from the volume."""
 indices = [slice(None), slice(None), slice(None)]
 indices[self._axis] = index
 return self._volume[tuple(indices)]
 im = self._volume[tuple(indices)]
 return (im.astype(np.float32) * (255 / im.max())).astype(np.uint8)

 def _create_server_callbacks(self, app):
 """Create the callbacks that run server-side."""
Expand All@@ -112,7 +109,6 @@ def _create_server_callbacks(self, app):
 )
 def upload_requested_slice(slice_index):
 slice = self._slice(slice_index)
 slice = (slice.astype(np.float32) * (255 / slice.max())).astype(np.uint8)
 return [slice_index, img_array_to_uri(slice)]

 def _create_client_callbacks(self, app):
Expand DownExpand Up@@ -158,7 +154,7 @@ def _create_client_callbacks(self, app):

 app.clientside_callback(
 """
 function handle_incoming_slice(index, index_and_data, ori_figure) {
 function handle_incoming_slice(index, index_and_data, ori_figure, lowres) {
 let new_index = index_and_data[0];
 let new_data = index_and_data[1];
 // Store data in cache
Expand All@@ -167,17 +163,18 @@ def _create_client_callbacks(self, app):
 slice_cache[new_index] = new_data;
 // Get the data we need *now*
 let data = slice_cache[index];
 //slice_cache[new_index] = undefined; // todo: disabled cache for now!
 // Maybe we do not need an update
 if (!data) {
return window.dash_clientside.no_update;
data = lowres[index];
 }
 if (data == ori_figure.layout.images[0].source) {
 if (data == ori_figure.data[0].source) {
 return window.dash_clientside.no_update;
 }
 // Otherwise, perform update
 console.log("updating figure");
 let figure = {...ori_figure};
 figure.layout.images[0].source = data;
 figure.data[0].source = data;
 return figure;
 }
 """.replace(
Expand All@@ -188,5 +185,8 @@ def _create_client_callbacks(self, app):
 Input(self._subid("slice-index"), "data"),
 Input(self._subid("_slice-data"), "data"),
 ],
 [State(self._subid("graph"), "figure")],
 [
 State(self._subid("graph"), "figure"),
 State(self._subid("_slice-data-lowres"), "data"),
 ],
 )

14 changes: 10 additions & 4 deletions
dash_3d_viewer/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,19 +1,25 @@
import io
import random
import base64

import PIL.Image
import skimage
from plotly.utils import ImageUriValidator


def gen_random_id(n=6):
 return "".join(random.choice("abcdefghijklmnopqrtsuvwxyz") for i in range(n))


def img_array_to_uri(img_array):
def img_array_to_uri(img_array, new_size=None):
 img_array = skimage.util.img_as_ubyte(img_array)
 # todo: leverage this Plotly util once it becomes part of the public API (also drops the Pillow dependency)
 # from plotly.express._imshow import _array_to_b64str
 # return _array_to_b64str(img_array)
 img_pil = PIL.Image.fromarray(img_array)
 uri = ImageUriValidator.pil_image_to_uri(img_pil)
 return uri
 if new_size:
 img_pil.thumbnail(new_size)
 # The below was taken from plotly.utils.ImageUriValidator.pil_image_to_uri()
 f = io.BytesIO()
 img_pil.save(f, format="PNG")
 base64_str = base64.b64encode(f.getvalue()).decode()
 return "data:image/png;base64," + base64_str