"""Volumetric datasets (x*y*z matrix)"""
from . import client
from . import utils
import numpy as np
import zlib
import json
import csv
import base64
from vbl_aquarium.models.urchin import VolumeMetaModel, VolumeDataChunk
counter = 0
CHUNK_LIMIT = 1000000
click_list = []
verbose = False
def _volume_click(data):
"""Internal callback function
"""
click_pos = json.loads(data)
if verbose:
print(click_pos)
click_list.append(click_pos)
[docs]def clear_clicks():
"""Clear the volumes click list
"""
global click_list
click_list = []
[docs]def save_clicks(fpath):
"""Save the current click list to a CSV file.
Use `urchin.volumes.clear_clicks()` before starting your click sequence.
Parameters
----------
fpath : string
Relative filepath
"""
global click_list
# Extract headers and data
headers = ['ap', 'ml', 'dv']
data = [[entry[header] for header in headers] for entry in click_list]
with open(fpath, mode='w', newline='') as file:
writer = csv.writer(file)
# Write headers
writer.writerow(headers)
# Write data
writer.writerows(data)
[docs]def clear():
"""Clear all custom meshes
"""
client.sio.emit('Clear','volume')
[docs]class Volume:
"""Volumetric dataset represented in a compressed format by using a colormap to translate
uint8 x/y/z data into full RGB color.
Volumes should be created in (AP, ML, DV)
"""
def __init__(self, volume_data, colormap = None):
"""_summary_
Parameters
----------
volume_data : _type_
_description_
colormap : _type_, optional
_description_, by default None
"""
global counter
self.id = f'volume{counter}'
counter += 1
volume_data[np.isnan(volume_data)] = 255
flattened_data = volume_data.flatten().astype(np.uint8).tobytes()
compressed_data = zlib.compress(flattened_data)
compressed_data = base64.b64encode(compressed_data).decode('utf-8')
if colormap is None:
colormap = ['#000000'] * 255
self.data = VolumeMetaModel(
name = f'volume{counter}',
n_bytes = len(compressed_data),
colormap = [utils.formatted_color(color) for color in colormap],
visible = True
)
self.update()
# send data packets
# split data into chunks
n_chunks = int(np.ceil(self.data.n_bytes / CHUNK_LIMIT))
print(f'Data fits in {n_chunks} chunks of 1MB or less')
offset = 0
for chunk in range(n_chunks):
# get the data
chunk_size = np.min((self.data.n_bytes - offset, CHUNK_LIMIT))
chunk_data = VolumeDataChunk(
name = self.data.name,
# bytes = base64.b64encode(compressed_data[offset : offset + chunk_size]).decode('utf-8')
bytes = compressed_data[offset : offset + chunk_size]
)
client.sio.emit('SetVolumeData', chunk_data.to_string())
offset += chunk_size
[docs] def update(self):
client.sio.emit('UpdateVolume', self.data.to_string())
[docs] def delete(self):
client.sio.emit('DeleteVolume', self.id)
[docs]def compress_volume(volume_data, n_colors=254):
"""Compress a volume of float data into a uint8 volume by quantiles.
NaN values are mapped to 255 (transparent) for Urchin.
This is required for use with the urchin.volume.Volume object type.
Parameters
----------
volume_data : float volume
3D matrix of float data
n_colors : int (optional)
Default to 254, number of un-reserved colors. 255 must always be reserved for NaN / transparency
Returns
-------
(uint8 volume, float[] map)
"""
valid_values = volume_data[~np.isnan(volume_data)]
quantiles = np.quantile(valid_values.flatten(), np.linspace(0,1,n_colors))
out = np.digitize(volume_data, quantiles, right=True).astype(np.uint8)
out[np.isnan(volume_data)] = 255
return out.astype(np.uint8), quantiles
[docs]def colormap(colormap_name='greens', reserved_colors=[], datapoints=None):
"""Build a colormap
This function has two parts:
1. It builds a standard colormap in indexes 0->n_colors
2. It leaves "reserved" colors at the end, by default this is just 255 which becomes
transparent in Urchin. But you can add a list of additional colors which will be added
to the end of the colormap. The order will match the list you pass in, so e.g.
3. If you pass in datapoints, it will generate a non-uniform colormap going from the min
to maximum value.
indexes: [0->252, 253->254, 255]
colors: [greens, your reserved colors, transparent]
Colormap options
----------
reds: 0->255 R channel
greens: 0->255 G channel
blues: 0->255 B channel
Parameters
----------
colormap_name : str, optional
_description_, by default 'greens'
reserved_colors : _type_, optional
_description_, by default None
Returns
-------
list of string
List of colormap hex colors in Urchin-compatible format
"""
colormap = []
n_unreserved = 254 - len(reserved_colors)
datapoints = (datapoints - np.min(datapoints)) / (np.max(datapoints) - np.min(datapoints))
datapoints = datapoints / np.max(datapoints)
for i in range(0, n_unreserved):
if datapoints is not None:
v = int(np.round(datapoints[i] * 255))
else:
v = int(np.round(i / n_unreserved * 255))
if colormap_name == 'reds':
colormap.append(utils.rgba_to_hex((v,0,0,255)))
elif colormap_name == 'greens':
colormap.append(utils.rgba_to_hex((0,v,0,255)))
elif colormap_name == 'blues':
colormap.append(utils.rgba_to_hex((0,0,v,255)))
else:
raise Exception(f'{colormap_name} is not a valid colormap option')
colormap.extend(reserved_colors)
return colormap