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Commit 63fe7b7

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kushalkolarkushalkolar
authored
Merge pull request #150 from kushalkolar/better-buffer-handling
better buffer handling
2 parents 9484594 + 216216a commit 63fe7b7
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4 files changed

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‎fastplotlib/graphics/features/_base.py

Copy file name to clipboardExpand all lines: fastplotlib/graphics/features/_base.py
+5-5Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
from typing import *
55

66
import numpy as np
7-
from pygfx import Buffer
7+
from pygfx import Buffer, Texture
88

99

1010
supported_dtypes = [
@@ -226,7 +226,7 @@ def _update_range(self, key):
226226

227227
@property
228228
@abstractmethod
229-
def _buffer(self) -> Buffer:
229+
def buffer(self) -> Union[Buffer, Texture]:
230230
pass
231231

232232
@property
@@ -238,21 +238,21 @@ def _update_range_indices(self, key):
238238
key = cleanup_slice(key, self._upper_bound)
239239

240240
if isinstance(key, int):
241-
self._buffer.update_range(key, size=1)
241+
self.buffer.update_range(key, size=1)
242242
return
243243

244244
# else if it's a slice obj
245245
if isinstance(key, slice):
246246
if key.step == 1: # we cleaned up the slice obj so step of None becomes 1
247247
# update range according to size using the offset
248-
self._buffer.update_range(offset=key.start, size=key.stop - key.start)
248+
self.buffer.update_range(offset=key.start, size=key.stop - key.start)
249249

250250
else:
251251
step = key.step
252252
# convert slice to indices
253253
ixs = range(key.start, key.stop, step)
254254
for ix in ixs:
255-
self._buffer.update_range(ix, size=1)
255+
self.buffer.update_range(ix, size=1)
256256
else:
257257
raise TypeError("must pass int or slice to update range")
258258

‎fastplotlib/graphics/features/_colors.py

Copy file name to clipboardExpand all lines: fastplotlib/graphics/features/_colors.py
+4-4Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,11 @@
77

88
class ColorFeature(GraphicFeatureIndexable):
99
@property
10-
def _buffer(self):
10+
def buffer(self):
1111
return self._parent.world_object.geometry.colors
1212

1313
def __getitem__(self, item):
14-
return self._buffer.data[item]
14+
return self.buffer.data[item]
1515

1616
def __init__(self, parent, colors, n_colors: int, alpha: float = 1.0, collection_index: int = None):
1717
"""
@@ -113,7 +113,7 @@ def __setitem__(self, key, value):
113113
raise ValueError("fancy indexing for colors must be 2-dimension, i.e. [n_datapoints, RGBA]")
114114

115115
# set the user passed data directly
116-
self._buffer.data[key] = value
116+
self.buffer.data[key] = value
117117

118118
# update range
119119
# first slice obj is going to be the indexing so use key[0]
@@ -162,7 +162,7 @@ def __setitem__(self, key, value):
162162
else:
163163
raise ValueError("numpy array passed to color must be of shape (4,) or (n_colors_modify, 4)")
164164

165-
self._buffer.data[key] = new_colors
165+
self.buffer.data[key] = new_colors
166166

167167
self._update_range(key)
168168
self._feature_changed(key, new_colors)

‎fastplotlib/graphics/features/_data.py

Copy file name to clipboardExpand all lines: fastplotlib/graphics/features/_data.py
+20-11Lines changed: 20 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
from typing import *
22

33
import numpy as np
4-
from pygfx import Buffer, Texture
4+
from pygfx import Buffer, Texture, TextureView
55

66
from ._base import GraphicFeatureIndexable, cleanup_slice, FeatureEvent, to_gpu_supported_dtype
77

@@ -16,11 +16,11 @@ def __init__(self, parent, data: Any, collection_index: int = None):
1616
super(PointsDataFeature, self).__init__(parent, data, collection_index=collection_index)
1717

1818
@property
19-
def _buffer(self) -> Buffer:
19+
def buffer(self) -> Buffer:
2020
return self._parent.world_object.geometry.positions
2121

2222
def __getitem__(self, item):
23-
return self._buffer.data[item]
23+
return self.buffer.data[item]
2424

2525
def _fix_data(self, data, parent):
2626
graphic_type = parent.__class__.__name__
@@ -54,7 +54,7 @@ def __setitem__(self, key, value):
5454
# otherwise assume that they have the right shape
5555
# numpy will throw errors if it can't broadcast
5656

57-
self._buffer.data[key] = value
57+
self.buffer.data[key] = value
5858
self._update_range(key)
5959
# avoid creating dicts constantly if there are no events to handle
6060
if len(self._event_handlers) > 0:
@@ -97,29 +97,33 @@ def __init__(self, parent, data: Any):
9797
"``[x_dim, y_dim]`` or ``[x_dim, y_dim, rgb]``"
9898
)
9999

100-
data = to_gpu_supported_dtype(data)
101100
super(ImageDataFeature, self).__init__(parent, data)
102101

103102
@property
104-
def _buffer(self) -> Texture:
103+
def buffer(self) -> Texture:
104+
"""Texture buffer for the image data"""
105105
return self._parent.world_object.geometry.grid.texture
106106

107+
def update_gpu(self):
108+
"""Update the GPU with the buffer"""
109+
self._update_range(None)
110+
107111
def __getitem__(self, item):
108-
return self._buffer.data[item]
112+
return self.buffer.data[item]
109113

110114
def __setitem__(self, key, value):
111115
# make sure float32
112116
value = to_gpu_supported_dtype(value)
113117

114-
self._buffer.data[key] = value
118+
self.buffer.data[key] = value
115119
self._update_range(key)
116120

117121
# avoid creating dicts constantly if there are no events to handle
118122
if len(self._event_handlers) > 0:
119123
self._feature_changed(key, value)
120124

121125
def _update_range(self, key):
122-
self._buffer.update_range((0, 0, 0), size=self._buffer.size)
126+
self.buffer.update_range((0, 0, 0), size=self.buffer.size)
123127

124128
def _feature_changed(self, key, new_data):
125129
if key is not None:
@@ -144,9 +148,14 @@ def _feature_changed(self, key, new_data):
144148

145149
class HeatmapDataFeature(ImageDataFeature):
146150
@property
147-
def _buffer(self) -> List[Texture]:
151+
def buffer(self) -> List[Texture]:
152+
"""list of Texture buffer for the image data"""
148153
return [img.geometry.grid.texture for img in self._parent.world_object.children]
149154

155+
def update_gpu(self):
156+
"""Update the GPU with the buffer"""
157+
self._update_range(None)
158+
150159
def __getitem__(self, item):
151160
return self._data[item]
152161

@@ -162,7 +171,7 @@ def __setitem__(self, key, value):
162171
self._feature_changed(key, value)
163172

164173
def _update_range(self, key):
165-
for buffer in self._buffer:
174+
for buffer in self.buffer:
166175
buffer.update_range((0, 0, 0), size=buffer.size)
167176

168177
def _feature_changed(self, key, new_data):

‎fastplotlib/graphics/image.py

Copy file name to clipboardExpand all lines: fastplotlib/graphics/image.py
+51-6Lines changed: 51 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,13 @@
22
from math import ceil
33
from itertools import product
44

5+
import numpy as np
56
import pygfx
67
from pygfx.utils import unpack_bitfield
78

89
from ._base import Graphic, Interaction, PreviouslyModifiedData
910
from .features import ImageCmapFeature, ImageDataFeature, HeatmapDataFeature, HeatmapCmapFeature
11+
from .features._base import to_gpu_supported_dtype
1012
from ..utils import quick_min_max
1113

1214

@@ -23,6 +25,7 @@ def __init__(
2325
vmax: int = None,
2426
cmap: str = 'plasma',
2527
filter: str = "nearest",
28+
isolated_buffer: bool = True,
2629
*args,
2730
**kwargs
2831
):
@@ -43,6 +46,10 @@ def __init__(
4346
colormap to use to display the image data, ignored if data is RGB
4447
filter: str, optional, default "nearest"
4548
interpolation filter, one of "nearest" or "linear"
49+
isolated_buffer: bool, default True
50+
If True, initialize a buffer with the same shape as the input data and then
51+
set the data, useful if the data arrays are ready-only such as memmaps.
52+
If False, the input array is itself used as the buffer.
4653
args:
4754
additional arguments passed to Graphic
4855
kwargs:
@@ -65,20 +72,29 @@ def __init__(
6572

6673
super().__init__(*args, **kwargs)
6774

68-
self.data = ImageDataFeature(self, data)
75+
data = to_gpu_supported_dtype(data)
76+
77+
# TODO: we need to organize and do this better
78+
if isolated_buffer:
79+
# initialize a buffer with the same shape as the input data
80+
# we do not directly use the input data array as the buffer
81+
# because if the input array is a read-only type, such as
82+
# numpy memmaps, we would not be able to change the image data
83+
buffer_init = np.zeros(shape=data.shape, dtype=data.dtype)
84+
else:
85+
buffer_init = data
6986

7087
if (vmin is None) or (vmax is None):
7188
vmin, vmax = quick_min_max(data)
7289

73-
texture_view = pygfx.Texture(self.data(), dim=2).get_view(filter=filter)
90+
texture_view = pygfx.Texture(buffer_init, dim=2).get_view(filter=filter)
7491

7592
geometry = pygfx.Geometry(grid=texture_view)
7693

7794
# if data is RGB
78-
if self.data().ndim == 3:
95+
if data.ndim == 3:
7996
self.cmap = None
8097
material = pygfx.ImageBasicMaterial(clim=(vmin, vmax))
81-
8298
# if data is just 2D without color information, use colormap LUT
8399
else:
84100
self.cmap = ImageCmapFeature(self, cmap)
@@ -89,6 +105,13 @@ def __init__(
89105
material
90106
)
91107

108+
self.data = ImageDataFeature(self, data)
109+
# TODO: we need to organize and do this better
110+
if isolated_buffer:
111+
# if the buffer was initialized with zeros
112+
# set it with the actual data
113+
self.data = data
114+
92115
@property
93116
def vmin(self) -> float:
94117
"""Minimum contrast limit."""
@@ -176,6 +199,7 @@ def __init__(
176199
cmap: str = 'plasma',
177200
filter: str = "nearest",
178201
chunk_size: int = 8192,
202+
isolated_buffer: bool = True,
179203
*args,
180204
**kwargs
181205
):
@@ -198,6 +222,10 @@ def __init__(
198222
interpolation filter, one of "nearest" or "linear"
199223
chunk_size: int, default 8192, max 8192
200224
chunk size for each tile used to make up the heatmap texture
225+
isolated_buffer: bool, default True
226+
If True, initialize a buffer with the same shape as the input data and then
227+
set the data, useful if the data arrays are ready-only such as memmaps.
228+
If False, the input array is itself used as the buffer.
201229
args:
202230
additional arguments passed to Graphic
203231
kwargs:
@@ -223,7 +251,17 @@ def __init__(
223251
if chunk_size > 8192:
224252
raise ValueError("Maximum chunk size is 8192")
225253

226-
self.data = HeatmapDataFeature(self, data)
254+
data = to_gpu_supported_dtype(data)
255+
256+
# TODO: we need to organize and do this better
257+
if isolated_buffer:
258+
# initialize a buffer with the same shape as the input data
259+
# we do not directly use the input data array as the buffer
260+
# because if the input array is a read-only type, such as
261+
# numpy memmaps, we would not be able to change the image data
262+
buffer_init = np.zeros(shape=data.shape, dtype=data.dtype)
263+
else:
264+
buffer_init = data
227265

228266
row_chunks = range(ceil(data.shape[0] / chunk_size))
229267
col_chunks = range(ceil(data.shape[1] / chunk_size))
@@ -249,7 +287,7 @@ def __init__(
249287
# x and y positions of the Tile in world space coordinates
250288
y_pos, x_pos = row_start, col_start
251289

252-
tex_view = pygfx.Texture(data[row_start:row_stop, col_start:col_stop], dim=2).get_view(filter=filter)
290+
tex_view = pygfx.Texture(buffer_init[row_start:row_stop, col_start:col_stop], dim=2).get_view(filter=filter)
253291
geometry = pygfx.Geometry(grid=tex_view)
254292
# material = pygfx.ImageBasicMaterial(clim=(0, 1), map=self.cmap())
255293

@@ -264,6 +302,13 @@ def __init__(
264302

265303
self.world_object.add(img)
266304

305+
self.data = HeatmapDataFeature(self, buffer_init)
306+
# TODO: we need to organize and do this better
307+
if isolated_buffer:
308+
# if the buffer was initialized with zeros
309+
# set it with the actual data
310+
self.data = data
311+
267312
@property
268313
def vmin(self) -> float:
269314
"""Minimum contrast limit."""

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