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basic image volume #401

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81 changes: 81 additions & 0 deletions examples/notebooks/volume.ipynb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,81 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "737b7aee-8cfb-47f0-b595-bc3749e995ea",
"metadata": {},
"outputs": [],
"source": [
"import fastplotlib as fpl\n",
"import imageio.v3 as iio\n",
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "92d3b41a-2d38-40b7-9156-1755711d4964",
"metadata": {},
"outputs": [],
"source": [
"voldata = iio.imread(\"imageio:stent.npz\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ef67db3d-484d-40c5-9725-f54b4f99d1d7",
"metadata": {},
"outputs": [],
"source": [
"voldata.dtype"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "28efdd55-a6fd-4ffd-a934-7a0b759cee96",
"metadata": {},
"outputs": [],
"source": [
"plot = fpl.Plot(camera=\"3d\")\n",
"\n",
"plot.add_volume(voldata)\n",
"\n",
"plot.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "80df1d1c-5ff7-4174-aeb7-4dbb534fd33f",
"metadata": {},
"outputs": [],
"source": [
"plot.controller = \"orbit\""
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.3"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
3 changes: 2 additions & 1 deletion fastplotlib/graphics/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
from .line import LineGraphic
from .scatter import ScatterGraphic
from .image import ImageGraphic, HeatmapGraphic
from .image import ImageGraphic, HeatmapGraphic, VolumeGraphic
from .text import TextGraphic
from .line_collection import LineCollection, LineStack

__all__ = [
"ImageGraphic",
"VolumeGraphic",
"ScatterGraphic",
"LineGraphic",
"HeatmapGraphic",
Expand Down
150 changes: 141 additions & 9 deletions fastplotlib/graphics/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,8 @@ def __init__(
vmin: int = None,
vmax: int = None,
cmap: str = "plasma",
filter: str = "nearest",
interpolation: str = "nearest",
map_interpolation: str = "linear",
isolated_buffer: bool = True,
*args,
**kwargs,
Expand All @@ -228,8 +229,11 @@ def __init__(
cmap: str, optional, default "plasma"
colormap to use to display the image data, ignored if data is RGB

filter: str, optional, default "nearest"
interpolation filter, one of "nearest" or "linear"
interpolation: str, optional, default "nearest"
interpolation of the data, one of "nearest" or "linear"

map_interpolation: str, optional, default "nearest"
interpolation of the cmap, one of "nearest" or "linear"

isolated_buffer: bool, default True
If True, initialize a buffer with the same shape as the input data and then
Expand Down Expand Up @@ -282,12 +286,16 @@ def __init__(
# if data is RGB or RGBA
if data.ndim > 2:
material = pygfx.ImageBasicMaterial(
clim=(vmin, vmax), map_interpolation=filter
clim=(vmin, vmax),
interpolation=interpolation,
map_interpolation=map_interpolation
)
# if data is just 2D without color information, use colormap LUT
else:
material = pygfx.ImageBasicMaterial(
clim=(vmin, vmax), map=self.cmap(), map_interpolation=filter
clim=(vmin, vmax), map=self.cmap(),
interpolation=interpolation,
map_interpolation=map_interpolation
)

world_object = pygfx.Image(geometry, material)
Expand Down Expand Up @@ -356,7 +364,8 @@ def __init__(
vmin: int = None,
vmax: int = None,
cmap: str = "plasma",
filter: str = "nearest",
interpolation: str = "nearest",
map_interpolation: str = "linear",
chunk_size: int = 8192,
isolated_buffer: bool = True,
*args,
Expand All @@ -381,8 +390,11 @@ def __init__(
cmap: str, optional, default "plasma"
colormap to use to display the data

filter: str, optional, default "nearest"
interpolation filter, one of "nearest" or "linear"
interpolation: str, optional, default "nearest"
interpolation of the data, one of "nearest" or "linear"

map_interpolation: str, optional, default "nearest"
interpolation of the cmap, one of "nearest" or "linear"

chunk_size: int, default 8192, max 8192
chunk size for each tile used to make up the heatmap texture
Expand Down Expand Up @@ -446,7 +458,10 @@ def __init__(

self.cmap = HeatmapCmapFeature(self, cmap)
self._material = pygfx.ImageBasicMaterial(
clim=(vmin, vmax), map=self.cmap(), map_interpolation=filter
clim=(vmin, vmax),
map=self.cmap(),
interpolation=interpolation,
map_interpolation=map_interpolation,
)

for start, stop, chunk in zip(start_ixs, stop_ixs, chunks):
Expand Down Expand Up @@ -485,3 +500,120 @@ def set_feature(self, feature: str, new_data: Any, indices: Any):

def reset_feature(self, feature: str):
pass


class VolumeGraphic(Graphic, Interaction):
feature_events = ("data", "cmap", "present")

def __init__(
self,
data: Any,
vmin: float = None,
vmax: float = None,
cmap: str = "plasma",
interpolation: str = "nearest",
map_interpolation: str = "linear",
isolated_buffer: bool = True,
*args,
**kwargs,
):
"""
Create an Image Volume Graphic

Parameters
----------
data: array-like
array-like, usually numpy.ndarray, must support ``memoryview()``
Tensorflow Tensors also work **probably**, but not thoroughly tested
| shape must be ``[x_dim, y_dim]`` or ``[x_dim, y_dim, rgb]``

vmin: int, optional
minimum value for color scaling, calculated from data if not provided

vmax: int, optional
maximum value for color scaling, calculated from data if not provided

cmap: str, optional, default "plasma"
colormap to use to display the image data, ignored if data is RGB

interpolation: str, optional, default "nearest"
interpolation of the data, one of "nearest" or "linear"

map_interpolation: str, optional, default "nearest"
interpolation of the cmap, one of "nearest" or "linear"

isolated_buffer: bool, default True
If True, initialize a buffer with the same shape as the input data and then
set the data, useful if the data arrays are ready-only such as memmaps.
If False, the input array is itself used as the buffer.

args:
additional arguments passed to Graphic

kwargs:
additional keyword arguments passed to Graphic

Features
--------

**data**: :class:`.ImageDataFeature`
Manages the data buffer displayed in the ImageGraphic

**cmap**: :class:`.ImageCmapFeature`
Manages the colormap

**present**: :class:`.PresentFeature`
Control the presence of the Graphic in the scene

"""

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

data = to_gpu_supported_dtype(data)

# TODO: we need to organize and do this better
if isolated_buffer:
# initialize a buffer with the same shape as the input data
# we do not directly use the input data array as the buffer
# because if the input array is a read-only type, such as
# numpy memmaps, we would not be able to change the image data
buffer_init = np.zeros(shape=data.shape, dtype=data.dtype)
else:
buffer_init = data

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

texture = pygfx.Texture(buffer_init, dim=3)

geometry = pygfx.Geometry(grid=texture)

self.cmap = ImageCmapFeature(self, cmap)

material = pygfx.VolumeRayMaterial(
clim=(vmin, vmax),
map=self.cmap(),
interpolation=interpolation,
map_interpolation=map_interpolation
)

world_object = pygfx.Volume(
geometry,
material
)

self._set_world_object(world_object)

self.cmap.vmin = vmin
self.cmap.vmax = vmax

self.data = ImageDataFeature(self, data)

if isolated_buffer:
self.data = data

def set_feature(self, feature: str, new_data: Any, indices: Any):
pass

def reset_feature(self, feature: str):
pass
65 changes: 61 additions & 4 deletions fastplotlib/layouts/graphic_methods_mixin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ def add_heatmap(self, data: Any, vmin: int = None, vmax: int = None, cmap: str =
"""
return self._create_graphic(HeatmapGraphic, data, vmin, vmax, cmap, filter, chunk_size, isolated_buffer, *args, **kwargs)

def add_image(self, data: Any, vmin: int = None, vmax: int = None, cmap: str = 'plasma', filter: str = 'nearest', isolated_buffer: bool = True, *args, **kwargs) -> ImageGraphic:
def add_image(self, data: Any, vmin: int = None, vmax: int = None, cmap: str = 'plasma', interpolation: str = 'nearest', map_interpolation: str = 'linear', isolated_buffer: bool = True, *args, **kwargs) -> ImageGraphic:
"""

Create an Image Graphic
Expand All @@ -103,8 +103,11 @@ def add_image(self, data: Any, vmin: int = None, vmax: int = None, cmap: str = '
cmap: str, optional, default "plasma"
colormap to use to display the image data, ignored if data is RGB

filter: str, optional, default "nearest"
interpolation filter, one of "nearest" or "linear"
interpolation: str, optional, default "nearest"
interpolation of the data, one of "nearest" or "linear"

map_interpolation: str, optional, default "nearest"
interpolation of the cmap, one of "nearest" or "linear"

isolated_buffer: bool, default True
If True, initialize a buffer with the same shape as the input data and then
Expand All @@ -131,7 +134,7 @@ def add_image(self, data: Any, vmin: int = None, vmax: int = None, cmap: str = '


"""
return self._create_graphic(ImageGraphic, data, vmin, vmax, cmap, filter, isolated_buffer, *args, **kwargs)
return self._create_graphic(ImageGraphic, data, vmin, vmax, cmap, interpolation, map_interpolation, isolated_buffer, *args, **kwargs)

def add_line_collection(self, data: List[numpy.ndarray], z_position: Union[List[float], float] = None, thickness: Union[float, List[float]] = 2.0, colors: Union[List[numpy.ndarray], numpy.ndarray] = 'w', alpha: float = 1.0, cmap: Union[List[str], str] = None, cmap_values: Union[numpy.ndarray, List] = None, name: str = None, metadata: Union[list, tuple, numpy.ndarray] = None, *args, **kwargs) -> LineCollection:
"""
Expand Down Expand Up @@ -409,3 +412,57 @@ def add_text(self, text: str, position: Tuple[int] = (0, 0, 0), size: int = 14,
"""
return self._create_graphic(TextGraphic, text, position, size, face_color, outline_color, outline_thickness, screen_space, anchor, *args, **kwargs)

def add_volume(self, data: Any, vmin: float = None, vmax: float = None, cmap: str = 'plasma', interpolation: str = 'nearest', map_interpolation: str = 'linear', isolated_buffer: bool = True, *args, **kwargs) -> VolumeGraphic:
"""

Create an Image Volume Graphic

Parameters
----------
data: array-like
array-like, usually numpy.ndarray, must support ``memoryview()``
Tensorflow Tensors also work **probably**, but not thoroughly tested
| shape must be ``[x_dim, y_dim]`` or ``[x_dim, y_dim, rgb]``

vmin: int, optional
minimum value for color scaling, calculated from data if not provided

vmax: int, optional
maximum value for color scaling, calculated from data if not provided

cmap: str, optional, default "plasma"
colormap to use to display the image data, ignored if data is RGB

interpolation: str, optional, default "nearest"
interpolation of the data, one of "nearest" or "linear"

map_interpolation: str, optional, default "nearest"
interpolation of the cmap, one of "nearest" or "linear"

isolated_buffer: bool, default True
If True, initialize a buffer with the same shape as the input data and then
set the data, useful if the data arrays are ready-only such as memmaps.
If False, the input array is itself used as the buffer.

args:
additional arguments passed to Graphic

kwargs:
additional keyword arguments passed to Graphic

Features
--------

**data**: :class:`.ImageDataFeature`
Manages the data buffer displayed in the ImageGraphic

**cmap**: :class:`.ImageCmapFeature`
Manages the colormap

**present**: :class:`.PresentFeature`
Control the presence of the Graphic in the scene


"""
return self._create_graphic(VolumeGraphic, data, vmin, vmax, cmap, interpolation, map_interpolation, isolated_buffer, *args, **kwargs)