Merge pull request #143 from kushalkolar/large-images

HeatmapGraphic, supports dims larger than 8192

fastplotlib/graphics/__init__.py

@@ -1,8 +1,8 @@
 from .histogram import HistogramGraphic
 from .line import LineGraphic
 from .scatter import ScatterGraphic
-from .image import ImageGraphic
-from .heatmap import HeatmapGraphic
+from .image import ImageGraphic, HeatmapGraphic
+# from .heatmap import HeatmapGraphic
 from .text import TextGraphic
 from .line_collection import LineCollection, LineStack
 

fastplotlib/graphics/features/__init__.py

@@ -1,5 +1,5 @@
-from ._colors import ColorFeature, CmapFeature, ImageCmapFeature
-from ._data import PointsDataFeature, ImageDataFeature
+from ._colors import ColorFeature, CmapFeature, ImageCmapFeature, HeatmapCmapFeature
+from ._data import PointsDataFeature, ImageDataFeature, HeatmapDataFeature
 from ._present import PresentFeature
 from ._thickness import ThicknessFeature
 from ._base import GraphicFeature, GraphicFeatureIndexable

fastplotlib/graphics/features/_base.py

@@ -7,6 +7,33 @@
 from pygfx import Buffer
 
 
+supported_dtypes = [
+    np.uint8,
+    np.uint16,
+    np.uint32,
+    np.int8,
+    np.int16,
+    np.int32,
+    np.float16,
+    np.float32
+]
+
+
+def to_gpu_supported_dtype(array):
+    if isinstance(array, np.ndarray):
+        if array.dtype not in supported_dtypes:
+            if np.issubdtype(array.dtype, np.integer):
+                warn(f"converting {array.dtype} array to int32")
+                return array.astype(np.int32)
+            elif np.issubdtype(array.dtype, np.floating):
+                warn(f"converting {array.dtype} array to float32")
+                return array.astype(np.float32, copy=False)
+            else:
+                raise TypeError("Unsupported type, supported array types must be int or float dtypes")
+
+    return array
+
+
 class FeatureEvent:
     """
     type: <feature_name>, example: "colors"
@@ -43,7 +70,7 @@ def __init__(self, parent, data: Any, collection_index: int = None):
         """
         self._parent = parent
         if isinstance(data, np.ndarray):
-            data = data.astype(np.float32)
+            data = to_gpu_supported_dtype(data)
 
         self._data = data
 
@@ -227,3 +254,4 @@ def _update_range_indices(self, key):
                     self._buffer.update_range(ix, size=1)
         else:
             raise TypeError("must pass int or slice to update range")
+

fastplotlib/graphics/features/_colors.py

@@ -238,3 +238,16 @@ def _feature_changed(self, key, new_data):
         event_data = FeatureEvent(type="cmap", pick_info=pick_info)
 
         self._call_event_handlers(event_data)
+
+
+class HeatmapCmapFeature(ImageCmapFeature):
+    """
+    Colormap for HeatmapGraphic
+    """
+
+    def _set(self, cmap_name: str):
+        self._parent._material.map.texture.data[:] = make_colors(256, cmap_name)
+        self._parent._material.map.texture.update_range((0, 0, 0), size=(256, 1, 1))
+        self.name = cmap_name
+
+        self._feature_changed(key=None, new_data=self.name)

fastplotlib/graphics/features/_data.py

@@ -3,14 +3,7 @@
 import numpy as np
 from pygfx import Buffer, Texture
 
-from ._base import GraphicFeatureIndexable, cleanup_slice, FeatureEvent
-
-
-def to_float32(array):
-    if isinstance(array, np.ndarray):
-        return array.astype(np.float32, copy=False)
-
-    return array
+from ._base import GraphicFeatureIndexable, cleanup_slice, FeatureEvent, to_gpu_supported_dtype
 
 
 class PointsDataFeature(GraphicFeatureIndexable):
@@ -102,7 +95,7 @@ def __init__(self, parent, data: Any):
                 "``[x_dim, y_dim]`` or ``[x_dim, y_dim, rgb]``"
             )
 
-        data = to_float32(data)
+        data = to_gpu_supported_dtype(data)
         super(ImageDataFeature, self).__init__(parent, data)
 
     @property
@@ -114,7 +107,7 @@ def __getitem__(self, item):
 
     def __setitem__(self, key, value):
         # make sure float32
-        value = to_float32(value)
+        value = to_gpu_supported_dtype(value)
 
         self._buffer.data[key] = value
         self._update_range(key)
@@ -145,3 +138,47 @@ def _feature_changed(self, key, new_data):
         event_data = FeatureEvent(type="data", pick_info=pick_info)
 
         self._call_event_handlers(event_data)
+
+
+class HeatmapDataFeature(ImageDataFeature):
+    @property
+    def _buffer(self) -> List[Texture]:
+        return [img.geometry.grid.texture for img in self._parent.world_object.children]
+
+    def __getitem__(self, item):
+        return self._data[item]
+
+    def __setitem__(self, key, value):
+        # make sure supported type, not float64 etc.
+        value = to_gpu_supported_dtype(value)
+
+        self._data[key] = value
+        self._update_range(key)
+
+        # avoid creating dicts constantly if there are no events to handle
+        if len(self._event_handlers) > 0:
+            self._feature_changed(key, value)
+
+    def _update_range(self, key):
+        for buffer in self._buffer:
+            buffer.update_range((0, 0, 0), size=buffer.size)
+
+    def _feature_changed(self, key, new_data):
+        if key is not None:
+            key = cleanup_slice(key, self._upper_bound)
+        if isinstance(key, int):
+            indices = [key]
+        elif isinstance(key, slice):
+            indices = range(key.start, key.stop, key.step)
+        elif key is None:
+            indices = None
+
+        pick_info = {
+            "index": indices,
+            "world_object": self._parent.world_object,
+            "new_data": new_data
+        }
+
+        event_data = FeatureEvent(type="data", pick_info=pick_info)
+
+        self._call_event_handlers(event_data)

fastplotlib/graphics/image.py

@@ -1,9 +1,12 @@
 from typing import *
+from math import ceil
+from itertools import product
 
 import pygfx
+from pygfx.utils import unpack_bitfield
 
 from ._base import Graphic, Interaction, PreviouslyModifiedData
-from .features import ImageCmapFeature, ImageDataFeature
+from .features import ImageCmapFeature, ImageDataFeature, HeatmapDataFeature, HeatmapCmapFeature
 from ..utils import quick_min_max
 
 
@@ -119,5 +122,176 @@ def _reset_feature(self, feature: str):
         pass
 
 
+class _ImageTile(pygfx.Image):
+    """
+    Similar to pygfx.Image, only difference is that it contains a few properties to keep track of
+    row chunk index, column chunk index
 
 
+    """
+    def _wgpu_get_pick_info(self, pick_value):
+        tex = self.geometry.grid
+        if hasattr(tex, "texture"):
+            tex = tex.texture  # tex was a view
+        # This should match with the shader
+        values = unpack_bitfield(pick_value, wobject_id=20, x=22, y=22)
+        x = values["x"] / 4194304 * tex.size[0] - 0.5
+        y = values["y"] / 4194304 * tex.size[1] - 0.5
+        ix, iy = int(x + 0.5), int(y + 0.5)
+        return {
+            "index": (ix, iy),
+            "pixel_coord": (x - ix, y - iy),
+            "row_chunk_index": self.row_chunk_index,
+            "col_chunk_index": self.col_chunk_index
+        }
+
+    @property
+    def row_chunk_index(self) -> int:
+        return self._row_chunk_index
+
+    @row_chunk_index.setter
+    def row_chunk_index(self, index: int):
+        self._row_chunk_index = index
+
+    @property
+    def col_chunk_index(self) -> int:
+        return self._col_chunk_index
+
+    @col_chunk_index.setter
+    def col_chunk_index(self, index: int):
+        self._col_chunk_index = index
+
+
+class HeatmapGraphic(Graphic, Interaction):
+    feature_events = (
+        "data",
+        "cmap",
+    )
+
+    def __init__(
+            self,
+            data: Any,
+            vmin: int = None,
+            vmax: int = None,
+            cmap: str = 'plasma',
+            filter: str = "nearest",
+            chunk_size: int = 8192,
+            *args,
+            **kwargs
+    ):
+        """
+        Create an Image 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]``
+        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 data
+        filter: str, optional, default "nearest"
+            interpolation filter, one of "nearest" or "linear"
+        chunk_size: int, default 8192, max 8192
+            chunk size for each tile used to make up the heatmap texture
+        args:
+            additional arguments passed to Graphic
+        kwargs:
+            additional keyword arguments passed to Graphic
+
+        Examples
+        --------
+        .. code-block:: python
+
+            from fastplotlib import Plot
+            # create a `Plot` instance
+            plot = Plot()
+            # make some random 2D image data
+            data = np.random.rand(512, 512)
+            # plot the image data
+            plot.add_image(data=data)
+            # show the plot
+            plot.show()
+        """
+
+        super().__init__(*args, **kwargs)
+
+        if chunk_size > 8192:
+            raise ValueError("Maximum chunk size is 8192")
+
+        self.data = HeatmapDataFeature(self, data)
+
+        row_chunks = range(ceil(data.shape[0] / chunk_size))
+        col_chunks = range(ceil(data.shape[1] / chunk_size))
+
+        chunks = list(product(row_chunks, col_chunks))
+        # chunks is the index position of each chunk
+
+        start_ixs = [list(map(lambda c: c * chunk_size, chunk)) for chunk in chunks]
+        stop_ixs = [list(map(lambda c: c + chunk_size, chunk)) for chunk in start_ixs]
+
+        self._world_object = pygfx.Group()
+
+        if (vmin is None) or (vmax is None):
+            vmin, vmax = quick_min_max(data)
+
+        self.cmap = HeatmapCmapFeature(self, cmap)
+        self._material = pygfx.ImageBasicMaterial(clim=(vmin, vmax), map=self.cmap())
+
+        for start, stop, chunk in zip(start_ixs, stop_ixs, chunks):
+            row_start, col_start = start
+            row_stop, col_stop = stop
+
+            # x and y positions of the Tile in world space coordinates
+            y_pos, x_pos = row_start, col_start
+
+            tex_view = pygfx.Texture(data[row_start:row_stop, col_start:col_stop], dim=2).get_view(filter=filter)
+            geometry = pygfx.Geometry(grid=tex_view)
+            # material = pygfx.ImageBasicMaterial(clim=(0, 1), map=self.cmap())
+
+            img = _ImageTile(geometry, self._material)
+
+            # row and column chunk index for this Tile
+            img.row_chunk_index = chunk[0]
+            img.col_chunk_index = chunk[1]
+
+            img.position.set_x(x_pos)
+            img.position.set_y(y_pos)
+
+            self.world_object.add(img)
+
+    @property
+    def vmin(self) -> float:
+        """Minimum contrast limit."""
+        return self._material.clim[0]
+
+    @vmin.setter
+    def vmin(self, value: float):
+        """Minimum contrast limit."""
+        self._material.clim = (
+            value,
+            self._material.clim[1]
+        )
+
+    @property
+    def vmax(self) -> float:
+        """Maximum contrast limit."""
+        return self._material.clim[1]
+
+    @vmax.setter
+    def vmax(self, value: float):
+        """Maximum contrast limit."""
+        self._material.clim = (
+            self._material.clim[0],
+            value
+        )
+
+    def _set_feature(self, feature: str, new_data: Any, indices: Any):
+        pass
+
+    def _reset_feature(self, feature: str):
+        pass

fastplotlib/layouts/_subplot.py

@@ -255,9 +255,6 @@ def add_graphic(self, graphic, center: bool = True):
         graphic.world_object.position.z = len(self._graphics)
         super(Subplot, self).add_graphic(graphic, center)
 
-        if isinstance(graphic, graphics.HeatmapGraphic):
-            self.controller.scale.y = copysign(self.controller.scale.y, -1)
-
     def set_axes_visibility(self, visible: bool):
         """Toggles axes visibility."""
         if visible: