figpack-spike-sorting 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

figpack_spike_sorting/views/TiledImage.py

@@ -0,0 +1,159 @@
+"""
+TiledImage view for figpack - displays large images using tiled rendering with deck.gl
+"""
+
+from io import BytesIO
+from tempfile import TemporaryDirectory
+from typing import Any, List, Union
+
+import numpy as np
+
+import figpack
+from ..spike_sorting_extension import spike_sorting_extension
+
+pyvips_installation_msg = "To use TiledImage you need to install pyvips (conda install -c conda-forge pyvips recommended)"
+
+
+class TiledImageLayer:
+    def __init__(self, label: str, data: Union[np.ndarray, Any]) -> None:
+        """
+        Initialize a TiledImageLayer
+
+        Args:
+            label: Label for the layer
+            data: Image data as numpy array (uint8, shape (height, width, 3) for RGB)
+                  or pyvips.Image object
+        """
+        try:
+            import pyvips
+        except ImportError:
+            raise ImportError(pyvips_installation_msg)
+
+        self.label = label
+        self.data = data
+
+        if isinstance(data, pyvips.Image):
+            image: pyvips.Image = data
+        else:
+            if not isinstance(data, np.ndarray):
+                raise TypeError("Data must be a numpy array or pyvips.Image")
+            if data.dtype != np.uint8:
+                raise ValueError("Data must be of type uint8")
+            # Convert numpy array to pyvips image
+            image: pyvips.Image = pyvips.Image.new_from_array(data)
+
+        self.image = image
+
+
+class TiledImage(figpack.ExtensionView):
+    """
+    A view that displays large images using tiled rendering for efficient viewing
+    """
+
+    def __init__(
+        self, *, tile_size: int, layers: List[TiledImageLayer], verbose: bool = False
+    ):
+        """
+        Initialize a TiledImage view
+
+        Args:
+            tile_size: Size of each tile in pixels (e.g., 256)
+            layers: List of TiledImageLayer objects
+            verbose: Whether to print verbose output during tile generation
+        """
+        super().__init__(
+            extension=spike_sorting_extension, view_type="spike_sorting.TiledImage"
+        )
+        self.tile_size = tile_size
+        self.layers = layers
+        self.verbose = verbose
+
+    def write_to_zarr_group(self, group: figpack.Group) -> None:
+        """
+        Write the TiledImage data to a Zarr group
+
+        Args:
+            group: Zarr group to write data into
+        """
+        import os
+        import pyvips
+
+        super().write_to_zarr_group(group)
+
+        group.attrs["tile_size"] = self.tile_size
+        group.attrs["num_layers"] = len(self.layers)
+
+        for layer_idx, layer in enumerate(self.layers):
+            if self.verbose:
+                print(
+                    f"Processing layer {layer_idx + 1}/{len(self.layers)}: {layer.label}"
+                )
+
+            layer_group = group.create_group(f"layer_{layer_idx}")
+            layer_group.attrs["label"] = layer.label
+
+            image: pyvips.Image = layer.image
+            layer_group.attrs["width"] = image.width
+            layer_group.attrs["height"] = image.height
+
+            # Generate tiled JPEG images using pyvips dzsave
+            with TemporaryDirectory() as tmpdir:
+                # Generate the tile pyramid
+                image.dzsave(
+                    f"{tmpdir}/output",
+                    overlap=0,
+                    tile_size=self.tile_size,
+                    layout=pyvips.enums.ForeignDzLayout.DZ,
+                )
+
+                output_dirname = f"{tmpdir}/output_files"
+
+                # Count zoom levels
+                num_zoom_levels = 0
+                z = 1
+                while True:
+                    dirname = f"{output_dirname}/{z}"
+                    if not os.path.exists(dirname):
+                        break
+                    num_zoom_levels = z
+                    z += 1
+
+                layer_group.attrs["num_zoom_levels"] = num_zoom_levels
+
+                # Store each tile as a zarr dataset containing JPEG bytes
+                tiles_group = layer_group.create_group("tiles")
+
+                for z in range(1, num_zoom_levels + 1):
+                    dirname = f"{output_dirname}/{z}"
+                    j = 0
+                    while True:
+                        if not os.path.exists(f"{dirname}/{j}_0.jpeg"):
+                            break
+                        k = 0
+                        while True:
+                            tile_path = f"{dirname}/{j}_{k}.jpeg"
+                            if not os.path.exists(tile_path):
+                                break
+
+                            # Read the JPEG file as bytes
+                            with open(tile_path, "rb") as f:
+                                jpeg_bytes = f.read()
+
+                            # Store as uint8 array in zarr
+                            tile_key = f"{z}_{j}_{k}"
+                            jpeg_array = np.frombuffer(jpeg_bytes, dtype=np.uint8)
+                            tiles_group.create_dataset(tile_key, data=jpeg_array)
+
+                            if self.verbose:
+                                print(
+                                    f"  Stored tile {tile_key}: {len(jpeg_bytes)} bytes"
+                                )
+
+                            k += 1
+                        j += 1
+
+                if self.verbose:
+                    print(
+                        f"  Layer {layer.label}: {image.width}x{image.height}, "
+                        f"{num_zoom_levels} zoom levels"
+                    )

figpack_spike_sorting/views/__init__.py

@@ -20,6 +20,7 @@ from .UnitMetricsGraph import (
     UnitMetricsGraphUnit,
 )
 from .SortingCuration import SortingCuration
+from .TiledImage import TiledImage, TiledImageLayer
 
 __all__ = [
     "Autocorrelograms",
@@ -42,4 +43,6 @@ __all__ = [
     "UnitMetricsGraphMetric",
     "UnitMetricsGraphUnit",
     "SortingCuration",
+    "TiledImage",
+    "TiledImageLayer",
 ]

{figpack_spike_sorting-0.1.6.dist-info → figpack_spike_sorting-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack_spike_sorting
-Version: 0.1.6
+Version: 0.1.8
 Summary: Spike Sorting specific extension for figpack
 Home-page: https://github.com/flatironinstitute/figpack
 Author: figpack contributors

{figpack_spike_sorting-0.1.6.dist-info → figpack_spike_sorting-0.1.8.dist-info}/RECORD

@@ -1,5 +1,5 @@
-figpack_spike_sorting/__init__.py,sha256=XWtb7794TixjHJDii3OeYOdM-GYVLsR0BEfiUMEP_vQ,100
-figpack_spike_sorting/figpack_spike_sorting.js,sha256=qxu-lFeqfIkWaRrZ9OX_MMjSrZ8zbD4Nz94kCoPmaRU,663123
+figpack_spike_sorting/__init__.py,sha256=X3iWqqx6ep-Gznn4FbdnV5eUsflN-q7z-JiF4IalB3M,100
+figpack_spike_sorting/figpack_spike_sorting.js,sha256=D3FB0vIMOM3WN-P5VUIZZIVI4iBMp7NjXpwSis5gMkw,1509907
 figpack_spike_sorting/spike_sorting_extension.py,sha256=ugpk8hDsO4RmyQRNjfhB4Pw5p10FmhQeu3koBynSPHU,755
 figpack_spike_sorting/style.css,sha256=R4pcnrpSMpOsBn7X1t-JBP8ODktsc5e8o95Fl_0LVps,3208
 figpack_spike_sorting/views/AutocorrelogramItem.py,sha256=qHmvIdHpbfVA_utPb5N2oP3hSP2cGnlT8VLaxOXV4UM,738
@@ -12,14 +12,15 @@ figpack_spike_sorting/views/RasterPlotItem.py,sha256=iW7fuDEjSfvf5YMIwrF_6cmKvD7
 figpack_spike_sorting/views/SortingCuration.py,sha256=J3p9vrhbnRt05qeihZk_i6EBWDcTGYs293WVW_9qLSk,1243
 figpack_spike_sorting/views/SpikeAmplitudes.py,sha256=H_VV0Z1kAVCztNaTYnOW8tqyu6FLtgFPWNrlmokVKeI,13290
 figpack_spike_sorting/views/SpikeAmplitudesItem.py,sha256=j5Na-diY-vRUAPu0t0VkyFCSKFnQ_f5HT077mB3Cy8c,1134
+figpack_spike_sorting/views/TiledImage.py,sha256=_nvFhvRoGWd7MN84d9CphB0bK4j0txlx035zm-hCDic,5457
 figpack_spike_sorting/views/UnitLocations.py,sha256=K18oJFnKshn0fZ9NtgKXcWGroJGc_OaF3f_ZEEInZPA,2336
 figpack_spike_sorting/views/UnitMetricsGraph.py,sha256=8YZo2-5d-RHKSfyUKYAfDvW9hZDCTzmnUAyb3fPWo3I,3373
 figpack_spike_sorting/views/UnitSimilarityScore.py,sha256=cJA9MkETos9qHhV1tqgA7SfNEaPo-duXYCE76hSFGnA,948
 figpack_spike_sorting/views/UnitsTable.py,sha256=8aluJ2tCnwsFOLbjbJDyY2z1ml9VK7Sz5_bxdRUAeDI,2758
 figpack_spike_sorting/views/UnitsTableColumn.py,sha256=zBnuoeILTuiVLDvtcOxqa37E5WlbR12rlwNJUeWXxY4,847
 figpack_spike_sorting/views/UnitsTableRow.py,sha256=rEb2hMTA_pl2fTW1nOvnGir0ysfNx4uww3aekZzfWjk,720
-figpack_spike_sorting/views/__init__.py,sha256=m7XRK-rCsqXXbNtilncHsUzDK09j3gWeTqfYWUs9_jM,1316
-figpack_spike_sorting-0.1.6.dist-info/METADATA,sha256=AFNFDdpxitRyp26XLKnKAh5E4Cyd0nq-ZV8J_a2m6rE,1218
-figpack_spike_sorting-0.1.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-figpack_spike_sorting-0.1.6.dist-info/top_level.txt,sha256=CAkWrQc1wGK5laYDkT2GBjGgAuNwWNXKodTQlTcpxus,22
-figpack_spike_sorting-0.1.6.dist-info/RECORD,,
+figpack_spike_sorting/views/__init__.py,sha256=gUt261Id35gNiJyne6GY-NzIGyTfRDmL25tNjyC2dLY,1409
+figpack_spike_sorting-0.1.8.dist-info/METADATA,sha256=48QIQNnjJ4_RpsX7uhn7fvtKN8kpJepvtM4Lxj1U78U,1218
+figpack_spike_sorting-0.1.8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+figpack_spike_sorting-0.1.8.dist-info/top_level.txt,sha256=CAkWrQc1wGK5laYDkT2GBjGgAuNwWNXKodTQlTcpxus,22
+figpack_spike_sorting-0.1.8.dist-info/RECORD,,

{figpack_spike_sorting-0.1.6.dist-info → figpack_spike_sorting-0.1.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any