Sc 45 instanseg

docs/api.md

@@ -57,6 +57,7 @@ Operations on image and labels layers.
     im.segment
     im.segment_points
     im.cellpose_callable
+    im.instanseg_callable
     im.add_grid_labels_layer
     im.expand_labels_layer
     im.align_labels_layers

setup.cfg

@@ -121,9 +121,7 @@ clustering =
     #napari-convpaint @ git+ssh://[email protected]/guiwitz/napari-convpaint.git
 
 instanseg =
-    instanseg
-    torchvision
-    monai
+    instanseg-torch
 
 [options.package_data]
 * = *.yaml

src/harpy/_tests/test_image/test_segmentation/test_segmentation.py

@@ -1,11 +1,13 @@
 import importlib.util
 
+import dask.array as da
 import dask.dataframe as dd
 import pandas as pd
 import pytest
 from dask.dataframe import DataFrame
 from spatialdata import SpatialData
 
+from harpy.image._image import _get_spatial_element
 from harpy.image.segmentation._segmentation import segment, segment_points
 from harpy.image.segmentation.segmentation_models._baysor import _dummy
 from harpy.image.segmentation.segmentation_models._cellpose import cellpose_callable
@@ -124,3 +126,40 @@ def test_segment_points(sdata_multi_c_no_backed: SpatialData):
         assert _output_labels_layer in sdata_multi_c_no_backed.labels
     for _output_shapes_layer in output_shapes_layer:
         assert _output_shapes_layer in sdata_multi_c_no_backed.shapes
+
+
+@pytest.mark.skipif(not importlib.util.find_spec("instanseg"), reason="requires the instanseg library")
+def test_segment_instanseg(sdata_multi_c_no_backed: SpatialData):
+    from instanseg import InstanSeg
+
+    from harpy.image.segmentation.segmentation_models._instanseg import instanseg_callable
+
+    instanseg_fluorescence = InstanSeg("fluorescence_nuclei_and_cells", verbosity=1, device="cpu")
+
+    output_labels_layer = ["labels_nuclei_instanseg", "labels_cells_instanseg"]
+    output_shapes_layer = ["shapes_nuclei_instanseg", "shapes_cells_instanseg"]
+    sdata_multi_c_no_backed = segment(
+        sdata_multi_c_no_backed,
+        img_layer="combine",
+        model=instanseg_callable,
+        output_labels_layer=output_labels_layer,
+        output_shapes_layer=output_shapes_layer,
+        labels_layer_align="labels_cells_instanseg",
+        trim=False,
+        chunks=50,
+        overwrite=True,
+        depth=30,
+        crd=[10, 110, 0, 100],
+        scale_factors=[2, 2, 2, 2],
+        instanseg_model=instanseg_fluorescence,
+        output="all_outputs",
+    )
+
+    for _output_labels_layer in output_labels_layer:
+        assert _output_labels_layer in sdata_multi_c_no_backed.labels
+    for _output_shapes_layer in output_shapes_layer:
+        assert _output_shapes_layer in sdata_multi_c_no_backed.shapes
+
+    for _output_labels_layer in output_labels_layer:
+        se = _get_spatial_element(sdata_multi_c_no_backed, layer=output_labels_layer[0])
+        assert da.any(se.data).compute()

src/harpy/_tests/test_notebooks.py

@@ -116,10 +116,8 @@ def test_notebooks_flowsom(notebook):
 
 @pytest.mark.skip
 @pytest.mark.skipif(
-    not importlib.util.find_spec("InstanSeg")
-    or not importlib.util.find_spec("monai")
-    or not importlib.util.find_spec("torchvision"),
-    reason="requires the InstanSeg, monai and torchvision libraries",
+    not importlib.util.find_spec("instanseg"),
+    reason="requires the instanseg library",
 )
 @pytest.mark.parametrize(
     "notebook",

src/harpy/image/__init__.py

@@ -23,3 +23,4 @@
 )
 from .segmentation._segmentation import segment, segment_points
 from .segmentation.segmentation_models._cellpose import cellpose_callable
+from .segmentation.segmentation_models._instanseg import instanseg_callable

src/harpy/image/segmentation/_align_masks.py

@@ -1,24 +1,11 @@
 from __future__ import annotations
 
-from typing import Any
-
-import dask.array as da
 import numpy as np
-from dask.array import Array
 from numpy.typing import NDArray
 from spatialdata import SpatialData
 from spatialdata.models.models import ScaleFactors_t
 
 from harpy.image.segmentation._map import map_labels
-from harpy.image.segmentation._utils import (
-    _SEG_DTYPE,
-    _add_depth_to_chunks_size,
-    _check_boundary,
-    _clean_up_masks,
-    _merge_masks,
-    _rechunk_overlap,
-    _substract_depth_from_chunks_size,
-)
 from harpy.utils.pylogger import get_pylogger
 
 log = get_pylogger(__name__)
@@ -117,100 +104,6 @@ def align_labels_layers(
     return sdata
 
 
-def _align_dask_arrays(
-    x_label_1: Array,
-    x_label_2: Array,
-    **kwargs: Any,  # keyword arguments to be passed to map_overlap/map_blocks
-):
-    # we will align labels of x_label_1 with labels of x_labels_2.
-
-    assert x_label_1.shape == x_label_2.shape, "Only arrays with same shape are currently supported."
-
-    chunks = kwargs.pop("chunks", None)
-    depth = kwargs.pop("depth", 100)
-    boundary = kwargs.pop("boundary", "reflect")
-
-    if isinstance(depth, int):
-        depth = {0: 0, 1: depth, 2: depth}
-    else:
-        assert len(depth) == x_label_1.ndim, f"Please provide depth for each dimension ({x_label_1.ndim})."
-        if x_label_1.ndim == 2:
-            depth = {0: 0, 1: depth[0], 2: depth[1]}
-
-    assert depth[0] == 0, "Depth not equal to 0 for 'z' dimension is not supported"
-
-    if chunks is None:
-        assert (
-            x_label_1.chunksize == x_label_2.chunksize
-        ), "If chunks is not specified, please ensure Dask arrays have the same chunksize."
-
-    _check_boundary(boundary)
-
-    _to_squeeze = False
-    if x_label_1.ndim == 2:
-        _to_squeeze = True
-        x_label_1 = x_label_1[None, ...]
-        x_label_2 = x_label_2[None, ...]
-
-    #  rechunk so that we ensure minimum chunksize, in order to control output_chunks sizes.
-    x_label_1 = _rechunk_overlap(x_label_1, depth=depth, chunks=chunks)
-    x_label_2 = _rechunk_overlap(x_label_2, depth=depth, chunks=chunks)
-
-    assert (
-        x_label_1.numblocks[0] == 1
-    ), f"Expected the number of blocks in the Z-dimension to be `1`, found `{x_label_1.numblocks[0]}`."
-    assert (
-        x_label_2.numblocks[0] == 1
-    ), f"Expected the number of blocks in the Z-dimension to be `1`, found `{x_label_2.numblocks[0]}`."
-
-    # output_chunks can be derived from either x_label_1 or x_label_2
-    output_chunks = _add_depth_to_chunks_size(x_label_1.chunks, depth)
-
-    x_labels = da.map_overlap(
-        lambda m, f: _relabel_array_1_to_array_2_per_chunk(m, f),
-        x_label_1,
-        x_label_2,
-        dtype=_SEG_DTYPE,
-        allow_rechunk=False,  # already dealed with correcting for case where depth > chunksize
-        chunks=output_chunks,  # e.g. ((1024+60, 1024+60, 452+60), (1024+60, 1024+60, 452+60) ),
-        depth=depth,
-        trim=False,
-        boundary="reflect",
-        # this reflect is useless for this use case, but clean_up_masks and _merge_masks only support
-        # results from map_overlap generated with "reflect", "nearest" and "constant"
-    )
-
-    x_labels = da.map_blocks(
-        _clean_up_masks,
-        x_labels,
-        dtype=_SEG_DTYPE,
-        depth=depth,
-    )
-
-    output_chunks = _substract_depth_from_chunks_size(x_labels.chunks, depth=depth)
-
-    x_labels = da.map_overlap(
-        _merge_masks,
-        x_labels,
-        dtype=_SEG_DTYPE,
-        num_blocks=x_labels.numblocks,
-        trim=False,
-        allow_rechunk=False,  # already dealed with correcting for case where depth > chunksize
-        chunks=output_chunks,  # e.g. ((7,) ,(1024, 1024, 452), (1024, 1024, 452), (1,) ),
-        depth=depth,
-        boundary="reflect",
-        _depth=depth,
-    )
-
-    x_labels = x_labels.rechunk(x_labels.chunksize)
-
-    # squeeze if a trivial dimension was added.
-    if _to_squeeze:
-        x_labels = x_labels.squeeze(0)
-
-    return x_labels
-
-
 def _relabel_array_1_to_array_2_per_chunk(array_1: NDArray, array_2: NDArray) -> NDArray:
     assert array_1.shape == array_2.shape
 

src/harpy/image/segmentation/_map.py

@@ -1,6 +1,10 @@
 from __future__ import annotations
 
+import os
+import shutil
+import uuid
 from collections.abc import Callable, Iterable, Mapping
+from pathlib import Path
 from types import MappingProxyType
 from typing import Any
 
@@ -11,6 +15,7 @@
 from spatialdata import SpatialData
 from spatialdata.models.models import ScaleFactors_t
 from spatialdata.transformations import Translation, get_transformation
+from upath import UPath
 
 from harpy.image._image import (
     _get_spatial_element,
@@ -154,9 +159,9 @@ def _get_layers(sdata: SpatialData, labels_layers: list[str]) -> tuple[list[Arra
             )
 
             # Ensure the translation is the same as the first label layer
-            assert (
-                transformations == first_transformations
-            ), f"Provided labels layers '{labels_layers}' should all have the same transformations defined on them."
+            assert transformations == first_transformations, (
+                f"Provided labels layers '{labels_layers}' should all have the same transformations defined on them."
+            )
 
             labels_data.append(x_label)
 
@@ -171,13 +176,19 @@ def _get_layers(sdata: SpatialData, labels_layers: list[str]) -> tuple[list[Arra
     kwargs.setdefault("iou_depth", iou_depth)
     kwargs.setdefault("iou_threshold", iou_threshold)
 
+    if sdata.is_backed():
+        _temp_path = UPath(sdata.path).parent / f"tmp_{uuid.uuid4()}"
+    else:
+        _temp_path = None
+
     # labels_arrays is a list of dask arrays
     # do some processing on the labels
     array = _combine_dask_arrays(
         labels_arrays,
         relabel_chunks=relabel_chunks,
         trim=trim,
         func=func,
+        temp_path=_temp_path,
         fn_kwargs=fn_kwargs,
         **kwargs,
     )
@@ -205,6 +216,10 @@ def _get_layers(sdata: SpatialData, labels_layers: list[str]) -> tuple[list[Arra
             overwrite=overwrite,
         )
 
+    if _temp_path is not None:
+        # TODO this will not work if sdata is remote (e.g. s3 bucket).
+        shutil.rmtree(_temp_path)
+
     return sdata
 
 
@@ -213,6 +228,7 @@ def _combine_dask_arrays(
     relabel_chunks: bool,
     trim: bool,
     func: Callable[..., NDArray],
+    temp_path: str | Path,
     fn_kwargs: Mapping[str, Any] = MappingProxyType({}),  # keyword arguments to be passed to func
     **kwargs: Any,  # keyword arguments to be passed to map_overlap/map_blocks
 ) -> Array:
@@ -268,9 +284,9 @@ def _fix_depth(_depth):
     for i, x_label in enumerate(_labels_arrays):
         #  rechunk so that we ensure minimum chunksize, in order to control output_chunks sizes.
         x_label = _rechunk_overlap(x_label, depth=depth, chunks=chunks)
-        assert (
-            x_label.numblocks[0] == 1
-        ), f"Expected the number of blocks in the Z-dimension to be `1`, found `{x_label.numblocks[0]}`."
+        assert x_label.numblocks[0] == 1, (
+            f"Expected the number of blocks in the Z-dimension to be `1`, found `{x_label.numblocks[0]}`."
+        )
 
         if i == 0:
             # output_chunks can be derived from any rechunked x_label in labels_arrays
@@ -307,6 +323,21 @@ def _fix_depth(_depth):
     # return x_labels.squeeze(0)
 
     if not trim:
+        # write to intermediate zarr store if sdata is backed to reduce ram memory.
+        if temp_path is not None:
+            zarr_path = os.path.join(temp_path, f"labels_{uuid.uuid4()}.zarr")
+            _chunks = x_labels.chunks
+            x_labels.rechunk(x_labels.chunksize).to_zarr(
+                zarr_path,
+                overwrite=False,
+            )
+            x_labels = da.from_zarr(zarr_path)
+            x_labels = x_labels.rechunk(_chunks)
+        else:
+            x_labels = x_labels.persist()
+
+        log.info("Linking labels across chunks.")
+
         iou_depth = da.overlap.coerce_depth(len(depth), iou_depth)
 
         if any(iou_depth[ax] > depth[ax] for ax in depth.keys()):