Visualize tracked cells and their features (#13)

* remove unused import * configurable logging levels * metadata options in reader functions * add tracking labels viewer * fix ambiguous variable name * only use labels layer for annotation * clean up arguments * todo comment * improve log message * format * fix exports * use unprojected embeddings * configurable feature files * test add widget * use default napari dependencies for dev * add optional dependencies also redo packaging with pyproject.toml * relax napari pin after napari-clusters-plotter update * format * wip: use xarray output zarr format for embeddings * construct index from xarray * fix index naming * bump iohub to 0.2.0a1 * add fake z axis for tracking * ci: use x86_64 runner for macos since higra is not available on arm64 * disable coverage * use precomputed umap * aggregate feature loading * update widget name in test * add 3.12 to test runners * make features optional this allows the widget to be used as a tracks viewer * fix fov name filtering * pin ncp to commit
czbiohub-sf · Oct 18, 2024 · 28c49c2 · 28c49c2
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commit 28c49c2
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -22,8 +22,8 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.10', '3.11']
+        platform: [ubuntu-latest, windows-latest, macos-13]
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v3
@@ -60,9 +60,6 @@ jobs:
         env:
           PLATFORM: ${{ matrix.platform }}
 
-      - name: Coverage
-        uses: codecov/codecov-action@v2
-
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
     # and requires that you have put your twine API key in your

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,12 +1,68 @@
 [build-system]
-requires = ["setuptools>=42.0.0", "wheel"]
+requires = ["setuptools>=42.0.0", "setuptools-scm[toml]"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "napari-iohub"
+description = "OME-Zarr viewer for napari with iohub as the I/O backend"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+authors = [
+  { name = "CZ Biohub SF and napari-iohub contributors", email = "[email protected]" },
+]
+dependencies = ["iohub>=0.1.0", "magicgui", "qtpy"]
+dynamic = ["version"]
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Framework :: napari",
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: BSD License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Image Processing",
+]
 
+[project.optional-dependencies]
+clustering = [
+  # https://github.com/BiAPoL/napari-clusters-plotter/pull/345
+  "napari-clusters-plotter@git+https://github.com/BiAPoL/napari-clusters-plotter.git@43f5f8297f41927eb5993b95092aaf9f90bb1583",
+  "ultrack",
+  "iohub==0.2.0a1",
+]
+all = ["napari[all]", "napari-iohub[clustering]"]
+dev = [
+  "tox",
+  "pytest",
+  "pytest-cov",
+  "pytest-qt",
+  "black",
+  "ruff",
+  "napari-iohub[all]",
+]
+
+[project.entry-points."napari.manifest"]
+"napari-iohub" = "napari_iohub:napari.yaml"
+
+[tool.setuptools_scm]
+write_to = "src/napari_iohub/_version.py"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
 
 [tool.black]
 line-length = 79
 
-[tool.isort]
-profile = "black"
-line_length = 79
+[tool.ruff]
+src = ["src"]
+lint.extend-select = ["I001"]
+lint.isort.known-first-party = ["napari_iohub"]
diff --git a/setup.cfg b/setup.cfg
diff --git a/src/napari_iohub/__init__.py b/src/napari_iohub/__init__.py
@@ -1,10 +1,17 @@
-__version__ = "0.0.1"
+import logging
+import os
 
+from ._edit_labels import EditLabelsWidget
 from ._reader import napari_get_reader
+from ._view_tracks import open_image_and_tracks
 from ._widget import MainWidget
 
 __all__ = (
     "napari_get_reader",
     "MainWidget",
-    "example_magic_widget",
+    "EditLabelsWidget",
+    "open_image_and_tracks",
 )
+
+_logger = logging.getLogger(__name__)
+_logger.setLevel(os.getenv("NAPARI_IOHUB_LOGGING_LEVEL", logging.DEBUG))
diff --git a/src/napari_iohub/_edit_labels.py b/src/napari_iohub/_edit_labels.py
@@ -3,13 +3,12 @@
 import logging
 import os
 import warnings
-from os.path import isdir, isfile
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-from napari import Viewer
 import numpy as np
 from iohub.ngff.nodes import Plate, Position, Row, Well, open_ome_zarr
+from napari import Viewer
 from qtpy.QtWidgets import (
     QFileDialog,
     QFormLayout,
@@ -27,7 +26,6 @@
     import napari
     from napari.types import LayerData
 _logger = logging.getLogger(__name__)
-_logger.setLevel(logging.DEBUG)
 
 
 class _LoadFOV(QWidget):

diff --git a/src/napari_iohub/_reader.py b/src/napari_iohub/_reader.py
@@ -10,9 +10,9 @@
     MultiScaleMeta,
     NGFFNode,
     OMEROMeta,
+    Plate,
     Position,
     Well,
-    Plate,
     _open_store,
     open_ome_zarr,
 )
@@ -69,9 +69,7 @@ def _get_node(path: StrOrBytesPath):
         zgroup.store.close()
         node = open_ome_zarr(store_path=path, layout="hcs", mode="r")
     else:
-        raise KeyError(
-            f"NGFF plate or well metadata not found under '{zgroup.name}'"
-        )
+        raise KeyError(f"NGFF plate or well metadata not found under '{zgroup.name}'")
     return node
 
 
@@ -80,8 +78,8 @@ def stitch_well_by_channel(well: Well, row_wrap: int):
     levels = []
     pyramids: list[list] = []
     for i, (_, pos) in enumerate(well.positions()):
-        l, ims = _get_multiscales(pos)
-        levels.append(l)
+        lv, ims = _get_multiscales(pos)
+        levels.append(lv)
         pyramids.append(ims)
         if i == 0:
             layers_kwargs = _ome_to_napari_by_channel(pos.metadata)
@@ -98,8 +96,8 @@ def stack_well_by_position(well: Well):
     levels = []
     pyramids: list[list] = []
     for i, (_, pos) in enumerate(well.positions()):
-        l, ims = _get_multiscales(pos)
-        levels.append(l)
+        lv, ims = _get_multiscales(pos)
+        levels.append(lv)
         pyramids.append(ims)
         if i == 0:
             layers_kwargs = _ome_to_napari_by_channel(pos.metadata)
@@ -118,9 +116,7 @@ def _get_multiscales(pos: Position):
         try:
             multiscales.append(da.from_zarr(pos[im]))
         except Exception as e:
-            logging.warning(
-                f"Skipped array '{im}' at position {pos.zgroup.name}: {e}"
-            )
+            logging.warning(f"Skipped array '{im}' at position {pos.zgroup.name}: {e}")
     return len(multiscales), multiscales
 
 
@@ -136,12 +132,12 @@ def _make_grid(elements: list[da.Array], cols: int):
     return grid
 
 
-def _ome_to_napari_by_channel(metadata):
+def _ome_to_napari_by_channel(metadata, parse_colormap: bool = True):
     omero: OMEROMeta = metadata.omero
     layers_kwargs = []
     for channel in omero.channels:
         metadata = {"name": channel.label}
-        if channel.color:
+        if channel.color and parse_colormap:
             # alpha channel is optional
             rgb = Color(channel.color).as_rgb_tuple(alpha=None)
             start = [0.0] * 3
@@ -153,6 +149,7 @@ def _ome_to_napari_by_channel(metadata):
                     [v / np.iinfo(np.uint8).max for v in rgb],
                 ]
             )
+            metadata["blending"] = "additive"
         layers_kwargs.append(metadata)
     return layers_kwargs
 
@@ -190,20 +187,20 @@ def layers_from_arrays(
     return layers
 
 
-def fov_to_layers(fov: Position):
-    layers_kwargs = _ome_to_napari_by_channel(fov.metadata)
+def fov_to_layers(fov: Position, layer_type: str = "image"):
+    layers_kwargs = _ome_to_napari_by_channel(
+        fov.metadata, parse_colormap=(layer_type == "image")
+    )
     ch_axis = _find_ch_axis(fov)
     arrays = [arr for _, arr in fov.images()]
-    return layers_from_arrays(layers_kwargs, ch_axis, arrays, mode="stitch")
+    return layers_from_arrays(
+        layers_kwargs, ch_axis, arrays, mode="stitch", layer_type=layer_type
+    )
 
 
-def well_to_layers(
-    well: Well, mode: Literal["stitch", "stack"], layer_type: str
-):
+def well_to_layers(well: Well, mode: Literal["stitch", "stack"], layer_type: str):
     if mode == "stitch":
-        layers_kwargs, ch_axis, arrays = stitch_well_by_channel(
-            well, row_wrap=4
-        )
+        layers_kwargs, ch_axis, arrays = stitch_well_by_channel(well, row_wrap=4)
     elif mode == "stack":
         layers_kwargs, ch_axis, arrays = stack_well_by_position(well)
     return layers_from_arrays(
@@ -234,9 +231,7 @@ def make_bbox(bbox_extents):
     maxr = bbox_extents[2]
     maxc = bbox_extents[3]
 
-    bbox_rect = np.array(
-        [[minr, minc], [maxr, minc], [maxr, maxc], [minr, maxc]]
-    )
+    bbox_rect = np.array([[minr, minc], [maxr, minc], [maxr, maxc], [minr, maxc]])
     bbox_rect = np.moveaxis(bbox_rect, 2, 0)
 
     return bbox_rect
@@ -276,9 +271,7 @@ def plate_to_layers(
                 ]
                 for k in range(len(boxes)):
                     boxes[k].append(box_extents[k] - 0.5)
-                properties["fov"].append(
-                    well_path + "/" + next(well.positions())[0]
-                )
+                properties["fov"].append(well_path + "/" + next(well.positions())[0])
             else:
                 row_arrays.append(None)
         plate_arrays.append(row_arrays)
@@ -291,9 +284,7 @@ def plate_to_layers(
             row_level = []
             for c in r:
                 if c is None:
-                    arr = da.zeros(
-                        shape=fill_args[level][0], dtype=fill_args[level][1]
-                    )
+                    arr = da.zeros(shape=fill_args[level][0], dtype=fill_args[level][1])
                 else:
                     arr = c[level]
                 row_level.append(arr)

diff --git a/src/napari_iohub/_tests/test_view_tracks.py b/src/napari_iohub/_tests/test_view_tracks.py
@@ -0,0 +1,3 @@
+def test_view_tracks_widget(make_napari_viewer):
+    viewer = make_napari_viewer()
+    _ = viewer.window.add_plugin_dock_widget("napari-iohub", "Single-cell features")