Visualize tracked cells and their features

.github/workflows/test_and_deploy.yml

@@ -22,7 +22,7 @@ jobs:
  runs-on: ${{ matrix.platform }}
  strategy:
  matrix:
- platform: [ubuntu-latest, windows-latest, macos-latest]
+ platform: [ubuntu-latest, windows-latest, macos-13]
  python-version: ['3.10', '3.11']
 
  steps:
@@ -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

pyproject.toml

@@ -1,12 +1,63 @@
 [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 = "iohub@czbiohub.org" },
+]
+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 = ["napari-clusters-plotter", "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"]

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))

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 import Plate, Position, Row, Well, open_ome_zarr
+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):

src/napari_iohub/_reader.py

@@ -6,13 +6,13 @@
 
 import dask.array as da
 import numpy as np
-from iohub.ngff import (
+from iohub.ngff.nodes import (
  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)

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", "View tracks")