diff --git a/poetry.lock b/poetry.lock
index b1a26c96be409c5baec23a71b5bf1abde57bec5f..6e46af5ca1f64617910dc6098addaef2a6f7d675 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -925,63 +925,63 @@ test-no-images = ["pytest"]
[[package]]
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+ {file = "coverage-7.2.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9d22e94e6dc86de981b1b684b342bec5e331401599ce652900ec59db52940005"},
+ {file = "coverage-7.2.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:507e4720791977934bba016101579b8c500fb21c5fa3cd4cf256477331ddd988"},
+ {file = "coverage-7.2.2-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:bc4803779f0e4b06a2361f666e76f5c2e3715e8e379889d02251ec911befd149"},
+ {file = "coverage-7.2.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:db8c2c5ace167fd25ab5dd732714c51d4633f58bac21fb0ff63b0349f62755a8"},
+ {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:4f68ee32d7c4164f1e2c8797535a6d0a3733355f5861e0f667e37df2d4b07140"},
+ {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:d52f0a114b6a58305b11a5cdecd42b2e7f1ec77eb20e2b33969d702feafdd016"},
+ {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:797aad79e7b6182cb49c08cc5d2f7aa7b2128133b0926060d0a8889ac43843be"},
+ {file = "coverage-7.2.2-cp39-cp39-win32.whl", hash = "sha256:db45eec1dfccdadb179b0f9ca616872c6f700d23945ecc8f21bb105d74b1c5fc"},
+ {file = "coverage-7.2.2-cp39-cp39-win_amd64.whl", hash = "sha256:8dbe2647bf58d2c5a6c5bcc685f23b5f371909a5624e9f5cd51436d6a9f6c6ef"},
+ {file = "coverage-7.2.2-pp37.pp38.pp39-none-any.whl", hash = "sha256:872d6ce1f5be73f05bea4df498c140b9e7ee5418bfa2cc8204e7f9b817caa968"},
+ {file = "coverage-7.2.2.tar.gz", hash = "sha256:36dd42da34fe94ed98c39887b86db9d06777b1c8f860520e21126a75507024f2"},
]
[package.extras]
@@ -1201,14 +1201,14 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
[[package]]
name = "filelock"
-version = "3.9.1"
+version = "3.10.0"
description = "A platform independent file lock."
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "filelock-3.9.1-py3-none-any.whl", hash = "sha256:4427cdda14a1c68e264845142842d6de2d0fa2c15ba31571a3d9c9a1ec9d191c"},
- {file = "filelock-3.9.1.tar.gz", hash = "sha256:e393782f76abea324dee598d2ea145b857a20df0e0ee4f80fcf35e72a341d2c7"},
+ {file = "filelock-3.10.0-py3-none-any.whl", hash = "sha256:e90b34656470756edf8b19656785c5fea73afa1953f3e1b0d645cef11cab3182"},
+ {file = "filelock-3.10.0.tar.gz", hash = "sha256:3199fd0d3faea8b911be52b663dfccceb84c95949dd13179aa21436d1a79c4ce"},
]
[package.extras]
@@ -1261,14 +1261,14 @@ six = ">=1.12,<2.0"
[[package]]
name = "fonttools"
-version = "4.39.0"
+version = "4.39.2"
description = "Tools to manipulate font files"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
- {file = "fonttools-4.39.0-py3-none-any.whl", hash = "sha256:f5e764e1fd6ad54dfc201ff32af0ba111bcfbe0d05b24540af74c63db4ed6390"},
- {file = "fonttools-4.39.0.zip", hash = "sha256:909c104558835eac27faeb56be5a4c32694192dca123d073bf746ce9254054af"},
+ {file = "fonttools-4.39.2-py3-none-any.whl", hash = "sha256:85245aa2fd4cf502a643c9a9a2b5a393703e150a6eaacc3e0e84bb448053f061"},
+ {file = "fonttools-4.39.2.zip", hash = "sha256:e2d9f10337c9e3b17f9bce17a60a16a885a7d23b59b7f45ce07ea643e5580439"},
]
[package.extras]
@@ -1711,14 +1711,14 @@ files = [
[[package]]
name = "identify"
-version = "2.5.20"
+version = "2.5.21"
description = "File identification library for Python"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "identify-2.5.20-py2.py3-none-any.whl", hash = "sha256:5dfef8a745ca4f2c95f27e9db74cb4c8b6d9916383988e8791f3595868f78a33"},
- {file = "identify-2.5.20.tar.gz", hash = "sha256:c8b288552bc5f05a08aff09af2f58e6976bf8ac87beb38498a0e3d98ba64eb18"},
+ {file = "identify-2.5.21-py2.py3-none-any.whl", hash = "sha256:69edcaffa8e91ae0f77d397af60f148b6b45a8044b2cc6d99cafa5b04793ff00"},
+ {file = "identify-2.5.21.tar.gz", hash = "sha256:7671a05ef9cfaf8ff63b15d45a91a1147a03aaccb2976d4e9bd047cbbc508471"},
]
[package.extras]
@@ -2237,19 +2237,19 @@ test = ["flaky", "pexpect", "pytest"]
[[package]]
name = "jupyter-core"
-version = "5.2.0"
+version = "5.3.0"
description = "Jupyter core package. A base package on which Jupyter projects rely."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_core-5.2.0-py3-none-any.whl", hash = "sha256:4bdc2928c37f6917130c667d8b8708f20aee539d8283c6be72aabd2a4b4c83b0"},
- {file = "jupyter_core-5.2.0.tar.gz", hash = "sha256:1407cdb4c79ee467696c04b76633fc1884015fa109323365a6372c8e890cc83f"},
+ {file = "jupyter_core-5.3.0-py3-none-any.whl", hash = "sha256:d4201af84559bc8c70cead287e1ab94aeef3c512848dde077b7684b54d67730d"},
+ {file = "jupyter_core-5.3.0.tar.gz", hash = "sha256:6db75be0c83edbf1b7c9f91ec266a9a24ef945da630f3120e1a0046dc13713fc"},
]
[package.dependencies]
platformdirs = ">=2.5"
-pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
traitlets = ">=5.3"
[package.extras]
@@ -2283,14 +2283,14 @@ test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=
[[package]]
name = "jupyter-server"
-version = "2.4.0"
+version = "2.5.0"
description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "jupyter_server-2.4.0-py3-none-any.whl", hash = "sha256:cc22792281bfb0131a728414f28ae74883b44ad6d009971aa975cae9bcc650de"},
- {file = "jupyter_server-2.4.0.tar.gz", hash = "sha256:f31f0ba2c3c44f07143bfa03fb07dd0253f857eb63f0c26f2fea955f04a49765"},
+ {file = "jupyter_server-2.5.0-py3-none-any.whl", hash = "sha256:e6bc1e9e96d7c55b9ce9699ff6cb9a910581fe7349e27c40389acb67632e24c0"},
+ {file = "jupyter_server-2.5.0.tar.gz", hash = "sha256:9fde612791f716fd34d610cd939704a9639643744751ba66e7ee8fdc9cead07e"},
]
[package.dependencies]
@@ -5063,14 +5063,14 @@ tune = ["pandas", "requests", "tabulate", "tensorboardX (>=1.9)"]
[[package]]
name = "readchar"
-version = "4.0.4"
+version = "4.0.5"
description = "Library to easily read single chars and key strokes"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "readchar-4.0.4-py3-none-any.whl", hash = "sha256:274e08aebb64542362ebf0b06cfa8e7ba7595dc419b812c19d6bc17c2d4fa4bb"},
- {file = "readchar-4.0.4.tar.gz", hash = "sha256:79b1d27eb9160568102219c872fef8d13bf7f16094c09ee287f620f6f2a7c031"},
+ {file = "readchar-4.0.5-py3-none-any.whl", hash = "sha256:76ec784a5dd2afac3b7da8003329834cdd9824294c260027f8c8d2e4d0a78f43"},
+ {file = "readchar-4.0.5.tar.gz", hash = "sha256:08a456c2d7c1888cde3f4688b542621b676eb38cd6cfed7eb6cb2e2905ddc826"},
]
[package.dependencies]
@@ -5938,14 +5938,14 @@ files = [
[[package]]
name = "tifffile"
-version = "2023.2.28"
+version = "2023.3.15"
description = "Read and write TIFF files"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
- {file = "tifffile-2023.2.28-py3-none-any.whl", hash = "sha256:8357cd8ccbdd4378ad4d6b84ffe3ab15b1d96630b1719f576d4de386f45546f1"},
- {file = "tifffile-2023.2.28.tar.gz", hash = "sha256:2d2baba8dea6609f553fe61853db9a61f715d60ba3bce6a20b5a1ab72407dfed"},
+ {file = "tifffile-2023.3.15-py3-none-any.whl", hash = "sha256:0ad708d0d5a45d068444e9036a20f1f8a237da008e35cc9cbc69bbb5602d6987"},
+ {file = "tifffile-2023.3.15.tar.gz", hash = "sha256:38e95a8f1b0cbcbf50d20011c3953db52c13a7e258afc391e7f681960303dd60"},
]
[package.dependencies]
@@ -6711,8 +6711,9 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
[extras]
omero = ["omero-py"]
+utils = []
[metadata]
lock-version = "2.0"
python-versions = ">=3.8, <3.11"
-content-hash = "d4e111afae2f7b8c182eeeb7c0ce36ef4b5c0f14ec03d90fb4aeb6c94c2bdcb6"
+content-hash = "f6f3a7589011cc602be1f18bc03b70a228f98becc80a305df3b78b44ef2d4507"
diff --git a/pyproject.toml b/pyproject.toml
index fc5db2ef787c5df56ecf2ebbab4a3661f9adc89f..e49b446f0c8d1d8c32d532c9c733d1c4afd9d231 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,9 @@ GitPython = "^3.1.27"
omero-py = { version = ">=5.6.2", optional = true } # contact omero server
[tool.poetry.extras]
-omero = [ "omero-py" ]
+omero = ["omero-py"]
+utils = ["napari", "torch", "pytorch-lightning", "torchvision", "trio", "grid-strategy"]
+
# Postprocessing
[tool.poetry.group.pp.dependencies]
@@ -108,6 +110,7 @@ torch = "^1.13.1"
pytorch-lightning = "^1.9.3"
torchvision = "^0.14.1"
trio = "^0.22.0"
+grid-strategy = "^0.0.1"
[tool.black]
line-length = 79
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index d2e502024b20bd4ebcba2db1c6c840c7c074bb6e..b4dd2e86ce7254721dcc2bfd9d48b3a5f473a174 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -19,6 +19,7 @@ from datetime import datetime
from pathlib import Path, PosixPath
import dask.array as da
+import numpy as np
import xmltodict
import zarr
from dask.array.image import imread
@@ -33,7 +34,9 @@ def get_examples_dir():
return files("aliby").parent.parent / "examples" / "tiler"
-def instatiate_image(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
+def instantiate_image(
+ source: t.Union[str, int, t.Dict[str, str], PosixPath], **kwargs
+):
"""Wrapper to instatiate the appropiate image
Parameters
@@ -44,18 +47,18 @@ def instatiate_image(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
Examples
--------
image_path = "path/to/image"]
- with instatiate_image(image_path) as img:
+ with instantiate_image(image_path) as img:
print(imz.data, img.metadata)
"""
- return dispatch_image(source)(source)
+ return dispatch_image(source)(source, **kwargs)
def dispatch_image(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
"""
Wrapper to pick the appropiate Image class depending on the source of data.
"""
- if isinstance(source, int):
+ if isinstance(source, (int, np.int64)):
from aliby.io.omero import Image
instatiator = Image
diff --git a/src/aliby/utils/imageViewer.py b/src/aliby/utils/imageViewer.py
index ec90a6fc48332ef7954bb1cc9fe8d274ab180401..e59da39303ce6b89cc1c406e09b0686965efbcd7 100644
--- a/src/aliby/utils/imageViewer.py
+++ b/src/aliby/utils/imageViewer.py
@@ -27,8 +27,7 @@ from PIL import Image
from skimage.morphology import dilation
from agora.io.cells import Cells
-from agora.io.writer import load_attributes
-from aliby.io.image import dispatch_image
+from agora.io.metadata import dispatch_metadata_parser
from aliby.tile.tiler import Tiler, TilerParameters
from aliby.utils.plot import stretch_clip
@@ -82,11 +81,14 @@ class BaseImageViewer(ABC):
def __init__(self, fpath):
self._fpath = fpath
- attrs = load_attributes(fpath)
+ attrs = dispatch_metadata_parser(fpath.parent)
self._logfiles_meta = {}
- self._logfiles_meta["channels"] = attrs["channels/channel"]
+ # self._logfiles_meta["channels"] =
self.image_id = attrs.get("image_id")
+ if self.image_id is None:
+ with h5py.File(fpath, "r") as f:
+ self.image_id = f.attrs.get("image_id")
assert self.image_id is not None, "No valid image_id found in metadata"
@@ -133,7 +135,7 @@ class LocalImageViewer(BaseImageViewer):
self.cells = Cells.from_source(results_path)
-class remoteImageViewer(BaseImageViewer):
+class RemoteImageViewer(BaseImageViewer):
"""
This ImageViewer combines fetching remote images with tiling and outline display.
"""
@@ -143,20 +145,16 @@ class remoteImageViewer(BaseImageViewer):
results_path: str,
server_info: t.Dict[str, str],
):
- self.super().__init__(results_path)
-
- from aliby.io.omero import Image as OImage
+ super().__init__(results_path)
- self._image_class = OImage
+ from aliby.io.omero import UnsafeImage as OImage
self._server_info = (
server_info or attrs["parameters"]["general"]["server_info"]
)
- with dispatch_image(self.image_id)(
- self.image_id, **self.server_info
- ) as image:
- self.tiler = Tiler.from_hdf5(image, results_path)
+ unsafe_image = OImage(self.image_id, **self._server_info)
+ self.tiler = Tiler.from_h5(unsafe_image, results_path)
self.cells = Cells.from_source(results_path)
@@ -232,6 +230,7 @@ class remoteImageViewer(BaseImageViewer):
z = z or self.tiler.ref_z
ch_tps = [(channels[0], tp) for tp in tps]
+
with self._image_class(self.image_id, **server_info) as image:
self.tiler.image = image.data
for ch, tp in ch_tps:
diff --git a/src/aliby/utils/vis_tools.py b/src/aliby/utils/vis_tools.py
index 523190127059c9322926a04a2fd51e542d994114..2215f2124fda30d15f2e5e1f2dcc0db5b416a1b0 100644
--- a/src/aliby/utils/vis_tools.py
+++ b/src/aliby/utils/vis_tools.py
@@ -11,7 +11,7 @@ from copy import copy
import numpy as np
from agora.io.cells import Cells
-from aliby.io.image import instatiate_image
+from aliby.io.image import instantiate_image
from aliby.tile.tiler import Tiler, TilerParameters
@@ -21,7 +21,7 @@ def fetch_tc(
"""
Return 3D ndarray with (Z,Y,X) for a given pair of time point and channel.
"""
- with instatiate_image(image_path) as img:
+ with instantiate_image(image_path) as img:
tiler = Tiler.from_h5(img, results_path, TilerParameters.default())
tc = tiler.get_tp_data(t, c)
return tc
@@ -55,7 +55,7 @@ def get_tiles_at_times(
"""
# Get the correct tile in space and time
- with instatiate_image(image_path) as image:
+ with instantiate_image(image_path) as image:
tiler = Tiler.from_h5(image, results_path, TilerParameters.default())
tp_channel_stack = [
_dispatch_tile_reduction(tile_reduction)(