diff --git a/aliby/tile/tiler.py b/aliby/tile/tiler.py
index 59e6463779b259126d391ac34627addf394762cf..2438d8dca3e0de2590f4438eba5cf2e6fd83e8d5 100644
--- a/aliby/tile/tiler.py
+++ b/aliby/tile/tiler.py
@@ -227,16 +227,8 @@ class Tiler(ProcessABC):
@lru_cache(maxsize=2)
def get_tc(self, t, c):
- # Get image by forcing loading it into cache. Assumes TCZYX dimensional order.
- # WORKAROUND around error (which arose on 2022/06/14) when fetching 3-D data.
- # full = np.stack(
- # [
- # self.image[t, c, z]
- # for z in range(self.image.shape[2])
- # ],
- # axis=0,
- # )
full = self.image[t, c].compute(scheduler='synchronous')
+
return full
###
diff --git a/poetry.lock b/poetry.lock
index e222acd83ada8f29aa7b280d0f5585214623603d..0959969b1077bef9f9f0984a41d20b9508b4cc34 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -75,7 +75,7 @@ python-versions = "*"
[[package]]
name = "aliby-agora"
-version = "0.2.28"
+version = "0.2.29"
description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
category = "main"
optional = false
@@ -92,7 +92,7 @@ scipy = ">=1.7.3"
[[package]]
name = "aliby-baby"
-version = "0.1.9"
+version = "0.1.10"
description = "Birth Annotator for Budding Yeast"
category = "main"
optional = false
@@ -103,7 +103,7 @@ colorama = ">=0.4.4,<0.5.0"
imageio = "2.8.0"
keras-tuner = "1.0.1"
matplotlib = ">=3.5.1,<4.0.0"
-numpy = ">=1.21.6,<2.0.0"
+numpy = "1.21.6"
pandas = "1.3.3"
Pillow = ">=9.0.0,<10.0.0"
ray = {version = "1.4.0", extras = ["tune"]}
@@ -199,7 +199,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>
[[package]]
name = "babel"
-version = "2.10.2"
+version = "2.10.3"
description = "Internationalization utilities"
category = "dev"
optional = false
@@ -260,7 +260,7 @@ python-versions = "*"
[[package]]
name = "certifi"
-version = "2022.5.18.1"
+version = "2022.6.15"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
@@ -299,7 +299,7 @@ python-versions = ">=3.6"
[[package]]
name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
description = "Cross-platform colored terminal text."
category = "main"
optional = false
@@ -482,7 +482,7 @@ scipy = ">=1.7.3,<2.0.0"
[[package]]
name = "google-api-core"
-version = "2.8.1"
+version = "2.8.2"
description = "Google API client core library"
category = "main"
optional = false
@@ -491,13 +491,11 @@ python-versions = ">=3.6"
[package.dependencies]
google-auth = ">=1.25.0,<3.0dev"
googleapis-common-protos = ">=1.56.2,<2.0dev"
-protobuf = ">=3.15.0,<4.0.0dev"
+protobuf = ">=3.15.0,<5.0.0dev"
requests = ">=2.18.0,<3.0.0dev"
[package.extras]
grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio-status (>=1.33.2,<2.0dev)"]
-grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"]
-grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"]
[[package]]
name = "google-auth"
@@ -673,7 +671,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[[package]]
name = "importlib-resources"
-version = "5.7.1"
+version = "5.8.0"
description = "Read resources from Python packages"
category = "main"
optional = false
@@ -2007,7 +2005,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[metadata]
lock-version = "1.1"
python-versions = ">=3.7.1,<3.11"
-content-hash = "090a627ee0f3ae896e04bd7835211beea28b812f6c64153065e00df8ce773975"
+content-hash = "2b6ad2d552e03121404a606ede71b793722be635dbdd4d2328656ccb23d62ffb"
[metadata.files]
absl-py = [
@@ -2105,12 +2103,12 @@ alabaster = [
{file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
]
aliby-agora = [
- {file = "aliby-agora-0.2.28.tar.gz", hash = "sha256:029a2aef0c62b0b0f3e7f0f3374f8307dc5bddba91b3906371dcd90a62442ade"},
- {file = "aliby_agora-0.2.28-py3-none-any.whl", hash = "sha256:54219b605e368a6ff883859c88e064009118653bac95b967e02750dbabf4ceb3"},
+ {file = "aliby-agora-0.2.29.tar.gz", hash = "sha256:5f8654085cbbf84199413cf44c3781a743d4fdceef523a7e7e97e78bb81df44d"},
+ {file = "aliby_agora-0.2.29-py3-none-any.whl", hash = "sha256:782785da7d1766600eb1d78e5d1fd094621cbb0b3f5908b14c5feafcfcd0186b"},
]
aliby-baby = [
- {file = "aliby-baby-0.1.9.tar.gz", hash = "sha256:d1f80d8187ae586ed037cba2f34af1b28c9e989075a4552d3ed93b402099144b"},
- {file = "aliby_baby-0.1.9-py3-none-any.whl", hash = "sha256:c5690556693e0404b54eb37f589ae3240d173119e6abc938a55f173daaf43105"},
+ {file = "aliby-baby-0.1.10.tar.gz", hash = "sha256:6d3be468c9ebd1968e4cc9aa535ed1c9669ca88321aaf5c33b4b597e50fb53a6"},
+ {file = "aliby_baby-0.1.10-py3-none-any.whl", hash = "sha256:af1fca10adff72ebd7b4fdb2b62586b7ed779e2ab2bed01fe4a2b9e5468c40eb"},
]
aliby-post = [
{file = "aliby-post-0.1.27.tar.gz", hash = "sha256:77f8763be9892b702483739f2abd84e2d4c1f568d60b03c93ba6400e6f69f464"},
@@ -2141,8 +2139,8 @@ attrs = [
{file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
]
babel = [
- {file = "Babel-2.10.2-py3-none-any.whl", hash = "sha256:81a3beca4d0cd40a9cfb9e2adb2cf39261c2f959b92e7a74750befe5d79afd7b"},
- {file = "Babel-2.10.2.tar.gz", hash = "sha256:7aed055f0c04c9e7f51a2f75261e41e1c804efa724cb65b60a970dd4448d469d"},
+ {file = "Babel-2.10.3-py3-none-any.whl", hash = "sha256:ff56f4892c1c4bf0d814575ea23471c230d544203c7748e8c68f0089478d48eb"},
+ {file = "Babel-2.10.3.tar.gz", hash = "sha256:7614553711ee97490f732126dc077f8d0ae084ebc6a96e23db1482afabdb2c51"},
]
black = [
{file = "black-22.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2497f9c2386572e28921fa8bec7be3e51de6801f7459dffd6e62492531c47e09"},
@@ -2182,8 +2180,8 @@ catch22 = [
{file = "catch22-0.2.0.tar.gz", hash = "sha256:f8e1382ec6db256ee5be83802334bf03d1b951ba85fa859fe537004bc07a127b"},
]
certifi = [
- {file = "certifi-2022.5.18.1-py3-none-any.whl", hash = "sha256:f1d53542ee8cbedbe2118b5686372fb33c297fcd6379b050cca0ef13a597382a"},
- {file = "certifi-2022.5.18.1.tar.gz", hash = "sha256:9c5705e395cd70084351dd8ad5c41e65655e08ce46f2ec9cf6c2c08390f71eb7"},
+ {file = "certifi-2022.6.15-py3-none-any.whl", hash = "sha256:fe86415d55e84719d75f8b69414f6438ac3547d2078ab91b67e779ef69378412"},
+ {file = "certifi-2022.6.15.tar.gz", hash = "sha256:84c85a9078b11105f04f3036a9482ae10e4621616db313fe045dd24743a0820d"},
]
charset-normalizer = [
{file = "charset-normalizer-2.0.12.tar.gz", hash = "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597"},
@@ -2198,8 +2196,8 @@ cloudpickle = [
{file = "cloudpickle-2.1.0.tar.gz", hash = "sha256:bb233e876a58491d9590a676f93c7a5473a08f747d5ab9df7f9ce564b3e7938e"},
]
colorama = [
- {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
- {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
+ {file = "colorama-0.4.5-py2.py3-none-any.whl", hash = "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da"},
+ {file = "colorama-0.4.5.tar.gz", hash = "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"},
]
cycler = [
{file = "cycler-0.11.0-py3-none-any.whl", hash = "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3"},
@@ -2310,8 +2308,8 @@ gaussianprocessderivatives = [
{file = "gaussianprocessderivatives-0.1.5.tar.gz", hash = "sha256:3bd2142668a0d9b8876ba1a15a406a7f9bcbb8564547a7027a9839024dd81838"},
]
google-api-core = [
- {file = "google-api-core-2.8.1.tar.gz", hash = "sha256:958024c6aa3460b08f35741231076a4dd9a4c819a6a39d44da9627febe8b28f0"},
- {file = "google_api_core-2.8.1-py3-none-any.whl", hash = "sha256:ce1daa49644b50398093d2a9ad886501aa845e2602af70c3001b9f402a9d7359"},
+ {file = "google-api-core-2.8.2.tar.gz", hash = "sha256:06f7244c640322b508b125903bb5701bebabce8832f85aba9335ec00b3d02edc"},
+ {file = "google_api_core-2.8.2-py3-none-any.whl", hash = "sha256:93c6a91ccac79079ac6bbf8b74ee75db970cc899278b97d53bc012f35908cf50"},
]
google-auth = [
{file = "google-auth-2.8.0.tar.gz", hash = "sha256:819b70140d05501739e1387291d39f0de3b4dff3b00ae4aff8e7a05369957f89"},
@@ -2503,8 +2501,8 @@ importlib-metadata = [
{file = "importlib_metadata-4.11.4.tar.gz", hash = "sha256:5d26852efe48c0a32b0509ffbc583fda1a2266545a78d104a6f4aff3db17d700"},
]
importlib-resources = [
- {file = "importlib_resources-5.7.1-py3-none-any.whl", hash = "sha256:e447dc01619b1e951286f3929be820029d48c75eb25d265c28b92a16548212b8"},
- {file = "importlib_resources-5.7.1.tar.gz", hash = "sha256:b6062987dfc51f0fcb809187cffbd60f35df7acb4589091f154214af6d0d49d3"},
+ {file = "importlib_resources-5.8.0-py3-none-any.whl", hash = "sha256:7952325ffd516c05a8ad0858c74dff2c3343f136fe66a6002b2623dd1d43f223"},
+ {file = "importlib_resources-5.8.0.tar.gz", hash = "sha256:568c9f16cb204f9decc8d6d24a572eeea27dacbb4cee9e6b03a8025736769751"},
]
iniconfig = [
{file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
diff --git a/pyproject.toml b/pyproject.toml
index 01cdab79e6a16554b79507fffcb580bb557e3fb2..7dfaf012b7babdd64dc57b489f2aa2c4b0275f19 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,9 +25,9 @@ h5py = "2.10" # I/O into files
imageio = "2.8.0"
omero-py = ">=5.6.2" # contact omero server
zeroc-ice = "3.6.5" # pin networking interface
-aliby-agora = "^0.2.28"
-aliby-baby = "^0.1.9"
-aliby-post = "^0.1.26"
+aliby-agora = "^0.2.29"
+aliby-baby = "^0.1.10"
+aliby-post = "^0.1.27"
p-tqdm = "^1.3.3" # Parallel progress bars
xmltodict = "^0.13.0" # read ome-tiff metadata
protobuf = "<=3.20.1" # For pytest to work