diff --git a/README.md b/README.md index c2ace9b8ceb48aa7f1a632f9072a726c221311b2..8af2c40fc1d8edc87ce72dcaa87cd0765536cb77 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ docker-compose stop ### Raw data access ```python -from argo.omero import Dataset, Image +from aliby.io.omero import Dataset, Image server_info= { "host": "host_address", @@ -62,7 +62,7 @@ with Image(list(image_ids.values())[0], **server_info) as image: A `Tiler` object performs trap registration. It is built in different ways, the easiest one is using an image and a the default parameters set. ```python -from agora.tile.tiler import Tiler, TilerParameters +from aliby.tile.tiler import Tiler, TilerParameters with Image(list(image_ids.values())[0], **server_info) as image: tiler = Tiler.from_image(image, TilerParameters.default()) ``` @@ -117,7 +117,7 @@ seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None, At the moment the best/only way to read matlab files is through a `matObject`: ```python -from core.io.matlab import matObject +from aliby.io.matlab import matObject cTimelapse = matObject('/path/to/cTimelapse.mat') ``` diff --git a/aliby/pipeline.py b/aliby/pipeline.py index 591dbd95be9b0fc82919174a06435a6031949995..35d5f070d69be0ce9506a76943336280c48206a0 100644 --- a/aliby/pipeline.py +++ b/aliby/pipeline.py @@ -20,11 +20,11 @@ from pathos.multiprocessing import Pool from aliby.experiment import MetaData from aliby.haystack import initialise_tf from aliby.baby_client import BabyRunner, BabyParameters -from agora.tile.tiler import Tiler, TilerParameters +from aliby.tile.tiler import Tiler, TilerParameters +from aliby.io.omero import Dataset, Image from agora.abc import ParametersABC, ProcessABC from agora.io.writer import TilerWriter, BabyWriter from agora.io.signal import Signal -from argo.io.omero import Dataset, Image from extraction.core.extractor import Extractor, ExtractorParameters from extraction.core.functions.defaults import exparams_from_meta from postprocessor.core.processor import PostProcessor, PostProcessorParameters diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py index b3f7abdcf862db6cc0fc1bb573668f26353b0e84..6acbf28d88ca5b85312d41f872453d6ba9b2deba 100644 --- a/extraction/core/extractor.py +++ b/extraction/core/extractor.py @@ -26,7 +26,7 @@ from extraction.core.functions.utils import depth from agora.abc import ProcessABC, ParametersABC from agora.io.writer import Writer, load_attributes from agora.io.cells import Cells -from agora.tile.tiler import Tiler +from aliby.tile.tiler import Tiler CELL_FUNS, TRAPFUNS, FUNS = load_funs() CUSTOM_FUNS, CUSTOM_ARGS = load_custom_args() diff --git a/pyproject.toml b/pyproject.toml index 67fb7fbe7567c1c38ecc056cef5b1ea4bee3cdf7..d5e8bee450e28372dbaf5223e35480c20ff2034d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ tensorflow = ">=1.15,<=2.3" aliby-agora = "*" aliby-baby = "*" aliby-post = "*" +omni-gaussian = "*" [tool.poetry.dev-dependencies] diff --git a/tests/aliby/test_pipeline.py b/tests/aliby/test_pipeline.py index a89d4bd7e2004501d0a91a5201dcf92aac025fd0..1adb44562ed13d594685c522472cdd639be7679c 100644 --- a/tests/aliby/test_pipeline.py +++ b/tests/aliby/test_pipeline.py @@ -5,7 +5,7 @@ from pathlib import Path from aliby.baby_client import BabyRunner from aliby.experiment import ExperimentOMERO from aliby.pipeline import ExperimentLocal -from agora.tile.tiler import Tiler +from aliby.tile.tiler import Tiler class TestLocal(unittest.TestCase): diff --git a/tests/aliby/test_segment.py b/tests/aliby/test_segment.py index f3045d19fcf83e7e319ef9fa2ba6ce0d860ea2a7..65c2bf6c969b546fa9062ff9ee000c2f1dd9c53b 100644 --- a/tests/aliby/test_segment.py +++ b/tests/aliby/test_segment.py @@ -1,7 +1,7 @@ import unittest import numpy as np -from agora.tile.tiler import align_timelapse_images +from aliby.tile.tiler import align_timelapse_images class TestCase(unittest.TestCase):