From 9daf33c54969aa4fc4142699c17b99f65bae6f75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 7 Jan 2022 18:49:03 +0000
Subject: [PATCH] rename imports
---
README.md | 6 +++---
aliby/pipeline.py | 4 ++--
extraction/core/extractor.py | 2 +-
pyproject.toml | 1 +
tests/aliby/test_pipeline.py | 2 +-
tests/aliby/test_segment.py | 2 +-
6 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index c2ace9b8..8af2c40f 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 591dbd95..35d5f070 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 b3f7abdc..6acbf28d 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 67fb7fbe..d5e8bee4 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 a89d4bd7..1adb4456 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 f3045d19..65c2bf6c 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):
--
GitLab