rename imports

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')
 ```
 

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

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()

pyproject.toml

@@ -32,6 +32,7 @@ tensorflow = ">=1.15,<=2.3"
 aliby-agora = "*"
 aliby-baby = "*"
 aliby-post = "*"
+omni-gaussian = "*"
 
 
 [tool.poetry.dev-dependencies]

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):

tests/aliby/test_segment.py

 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):