From 1e07254b634f75c1a6e8fb1005a3de296df6a350 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 28 Feb 2024 16:52:06 +0100
Subject: [PATCH] Standardized all references to model_server.
---
model_server/base/roiset.py | 6 +++---
model_server/extensions/ilastik/models.py | 2 +-
model_server/extensions/ilastik/workflows.py | 3 ++-
tests/test_accessors.py | 3 +--
tests/test_process.py | 2 +-
5 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 936b5368..2f20ba9a 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -16,9 +16,9 @@ from sklearn.linear_model import LinearRegression
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.base.models import InstanceSegmentationModel
from model_server.base.process import pad, rescale, resample_to_8bit, make_rgb
-from base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
-from base.accessors import PatchStack
-from base.process import mask_largest_object
+from model_server.base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
+from model_server.base.accessors import PatchStack
+from model_server.base.process import mask_largest_object
class PatchParams(BaseModel):
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 91493a2b..de25566a 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -5,7 +5,7 @@ import numpy as np
import vigra
import model_server.extensions.ilastik.conf
-from base.accessors import PatchStack
+from model_server.base.accessors import PatchStack
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.base.models import Model, ImageToImageModel, InstanceSegmentationModel, InvalidInputImageError, ParameterExpectedError, SemanticSegmentationModel
diff --git a/model_server/extensions/ilastik/workflows.py b/model_server/extensions/ilastik/workflows.py
index aed4b8f2..bbe21e41 100644
--- a/model_server/extensions/ilastik/workflows.py
+++ b/model_server/extensions/ilastik/workflows.py
@@ -4,11 +4,12 @@ Implementation of image analysis work behind API endpoints, without knowledge of
from pathlib import Path
from typing import Dict
+from pydantic import BaseModel
+
from model_server.extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file
from model_server.base.workflows import Timer
-from pydantic import BaseModel
class WorkflowRunRecord(BaseModel):
pixel_model_id: str
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index d622a368..f85920ba 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -2,8 +2,7 @@ import unittest
import numpy as np
-from base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
-from conf.testing import monozstackmask
+from model_server.base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
from model_server.conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
from model_server.base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
diff --git a/tests/test_process.py b/tests/test_process.py
index 454151bc..569ac1b7 100644
--- a/tests/test_process.py
+++ b/tests/test_process.py
@@ -2,7 +2,7 @@ import unittest
import numpy as np
-from base.process import mask_largest_object
+from model_server.base.process import mask_largest_object
from model_server.base.process import pad
class TestProcessingUtilityMethods(unittest.TestCase):
--
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