diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 8b7642774a4e84c9f476b5aa744ec62652ed551e..cfeec9eec6d4de1e2d56a358055140a58893b4a6 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -954,7 +954,7 @@ class RoiSet(object):
return interm
- def serialize(self, where: Path, prefix='') -> dict:
+ def serialize(self, where: Path, prefix='roiset') -> dict:
"""
Export the minimal information needed to recreate RoiSet object, i.e. CSV data file and tight patch masks
:param where: path of directory in which to write files
diff --git a/model_server/conf/testing.py b/model_server/conf/testing.py
index 12d93c8b884dfad672a5e7adf0f5cbe05c60eeba..042a95512bb4417efd0e09f1359db11a37e4ff45 100644
--- a/model_server/conf/testing.py
+++ b/model_server/conf/testing.py
@@ -1,13 +1,18 @@
import json
import os
import unittest
+from math import floor
from multiprocessing import Process
from pathlib import Path
from shutil import copyfile
+import numpy as np
import requests
from urllib3 import Retry
+from ..base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
+from ..base.models import SemanticSegmentationModel, InstanceSegmentationModel
+
from ..base.accessors import generate_file_accessor
class TestServerBaseClass(unittest.TestCase):
@@ -77,9 +82,21 @@ def setup_test_data():
:return:
meta (dict) of test data and paths
"""
+
+ def _winpath(f):
+ if not isinstance(f, str):
+ return f
+ p = f.split('/')
+ if len(p) > 1:
+ p[1] = p[1] + ':'
+ return '\\'.join(p[1:])
+ else:
+ return f
+
# places to look for test data
data_paths = [
os.environ.get('UNITTEST_DATA_ROOT'),
+ _winpath(os.environ.get('UNITTEST_DATA_ROOT')),
Path.home() / 'model_server' / 'testing',
os.getcwd(),
]
@@ -100,8 +117,7 @@ def setup_test_data():
raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
meta['root'] = Path(root)
- op_ev = os.environ.get('UNITTEST_OUTPUT', (meta['root'] / 'test_output'))
- meta['output_path'] = Path(op_ev)
+ meta['output_path'] = meta['root'] / 'test_output'
meta['output_path'].mkdir(parents=True, exist_ok=True)
# resolve relative paths
@@ -117,4 +133,49 @@ def setup_test_data():
return meta
# object containing test data paths and metadata, for import into unittest modules
-meta = setup_test_data()
\ No newline at end of file
+meta = setup_test_data()
+
+
+class DummySemanticSegmentationModel(SemanticSegmentationModel):
+
+ model_id = 'dummy_make_white_square'
+
+ def load(self):
+ return True
+
+ def infer(self, img: GenericImageDataAccessor) -> (GenericImageDataAccessor, dict):
+ super().infer(img)
+ w = img.shape_dict['X']
+ h = img.shape_dict['Y']
+ result = np.zeros([h, w], dtype='uint8')
+ result[floor(0.25 * h) : floor(0.75 * h), floor(0.25 * w) : floor(0.75 * w)] = 255
+ return InMemoryDataAccessor(data=result), {'success': True}
+
+ def label_pixel_class(
+ self, img: GenericImageDataAccessor, **kwargs) -> GenericImageDataAccessor:
+ mask, _ = self.infer(img)
+ return mask
+
+
+class DummyInstanceSegmentationModel(InstanceSegmentationModel):
+
+ model_id = 'dummy_pass_input_mask'
+
+ def load(self):
+ return True
+
+ def infer(
+ self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor
+ ) -> (GenericImageDataAccessor, dict):
+ return img.__class__(
+ (mask.data / mask.data.max()).astype('uint16')
+ )
+
+ def label_instance_class(
+ self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
+ ) -> GenericImageDataAccessor:
+ """
+ Returns a trivial segmentation, i.e. the input mask with value 1
+ """
+ super(DummyInstanceSegmentationModel, self).label_instance_class(img, mask, **kwargs)
+ return self.infer(img, mask)
diff --git a/pyproject.toml b/pyproject.toml
index d00d683d3e31b3bf58975c2cd9342c4a0c8ab298..882ad79c5a6e8bf5d99116212482db65478df8a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "model_server"
license = {file = "LICENSE"}
-version = "2024.09.30"
+version = "2024.10.01"
authors = [
{ name="Christopher Rhodes", email="christopher.rhodes@embl.de" },
]
diff --git a/tests/base/test_api.py b/tests/base/test_api.py
index f368dc05212c59f1b2ece208a719b4e249cedf70..e31b4366f3d4baa9371fcd80c3338cc2c5fbb013 100644
--- a/tests/base/test_api.py
+++ b/tests/base/test_api.py
@@ -8,7 +8,7 @@ import model_server.conf.testing as conf
from model_server.base.accessors import InMemoryDataAccessor
from model_server.base.api import app
from model_server.base.session import session
-from tests.base.test_model import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
+from model_server.conf.testing import DummySemanticSegmentationModel, DummyInstanceSegmentationModel
czifile = conf.meta['image_files']['czifile']
diff --git a/tests/base/test_model.py b/tests/base/test_model.py
index fb5a8f21e263ea5ab5f08d31f727ddcd24386e63..d975f7cd8725e0215391b4a526feab7cd69eeb31 100644
--- a/tests/base/test_model.py
+++ b/tests/base/test_model.py
@@ -1,58 +1,12 @@
-from math import floor
import unittest
-import numpy as np
-
import model_server.conf.testing as conf
-from model_server.base.accessors import CziImageFileAccessor, GenericImageDataAccessor, InMemoryDataAccessor
-from model_server.base.models import CouldNotLoadModelError, InstanceSegmentationModel, SemanticSegmentationModel, BinaryThresholdSegmentationModel
+from model_server.conf.testing import DummySemanticSegmentationModel, DummyInstanceSegmentationModel
+from model_server.base.accessors import CziImageFileAccessor
+from model_server.base.models import CouldNotLoadModelError, BinaryThresholdSegmentationModel
czifile = conf.meta['image_files']['czifile']
-class DummySemanticSegmentationModel(SemanticSegmentationModel):
-
- model_id = 'dummy_make_white_square'
-
- def load(self):
- return True
-
- def infer(self, img: GenericImageDataAccessor) -> (GenericImageDataAccessor, dict):
- super().infer(img)
- w = img.shape_dict['X']
- h = img.shape_dict['Y']
- result = np.zeros([h, w], dtype='uint8')
- result[floor(0.25 * h) : floor(0.75 * h), floor(0.25 * w) : floor(0.75 * w)] = 255
- return InMemoryDataAccessor(data=result), {'success': True}
-
- def label_pixel_class(
- self, img: GenericImageDataAccessor, **kwargs) -> GenericImageDataAccessor:
- mask, _ = self.infer(img)
- return mask
-
-
-class DummyInstanceSegmentationModel(InstanceSegmentationModel):
-
- model_id = 'dummy_pass_input_mask'
-
- def load(self):
- return True
-
- def infer(
- self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor
- ) -> (GenericImageDataAccessor, dict):
- return img.__class__(
- (mask.data / mask.data.max()).astype('uint16')
- )
-
- def label_instance_class(
- self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
- ) -> GenericImageDataAccessor:
- """
- Returns a trivial segmentation, i.e. the input mask with value 1
- """
- super(DummyInstanceSegmentationModel, self).label_instance_class(img, mask, **kwargs)
- return self.infer(img, mask)
-
class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/base/test_pipelines.py b/tests/base/test_pipelines.py
index 2a97c5b4088976f96a4973e0f70e8472fc722047..9f1b0303cbacf9fe9fe9969f7beadfe1ce942711 100644
--- a/tests/base/test_pipelines.py
+++ b/tests/base/test_pipelines.py
@@ -4,7 +4,7 @@ from model_server.base.accessors import generate_file_accessor, write_accessor_d
from model_server.base.pipelines import router, segment, segment_zproj
import model_server.conf.testing as conf
-from tests.base.test_model import DummySemanticSegmentationModel
+from model_server.conf.testing import DummySemanticSegmentationModel
czifile = conf.meta['image_files']['czifile']
zstack = conf.meta['image_files']['tifffile']
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 0a03973e78ca824083f2821157c70bb9adc77265..785358c92961662273f97f8f8c74037e03fc3cf3 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -11,7 +11,7 @@ from model_server.base.roiset import filter_df_overlap_bbox, filter_df_overlap_s
from model_server.base.roiset import RoiSet
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
import model_server.conf.testing as conf
-from tests.base.test_model import DummyInstanceSegmentationModel
+from model_server.conf.testing import DummyInstanceSegmentationModel
data = conf.meta['image_files']
output_path = conf.meta['output_path']
diff --git a/tests/base/test_roiset_derived.py b/tests/base/test_roiset_derived.py
index 52e7f6fc0a917d719262dcd0c19f3170414f2f18..156ef9fe42c472dc829085ed3b8c26bb46ac003a 100644
--- a/tests/base/test_roiset_derived.py
+++ b/tests/base/test_roiset_derived.py
@@ -7,7 +7,7 @@ from model_server.base.roiset import RoiSetWithDerivedChannelsExportParams, RoiS
from model_server.base.roiset import RoiSetWithDerivedChannels
from model_server.base.accessors import generate_file_accessor, PatchStack
import model_server.conf.testing as conf
-from tests.base.test_model import DummyInstanceSegmentationModel
+from model_server.conf.testing import DummyInstanceSegmentationModel
data = conf.meta['image_files']
params = conf.meta['roiset']