diff --git a/.idea/model_server.iml b/.idea/model_server.iml
index 167262fe593bfe12ad8b4ccee58da6af496a3f21..57c52987a7d5da8ba7e7a5c64de0344a03c7099c 100644
--- a/.idea/model_server.iml
+++ b/.idea/model_server.iml
@@ -1,7 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
- <content url="file://$MODULE_DIR$" />
+ <content url="file://$MODULE_DIR$">
+ <sourceFolder url="file://$MODULE_DIR$/model_server" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="false" />
+ </content>
<orderEntry type="jdk" jdkName="Python 3.9 (model_server_env)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 86b6afe42c62b8865f1b7826f89501e0c8ecb754..f74a804816d1031d6b9d6976be2d2318bf0fca76 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -8,8 +8,8 @@ from skimage.io import imread, imsave
import czifile
import tifffile
-from model_server.base.process import make_rgb
-from model_server.base.process import is_mask
+from base.process import make_rgb
+from base.process import is_mask
class GenericImageDataAccessor(ABC):
diff --git a/model_server/base/annotators.py b/model_server/base/annotators.py
index f0e1df914b0c04fbdf93f68a0d78c85469870dd8..9c13dafbc559b647aa1c1796e9f20fb0f90cf32e 100644
--- a/model_server/base/annotators.py
+++ b/model_server/base/annotators.py
@@ -2,7 +2,7 @@ import numpy as np
from matplotlib import font_manager
from PIL import Image, ImageDraw, ImageFont
-from model_server.base.process import rescale
+from base.process import rescale
def _get_font(font_size=18):
return ImageFont.truetype(
diff --git a/model_server/base/api.py b/model_server/base/api.py
index 13abef8ee4d76157d91dd7e4c5227238161366c9..22554a062c65bb468b570522b6b96a17ca716b2d 100644
--- a/model_server/base/api.py
+++ b/model_server/base/api.py
@@ -1,11 +1,11 @@
from fastapi import FastAPI, HTTPException
from pydantic import BaseModel
-from model_server.base.models import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
-from model_server.base.session import Session, InvalidPathError
-from model_server.base.validators import validate_workflow_inputs
-from model_server.base.workflows import classify_pixels
-from model_server.extensions.ilastik.workflows import infer_px_then_ob_model
+from base.models import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
+from base.session import Session, InvalidPathError
+from base.validators import validate_workflow_inputs
+from base.workflows import classify_pixels
+from extensions.ilastik.workflows import infer_px_then_ob_model
app = FastAPI(debug=True)
session = Session()
diff --git a/model_server/base/czi_util.py b/model_server/base/czi_util.py
index 6c8c5db8c27eeefea2e4bad32122d34f306bf16e..3facb61ae513bb8009beef7ad33c63f304f754c5 100644
--- a/model_server/base/czi_util.py
+++ b/model_server/base/czi_util.py
@@ -5,7 +5,7 @@ import czifile
import numpy as np
import pandas as pd
-from model_server.base.accessors import InMemoryDataAccessor
+from base.accessors import InMemoryDataAccessor
def dump_czi_subblock_table(czif: czifile.CziFile, where: Path):
diff --git a/model_server/base/models.py b/model_server/base/models.py
index 228bcb66a7451837eaa6fd3b23a4fe489c335b95..264230b991df744bbf098a796be5ab3627517fe1 100644
--- a/model_server/base/models.py
+++ b/model_server/base/models.py
@@ -5,7 +5,7 @@ from typing import Union
import numpy as np
from pydantic import BaseModel
-from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, PatchStack
+from base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, PatchStack
class Model(ABC):
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 68ee831a58a7088d74e8959e8e47e5734780ac6e..847c255187da7a22c94302cdca11c4e28edb6414 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -14,12 +14,12 @@ from skimage.measure import label, regionprops_table, shannon_entropy, find_cont
from sklearn.preprocessing import PolynomialFeatures
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 get_safe_contours, pad, rescale, resample_to_8bit, make_rgb
-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 generate_file_accessor, PatchStack
-from model_server.base.process import mask_largest_object
+from base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+from base.models import InstanceSegmentationModel
+from base.process import get_safe_contours, 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 generate_file_accessor, PatchStack
+from base.process import mask_largest_object
class PatchParams(BaseModel):
diff --git a/model_server/base/session.py b/model_server/base/session.py
index 6916f5b6462293bf86f6d186249d80163576bfd8..20987ba556138ff65850b1f0f73b9ce2f8bc68cd 100644
--- a/model_server/base/session.py
+++ b/model_server/base/session.py
@@ -8,8 +8,8 @@ from typing import Union
import pandas as pd
-import model_server.conf.defaults
-from model_server.base.models import Model
+import conf.defaults
+from base.models import Model
logger = logging.getLogger(__name__)
@@ -97,13 +97,13 @@ class Session(object, metaclass=Singleton):
:return: dictionary of session paths
"""
if root is None:
- root_path = Path(model_server.conf.defaults.root)
+ root_path = Path(conf.defaults.root)
else:
root_path = Path(root)
sid = Session.create_session_id(root_path)
paths = {'root': root_path}
for pk in ['inbound_images', 'outbound_images', 'logs', 'tables']:
- pa = root_path / sid / model_server.conf.defaults.subdirectories[pk]
+ pa = root_path / sid / conf.defaults.subdirectories[pk]
paths[pk] = pa
try:
pa.mkdir(parents=True, exist_ok=True)
diff --git a/model_server/base/util.py b/model_server/base/util.py
index 112118832acb0d15caed1ef29118c3bcc43ea7df..15a2021c09399d4d6773ef12a4cb6ff6a7c189e8 100644
--- a/model_server/base/util.py
+++ b/model_server/base/util.py
@@ -6,8 +6,8 @@ from typing import List
import pandas as pd
-from model_server.base.accessors import InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.base.models import Model
+from base.accessors import InMemoryDataAccessor, write_accessor_data_to_file
+from base.models import Model
def autonumber_new_directory(where: str, prefix: str) -> str:
"""
diff --git a/model_server/base/validators.py b/model_server/base/validators.py
index b4142b0f6ef99904d3bdb13fd7c5494e5df4fe18..c55adb192826bba255de2d86b2e6195c57b25083 100644
--- a/model_server/base/validators.py
+++ b/model_server/base/validators.py
@@ -1,6 +1,6 @@
from fastapi import HTTPException
-from model_server.base.session import Session
+from base.session import Session
session = Session()
diff --git a/model_server/base/workflows.py b/model_server/base/workflows.py
index 9ff6f57c04c4278a59fd683040d42ce6111cae52..5e712106e25cc0a5080179bb2450a83a7f13c7e9 100644
--- a/model_server/base/workflows.py
+++ b/model_server/base/workflows.py
@@ -6,8 +6,8 @@ from pathlib import Path
from time import perf_counter
from typing import Dict
-from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file
-from model_server.base.models import SemanticSegmentationModel
+from base.accessors import generate_file_accessor, write_accessor_data_to_file
+from base.models import SemanticSegmentationModel
from pydantic import BaseModel
diff --git a/model_server/scripts/run_server.py b/model_server/scripts/run_server.py
index 2ca5e559019e3444c3f135450db749736e88bf29..07236bd9555eb4051e1db7a9f2953c7054efec62 100644
--- a/model_server/scripts/run_server.py
+++ b/model_server/scripts/run_server.py
@@ -6,7 +6,7 @@ from urllib3 import Retry
import uvicorn
import webbrowser
-from model_server.conf.defaults import server_conf
+from conf.defaults import server_conf
def parse_args():
parser = argparse.ArgumentParser(
diff --git a/model_server/scripts/verify_multichannel_ilastik_inputs.py b/model_server/scripts/verify_multichannel_ilastik_inputs.py
index 1159b3f1ae42d9902474a854c7f85f1134748fe5..ec0e53fa38575a4a9d24e3e8959e7ee43236b665 100644
--- a/model_server/scripts/verify_multichannel_ilastik_inputs.py
+++ b/model_server/scripts/verify_multichannel_ilastik_inputs.py
@@ -4,8 +4,8 @@ import h5py
import numpy as np
import pandas as pd
-from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file, InMemoryDataAccessor
-from model_server.extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
+from base.accessors import generate_file_accessor, write_accessor_data_to_file, InMemoryDataAccessor
+from extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
def get_input_files(where_ilp: Path) -> list:
files = []
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 014eda2c283ce9297f3084513abad66497303cbd..1f730c47b057ae546adee419019edffeec9762a6 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -2,10 +2,10 @@ import unittest
import numpy as np
-from model_server.base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
+from 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
+from conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
+from base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
def _random_int(*args):
return np.random.randint(0, 2 ** 8, size=args, dtype='uint8')
diff --git a/tests/test_api.py b/tests/test_api.py
index 6e336a9c0e46fddf1f627667618ff13516a58fa6..562982e497abcd5c9396836df490f791b8d0da58 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -6,7 +6,7 @@ import requests
import unittest
from urllib3 import Retry
-from model_server.conf.testing import czifile
+from conf.testing import czifile
class TestServerBaseClass(unittest.TestCase):
diff --git a/tests/test_model.py b/tests/test_model.py
index 91043f24e7ec354759dafa2c61b833b1dbd78688..7c0c0ec7030aea515fa444adc6e4c8fb294312a8 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -1,7 +1,7 @@
import unittest
-from model_server.conf.testing import czifile
-from model_server.base.accessors import CziImageFileAccessor
-from model_server.base.models import DummySemanticSegmentationModel, DummyInstanceSegmentationModel, CouldNotLoadModelError
+from conf.testing import czifile
+from base.accessors import CziImageFileAccessor
+from base.models import DummySemanticSegmentationModel, DummyInstanceSegmentationModel, CouldNotLoadModelError
class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_process.py b/tests/test_process.py
index d2fb33b9cc9a8b6af04c8eacd99b6b87d7d64527..63d8bf41d070629be2ae7b8f222eb4d47a167333 100644
--- a/tests/test_process.py
+++ b/tests/test_process.py
@@ -1,10 +1,9 @@
import unittest
import numpy as np
-from skimage.measure import find_contours
-from model_server.base.annotators import draw_contours_on_patch
-from model_server.base.process import get_safe_contours, mask_largest_object, pad
+from base.annotators import draw_contours_on_patch
+from base.process import get_safe_contours, mask_largest_object, pad
class TestProcessingUtilityMethods(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index 98e07ef2de36564ff278d2643860393a0ba620c1..c798fa8bacdc1bd26591f33aa1ba7a74e7a8ea99 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -9,10 +9,10 @@ import pandas as pd
from model_server.conf.testing import output_path, roiset_test_data
-from model_server.base.roiset import RoiSetExportParams, RoiSetMetaParams
-from model_server.base.roiset import RoiSet
-from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
-from model_server.base.models import DummyInstanceSegmentationModel
+from base.roiset import RoiSetExportParams, RoiSetMetaParams
+from base.roiset import RoiSet
+from base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
+from base.models import DummyInstanceSegmentationModel
class BaseTestRoiSetMonoProducts(object):
diff --git a/tests/test_session.py b/tests/test_session.py
index 7626faa672496c291800397d1c9ce90a2b6cc287..ce49dbceef0d43620cf94f41a9fbed05fb2cf6e0 100644
--- a/tests/test_session.py
+++ b/tests/test_session.py
@@ -3,8 +3,8 @@ import pathlib
from pydantic import BaseModel
import unittest
-from model_server.base.models import DummySemanticSegmentationModel
-from model_server.base.session import Session
+from base.models import DummySemanticSegmentationModel
+from base.session import Session
class TestGetSessionObject(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
index 6e9603ea7418ba367b482a00b8dd8c9aafa8820d..cc66cf2109433f4a2b544e7930de8c29fbae8969 100644
--- a/tests/test_workflow.py
+++ b/tests/test_workflow.py
@@ -1,8 +1,8 @@
import unittest
-from model_server.conf.testing import czifile, output_path
-from model_server.base.models import DummySemanticSegmentationModel
-from model_server.base.workflows import classify_pixels
+from conf.testing import czifile, output_path
+from base.models import DummySemanticSegmentationModel
+from base.workflows import classify_pixels
class TestGetSessionObject(unittest.TestCase):