diff --git a/api.py b/api.py
index abd27bbfe85291362ae5d9e1691d6d3393154b09..45ee844fcd17d6f33a657b615aba446c02a6608f 100644
--- a/api.py
+++ b/api.py
@@ -1,10 +1,10 @@
from fastapi import FastAPI, HTTPException
-from model_server.ilastik import IlastikImageToImageModel, IlastikPixelClassifierModel, IlastikObjectClassifierModel
-from model_server.model import DummyImageToImageModel, ParameterExpectedError
+from extensions.ilastik.models import IlastikImageToImageModel, IlastikPixelClassifierModel, IlastikObjectClassifierModel
+from model_server.models import DummyImageToImageModel, ParameterExpectedError
from model_server.session import Session
-from model_server.workflow import infer_image_to_image
-from model_server.workflow_ilastik import infer_px_then_ob_model
+from model_server.workflows import infer_image_to_image
+from extensions.ilastik.workflows import infer_px_then_ob_model
app = FastAPI(debug=True)
session = Session()
diff --git a/extensions/__init__.py b/extensions/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/extensions/examples/__init__.py b/extensions/examples/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/ilastik3d.py b/extensions/examples/ilastik3d.py
similarity index 100%
rename from examples/ilastik3d.py
rename to extensions/examples/ilastik3d.py
diff --git a/extensions/ilastik/__init__.py b/extensions/ilastik/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/conf/ilastik.py b/extensions/ilastik/conf.py
similarity index 100%
rename from conf/ilastik.py
rename to extensions/ilastik/conf.py
diff --git a/model_server/ilastik.py b/extensions/ilastik/models.py
similarity index 91%
rename from model_server/ilastik.py
rename to extensions/ilastik/models.py
index aad0f38cc3adba237fd3161f7f9badb4cc62a344..ddcb0db5d6f4496e70196781d485e4da2ab43257 100644
--- a/model_server/ilastik.py
+++ b/extensions/ilastik/models.py
@@ -4,9 +4,9 @@ from pathlib import Path
import numpy as np
import vigra
-import conf.ilastik
-from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
-from model_server.model import ImageToImageModel, ParameterExpectedError
+import extensions.ilastik.conf
+from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor
+from model_server.models import ImageToImageModel, ParameterExpectedError
class IlastikImageToImageModel(ImageToImageModel):
@@ -14,7 +14,7 @@ class IlastikImageToImageModel(ImageToImageModel):
def __init__(self, params, autoload=True):
self.project_file = Path(params['project_file'])
params['project_file'] = self.project_file.__str__()
- pap = conf.ilastik.paths['project_files'] / self.project_file
+ pap = extensions.ilastik.conf.paths['project_files'] / self.project_file
self.project_file_abspath = pap
if not pap.exists():
raise FileNotFoundError(f'Project file does not exist: {pap}')
@@ -53,7 +53,7 @@ class IlastikPixelClassifierModel(IlastikImageToImageModel):
@staticmethod
def get_workflow():
- from ilastik.workflows.pixelClassification import PixelClassificationWorkflow
+ from ilastik.workflows import PixelClassificationWorkflow
return PixelClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor) -> (np.ndarray, dict):
diff --git a/extensions/ilastik/tests/__init__.py b/extensions/ilastik/tests/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/test_ilastik.py b/extensions/ilastik/tests/test_ilastik.py
similarity index 96%
rename from tests/test_ilastik.py
rename to extensions/ilastik/tests/test_ilastik.py
index 747de17a76d1cd487dd3c304f002b1d4a1029b83..f8ec7e9e683e4a96c605a0c748e8d6ed1b5fd04a 100644
--- a/tests/test_ilastik.py
+++ b/extensions/ilastik/tests/test_ilastik.py
@@ -4,9 +4,9 @@ import unittest
import numpy as np
import conf.testing
-from model_server.image import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.ilastik import IlastikObjectClassifierModel, IlastikPixelClassifierModel
-from model_server.workflow import infer_image_to_image
+from model_server.accessors import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+from extensions.ilastik.models import IlastikObjectClassifierModel, IlastikPixelClassifierModel
+from model_server.workflows import infer_image_to_image
from tests.test_api import TestServerBaseClass
class TestIlastikPixelClassification(unittest.TestCase):
diff --git a/model_server/workflow_ilastik.py b/extensions/ilastik/workflows.py
similarity index 88%
rename from model_server/workflow_ilastik.py
rename to extensions/ilastik/workflows.py
index db412bb4b9b2ba1e33b0ba42d9d5108bbfcdce5d..45763ad7415600e6b6dc441c33dee4c0cc8dc647 100644
--- a/model_server/workflow_ilastik.py
+++ b/extensions/ilastik/workflows.py
@@ -2,13 +2,11 @@
Implementation of image analysis work behind API endpoints, without knowledge of persistent data in server session.
"""
from pathlib import Path
-from time import perf_counter
from typing import Dict
-from model_server.ilastik import IlastikPixelClassifierModel, IlastikObjectClassifierModel
-from model_server.image import generate_file_accessor, write_accessor_data_to_file
-from model_server.model import Model
-from model_server.workflow import Timer
+from extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierModel
+from model_server.accessors import generate_file_accessor, write_accessor_data_to_file
+from model_server.workflows import Timer
from pydantic import BaseModel
diff --git a/model_server/image.py b/model_server/accessors.py
similarity index 100%
rename from model_server/image.py
rename to model_server/accessors.py
diff --git a/model_server/model.py b/model_server/models.py
similarity index 96%
rename from model_server/model.py
rename to model_server/models.py
index a2d75c7b5453a8ad14092f6ea61a57d6860ea0fb..4285b49c4d8a55bb3b77135d9e578546ea851d4c 100644
--- a/model_server/model.py
+++ b/model_server/models.py
@@ -4,7 +4,7 @@ import os
import numpy as np
-from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
+from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor
class Model(ABC):
diff --git a/model_server/session.py b/model_server/session.py
index eb82d1b6f089ccf990b4ca8fadff93f893e88a20..3d5db0bc16cb37fbb01f505ae143282294779e03 100644
--- a/model_server/session.py
+++ b/model_server/session.py
@@ -6,9 +6,9 @@ from time import strftime, localtime
from typing import Dict
import conf.defaults
-from model_server.model import Model
+from model_server.models import Model
from model_server.share import SharedImageDirectory
-from model_server.workflow import WorkflowRunRecord
+from model_server.workflows import WorkflowRunRecord
def create_manifest_json():
pass
@@ -17,9 +17,6 @@ class Session(object):
"""
Singleton class for a server session that persists data between API calls
"""
- # inbound = SharedImageDirectory(conf.defaults.paths['inbound_images'])
- # outbound = SharedImageDirectory(conf.defaults.paths['outbound_images'])
- # where_records = conf.defaults.paths['logs']
def __new__(cls):
if not hasattr(cls, 'instance'):
@@ -31,8 +28,6 @@ class Session(object):
self.models = {} # model_id : model object
self.manifest = [] # paths to data as well as other metadata from each inference run
self.paths = self.make_paths(root)
- # self.session_id = self.create_session_id(self.paths['logs'])
- # self.session_id = self.create_session_id(self.paths)
self.session_log = self.paths['logs'] / f'session.log'
self.log_event('Initialized session')
self.manifest_json = self.paths['logs'] / f'manifest.json'
diff --git a/model_server/share.py b/model_server/share.py
index e270dea6d75bc59d2cf4fe5394775672b1aa509c..fad2b2f03d1a6c19909215a3f34c28867c37ac71 100644
--- a/model_server/share.py
+++ b/model_server/share.py
@@ -1,3 +1,8 @@
+"""
+Classes that manage data sharing between server and outside processes. Currently just a directory on a shared
+filesystem; but may expand to include data transfer over API, shared memory objects, etc.
+"""
+
import os
import pathlib
diff --git a/model_server/workflow.py b/model_server/workflows.py
similarity index 92%
rename from model_server/workflow.py
rename to model_server/workflows.py
index 7c09bc46835eacb04a31871534a91786991267ec..c81d2afdc3e59e8153e1710524e286961ecd7746 100644
--- a/model_server/workflow.py
+++ b/model_server/workflows.py
@@ -5,8 +5,8 @@ from pathlib import Path
from time import perf_counter
from typing import Dict
-from model_server.image import generate_file_accessor, write_accessor_data_to_file
-from model_server.model import Model
+from model_server.accessors import generate_file_accessor, write_accessor_data_to_file
+from model_server.models import Model
from pydantic import BaseModel
diff --git a/simulate_automic.py b/simulate_automic.py
deleted file mode 100644
index 94e042c8b0596aeb5bbb7ae493b1569fec4aedf8..0000000000000000000000000000000000000000
--- a/simulate_automic.py
+++ /dev/null
@@ -1,55 +0,0 @@
-from multiprocessing import Process
-import os
-import requests
-import unittest
-
-import uvicorn
-
-import conf.server
-
-# run server in subprocess
-
-host = '127.0.0.1'
-port = 5000
-server_process = Process(
- target=uvicorn.run,
- args=('api:app', ),
- kwargs={'host': host, 'port': port, 'log_level': 'debug'},
- daemon=True
-)
-uri = f'http://{host}:{port}/'
-server_process.start()
-
-# configure and validate folders etc.
-paths = conf.server.paths
-paths['automic_watch_folder'] = paths['images']['inbound']
-paths['test_source_files'] = ''
-
-# load models by API
-
-# prompt user start AutoMic loop
-
-# move files from one folder to another
-def copy_one_input_image_files(copy=True):
- pattern = ''
- os.listdir(paths['test_source_files'])
-
- # order by increaseing alpha order? timestamp?
-
-
- if copy:
- # copy image from test source files to automic watch folder
- else:
- # move them
-
- # recursive repeat until nothign is left
-
-# point to server session logs
-
-
-# shut down server
-server_process.terminate()
-
-
-# do something with the data?
-
diff --git a/tests/test_api.py b/tests/test_api.py
index 40ecfd2985e6a9450fe1bf273eddd18a8890fb55..778c378f725c094e9472df0d76f6104bc9166975 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -4,7 +4,7 @@ import requests
import unittest
from conf.testing import czifile
-from model_server.model import DummyImageToImageModel
+from model_server.models import DummyImageToImageModel
class TestServerBaseClass(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_image.py b/tests/test_image.py
index 6c085b6cb03b52cabbf7eb230792058e8618a966..3d590990062101a8ccfaa2420735f0ddc7532161 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -3,7 +3,7 @@ import unittest
import numpy as np
from conf.testing import czifile, output_path
-from model_server.image import CziImageFileAccessor, DataShapeError, InMemoryDataAccessor, write_accessor_data_to_file
+from model_server.accessors import CziImageFileAccessor, DataShapeError, InMemoryDataAccessor, write_accessor_data_to_file
class TestCziImageFileAccess(unittest.TestCase):
diff --git a/tests/test_model.py b/tests/test_model.py
index a265cbe4bd9860b8b053ca9ad768a7ca41885554..661aeadf93825afc430e55f56326def0fe3f43b0 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -1,7 +1,7 @@
import unittest
from conf.testing import czifile
-from model_server.image import CziImageFileAccessor
-from model_server.model import DummyImageToImageModel, CouldNotLoadModelError
+from model_server.accessors import CziImageFileAccessor
+from model_server.models import DummyImageToImageModel, CouldNotLoadModelError
class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
diff --git a/tests/test_session.py b/tests/test_session.py
index a03e1ad1b45a43ef5fe217935c5ed13a8431410c..fd4b79c94c64b6bd11fa679244d766a6671a3ceb 100644
--- a/tests/test_session.py
+++ b/tests/test_session.py
@@ -1,5 +1,5 @@
import unittest
-from model_server.model import DummyImageToImageModel
+from model_server.models import DummyImageToImageModel
from model_server.session import Session
class TestGetSessionObject(unittest.TestCase):
@@ -38,7 +38,7 @@ class TestGetSessionObject(unittest.TestCase):
def test_session_records_workflow(self):
import json
- from model_server.workflow import WorkflowRunRecord
+ from model_server.workflows import WorkflowRunRecord
sesh = Session()
di = WorkflowRunRecord(
model_id='test_model',
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
index 6bc8d56d88f960d63cdada4efe68e65c6ecd572f..2cab499d04c222651894d9064c1f7f990050d626 100644
--- a/tests/test_workflow.py
+++ b/tests/test_workflow.py
@@ -1,8 +1,8 @@
import unittest
from conf.testing import czifile, output_path
-from model_server.model import DummyImageToImageModel
-from model_server.workflow import infer_image_to_image
+from model_server.models import DummyImageToImageModel
+from model_server.workflows import infer_image_to_image
class TestGetSessionObject(unittest.TestCase):