From 9010a5a196f2fe8a7325ef22c4f2d56677324d4d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 30 Aug 2023 16:44:59 +0200
Subject: [PATCH] Stuck on type validation in test. def
test_load_ilastik_model()
---
api.py | 13 ++++++++++---
model_server/ilastik.py | 32 +++++++++++++++++++-------------
model_server/model.py | 11 -----------
model_server/model_registry.py | 17 +++++++++++++++++
model_server/session.py | 3 ++-
run_server.py | 7 +++++++
tests/test_api.py | 12 +++++++++++-
tests/test_ilastik.py | 25 ++++++++++++++++++++++++-
8 files changed, 90 insertions(+), 30 deletions(-)
create mode 100644 model_server/model_registry.py
create mode 100644 run_server.py
diff --git a/api.py b/api.py
index 32eea187..0167a17c 100644
--- a/api.py
+++ b/api.py
@@ -2,7 +2,7 @@ from typing import Dict
from fastapi import FastAPI, HTTPException
-from model_server.session import Session
+from model_server.session import CouldNotFindModelError, Session
from model_server.workflow import infer_image_to_image
app = FastAPI(debug=True)
@@ -21,13 +21,20 @@ def list_active_models():
return session.describe_loaded_models()
@app.put('/models/load/')
-def load_model(model_id: str, params: Dict[str, str] = None) -> dict:
+# def load_model(model_id: str, misc: Dict[str, str]) -> dict:
+def load_model(model_id: str, misc: dict) -> dict:
if model_id in session.models.keys():
raise HTTPException(
status_code=409,
detail=f'Model with id {model_id} has already been loaded'
)
- session.load_model(model_id, params=params)
+ try:
+ session.load_model(model_id, params=misc)
+ except CouldNotFindModelError:
+ raise HTTPException(
+ status_code=404,
+ detail=f'Could not find {model_id} in defined models'
+ )
return session.describe_loaded_models()
@app.put('/i2i/infer/')
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index 99a812a7..606c93d4 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -1,11 +1,5 @@
import os
-from ilastik import app
-from ilastik.applets.dataSelection import DatasetInfo, FilesystemDatasetInfo
-from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo
-from ilastik.workflows.pixelClassification import PixelClassificationWorkflow
-from ilastik.workflows.objectClassification.objectClassificationWorkflow import ObjectClassificationWorkflow
-
import numpy as np
import vigra
@@ -20,11 +14,15 @@ class IlastikImageToImageModel(ImageToImageModel):
raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
self.project_file = str(params['project_file'])
self.shell = None
- # self.operator = None
super().__init__(autoload, params)
def load(self):
+ from ilastik import app
+ from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo
+
+ self.PreloadedArrayDatasetInfo = PreloadedArrayDatasetInfo
+
os.environ["LAZYFLOW_THREADS"] = "8"
os.environ["LAZYFLOW_TOTAL_RAM_MB"] = "24000"
@@ -33,7 +31,7 @@ class IlastikImageToImageModel(ImageToImageModel):
args.project = self.project_file
shell = app.main(args)
- if not isinstance(shell.workflow, self.workflow):
+ if not isinstance(shell.workflow, self.get_workflow()):
raise ParameterExpectedError(
f'Ilastik project file {self.project_file} does not describe an instance of {shell.workflow.__class__}'
)
@@ -44,13 +42,17 @@ class IlastikImageToImageModel(ImageToImageModel):
class IlastikPixelClassifierModel(IlastikImageToImageModel):
model_id = 'ilastik_pixel_classification'
- workflow = PixelClassificationWorkflow
+
+ @staticmethod
+ def get_workflow():
+ from ilastik.workflows.pixelClassification import PixelClassificationWorkflow
+ return PixelClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor) -> (np.ndarray, dict):
tagged_input_data = vigra.taggedView(input_img.data, 'xycz')
dsi = [
{
- 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
+ 'Raw Data': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
}
]
pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True) # [1 x w x h x n]
@@ -66,7 +68,11 @@ class IlastikPixelClassifierModel(IlastikImageToImageModel):
class IlastikObjectClassifierModel(IlastikImageToImageModel):
model_id = 'ilastik_object_classification'
- workflow = ObjectClassificationWorkflow
+
+ @staticmethod
+ def get_workflow():
+ from ilastik.workflows.objectClassification.objectClassificationWorkflow import ObjectClassificationWorkflow
+ return ObjectClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor, pxmap_img: GenericImageDataAccessor) -> (np.ndarray, dict):
tagged_input_data = vigra.taggedView(input_img.data, 'xycz')
@@ -74,8 +80,8 @@ class IlastikObjectClassifierModel(IlastikImageToImageModel):
dsi = [
{
- 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
- 'Prediction Maps': PreloadedArrayDatasetInfo(preloaded_array=tagged_pxmap_data),
+ 'Raw Data': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
+ 'Prediction Maps': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_pxmap_data),
}
]
diff --git a/model_server/model.py b/model_server/model.py
index 7ee63af4..a2d75c7b 100644
--- a/model_server/model.py
+++ b/model_server/model.py
@@ -27,17 +27,6 @@ class Model(ABC):
raise CouldNotLoadModelError()
return None
- @classmethod
- def get_all_subclasses(cls):
- """
- Recursively find all subclasses of Model
- :return: set of all subclasses of Model
- """
- def get_all_subclasses_of(cc):
- return set(cc.__subclasses__()).union(
- [s for c in cc.__subclasses__() for s in get_all_subclasses_of(c)])
- return get_all_subclasses_of(cls)
-
@abstractmethod
def load(self):
"""
diff --git a/model_server/model_registry.py b/model_server/model_registry.py
new file mode 100644
index 00000000..f6686dc0
--- /dev/null
+++ b/model_server/model_registry.py
@@ -0,0 +1,17 @@
+import model_server.ilastik
+import model_server.model
+
+def get_all_model_subclasses():
+ """
+ Recursively find all subclasses of Model
+ :return: set of all subclasses of Model
+ """
+
+ def get_all_subclasses_of(cc):
+ return set(cc.__subclasses__()).union(
+ [s for c in cc.__subclasses__() for s in get_all_subclasses_of(c)])
+
+ return get_all_subclasses_of(model_server.model.Model)
+
+if __name__ == '__main__':
+ print(get_all_model_subclasses())
\ No newline at end of file
diff --git a/model_server/session.py b/model_server/session.py
index 7508f103..69a94fcb 100644
--- a/model_server/session.py
+++ b/model_server/session.py
@@ -7,6 +7,7 @@ from typing import Dict
from conf.server import paths
from model_server.model import Model
+from model_server.model_registry import get_all_model_subclasses
from model_server.share import SharedImageDirectory
from model_server.workflow import WorkflowRunRecord
@@ -70,7 +71,7 @@ class Session(object):
:param params: optional parameters that are passed upon loading a model
:return: True if model successfully loaded, False if not
"""
- models = Model.get_all_subclasses()
+ models = get_all_model_subclasses()
for mc in models:
if hasattr(mc, 'model_id') and getattr(mc, 'model_id') == model_id:
try:
diff --git a/run_server.py b/run_server.py
new file mode 100644
index 00000000..1e90251c
--- /dev/null
+++ b/run_server.py
@@ -0,0 +1,7 @@
+import uvicorn
+
+host = '127.0.0.1'
+port = 8001
+
+if __name__ == '__main__':
+ uvicorn.run('api:app', **{'host': host, 'port': port, 'log_level': 'debug'}, reload=True)
\ No newline at end of file
diff --git a/tests/test_api.py b/tests/test_api.py
index 0b2e844b..bcb366ec 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -6,7 +6,7 @@ import unittest
from conf.testing import czifile
from model_server.model import DummyImageToImageModel
-class TestApiFromAutomatedClient(unittest.TestCase):
+class TestServerBaseClass(unittest.TestCase):
def setUp(self) -> None:
import uvicorn
host = '127.0.0.1'
@@ -37,6 +37,7 @@ class TestApiFromAutomatedClient(unittest.TestCase):
def tearDown(self) -> None:
self.server_process.terminate()
+class TestApiFromAutomatedClient(TestServerBaseClass):
def test_trivial_api_response(self):
resp = requests.get(self.uri, )
self.assertEqual(resp.status_code, 200)
@@ -59,6 +60,15 @@ class TestApiFromAutomatedClient(unittest.TestCase):
self.assertEqual(rj[model_id]['class'], 'DummyImageToImageModel')
return model_id
+ def test_respond_with_error_when_invalid_model_loaded(self):
+ model_id = 'not_a_real_model'
+ resp = requests.put(
+ self.uri + f'models/load',
+ params={'model_id': model_id}
+ )
+ self.assertEqual(resp.status_code, 404)
+ print(resp.content)
+
def test_respond_with_error_when_invalid_filepath_requested(self):
model_id = self.test_load_dummy_model()
resp = requests.put(
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index a2d204e6..643225b2 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -1,3 +1,4 @@
+import requests
import unittest
import numpy as np
@@ -5,7 +6,9 @@ import numpy as np
from conf.testing import czifile, ilastik, output_path
from model_server.image import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.ilastik import IlastikObjectClassifierModel, IlastikPixelClassifierModel
+from model_server.model import Model
from model_server.workflow import infer_image_to_image
+from tests.test_api import TestServerBaseClass
class TestIlastikPixelClassification(unittest.TestCase):
def setUp(self) -> None:
@@ -31,6 +34,10 @@ class TestIlastikPixelClassification(unittest.TestCase):
with self.assertRaises(AttributeError):
pxmap , _= model.infer(input_img)
+ def test_ilastik_subclasses_are_found(self):
+ self.assertIn(IlastikPixelClassifierModel, Model.get_all_subclasses())
+ self.assertIn(IlastikObjectClassifierModel, Model.get_all_subclasses())
+
def test_run_pixel_classifier_on_random_data(self):
model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
w = 512
@@ -89,4 +96,20 @@ class TestIlastikPixelClassification(unittest.TestCase):
channel=0,
)
self.assertTrue(result.success)
- self.assertGreater(result.timer_results['inference'], 1.0)
\ No newline at end of file
+ self.assertGreater(result.timer_results['inference'], 1.0)
+
+class TestIlastikOverApi(TestServerBaseClass):
+ def test_load_ilastik_model(self):
+ model_id = IlastikPixelClassifierModel.model_id
+ resp_load = requests.put(
+ self.uri + f'models/load',
+ params={'model_id': model_id},
+ # data={'project_file': str(ilastik['pixel_classifier'])},
+ data={'project_file': 'hii',},
+ )
+ self.assertEqual(resp_load.status_code, 200, resp_load.content)
+ # resp_list = requests.get(self.uri + 'models')
+ # self.assertEqual(resp_list.status_code, 200)
+ # rj = resp_list.json()
+ # self.assertEqual(rj[model_id]['class'], 'DummyImageToImageModel')
+ # return model_id
\ No newline at end of file
--
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