From b9f27095a0ca3494043beed30afb927fe66add30 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 31 Aug 2023 16:33:41 +0200
Subject: [PATCH] Can now load ilastik models by API
---
api.py | 36 ++++++++++++++----------------------
tests/test_api.py | 1 -
tests/test_ilastik.py | 39 ++++++++++++++++++++++++---------------
3 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/api.py b/api.py
index 1c168b44..ea23b59e 100644
--- a/api.py
+++ b/api.py
@@ -27,30 +27,22 @@ def load_dummy_model() -> dict:
return {'model_id': session.load_model(DummyImageToImageModel)}
@app.put('/models/ilastik/pixel_classification/load/')
-def load_ilastik_pixel_classification_model(params: str) -> dict:
- return {'model_id': session.load_model(IlastikPixelClassifierModel, params)}
+def load_ilastik_pixel_classification_model(project_file: str) -> dict:
+ return {
+ 'model_id': session.load_model(
+ IlastikPixelClassifierModel,
+ {'project_file': project_file}
+ )
+ }
@app.put('/models/ilastik/object_classification/load/')
-def load_ilastik_object_classification_model(params: str) -> dict:
- return {'model_id': session.load_model(IlastikObjectClassifierModel, params)}
-
-# @app.put('/models/ilastik/pixel_classification/load/')
-# def infer_ilastik_pixel_classification_from_file(input_filename: str, channel: int = None) -> dict:
-# inpath = session.inbound.path / input_filename
-# if not inpath.exists():
-# raise HTTPException(
-# status_code=404,
-# detail=f'Could not find file:\n{inpath}'
-# )
-#
-# record = infer_image_to_image(
-# inpath,
-# session.models[model_id]['object'],
-# session.outbound.path,
-# channel=channel,
-# )
-# session.record_workflow_run(record)
-# return record
+def load_ilastik_object_classification_model(project_file: str) -> dict:
+ return {
+ 'model_id': session.load_model(
+ IlastikObjectClassifierModel,
+ {'project_file': project_file}
+ )
+ }
@app.put('/infer/from_image_file')
def infer_img(model_id: str, input_filename: str, channel: int = None) -> dict:
diff --git a/tests/test_api.py b/tests/test_api.py
index c61e4c2b..e4091cb2 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -47,7 +47,6 @@ class TestApiFromAutomatedClient(TestServerBaseClass):
self.assertEqual(resp.content, b'{}')
def test_load_dummy_model(self):
- # model_key = DummyImageToImageModel.__name__ + '_00'
resp_load = requests.put(
self.uri + f'models/dummy/load',
)
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index 643225b2..8b687874 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -34,9 +34,6 @@ 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']})
@@ -48,6 +45,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
pxmap, _ = model.infer(input_img)
self.assertEqual(pxmap.shape, (w, h, 2, 1))
+
def test_run_pixel_classifier(self):
channel = 0
model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
@@ -99,17 +97,28 @@ class TestIlastikPixelClassification(unittest.TestCase):
self.assertGreater(result.timer_results['inference'], 1.0)
class TestIlastikOverApi(TestServerBaseClass):
- def test_load_ilastik_model(self):
- model_id = IlastikPixelClassifierModel.model_id
+ def test_load_ilastik_pixel_model(self):
+ resp_load = requests.put(
+ self.uri + 'models/ilastik/pixel_classification/load/',
+ params={'project_file': str(ilastik['pixel_classifier'])},
+ )
+ model_id = resp_load.json()['model_id']
+
+ self.assertEqual(resp_load.status_code, 200, resp_load.json())
+ resp_list = requests.get(self.uri + 'models')
+ self.assertEqual(resp_list.status_code, 200)
+ rj = resp_list.json()
+ self.assertEqual(rj[model_id]['class'], 'IlastikPixelClassifierModel')
+
+ def test_load_ilastik_object_model(self):
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.uri + 'models/ilastik/object_classification/load/',
+ params={'project_file': str(ilastik['object_classifier'])},
)
- 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
+ model_id = resp_load.json()['model_id']
+
+ self.assertEqual(resp_load.status_code, 200, resp_load.json())
+ resp_list = requests.get(self.uri + 'models')
+ self.assertEqual(resp_list.status_code, 200)
+ rj = resp_list.json()
+ self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierModel')
\ No newline at end of file
--
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