From 5dc646d95c2784e6ff3bedb1db0b8b1af409d50d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 16 Oct 2023 16:27:52 +0200
Subject: [PATCH] Made the one implemented ilastik object classification model
accomodate only the ilastik workflow that requires pixel prediction maps
---
extensions/ilastik/models.py | 8 ++++----
extensions/ilastik/router.py | 4 ++--
extensions/ilastik/tests/test_ilastik.py | 6 +++---
extensions/ilastik/workflows.py | 6 +++---
4 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/extensions/ilastik/models.py b/extensions/ilastik/models.py
index 47c81abb..a6daf81a 100644
--- a/extensions/ilastik/models.py
+++ b/extensions/ilastik/models.py
@@ -77,13 +77,13 @@ class IlastikPixelClassifierModel(IlastikImageToImageModel):
)
return InMemoryDataAccessor(data=yxcz), {'success': True}
-class IlastikObjectClassifierModel(IlastikImageToImageModel):
- model_id = 'ilastik_object_classification'
+class IlastikObjectClassifierFromPixelPredictionsModel(IlastikImageToImageModel):
+ model_id = 'ilastik_object_classification_from_pixel_predictions'
@staticmethod
def get_workflow():
- from ilastik.workflows.objectClassification.objectClassificationWorkflow import ObjectClassificationWorkflow
- return ObjectClassificationWorkflow
+ from ilastik.workflows.objectClassification.objectClassificationWorkflow import ObjectClassificationWorkflowPrediction
+ return ObjectClassificationWorkflowPrediction
def infer(self, input_img: GenericImageDataAccessor, pxmap_img: GenericImageDataAccessor) -> (np.ndarray, dict):
tagged_input_data = vigra.taggedView(input_img.data, 'yxcz')
diff --git a/extensions/ilastik/router.py b/extensions/ilastik/router.py
index 155d8fa0..3287dc47 100644
--- a/extensions/ilastik/router.py
+++ b/extensions/ilastik/router.py
@@ -3,7 +3,7 @@ from fastapi import APIRouter, HTTPException
from model_server.session import Session
from model_server.validators import validate_workflow_inputs
-from extensions.ilastik.models import IlastikImageToImageModel, IlastikPixelClassifierModel, IlastikObjectClassifierModel
+from extensions.ilastik.models import IlastikImageToImageModel, IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
from model_server.models import ParameterExpectedError
from extensions.ilastik.workflows import infer_px_then_ob_model
@@ -46,7 +46,7 @@ def load_ilastik_pixel_classification_model(project_file: str, duplicate: bool =
@router.put('/object_classification/load/')
def load_ilastik_object_classification_model(project_file: str, duplicate: bool = True) -> dict:
- return load_ilastik_model(IlastikObjectClassifierModel, project_file, duplicate=duplicate)
+ return load_ilastik_model(IlastikObjectClassifierFromPixelPredictionsModel, project_file, duplicate=duplicate)
@router.put('/pixel_then_object_classification/infer')
def infer_px_then_ob_maps(px_model_id: str, ob_model_id: str, input_filename: str, channel: int = None) -> dict:
diff --git a/extensions/ilastik/tests/test_ilastik.py b/extensions/ilastik/tests/test_ilastik.py
index 555d8286..348f955e 100644
--- a/extensions/ilastik/tests/test_ilastik.py
+++ b/extensions/ilastik/tests/test_ilastik.py
@@ -5,7 +5,7 @@ import numpy as np
import conf.testing
from model_server.accessors import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
-from extensions.ilastik.models import IlastikObjectClassifierModel, IlastikPixelClassifierModel
+from extensions.ilastik.models import IlastikObjectClassifierFromPixelPredictionsModel, IlastikPixelClassifierModel
from model_server.workflows import infer_image_to_image
from tests.test_api import TestServerBaseClass
@@ -83,7 +83,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_object_classifier(self):
self.test_run_pixel_classifier()
fp = conf.testing.czifile['path']
- model = IlastikObjectClassifierModel(
+ model = IlastikObjectClassifierFromPixelPredictionsModel(
{'project_file': conf.testing.ilastik['object_classifier']}
)
objmap, _ = model.infer(self.mono_image, self.pxmap)
@@ -167,7 +167,7 @@ class TestIlastikOverApi(TestServerBaseClass):
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')
+ self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierFromPixelPredictionsModel')
return model_id
def test_ilastik_infer_pixel_probability(self):
diff --git a/extensions/ilastik/workflows.py b/extensions/ilastik/workflows.py
index 45763ad7..1f622b67 100644
--- a/extensions/ilastik/workflows.py
+++ b/extensions/ilastik/workflows.py
@@ -4,7 +4,7 @@ Implementation of image analysis work behind API endpoints, without knowledge of
from pathlib import Path
from typing import Dict
-from extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierModel
+from extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
from model_server.accessors import generate_file_accessor, write_accessor_data_to_file
from model_server.workflows import Timer
@@ -23,7 +23,7 @@ class WorkflowRunRecord(BaseModel):
def infer_px_then_ob_model(
fpi: Path,
px_model: IlastikPixelClassifierModel,
- ob_model: IlastikObjectClassifierModel,
+ ob_model: IlastikObjectClassifierFromPixelPredictionsModel,
where_output: Path,
**kwargs
) -> WorkflowRunRecord:
@@ -38,7 +38,7 @@ def infer_px_then_ob_model(
:return:
"""
assert isinstance(px_model, IlastikPixelClassifierModel)
- assert isinstance(ob_model, IlastikObjectClassifierModel)
+ assert isinstance(ob_model, IlastikObjectClassifierFromPixelPredictionsModel)
ti = Timer()
ch = kwargs.get('channel')
--
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