From a0b7809f5d63247ad61047eb2ec2cdfa64ea7229 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 31 Oct 2023 15:09:07 +0100
Subject: [PATCH] Merge in ilastik API support for segmentation-to-object
workflow
---
.gitignore | 4 +-
conf/testing.py | 7 +-
extensions/ilastik/router.py | 20 +++---
extensions/ilastik/tests/test_ilastik.py | 82 ++++++++++++++----------
4 files changed, 67 insertions(+), 46 deletions(-)
diff --git a/.gitignore b/.gitignore
index f5570b3f..7efb7f0b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
*/.idea/*
-*__pycache__*
\ No newline at end of file
+*__pycache__*
+/clients/imagej/.idea/workspace.xml
+/clients/imagej/.idea/
diff --git a/conf/testing.py b/conf/testing.py
index 3c52b95c..1c2b0cf3 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -53,9 +53,10 @@ monozstackmask = {
'z': 85
}
-ilastik = {
- 'pixel_classifier': 'demo_px.ilp',
- 'object_classifier': 'demo_obj.ilp',
+ilastik_classifiers = {
+ 'px': 'demo_px.ilp',
+ 'pxmap_to_obj': 'demo_obj.ilp',
+ 'seg_to_obj': 'new_auto_obj.ilp',
}
output_path = root / 'testing_output'
diff --git a/extensions/ilastik/router.py b/extensions/ilastik/router.py
index 3287dc47..ba01d1b9 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, IlastikObjectClassifierFromPixelPredictionsModel
+from extensions.ilastik import models as ilm
from model_server.models import ParameterExpectedError
from extensions.ilastik.workflows import infer_px_then_ob_model
@@ -14,7 +14,7 @@ router = APIRouter(
session = Session()
-def load_ilastik_model(model_class: IlastikImageToImageModel, project_file: str, duplicate=True) -> dict:
+def load_ilastik_model(model_class: ilm.IlastikImageToImageModel, project_file: str, duplicate=True) -> dict:
"""
Load an ilastik model of a given class and project filename.
:param model_class:
@@ -40,13 +40,17 @@ def load_ilastik_model(model_class: IlastikImageToImageModel, project_file: str,
)
return result
-@router.put('/pixel_classification/load/')
-def load_ilastik_pixel_classification_model(project_file: str, duplicate: bool = True) -> dict:
- return load_ilastik_model(IlastikPixelClassifierModel, project_file, duplicate=duplicate)
+@router.put('/px/load/')
+def load_px_model(project_file: str, duplicate: bool = True) -> dict:
+ return load_ilastik_model(ilm.IlastikPixelClassifierModel, project_file, duplicate=duplicate)
-@router.put('/object_classification/load/')
-def load_ilastik_object_classification_model(project_file: str, duplicate: bool = True) -> dict:
- return load_ilastik_model(IlastikObjectClassifierFromPixelPredictionsModel, project_file, duplicate=duplicate)
+@router.put('/pxmap_to_obj/load/')
+def load_pxmap_to_obj_model(project_file: str, duplicate: bool = True) -> dict:
+ return load_ilastik_model(ilm.IlastikObjectClassifierFromPixelPredictionsModel, project_file, duplicate=duplicate)
+
+@router.put('/seg_to_obj/load/')
+def load_seg_to_obj_model(project_file: str, duplicate: bool = True) -> dict:
+ return load_ilastik_model(ilm.IlastikObjectClassifierFromSegmentationModel, 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 217b00c9..d2498af2 100644
--- a/extensions/ilastik/tests/test_ilastik.py
+++ b/extensions/ilastik/tests/test_ilastik.py
@@ -3,15 +3,15 @@ import unittest
import numpy as np
-import conf.testing
+from conf.testing import czifile, ilastik_classifiers, output_path
from model_server.accessors import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
-from extensions.ilastik.models import IlastikObjectClassifierFromPixelPredictionsModel, IlastikPixelClassifierModel
+from extensions.ilastik import models as ilm
from model_server.workflows import infer_image_to_image
from tests.test_api import TestServerBaseClass
class TestIlastikPixelClassification(unittest.TestCase):
def setUp(self) -> None:
- self.cf = CziImageFileAccessor(conf.testing.czifile['path'])
+ self.cf = CziImageFileAccessor(czifile['path'])
def test_faulthandler(self): # recreate error that is messing up ilastik
@@ -24,8 +24,8 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_raise_error_if_autoload_disabled(self):
- model = IlastikPixelClassifierModel(
- {'project_file': conf.testing.ilastik['pixel_classifier']},
+ model = ilm.IlastikPixelClassifierModel(
+ {'project_file': ilastik_classifiers['px']},
autoload=False
)
w = 512
@@ -38,8 +38,8 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_pixel_classifier_on_random_data(self):
- model = IlastikPixelClassifierModel(
- {'project_file': conf.testing.ilastik['pixel_classifier']},
+ model = ilm.IlastikPixelClassifierModel(
+ {'project_file': ilastik_classifiers['px']},
)
w = 512
h = 256
@@ -52,16 +52,16 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_pixel_classifier(self):
channel = 0
- model = IlastikPixelClassifierModel(
- {'project_file': conf.testing.ilastik['pixel_classifier']}
+ model = ilm.IlastikPixelClassifierModel(
+ {'project_file': ilastik_classifiers['px']}
)
cf = CziImageFileAccessor(
- conf.testing.czifile['path']
+ czifile['path']
)
mono_image = cf.get_one_channel_data(channel)
- self.assertEqual(mono_image.shape_dict['X'], conf.testing.czifile['w'])
- self.assertEqual(mono_image.shape_dict['Y'], conf.testing.czifile['h'])
+ self.assertEqual(mono_image.shape_dict['X'], czifile['w'])
+ self.assertEqual(mono_image.shape_dict['Y'], czifile['h'])
self.assertEqual(mono_image.shape_dict['C'], 1)
self.assertEqual(mono_image.shape_dict['Z'], 1)
@@ -72,7 +72,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
self.assertEqual(pxmap.shape_dict['Z'], 1)
self.assertTrue(
write_accessor_data_to_file(
- conf.testing.output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
+ output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
pxmap
)
)
@@ -82,15 +82,15 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_object_classifier(self):
self.test_run_pixel_classifier()
- fp = conf.testing.czifile['path']
- model = IlastikObjectClassifierFromPixelPredictionsModel(
- {'project_file': conf.testing.ilastik['object_classifier']}
+ fp = czifile['path']
+ model = ilm.IlastikObjectClassifierFromPixelPredictionsModel(
+ {'project_file': ilastik_classifiers['pxmap_to_obj']}
)
objmap, _ = model.infer(self.mono_image, self.pxmap)
self.assertTrue(
write_accessor_data_to_file(
- conf.testing.output_path / f'obmap_{fp.stem}.tif',
+ output_path / f'obmap_{fp.stem}.tif',
objmap,
)
)
@@ -98,11 +98,11 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_ilastik_pixel_classification_as_workflow(self):
result = infer_image_to_image(
- conf.testing.czifile['path'],
- IlastikPixelClassifierModel(
- {'project_file': conf.testing.ilastik['pixel_classifier']}
+ czifile['path'],
+ ilm.IlastikPixelClassifierModel(
+ {'project_file': ilastik_classifiers['px']}
),
- conf.testing.output_path,
+ output_path,
channel=0,
)
self.assertTrue(result.success)
@@ -112,7 +112,7 @@ class TestIlastikOverApi(TestServerBaseClass):
def test_httpexception_if_incorrect_project_file_loaded(self):
resp_load = requests.put(
- self.uri + 'ilastik/pixel_classification/load/',
+ self.uri + 'ilastik/px/load/',
params={'project_file': 'improper.ilp'},
)
self.assertEqual(resp_load.status_code, 404)
@@ -120,8 +120,8 @@ class TestIlastikOverApi(TestServerBaseClass):
def test_load_ilastik_pixel_model(self):
resp_load = requests.put(
- self.uri + 'ilastik/pixel_classification/load/',
- params={'project_file': str(conf.testing.ilastik['pixel_classifier'])},
+ self.uri + 'ilastik/px/load/',
+ params={'project_file': str(ilastik_classifiers['px'])},
)
model_id = resp_load.json()['model_id']
@@ -137,18 +137,18 @@ class TestIlastikOverApi(TestServerBaseClass):
resp_list_1st = requests.get(self.uri + 'models').json()
self.assertEqual(len(resp_list_1st), 1, resp_list_1st)
resp_load_2nd = requests.put(
- self.uri + 'ilastik/pixel_classification/load/',
+ self.uri + 'ilastik/px/load/',
params={
- 'project_file': str(conf.testing.ilastik['pixel_classifier']),
+ 'project_file': str(ilastik_classifiers['px']),
'duplicate': True,
},
)
resp_list_2nd = requests.get(self.uri + 'models').json()
self.assertEqual(len(resp_list_2nd), 2, resp_list_2nd)
resp_load_3rd = requests.put(
- self.uri + 'ilastik/pixel_classification/load/',
+ self.uri + 'ilastik/px/load/',
params={
- 'project_file': str(conf.testing.ilastik['pixel_classifier']),
+ 'project_file': str(ilastik_classifiers['px']),
'duplicate': False,
},
)
@@ -156,10 +156,10 @@ class TestIlastikOverApi(TestServerBaseClass):
self.assertEqual(len(resp_list_3rd), 2, resp_list_3rd)
- def test_load_ilastik_object_model(self):
+ def test_load_ilastik_pxmap_to_obj_model(self):
resp_load = requests.put(
- self.uri + 'ilastik/object_classification/load/',
- params={'project_file': str(conf.testing.ilastik['object_classifier'])},
+ self.uri + 'ilastik/pxmap_to_obj/load/',
+ params={'project_file': str(ilastik_classifiers['pxmap_to_obj'])},
)
model_id = resp_load.json()['model_id']
@@ -170,6 +170,20 @@ class TestIlastikOverApi(TestServerBaseClass):
self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierFromPixelPredictionsModel')
return model_id
+ def test_load_ilastik_seg_to_obj_model(self):
+ resp_load = requests.put(
+ self.uri + 'ilastik/seg_to_obj/load/',
+ params={'project_file': str(ilastik_classifiers['seg_to_obj'])},
+ )
+ 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'], 'IlastikObjectClassifierFromSegmentationModel')
+ return model_id
+
def test_ilastik_infer_pixel_probability(self):
self.copy_input_file_to_server()
model_id = self.test_load_ilastik_pixel_model()
@@ -178,7 +192,7 @@ class TestIlastikOverApi(TestServerBaseClass):
self.uri + f'infer/from_image_file',
params={
'model_id': model_id,
- 'input_filename': conf.testing.czifile['filename'],
+ 'input_filename': czifile['filename'],
'channel': 0,
},
)
@@ -187,14 +201,14 @@ class TestIlastikOverApi(TestServerBaseClass):
def test_ilastik_infer_px_then_ob(self):
self.copy_input_file_to_server()
px_model_id = self.test_load_ilastik_pixel_model()
- ob_model_id = self.test_load_ilastik_object_model()
+ ob_model_id = self.test_load_ilastik_pxmap_to_obj_model()
resp_infer = requests.put(
self.uri + f'ilastik/pixel_then_object_classification/infer/',
params={
'px_model_id': px_model_id,
'ob_model_id': ob_model_id,
- 'input_filename': conf.testing.czifile['filename'],
+ 'input_filename': czifile['filename'],
'channel': 0,
}
)
--
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