From 7d7f0552c287e469e04639d5a42e5d5380588128 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 1 Sep 2023 14:55:44 +0200
Subject: [PATCH] Pass notebook filename and not path to load an ilastik model;
assumes project files are in conf.server.paths['ilastik']
---
conf/server.py | 4 ++--
conf/testing.py | 9 +++++--
model_server/ilastik.py | 12 +++++++---
tests/test_ilastik.py | 53 +++++++++++++++++++++++++----------------
4 files changed, 51 insertions(+), 27 deletions(-)
diff --git a/conf/server.py b/conf/server.py
index a143374d..707b60ac 100644
--- a/conf/server.py
+++ b/conf/server.py
@@ -9,8 +9,8 @@ paths = {
'inbound': root / 'images' / 'inbound',
'outbound': root / 'images' / 'outbound',
},
- 'ilastik' : {
- 'projects' : root / 'ilastik'
+ 'ilastik': {
+ 'projects': root / 'ilastik'
}
}
diff --git a/conf/testing.py b/conf/testing.py
index 7e76e6b0..cd6088e5 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -11,9 +11,14 @@ czifile = {
'z': 1,
}
+# ilastik = {
+# 'pixel_classifier': root / 'testdata' / 'ilastik' / 'demo_px.ilp',
+# 'object_classifier': root / 'testdata' / 'ilastik' / 'demo_obj.ilp',
+# }
+
ilastik = {
- 'pixel_classifier': root / 'testdata' / 'ilastik' / 'demo_px.ilp',
- 'object_classifier': root / 'testdata' / 'ilastik' / 'demo_obj.ilp',
+ 'pixel_classifier': 'demo_px.ilp',
+ 'object_classifier': 'demo_obj.ilp',
}
output_path = root / 'testing_output'
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index 606c93d4..54419f78 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -1,8 +1,10 @@
import os
+import pathlib
import numpy as np
import vigra
+import conf.server
from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.model import ImageToImageModel, ParameterExpectedError
@@ -10,9 +12,13 @@ from model_server.model import ImageToImageModel, ParameterExpectedError
class IlastikImageToImageModel(ImageToImageModel):
def __init__(self, params, autoload=True):
- if 'project_file' not in params or not os.path.exists(params['project_file']):
- raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
self.project_file = str(params['project_file'])
+ self.project_file_abspath = pathlib.Path(
+ conf.server.paths['ilastik']['projects'] / self.project_file,
+ )
+ if 'project_file' not in params or not self.project_file_abspath.exists():
+ raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
+
self.shell = None
super().__init__(autoload, params)
@@ -28,7 +34,7 @@ class IlastikImageToImageModel(ImageToImageModel):
args = app.parse_args([])
args.headless = True
- args.project = self.project_file
+ args.project = self.project_file_abspath.__str__()
shell = app.main(args)
if not isinstance(shell.workflow, self.get_workflow()):
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index 01ac4306..204ad237 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -3,7 +3,7 @@ import unittest
import numpy as np
-from conf.testing import czifile, ilastik, output_path
+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.model import Model
@@ -12,7 +12,7 @@ from tests.test_api import TestServerBaseClass
class TestIlastikPixelClassification(unittest.TestCase):
def setUp(self) -> None:
- self.cf = CziImageFileAccessor(czifile['path'])
+ self.cf = CziImageFileAccessor(conf.testing.czifile['path'])
def test_faulthandler(self): # recreate error that is messing up ilastik
@@ -25,18 +25,23 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_raise_error_if_autoload_disabled(self):
- model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']}, autoload=False)
+ model = IlastikPixelClassifierModel(
+ {'project_file': conf.testing.ilastik['pixel_classifier']},
+ autoload=False
+ )
w = 512
h = 256
input_img = InMemoryDataAccessor(data=np.random.rand(w, h, 1, 1))
with self.assertRaises(AttributeError):
- pxmap , _= model.infer(input_img)
+ pxmap, _ = model.infer(input_img)
def test_run_pixel_classifier_on_random_data(self):
- model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
+ model = IlastikPixelClassifierModel(
+ {'project_file': conf.testing.ilastik['pixel_classifier']},
+ )
w = 512
h = 256
@@ -48,12 +53,16 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_pixel_classifier(self):
channel = 0
- model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
- cf = CziImageFileAccessor(czifile['path'])
+ model = IlastikPixelClassifierModel(
+ {'project_file': conf.testing.ilastik['pixel_classifier']}
+ )
+ cf = CziImageFileAccessor(
+ conf.testing.czifile['path']
+ )
mono_image = cf.get_one_channel_data(channel)
- self.assertEqual(mono_image.shape_dict['X'], czifile['w'])
- self.assertEqual(mono_image.shape_dict['Y'], czifile['h'])
+ 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['C'], 1)
self.assertEqual(mono_image.shape_dict['Z'], 1)
@@ -64,7 +73,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
self.assertEqual(pxmap.shape_dict['Z'], 1)
self.assertTrue(
write_accessor_data_to_file(
- output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
+ conf.testing.output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
pxmap
)
)
@@ -74,13 +83,15 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_run_object_classifier(self):
self.test_run_pixel_classifier()
- fp = czifile['path']
- model = IlastikObjectClassifierModel({'project_file': ilastik['object_classifier']})
+ fp = conf.testing.czifile['path']
+ model = IlastikObjectClassifierModel(
+ {'project_file': conf.testing.ilastik['object_classifier']}
+ )
objmap, _ = model.infer(self.mono_image, self.pxmap)
self.assertTrue(
write_accessor_data_to_file(
- output_path / f'obmap_{fp.stem}.tif',
+ conf.testing.output_path / f'obmap_{fp.stem}.tif',
objmap,
)
)
@@ -88,9 +99,11 @@ class TestIlastikPixelClassification(unittest.TestCase):
def test_ilastik_pixel_classification_as_workflow(self):
result = infer_image_to_image(
- czifile['path'],
- IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']}),
- output_path,
+ conf.testing.czifile['path'],
+ IlastikPixelClassifierModel(
+ {'project_file': conf.testing.ilastik['pixel_classifier']}
+ ),
+ conf.testing.output_path,
channel=0,
)
self.assertTrue(result.success)
@@ -100,7 +113,7 @@ class TestIlastikOverApi(TestServerBaseClass):
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'])},
+ params={'project_file': str(conf.testing.ilastik['pixel_classifier'])},
)
model_id = resp_load.json()['model_id']
@@ -116,7 +129,7 @@ class TestIlastikOverApi(TestServerBaseClass):
def test_load_ilastik_object_model(self):
resp_load = requests.put(
self.uri + 'models/ilastik/object_classification/load/',
- params={'project_file': str(ilastik['object_classifier'])},
+ params={'project_file': str(conf.testing.ilastik['object_classifier'])},
)
model_id = resp_load.json()['model_id']
@@ -134,8 +147,8 @@ class TestIlastikOverApi(TestServerBaseClass):
self.uri + f'infer/from_image_file',
params={
'model_id': model_id,
- 'input_filename': czifile['filename'],
- 'channel': 2,
+ 'input_filename': conf.testing.czifile['filename'],
+ 'channel': 0,
},
)
self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
--
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