From ef4c894392371eafc2f592912da6f4ee8a2807b6 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 5 Sep 2023 13:21:40 +0200
Subject: [PATCH] Moved ilastik configuration into its own file
---
conf/defaults.py | 11 ++---------
conf/ilastik.py | 5 +++++
conf/testing.py | 5 -----
model_server/ilastik.py | 10 +++++-----
model_server/session.py | 11 ++++++-----
tests/test_api.py | 22 +++++++++++-----------
tests/test_ilastik.py | 2 +-
tests/test_session.py | 6 +++---
8 files changed, 33 insertions(+), 39 deletions(-)
create mode 100644 conf/ilastik.py
diff --git a/conf/defaults.py b/conf/defaults.py
index 39e07c4e..91675a25 100644
--- a/conf/defaults.py
+++ b/conf/defaults.py
@@ -1,16 +1,9 @@
from pathlib import Path
-root = Path('c:/Users/rhodes/projects/proj0015-model-server/resources')
-# paths = {
-# 'logs': root / 'logs' / 'session',
-# 'inbound_images': root / 'images' / 'inbound',
-# 'outbound_images': root / 'images' / 'outbound',
-# 'ilastik_projects': root / 'ilastik',
-# }
+root = Path.home() / 'model-server' / 'resources'
subdirectories = {
- 'logs': 'logs/session',
+ 'logs': 'logs',
'inbound_images': 'images/inbound',
'outbound_images': 'images/outbound',
- 'ilastik_projects': 'ilastik',
}
\ No newline at end of file
diff --git a/conf/ilastik.py b/conf/ilastik.py
new file mode 100644
index 00000000..de14a50c
--- /dev/null
+++ b/conf/ilastik.py
@@ -0,0 +1,5 @@
+from pathlib import Path
+
+paths = {
+ 'project_files': Path.home() / 'model-server' / 'ilastik'
+}
\ No newline at end of file
diff --git a/conf/testing.py b/conf/testing.py
index cd6088e5..b8ac1214 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -11,11 +11,6 @@ czifile = {
'z': 1,
}
-# ilastik = {
-# 'pixel_classifier': root / 'testdata' / 'ilastik' / 'demo_px.ilp',
-# 'object_classifier': root / 'testdata' / 'ilastik' / 'demo_obj.ilp',
-# }
-
ilastik = {
'pixel_classifier': 'demo_px.ilp',
'object_classifier': 'demo_obj.ilp',
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index c4b876de..2440b2a3 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -1,10 +1,9 @@
import os
-import pathlib
import numpy as np
import vigra
-import conf.defaults
+import conf.ilastik
from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.model import ImageToImageModel, ParameterExpectedError
@@ -13,9 +12,10 @@ class IlastikImageToImageModel(ImageToImageModel):
def __init__(self, params, autoload=True):
self.project_file = str(params['project_file'])
- self.project_file_abspath = pathlib.Path(
- conf.defaults.paths['ilastik_projects'] / self.project_file,
- )
+ pap = conf.ilastik.paths['project_files'] / self.project_file
+ self.project_file_abspath = pap
+ if not pap.exists():
+ raise FileNotFoundError(f'Project file does not exist: {pap}')
if 'project_file' not in params or not self.project_file_abspath.exists():
raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
diff --git a/model_server/session.py b/model_server/session.py
index f5225743..bea41e60 100644
--- a/model_server/session.py
+++ b/model_server/session.py
@@ -31,10 +31,11 @@ class Session(object):
self.models = {} # model_id : model object
self.manifest = [] # paths to data as well as other metadata from each inference run
self.paths = self.make_paths(root)
- self.session_id = self.create_session_id(self.paths['logs'])
- self.session_log = self.paths['logs'] / f'{self.session_id}.log'
+ # self.session_id = self.create_session_id(self.paths['logs'])
+ # self.session_id = self.create_session_id(self.paths)
+ self.session_log = self.paths['logs'] / f'session.log'
self.log_event('Initialized session')
- self.manifest_json = self.paths['logs'] / f'{self.session_id}-manifest.json'
+ self.manifest_json = self.paths['logs'] / f'manifest.json'
open(self.manifest_json, 'w').close() # instantiate empty json file
def get_paths(self):
@@ -47,12 +48,12 @@ class Session(object):
:param root: absolute path to top-level directory
:return: dictionary of session paths
"""
- paths = {}
if root is None:
root_path = Path(conf.defaults.root)
else:
root_path = Path(root)
sid = Session.create_session_id(root_path)
+ paths = {'root': root_path}
for pk in ['inbound_images', 'outbound_images', 'logs']:
pa = root_path / sid / conf.defaults.subdirectories[pk]
paths[pk] = pa
@@ -69,7 +70,7 @@ class Session(object):
"""
yyyymmdd = strftime('%Y%m%d', localtime())
idx = 0
- while os.path.exists(look_where / f'{yyyymmdd}-{idx:04d}.log'):
+ while os.path.exists(look_where / f'{yyyymmdd}-{idx:04d}'):
idx += 1
return f'{yyyymmdd}-{idx:04d}'
diff --git a/tests/test_api.py b/tests/test_api.py
index d09108e6..09baa8a4 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -21,6 +21,17 @@ class TestServerBaseClass(unittest.TestCase):
self.uri = f'http://{host}:{port}/'
self.server_process.start()
+ def copy_input_file_to_server(self):
+ from shutil import copyfile
+
+ resp = requests.get(self.uri + 'paths')
+ pa = resp.json()['inbound_images']
+ outpath = Path(pa) / czifile['filename']
+ copyfile(
+ czifile['path'],
+ outpath
+ )
+
def tearDown(self) -> None:
self.server_process.terminate()
@@ -89,17 +100,6 @@ class TestApiFromAutomatedClient(TestServerBaseClass):
)
self.assertEqual(resp.status_code, 409, resp.content.decode())
- def copy_input_file_to_server(self):
- from shutil import copyfile
-
- resp = requests.get(self.uri + 'paths')
- pa = resp.json()['inbound_images']
- outpath = Path(pa) / czifile['filename']
- copyfile(
- czifile['path'],
- outpath
- )
-
def test_i2i_dummy_inference_by_api(self):
model_id = self.test_load_dummy_model()
self.copy_input_file_to_server()
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index fba595e1..0ef8d0c4 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -139,7 +139,7 @@ class TestIlastikOverApi(TestServerBaseClass):
self.assertEqual(rj[model_id]['class'], 'IlastikObjectClassifierModel')
def test_ilastik_infer_pixel_probability(self):
- TestServerBaseClass.copy_input_file_to_server()
+ self.copy_input_file_to_server()
model_id = self.test_load_ilastik_pixel_model()
resp_infer = requests.put(
diff --git a/tests/test_session.py b/tests/test_session.py
index 9846dcfe..5055d5c9 100644
--- a/tests/test_session.py
+++ b/tests/test_session.py
@@ -25,12 +25,14 @@ class TestGetSessionObject(unittest.TestCase):
for k in old_paths.keys():
self.assertTrue(new_paths[k].__str__().startswith(newroot.__str__()))
+
+
def test_restart_session(self):
sesh = Session()
logfile1 = sesh.session_log
sesh.restart()
logfile2 = sesh.session_log
- self.assertIsNot(logfile1, logfile2, 'Restarting session does not generate new logfile')
+ self.assertNotEqual(logfile1, logfile2, 'Restarting session does not generate new logfile')
def test_session_records_workflow(self):
import json
@@ -55,7 +57,6 @@ class TestGetSessionObject(unittest.TestCase):
success = sesh.load_model(MC)
self.assertTrue(success)
loaded_models = sesh.describe_loaded_models()
- print(loaded_models)
self.assertTrue(
(MC.__name__ + '_00') in loaded_models.keys()
)
@@ -69,7 +70,6 @@ class TestGetSessionObject(unittest.TestCase):
MC = DummyImageToImageModel
sesh.load_model(MC)
sesh.load_model(MC)
- print(sesh.models.keys())
self.assertIn(MC.__name__ + '_00', sesh.models.keys())
self.assertIn(MC.__name__ + '_01', sesh.models.keys())
--
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