From 125847bcaa9a6e6fe53a4fdb523229a138792c3a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 28 Aug 2023 15:08:13 +0200
Subject: [PATCH] Reconfigured inference endpoint as pure PUT; can now pass
params to model inference method
---
api.py | 18 +++++++++---------
model_server/model.py | 24 +++++++++++++++---------
model_server/session.py | 28 +++++++++++++++++++++-------
tests/test_api.py | 14 +++++++++++---
tests/test_session.py | 4 ++--
5 files changed, 58 insertions(+), 30 deletions(-)
diff --git a/api.py b/api.py
index f5d7976f..89e42d8f 100644
--- a/api.py
+++ b/api.py
@@ -1,4 +1,4 @@
-from pathlib import Path
+from typing import Dict
from fastapi import FastAPI, HTTPException
@@ -18,21 +18,21 @@ def read_root():
@app.get('/models')
def list_active_models():
- return session.describe_models()
+ return session.describe_loaded_models()
-@app.get('/models/{model_id}/load/')
-def load_model(model_id: str) -> dict:
+@app.put('/models/load/')
+def load_model(model_id: str, params: Dict[str, str] = None) -> dict:
if model_id in session.models.keys():
raise HTTPException(
status_code=409,
detail=f'Model with id {model_id} has already been loaded'
)
- session.load_model(model_id)
- return session.describe_models()
+ session.load_model(model_id, params=params)
+ return session.describe_loaded_models()
@app.put('/i2i/infer/{model_id}') # image file in, image file out
def infer_img(model_id: str, input_filename: str, channel: int = None) -> dict:
- if model_id not in session.describe_models().keys():
+ if model_id not in session.describe_loaded_models().keys():
raise HTTPException(
status_code=409,
detail=f'Model {model_id} has not been loaded'
@@ -43,10 +43,10 @@ def infer_img(model_id: str, input_filename: str, channel: int = None) -> dict:
status_code=404,
detail=f'Could not find file:\n{inpath}'
)
-
+ model = session.models[model_id]['object']
record = infer_image_to_image(
inpath,
- session.models[model_id],
+ session.models[model_id]['object'],
session.outbound.path,
channel=channel,
# TODO: optional callback for status reporting
diff --git a/model_server/model.py b/model_server/model.py
index 7c9d84e1..d483744a 100644
--- a/model_server/model.py
+++ b/model_server/model.py
@@ -1,5 +1,6 @@
from abc import ABC, abstractmethod
from math import floor
+import os
import numpy as np
@@ -8,13 +9,15 @@ from model_server.image import GenericImageFileAccessor
class Model(ABC):
- def __init__(self, autoload=True):
+ def __init__(self, autoload=True, params=None):
"""
Abstract base class for an inference model that uses image data as an input.
:param autoload: automatically load model and dependencies into memory if True
+ :param params: Dict[str, str] of arguments e.g. configuration files required to load model
"""
self.autoload = autoload
+ self.params = params
if self.load():
self.loaded = True
else:
@@ -58,20 +61,20 @@ class Model(ABC):
class ImageToImageModel(Model):
-
- def __init__(self, **kwargs):
- """
- Abstract class for models that receive an image and return an image of the same size
- :param kwargs: variable length keyword arguments
- """
- return super().__init__(**kwargs)
+ """
+ Abstract class for models that receive an image and return an image of the same size
+ """
@abstractmethod
def infer(self, img, channel=None) -> (np.ndarray, dict):
super().infer(img, channel)
class IlastikImageToImageModel(ImageToImageModel):
- pass
+ def load(self):
+ if 'project_file' not in self.params or not os.path.exists(self.params['project_file']):
+ raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
+ self.project_file = self.params['project_file']
+
class DummyImageToImageModel(ImageToImageModel):
@@ -96,4 +99,7 @@ class ChannelTooHighError(Error):
pass
class CouldNotLoadModelError(Error):
+ pass
+
+class ParameterExpectedError(Error):
pass
\ No newline at end of file
diff --git a/model_server/session.py b/model_server/session.py
index f3b65d62..5ab27fe9 100644
--- a/model_server/session.py
+++ b/model_server/session.py
@@ -3,6 +3,7 @@ import os
from pathlib import Path
from time import strftime, localtime
+from typing import Dict
from conf.server import paths
from model_server.model import Model
@@ -61,27 +62,37 @@ class Session(object):
with open(self.manifest_json, 'w+') as fh:
json.dump(record.dict(), fh)
- def load_model(self, model_id: str) -> bool:
+ def load_model(self, model_id: str, params: Dict[str, str] = None) -> bool:
"""
Load an instance of first model class that matches model_id string
- :param model_id:
+ :param model_id: string that uniquely defines a class of model
+ :param params: optional parameters that are passed upon loading a model
:return: True if model successfully loaded, False if not
"""
models = Model.get_all_subclasses()
for mc in models:
if hasattr(mc, 'model_id') and getattr(mc, 'model_id') == model_id:
- mi = mc()
- assert mi.loaded
- self.models[model_id] = mi
+ try:
+ mi = mc(params)
+ assert mi.loaded
+ except:
+ raise CouldNotInstantiateModelError()
+ self.models[model_id] = {
+ 'object': mi,
+ 'params': params,
+ }
return True
raise CouldNotFindModelError(
f'Could not find {model_id} in:\n{models}',
)
return False
- def describe_models(self) -> dict:
+ def describe_loaded_models(self) -> dict:
return {
- k: self.models[k].__class__.__name__
+ k: {
+ 'class': self.models[k]['object'].__class__.__name__,
+ 'params': self.models[k]['params'],
+ }
for k in self.models.keys()
}
@@ -95,4 +106,7 @@ class CouldNotFindModelError(Error):
pass
class InferenceRecordError(Error):
+ pass
+
+class CouldNotInstantiateModelError(Error):
pass
\ No newline at end of file
diff --git a/tests/test_api.py b/tests/test_api.py
index ecc0296c..e290d163 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -48,11 +48,16 @@ class TestApiFromAutomatedClient(unittest.TestCase):
def test_load_model(self):
model_id = DummyImageToImageModel.model_id
- resp_load = requests.get(self.uri + f'models/{model_id}/load')
+ resp_load = requests.put(
+ self.uri + f'models/load',
+ params={'model_id': model_id}
+ )
self.assertEqual(resp_load.status_code, 200)
resp_list = requests.get(self.uri + 'models')
self.assertEqual(resp_list.status_code, 200)
- self.assertEqual(resp_list.content, b'{"dummy_make_white_square":"DummyImageToImageModel"}')
+ rj = resp_list.json()
+ self.assertEqual(rj[model_id]['class'], 'DummyImageToImageModel')
+
def test_i2i_inference_errors_model_not_found(self):
model_id = 'not_a_real_model'
@@ -65,7 +70,10 @@ class TestApiFromAutomatedClient(unittest.TestCase):
def test_i2i_dummy_inference_by_api(self):
model = DummyImageToImageModel()
- resp_load = requests.get(self.uri + f'models/{model.model_id}/load')
+ resp_load = requests.put(
+ self.uri + f'models/load',
+ params={'model_id': model.model_id}
+ )
self.assertEqual(resp_load.status_code, 200, f'Error loading {model.model_id}')
self.copy_input_file_to_server()
resp_infer = requests.put(
diff --git a/tests/test_session.py b/tests/test_session.py
index 2538d3d2..99fd6c6d 100644
--- a/tests/test_session.py
+++ b/tests/test_session.py
@@ -42,9 +42,9 @@ class TestGetSessionObject(unittest.TestCase):
model_id = DummyImageToImageModel.model_id
success = sesh.load_model(model_id)
self.assertTrue(success)
- loaded_models = sesh.describe_models()
+ loaded_models = sesh.describe_loaded_models()
self.assertTrue(model_id in loaded_models.keys())
self.assertEqual(
- loaded_models[model_id],
+ loaded_models[model_id]['class'],
DummyImageToImageModel.__name__
)
\ No newline at end of file
--
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