From e9da5e6abb6e91251531da68e617b3030d1de3ba Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 8 Aug 2024 15:42:44 +0200
Subject: [PATCH] Session can add and delete accessors to its scope
---
model_server/base/accessors.py | 15 ++++++++++++-
model_server/base/session.py | 41 +++++++++++++++++++++++++++++++++-
tests/base/test_session.py | 17 +++++++++++++-
3 files changed, 70 insertions(+), 3 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 5be57a4b..271b8d4a 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -153,6 +153,14 @@ class GenericImageDataAccessor(ABC):
func(self.data)
)
+ @property
+ def info(self):
+ return {
+ 'shape_dict': self.shape_dict,
+ 'dtype': self.dtype,
+ 'loaded': True,
+ }
+
class InMemoryDataAccessor(GenericImageDataAccessor):
def __init__(self, data):
self._data = self.conform_data(data)
@@ -172,6 +180,12 @@ class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded
def read(fp: Path):
return generate_file_accessor(fp)
+ @property
+ def info(self):
+ d = super().info()
+ d['filepath'] = self.fpath.__str__()
+ return d
+
class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
def __init__(self, fpath: Path):
super().__init__(fpath)
@@ -470,7 +484,6 @@ def make_patch_stack_from_file(fpath): # interpret t-dimension as patch positio
return PatchStack(pyxcz)
-
class Error(Exception):
pass
diff --git a/model_server/base/session.py b/model_server/base/session.py
index 24c5b31c..3876a769 100644
--- a/model_server/base/session.py
+++ b/model_server/base/session.py
@@ -1,3 +1,4 @@
+from collections import OrderedDict
import logging
import os
@@ -9,11 +10,11 @@ from typing import Union
import pandas as pd
from ..conf import defaults
+from .accessors import GenericImageDataAccessor
from .models import Model
logger = logging.getLogger(__name__)
-
class CsvTable(object):
def __init__(self, fpath: Path):
self.path = fpath
@@ -40,6 +41,7 @@ class _Session(object):
def __init__(self, root: str = None):
self.models = {} # model_id : model object
self.paths = self.make_paths(root)
+ self.accessors = OrderedDict()
self.logfile = self.paths['logs'] / f'session.log'
logging.basicConfig(filename=self.logfile, level=logging.INFO, force=True, format=self.log_format)
@@ -80,6 +82,40 @@ class _Session(object):
raise InvalidPathError(f'Could not find {path}')
self.paths[key] = Path(path)
+ def add_accessor(self, acc: GenericImageDataAccessor, accessor_id: str = None):
+ """
+ Add an accessor to session context
+ :param acc: accessor to add
+ :param accessor_id: unique ID, or autogenerate if None
+ :return: ID of accessor
+ """
+ if accessor_id in self.accessors.keys():
+ raise AccessorIdError(f'Access with ID {accessor_id} already exists')
+ if accessor_id is None:
+ idx = len(self.accessors)
+ accessor_id = f'auto_{idx:06d}'
+ self.accessors[accessor_id] = acc
+ return accessor_id
+
+ def del_accessor(self, accessor_id: str):
+ """
+ Replace accessor object with its info dictionary
+ :param accessor_id: accessor's ID
+ :return: ID of accessor
+ """
+ if accessor_id not in self.accessors.keys():
+ raise AccessorIdError(f'No accessor with ID {accessor_id} is registered')
+ v = self.accessors[accessor_id]
+ if isinstance(v, dict) and v['loaded'] is False:
+ logger.warning(f'Accessor {accessor_id} is already deleted')
+ info = v
+ else:
+ assert isinstance(v, GenericImageDataAccessor)
+ info = v.info
+ info['loaded'] = False
+ self.accessors[accessor_id] = info
+ return accessor_id
+
@staticmethod
def make_paths(root: str = None) -> dict:
"""
@@ -208,6 +244,9 @@ class InferenceRecordError(Error):
class CouldNotInstantiateModelError(Error):
pass
+class AccessorIdError(Error):
+ pass
+
class CouldNotCreateDirectory(Error):
pass
diff --git a/tests/base/test_session.py b/tests/base/test_session.py
index 56ce4632..1e333844 100644
--- a/tests/base/test_session.py
+++ b/tests/base/test_session.py
@@ -1,8 +1,9 @@
from os.path import exists
import pathlib
-from pydantic import BaseModel
import unittest
+import numpy as np
+from model_server.base.accessors import InMemoryDataAccessor
from model_server.base.session import session
class TestGetSessionObject(unittest.TestCase):
@@ -85,3 +86,17 @@ class TestGetSessionObject(unittest.TestCase):
self.assertEqual(len(dfv), len(data))
self.assertEqual(dfv.columns[0], 'X')
self.assertEqual(dfv.columns[1], 'Y')
+
+
+ def test_add_and_remove_accessor(self):
+ w = 256
+ h = 512
+ nc = 4
+ nz = 11
+ sh = (h, w, nc, nz)
+ acc = InMemoryDataAccessor(np.random.randint(0, 2 ** 8, size=sh, dtype='uint8'))
+ acc_id = session.add_accessor(acc)
+ shd = acc.shape_dict
+ self.assertEqual(session.accessors[acc_id].shape, sh)
+ session.del_accessor(acc_id)
+ self.assertEqual(session.accessors[acc_id]['shape_dict'], shd)
--
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