From beac602cb08a69a8ef7d0fa7bac3935e26120d78 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 30 Oct 2023 16:54:48 +0100
Subject: [PATCH] Merged in from master
---
model_server/accessors.py | 11 +++--------
model_server/process.py | 14 ++++++++++++++
model_server/util.py | 4 ----
tests/test_api.py | 2 +-
4 files changed, 18 insertions(+), 13 deletions(-)
diff --git a/model_server/accessors.py b/model_server/accessors.py
index 1bb5b6b4..0e5e2cc9 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -1,7 +1,6 @@
from abc import ABC, abstractmethod
import os
from pathlib import Path
-from typing import Dict
import numpy as np
from skimage.io import imread
@@ -9,6 +8,8 @@ from skimage.io import imread
import czifile
import tifffile
+from model_server.process import is_mask
+
class GenericImageDataAccessor(ABC):
@abstractmethod
@@ -34,13 +35,7 @@ class GenericImageDataAccessor(ABC):
return True if self.shape_dict['Z'] > 1 else False
def is_mask(self):
- if self._data.dtype == 'bool':
- return True
- elif self._data.dtype == 'uint8':
- unique = np.unique(self._data)
- if unique.shape[0] == 2 and np.all(unique == [0, 255]):
- return True
- return False
+ return is_mask(self._data)
def get_one_channel_data (self, channel: int):
c = int(channel)
diff --git a/model_server/process.py b/model_server/process.py
index 767cd1f6..48128223 100644
--- a/model_server/process.py
+++ b/model_server/process.py
@@ -6,6 +6,20 @@ from math import ceil, floor
import numpy as np
from skimage.exposure import rescale_intensity
+
+def is_mask(img):
+ """
+ Return True if an image represents a binary mask
+ :param img: np.ndarray
+ """
+ if img.dtype == 'bool':
+ return True
+ elif img.dtype == 'uint8':
+ unique = np.unique(img)
+ if unique.shape[0] == 2 and np.all(unique == [0, 255]):
+ return True
+ return False
+
def pad(yxcz, mpx: int):
"""
Pad and crop image data in Y and X axes to meet specific dimension
diff --git a/model_server/util.py b/model_server/util.py
index 1cc33753..8bc071ab 100644
--- a/model_server/util.py
+++ b/model_server/util.py
@@ -1,12 +1,10 @@
from pathlib import Path
import re
from time import localtime, strftime
-from typing import List
import pandas as pd
from model_server.accessors import InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.models import Model
def autonumber_new_directory(where: str, prefix: str) -> str:
"""
@@ -77,7 +75,6 @@ def loop_workflow(
files: list,
output_folder_path: str,
workflow_func: callable,
- models: List[Model],
params: dict,
export_batch_csvs: bool = True,
write_intermediate_products: bool = True,
@@ -98,7 +95,6 @@ def loop_workflow(
export_kwargs = {
'input_file_path': ff,
'output_folder_path': output_folder_path,
- 'models': models,
**params,
}
diff --git a/tests/test_api.py b/tests/test_api.py
index 778c378f..e8e11056 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -14,7 +14,7 @@ class TestServerBaseClass(unittest.TestCase):
self.server_process = Process(
target=uvicorn.run,
- args=('api:app', ),
+ args=('model_server.api:app', ),
kwargs={'host': host, 'port': port, 'log_level': 'debug'},
daemon=True
)
--
GitLab