From 97528dd7b7c147b85ca1a3509e5f52d2177a84c3 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 26 Jan 2023 17:23:54 +0000
Subject: [PATCH] Allow local runs without the omero module
---
src/aliby/io/dataset.py | 6 ++++--
src/aliby/io/image.py | 47 ++++++++++++++++++++++++++++-------------
src/aliby/io/omero.py | 6 +++++-
3 files changed, 41 insertions(+), 18 deletions(-)
diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py
index eaec2688..b09567ed 100644
--- a/src/aliby/io/dataset.py
+++ b/src/aliby/io/dataset.py
@@ -13,8 +13,10 @@ from abc import ABC, abstractproperty, abstractmethod
from pathlib import Path, PosixPath
from typing import Union
-import omero
-
+try:
+ import omero
+except ModuleNotFoundError:
+ print("Warning: Cannot import omero.")
from agora.io.bridge import BridgeH5
from aliby.io.image import ImageLocalOME
from aliby.io.omero import BridgeOmero
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index fd910963..fe6c0759 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -10,25 +10,41 @@ import numpy as np
import xmltodict
from dask import delayed
from dask.array.image import imread
-from omero.model import enums as omero_enums
+
+try:
+ from omero.model import enums as omero_enums
+except ModuleNotFoundError:
+ print("Warning: Cannot import omero_enums.")
from tifffile import TiffFile
from yaml import safe_load
from agora.io.bridge import BridgeH5
from agora.io.metadata import dir_to_meta
-from aliby.io.omero import BridgeOmero
+
+try:
+ from aliby.io.omero import BridgeOmero
+except ModuleNotFoundError:
+
+ class BridgeOmero:
+ # dummy class necessary when the omero module is not installed
+ pass
+
+ print("Warning: Cannot import BridgeOmero.")
# convert OMERO definitions into numpy types
-PIXEL_TYPES = {
- omero_enums.PixelsTypeint8: np.int8,
- omero_enums.PixelsTypeuint8: np.uint8,
- omero_enums.PixelsTypeint16: np.int16,
- omero_enums.PixelsTypeuint16: np.uint16,
- omero_enums.PixelsTypeint32: np.int32,
- omero_enums.PixelsTypeuint32: np.uint32,
- omero_enums.PixelsTypefloat: np.float32,
- omero_enums.PixelsTypedouble: np.float64,
-}
+try:
+ PIXEL_TYPES = {
+ omero_enums.PixelsTypeint8: np.int8,
+ omero_enums.PixelsTypeuint8: np.uint8,
+ omero_enums.PixelsTypeint16: np.int16,
+ omero_enums.PixelsTypeuint16: np.uint16,
+ omero_enums.PixelsTypeint32: np.int32,
+ omero_enums.PixelsTypeuint32: np.uint32,
+ omero_enums.PixelsTypefloat: np.float32,
+ omero_enums.PixelsTypedouble: np.float64,
+ }
+except NameError:
+ print("Warning: PIXEL_TYPES are not defined.")
def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
@@ -266,12 +282,12 @@ class ImageDir(BaseLocalImage):
class Image(BridgeOmero):
"""
- Loads images from OMERO and gives access to the data and metadata.
+ Load images from OMERO and gives access to the data and metadata.
"""
def __init__(self, image_id: int, **server_info):
"""
- Establishes the connection to the OMERO server via the Argo
+ Establish the connection to the OMERO server via the Argo
base class.
Parameters
@@ -292,7 +308,8 @@ class Image(BridgeOmero):
cls,
filepath: t.Union[str, PosixPath],
):
- """Instatiate Image from a hdf5 file.
+ """
+ Instantiate Image from a hdf5 file.
Parameters
----------
diff --git a/src/aliby/io/omero.py b/src/aliby/io/omero.py
index af8f451b..9ae5ffba 100644
--- a/src/aliby/io/omero.py
+++ b/src/aliby/io/omero.py
@@ -4,7 +4,11 @@ from pathlib import PosixPath
import re
from agora.io.bridge import BridgeH5
-from omero.gateway import BlitzGateway
+
+try:
+ from omero.gateway import BlitzGateway
+except ModuleNotFoundError:
+ print("Warning: Cannot import BlitzGateway.")
from yaml import safe_load
--
GitLab