diff --git a/src/wela/imageviewer.py b/src/wela/imageviewer.py
index 84be7cf4a31926a5f94cbbe94c9d42cddc1c6b53..75f5363fed233fc4da0580ff8b6e8015594b6f46 100644
--- a/src/wela/imageviewer.py
+++ b/src/wela/imageviewer.py
@@ -1,5 +1,3 @@
-import typing as t
-from abc import ABC
from pathlib import Path
import h5py
@@ -12,25 +10,57 @@ from aliby.io.omero import UnsafeImage as OImage
from aliby.tile.tiler import Tiler
-def colormap(channel):
- """Find default colormap."""
- if "GFP" in channel:
- colormap = "green"
- elif "Cherry" in channel or "RFP" in channel:
- colormap = "red"
- else:
- colormap = "gray"
- return colormap
+class ImageViewer:
+ def __init__(self, h5file):
+ self.h5file_path = Path(h5file)
+ print(f"Viewing {str(self.h5file_path)}")
+ self.full = {}
-class BaseImageViewer(ABC):
- """Base class for all ImageViewers."""
+ @classmethod
+ def local(cls, h5file: str, image_file: str):
+ """
+ View images from local files.
- def __init__(self, h5file_path):
- """Initialise from a Path to a h5 file."""
- self.h5file_path = h5file_path
- print(f"Viewing {str(h5file_path)}")
- self.full = {}
+ Files are either zarr or organised in directories.
+ """
+ iv = cls(h5file)
+ image_file_path = Path(image_file)
+ if iv.h5file_path.exists() and image_file_path.exists():
+ with dispatch_image(image_file_path)(image_file_path) as image:
+ tiler = Tiler.from_h5(image, iv.h5file_path)
+ cells = Cells.from_source(iv.h5file_path)
+ iv.tiler = tiler
+ iv.cells = cells
+ return iv
+ else:
+ if not iv.h5file_path.exists():
+ print(f" Trouble loading {h5file}.")
+ if not image_file_path.exists():
+ print(f" Trouble loading {image_file}.")
+
+ @classmethod
+ def remote(cls, h5file: str, server_info: dict, omero_id: int):
+ """View images from OMERO."""
+ iv = cls(h5file)
+ with h5py.File(iv.h5file_path, "r") as f:
+ # get image_id from the h5 file
+ image_id = f.attrs.get("image_id")
+ if image_id is None:
+ # get image_id from OMERO
+ with Dataset(omero_id, **server_info) as dataset_om:
+ positions = dataset_om.get_position_ids()
+ image_id = positions.get(iv.h5file_path.name.split(".")[0])
+ if image_id is None:
+ print("Can't find an image.")
+ else:
+ print(f"Using image ID {image_id}.")
+ iv.image_id = image_id
+ image = OImage(image_id, **server_info)
+ print("Connected to OMERO.")
+ iv.tiler = Tiler.from_h5(image, iv.h5file_path)
+ iv.cells = Cells.from_source(iv.h5file_path)
+ return iv
def find_traps_with_cells(self, tpt_end, tpt_start=0):
"""List traps with cells."""
@@ -192,55 +222,66 @@ class BaseImageViewer(ABC):
)
-class LocalImageViewer(BaseImageViewer):
- """
- View images from local files.
+# class LocalImageViewer(BaseImageViewer):
+# """
+# View images from local files.
- Files are either zarr or organised in directories.
- """
+# Files are either zarr or organised in directories.
+# """
- def __init__(self, h5file: str, image_file: str):
- """Initialise using a h5file and a zarr file of images."""
- h5file_path = Path(h5file)
- image_file_path = Path(image_file)
- if h5file_path.exists() and image_file_path.exists():
- super().__init__(h5file_path)
- with dispatch_image(image_file_path)(image_file_path) as image:
- self.tiler = Tiler.from_h5(image, h5file_path)
- self.cells = Cells.from_source(h5file_path)
- else:
- if not h5file_path.exists():
- print(f" Trouble loading {h5file}.")
- if not image_file_path.exists():
- print(f" Trouble loading {image_file}.")
+# def __init__(self, h5file: str, image_file: str):
+# """Initialise using a h5file and a zarr file of images."""
+# h5file_path = Path(h5file)
+# image_file_path = Path(image_file)
+# if h5file_path.exists() and image_file_path.exists():
+# super().__init__(h5file_path)
+# with dispatch_image(image_file_path)(image_file_path) as image:
+# self.tiler = Tiler.from_h5(image, h5file_path)
+# self.cells = Cells.from_source(h5file_path)
+# else:
+# if not h5file_path.exists():
+# print(f" Trouble loading {h5file}.")
+# if not image_file_path.exists():
+# print(f" Trouble loading {image_file}.")
-class RemoteImageViewer(BaseImageViewer):
- """View images from OMERO."""
+# class RemoteImageViewer(BaseImageViewer):
+# """View images from OMERO."""
- def __init__(
- self, h5file: str, server_info: t.Dict[str, str], omero_id: int
- ):
- """Initialise using a h5file and importing aliby.io.omero."""
- h5file_path = Path(h5file)
- super().__init__(h5file_path)
- with h5py.File(h5file_path, "r") as f:
- # get image_id from the h5 file
- image_id = f.attrs.get("image_id")
- if image_id is None:
- # get image_id from OMERO
- with Dataset(omero_id, **server_info) as dataset_om:
- positions = dataset_om.get_position_ids()
- image_id = positions.get(h5file_path.name.split(".")[0])
- if image_id is None:
- print("Can't find an image.")
- else:
- print(f"Using image ID {image_id}.")
- self.image_id = image_id
- image = OImage(image_id, **server_info)
- print("Connected to OMERO.")
- self.tiler = Tiler.from_h5(image, h5file_path)
- self.cells = Cells.from_source(h5file_path)
+# def __init__(
+# self, h5file: str, server_info: t.Dict[str, str], omero_id: int
+# ):
+# """Initialise using a h5file and importing aliby.io.omero."""
+# h5file_path = Path(h5file)
+# super().__init__(h5file_path)
+# with h5py.File(h5file_path, "r") as f:
+# # get image_id from the h5 file
+# image_id = f.attrs.get("image_id")
+# if image_id is None:
+# # get image_id from OMERO
+# with Dataset(omero_id, **server_info) as dataset_om:
+# positions = dataset_om.get_position_ids()
+# image_id = positions.get(h5file_path.name.split(".")[0])
+# if image_id is None:
+# print("Can't find an image.")
+# else:
+# print(f"Using image ID {image_id}.")
+# self.image_id = image_id
+# image = OImage(image_id, **server_info)
+# print("Connected to OMERO.")
+# self.tiler = Tiler.from_h5(image, h5file_path)
+# self.cells = Cells.from_source(h5file_path)
+
+
+def colormap(channel):
+ """Find default colormap."""
+ if "GFP" in channel:
+ colormap = "green"
+ elif "Cherry" in channel or "RFP" in channel:
+ colormap = "red"
+ else:
+ colormap = "gray"
+ return colormap
def get_files(