change(aliby): move omero Image to omero.py

src/aliby/io/image.py

@@ -6,29 +6,11 @@ from datetime import datetime
 from pathlib import Path, PosixPath
 
 import dask.array as da
-import numpy as np
 import xmltodict
-from dask import delayed
 from dask.array.image import imread
-from omero.model import enums as 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
-
-# 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,
-}
 
 
 def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
@@ -36,6 +18,8 @@ def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
     Wrapper to pick the appropiate Image class depending on the source of data.
     """
     if isinstance(source, int):
+        from aliby.io.omero import Image
+
         instatiator = Image
     elif isinstance(source, dict) or (
         isinstance(source, (str, PosixPath)) and Path(source).is_dir()
@@ -262,138 +246,3 @@ class ImageDir(BaseLocalImage):
         return [
             k.split("_")[-1] for k in self._meta.keys() if k.startswith("size")
         ]
-
-
-class Image(BridgeOmero):
-    """
-    Loads 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
-        base class.
-
-        Parameters
-        ----------
-        image_id: integer
-        server_info: dictionary
-            Specifies the host, username, and password as strings
-        """
-        self.ome_id = image_id
-        super().__init__(**server_info)
-
-    def init_interface(self, ome_id: int):
-        self.set_id(ome_id)
-        self.ome_class = self.conn.getObject("Image", ome_id)
-
-    @classmethod
-    def from_h5(
-        cls,
-        filepath: t.Union[str, PosixPath],
-    ):
-        """Instatiate Image from a hdf5 file.
-
-        Parameters
-        ----------
-        cls : Image
-            Image class
-        filepath : t.Union[str, PosixPath]
-            Location of hdf5 file.
-
-        Examples
-        --------
-        FIXME: Add docs.
-
-        """
-        # metadata = load_attributes(filepath)
-        bridge = BridgeH5(filepath)
-        image_id = bridge.meta_h5["image_id"]
-        # server_info = safe_load(bridge.meta_h5["parameters"])["general"][
-        #     "server_info"
-        # ]
-        return cls(image_id, **cls.server_info_from_h5(filepath))
-
-    @property
-    def name(self):
-        return self.ome_class.getName()
-
-    @property
-    def data(self):
-        return get_data_lazy(self.ome_class)
-
-    @property
-    def metadata(self):
-        """
-        Store metadata saved in OMERO: image size, number of time points,
-        labels of channels, and image name.
-        """
-        meta = dict()
-        meta["size_x"] = self.ome_class.getSizeX()
-        meta["size_y"] = self.ome_class.getSizeY()
-        meta["size_z"] = self.ome_class.getSizeZ()
-        meta["size_c"] = self.ome_class.getSizeC()
-        meta["size_t"] = self.ome_class.getSizeT()
-        meta["channels"] = self.ome_class.getChannelLabels()
-        meta["name"] = self.ome_class.getName()
-        return meta
-
-
-class UnsafeImage(Image):
-    """
-    Loads images from OMERO and gives access to the data and metadata.
-    This class is a temporary solution while we find a way to use
-    context managers inside napari. It risks resulting in zombie connections
-    and producing freezes in an OMERO server.
-
-    """
-
-    def __init__(self, image_id, **server_info):
-        """
-        Establishes the connection to the OMERO server via the Argo
-        base class.
-
-        Parameters
-        ----------
-        image_id: integer
-        server_info: dictionary
-            Specifies the host, username, and password as strings
-        """
-        super().__init__(image_id, **server_info)
-        self.create_gate()
-        self.init_wrapper()
-
-    @property
-    def data(self):
-        try:
-            return get_data_lazy(self.ome_class)
-        except Exception as e:
-            print(f"ERROR: Failed fetching image from server: {e}")
-            self.conn.connect(False)
-
-
-def get_data_lazy(image) -> da.Array:
-    """
-    Get 5D dask array, with delayed reading from OMERO image.
-    """
-    nt, nc, nz, ny, nx = [getattr(image, f"getSize{x}")() for x in "TCZYX"]
-    pixels = image.getPrimaryPixels()
-    dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
-    # using dask
-    get_plane = delayed(lambda idx: pixels.getPlane(*idx))
-
-    def get_lazy_plane(zct):
-        return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
-
-    # 5D stack: TCZXY
-    t_stacks = []
-    for t in range(nt):
-        c_stacks = []
-        for c in range(nc):
-            z_stack = []
-            for z in range(nz):
-                z_stack.append(get_lazy_plane((z, c, t)))
-            c_stacks.append(da.stack(z_stack))
-        t_stacks.append(da.stack(c_stacks))
-
-    return da.stack(t_stacks)

src/aliby/io/omero.py

+"""
+Tools to manage I/O using a remote OMERO server.
+"""
+
 import re
 import typing as t
 from abc import abstractmethod
 from pathlib import PosixPath
 
+import dask.array as da
+import numpy as np
 import omero
+from dask import delayed
 from omero.gateway import BlitzGateway
+from omero.model import enums as omero_enums
 from yaml import safe_load
 
 from agora.io.bridge import BridgeH5
+from aliby.io.omero 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,
+}
 
 
 class BridgeOmero:
@@ -195,7 +216,7 @@ class Dataset(BridgeOmero):
 
     def cache_logs(self, root_dir):
         valid_suffixes = ("txt", "log")
-        for name, annotation in self.files.items():
+        for _, annotation in self.files.items():
             filepath = root_dir / annotation.getFileName().replace("/", "_")
             if (
                 any([str(filepath).endswith(suff) for suff in valid_suffixes])
@@ -234,3 +255,138 @@ class Dataset(BridgeOmero):
                 return cls(
                     bridge.meta_h5[k], **cls.server_info_from_h5(filepath)
                 )
+
+
+class Image(BridgeOmero):
+    """
+    Loads 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
+        base class.
+
+        Parameters
+        ----------
+        image_id: integer
+        server_info: dictionary
+            Specifies the host, username, and password as strings
+        """
+        self.ome_id = image_id
+        super().__init__(**server_info)
+
+    def init_interface(self, ome_id: int):
+        self.set_id(ome_id)
+        self.ome_class = self.conn.getObject("Image", ome_id)
+
+    @classmethod
+    def from_h5(
+        cls,
+        filepath: t.Union[str, PosixPath],
+    ):
+        """Instatiate Image from a hdf5 file.
+
+        Parameters
+        ----------
+        cls : Image
+            Image class
+        filepath : t.Union[str, PosixPath]
+            Location of hdf5 file.
+
+        Examples
+        --------
+        FIXME: Add docs.
+
+        """
+        # metadata = load_attributes(filepath)
+        bridge = BridgeH5(filepath)
+        image_id = bridge.meta_h5["image_id"]
+        # server_info = safe_load(bridge.meta_h5["parameters"])["general"][
+        #     "server_info"
+        # ]
+        return cls(image_id, **cls.server_info_from_h5(filepath))
+
+    @property
+    def name(self):
+        return self.ome_class.getName()
+
+    @property
+    def data(self):
+        return get_data_lazy(self.ome_class)
+
+    @property
+    def metadata(self):
+        """
+        Store metadata saved in OMERO: image size, number of time points,
+        labels of channels, and image name.
+        """
+        meta = dict()
+        meta["size_x"] = self.ome_class.getSizeX()
+        meta["size_y"] = self.ome_class.getSizeY()
+        meta["size_z"] = self.ome_class.getSizeZ()
+        meta["size_c"] = self.ome_class.getSizeC()
+        meta["size_t"] = self.ome_class.getSizeT()
+        meta["channels"] = self.ome_class.getChannelLabels()
+        meta["name"] = self.ome_class.getName()
+        return meta
+
+
+class UnsafeImage(Image):
+    """
+    Loads images from OMERO and gives access to the data and metadata.
+    This class is a temporary solution while we find a way to use
+    context managers inside napari. It risks resulting in zombie connections
+    and producing freezes in an OMERO server.
+
+    """
+
+    def __init__(self, image_id, **server_info):
+        """
+        Establishes the connection to the OMERO server via the Argo
+        base class.
+
+        Parameters
+        ----------
+        image_id: integer
+        server_info: dictionary
+            Specifies the host, username, and password as strings
+        """
+        super().__init__(image_id, **server_info)
+        self.create_gate()
+        self.init_wrapper()
+
+    @property
+    def data(self):
+        try:
+            return get_data_lazy(self.ome_class)
+        except Exception as e:
+            print(f"ERROR: Failed fetching image from server: {e}")
+            self.conn.connect(False)
+
+
+def get_data_lazy(image) -> da.Array:
+    """
+    Get 5D dask array, with delayed reading from OMERO image.
+    """
+    nt, nc, nz, ny, nx = [getattr(image, f"getSize{x}")() for x in "TCZYX"]
+    pixels = image.getPrimaryPixels()
+    dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
+    # using dask
+    get_plane = delayed(lambda idx: pixels.getPlane(*idx))
+
+    def get_lazy_plane(zct):
+        return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
+
+    # 5D stack: TCZXY
+    t_stacks = []
+    for t in range(nt):
+        c_stacks = []
+        for c in range(nc):
+            z_stack = []
+            for z in range(nz):
+                z_stack.append(get_lazy_plane((z, c, t)))
+            c_stacks.append(da.stack(z_stack))
+        t_stacks.append(da.stack(c_stacks))
+
+    return da.stack(t_stacks)