diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 5af04ca679d92fe9d40ca33f029b9553f42a9dc2..42005645b6935e07ff264f8e4b699258d2c75d37 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -29,15 +29,11 @@ from tifffile import TiffFile
from agora.io.metadata import dir_to_meta, dispatch_metadata_parser
-def get_examples_dir():
- """Get examples directory that stores dummy image for tiler."""
- return files("aliby").parent.parent / "examples" / "tiler"
-
-
def instantiate_image(
source: t.Union[str, int, t.Dict[str, str], Path], **kwargs
):
- """Wrapper to instantiate the appropriate image
+ """
+ Instantiate the image.
Parameters
----------
@@ -46,10 +42,9 @@ def instantiate_image(
Examples
--------
- image_path = "path/to/image"]
+ image_path = "path/to/image"
with instantiate_image(image_path) as img:
print(imz.data, img.metadata)
-
"""
return dispatch_image(source)(source, **kwargs)
@@ -63,14 +58,12 @@ def dispatch_image(source: t.Union[str, int, t.Dict[str, str], Path]):
elif isinstance(source, dict) or (
isinstance(source, (str, Path)) and Path(source).is_dir()
):
+ # zarr files are considered directories
if Path(source).suffix == ".zarr":
instantiator = ImageZarr
else:
instantiator = ImageDir
- elif isinstance(source, Path) and source.is_file():
- # my addition
- instantiator = ImageLocalOME
- elif isinstance(source, str) and Path(source).is_file():
+ elif isinstance(source, (str, Path)) and Path(source).is_file():
instantiator = ImageLocalOME
else:
raise Exception(f"Invalid data source at {source}")
@@ -78,9 +71,7 @@ def dispatch_image(source: t.Union[str, int, t.Dict[str, str], Path]):
class BaseLocalImage(ABC):
- """
- Base Image class to set path and provide context management method.
- """
+ """Set path and provide method for context management."""
# default image order
_default_dimorder = "tczyx"
@@ -112,30 +103,35 @@ class BaseLocalImage(ABC):
)
return self._rechunked_img
+ @property
+ def data(self):
+ """Get data."""
+ return self.get_data_lazy()
+
+ @property
+ def metadata(self):
+ """Get metadata."""
+ return self._meta
+
+ def set_meta(self):
+ """Load metadata using parser dispatch."""
+ self._meta = dispatch_metadata_parser(self.path)
+
@abstractmethod
def get_data_lazy(self) -> da.Array:
+ """Define in child class."""
pass
@abstractproperty
def name(self):
+ """Define in child class."""
pass
@abstractproperty
def dimorder(self):
+ """Define in child class."""
pass
- @property
- def data(self):
- return self.get_data_lazy()
-
- @property
- def metadata(self):
- return self._meta
-
- def set_meta(self):
- """Load metadata using parser dispatch"""
- self._meta = dispatch_metadata_parser(self.path)
-
class ImageLocalOME(BaseLocalImage):
"""
@@ -146,11 +142,13 @@ class ImageLocalOME(BaseLocalImage):
"""
def __init__(self, path: str, dimorder=None, **kwargs):
+ """Initialise using file name."""
super().__init__(path)
self._id = str(path)
self.set_meta(str(path))
def set_meta(self, path):
+ """Get metadata from the associated tiff file."""
meta = dict()
try:
with TiffFile(path) as f:
@@ -194,7 +192,7 @@ class ImageLocalOME(BaseLocalImage):
@property
def dimorder(self):
- """Order of dimensions in image"""
+ """Return order of dimensions in the image."""
if not hasattr(self, "_dimorder"):
self._dimorder = self._meta["Image"]["Pixels"]["@DimensionOrder"]
return self._dimorder
@@ -205,16 +203,16 @@ class ImageLocalOME(BaseLocalImage):
return self._dimorder
def get_data_lazy(self) -> da.Array:
- """Return 5D dask array. For lazy-loading multidimensional tiff files"""
-
+ """Return 5D dask array via lazy-loading of tiff files."""
if not hasattr(self, "formatted_img"):
- if not hasattr(self, "ids"): # Standard dimension order
+ if not hasattr(self, "ids"):
+ # standard order of image dimensions
img = (imread(str(self.path))[0],)
- else: # Custom dimension order, we rearrange the axes for compatibility
+ else:
+ # bespoke order, so rearrange axes for compatibility
img = imread(str(self.path))[0]
for i, d in enumerate(self._dimorder):
self._meta["size_" + d.lower()] = img.shape[i]
-
target_order = (
*self.ids,
*[
@@ -233,12 +231,13 @@ class ImageLocalOME(BaseLocalImage):
img = da.moveaxis(
reshaped, range(len(reshaped.shape)), target_order
)
-
return self.rechunk_data(img)
class ImageDir(BaseLocalImage):
"""
+ Standard image class for tiff files.
+
Image class for the case in which all images are split in one or
multiple folders with time-points and channels as independent files.
It inherits from BaseLocalImage so we only override methods that are critical.
@@ -247,28 +246,23 @@ class ImageDir(BaseLocalImage):
- One folder per position.
- Images are flat.
- Channel, Time, z-stack and the others are determined by filenames.
- - Provides Dimorder as it is set in the filenames, or expects order during instatiation
+ - Provides Dimorder as it is set in the filenames, or expects order
"""
def __init__(self, path: t.Union[str, Path], **kwargs):
+ """Initialise using file name."""
super().__init__(path)
self.image_id = str(self.path.stem)
-
self._meta = dir_to_meta(self.path)
def get_data_lazy(self) -> da.Array:
- """Return 5D dask array. For lazy-loading local multidimensional tiff files"""
-
+ """Return 5D dask array."""
img = imread(str(self.path / "*.tiff"))
-
# If extra channels, pick the first stack of the last dimensions
-
while len(img.shape) > 3:
img = img[..., 0]
-
if self._meta:
self._meta["size_x"], self._meta["size_y"] = img.shape[-2:]
-
# Reshape using metadata
# img = da.reshape(img, (*self._meta, *img.shape[1:]))
img = da.reshape(img, self._meta.values())
@@ -289,6 +283,7 @@ class ImageDir(BaseLocalImage):
@property
def name(self):
+ """Return name of image directory."""
return self.path.stem
@property
@@ -302,24 +297,27 @@ class ImageDir(BaseLocalImage):
class ImageZarr(BaseLocalImage):
"""
Read zarr compressed files.
- These are outputed by the script
+
+ These files are generated by the script
skeletons/scripts/howto_omero/convert_clone_zarr_to_tiff.py
"""
def __init__(self, path: t.Union[str, Path], **kwargs):
+ """Initialise using file name."""
super().__init__(path)
self.set_meta()
try:
self._img = zarr.open(self.path)
self.add_size_to_meta()
except Exception as e:
- print(f"Could not add size info to metadata: {e}")
+ print(f"ImageZarr: Could not add size info to metadata: {e}.")
def get_data_lazy(self) -> da.Array:
"""Return 5D dask array for lazy-loading local multidimensional zarr files."""
return self._img
def add_size_to_meta(self):
+ """Add shape of image array to metadata."""
self._meta.update(
{
f"size_{dim}": shape
@@ -329,16 +327,13 @@ class ImageZarr(BaseLocalImage):
@property
def name(self):
+ """Return name of zarr directory."""
return self.path.stem
@property
def dimorder(self):
- # FIXME hardcoded order based on zarr compression/cloning script
+ """Impose a hard-coded order of dimensions based on the zarr compression script."""
return "TCZYX"
- # Assumes only dimensions start with "size"
- # return [
- # k.split("_")[-1] for k in self._meta.keys() if k.startswith("size")
- # ]
class ImageDummy(BaseLocalImage):
diff --git a/src/aliby/io/omero.py b/src/aliby/io/omero.py
index 0ea37359360598a7335db55081ab9500e91c3efc..8cc4fd939dcf1aacd0ac2e8cb84a48ae87a4f292 100644
--- a/src/aliby/io/omero.py
+++ b/src/aliby/io/omero.py
@@ -253,7 +253,8 @@ class Dataset(BridgeOmero):
cls,
filepath: t.Union[str, Path],
):
- """Instatiate Dataset from a hdf5 file.
+ """
+ Instantiate data set from a h5 file.
Parameters
----------
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index b0fdbefcce328faefa1425fcaa2886bf38c5d278..b35ca5c10e6611d9eb928c2fc44f2b4b7391e639 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -320,7 +320,7 @@ class Tiler(StepABC):
image.data,
metadata,
parameters,
- tile_locs=tile_locs,
+ tile_locations=tile_locs,
)
if hasattr(tile_locs, "drifts"):
tiler.no_processed = len(tile_locs.drifts)
diff --git a/src/aliby/utils/imageViewer.py b/src/aliby/utils/imageViewer.py
index fd529108dd9091b7ec19041ccc8cf2d265af2fa9..52a15ee763f776aba369276e34748b1becff76c0 100644
--- a/src/aliby/utils/imageViewer.py
+++ b/src/aliby/utils/imageViewer.py
@@ -17,17 +17,22 @@ riv.plot_labelled_trap(tile_id, trange, [0], ncols=ncols)
import re
import typing as t
+from abc import ABC
import h5py
-from abc import ABC
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
-from PIL import Image
from skimage.morphology import dilation
from agora.io.cells import Cells
from agora.io.metadata import dispatch_metadata_parser
+from aliby.io.image import ImageDir, ImageZarr, dispatch_image
+
+try:
+ from aliby.io.omero import UnsafeImage as OImage
+except ModuleNotFoundError:
+ print("Viewing available only for local files.")
from aliby.tile.tiler import Tiler, TilerParameters
from aliby.utils.plot import stretch_clip
@@ -40,9 +45,7 @@ default_colours = {
def custom_imshow(a, norm=None, cmap=None, *args, **kwargs):
- """
- Wrapper on plt.imshow function.
- """
+ """Wrap plt.imshow."""
if cmap is None:
cmap = "Greys_r"
return plt.imshow(
@@ -57,16 +60,13 @@ def custom_imshow(a, norm=None, cmap=None, *args, **kwargs):
class BaseImageViewer(ABC):
def __init__(self, fpath):
-
self._fpath = fpath
- attrs = dispatch_metadata_parser(fpath.parent)
+ self.attrs = dispatch_metadata_parser(fpath.parent)
self._logfiles_meta = {}
-
- self.image_id = attrs.get("image_id")
+ self.image_id = self.attrs.get("image_id")
if self.image_id is None:
with h5py.File(fpath, "r") as f:
self.image_id = f.attrs.get("image_id")
-
assert self.image_id is not None, "No valid image_id found in metadata"
@property
@@ -75,42 +75,39 @@ class BaseImageViewer(ABC):
@property
def ntraps(self):
+ """Find the number of traps available."""
return self.cells.ntraps
@property
def max_labels(self):
- # Print max cell label in whole experiment
+ """Find maximum cell label in whole experiment."""
return [max(x) for x in self.cells.labels]
def labels_at_time(self, tp: int):
- # Print cell label at a given time-point
+ """Find cell label at a given time point."""
return self.cells.labels_at_time(tp)
class LocalImageViewer(BaseImageViewer):
"""
- Tool to generate figures from local files, either zarr or files organised
- in directories.
+ Generate figures from local files.
+
+ File are either zarr or organised in directories.
TODO move common functionality from RemoteImageViewer to BaseImageViewer
"""
- def __init__(self, results_path: str, data_path: str):
- super().__init__(results_path)
-
- from aliby.io.image import ImageDir, ImageZarr
-
+ def __init__(self, h5file_path: str, data_path: str):
+ super().__init__(h5file_path)
self._image_class = (
- ImageZarr if data_path.endswith(".zar") else ImageDir
+ ImageZarr if str(data_path).endswith(".zarr") else ImageDir
)
-
- with dispatch_image(data_path)(data_path) as image:
- self.tiler = Tiler(
- image.data,
- self._meta if hasattr(self, "_meta") else self._logfiles_meta,
- TilerParameters.default(),
- )
-
- self.cells = Cells.from_source(results_path)
+ image = ImageZarr(data_path)
+ self.tiler = Tiler(
+ image.data,
+ self._meta if hasattr(self, "_meta") else self._logfiles_meta,
+ TilerParameters.default(),
+ )
+ self.cells = Cells.from_source(h5file_path)
class RemoteImageViewer(BaseImageViewer):
@@ -126,16 +123,12 @@ class RemoteImageViewer(BaseImageViewer):
server_info: t.Dict[str, str],
):
super().__init__(results_path)
-
- from aliby.io.omero import UnsafeImage as OImage
-
self._server_info = server_info or {
- k: attrs["parameters"]["general"][k] for k in self._credentials
+ k: self.attrs["parameters"]["general"][k]
+ for k in self._credentials
}
-
self._image_instance = OImage(self.image_id, **self._server_info)
self.tiler = Tiler.from_h5(self._image_instance, results_path)
-
self.cells = Cells.from_source(results_path)
def random_valid_trap_tp(
@@ -194,7 +187,6 @@ class RemoteImageViewer(BaseImageViewer):
z: int = None,
server_info=None,
):
-
if tps and not isinstance(tps, t.Collection):
tps = range(tps)
diff --git a/src/aliby/utils/plot.py b/src/aliby/utils/plot.py
index 3f0a66c0849839fac357851ade037e78e8d17634..8a34c3b7ade6c8abe68e1491d2b0885d815def4a 100644
--- a/src/aliby/utils/plot.py
+++ b/src/aliby/utils/plot.py
@@ -52,7 +52,7 @@ def plot_in_square(data: t.Iterable):
def stretch_clip(image, clip=True):
"""
- Performs contrast stretching on an input image.
+ Perform contrast stretching on an input image.
This function takes an array-like input image and enhances its contrast by adjusting
the dynamic range of pixel values. It first scales the pixel values between 0 and 255,