From 4dd9423f628b7d7e0fa39626951bd3e1be3052fb Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 23 May 2024 15:26:11 +0100
Subject: [PATCH] fix(imageviewer): checks correctly for empty traps
---
src/wela/imageviewer.py | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)
diff --git a/src/wela/imageviewer.py b/src/wela/imageviewer.py
index 5a94cb7..84be7cf 100644
--- a/src/wela/imageviewer.py
+++ b/src/wela/imageviewer.py
@@ -24,7 +24,7 @@ def colormap(channel):
class BaseImageViewer(ABC):
- """Base class with routines common to all ImageViewers."""
+ """Base class for all ImageViewers."""
def __init__(self, h5file_path):
"""Initialise from a Path to a h5 file."""
@@ -32,13 +32,18 @@ class BaseImageViewer(ABC):
print(f"Viewing {str(h5file_path)}")
self.full = {}
- def print_trap_info(self, cells):
- """List available traps - those with identified cells."""
- traps_with_labels = [
- i for i, labels in enumerate(cells.labels) if labels
- ]
- print(f"Traps with labelled cells {traps_with_labels}.")
- print(f"Maximum number of time points {cells.ntimepoints}.")
+ def find_traps_with_cells(self, tpt_end, tpt_start=0):
+ """List traps with cells."""
+ cells = self.cells
+ tpts = range(tpt_start, tpt_end)
+ traps_with_cells = []
+ for trap_id in cells.traps:
+ for tpt in tpts:
+ if tpt in cells.nonempty_tp_in_trap(trap_id):
+ traps_with_cells.append(trap_id)
+ break
+ print(f"Traps with cells {traps_with_cells}")
+ return traps_with_cells
def get_tiles(self, trap_id, tps, channels_to_skip=None, cell_only=True):
"""Get dict of tiles with channel indices as keys."""
@@ -148,7 +153,7 @@ class BaseImageViewer(ABC):
ts_labels[tp_index, 0, ...] = outlines[tp_index]
return ts_images, ts_labels, channels
- def view(self, trap_id, tps=10, channels_to_skip=None):
+ def view(self, trap_id, tpt_end=10, tpt_start=0, channels_to_skip=None):
"""
Use Napari to view all channels and outlines for a particular trap.
@@ -164,10 +169,7 @@ class BaseImageViewer(ABC):
If None, all time points will be viewed, but gathering the images
will be slow.
"""
- if tps is None:
- tps = np.arange(self.cells.ntimepoints)
- elif type(tps) is int:
- tps = np.arange(tps)
+ tps = np.arange(tpt_start, tpt_end + 1)
ts_images, ts_labels, channels = self.get_data_for_viewing(
trap_id, tps, channels_to_skip
)
@@ -194,7 +196,7 @@ class LocalImageViewer(BaseImageViewer):
"""
View images from local files.
- File are either zarr or organised in directories.
+ Files are either zarr or organised in directories.
"""
def __init__(self, h5file: str, image_file: str):
@@ -206,7 +208,6 @@ class LocalImageViewer(BaseImageViewer):
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)
- self.print_trap_info(self.cells)
else:
if not h5file_path.exists():
print(f" Trouble loading {h5file}.")
@@ -215,7 +216,7 @@ class LocalImageViewer(BaseImageViewer):
class RemoteImageViewer(BaseImageViewer):
- """Fetching remote images with tiling and outline display."""
+ """View images from OMERO."""
def __init__(
self, h5file: str, server_info: t.Dict[str, str], omero_id: int
@@ -234,12 +235,12 @@ class RemoteImageViewer(BaseImageViewer):
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)
- self.print_trap_info(self.cells)
def get_files(
@@ -253,4 +254,4 @@ def get_files(
h5file = [f for f in h5files if position in f][0]
image_file_name = h5file.split("/")[-1].split(".")[0] + ".zarr"
image_file = str(Path(aliby_input) / omero_name / image_file_name)
- return [h5file, image_file]
+ return {"h5file": h5file, "image_file": image_file}
--
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