From 3e5f041e64613d7c998ebeef8f274afdd3ed9baa Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 20 Jun 2024 12:08:55 +0100
Subject: [PATCH] feature(imageviewer): dded sample_traps_with_cells
---
examples/run_imageviewer.py | 3 ++-
src/wela/imageviewer.py | 27 ++++++++++++++++++++++++---
src/wela/plotting.py | 6 +++---
3 files changed, 29 insertions(+), 7 deletions(-)
diff --git a/examples/run_imageviewer.py b/examples/run_imageviewer.py
index 6afe25e..40ccbdc 100644
--- a/examples/run_imageviewer.py
+++ b/examples/run_imageviewer.py
@@ -14,12 +14,13 @@ server_info = {
h5file = f"{aliby_output}{omero_name}/{position}.h5"
iv = ImageViewer.remote(h5file, server_info, 2104)
tpt_end = 10
+no_cells = 4
# for information only
iv.print_traps_with_cells(tpt_end)
# use Napari to view cells
# python -m pip install "napari[all]" --upgrade
iv.view(
- trap_ids=[4, 8, 13],
+ trap_ids=iv.sample_traps_with_cells(tpt_end=tpt_end, no_cells=no_cells),
tpt_end=tpt_end,
channels_to_skip=["cy5"],
no_vertical_tiles=1,
diff --git a/src/wela/imageviewer.py b/src/wela/imageviewer.py
index b251a08..629d69e 100644
--- a/src/wela/imageviewer.py
+++ b/src/wela/imageviewer.py
@@ -1,7 +1,14 @@
from pathlib import Path
import h5py
-import napari
+
+try:
+ import napari
+except ModuleNotFoundError:
+ print(
+ "Napari cannot be imported.\nRun",
+ ' python -m pip install "napari[all]"',
+ )
import numpy as np
from agora.io.cells import Cells
from aliby.io.image import dispatch_image
@@ -62,7 +69,7 @@ class ImageViewer:
iv.cells = Cells.from_source(iv.h5file_path)
return iv
- def print_traps_with_cells(self, tpt_end, tpt_start=0):
+ def get_all_traps_with_cells(self, tpt_end, tpt_start=0, display=True):
"""List traps with cells."""
cells = self.cells
tpts = range(tpt_start, tpt_end)
@@ -72,9 +79,23 @@ class ImageViewer:
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}")
+ if display:
+ print(f"Traps with cells {traps_with_cells}")
return traps_with_cells
+ def sample_traps_with_cells(self, no_cells, tpt_end, tpt_start=0):
+ """Sample some traps that have cells."""
+ traps_with_cells = self.get_all_traps_with_cells(
+ tpt_end, tpt_start, display=False
+ )
+ rng = np.random.default_rng()
+ samples = rng.integers(
+ low=0,
+ high=len(traps_with_cells),
+ size=np.min([no_cells, len(traps_with_cells)]),
+ )
+ return samples
+
def get_tiles(self, trap_id, tps, channels_to_skip=None, cell_only=True):
"""Get dict of tiles with channel indices as keys."""
tiles_dict = {}
diff --git a/src/wela/plotting.py b/src/wela/plotting.py
index 5040d7e..56a412e 100644
--- a/src/wela/plotting.py
+++ b/src/wela/plotting.py
@@ -496,7 +496,7 @@ def plot2Dhist(
--------
Load data:
>>> from wela.dataloader import dataloader
- >>> from wela.plotting import plothist
+ >>> from wela.plotting import plot2Dhist
>>> dl = dataloader()
>>> dl.load("1334_2023_03_28_pyrTo2Gal_01glc_00", use_tsv=True)
>>> dlc = dataloader()
@@ -507,8 +507,8 @@ def plot2Dhist(
>>> tc, dc = dlc.get_time_series("median_GFP")
Plot both data sets using axes with the same range:
- >>> bins = plothist(t, dc, title="2% Gal", figsize=(4, 3))[0]
- >>> plothist(t, d, title="2% Gal and 0.1% Glu", bins=bins, figsize=(4, 3))
+ >>> bins = plot2Dhist(t, dc, title="2% Gal", figsize=(4, 3))[0]
+ >>> plot2Dhist(t, d, title="2% Gal and 0.1% Glu", bins=bins, figsize=(4, 3))
"""
if x.ndim == 1:
# make into a 2D array
--
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