From c48848838cced3ebab0273806b70ece82fba461d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 9 Oct 2023 16:42:35 +0200
Subject: [PATCH] Focus 3d patches now brought into workflow parameters
---
extensions/chaeo/products.py | 24 +++++++++++++++---------
extensions/chaeo/workflows.py | 28 ++++++++++++----------------
2 files changed, 27 insertions(+), 25 deletions(-)
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index 98a087e8..0595e6a3 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -13,6 +13,16 @@ from extensions.chaeo.annotators import draw_box_on_patch
from model_server.accessors import GenericImageDataAccessor
from model_server.process import pad, rescale, resample_to_8bit
+def _focus_metrics():
+ return {
+ 'max_intensity': lambda x: np.max(x),
+ 'stdev': lambda x: np.std(x),
+ 'max_sobel': lambda x: np.max(sobel(x)),
+ 'rms_sobel': lambda x: sqrt(np.mean(sobel(x) ** 2)),
+ 'entropy': lambda x: shannon_entropy(x),
+ 'moment': lambda x: moment(x.flatten(), moment=2),
+ }
+
def _write_patch_to_file(where, fname, data):
ext = fname.split('.')[-1].upper()
where.mkdir(parents=True, exist_ok=True)
@@ -41,6 +51,7 @@ def export_patches_from_zstack(
pad_to: int = 256,
make_3d: bool = False,
prefix='patch',
+ focus_metric: str = None,
**kwargs
):
assert stack.chroma == 1, 'Expecting monochromatic image data'
@@ -65,7 +76,9 @@ def export_patches_from_zstack(
patch = patch3d
# make a 2d patch, find optimal z-position determined by focus_metric function
- elif foc := kwargs.get('focus_metric'):
+ elif focus_metric is not None:
+ foc = _focus_metrics()[focus_metric]
+
sp_sl = np.s_[y0: y1, x0: x1, :, :]
subpatch = patch3d[sp_sl]
@@ -125,14 +138,7 @@ def export_3d_patches_with_focus_metrics(
def get_zstack_focus_metrics(zs):
nz = zs.shape[3]
- me = {
- 'max_intensity': lambda x: np.max(x),
- 'stdev': lambda x: np.std(x),
- 'max_sobel': lambda x: np.max(sobel(x)),
- 'rms_sobel': lambda x: sqrt(np.mean(sobel(x) ** 2)),
- 'entropy': lambda x: shannon_entropy(x),
- 'moment': lambda x: moment(x.flatten(), moment=2),
- }
+ me = _focus_metrics()
dd = {}
for zi in range(0, nz):
spf = zs[:, :, :, zi]
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index b0d6287a..50b9ec52 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -60,33 +60,29 @@ def export_patches_from_multichannel_zstack(
zmask_acc = InMemoryDataAccessor(zmask)
ti.click('generate_zmasks')
- # export patches
- import numpy as np
- from skimage.filters import gaussian, sobel
-
- # def zs_projector(zs):
- # sigma = 1.5
- # blur = gaussian(sobel(zs), sigma)
- # argmax = np.argmax(blur, axis=3, keepdims=True)
- # return np.take_along_axis(zs, argmax, axis=3)
- #
- # def zs_annotate_best_focus(zs):
- # pass
-
files = export_patches_from_zstack(
- # Path(where_output) / '2d_patches',
Path(where_output) / '3d_patches',
stack.get_one_channel_data(patches_channel),
zmask_meta,
prefix=fstem,
- # draw_bounding_box=True,
draw_bounding_box=False,
rescale_clip=0.0,
- # projector=zs_projector,
make_3d=True,
)
ti.click('export_patches')
+ files = export_patches_from_zstack(
+ Path(where_output) / '2d_patches',
+ stack.get_one_channel_data(patches_channel),
+ zmask_meta,
+ prefix=fstem,
+ draw_bounding_box=False,
+ rescale_clip=0.0,
+ make_3d=False,
+ focus_metric='max_sobel',
+ )
+ ti.click('export_patches')
+
# export annotated zstack
annotated = InMemoryDataAccessor(
draw_boxes_on_3d_image(
--
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