From aade8740275447090fb2f20555e277cd2e6de3bf Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 10 Oct 2023 14:36:36 +0200
Subject: [PATCH] Chasing down bug in overlay annotations
---
extensions/chaeo/annotators.py | 5 ++--
.../chaeo/examples/batch_run_patches.py | 2 +-
extensions/chaeo/products.py | 12 ++++++---
extensions/chaeo/tests/test_zstack.py | 10 +++++++
extensions/chaeo/workflows.py | 26 ++++++++++++++++---
5 files changed, 44 insertions(+), 11 deletions(-)
diff --git a/extensions/chaeo/annotators.py b/extensions/chaeo/annotators.py
index 3e84d0b1..0c25647e 100644
--- a/extensions/chaeo/annotators.py
+++ b/extensions/chaeo/annotators.py
@@ -58,11 +58,10 @@ def draw_box_on_patch(patch, bbox, linewidth=1):
draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=linewidth)
return np.array(pilimg)
-def draw_contours_on_patch(patch, contours, offset, linewidth=1):
+def draw_contours_on_patch(patch, contours, linewidth=1):
assert len(patch.shape) == 2
pilimg = Image.fromarray(patch) # drawing modifies array in-place
draw = ImageDraw.Draw(pilimg)
- x0, y0 = offset
for co in contours:
- draw.line([(p[1] + y0, p[0] + x0) for p in co], width=linewidth)
+ draw.line([(p[1], p[0]) for p in co], width=linewidth)
return np.array(pilimg)
\ No newline at end of file
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index f2fd45d9..0c27af40 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -38,7 +38,7 @@ if __name__ == '__main__':
ma = re.match(pattern, ff.stem)
print(ff)
- if not ff.suffix.upper () == '.CZI':
+ if not ff.suffix.upper() == '.CZI':
continue
if int(ma.groups()[1]) > 10: # skip second half of set
continue
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index 006244e2..bab25537 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -146,16 +146,22 @@ def export_patches_from_zstack(
if kwargs.get('draw_mask'):
mci = kwargs.get('mask_channel', 0)
+ mask = np.zeros(patch.shape[0:2], dtype=bool)
+ mask[sp_sl[0:2]] = mi['mask']
for zi in range(0, patch.shape[3]):
- patch[sp_sl][:, :, mci, zi] = np.invert(mi['mask']) * patch[sp_sl][:, :, mci, zi]
+ patch[:, :, mci, zi] = np.invert(mask) * patch[:, :, mci, zi]
if kwargs.get('draw_contour'):
mci = kwargs.get('contour_channel', 0)
+ mask = np.zeros(patch.shape[0:2], dtype=bool)
+ try:
+ mask[sp_sl[0:2]] = mi['mask']
+ except Exception:
+ a=1
for zi in range(0, patch.shape[3]):
patch[:, :, mci, zi] = draw_contours_on_patch(
patch[:, :, mci, zi],
- find_contours(mi['mask']),
- offset=(x0, y0)
+ find_contours(mask)
)
if pad_to:
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 89e69db1..35f14666 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -132,6 +132,11 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
self.assertGreaterEqual(len(files), 1)
+ def test_make_multichannel_2d_patches_with_mask_overlay(self):
+ zmask, meta = self.test_zmask_makes_correct_boxes(
+ filters={'area': (1e3, 1e4)},
+ expand_box_by=(128, 2)
+ )
files = export_multichannel_patches_from_zstack(
output_path / '2d_patches_chlorophyl_mask_overlay',
InMemoryDataAccessor(self.stack.data),
@@ -144,6 +149,11 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
self.assertGreaterEqual(len(files), 1)
+ def test_make_multichannel_2d_patches_with_contour_overlay(self):
+ zmask, meta = self.test_zmask_makes_correct_boxes(
+ filters={'area': (1e3, 1e4)},
+ expand_box_by=(128, 2)
+ )
files = export_multichannel_patches_from_zstack(
output_path / '2d_patches_chlorophyl_contour_overlay',
InMemoryDataAccessor(self.stack.data),
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 7f2df928..6b23ca80 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -3,7 +3,7 @@ from typing import Dict
from extensions.ilastik.models import IlastikPixelClassifierModel
from extensions.chaeo.annotators import draw_boxes_on_3d_image
-from extensions.chaeo.products import export_patches_from_zstack, export_patch_masks_from_zstack
+from extensions.chaeo.products import export_patches_from_zstack, export_patch_masks_from_zstack, export_multichannel_patches_from_zstack
from extensions.chaeo.zmask import build_zmask_from_object_mask, project_stack_from_focal_points
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.workflows import Timer
@@ -78,16 +78,34 @@ def export_patches_from_multichannel_zstack(
)
ti.click('export_3d_patches')
+ # if export_2d_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_2d_patches')
+
if export_2d_patches:
- files = export_patches_from_zstack(
- Path(where_output) / '2d_patches',
- stack.get_one_channel_data(patches_channel),
+ files = export_multichannel_patches_from_zstack(
+ Path(where_output) / '2d_patches_chlorophyl_contour',
+ stack,
zmask_meta,
prefix=fstem,
draw_bounding_box=False,
rescale_clip=0.0,
make_3d=False,
focus_metric='max_sobel',
+ ch_white=4,
+ ch_rgb_overlay=(3, None, None),
+ draw_contour=True,
+ contour_channel=1,
+ overlay_gain=(0.1, 1.0, 1.0)
)
ti.click('export_2d_patches')
--
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