From f9a04f7d3c5f9782dcca467155d883db334e3d22 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 7 Feb 2024 15:14:15 +0100
Subject: [PATCH] Combined mono and multichannel patch export methods
---
model_server/extensions/chaeo/products.py | 22 +------------------
.../extensions/chaeo/tests/test_zstack.py | 20 ++++++-----------
model_server/extensions/chaeo/zmask.py | 6 ++---
3 files changed, 11 insertions(+), 37 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index f7782f8c..484756fa 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -247,24 +247,4 @@ def export_patches_from_zstack(
for roi in patches_df.itertuples(): # just used for label info
_export_patch(roi)
- return exported
-
-
-def export_multichannel_patches_from_zstack(
- where: Path,
- roiset,
- rgb_overlay_channels: list = None,
- rgb_overlay_weights: list = [1.0, 1.0, 1.0],
- white_channel: int = None,
- **kwargs
-):
- """
- Export RGB patches where each patch is assignable to a channel of the input stack
- :param ch_rgb_overlay: tuple of integers (R, G, B) that assign a stack channel index to an RGB channel
- :param overlay_gain: optional, tuple of float (R, G, B) multipliers that can be used to balance relative brightness
- :param rgb_white_channel: int, index of stack channel that becomes grayscale signal in export patches
- """
- kwargs['white_channel'] = white_channel
- kwargs['rgb_overlay_channels'] = rgb_overlay_channels
- kwargs['rgb_overlay_weights'] = rgb_overlay_weights
- return export_patches_from_zstack(where, roiset, **kwargs)
\ No newline at end of file
+ return exported
\ No newline at end of file
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index 41571203..35d73f26 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -7,7 +7,7 @@ from model_server.conf.testing import output_path
from model_server.extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
from extensions.chaeo.params import RoiSetExportParams, RoiSetMetaParams
-from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack
+from model_server.extensions.chaeo.products import export_patches_from_zstack
from model_server.extensions.chaeo.workflows import infer_object_map_from_zstack
from model_server.extensions.chaeo.zmask import get_label_ids, RoiSet
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
@@ -248,8 +248,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
)
def test_multichannel_to_mono_2d_patches(self):
-
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
output_path / 'multichannel' / 'mono_2d_patches',
self.roiset,
white_channel=3,
@@ -259,7 +258,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.chroma, 1)
def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
output_path / 'multichannel' / 'mono_2d_patches_rgb_bbox',
self.roiset,
white_channel=3,
@@ -270,7 +269,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.chroma, 3)
def test_multichannnel_to_rgb_2d_patches_bbox(self):
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
output_path / 'multichannel' / 'rgb_2d_patches_bbox',
self.roiset,
white_channel=4,
@@ -283,7 +282,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.chroma, 3)
def test_multichannnel_to_rgb_2d_patches_contour(self):
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
output_path / 'multichannel' / 'rgb_2d_patches_contour',
self.roiset,
rgb_overlay_channels=(3, None, None),
@@ -296,7 +295,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.get_one_channel_data(2).data.max(), 0) # blue channel is black
def test_multichannel_to_multichannel_tif_patches(self):
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
output_path / 'multichannel' / 'multichannel_tif_patches',
self.roiset,
)
@@ -309,9 +308,4 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
'test_multichannel_annotated_zstack',
)
- # files = export_multichannel_patches_from_zstack(
- # output_path / 'multichannel_to_multichannel_tif_patches',
- # self.roiset,
- # )
- # result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
- # self.assertEqual(result.chroma, 5)
+
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 55030731..ef30936d 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -14,7 +14,7 @@ from model_server.base.models import InstanceSegmentationModel
from model_server.base.process import pad, rescale, resample_to_8bit
from model_server.extensions.chaeo.annotators import draw_boxes_on_3d_image
-from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack
+from model_server.extensions.chaeo.products import export_patches_from_zstack
from extensions.chaeo.params import RoiFilter, RoiSetMetaParams, RoiSetExportParams
from model_server.extensions.chaeo.accessors import MonoPatchStack, Multichannel3dPatchStack
from model_server.extensions.chaeo.process import mask_largest_object
@@ -247,12 +247,12 @@ class RoiSet(object):
subdir, self, white_channel=channel, prefix=pr, make_3d=True, **kp
)
if k == 'annotated_patches_2d':
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
subdir, self, prefix=pr, make_3d=False, white_channel=channel,
bounding_box_channel=1, bounding_box_linewidth=2, **kp,
)
if k == 'patches_2d':
- files = export_multichannel_patches_from_zstack(
+ files = export_patches_from_zstack(
subdir, self, white_channel=channel, prefix=pr, make_3d=False, **kp
)
df_patches = pd.DataFrame(files)
--
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