From 2bd47356f6c0377c9f242b9e7ee8f1dc45db4e8c Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 29 Sep 2023 09:06:38 +0200
Subject: [PATCH] Cleaning up zmask builder
---
extensions/chaeo/test_zstack.py | 5 ++---
extensions/chaeo/{zstack.py => zmask.py} | 20 +++++++++++++-------
2 files changed, 15 insertions(+), 10 deletions(-)
rename extensions/chaeo/{zstack.py => zmask.py} (88%)
diff --git a/extensions/chaeo/test_zstack.py b/extensions/chaeo/test_zstack.py
index 4dfe7ec6..e423d0c5 100644
--- a/extensions/chaeo/test_zstack.py
+++ b/extensions/chaeo/test_zstack.py
@@ -5,7 +5,7 @@ import numpy as np
from conf.testing import output_path
from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
-from extensions.chaeo.zstack import build_stack_mask
+from extensions.chaeo.zmask import build_zmask_from_object_mask
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from extensions.ilastik.models import IlastikObjectClassifierModel, IlastikPixelClassifierModel
@@ -26,8 +26,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
# write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
def test_zmask_makes_correct_boxes(self, mask_type='boxes', filters=None):
- zmask, meta = build_stack_mask(
- 'test_zmask_with boxes',
+ zmask, meta = build_zmask_from_object_mask(
self.obmap.get_one_channel_data(0),
self.stack.get_one_channel_data(0),
mask_type=mask_type,
diff --git a/extensions/chaeo/zstack.py b/extensions/chaeo/zmask.py
similarity index 88%
rename from extensions/chaeo/zstack.py
rename to extensions/chaeo/zmask.py
index 63152287..0141386b 100644
--- a/extensions/chaeo/zstack.py
+++ b/extensions/chaeo/zmask.py
@@ -6,21 +6,27 @@ from skimage.measure import find_contours, label, regionprops_table
from model_server.accessors import GenericImageDataAccessor
# build a single boolean 3d mask (objects v. bboxes) and return bounding boxes
-def build_stack_mask(desc, obmap: GenericImageDataAccessor, stack: GenericImageDataAccessor, filters=None, mask_type='contour', expand_box_by=(0, 0)): # TODO: specify boxes data type
+def build_zmask_from_object_mask(
+ obmask: GenericImageDataAccessor,
+ stack: GenericImageDataAccessor,
+ filters=None,
+ mask_type='contour',
+ expand_box_by=(0, 0)
+):
"""
-
+ Given a 2D
filters: dict of (min, max) tuples
expand_box_by: (xy, z) pixelsf
"""
# validate inputs
- # assert len(stack.shape) == 3, stack.shape
assert stack.chroma == 1
assert stack.shape_dict['Z'] > 1
- assert mask_type in ('contours', 'boxes'), mask_type # TODO: replace with call to validator
-
- assert obmap.is_mask()
- lamap = label(obmap.data[:, :, 0, 0])
+ assert mask_type in ('contours', 'boxes'), mask_type
+ assert obmask.is_mask()
+ assert obmask.chroma == 1
+ assert obmask.shape_dict['Z'] == 1
+ lamap = label(obmask.data[:, :, 0, 0])
# build object query
query_str = 'label > 0' # always true
--
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