From 5bb914c7bf3446745f06a681fc592c30b7b01c66 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Nov 2024 14:41:07 +0100
Subject: [PATCH] Optional intensity threshold for weight deprojection
---
model_server/base/roiset.py | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index a4397d5b..8dc5ff05 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -57,6 +57,7 @@ class RoiSetMetaParams(BaseModel):
filters: Union[RoiFilter, None] = None
expand_box_by: List[int] = [128, 0]
deproject_channel: Union[int, None] = None
+ deproject_intensity_threshold: float = 0.0
class RoiSetExportParams(BaseModel):
@@ -222,13 +223,22 @@ def filter_df_overlap_seg(df1: pd.DataFrame, df2: pd.DataFrame = None) -> pd.Dat
return dfbb
-def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by, deproject_channel=None, filters=None) -> pd.DataFrame:
+def make_df_from_object_ids(
+ acc_raw,
+ acc_obj_ids,
+ expand_box_by,
+ deproject_channel=None,
+ filters=None,
+ deproject_intensity_threshold=0.0
+) -> pd.DataFrame:
"""
Build dataframe that associate object IDs with summary stats;
:param acc_raw: accessor to raw image data
:param acc_obj_ids: accessor to map of object IDs
:param expand_box_by: number of pixels to expand bounding box in all directions (without exceeding image boundary)
:param deproject_channel: if objects' z-coordinates are not specified, compute them based on argmax of this channel
+ :param deproject_intensity_threshold: when deprojecting, round MIP deprojection_channel to zero if below this
+ threshold (as fraction of full range, 0.0 to 1.0)
:return: pd.DataFrame
"""
# build dataframe of objects, assign z index to each object
@@ -244,10 +254,11 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by, deproject_chann
)
mono = acc_raw.get_mono(deproject_channel)
- mip = mono.get_mip()
+ intensity_weight = mono.get_mip().data_yx
+ intensity_weight[intensity_weight < (deproject_intensity_threshold * mono.dtype_max)] = 0
zi_map = np.stack([
- mip.data_yx,
- mono.get_z_argmax().data_yx * mip.data_yx
+ intensity_weight,
+ mono.get_z_argmax().data_yx * intensity_weight,
], axis=-1)
assert len(zi_map.shape) == 3
@@ -414,6 +425,7 @@ class RoiSet(object):
acc_raw, acc_obj_ids,
expand_box_by=params.expand_box_by,
deproject_channel=params.deproject_channel,
+ deproject_intensity_threshold=params.deproject_intensity_threshold,
filters=params.filters,
)
--
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