From f9f8621180a9dd5e837b3f62f1e0d066e03752ec Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 30 Oct 2024 10:17:36 +0100
Subject: [PATCH] Moved intensity gate model to RoiSet module
---
model_server/base/api.py | 4 ++--
model_server/base/models.py | 25 ------------------------
model_server/base/roiset.py | 38 +++++++++++++++++++++++++++++++++++++
tests/base/test_model.py | 6 ------
tests/base/test_roiset.py | 17 ++++++++++++++---
5 files changed, 54 insertions(+), 36 deletions(-)
diff --git a/model_server/base/api.py b/model_server/base/api.py
index 6d9f5814..081b3b03 100644
--- a/model_server/base/api.py
+++ b/model_server/base/api.py
@@ -3,8 +3,8 @@ from typing import List, Union
from fastapi import FastAPI, HTTPException
from .accessors import generate_file_accessor
-from .models import BinaryThresholdSegmentationModel, IntensityThresholdInstanceMaskSegmentationModel
-from .roiset import RoiSetExportParams, SerializeRoiSetError
+from .models import BinaryThresholdSegmentationModel
+from .roiset import IntensityThresholdInstanceMaskSegmentationModel, RoiSetExportParams, SerializeRoiSetError
from .session import session, AccessorIdError, InvalidPathError, RoiSetIdError, WriteAccessorError
app = FastAPI(debug=True)
diff --git a/model_server/base/models.py b/model_server/base/models.py
index 3e026143..800ec951 100644
--- a/model_server/base/models.py
+++ b/model_server/base/models.py
@@ -158,31 +158,6 @@ class InstanceMaskSegmentationModel(ImageToImageModel):
return PatchStack(data)
-class IntensityThresholdInstanceMaskSegmentationModel(InstanceMaskSegmentationModel):
- def __init__(self, tr: float = 0.5, channel: int = 0):
- """
- Model that labels all objects as class 1 if the intensity in specified channel exceeds a threshold; labels all
- objects as class 1 if threshold = 0.0
- :param tr: threshold in range of 0.0 to 1.0; model handles normalization to full pixel intensity range
- :param channel: channel to use for thresholding
- """
- self.tr = tr
- self.channel = channel
- self.loaded = self.load()
- super().__init__(info={'tr': tr, 'channel': channel})
-
- def load(self):
- return True
-
- def infer(self, acc: GenericImageDataAccessor, mask: GenericImageDataAccessor) -> GenericImageDataAccessor:
- return mask.apply(lambda x: (1 * (x > self.tr)).astype(acc.dtype))
-
- def label_instance_class(
- self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
- ) -> GenericImageDataAccessor:
- super().label_instance_class(img, mask, **kwargs)
- return self.infer(img, mask)
-
class Error(Exception):
pass
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index ba7c6b06..ac93238b 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -1081,6 +1081,7 @@ class RoiSet(object):
class RoiSetWithDerivedChannelsExportParams(RoiSetExportParams):
derived_channels: bool = False
+
class RoiSetWithDerivedChannels(RoiSet):
def __init__(self, *a, **k):
@@ -1165,32 +1166,69 @@ class RoiSetWithDerivedChannels(RoiSet):
record[k].append(str(fp))
return record
+
+class IntensityThresholdInstanceMaskSegmentationModel(InstanceMaskSegmentationModel):
+ def __init__(self, tr: float = 0.5, channel: int = 0):
+ """
+ Model that labels all objects as class 1 if the intensity in specified channel exceeds a threshold; labels all
+ objects as class 1 if threshold = 0.0
+ :param tr: threshold in range of 0.0 to 1.0; model handles normalization to full pixel intensity range
+ :param channel: channel to use for thresholding
+ """
+ self.tr = tr
+ self.channel = channel
+ self.loaded = self.load()
+ super().__init__(info={'tr': tr, 'channel': channel})
+
+ def load(self):
+ return True
+
+ def infer(self, acc: GenericImageDataAccessor, mask: GenericImageDataAccessor) -> GenericImageDataAccessor:
+ # TODO: gate by intensity in image, not threshold in mask channel; this will require iterating on labeled objects
+ return mask.apply(lambda x: (1 * (x > self.tr)).astype(acc.dtype))
+
+ def label_instance_class(
+ self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
+ ) -> GenericImageDataAccessor:
+ super().label_instance_class(img, mask, **kwargs)
+ return self.infer(img, mask)
+
+
class Error(Exception):
pass
+
class BoundingBoxError(Error):
pass
+
class DeserializeRoiSetError(Error):
pass
+
class SerializeRoiSetError(Error):
pass
+
class NoDeprojectChannelSpecifiedError(Error):
pass
+
class DerivedChannelError(Error):
pass
+
class MissingSegmentationError(Error):
pass
+
class PatchMaskShapeError(Error):
pass
+
class ShapeMismatchError(Error):
pass
+
class MissingInstanceLabelsError(Error):
pass
\ No newline at end of file
diff --git a/tests/base/test_model.py b/tests/base/test_model.py
index e5c96894..8b4aa3a7 100644
--- a/tests/base/test_model.py
+++ b/tests/base/test_model.py
@@ -68,9 +68,3 @@ class TestCziImageFileAccess(unittest.TestCase):
obmap = model.label_instance_class(img, mask)
self.assertTrue(all(obmap.unique()[0] == [0, 1]))
self.assertTrue(all(obmap.unique()[1] > 0))
-
- def test_permissive_instance_segmentation(self):
- img, mask = self.test_dummy_pixel_segmentation()
- model = IntensityThresholdInstanceMaskSegmentationModel()
- obmap = model.label_instance_class(img, mask)
- self.assertTrue(np.all(mask.data == 255 * obmap.data))
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index c510510a..b9b89410 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -7,9 +7,8 @@ from pathlib import Path
import pandas as pd
from model_server.base.process import smooth
-from model_server.base.roiset import filter_df_overlap_bbox, filter_df_overlap_seg, RoiSetExportParams, RoiSetMetaParams
-from model_server.base.roiset import RoiSet
-from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
+from model_server.base.roiset import filter_df_overlap_bbox, filter_df_overlap_seg, RoiSet, RoiSetExportParams, RoiSetMetaParams
+from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
import model_server.conf.testing as conf
from model_server.conf.testing import DummyInstanceMaskSegmentationModel
@@ -819,3 +818,15 @@ class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
self.assertTrue((res.bbox_intersec == 2).all())
self.assertTrue((res.loc[res.seg_overlaps, :].index == [1]).all())
self.assertTrue((res.loc[res.seg_overlaps, 'seg_iou'] == 0.4).all())
+
+class TestIntensityThresholdObjectModel(BaseTestRoiSetMonoProducts, unittest.TestCase):
+ def test_permissive_instance_segmentation(self):
+ from model_server.base.roiset import IntensityThresholdInstanceMaskSegmentationModel
+
+ img = self.stack.get_mono(channel=0, mip=True)
+ mask = self.seg_mask
+
+ # TODO: test on actual binary mask, not dummy square mask
+ model = IntensityThresholdInstanceMaskSegmentationModel()
+ obmap = model.label_instance_class(img, mask)
+ self.assertTrue(np.all(mask.data == 255 * obmap.data))
\ No newline at end of file
--
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