From 976206d74445dfc43edce46cc1ffae749170bf8a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 14 Aug 2024 16:49:18 +0200
Subject: [PATCH] Put simplest functional RoiSet pipeline model_server for now;
derived channel and boundary seg alternatives in trec-adaptive-feedback
---
model_server/base/pipelines/roiset_obmap.py | 56 ++-------------------
tests/test_ilastik/test_roiset_workflow.py | 42 ++++++++--------
2 files changed, 26 insertions(+), 72 deletions(-)
diff --git a/model_server/base/pipelines/roiset_obmap.py b/model_server/base/pipelines/roiset_obmap.py
index 8a891b4d..38313675 100644
--- a/model_server/base/pipelines/roiset_obmap.py
+++ b/model_server/base/pipelines/roiset_obmap.py
@@ -7,8 +7,9 @@ from pydantic import Field
from model_server.base.accessors import GenericImageDataAccessor, PatchStack
from model_server.base.pipelines.params import PipelineParams, PipelineRecord
+from model_server.base.pipelines.segment import segment_pipeline
from model_server.base.pipelines.util import call_pipeline
-from model_server.base.roiset import RoiSet, RoiSetMetaParams, RoiSetExportParams
+from model_server.base.roiset import get_label_ids, RoiSet, RoiSetMetaParams, RoiSetExportParams
from model_server.base.session import session
from model_server.base.util import PipelineTrace
@@ -73,8 +74,6 @@ class RoiSetObjectMapParams(PipelineParams):
None,
description='Derived channels to send to object classifier; use all if empty'
)
- # TODO: move to subclassed pipeline
- # label_params: Union[LabelFromBoundarySegParams, None] = None
export_label_interm: bool = False
@@ -92,7 +91,6 @@ def roiset_object_map(p: RoiSetObjectMapParams) -> RoiSetToObjectMapRecord:
assert isinstance(rois, RoiSet)
table = rois.get_serializable_dataframe()
-
# TODO: instead, explicitly let trace include RoiSets
session.write_to_table('RoiSet', {'input_filename': p.accessor_id}, table)
ret = RoiSetToObjectMapRecord(
@@ -101,20 +99,6 @@ def roiset_object_map(p: RoiSetObjectMapParams) -> RoiSetToObjectMapRecord:
)
return ret
-# def _segment(d: PipelineTrace, models: Dict[str, Model], **k) -> PipelineTrace:
-# # MIP if no zmask z-index is given, then classify pixels
-# zmi = k['zmask_zindex']
-# sch = k['segmentation_channel']
-#
-# if isinstance(zmi, int):
-# assert 0 < zmi < d.last.nz
-# d['mip'] = d.last.get_mono(channel=sch).get_zi(zmi)
-# else:
-# d['mip'] = d.last.get_mono(channel=sch).apply(lambda x: x.max(axis=-1, keepdims=True))
-#
-# d['mip_mask'] = models['pixel_classifier_segmentation_model'].label_pixel_class(d.last)
-# return d
-
def roiset_object_map_pipeline(
accessors: Dict[str, GenericImageDataAccessor],
@@ -124,10 +108,7 @@ def roiset_object_map_pipeline(
if not isinstance(models['pixel_classifier_segmentation_model'], SemanticSegmentationModel):
raise IncompatibleModelsError('Expecting a pixel classification model')
- d = PipelineTrace()
- d['raw'] = accessors['accessor']
- # d = _segment(d, models, **k)
-
+ d = PipelineTrace(accessors['accessor'])
zmi = k['zmask_zindex']
sch = k['segmentation_channel']
@@ -138,28 +119,8 @@ def roiset_object_map_pipeline(
d['mip'] = d.last.get_mono(channel=sch).apply(lambda x: x.max(axis=-1, keepdims=True))
d['mip_mask'] = models['pixel_classifier_segmentation_model'].label_pixel_class(d.last)
-
- rois = RoiSet.from_binary_mask(d['raw'], d.last, RoiSetMetaParams(**k['roi_params']))
-
- # TODO: split out derived channel logic
- # # optionally derive additional inputs for object classification
- # if dpmod := models.get('pixel_classifier_derived_model'):
- # ic = k['derived_channels_input_channel']
- # ocs = k['derived_channels_output_channels']
- # assert ic < d['raw'].chroma
- # if not isinstance(dpmod, SemanticSegmentationModel):
- # raise IncompatibleModelsError('Expecting pixel_classifier_derived to be a pixel classification model')
- #
- # def _derive(acc: GenericImageDataAccessor, oc: int):
- # acc_mono = acc.get_channels([ic])
- # pxmap = dpmod.infer_patch_stack(acc_mono)[0]
- # assert oc < pxmap.chroma
- # return PatchStack((pxmap.get_channels([oc]).data * 255).astype('uint8'))
- # derived_channel_handles = [
- # lambda a: _derive(a, oc) for oc in ocs
- # ]
- # else:
- # derived_channel_handles = None
+ d['segmentation'] = get_label_ids(d.last)
+ rois = RoiSet.from_object_ids(d['input'], d['segmentation'], RoiSetMetaParams(**k['roi_params']))
# optionally run an object classifier if specified
if obmod := models.get('object_classifier_model'):
@@ -169,16 +130,9 @@ def roiset_object_map_pipeline(
obmod_name,
[k['patches_channel']],
obmod,
- # derived_channel_functions=derived_channel_handles
)
- # TODO: split out derived channel logic
- # # add derived channels to intermediate data
- # for di, dacc in enumerate(rois.accs_derived):
- # d[f'derived_{di:02d}'] = dacc
-
d[obmod_name] = rois.get_object_class_map(obmod_name)
-
return d, rois
class Error(Exception):
diff --git a/tests/test_ilastik/test_roiset_workflow.py b/tests/test_ilastik/test_roiset_workflow.py
index 27fd0d7f..bfe51ed0 100644
--- a/tests/test_ilastik/test_roiset_workflow.py
+++ b/tests/test_ilastik/test_roiset_workflow.py
@@ -118,27 +118,27 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
self.assertEqual(len(trace['ob_id']._unique()[0]), 2)
- def test_object_map_workflow_with_derived_channels(self):
- acc_in = generate_file_accessor(self.fpi)
- params = RoiSetObjectMapParams(
- **self._pipeline_params(),
- pixel_classifier_derived_model_id='id_px',
- derived_channels_input_channel=0,
- derived_channels_output_channels=[1],
- )
- models = self._get_models()
- models['pixel_classifier_derived'] = models['pixel_classifier_segmentation'] # re-use same classifier
-
- trace, _ = roiset_object_map_pipeline(
- {'accessor': acc_in},
- {f'{k}_model': v['model'] for k, v in models.items()},
- **params.dict()
- )
-
- self.assertTrue('ob_id' in trace.keys())
- self.assertEqual(len(trace['ob_id']._unique()[0]), 2)
- self.assertTrue('derived_00' in trace.keys())
- self.assertEqual(trace['derived_00'].chroma, 1)
+ # def test_object_map_workflow_with_derived_channels(self):
+ # acc_in = generate_file_accessor(self.fpi)
+ # params = RoiSetObjectMapParams(
+ # **self._pipeline_params(),
+ # pixel_classifier_derived_model_id='id_px',
+ # derived_channels_input_channel=0,
+ # derived_channels_output_channels=[1],
+ # )
+ # models = self._get_models()
+ # models['pixel_classifier_derived'] = models['pixel_classifier_segmentation'] # re-use same classifier
+ #
+ # trace, _ = roiset_object_map_pipeline(
+ # {'accessor': acc_in},
+ # {f'{k}_model': v['model'] for k, v in models.items()},
+ # **params.dict()
+ # )
+ #
+ # self.assertTrue('ob_id' in trace.keys())
+ # self.assertEqual(len(trace['ob_id']._unique()[0]), 2)
+ # self.assertTrue('derived_00' in trace.keys())
+ # self.assertEqual(trace['derived_00'].chroma, 1)
class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProducts):
--
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