From 3fa8292a1da8b43c623f5c346af9407d82f21789 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 15 Aug 2024 16:46:49 +0200
Subject: [PATCH] API maps RoiSet products as accessors
---
model_server/base/models.py | 3 +--
model_server/base/pipelines/roiset_obmap.py | 19 +++++--------------
model_server/base/session.py | 7 +++++--
tests/test_ilastik/test_roiset_workflow.py | 12 ++++--------
4 files changed, 15 insertions(+), 26 deletions(-)
diff --git a/model_server/base/models.py b/model_server/base/models.py
index ffaa346f..eaded2c9 100644
--- a/model_server/base/models.py
+++ b/model_server/base/models.py
@@ -50,7 +50,7 @@ class Model(ABC):
@property
def name(self):
- return f'{self.__class__}'
+ return f'{self.__class__.__name__}'
@@ -131,7 +131,6 @@ class InstanceSegmentationModel(ImageToImageModel):
class BinaryThresholdSegmentationModel(SemanticSegmentationModel):
- # TODO: also allow relative threshold
def __init__(self, tr: float = 0.5):
self.tr = tr
diff --git a/model_server/base/pipelines/roiset_obmap.py b/model_server/base/pipelines/roiset_obmap.py
index 376dbe3c..96e03390 100644
--- a/model_server/base/pipelines/roiset_obmap.py
+++ b/model_server/base/pipelines/roiset_obmap.py
@@ -53,20 +53,7 @@ class RoiSetObjectMapParams(PipelineParams):
},
'expand_box_by': [128, 2]
})
- # TODO: maybe don't support all these exports here; instead leverage interm accessors
- export_params: RoiSetExportParams = RoiSetExportParams(**{
- 'annotated_patches_2d': {
- 'draw_bounding_box': True,
- 'pad_to': 256,
- },
- 'patches_2d': {
- 'draw_bounding_box': True,
- 'draw_mask': False,
- },
- 'patch_masks': {},
- 'object_classes': True,
- 'dataframe': True,
- })
+ export_params: RoiSetExportParams = RoiSetExportParams()
derived_channels_input_channel: Union[int, None] = Field(
None,
description='Channel of input image from which to compute derived channels; use all if empty'
@@ -114,6 +101,10 @@ def roiset_object_map_pipeline(
d['labeled'] = get_label_ids(d.last)
rois = RoiSet.from_object_ids(d['input'], d['labeled'], RoiSetMetaParams(**k['roi_params']))
+ # optionally append RoiSet products
+ for ki, vi in rois.get_export_product_accessors(k['patches_channel'], RoiSetExportParams(**k['export_params'])).items():
+ d[ki] = vi
+
# optionally run an object classifier if specified
if obmod := models.get('object_classifier_model'):
obmod_name = k['object_classifier_model_id']
diff --git a/model_server/base/session.py b/model_server/base/session.py
index 8358a957..f22655c6 100644
--- a/model_server/base/session.py
+++ b/model_server/base/session.py
@@ -10,7 +10,7 @@ from typing import Union
import pandas as pd
from ..conf import defaults
-from .accessors import GenericImageDataAccessor
+from .accessors import GenericImageDataAccessor, PatchStack
from .models import Model
logger = logging.getLogger(__name__)
@@ -166,7 +166,10 @@ class _Session(object):
f'Cannot overwrite accessor that is already written to {old_fp}'
)
- acc.write(fp)
+ if isinstance(acc, PatchStack):
+ acc.export_pyxcz(fp)
+ else:
+ acc.write(fp)
self.accessors[acc_id]['filepath'] = fp.__str__()
return fp.name
diff --git a/tests/test_ilastik/test_roiset_workflow.py b/tests/test_ilastik/test_roiset_workflow.py
index cd6d2ded..c02dd6d9 100644
--- a/tests/test_ilastik/test_roiset_workflow.py
+++ b/tests/test_ilastik/test_roiset_workflow.py
@@ -39,8 +39,7 @@ class BaseTestRoiSetMonoProducts(object):
def _get_export_params(self):
return {
- 'pixel_probabilities': True,
- 'patches_3d': {},
+ 'patches_3d': None,
'annotated_patches_2d': {
'draw_bounding_box': True,
'rgb_overlay_channels': [3, None, None],
@@ -51,12 +50,8 @@ class BaseTestRoiSetMonoProducts(object):
'draw_bounding_box': False,
'draw_mask': False,
},
- 'patch_masks': {
- 'pad_to': 256,
- },
- 'annotated_zstacks': {},
+ 'annotated_zstacks': None,
'object_classes': True,
- 'dataframe': True,
}
def _get_roi_params(self):
@@ -119,7 +114,8 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
{f'{k}_model': v['model'] for k, v in self._get_models().items()},
**params.dict()
)
-
+ self.assertEqual(trace.pop('annotated_patches_2d').count, 13)
+ self.assertEqual(trace.pop('patches_2d').count, 13)
trace.write_interm(Path(output_path) / 'trace', 'roiset_worfklow_trace', skip_first=False, skip_last=False)
self.assertTrue('ob_id' in trace.keys())
self.assertEqual(len(trace['labeled'].unique()[0]), 14)
--
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