From c1cd28eb667555ba0b9fa03adc68945fdec5233d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 13 Aug 2024 17:35:24 +0200
Subject: [PATCH] Test covers derived inputs pipeline method directly
---
model_server/base/pipelines/roiset_obmap.py | 10 ++-
tests/test_ilastik/test_roiset_workflow.py | 74 +--------------------
2 files changed, 11 insertions(+), 73 deletions(-)
diff --git a/model_server/base/pipelines/roiset_obmap.py b/model_server/base/pipelines/roiset_obmap.py
index 1bd9220a..3efa5189 100644
--- a/model_server/base/pipelines/roiset_obmap.py
+++ b/model_server/base/pipelines/roiset_obmap.py
@@ -139,7 +139,7 @@ def roiset_object_map_pipeline(
rois = RoiSet.from_binary_mask(d['raw'], d.last, RoiSetMetaParams(**k['roi_params']))
# optionally derive additional inputs for object classification
- if dpmod := models.get('pixel_classifier_derived'):
+ 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
@@ -157,7 +157,7 @@ def roiset_object_map_pipeline(
else:
derived_channel_handles = None
- # optionally classify if an object classifier is passed
+ # optionally run an object classifier if specified
if obmod := models.get('object_classifier_model'):
obmod_name = k['object_classifier_model_id']
assert isinstance(obmod, InstanceSegmentationModel)
@@ -167,8 +167,14 @@ def roiset_object_map_pipeline(
obmod,
derived_channel_functions=derived_channel_handles
)
+ # 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)
+
+
# TODO: subclass this boundary pipeline in separate module
# if p.label_params and p.export_label_interm:
# fp_la_interm = Path(output_folder_path) / 'mip_masks' / f'interm_{fstem}.png'
diff --git a/tests/test_ilastik/test_roiset_workflow.py b/tests/test_ilastik/test_roiset_workflow.py
index 860d8089..27fd0d7f 100644
--- a/tests/test_ilastik/test_roiset_workflow.py
+++ b/tests/test_ilastik/test_roiset_workflow.py
@@ -1,15 +1,11 @@
-import shutil
from pathlib import Path
-from shutil import copyfile
import unittest
import numpy as np
-import model_server.conf.testing as conf
from model_server.base.accessors import generate_file_accessor
from tests.base.test_model import DummyInstanceSegmentationModel
-from model_server.base.roiset import RoiSetMetaParams, RoiSetExportParams
import model_server.conf.testing as conf
from model_server.base.pipelines.roiset_obmap import RoiSetObjectMapParams, roiset_object_map_pipeline
@@ -121,6 +117,7 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
self.assertTrue('ob_id' in trace.keys())
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(
@@ -140,7 +137,8 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
self.assertTrue('ob_id' in trace.keys())
self.assertEqual(len(trace['ob_id']._unique()[0]), 2)
- self.assertTrue(all([Path(pa).exists() for pa in record['interm']['derived_channels']]))
+ self.assertTrue('derived_00' in trace.keys())
+ self.assertEqual(trace['derived_00'].chroma, 1)
class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProducts):
@@ -255,69 +253,3 @@ class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProd
# self.assertTrue(all(np.unique(acc_obmap.data) == [0, 1]))
-
-class TestRoiSetWithDerivedChannels(conf.TestServerBaseClass):
-
- app_name = 'api:app'
- input_data = data['multichannel_zstack_raw']
-
- # def test_object_map_workflow_with_derived_channels(self):
- # models = _get_models()
- # models['pixel_classifier_derived'] = models['pixel_classifier_segmentation'] # re-use same classifier
- # where_out = output_path / 'roiset' / 'workflow'
- #
- # p = ClassifyZStackApiParams(
- # input_filename=str(data['multichannel_zstack_raw']['path']),
- # model_ids={
- # 'pixel_classifier_segmentation': 'id_px',
- # 'object_classifier': 'id_ob',
- # 'pixel_classifier_derived': 'id_px',
- # },
- # derived_channels_input_channel=0,
- # derived_channels_output_channels=[1],
- # segmentation_channel=test_params['segmentation_channel'],
- # patches_channel=test_params['patches_channel'],
- # roi_params=_get_roi_params(),
- # export_params=_get_export_params(),
- # )
- #
- # record = export_zstack_roiset(
- # data['multichannel_zstack_raw']['path'],
- # where_out,
- # models,
- # p
- # )
- # self.assertTrue(all([Path(pa).exists() for pa in record['interm']['derived_channels']]))
-
- def test_derived_channels_api(self):
- resp = self._put(
- 'ilastik/seg/load/',
- body={'project_file': _get_model_params()['pixel_classifier_segmentation']['project_file'].__str__()},
- )
- self.assertEqual(resp.status_code, 200)
- mid_px = resp.json()['model_id']
- resp = self._put(f'models/dummy_instance/load')
- mid_ob = resp.json()['model_id']
-
-
- p = ClassifyZStackApiParams(
- input_filename=data['multichannel_zstack_raw']['path'].__str__(),
- model_ids={
- 'pixel_classifier_segmentation': mid_px,
- 'object_classifier': mid_ob,
- 'pixel_classifier_derived': mid_px,
- },
- derived_channels_input_channel=0,
- derived_channels_output_channels=[1],
- segmentation_channel=test_params['segmentation_channel'],
- patches_channel=test_params['patches_channel'],
- roi_params=_get_roi_params(),
- export_params=_get_export_params(),
- )
- resp = self._put('chaeo/classify_zstack/infer', body=p.dict())
- self.assertEqual(resp.status_code, 200, resp.json())
- omfp = resp.json()['object_map_filepath']
- self.assertTrue(Path(omfp).exists())
- acc_obmap = generate_file_accessor(omfp)
- self.assertTrue(all(np.unique(acc_obmap.data) == [0, 1]))
-
--
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