Small changes that slipped through merge, also changed test with updated RoiSet parameter

model_server/base/accessors.py

@@ -61,6 +61,11 @@ class GenericImageDataAccessor(ABC):
             )
         )
 
+    def get_mip(self):
+        """
+        Return a new accessor of maximum intensity projection (MIP) along z-axis
+        """
+        return self.apply(lambda x: x.max(axis=self._ga('Z'), keepdims=True))
 
     def get_mono(self, channel: int, mip: bool = False):
         return self.get_channels([channel], mip=mip)

model_server/base/pipelines/roiset_obmap.py

 from typing import Dict, Union
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, validator
 
 from ..accessors import GenericImageDataAccessor
 from .router import router
@@ -51,7 +51,8 @@ class RoiSetObjectMapParams(PipelineParams):
         'filters': {
             'area': {'min': 1e3, 'max': 1e8}
         },
-        'expand_box_by': [128, 2]
+        'expand_box_by': [128, 2],
+        'deproject_channel': None,
     })
     export_params: RoiSetExportParams = RoiSetExportParams()
     derived_channels_input_channel: Union[int, None] = Field(

model_server/base/roiset.py

@@ -62,6 +62,7 @@ class RoiSetExportParams(BaseModel):
     patches_2d: Union[PatchParams, None] = None
     annotated_zstacks: Union[AnnotatedZStackParams, None] = None
     object_classes: bool = False
+    derived_channels: bool = False
 
 
 def get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, connect_3d=True) -> InMemoryDataAccessor:
@@ -1091,7 +1092,7 @@ class RoiSetWithDerivedChannels(RoiSet):
 
     def __init__(self, *a, **k):
         self.accs_derived = []
-        return super().__init__(*a, **k)
+        super().__init__(*a, **k)
 
     def classify_by(
             self, name: str, channels: list[int],

tests/base/test_roiset_derived.py

@@ -29,6 +29,7 @@ class TestDerivedChannels(unittest.TestCase):
             self.seg_mask,
             params=RoiSetMetaParams(
                 filters={'area': {'min': 1e3, 'max': 1e4}},
+                deproject_channel=0,
             )
         )
         self.assertIsInstance(roiset, RoiSetWithDerivedChannels)

tests/test_ilastik/test_roiset_workflow.py

@@ -60,7 +60,8 @@ class BaseTestRoiSetMonoProducts(object):
             'filters': {
                 'area': {'min': 1e0, 'max': 1e8}
             },
-            'expand_box_by': [128, 2]
+            'expand_box_by': [128, 2],
+            'deproject_channel': 0,
         }
 
     def _get_models(self): # tests can either use model objects directly, or load in API via project file string