Merged in RoiSet polygon logic so far from YOLO dev branch

model_server/base/roiset.py

@@ -288,7 +288,6 @@ def make_object_ids_from_df(df: pd.DataFrame, sd: dict) -> InMemoryDataAccessor:
 
 class RoiSet(object):
 
-    # TODO: __init__ to take bounding boxes e.g. from obj det model; flag if overlaps are allowed
     def __init__(
             self,
             acc_raw: GenericImageDataAccessor,
@@ -302,15 +301,12 @@ class RoiSet(object):
         :param df: dataframe containing at minimum bounding box and segmentation mask information
         :param params: optional arguments that influence the definition and representation of ROIs
         """
-        # assert acc_obj_ids.chroma == 1
-        # self.acc_obj_ids = acc_obj_ids
         self.acc_raw = acc_raw
         self.accs_derived = []
         self.params = params
 
         self._df = df
         self.count = len(self._df)
-        # self.object_class_maps = {}  # classification results
 
     def __iter__(self):
         """Expose ROI meta information via the Pandas.DataFrame API"""
@@ -342,7 +338,6 @@ class RoiSet(object):
         return RoiSet(acc_raw, df, params)
 
 
-    # TODO: add a generator for the object detection case
     @staticmethod
     def from_bounding_boxes(
         acc_raw: GenericImageDataAccessor,
@@ -857,7 +852,6 @@ class RoiSet(object):
     def acc_obj_ids(self):
         return make_object_ids_from_df(self._df, self.acc_raw.shape_dict)
 
-    # TODO: make this work with obj det dataset
     @staticmethod
     def deserialize(acc_raw: GenericImageDataAccessor, where: Path, prefix=''):
         """

tests/test_ilastik/test_ilastik.py

@@ -5,7 +5,7 @@ import numpy as np
 from model_server.base.accessors import CziImageFileAccessor, generate_file_accessor, InMemoryDataAccessor, PatchStack, write_accessor_data_to_file
 from model_server.extensions.ilastik import models as ilm
 from model_server.extensions.ilastik.pipelines.px_then_ob import infer_px_then_ob_model
-from model_server.base.roiset import _get_label_ids, RoiSet, RoiSetMetaParams
+from model_server.base.roiset import get_label_ids, RoiSet, RoiSetMetaParams
 from model_server.base.pipelines.segment import classify_pixels
 import model_server.conf.testing as conf
 
@@ -399,9 +399,9 @@ class TestIlastikObjectClassification(unittest.TestCase):
         stack_ch_pa = stack.get_mono(conf.meta['roiset']['patches_channel'])
         seg_mask = generate_file_accessor(data['multichannel_zstack_mask2d']['path'])
 
-        self.roiset = RoiSet(
+        self.roiset = RoiSet.from_binary_mask(
             stack_ch_pa,
-            _get_label_ids(seg_mask),
+            seg_mask,
             params=RoiSetMetaParams(
                 mask_type='boxes',
                 filters={'area': {'min': 1e3, 'max': 1e4}},