Combined mono and multichannel patch export methods

model_server/extensions/chaeo/products.py

@@ -247,24 +247,4 @@ def export_patches_from_zstack(
     for roi in patches_df.itertuples():  # just used for label info
         _export_patch(roi)
 
-    return exported
-
-
-def export_multichannel_patches_from_zstack(
-    where: Path,
-    roiset,
-    rgb_overlay_channels: list = None,
-    rgb_overlay_weights: list = [1.0, 1.0, 1.0],
-    white_channel: int = None,
-    **kwargs
-):
-    """
-    Export RGB patches where each patch is assignable to a channel of the input stack
-    :param ch_rgb_overlay: tuple of integers (R, G, B) that assign a stack channel index to an RGB channel
-    :param overlay_gain: optional, tuple of float (R, G, B) multipliers that can be used to balance relative brightness
-    :param rgb_white_channel: int, index of stack channel that becomes grayscale signal in export patches
-    """
-    kwargs['white_channel'] = white_channel
-    kwargs['rgb_overlay_channels'] = rgb_overlay_channels
-    kwargs['rgb_overlay_weights'] = rgb_overlay_weights
-    return export_patches_from_zstack(where, roiset, **kwargs)
\ No newline at end of file
+    return exported
\ No newline at end of file

model_server/extensions/chaeo/tests/test_zstack.py

@@ -7,7 +7,7 @@ from model_server.conf.testing import output_path
 
 from model_server.extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
 from extensions.chaeo.params import RoiSetExportParams, RoiSetMetaParams
-from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack
+from model_server.extensions.chaeo.products import export_patches_from_zstack
 from model_server.extensions.chaeo.workflows import infer_object_map_from_zstack
 from model_server.extensions.chaeo.zmask import get_label_ids, RoiSet
 from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
@@ -248,8 +248,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         )
 
     def test_multichannel_to_mono_2d_patches(self):
-
-        files = export_multichannel_patches_from_zstack(
+        files = export_patches_from_zstack(
             output_path / 'multichannel' / 'mono_2d_patches',
             self.roiset,
             white_channel=3,
@@ -259,7 +258,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.chroma, 1)
 
     def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
-        files = export_multichannel_patches_from_zstack(
+        files = export_patches_from_zstack(
             output_path / 'multichannel' / 'mono_2d_patches_rgb_bbox',
             self.roiset,
             white_channel=3,
@@ -270,7 +269,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.chroma, 3)
 
     def test_multichannnel_to_rgb_2d_patches_bbox(self):
-        files = export_multichannel_patches_from_zstack(
+        files = export_patches_from_zstack(
             output_path / 'multichannel' / 'rgb_2d_patches_bbox',
             self.roiset,
             white_channel=4,
@@ -283,7 +282,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.chroma, 3)
 
     def test_multichannnel_to_rgb_2d_patches_contour(self):
-        files = export_multichannel_patches_from_zstack(
+        files = export_patches_from_zstack(
             output_path / 'multichannel' / 'rgb_2d_patches_contour',
             self.roiset,
             rgb_overlay_channels=(3, None, None),
@@ -296,7 +295,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.get_one_channel_data(2).data.max(), 0)  # blue channel is black
 
     def test_multichannel_to_multichannel_tif_patches(self):
-        files = export_multichannel_patches_from_zstack(
+        files = export_patches_from_zstack(
             output_path / 'multichannel' / 'multichannel_tif_patches',
             self.roiset,
         )
@@ -309,9 +308,4 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
             'test_multichannel_annotated_zstack',
 
         )
-        # files = export_multichannel_patches_from_zstack(
-        #     output_path / 'multichannel_to_multichannel_tif_patches',
-        #     self.roiset,
-        # )
-        # result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
-        # self.assertEqual(result.chroma, 5)
+

model_server/extensions/chaeo/zmask.py

@@ -14,7 +14,7 @@ from model_server.base.models import InstanceSegmentationModel
 from model_server.base.process import pad, rescale, resample_to_8bit
 
 from model_server.extensions.chaeo.annotators import draw_boxes_on_3d_image
-from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack
+from model_server.extensions.chaeo.products import export_patches_from_zstack
 from extensions.chaeo.params import RoiFilter, RoiSetMetaParams, RoiSetExportParams
 from model_server.extensions.chaeo.accessors import MonoPatchStack, Multichannel3dPatchStack
 from model_server.extensions.chaeo.process import mask_largest_object
@@ -247,12 +247,12 @@ class RoiSet(object):
                     subdir, self, white_channel=channel, prefix=pr, make_3d=True, **kp
                 )
             if k == 'annotated_patches_2d':
-                files = export_multichannel_patches_from_zstack(
+                files = export_patches_from_zstack(
                     subdir, self, prefix=pr, make_3d=False, white_channel=channel,
                     bounding_box_channel=1, bounding_box_linewidth=2, **kp,
                 )
             if k == 'patches_2d':
-                files = export_multichannel_patches_from_zstack(
+                files = export_patches_from_zstack(
                     subdir, self, white_channel=channel, prefix=pr, make_3d=False, **kp
                 )
                 df_patches = pd.DataFrame(files)