diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index 796469e9d7cd52b9af9c3d852b0af1dd1f10a0bd..fccc4f0bae2943ed0ab63f2a1a298d15dda71e0f 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -11,6 +11,7 @@ class PatchParams(BaseModel):
focus_metric: str = 'max_sobel'
rgb_overlay_channels: List[Union[int, None]] = [None, None, None]
rgb_overlay_weights: List[float] = [1.0, 1.0, 1.0]
+ pad_to: int = 256
class AnnotatedZStackParams(BaseModel):
@@ -18,6 +19,7 @@ class AnnotatedZStackParams(BaseModel):
class RoiSetExportParams(BaseModel):
+ expand_box_by: List[int] = [128, 0]
pixel_probabilities: bool = False
patches_3d: Union[PatchParams, None] = None
patches_2d_for_annotation: Union[PatchParams, None] = None
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 357a0ca6feba201097a27782c4ca4d4717f3729f..a78fbea4e9b4721fb19d10c60c86688cbdc15edb 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -211,18 +211,27 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
export_params = RoiSetExportParams(**{
'pixel_probabilities': True,
'patches_3d': {},
- # 'patches_2d_for_annotation': {
- # 'draw_bounding_box': True,
- # 'rgb_overlay_channels': [4, 2, None]
- # }
+ 'patches_2d_for_annotation': {
+ 'draw_bounding_box': True,
+ 'rgb_overlay_channels': [3, None, None],
+ 'rgb_overlay_weights': [0.2, 1.0, 1.0],
+ 'pad_to': 512,
+ },
+ 'patches_2d_for_training': {
+ 'draw_bounding_box': False,
+ 'draw_mask': False,
+ },
+ 'patch_masks': True,
+ 'annotated_z_stack': {}
})
infer_object_map_from_zstack(
multichannel_zstack['path'],
- output_path / 'workflow',
+ output_path / 'roiset' / 'workflow',
models,
pxmap_foreground_channel=pp['pxmap_channel'],
pxmap_threshold=pp['pxmap_threshold'],
segmentation_channel=pp['segmentation_channel'],
patches_channel=pp['patches_channel'],
- # exports=export_params,
- )
\ No newline at end of file
+ exports=export_params,
+ )
+
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 46e693b159ea33d2b6b431ef66b3554a9d71ad77..91b09c9d45178659a740efa85551b9caa6486776 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -286,7 +286,7 @@ def infer_object_map_from_zstack(
stack,
mask_type=zmask_type,
filters=zmask_filters,
- expand_box_by=kwargs.get('zmask_expand_box_by', (0, 0)),
+ expand_box_by=exports.expand_box_by,
)
ti.click('generate_zmasks')
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 886dcf1c7ab5a713d5064706441f5ac2707b0be8..31bf51702d539affc825cea8e0e437ca28b00e8d 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -53,36 +53,29 @@ class RoiSet(object):
make_3d=True,
)
- def export_2d_patches_for_annotation(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_2d_patches_for_training(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
where,
- self.acc_raw.get_one_channel_data(channel),
+ self.acc_raw,
self.zmask_meta,
+ ch_white=channel,
prefix=prefix,
- draw_bounding_box=params.draw_bounding_box,
rescale_clip=params.rescale_clip,
make_3d=False,
focus_metric=params.focus_metric,
- ch_white=channel,
- ch_rgb_overlay=params.rgb_overlay_channels,
- bounding_box_channel=1,
- bounding_box_linewidth=2,
- draw_contour=params.draw_contour,
- draw_mask=params.draw_mask,
- overlay_gain=params.rgb_overlay_weights,
)
df_patches = pd.DataFrame(files)
self.df = pd.merge(self.df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
self.df['patch_id'] = self.df.apply(lambda _: uuid4(), axis=1)
- def export_2d_patches_for_training(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_2d_patches_for_annotation(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
where,
- self.acc_raw.get_one_channel_data(channel),
+ self.acc_raw,
self.zmask_meta,
prefix=prefix,
draw_bounding_box=params.draw_bounding_box,
@@ -96,22 +89,7 @@ class RoiSet(object):
draw_contour=params.draw_contour,
draw_mask=params.draw_mask,
overlay_gain=params.rgb_overlay_weights,
- )
- df_patches = pd.DataFrame(files)
- self.df = pd.merge(self.df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
- self.df['patch_id'] = self.df.apply(lambda _: uuid4(), axis=1)
-
- def export_2d_patches_for_annotation(self, where, prefix, channel, params: RoiSetExportParams):
- if not self.count:
- return
- files = export_multichannel_patches_from_zstack(
- where,
- self.acc_raw.get_one_channel_data(channel),
- self.zmask_meta,
- prefix=prefix,
- rescale_clip=params.rescale_clip,
- make_3d=False,
- focus_metric=params.focus_metric,
+ pad_to=params.pad_to,
)
def export_patch_masks(self, where, prefix, channel, params: RoiSetExportParams):
@@ -152,7 +130,10 @@ class RoiSet(object):
return projected
def get_raw_patches(self, channel):
- return get_patches_from_zmask_meta(self.acc_raw, self.zmask_meta).get_one_channel_data(channel)
+ return get_patches_from_zmask_meta(
+ self.acc_raw.get_one_channel_data(channel),
+ self.zmask_meta
+ )
def get_patch_masks(self):
return get_patch_masks_from_zmask_meta(self.acc_raw, self.zmask_meta)