From 6d9f27b0f3129a97a9a4c4bed1401e89aedb47d7 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 14:51:03 +0100
Subject: [PATCH] Dummy object classification exports map
---
extensions/chaeo/params.py | 1 +
extensions/chaeo/tests/test_zstack.py | 3 ++-
extensions/chaeo/workflows.py | 18 +++++-------------
extensions/chaeo/zmask.py | 13 ++++++-------
model_server/models.py | 6 ++++--
5 files changed, 18 insertions(+), 23 deletions(-)
diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index 5a226925..0ba956fb 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -39,5 +39,6 @@ class RoiSetExportParams(BaseModel):
patches_2d_for_training: Union[PatchParams, None] = None
patch_masks: bool = False
annotated_zstacks: Union[AnnotatedZStackParams, None] = None
+ object_classes: bool = False
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 9e6e3a74..7778370a 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -229,7 +229,8 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
'draw_mask': False,
},
'patch_masks': True,
- 'annotated_zstacks': {}
+ 'annotated_zstacks': {},
+ 'object_classes': True
})
infer_object_map_from_zstack(
multichannel_zstack['path'],
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 4b3f380d..7a0e0941 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -54,33 +54,25 @@ def infer_object_map_from_zstack(
mip = InMemoryDataAccessor(
zmask_data,
)
- # pxmap, _ = pixel_classifier.infer(mip)
+
mip_mask = pixel_classifier.label_pixel_class(mip, pixel_class, pixel_probability_threshold,)
ti.click('classify_pixels')
# make zmask
- # rois = RoiSet(mip_mask, stack, mask_type=zmask_type, filters=zmask_filters, expand_box_by=meta.expand_box_by)
rois = RoiSet(mip_mask, stack, params=roi_params)
ti.click('generate_zmasks')
- object_class_map = rois.classify_by(patches_channel, object_classifier)
-
- # TODO: add ZMaskObjectTable method to export object map
- output_path = Path(output_folder_path) / ('obj_classes_' + (fstem + '.tif'))
- write_accessor_data_to_file(
- output_path,
- object_class_map
- )
- ti.click('export_object_classes')
+ rois.classify_by(patches_channel, object_classifier)
+ ti.click('classify_objects')
rois.run_exports(Path(output_folder_path), patches_channel, fstem, export_params)
ti.click('export_roi_products')
return {
'timer_results': ti.events,
- 'dataframe': rois.df,
+ 'dataframe': rois.df,
'interm': {},
- 'output_path': output_path.__str__(),
+ 'output_path': output_folder_path,
}
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 13c54b7d..1441e9ae 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -32,6 +32,7 @@ class RoiSet(object):
self.acc_raw = acc_raw
self.count = len(self.zmask_meta)
self.object_id_labels = self.interm['label_map']
+ self.object_class_map = None
def get_argmax(self):
return self.interm.argmax
@@ -67,7 +68,7 @@ class RoiSet(object):
)
lamap = self.object_id_labels
- output_map = np.zeros(lamap.shape, dtype=lamap.dtype)
+ om = np.zeros(lamap.shape, dtype=lamap.dtype)
self.df['instance_class'] = np.nan
# assign labels to object map:
@@ -75,10 +76,10 @@ class RoiSet(object):
object_id = self.zmask_meta[ii]['info'].label
result_patch = mask_largest_object(obmap_patches.iat(ii))
object_class = np.unique(result_patch)[1]
- output_map[self.object_id_labels == object_id] = object_class
+ om[self.object_id_labels == object_id] = object_class
self.df[object_id, 'instance_class'] = object_class
- return InMemoryDataAccessor(output_map)
+ self.object_class_map = InMemoryDataAccessor(om)
# TODO: test
def get_object_mask_by_id(self, obj_id):
@@ -91,9 +92,6 @@ class RoiSet(object):
def get_object_patch_by_id(self, obj_id):
pass
- def get_object_map(self, filters: RoiFilter):
- pass
-
def run_exports(self, where, channel, prefix, params: RoiSetExportParams):
if not self.count:
return
@@ -129,7 +127,8 @@ class RoiSet(object):
draw_boxes_on_3d_image(raw_ch.data, self.zmask_meta, **kp)
)
write_accessor_data_to_file(subdir / (pr + '.tif'), annotated)
-
+ if k == 'object_classes':
+ write_accessor_data_to_file(subdir / (pr + '.tif'), self.object_class_map)
diff --git a/model_server/models.py b/model_server/models.py
index 06bef01c..8239d1ca 100644
--- a/model_server/models.py
+++ b/model_server/models.py
@@ -120,13 +120,15 @@ class DummyInstanceSegmentationModel(InstanceSegmentationModel):
def infer(
self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor
) -> (GenericImageDataAccessor, dict):
- return mask
+ return img.__class__(
+ (mask.data / mask.data.max()).astype('uint16')
+ )
def label_instance_class(
self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
) -> GenericImageDataAccessor:
"""
- Returns a trivial segmentation, i.e. the input mask
+ Returns a trivial segmentation, i.e. the input mask with value 1
"""
super(DummyInstanceSegmentationModel, self).label_instance_class(img, mask, **kwargs)
return self.infer(img, mask)
--
GitLab