From 29bbcf6f8b16aacd3dd6a0f413afe889e7411de5 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 23 Sep 2024 11:24:15 +0200
Subject: [PATCH] Implemented and tested serialize/deserialize methods on
object detection RoiSets
---
model_server/base/roiset.py | 77 ++++++++++++++++++++++---------------
tests/base/test_roiset.py | 18 +++++++--
2 files changed, 62 insertions(+), 33 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 3e99eaef..4eeda490 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -427,10 +427,11 @@ class RoiSet(object):
bbox_df['x0'] = bbox_df['x']
bbox_df['y1'] = bbox_df['y0'] + bbox_df['h']
bbox_df['x1'] = bbox_df['x0'] + bbox_df['w']
+ bbox_df['label'] = bbox_df.index
df = df_insert_slices(
- bbox_df[['y0', 'x0', 'y1', 'x1', 'zi']],
+ bbox_df[['y0', 'x0', 'y1', 'x1', 'zi', 'label']],
acc_raw.shape_dict,
params.expand_box_by,
)
@@ -924,7 +925,7 @@ class RoiSet(object):
return record
- def serialize(self, where: Path, prefix='') -> dict:
+ def serialize(self, where: Path, prefix='roiset') -> dict:
"""
Export the minimal information needed to recreate RoiSet object, i.e. CSV data file and tight patch masks
:param where: path of directory in which to write files
@@ -932,18 +933,20 @@ class RoiSet(object):
:return: nested dict of Path objects describing the locations of export products
"""
record = {}
- df_exp = self.export_patch_masks(
- where / 'tight_patch_masks',
- prefix=prefix,
- pad_to=None,
- expanded=False
- )
- # record patch masks paths to dataframe, then save static columns to CSV
- se_pa = df_exp.patch_mask_path.apply(
- lambda x: str(Path('tight_patch_masks') / x)
- ).rename('tight_patch_masks_path')
+ if not self._df.binary_mask.apply(lambda x: np.all(x)).all(): # binary masks aren't just all True
+ df_exp = self.export_patch_masks(
+ where / 'tight_patch_masks',
+ prefix=prefix,
+ pad_to=None,
+ expanded=False
+ )
+ # record patch masks paths to dataframe, then save static columns to CSV
+ se_pa = df_exp.patch_mask_path.apply(
+ lambda x: str(Path('tight_patch_masks') / x)
+ ).rename('tight_patch_masks_path')
+ self._df = self._df.join(se_pa)
+ record['tight_patch_masks'] = list(se_pa)
- self._df = self._df.join(se_pa)
csv_path = where / 'dataframe' / (prefix + '.csv')
csv_path.parent.mkdir(parents=True, exist_ok=True)
self._df.drop(
@@ -952,9 +955,10 @@ class RoiSet(object):
).to_csv(csv_path, index=False)
record['dataframe'] = str(Path('dataframe') / csv_path.name)
- record['tight_patch_masks'] = list(se_pa)
+
return record
+
def get_polygons(self, poly_threshold=0, dilation_radius=1) -> pd.DataFrame:
self.coordinates_ = """
Fit polygons to all object boundaries in the RoiSet
@@ -994,9 +998,8 @@ 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='') -> Self:
+ def deserialize(acc_raw: GenericImageDataAccessor, where: Path, prefix='roiset') -> Self:
"""
Create an RoiSet object from saved files and an image accessor
:param acc_raw: accessor to image that contains ROIs
@@ -1006,20 +1009,34 @@ class RoiSet(object):
:return: RoiSet object
"""
df = pd.read_csv(where / 'dataframe' / (prefix + '.csv'))[['label', 'zi', 'y0', 'y1', 'x0', 'x1']]
-
- def _read_binary_mask(r):
- ext = 'png'
- fname = f'{prefix}-la{r.label:04d}-zi{r.zi:04d}.{ext}'
- try:
- ma_acc = generate_file_accessor(where / 'tight_patch_masks' / fname)
- assert ma_acc.chroma == 1 and ma_acc.nz == 1
- mask_data = ma_acc.data_xy / np.iinfo(ma_acc.data.dtype).max
- return mask_data
- except Exception as e:
- raise DeserializeRoiSet(e)
- df['binary_mask'] = df.apply(_read_binary_mask, axis=1)
- id_mask = make_object_ids_from_df(df, acc_raw.shape_dict)
- return RoiSet.from_object_ids(acc_raw, id_mask)
+ pa_masks = where / 'tight_patch_masks'
+
+ if pa_masks.exists(): # import segmentation masks
+ def _read_binary_mask(r):
+ ext = 'png'
+ fname = f'{prefix}-la{r.label:04d}-zi{r.zi:04d}.{ext}'
+ try:
+ ma_acc = generate_file_accessor(pa_masks / fname)
+ assert ma_acc.chroma == 1 and ma_acc.nz == 1
+ mask_data = ma_acc.data_xy / np.iinfo(ma_acc.data.dtype).max
+ return mask_data
+ except Exception as e:
+ raise DeserializeRoiSet(e)
+
+ df['binary_mask'] = df.apply(_read_binary_mask, axis=1)
+ id_mask = make_object_ids_from_df(df, acc_raw.shape_dict)
+ return RoiSet.from_object_ids(acc_raw, id_mask)
+
+ else: # assume bounding boxes only
+ df['y'] = df['y0']
+ df['x'] = df['x0']
+ df['h'] = df['y1'] - df['y0']
+ df['w'] = df['x1'] - df['x0']
+ return RoiSet.from_bounding_boxes(
+ acc_raw,
+ df[['y', 'x', 'h', 'w']].to_dict(orient='records'),
+ list(df['zi'])
+ )
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 9de818ee..93e96df7 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -637,7 +637,6 @@ class TestRoiSetObjectDetection(unittest.TestCase):
def test_create_roiset_from_bounding_boxes(self):
from skimage.measure import label, regionprops, regionprops_table
-
mask = self.seg_mask_3d
labels = label(mask.data_xyz, connectivity=3)
table = pd.DataFrame(
@@ -651,12 +650,12 @@ class TestRoiSetObjectDetection(unittest.TestCase):
table['h'] = table['y1'] - table['y']
bboxes = table[['y', 'x', 'h', 'w']].to_dict(orient='records')
-
roiset_bbox = RoiSet.from_bounding_boxes(self.stack_ch_pa, bboxes)
-
+ self.assertTrue('label' in roiset_bbox.get_df().columns)
patches_bbox = roiset_bbox.get_patches_acc()
self.assertEqual(len(table), patches_bbox.count)
+
# roiset w/ seg for comparison
roiset_seg = RoiSet.from_binary_mask(self.stack_ch_pa, mask, allow_3d=True)
patches_seg = roiset_seg.get_patches_acc()
@@ -666,6 +665,19 @@ class TestRoiSetObjectDetection(unittest.TestCase):
for i in range(0, roiset_seg.count):
self.assertEqual(patches_seg.iat(0, crop=True).shape, patches_bbox.iat(0, crop=True).shape)
+ # test that serialization does not write patch masks
+ roiset_ser_path = output_path / 'roiset_from_bbox'
+ dd = roiset_bbox.serialize(roiset_ser_path)
+ self.assertTrue('tight_patch_masks' not in dd.keys())
+ self.assertFalse((roiset_ser_path / 'tight_patch_masks').exists())
+
+ # test that deserialized RoiSet matches the original
+ roiset_des = RoiSet.deserialize(self.stack_ch_pa, roiset_ser_path)
+ self.assertEqual(roiset_des.count, roiset_bbox.count)
+ for i in range(0, roiset_des.count):
+ self.assertEqual(patches_seg.iat(0, crop=True).shape, patches_bbox.iat(0, crop=True).shape)
+ self.assertTrue((roiset_bbox.get_zmask() == roiset_des.get_zmask()).all())
+
class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
--
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