From ce711cba1966178fa4f9ed19cf34db1ebb07248c Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 3 Feb 2024 21:53:38 +0100
Subject: [PATCH] slice and mask array objects now in RoiSet's dataframe
---
model_server/extensions/chaeo/products.py | 3 +-
.../extensions/chaeo/tests/test_zstack.py | 8 +--
model_server/extensions/chaeo/zmask.py | 59 +++++++++----------
3 files changed, 32 insertions(+), 38 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index 82699fb2..84535d73 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -61,9 +61,8 @@ def write_patch_to_file(where, fname, yxcz):
def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
patches = []
for ob in roiset.get_df().itertuples('Roi'):
- sp_sl = roiset.get_rel_slice_at(ob.Index)
patch = np.zeros((ob.ebb_h, ob.ebb_w, 1, 1), dtype='uint8')
- patch[sp_sl][:, :, 0, 0] = roiset.get_mask_at(ob.Index) * 255
+ patch[ob.relative_slice][:, :, 0, 0] = ob.mask * 255
if pad_to:
patch = pad(patch, pad_to)
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index cc9a4297..6fca51b8 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -96,20 +96,18 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
def test_zmask_slices_are_valid(self):
roiset = self.test_zmask_makes_correct_boxes()
- slices = [roiset.get_slice_at(i) for i in roiset.get_df().index]
- for s in slices:
+ for s in roiset.get_slices():
ebb = roiset.acc_raw.data[s]
self.assertEqual(len(ebb.shape), 4)
self.assertTrue(np.all([si >= 1 for si in ebb.shape]))
def test_zmask_rel_slices_are_valid(self):
roiset = self.test_zmask_makes_correct_boxes()
- slices = [roiset.get_slice_at(i) for i in roiset.get_df().index]
- rel_slices = [roiset.get_rel_slice_at(i) for i in roiset.get_df().index]
- for i, s in enumerate(slices):
+ for i, s in enumerate(roiset.get_slices()):
ebb = roiset.acc_raw.data[s]
self.assertEqual(len(ebb.shape), 4)
self.assertTrue(np.all([si >= 1 for si in ebb.shape]))
+ rel_slices = roiset.get_df()['relative_slice']
rbb = ebb[rel_slices[i]]
self.assertEqual(len(rbb.shape), 4)
self.assertTrue(np.all([si >= 1 for si in rbb.shape]))
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 2cef8230..b06c276f 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -36,7 +36,9 @@ class RoiSet(object):
self.acc_raw = acc_raw
self._df = self.filter_df(
- self.make_df(self.acc_raw, self.acc_obj_ids, expand_box_by=params.expand_box_by),
+ self.make_df(
+ self.acc_raw, self.acc_obj_ids, expand_box_by=params.expand_box_by
+ ),
params.filters,
)
@@ -78,7 +80,14 @@ class RoiSet(object):
self.object_class_map = None
@staticmethod
- def make_df(acc_raw, acc_obj_ids, expand_box_by):
+ def make_df(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame:
+ """
+ Build dataframe associate object IDs with summary stats
+ :param acc_raw: accessor to raw image data
+ :param acc_obj_ids: accessor to map of object IDs
+ :param expand_box_by: number of pixels to expand bounding box in all directions (without exceeding image boundary)
+ :return: pd.DataFrame
+ """
# build dataframe of objects, assign z index to each object
argmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
df = (
@@ -117,36 +126,22 @@ class RoiSet(object):
assert np.all(df['rel_x1'] <= (df['ebb_x1'] - df['ebb_x0']))
assert np.all(df['rel_y1'] <= (df['ebb_x1'] - df['ebb_x0']))
+ df['slice'] = df.apply(
+ lambda r:
+ np.s_[int(r.ebb_y0): int(r.ebb_y1), int(r.ebb_x0): int(r.ebb_x1), :, int(r.ebb_z0): int(r.ebb_z1) + 1],
+ axis=1
+ )
+ df['relative_slice'] = df.apply(
+ lambda r:
+ np.s_[int(r.rel_y0): int(r.rel_y1), int(r.rel_x0): int(r.rel_x1), :, :],
+ axis=1
+ )
+ df['mask'] = df.apply(
+ lambda r: (acc_obj_ids == r.label)[r.y0: r.y1, r.x0: r.x1],
+ axis=1
+ )
return df
- def get_slice_at(self, idx) -> tuple:
- """
- Return slice object in np.s_ format that defines expanded bounding box of object
- :param idx: object index (Index in DataFrame, does not necessarily start at zero)
- :return: slice object
- """
- ob = self.get_df().loc[idx, :].astype('int64')
- return np.s_[ob.ebb_y0: ob.ebb_y1, ob.ebb_x0: ob.ebb_x1, :, ob.ebb_z0: ob.ebb_z1 + 1]
-
- def get_rel_slice_at(self, idx) -> tuple:
- """
- Return slice object in np.s_ format that defines bounding box of an object within its expanded bounding box
- :param idx: object index (Index in DataFrame, does not necessarily start at zero)
- :return: slice object
- """
- ob = self.get_df().loc[idx, :].astype('int64')
- return np.s_[ob.rel_y0: ob.rel_y1, ob.rel_x0: ob.rel_x1, :, :]
-
-
- def get_mask_at(self, idx) -> np.ndarray:
- """
- Return 2D array describing object mask that fills (unexpanded) bounding box at index idx
- :param idx: object index (Index in DataFrame, does not necessarily start at zero)
- :return: np.ndarray boolean mask
- """
- ob = self.get_df().loc[idx, :].astype('int64')
- obmask = (self.acc_obj_ids == ob.label)
- return obmask[ob.y0: ob.y1, ob.x0: ob.x1]
@staticmethod
def filter_df(df: pd.DataFrame, filters: RoiFilter = None) -> pd.DataFrame:
@@ -158,12 +153,14 @@ class RoiSet(object):
vmax = val['max']
assert vmin >= 0
query_str = query_str + f' & {k} > {vmin} & {k} < {vmax}'
- # df.loc[df.query(query_str).index, 'keeper'] = True
return df.loc[df.query(query_str).index, :]
def get_df(self) -> pd.DataFrame: # TODO: exclude columns that refer to objects
return self._df
+ def get_slices(self) -> pd.Series:
+ return self.get_df()['slice']
+
def add_df_col(self, name, se: pd.Series) -> None:
self._df[name] = se
--
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