From d436bb0d702c66b08ff7711cb8623c9bb40ca14a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 3 Feb 2024 16:44:15 +0100
Subject: [PATCH] Moved expanded and relative bounding box calcs in to DF
creation
---
model_server/extensions/chaeo/products.py | 6 +-
model_server/extensions/chaeo/zmask.py | 87 ++++++++++++++++++++---
2 files changed, 80 insertions(+), 13 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index d68b4c36..c9acc1fd 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -63,7 +63,7 @@ def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
for mi in roiset.zmask_meta:
sl = mi['slice']
- rbb = mi['relative_bounding_box']
+ rbb = mi['relative_bounding_box'] # TODO: call DF rbb fields
x0 = rbb['x0']
y0 = rbb['y0']
x1 = rbb['x1']
@@ -111,7 +111,7 @@ def get_patches_from_zmask_meta(
for mi in zmask_meta:
sl = mi['slice']
- rbb = mi['relative_bounding_box']
+ rbb = mi['relative_bounding_box'] # TODO: call rel_ fields in DF
idx = mi['df_index']
x0 = rbb['x0']
@@ -267,7 +267,7 @@ def export_3d_patches_with_focus_metrics(
for mi in zmask_meta:
obj = mi['info']
sl = mi['slice']
- rbb = mi['relative_bounding_box']
+ rbb = mi['relative_bounding_box'] # TODO: use rel_ fields in DF
idx = mi['df_index']
patch = stack.data[sl]
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 37996a0d..7e852e6d 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -67,25 +67,66 @@ class RoiSet(object):
self.acc_obj_ids = acc_obj_ids
self.acc_raw = acc_raw
+
+
self._df = self.filter_df(
- self.make_df(self.acc_raw, self.acc_obj_ids),
+ self.make_df(self.acc_raw, self.acc_obj_ids, expand_box_by=params.expand_box_by),
params.filters,
)
+ # self._df = self.make_slices(
+ # self._df,
+ # expand_box_by=params.expand_box_by,
+ # shape=acc_raw.shape
+ # )
+
# remaining zmask_meta write ops
- self.zmask_meta, _, self.interm = build_zmask_from_object_mask(
- acc_obj_ids,
- acc_raw,
- self.get_df(),
- params=params,
- )
+ # self.zmask_meta, _, self.interm = build_zmask_from_object_mask(
+ # acc_obj_ids,
+ # acc_raw,
+ # self.get_df(),
+ # params=params,
+ # )
+
+ # temporarily build zmask meta here
+ meta = []
+ for ob in self.get_df().itertuples(name='LabeledObject'):
+ sl = np.s_[ob.ebb_y0: ob.ebb_y1, ob.ebb_x0: ob.ebb_x1, :, ob.ebb_z0: ob.ebb_z1 + 1] # TODO: on-the-fly in RoiSet, given DF
+
+ # compute contours
+ obmask = (acc_obj_ids == ob.label) # TODO: on-the-fly
+ contour = find_contours(obmask) # TODO: on-the-fly
+ mask = obmask[ob.y0: ob.y1, ob.x0: ob.x1]
+
+ rbb = { # TODO: just put in the DF
+ 'y0': ob.rel_y0,
+ 'y1': ob.rel_y1,
+ 'x0': ob.rel_x0,
+ 'x1': ob.rel_x1,
+ }
+
+ meta.append({
+ 'df_index': ob.Index,
+ 'info': ob,
+ 'slice': sl,
+ 'relative_bounding_box': rbb, # TODO: put in DF
+ 'contour': contour, # TODO: delegate to getter
+ 'mask': mask # TODO: delegate to getter
+ })
+ self.zmask_meta = meta
+
+ # return intermediate image arrays # TODO: make on-the-fly
+ self.interm = {
+ 'label_map': acc_obj_ids,
+ 'argmax': acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16'),
+ }
self.count = len(self.zmask_meta)
self.object_id_labels = self.interm['label_map']
self.object_class_map = None
@staticmethod
- def make_df(acc_raw, acc_obj_ids):
+ def make_df(acc_raw, acc_obj_ids, expand_box_by):
# build dataframe of objects, assign z index to each object
argmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
df = (
@@ -101,8 +142,34 @@ class RoiSet(object):
)
)
df['zi'] = df['intensity_mean'].round().astype('int')
+
+ # compute expanded bounding boxes
+ h, w, c, nz = acc_raw.shape
+ ebxy, ebz = expand_box_by
+ df['ebb_y0'] = (df.y0 - ebxy).apply(lambda x: max(x, 0))
+ df['ebb_y1'] = (df.y1 + ebxy).apply(lambda x: min(x, h))
+ df['ebb_x0'] = (df.x0 - ebxy).apply(lambda x: max(x, 0))
+ df['ebb_x1'] = (df.x1 + ebxy).apply(lambda x: min(x, w))
+ df['ebb_z0'] = (df.zi - ebz).apply(lambda x: max(x, 0))
+ df['ebb_z1'] = (df.zi + ebz).apply(lambda x: min(x, nz))
+
+ # compute relative bounding boxes
+ df['rel_y0'] = df.y0 - df.ebb_y0
+ df['rel_y1'] = df.y1 - df.ebb_y1
+ df['rel_x0'] = df.x0 - df.ebb_x0
+ df['rel_x1'] = df.x1 - df.ebb_x1
+
+ assert np.all(df['rel_x1'] <= (df['ebb_x1'] - df['ebb_x0']))
+ assert np.all(df['rel_y1'] <= (df['ebb_x1'] - df['ebb_x0']))
+
return df
+ # def get_slices(self): # TODO: actually map to DF index as new column
+ # sl = []
+ # for ob in self.get_df().itertuples(name='LabeledObject'):
+ # sl.append(np.s_[ob.ebb_y0: ob.ebb_y1, ob.ebb_x0: ob.ebb_x1, :, ob.ebb_z0: ob.ebb_z1 + 1])
+ # return sl
+
@staticmethod
def filter_df(df: pd.DataFrame, filters: RoiFilter = None) -> pd.DataFrame:
query_str = 'label > 0' # always true
@@ -116,7 +183,7 @@ class RoiSet(object):
# df.loc[df.query(query_str).index, 'keeper'] = True
return df.loc[df.query(query_str).index, :]
- def get_df(self) -> pd.DataFrame:
+ def get_df(self) -> pd.DataFrame: # TODO: exclude columns that refer to objects
return self._df
def add_df_col(self, name, se: pd.Series) -> None:
@@ -344,7 +411,7 @@ def build_zmask_from_object_mask(
meta.append({
'df_index': ob.Index,
'info': ob,
- 'slice': sl,
+ # 'slice': sl,
'relative_bounding_box': rbb, # TODO: put in DF
'contour': contour, # TODO: delegate to getter
'mask': mask # TODO: delegate to getter
--
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