From 3e7e34c7eb682ea9167c54da1da3b838ef9430aa Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 5 Feb 2024 11:03:47 +0100
Subject: [PATCH] get_patches now returns an extended DataFrame with a patch
column, so that exporters have access to patch metadata with no risk of
mixing up indexing
---
model_server/extensions/chaeo/products.py | 45 ++++++++++++-----------
model_server/extensions/chaeo/zmask.py | 10 ++---
2 files changed, 27 insertions(+), 28 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index 679271ee..57ff9cbe 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -85,31 +85,20 @@ def export_patch_masks(roiset, where: Path, pad_to: int = 256, prefix='mask') ->
def get_patches_from_zmask_meta(
- # stack: GenericImageDataAccessor,
- # zmask_meta: list,
roiset,
rescale_clip: float = 0.0,
pad_to: int = 256,
make_3d: bool = False,
focus_metric: str = None,
**kwargs
-) -> MonoPatchStack:
- patches = []
+) -> pd.DataFrame:
+ # patches = []
# for mi in zmask_meta:
- for i, roi in enumerate(roiset.get_df().itertuples()): # TODO: call RoiSet.iter() when implemented
-
- # sl = roi['slice']
- # rbb = mi['relative_bounding_box'] # TODO: call rel_ fields in DF
- # idx = mi['df_index']
- #
- # x0 = rbb['x0']
- # y0 = rbb['y0']
- # x1 = rbb['x1']
- # y1 = rbb['y1']
- #
- # sp_sl = np.s_[y0: y1, x0: x1, :, :]
+ # dfe = roiset.get_df().assign(patch=object())
+ # for i, roi in enumerate(dfe.itertuples()):
+ def _make_patch(roi):
patch3d = roiset.acc_raw.data[roi.slice]
ph, pw, pc, pz = patch3d.shape
subpatch = patch3d[roi.relative_slice]
@@ -173,12 +162,17 @@ def get_patches_from_zmask_meta(
if pad_to:
patch = pad(patch, pad_to)
- patches.append(patch)
+ # patches.append(patch)
+ return patch
+ # dfe.loc[i, 'patch'] = patch
+ dfe = roiset.get_df()
+ dfe['patch'] = roiset.get_df().apply(lambda r: _make_patch(r), axis=1)
+ return dfe
- if not make_3d and pc == 1:
- return MonoPatchStack(patches)
- else:
- return Multichannel3dPatchStack(patches)
+ # if not make_3d and pc == 1:
+ # return MonoPatchStack(patches)
+ # else:
+ # return Multichannel3dPatchStack(patches)
def export_patches_from_zstack(
where: Path,
@@ -192,7 +186,7 @@ def export_patches_from_zstack(
focus_metric: str = None,
**kwargs
):
- patches_acc = get_patches_from_zmask_meta(
+ patches_df = get_patches_from_zmask_meta(
roiset,
# stack,
# zmask_meta,
@@ -203,6 +197,13 @@ def export_patches_from_zstack(
**kwargs
)
+ pc = roiset.acc_raw.chroma
+ patches = list(patches_df['patch'])
+ if not make_3d and pc == 1:
+ patches_acc = MonoPatchStack(patches)
+ else:
+ patches_acc = Multichannel3dPatchStack(patches)
+
exported = []
for i, roi in enumerate(roiset.get_df().itertuples()): # just used for label info
# for i in range(0, len(zmask_meta)):
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 117e189a..83cf744a 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -80,6 +80,7 @@ class RoiSet(object):
self.object_id_labels = self.interm['label_map']
self.object_class_map = None
+
@staticmethod
def make_df(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame:
"""
@@ -185,11 +186,8 @@ class RoiSet(object):
def export_patch_masks(self, where, **kwargs) -> list:
return export_patch_masks(self, where, **kwargs)
- def get_raw_patches(self, channel):
- return get_patches_from_zmask_meta(
- self.acc_raw.get_one_channel_data(channel),
- self.zmask_meta
- )
+ def get_raw_patches(self, channel): # tight, un-annotated 2d patches
+ return get_patches_from_zmask_meta(self, pad_to=None)
def get_zmask(self, mask_type='boxes'):
"""
@@ -285,7 +283,7 @@ class RoiSet(object):
self.export_patch_masks(subdir, prefix=pr, **params.patch_masks)
if k == 'annotated_zstacks':
annotated = InMemoryDataAccessor(
- draw_boxes_on_3d_image(raw_ch.data, self.zmask_meta, **kp)
+ draw_boxes_on_3d_image(raw_ch.data, self.zmask_meta, **kp) # TODO remove zmask_meta ref
)
write_accessor_data_to_file(subdir / (pr + '.tif'), annotated)
if k == 'object_classes':
--
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