From e39fcf731d8d25dccbba62db7cb07964aa56e099 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 3 Feb 2024 20:20:29 +0100
Subject: [PATCH] Starting to phase out use of zmask_meta
---
model_server/extensions/chaeo/products.py | 22 ++++++----------------
model_server/extensions/chaeo/zmask.py | 4 ++--
2 files changed, 8 insertions(+), 18 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index c9acc1fd..82699fb2 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -57,23 +57,13 @@ def write_patch_to_file(where, fname, yxcz):
raise Exception(f'Unsupported file extension: {ext}')
-def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
+def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
patches = []
- for mi in roiset.zmask_meta:
- sl = mi['slice']
-
- rbb = mi['relative_bounding_box'] # TODO: call DF rbb fields
- x0 = rbb['x0']
- y0 = rbb['y0']
- x1 = rbb['x1']
- y1 = rbb['y1']
-
- sp_sl = np.s_[y0: y1, x0: x1, :, :]
-
- h, w = roiset.acc_raw.data[sl].shape[0:2]
- patch = np.zeros((h, w, 1, 1), dtype='uint8')
- patch[sp_sl][:, :, 0, 0] = mi['mask'] * 255
+ 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
if pad_to:
patch = pad(patch, pad_to)
@@ -82,7 +72,7 @@ def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
return MonoPatchStack(patches)
-def export_patch_masks_from_zstack(roiset, where: Path, pad_to: int = 256, prefix='mask') -> list:
+def export_patch_masks(roiset, where: Path, pad_to: int = 256, prefix='mask') -> list:
patches_acc = roiset.get_patch_masks(pad_to=pad_to)
exported = []
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index b70afeb3..2cef8230 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -18,7 +18,7 @@ from model_server.extensions.chaeo.products import export_patches_from_zstack, e
from extensions.chaeo.params import RoiFilter, RoiSetMetaParams, RoiSetExportParams
from model_server.extensions.chaeo.accessors import MonoPatchStack
from model_server.extensions.chaeo.process import mask_largest_object
-from model_server.extensions.chaeo.products import get_patches_from_zmask_meta, get_patch_masks, export_patch_masks_from_zstack
+from model_server.extensions.chaeo.products import get_patches_from_zmask_meta, get_patch_masks, export_patch_masks
def get_label_ids(acc_seg_mask):
@@ -188,7 +188,7 @@ class RoiSet(object):
return get_patch_masks(self, **kwargs)
def export_patch_masks(self, where, **kwargs) -> list:
- return export_patch_masks_from_zstack(self, where, **kwargs)
+ return export_patch_masks(self, where, **kwargs)
def get_raw_patches(self, channel):
return get_patches_from_zmask_meta(
--
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