From ffd3a19dc0b4cea718647eaf38c9a3bc47d0139b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 6 Feb 2024 18:10:01 +0100
Subject: [PATCH] Progress on running workflow, still throwing errors but
suspect these just require method signature updates
---
model_server/extensions/chaeo/accessors.py | 1 +
model_server/extensions/chaeo/zmask.py | 10 +++++-----
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
index 31d043e3..bc65c6f3 100644
--- a/model_server/extensions/chaeo/accessors.py
+++ b/model_server/extensions/chaeo/accessors.py
@@ -77,6 +77,7 @@ class MonoPatchStackFromFile(MonoPatchStack):
def fpath(self):
return self.file_acc.fpath
+# TODO: unify this into one accessor
class Multichannel3dPatchStack(InMemoryDataAccessor):
def __init__(self, data):
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 242033d8..02e5922a 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -195,7 +195,7 @@ class RoiSet(object):
else:
patches_df = get_patches_from_zmask_meta(self, pad_to=pad_to)
patches = list(patches_df['patch'])
- if self.acc_raw.chroma == 1:
+ if channel is not None or self.acc_raw.chroma == 1:
return MonoPatchStack(patches)
else:
return Multichannel3dPatchStack(patches)
@@ -256,13 +256,13 @@ class RoiSet(object):
# df['classify_by_' + f]
# assign labels to object map:
- for i in idx:
+ for i in range(0, len(idx)):
# object_id = self.zmask_meta[i]['info'].label
- object_id = df.loc[i, 'label']
+ object_id = df.loc[idx[i], 'label']
result_patch = mask_largest_object(obmap_patches.iat(i))
object_class = np.unique(result_patch)[1]
om[self.object_id_labels == object_id] = object_class
- se.loc[i] = object_class
+ se.loc[idx[i]] = object_class
self.add_df_col('classify_by_' + name, se)
self.object_class_map[name] = InMemoryDataAccessor(om)
@@ -279,7 +279,7 @@ class RoiSet(object):
continue
if k == 'patches_3d':
files = export_patches_from_zstack(
- subdir, raw_ch, self.zmask_meta, prefix=pr, make_3d=True, **kp
+ subdir, self, white_channel=channel, prefix=pr, make_3d=True, **kp
)
if k == 'patches_2d_for_annotation':
files = export_multichannel_patches_from_zstack(
--
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