From 14d76dfa58cc336021be87af53eb1d0439aca257 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 15:13:25 +0100
Subject: [PATCH] Export DataFrame from workflow
---
extensions/chaeo/params.py | 1 +
extensions/chaeo/tests/test_zstack.py | 3 ++-
extensions/chaeo/zmask.py | 13 ++++---------
3 files changed, 7 insertions(+), 10 deletions(-)
diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index a1f6aa8c..e9fc2461 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -40,5 +40,6 @@ class RoiSetExportParams(BaseModel):
patch_masks: bool = False
annotated_zstacks: Union[AnnotatedZStackParams, None] = None
object_classes: bool = False
+ dataframe: bool = False
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 1779286b..45256258 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -232,7 +232,8 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
},
'patch_masks': True,
'annotated_zstacks': {},
- 'object_classes': True
+ 'object_classes': True,
+ 'dataframe': True,
})
infer_object_map_from_zstack(
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 053f1d44..d1e9301e 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -81,17 +81,9 @@ class RoiSet(object):
self.object_class_map = InMemoryDataAccessor(om)
- # TODO: test
- def get_object_mask_by_id(self, obj_id):
- return self.object_id_labels == obj_id
-
def get_object_mask_by_class(self, class_id):
return self.object_id_labels == class_id
- # TODO: implement
- def get_object_patch_by_id(self, obj_id):
- pass
-
def run_exports(self, where, channel, prefix, params: RoiSetExportParams):
if not self.count:
return
@@ -129,7 +121,10 @@ class RoiSet(object):
write_accessor_data_to_file(subdir / (pr + '.tif'), annotated)
if k == 'object_classes':
write_accessor_data_to_file(subdir / (pr + '.tif'), self.object_class_map)
-
+ if k == 'dataframe':
+ dfpa = subdir / (pr + '.csv')
+ dfpa.parent.mkdir(parents=True, exist_ok=True)
+ self.df.to_csv(dfpa, index=False)
def build_zmask_from_object_mask(
--
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