From 99aeda1c24246ca1b5dab826d4f01f9a5a27648a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 7 Mar 2024 10:41:18 +0100
Subject: [PATCH] Standardize that export record is a dict of pathlib.Path
objects
---
model_server/base/roiset.py | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 1a33c090..c44023db 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -474,7 +474,15 @@ class RoiSet(object):
dfe['patch'] = self._df.apply(lambda r: _make_patch(r), axis=1)
return dfe
- def run_exports(self, where, channel, prefix, params: RoiSetExportParams):
+ def run_exports(self, where: Path, channel, prefix, params: RoiSetExportParams) -> dict:
+ """
+ Export various representations of ROIs, e.g. patches, annotated stacks, and object maps.
+ :param where: path of directory in which to write all export products
+ :param channel: color channel of products to export
+ :param prefix: prefix of the name of each product's file or subfolder
+ :param params: RoiSetExportParams object describing which products to export and with which parameters
+ :return: dict of Path objects describing the location of single-file export products
+ """
record = {}
if not self.count:
return
@@ -506,11 +514,10 @@ class RoiSet(object):
if k == 'annotated_zstacks':
self.export_annotated_zstack(subdir, prefix=pr, **kp)
if k == 'object_classes':
- # record[k] = {}
for kc, acc in self.object_class_maps.items():
fp = subdir / kc / (pr + '.tif')
write_accessor_data_to_file(fp, acc)
- record[f'{k}_{kc}'] = fp.__str__()
+ record[f'{k}_{kc}'] = fp
if k == 'dataframe':
dfpa = subdir / (pr + '.csv')
dfpa.parent.mkdir(parents=True, exist_ok=True)
--
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