From 9431f5c6de9a02f6b0403c5bdb9268e8c03ce45c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sophia=20M=C3=A4dler?=
 <15019107+sophiamaedler@users.noreply.github.com>
Date: Tue, 5 Nov 2024 12:07:06 +0100
Subject: [PATCH 1/2] truncate image paths in BIAS generated XML

---
 src/scportrait/tools/stitch/_utils/filewriters.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/scportrait/tools/stitch/_utils/filewriters.py b/src/scportrait/tools/stitch/_utils/filewriters.py
index 6a55ac0f..e6e49340 100644
--- a/src/scportrait/tools/stitch/_utils/filewriters.py
+++ b/src/scportrait/tools/stitch/_utils/filewriters.py
@@ -164,6 +164,8 @@ def write_xml(image_paths: list[str], channels: list[str], slidename: str, outdi
                         text(channel)
         with tag("images"):
             for i, image_path in enumerate(image_paths):
+                # truncate image_path to only include the filename
+                image_path = os.path.basename(image_path)
                 with tag("image", url=str(image_path)):
                     with tag("channel"):
                         text(str(i + 1))

From c4e37894761b6eac01c8a2d709432d0a4f93bb5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sophia=20M=C3=A4dler?=
 <15019107+sophiamaedler@users.noreply.github.com>
Date: Wed, 6 Nov 2024 19:22:45 +0100
Subject: [PATCH 2/2] fix rescaling for thumbnail generation during stitching

---
 src/scportrait/tools/stitch/_stitch.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/scportrait/tools/stitch/_stitch.py b/src/scportrait/tools/stitch/_stitch.py
index 78821879..c6d27d6c 100644
--- a/src/scportrait/tools/stitch/_stitch.py
+++ b/src/scportrait/tools/stitch/_stitch.py
@@ -329,7 +329,14 @@ def generate_thumbnail(self, scale=0.05):
         self.thumbnail = thumbnail.make_thumbnail(self.reader, channel=self.stitching_channel_id, scale=scale)
 
         # rescale thumbnail to 0-1 range
-        self.thumbnail = rescale_image(self.thumbnail, self.rescale_range[self.stitching_channel])
+        # if all channels should be rescaled to the same range, initialize dictionary with all channels
+        if type(self.rescale_range) is tuple:
+            rescale_range = {k: self.rescale_range for k in self.channel_names}
+        else:
+            rescale_range = self.rescale_range[self.stitching_channel]
+
+        # rescale generated thumbnail
+        self.thumbnail = rescale_image(self.thumbnail, rescale_range)
 
     def initialize_aligner(self):
         """