From fed8217335e44b00780048e4c25025595ac2a7da Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Tue, 2 Apr 2019 22:07:33 +0200
Subject: [PATCH] Fix bug correct_and_project() when model is None
---
src/imcflibs/imagej/shading.py | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index 6eda795..bd66e18 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -89,8 +89,10 @@ def correct_and_project(filename, path, model, proj, fmt):
imps = bioformats.import_image(filename, split_c=True)
if model is not None:
log.debug("Applying shading correction on [%s]...", filename)
- imps = apply_model(imps, model)
- bioformats.export_using_orig_name(imps, path, filename, "", fmt, True)
+ imp = apply_model(imps, model)
+ bioformats.export_using_orig_name(imp, path, filename, "", fmt, True)
+ # imps needs to be updated with the new (=merged) stack:
+ imps = [imp]
if proj == 'None':
projs = []
@@ -98,10 +100,10 @@ def correct_and_project(filename, path, model, proj, fmt):
projs = ['Average', 'Maximum']
else:
projs = [proj]
- projections.create_and_save(imps, projs, path, filename, fmt)
+ for imp in imps:
+ projections.create_and_save(imp, projs, path, filename, fmt)
+ imp.close()
- # imps.show()
- imps.close()
log.debug("Done processing [%s].", os.path.basename(filename))
--
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