From ab1d6ed7ce0c39020e9bd1fbd9ace47e8ba6c66b Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 25 Feb 2019 17:25:32 +0100
Subject: [PATCH] Allow model file to be '-' or 'None' to disable shading
correction
---
src/imcflibs/imagej/shading.py | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index f1aeb14..18f66ac 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -116,15 +116,23 @@ def process_folder(path, suffix, outpath, model_file, fmt):
The output folder where results will be stored. Existing files will be
overwritten.
model_file : str
- The full path to a normalized 32-bit shading model image.
+ The full path to a normalized 32-bit shading model image. If set to '-'
+ or 'NONE', no shading correction will be applied.
fmt : str
The file format suffix for storing the results.
"""
- imp = ij.IJ.openImage(model_file)
+ if model_file in ["-", "NONE"]:
+ model = None
+ else:
+ model = ij.IJ.openImage(model_file)
+ model.show() # required, otherwise the IJ.run() call ignores the model
+
matching_files = listdir_matching(path, suffix)
+ log.info("Running shading correction and projections on %s files...",
+ len(matching_files))
- imp.show() # required, otherwise the IJ.run() call will ignore the imp
for orig_file in matching_files:
in_file = os.path.join(path, orig_file)
- correct_and_project(in_file, outpath, imp, 'ALL', fmt)
- imp.close()
+ correct_and_project(in_file, outpath, model, 'ALL', fmt)
+ if model:
+ model.close()
--
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