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Commit ab1d6ed7 authored by Niko Ehrenfeuchter's avatar Niko Ehrenfeuchter :keyboard:
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Allow model file to be '-' or 'None' to disable shading correction

parent 25b8746f
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......@@ -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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