From 5d3b5f32fa00332b97d902ec9e26e6d8f87e1321 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Fri, 5 Apr 2019 18:28:28 +0200
Subject: [PATCH] Split process_files() out from process_folder()
---
src/imcflibs/imagej/shading.py | 32 ++++++++++++++++++++++++++------
1 file changed, 26 insertions(+), 6 deletions(-)
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index 8e30c2a..c0a20a3 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -138,6 +138,30 @@ def process_folder(path, suffix, outpath, model_file, fmt):
fmt : str
The file format suffix for storing the results.
"""
+ matching_files = listdir_matching(path, suffix, fullpath=True)
+ process_files(matching_files, outpath, model_file, fmt)
+
+
+def process_files(files, outpath, model_file, fmt):
+ """Run shading correction and projections on a list of files.
+
+ Parameters
+ ----------
+ files : list(str)
+ The files to be processed, as a list of strings with the full path.
+ outpath : str
+ 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. If set to '-'
+ or 'NONE', no shading correction will be applied, i.e. only the
+ projection step will have an effect.
+ fmt : str
+ The file format suffix for storing the results.
+ """
+ log.info("Running shading correction and projections on %s files...",
+ len(files))
+
if model_file.upper() in ["-", "NONE"]:
model = None
else:
@@ -152,12 +176,8 @@ def process_folder(path, suffix, outpath, model_file, fmt):
except AttributeError:
misc.error_exit("Opening shading model [%s] failed!" % model_file)
- matching_files = listdir_matching(path, suffix)
- log.info("Running shading correction and projections on %s files...",
- len(matching_files))
-
- for orig_file in matching_files:
- in_file = os.path.join(path, orig_file)
+ for in_file in files:
correct_and_project(in_file, outpath, model, 'ALL', fmt)
+
if model:
model.close()
--
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