From 0aa41d09badbce912a32828edb7f5b7b623331a1 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Wed, 9 Jan 2019 11:41:09 +0100
Subject: [PATCH] Only create shading-corrected images if they don't exist yet
---
src/imcflibs/imagej/shading.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index 7bb69ab..0121198 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -7,7 +7,7 @@ from ij.plugin import ImageCalculator, RGBStackMerge
from ..imagej import bioformats
from ..imagej import projections
-from ..pathtools import listdir_matching
+from ..pathtools import listdir_matching, gen_name_from_orig
from ..log import LOG as log
@@ -55,6 +55,11 @@ def apply_model(imps, model, merge=True):
def correct_and_project(filename, path, model, proj, fmt):
"""Apply a shading correction to an image and create a projection.
+ In case the target file for the shading corrected image already exists,
+ nothing is done - neither the shading correction is re-created nor any
+ projections will be done (independent on whether the latter one already
+ exist or not).
+
Parameters
----------
filename : str
@@ -71,7 +76,12 @@ def correct_and_project(filename, path, model, proj, fmt):
The file format suffix to be used for the results and projections, e.g.
'.ics' for ICS2 etc. See the Bio-Formats specification for details.
"""
- log.debug("Processing [%s]...", filename)
+ target = gen_name_from_orig(path, filename, "", fmt)
+ if os.path.exists(target):
+ log.info("Found shading corrected file, not re-creating: %s", target)
+ return
+
+ log.debug("Applying shading correction on [%s]...", filename)
if not os.path.exists(path):
os.makedirs(path)
--
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