From dec2f94747df965d1123e2cb8ef32833f1d64f13 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 25 Feb 2019 17:19:57 +0100
Subject: [PATCH] Use fully-qualified calls
---
src/imcflibs/imagej/shading.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index 0121198..8417631 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -2,8 +2,7 @@
import os
-from ij import IJ
-from ij.plugin import ImageCalculator, RGBStackMerge
+import ij # pylint: disable-msg=import-error
from ..imagej import bioformats
from ..imagej import projections
@@ -39,7 +38,7 @@ def apply_model(imps, model, merge=True):
The merged ImagePlus with all channels, or the original list of stacks
with the shading-corrected image planes.
"""
- calc = ImageCalculator()
+ calc = ij.plugin.ImageCalculator()
for stack in imps:
# log.debug("Processing channel...")
calc.run("Divide stack", stack, model)
@@ -47,7 +46,7 @@ def apply_model(imps, model, merge=True):
if not merge:
return imps
- merger = RGBStackMerge()
+ merger = ij.plugin.RGBStackMerge()
merged_imp = merger.mergeChannels(imps, False)
return merged_imp
@@ -119,9 +118,9 @@ def process_folder(path, suffix, outpath, model_file, fmt):
fmt : str
The file format suffix for storing the results.
"""
+ imp = ij.IJ.openImage(model_file)
matching_files = listdir_matching(path, suffix)
- imp = IJ.openImage(model_file)
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)
--
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