From eabdfcf80a42b751cf6c92c44e20fc128cd25d16 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 7 Jan 2019 17:37:04 +0100
Subject: [PATCH] Re-activate logging in imagej.projections and imagej.shading
---
src/imcflibs/imagej/projections.py | 7 ++++---
src/imcflibs/imagej/shading.py | 4 +++-
2 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/src/imcflibs/imagej/projections.py b/src/imcflibs/imagej/projections.py
index d8ccf2d..ab332f3 100644
--- a/src/imcflibs/imagej/projections.py
+++ b/src/imcflibs/imagej/projections.py
@@ -1,6 +1,7 @@
"""Functions for creating Z projections."""
from .bioformats import export_using_orig_name
+from ..log import LOG as log
from ij.plugin import ZProjector
@@ -18,7 +19,7 @@ def average(imp):
ij.ImagePlus
The result of the projection.
"""
- # log.debug("Creating average projection...")
+ log.debug("Creating average projection...")
proj = ZProjector.run(imp, "avg")
return proj
@@ -36,7 +37,7 @@ def maximum(imp):
ij.ImagePlus
The result of the projection.
"""
- # log.debug("Creating maximum intensity projection...")
+ log.debug("Creating maximum intensity projection...")
proj = ZProjector.run(imp, "max")
return proj
@@ -64,7 +65,7 @@ def create_and_save(imp, projections, path, filename, export_format):
'Sum': 'sum',
}
for projection in projections:
- # log.debug("Creating '%s' projection..." % projection)
+ log.debug("Creating '%s' projection...", projection)
proj = ZProjector.run(imp, command[projection])
export_using_orig_name(proj,
path, filename,
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index 5f056af..eeaeff1 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -5,6 +5,7 @@ import os
from ..imagej import bioformats
from ..imagej import projections
from ..pathtools import listdir_matching
+from ..log import LOG as log
from ij import IJ
from ij.plugin import ImageCalculator, RGBStackMerge
@@ -70,6 +71,7 @@ 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)
if not os.path.exists(path):
os.makedirs(path)
@@ -87,7 +89,7 @@ def correct_and_project(filename, path, model, proj, fmt):
# corrected.show()
corrected.close()
- # log.debug("Done processing [%s]" % os.path.basename(in_file))
+ log.debug("Done processing [%s].", os.path.basename(filename))
def process_folder(path, suffix, outpath, model_file, fmt):
--
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