From 14106fe0affbf87e072b0006e13996c82cb5df51 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 7 Jan 2019 17:30:11 +0100
Subject: [PATCH] Re-activate logging calls in imagej.bioformats
---
src/imcflibs/imagej/bioformats.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/src/imcflibs/imagej/bioformats.py b/src/imcflibs/imagej/bioformats.py
index 6e6477a..9ec73e5 100644
--- a/src/imcflibs/imagej/bioformats.py
+++ b/src/imcflibs/imagej/bioformats.py
@@ -14,6 +14,7 @@ from loci.plugins import BF
from loci.plugins.in import ImporterOptions
from ..pathtools import image_basename
+from ..log import LOG as log
def import_image(filename,
@@ -52,7 +53,7 @@ def import_image(filename,
options.setSplitFocalPlanes(split_z)
options.setSplitTimepoints(split_t)
options.setId(filename)
- # log.info("Reading [%s]" % filename)
+ log.info("Reading [%s]", filename)
orig_imps = BF.openImagePlus(options)
return orig_imps
@@ -70,14 +71,15 @@ def export(imp, filename, overwrite=False):
A switch to indicate existing files should be overwritten. Default is to
keep existing files, in this case an IOError is raised.
"""
- # log.info("Exporting to [%s]" % out_file)
+ log.info("Exporting to [%s]", filename)
if os.path.exists(filename):
if not overwrite:
raise IOError('file [%s] already exists!' % filename)
+ log.debug("Removing existing file [%s]...", filename)
os.remove(filename)
IJ.run(imp, "Bio-Formats Exporter", "save=[" + filename + "]")
- # log.debug("Exporting finished.")
+ log.debug("Exporting finished.")
def export_using_orig_name(imp, path, orig_name, tag, suffix, overwrite=False):
--
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