From d24887a2d528a472cde0b60e9f6e69768d5c7186 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 7 Jan 2019 17:20:45 +0100
Subject: [PATCH] Add 'overwrite' switch to export() and
export_using_orig_name()
---
src/imcflibs/imagej/bioformats.py | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/src/imcflibs/imagej/bioformats.py b/src/imcflibs/imagej/bioformats.py
index 6661348..6e6477a 100644
--- a/src/imcflibs/imagej/bioformats.py
+++ b/src/imcflibs/imagej/bioformats.py
@@ -57,7 +57,7 @@ def import_image(filename,
return orig_imps
-def export(imp, filename):
+def export(imp, filename, overwrite=False):
"""Simple wrapper to export an image to a given file.
Parameters
@@ -66,13 +66,21 @@ def export(imp, filename):
The ImagePlus object to be exported by Bio-Formats.
filename : str
The output filename, may include a full path.
+ overwrite : bool
+ 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)
+ if os.path.exists(filename):
+ if not overwrite:
+ raise IOError('file [%s] already exists!' % filename)
+ os.remove(filename)
+
IJ.run(imp, "Bio-Formats Exporter", "save=[" + filename + "]")
# log.debug("Exporting finished.")
-def export_using_orig_name(imp, path, orig_name, tag, suffix):
+def export_using_orig_name(imp, path, orig_name, tag, suffix, overwrite=False):
"""Export an image to a given path, deriving the name from the input file.
The input filename is stripped to its pure file name, without any path or
@@ -92,6 +100,8 @@ def export_using_orig_name(imp, path, orig_name, tag, suffix):
to denote information like "-avg" for an average projection image.
suffix : str
The new file name suffix, which also sets the file format for BF.
+ overwrite : bool
+ A switch to indicate existing files should be overwritten.
Returns
-------
@@ -99,5 +109,5 @@ def export_using_orig_name(imp, path, orig_name, tag, suffix):
The full name of the exported file.
"""
out_file = os.path.join(path, image_basename(orig_name) + tag + suffix)
- export(imp, out_file)
+ export(imp, out_file, overwrite)
return out_file
--
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