From f6f545ec7b8f42c90efd0b1545a383f352d97825 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 4 Mar 2019 11:43:03 +0100
Subject: [PATCH] Add workaround for uncalibrated ICS/IDS exports in BF 6.0
series
---
src/imcflibs/imagej/bioformats.py | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/src/imcflibs/imagej/bioformats.py b/src/imcflibs/imagej/bioformats.py
index 1a9d125..69cc5cb 100644
--- a/src/imcflibs/imagej/bioformats.py
+++ b/src/imcflibs/imagej/bioformats.py
@@ -72,6 +72,17 @@ def export(imp, filename, overwrite=False):
keep existing files, in this case an IOError is raised.
"""
log.info("Exporting to [%s]", filename)
+ suffix = filename[-3:].lower()
+ try:
+ unit = imp.calibration.unit
+ log.debug("Detected calibration unit: %s", unit)
+ except Error as err:
+ log.error("Unable to detect spatial unit: %s", err)
+ raise RuntimeError("Error detecting image calibration!")
+ if unit == 'pixel' and (suffix == 'ics' or suffix == 'ids'):
+ log.warn("Forcing unit to be 'm' instead of 'pixel' to avoid "
+ "Bio-Formats 6.0.x Exporter bug!")
+ imp.calibration.unit = 'm'
if os.path.exists(filename):
if not overwrite:
raise IOError('file [%s] already exists!' % filename)
--
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