From c5cf6a5ecf72fc3afc05aba4332cf340b2a2d297 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Fri, 13 Apr 2018 11:45:52 +0200
Subject: [PATCH] Add script to collect acquisition metadata
---
.../NoiSee/NoiSee_Results_Annotate_Beads.py | 71 +++++++++++++++++++
1 file changed, 71 insertions(+)
create mode 100644 src/main/resources/scripts/Plugins/NoiSee/NoiSee_Results_Annotate_Beads.py
diff --git a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Results_Annotate_Beads.py b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Results_Annotate_Beads.py
new file mode 100644
index 0000000..c59a7c0
--- /dev/null
+++ b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Results_Annotate_Beads.py
@@ -0,0 +1,71 @@
+############ NoiSee Results - Annotate Bead Measurements
+## Signal-to-Noise-Ratio evaluation suite
+## written by Kai Schleicher, Niko Ehrenfeuchter, IMCF Basel
+## licence: GPLv3
+
+
+#@ String(visibility=MESSAGE, label="NoiSee Results -", value="Annotate Bead Measurements", persist=false) msg_title
+#@ File(label="NoiSee Beads Results Directory",style="directory") noisee_beads_resdir
+#@ String(label="Microscope Name", description="e.g. 'LSM700'") noisee_beads_mic_name
+#@ Date(label="Acquisition Date",required=false) noisee_beads_date
+#@ String(label="Objective", description="e.g. 63x, 40x-Water") noisee_beads_objective
+#@ String(label="Detector", description="e.g. PMT2, HyD3, GaAsP1") noisee_beads_detector
+#@ Float(label="Laser Power (in percent)") noisee_beads_lpp
+#@ Float(label="Laser Power (in µW)", description="e.g. '0,92'") noisee_beads_lpuw
+#@ Integer(label="Gain") noisee_beads_gain
+#@ Integer(label="Pixel Dwell") noisee_beads_dwell
+
+#@ LogService log
+
+
+import sys
+import datetime
+import os
+import os.path
+
+# we usually need the string, not the java File object:
+resdir = noisee_beads_resdir.getPath()
+
+if not os.path.isdir(resdir):
+ sys.exit("Results directory not existing: " + resdir)
+
+outfname = resdir + "/metadata.txt"
+if os.path.exists(outfname):
+ tstamp = datetime.datetime.now().strftime("%Y-%m-%d-%H%M%S")
+ try:
+ preserve = resdir + "/metadata_pre-" + tstamp + ".txt"
+ log.info("Preserving existing metadata as: %s" % preserve)
+ os.rename(outfname, preserve)
+ except Exception as err:
+ sys.exit("Unable to preserve existing metadata file: %s" % err)
+
+
+meta = {
+ 'microscope': noisee_beads_mic_name,
+ 'objective': noisee_beads_objective,
+ 'detector': noisee_beads_detector,
+ 'laserpower_pct': noisee_beads_lpp,
+ 'laserpower_uW': noisee_beads_lpuw,
+ 'gain': noisee_beads_gain,
+ 'dwell': noisee_beads_dwell
+}
+
+
+if noisee_beads_date is None:
+ meta['date'] = datetime.datetime.now().strftime("%Y-%m-%d")
+ log.info("No date given, using today: %s" % meta['date'])
+else:
+ meta['date'] = "%s-%02d-%02d" % (noisee_beads_date.year + 1900,
+ noisee_beads_date.month + 1,
+ noisee_beads_date.date)
+
+try:
+ log.info("Saving metadata file: %s" %outfname)
+ with open(outfname, "w") as outfile:
+ for key, val in meta.items():
+ formatted = "%s:%s" % (key, val)
+ log.info(" %s" % formatted)
+ outfile.write("%s\n" % formatted)
+ log.info("Done.")
+except Exception as err:
+ sys.exit("Error saving metadata: %s" % err)
--
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