From 58ab5218b78cc7f967129e98cfe3269ec0264fab Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Fri, 1 Mar 2019 09:28:23 +0100
Subject: [PATCH] Add 'imagej.stitching' module
---
src/imcflibs/imagej/stitching.py | 116 +++++++++++++++++++++++++++++++
1 file changed, 116 insertions(+)
create mode 100644 src/imcflibs/imagej/stitching.py
diff --git a/src/imcflibs/imagej/stitching.py b/src/imcflibs/imagej/stitching.py
new file mode 100644
index 0000000..29fd30b
--- /dev/null
+++ b/src/imcflibs/imagej/stitching.py
@@ -0,0 +1,116 @@
+"""Functions to work on stitching datasets."""
+
+from os.path import join
+
+from java.lang.System import getProperty # pylint: disable-msg=import-error
+
+import micrometa # pylint: disable-msg=import-error
+import ij # pylint: disable-msg=import-error
+
+from imcflibs.imagej.misc import show_status, show_progress, error_exit
+from ..strtools import flatten
+from ..log import LOG as log
+
+
+def process_fluoview_project(infile):
+ """Process a FluoView mosaic project file.
+
+ Parameters
+ ----------
+ infile : str
+ The full path to either an `MATL_Mosaic.log` or any `*.omp2info` file
+ from a FluoView MATL acquisition.
+
+ Returns
+ -------
+ micrometa.experiment.MosaicExperiment
+ The mosaic object if parsing the project file has been successful.
+ """
+ if infile[-9:] == '.omp2info':
+ mosaicclass = micrometa.fluoview.FluoView3kMosaic
+ elif infile[-4:] == '.log':
+ mosaicclass = micrometa.fluoview.FluoViewMosaic
+ else:
+ error_exit('Unsupported input file: %s' % infile)
+
+ log.info("Parsing project file: [%s]", infile)
+ ij.IJ.showStatus("Parsing mosaics...")
+
+ mosaics = mosaicclass(infile, runparser=False)
+ total = len(mosaics.mosaictrees)
+ ij.IJ.showProgress(0.0)
+ show_status("Parsed %s / %s mosaics" % (0, total))
+ for i, subtree in enumerate(mosaics.mosaictrees):
+ log.info("Parsing mosaic %s...", i+1)
+ try:
+ mosaics.add_mosaic(subtree, i)
+ except (ValueError, IOError) as err:
+ log.warn('Skipping mosaic %s: %s', i, err)
+ except RuntimeError as err:
+ log.warn('Error parsing mosaic %s, SKIPPING: %s', i, err)
+ show_progress(i, total)
+ show_status("Parsed %s / %s mosaics" % (i+1, total))
+ show_progress(total, total)
+ show_status("Parsed %i mosaics." % total)
+
+ if not mosaics:
+ error_exit("Couldn't find any (valid) mosaics in the project file!")
+ log.info(mosaics.summarize())
+
+ return mosaics
+
+
+def gen_macro(mosaics, indir, outfile=None, opts=None):
+ """Generate stitcher macro code and optionally save it in a file.
+
+ Parameters
+ ----------
+ mosaics : micrometa.experiment.MosaicExperiment
+ The mosaic object of the stitching experiment.
+ indir : str
+ The path to use as input directory *INSIDE* the macro.
+ outfile : str (optional)
+ The path to a file for saving the generated macro code.
+ opts : dict (optional)
+ A dict to be passed on to micrometa.imagej.gen_stitching_macro().
+
+ Returns
+ -------
+ list(str)
+ The generated macro code as a list of strings (one str per line).
+ """
+ templates = join(getProperty('fiji.dir'), 'jars', 'python-micrometa.jar')
+ log.info("Using macro templates from [%s].", templates)
+ log.info("Using [%s] as base directory.", indir)
+
+ # set the default stitcher options
+ stitcher_options = {
+ 'export_format': '".ids"',
+ 'split_z_slices': 'false',
+ 'rotation_angle': 0,
+ 'stitch_regression': 0.3,
+ 'stitch_maxavg_ratio': 2.5,
+ 'stitch_abs_displace': 3.5,
+ 'compute' : 'false',
+ }
+ # merge explicit options, overriding the defaults from above if applicable:
+ if opts:
+ stitcher_options.update(opts)
+
+ code = micrometa.imagej.gen_stitching_macro(
+ name=mosaics.infile['dname'],
+ path=indir,
+ tplpfx='templates/imagej-macro/stitching',
+ tplpath=templates,
+ opts=stitcher_options
+ )
+
+ log.debug("============= begin of generated macro code =============")
+ log.debug(flatten(code))
+ log.debug("============= end of generated macro code =============")
+
+ if outfile is not None:
+ log.info('Writing stitching macro.')
+ micrometa.imagej.write_stitching_macro(code, outfile)
+
+ return code
--
GitLab