Add 'imagej.stitching' module

Author: ehrenfeu

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