def run_calculations(self):
"""Collect the settings and launch the calculation."""
statusmsg = self.statusbar.showMessage
button_ok = self.bb_ok_cancel.button(QtGui.QDialogButtonBox.Ok)
button_ok.setEnabled(False)
infile = str(self.le_infile.text())
outfile = filehandle(str(self.le_outfile.text()), 'w')
xmax = self.dsb_1.value()
ymax = self.dsb_2.value()
if (xmax + ymax) == 0:
statusmsg('Input size required!')
button_ok.setEnabled(True)
return
xtgt = self.sb_1.value()
ytgt = self.sb_2.value()
set_loglevel(self.sl_verbosity.value())
statusmsg('Parsing XML file...')
spots = StatisticsSpots(infile)
spots.set_limits(xmax=xmax, ymax=ymax)
statusmsg('Generating bitmap...')
bitmap = spots.gen_bitmap((xtgt, ytgt), delta=50)
statusmsg('Writing output file...')
savetxt(outfile, bitmap, fmt='%i')
statusmsg('Finished writing bitmap (%i x %i).' % (xtgt, ytgt))
button_ok.setEnabled(True)
def main_noninteractive():
"""The main routine for running non-interactively."""
global imcftpl
args = parse_arguments()
set_loglevel(args.verbose)
log.info('Running in non-interactive mode.')
log.debug('Python FluoView package file: %s' % fv.__file__)
base = dirname(args.mosaiclog)
fname = basename(args.mosaiclog)
mosaics = fv.FluoViewMosaic(join(base, fname))
log.warn(gen_mosaic_details(mosaics))
if args.templates is not None:
imcftpl = args.templates
code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
path=base, tplpath=imcftpl)
if not args.dryrun:
log.info('Writing stitching macro.')
imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
log.info('Writing tile configuration files.')
imagej.write_all_tile_configs(mosaics, fixsep=True)
log.info('Launching stitching macro.')
IJ.runMacro(flatten(code))
else:
log.info('Dry-run was selected. Printing generated macro:')
log.warn(flatten(code))
def main():
"""Parse the commandline and dispatch the calculations."""
args = parse_arguments()
set_loglevel(args.verbosity)
spots_r = parse_coordinates(args.reference, 'reference')
spots_c = parse_coordinates(args.candidate, 'candidate')
(edm, pairs) = closest_pairs(spots_r, spots_c)
if (args.csv.name != '<stdout>'):
for pair in pairs:
csv_write_distances(args.csv, edm, pair[0])
def main():
"""Create the junction object and do the requested tasks."""
args = parse_arguments()
set_loglevel(args.verbosity)
junction = vp.CellJunction(args.p3d, args.edges)
if args.outfile:
junction.write_output(args.outfile, args.infile)
if args.plot or args.export_plot:
plot.junction(junction, args.plot, args.export_plot)
def main():
"""Parse commandline arguments and run parser."""
args = parse_arguments()
set_loglevel(args.verbosity)
log.debug("Using 'olefile' version %s (%s)." %
(olefile.__version__, olefile.__date__))
ole = olefile.OleFileIO(args.oib)
stream = ole.openstream(['OibInfo.txt'])
# stream = ole.openstream(['Storage00001', 'Stream00060'])
conv = codecs.decode(stream.read(), 'utf16')
log.warn(conv)
def main():
"""Parse commandline arguments and run parser."""
args = parse_arguments()
set_loglevel(args.verbosity)
dname = dirname(args.mosaic.name)
fname = basename(args.mosaic.name)
if args.out == '':
dout = dname
else:
dout = args.out
mosaic = fv.FluoViewMosaic(args.mosaic.name)
ij.write_all_tile_configs(mosaic, fixsep=args.fixsep)
code = ij.gen_stitching_macro_code(mosaic, 'stitching', path=dname)
ij.write_stitching_macro(code, 'stitch_all.ijm', dout)
def run_calculations(self):
"""Collect the settings and launch the calculation."""
statusmsg = self.statusbar.showMessage
button_ok = self.bb_ok_cancel.button(QtGui.QDialogButtonBox.Ok)
button_ok.setEnabled(False)
in_csv = str(self.le_infile.text())
out_csv = filehandle(str(self.le_outfile.text()), 'w')
set_loglevel(self.sl_verbosity.value())
statusmsg('Parsing junction files...')
junction = vp.CellJunction(in_csv)
statusmsg('Writing output files...')
junction.write_output(out_csv, in_csv)
if (self.cb_option.checkState() == 2):
statusmsg('Showing plot...')
plot.junction(junction, True, False)
statusmsg('Finished.')
button_ok.setEnabled(True)
def main():
"""Parse commandline arguments and run distance calculations."""
args = parse_arguments()
set_loglevel(args.verbosity)
log.warn("Calculating distances to WingJ structures...")
if args.imsxml is not None:
coords = ix.ImarisXML(args.imsxml).coordinates_2d("Position")
elif args.ijroi is not None:
coords = read_csv_com(args.ijroi)
coords *= args.pixelsize
else:
# this shouldn't happen with argparse, but you never know...
raise AttributeError("no reference file given!")
wingj = WingJStructure(args.directory, args.pixelsize)
wingj.min_dist_csv_export(coords, args.directory)
log.warn("Finished.")
#!/usr/bin/python """Tests the volpy filament parser.""" # TODO: this is not doing any useful automated tests yet, integrate a # run_test() function and add some useful datasets! # For the time being, this just serves as an example how to test the modules' # functionality. from log import set_loglevel import fluoview from os.path import dirname reload(fluoview) set_loglevel(3) basedir = 'TESTDATA/fluoview/' testfile = basedir + 'minimal_1mosaic_15pct/' + 'MATL_Mosaic.log' mosaic_exp = fluoview.FluoViewMosaic(testfile) mdc = mosaic_exp[0] mdc.dim mdc.get_overlap() mdc.storage oifds = mdc.subvol[3] oifds.get_dimensions() oifds.position oifds.storage
TAG_RE = re.compile(r'<[^>]+>')
def remove_tags(text):
return TAG_RE.sub('', text)
def escape_xml(s):
s = s.replace('&', '&')
s = s.replace('"', '"')
s = s.replace('\'', ''')
s = s.replace('<', '<')
s = s.replace('>', '>')
return s
if __name__ == '__main__':
log.set_loglevel(6)
g2p = G2p()
root = minidom.Document()
xml = root.createElement('result')
root.appendChild(xml)
#cmudict_help = minidom.parseString("<help>"+PhonemeSet+"</help>").firstChild
cmudict_help = root.createElement('help')
link = root.createElement('a')
link.setAttribute('href', "http://www.speech.cs.cmu.edu/cgi-bin/cmudict")
cmudict_help.appendChild(link)
link = root.createElement('a')
link.setAttribute('href', "https://en.wikipedia.org/wiki/ARPABET")
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'output_dir', help='output directory for backup'
)
parser.add_argument(
'-d', '--debug', action='store_true',
help='run in debug mode and output verbose logging'
)
parser.add_argument(
'-p', '--per-page', default=500, type=int, nargs='?',
help='number of photos per page'
)
parser.add_argument(
'-s', '--search-dirs', nargs='*',
help='list of directories to search'
)
args = parser.parse_args()
loglevel = logging.INFO
if args.debug:
loglevel = logging.DEBUG
log.set_loglevel(loglevel)
touchr = ZooomrTouchr(args.output_dir, args.search_dirs)
## create outputdir if it does not exist
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
resp = touchr.zapi.people_getPhotos(
user_id=touchr.zapi.nsid,
per_page=args.per_page
)
total_photos = int(resp.find('photos').get('total'))
total_pages = int(resp.find('photos').get('pages'))
logger.info("Downloading %d photos on %d pages.", total_photos, total_pages)
def extra_photo_ids(xml):
dct = []
for photo_elem in xml.findall('photos/photo'):
dct.append(photo_elem.get('id'))
return dct
## process initial page in 'resp'
photo_ids = extra_photo_ids(resp)
## process following pages
for page_idx in range(2, total_pages+1):
resp = touchr.zapi.people_getPhotos(
user_id=touchr.zapi.nsid,
page=page_idx,
per_page=args.per_page
)
photo_ids.extend(extra_photo_ids(resp))
assert(len(photo_ids) == total_photos)
logger.debug('List of photo IDs: %s', photo_ids)
for photo_id in photo_ids:
download_data = touchr.download_photo(photo_id)
if download_data is not None:
filename, metadata = download_data
## store metadata in photo
touchr.meta_handler.store_metadata(
os.path.join(touchr.output_dir, filename),
metadata
)
if os.path.getsize(ERROR_LOG) > 0:
logger.info(
'errors during processing. see %s.log for details.',
ERROR_LOG
)
else:
logger.info('Yeah!!! All photos backuped successfully.')
from volpy import Filament
from log import set_loglevel, set_filehandler
def run_test(fin, fout, flog):
set_filehandler(flog, no_stderr=True, mode='w')
flmnt = Filament(fin)
output = open(fout, 'w')
output.write(str(flmnt.get_coords()))
print 'Parsed %i points from "%s"' % \
(len(flmnt.get_coords()), fin)
print('Written results to "%s"' % fout)
set_loglevel(2)
basedir = 'TESTDATA/filaments/'
infile = basedir + 'testdata-filaments-small.csv'
outfile = basedir + 'result_filaments-small.coords.txt'
logfile = basedir + 'result_filaments-small.stderr.txt'
run_test(infile, outfile, logfile)
infile = basedir + 'testdata-filaments-manual.csv'
outfile = basedir + 'result_filaments-manual.coords.txt'
logfile = basedir + 'result_filaments-manual.stderr.txt'
run_test(infile, outfile, logfile)
infile = basedir + 'testdata-junction-wt-001.csv'
outfile = basedir + 'result_junction-wt-001.coords.txt'
logfile = basedir + 'result_junction-wt-001.stderr.txt'
