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'