def moveTeraStitcherStackToFileList(source, sink, deleteDirectory = True, verbose = True):
"""Moves image files from TeraSticher file structure to a list of files
Arguments:
source (str): base directory of the TeraStitcher files
sink (str): regular expression of the files to copy to
verbose (bool): show progress
Returns:
str: sink regular expression
"""
fns = glob.glob(os.path.join(source, '*/*/*'));
fns = natsort.natsorted(fns);
io.createDirectory(sink);
for i,f in enumerate(fns):
fn = filelist.fileExpressionToFileName(sink, i);
if verbose:
print '%s -> %s' % (f,fn)
shutil.move(f, fn);
if deleteDirectory:
p,_ = os.path.split(fns[0]);
p = p.split(os.path.sep);
p = p[:-2];
p = os.path.sep.join(p);
shutil.rmtree(p);
return sink;
def copyTeraStitcherStackToFileList(source, sink, verbose = True):
"""Copies image files from TeraSticher file structure to a list of files
Arguments:
source (str): base directory of the TeraStitcher files
sink (str): regular expression of the files to copy to
verbose (bool): show progress
Returns:
str: sink regular expression
"""
#TODO: multiple tiles !
fns = glob.glob(os.path.join(source, '*/*/*'));
fns = natsort.natsorted(fns);
#print fns
io.createDirectory(sink);
for i,f in enumerate(fns):
fn = filelist.fileExpressionToFileName(sink, i);
if verbose:
print '%s -> %s' % (f,fn)
shutil.copyfile(f, fn);
return sink;
def stitchData(xmlPlacementFile, resultPath, algorithm = None, resolutions = None, form = None, channel = None, subRegion = None, bitDepth = None, blockSize = None, cleanup = True, compress = False):
"""Runs the final stiching step of TeraSticher
Arguments:
xmlPlacementFile (str or None): the xml placement descriptor
resultPath (str): result path, file name or file expression for the stiched data
algorithm (str or None): optional algorithm to use for placement:
'NOBLEND' for no blending
'SINBLEND' for sinusoidal blending
resolutions (tuple or None): the different resolutions to produce
form (str or None): the output form, if None determined automatically
channel (str or None): the channels to use, 'R', 'G', 'B' or 'all'
subRegion (tuple or None): optional sub region in the form ((xmin,xmax),(ymin,ymax), (zmin, zmax))
bitDepth (int or None): the pits per pixel to use, default is 8
blockSize (tuple): the sizes of various blocks to save stiched image into
cleanup (bool): if True delete the TeraSticher file structure
compress (bool): if True compress final tif images
Returns:
str : the result path or file name of the stiched data
See also:
`TeraStitcher project step <https://github.com/abria/TeraStitcher/wiki/Step-6:-Merge>`_.
"""
checkSticherInitialized();
global TeraStitcherBinary;
cmd = TeraStitcherBinary + ' --merge --imout_format="tif" ';
cmd = cmd + '--projin="' + xmlPlacementFile + '" ';
if len(resultPath) > 3 and resultPath[-4:] == '.tif':
if io.isFileExpression(resultPath, check = False):
form = 'TiledXY|2Dseries';
resultPath, filename = os.path.split(resultPath);
else:
form = 'TiledXY|3Dseries';
resultPath, filename = os.path.split(resultPath);
else:
filename = None;
cmd = cmd + '--volout="' + resultPath + '" ';
if algorithm is not None:
cmd = cmd + ' --algorithm="' + algorithm + '" ';
if resolutions is not None:
cmd = cmd + '--resolutions="'
for r in sorted(resolutions):
cmd = cmd + str(r);
cmd = cmd + ' ';
if form is not None:
cmd = cmd + '--volout_plugin="' + form + '" ';
if channel is not None:
cmd = cmd + '--imin_channel="' + channel + '" ';
if subRegion is not None:
sns = (('--R0=', '--R1='), ('--C0=', '--C1='), ('--D0=', '--D1-'));
for d in range(3):
for m in range(2):
if subRegion[d][m] is not None:
cmd = cmd + sns[d][m] + str(subRegion[d][m]) + ' ';
if blockSize is not None:
bs = ('--slicewidth=', '--sliceheight=', '--slicedepth=');
for d in range(3):
if blockSize[d] is not None:
cmd = cmd + bs[d] + str(blockSize[d]) + ' ';
if bitDepth is not None:
cmd = cmd + '--imout_depth=' + str(bitDepth) + ' ';
if not compress:
cmd = cmd + '--libtiff_uncompress ';
#print resultPath
io.createDirectory(resultPath, split = False)
print 'running: ' + cmd;
res = os.system(cmd);
if res != 0:
raise RuntimeError('stitchData: failed executing: ' + cmd);
if filename is not None:
if io.isFileExpression(filename, check = False): # convert list of files in TeraSticher from
#TODO: multiple resolutions
basedir = max(glob.glob(os.path.join(resultPath, '*')), key = os.path.getmtime);
if cleanup:
moveTeraStitcherStackToFileList(basedir, os.path.join(resultPath, filename), deleteDirectory=True);
#shutil.rmtree(basedir);
else:
copyTeraStitcherStackToFileList(basedir, os.path.join(resultPath, filename));
else: # single file in TeraSticher folder
#get most recent created file
#TODO: test if this works
imgfile = max(glob.glob(os.path.join(resultPath, '*/*/*/*')), key = os.path.getmtime);
filename = os.path.join(resultPath, filename);
os.rename(imgfile, filename);
if cleanup:
imgpath = os.path.sep.join(imgfile.split(os.path.sep)[:-3]);
shutil.rmtree(imgpath)
return filename;
else:
return resultPath;
