def filter_ransac(corr_file, compared_url, out_fname, jar_file, conf=None):
# When matching layers, no need to take bounding box into account
conf_args = utils.conf_args_from_file(conf, 'FilterRansac')
java_cmd = 'java -Xmx3g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.FilterRansac --inputfile {1} --comparedUrl {2} \
--targetPath {3} {4}'.format(jar_file, utils.path2url(corr_file),
compared_url, out_fname, conf_args)
utils.execute_shell_command(java_cmd)
def filter_local_smoothness(corr_file, out_fname, jar_file, conf=None):
# When matching layers, no need to take bounding box into account
conf_args = utils.conf_args_from_file(conf, 'FilterLocalSmoothness')
java_cmd = 'java -Xmx3g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.FilterLocalSmoothness --inputfile {1} \
--targetPath {2} {3}'.format(
jar_file,
utils.path2url(corr_file),
out_fname,
conf_args)
utils.execute_shell_command(java_cmd)
def optimize_elastic_transform(correspondence_file, tilespec_file, fixed_tiles, output_file, jar_file, conf_fname=None):
corr_url = utils.path2url(correspondence_file)
tiles_url = utils.path2url(tilespec_file)
conf_args = utils.conf_args_from_file(conf_fname, 'OptimizeMontageElastic')
fixed_str = ""
if fixed_tiles != None:
fixed_str = "--fixedTiles {0}".format(" ".join(map(str, fixed_tiles)))
java_cmd = 'java -Xmx10g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.OptimizeMontageElastic {1} --corrfile {2} --tilespecfile {3} {4} --targetPath {5}'.format(\
jar_file, conf_args, corr_url, tiles_url, fixed_str, output_file)
utils.execute_shell_command(java_cmd)
def match_single_sift_features_and_filter(tiles_file,
features_file1,
features_file2,
jar,
out_fname,
index_pair,
conf_fname=None):
tiles_url = utils.path2url(os.path.abspath(tiles_file))
conf_args = utils.conf_args_from_file(conf_fname,
'MatchSiftFeaturesAndFilter')
java_cmd = 'java -Xmx3g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.MatchSiftFeaturesAndFilter \
--tilespecfile {1} --featurefile1 {2} --featurefile2 {3} --indices {4} --targetPath {5} {6}'.format(
jar, tiles_url, features_file1, features_file2,
"{}:{}".format(index_pair[0], index_pair[1]), out_fname, conf_args)
utils.execute_shell_command(java_cmd)
def create_layer_sift_features(tiles_fname,
out_fname,
jar_file,
meshes_dir=None,
conf=None,
threads_num=4):
meshes_str = ''
if meshes_dir is not None:
meshes_str = '--meshesDir "{0}"'.format(meshes_dir)
tiles_url = utils.path2url(os.path.abspath(tiles_fname))
conf_args = utils.conf_args_from_file(conf, 'ComputeSiftFeatures')
# Compute the Sift features `for each tile in the tile spec file
java_cmd = 'java -Xmx11g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.ComputeLayerSiftFeatures --url {1} --targetPath {2} --threads {3} {4} {5}'.format(\
jar_file, tiles_url, out_fname, threads_num, meshes_str, conf_args)
utils.execute_shell_command(java_cmd)
def match_layers_sift_features(tiles_file1,
features_file1,
tiles_file2,
features_file2,
out_fname,
jar_file,
conf=None,
threads_num=4):
# When matching layers, no need to take bounding box into account
conf_args = utils.conf_args_from_file(conf, 'MatchSiftFeatures')
java_cmd = 'java -Xmx3g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.MatchLayersSiftFeatures --threads {1} --tilespec1 {2} \
--featurefile1 {3} --tilespec2 {4} --featurefile2 {5} --targetPath {6} {7}'.format(
jar_file, threads_num, utils.path2url(tiles_file1),
utils.path2url(features_file1), utils.path2url(tiles_file2),
utils.path2url(features_file2), out_fname, conf_args)
utils.execute_shell_command(java_cmd)
def create_sift_features(tiles_fname,
out_fname,
index,
jar_file,
conf_fname=None,
threads_num=None):
threads_str = ""
if threads_num != None:
threads_str = "--threads {0}".format(threads_num)
tiles_url = utils.path2url(os.path.abspath(tiles_fname))
conf_args = utils.conf_args_from_file(conf_fname, 'ComputeSiftFeatures')
# Compute the Sift features `for each tile in the tile spec file
java_cmd = 'java -Xmx5g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.ComputeSiftFeatures --index {1} \
--url {2} --targetPath {3} {4} {5}' .format(\
jar_file, index, tiles_url, out_fname, threads_str, conf_args)
utils.execute_shell_command(java_cmd)
def match_layers_by_max_pmcc(jar_file,
tiles_file1,
tiles_file2,
models_file,
image_width,
image_height,
fixed_layers,
out_fname,
meshes_dir1=None,
meshes_dir2=None,
conf=None,
threads_num=None,
auto_add_model=False):
conf_args = utils.conf_args_from_file(conf, 'MatchLayersByMaxPMCC')
meshes_str = ''
if meshes_dir1 is not None:
meshes_str += ' --meshesDir1 "{0}"'.format(meshes_dir1)
if meshes_dir2 is not None:
meshes_str += ' --meshesDir2 "{0}"'.format(meshes_dir2)
fixed_str = ""
if fixed_layers != None:
fixed_str = "--fixedLayers {0}".format(" ".join(map(str,
fixed_layers)))
threads_str = ""
if threads_num != None:
threads_str = "--threads {0}".format(threads_num)
auto_add_model_str = ""
if auto_add_model:
auto_add_model_str = "--autoAddModel"
java_cmd = 'java -Xmx16g -XX:ParallelGCThreads={0} -Djava.awt.headless=true -cp "{1}" org.janelia.alignment.MatchLayersByMaxPMCC --inputfile1 {2} --inputfile2 {3} \
--modelsfile1 {4} --imageWidth {5} --imageHeight {6} {7} {8} {9} --targetPath {10} {11} {12}'.format(
utils.get_gc_threads_num(threads_num), jar_file,
utils.path2url(tiles_file1), utils.path2url(tiles_file2),
utils.path2url(models_file), int(image_width), int(image_height),
threads_str, auto_add_model_str, meshes_str, out_fname, fixed_str,
conf_args)
utils.execute_shell_command(java_cmd)
def main():
# Command line parser
parser = argparse.ArgumentParser(
description=
'Iterates over the tilespecs in a file, computing matches for each overlapping tile.'
)
parser.add_argument('tiles_file',
metavar='tiles_file',
type=str,
help='the json file of tilespecs')
parser.add_argument('features_file',
metavar='features_file',
type=str,
help='the json file of features')
parser.add_argument(
'-o',
'--output_file',
type=str,
help=
'an output correspondent_spec file, that will include the sift features for each tile (default: ./matches.json)',
default='./matches.json')
parser.add_argument(
'-j',
'--jar_file',
type=str,
help=
'the jar file that includes the render (default: ../target/render-0.0.1-SNAPSHOT.jar)',
default='../target/render-0.0.1-SNAPSHOT.jar')
parser.add_argument(
'-c',
'--conf_file_name',
type=str,
help=
'the configuration file with the parameters for each step of the alignment process in json format (uses default parameters, if not supplied)',
default=None)
args = parser.parse_args()
match_sift_features(args.tiles_file, args.features_file, args.output_file, args.jar_file, \
conf=utils.conf_args_from_file(args.conf_file_name, "MatchSiftFeatures"))
def optimize_layers_affine(tile_files,
corr_files,
model_files,
fixed_layers,
out_dir,
max_layer_distance,
jar_file,
conf=None,
skip_layers=None,
threads_num=4,
manual_matches=None):
conf_args = utils.conf_args_from_file(conf, 'OptimizeLayersAffine')
fixed_str = ""
if fixed_layers != None:
fixed_str = " ".join("--fixedLayers {0}".format(str(fixed_layer))
for fixed_layer in fixed_layers)
skip_str = ""
if skip_layers != None:
skip_str = "--skipLayers {0}".format(skip_layers)
manual_matches_str = ""
if manual_matches is not None:
manual_matches_str = " ".join("--manualMatches {}".format(a)
for a in manual_matches)
# Assuming that at least 4 threads will be allocated for this job, and increasing the number of gc threads to 4 will make it faster
java_cmd = 'java -Xmx46g -XX:ParallelGCThreads={0} -Djava.awt.headless=true -cp "{1}" org.janelia.alignment.OptimizeLayersAffine --tilespecFiles {2} --corrFiles {3} \
--modelFiles {4} {5} {6} --threads {7} --maxLayersDistance {8} {9} --targetDir {10} {11}'.format(
utils.get_gc_threads_num(threads_num), jar_file,
" ".join(utils.path2url(f) for f in tile_files),
" ".join(utils.path2url(f) for f in corr_files),
" ".join(utils.path2url(f)
for f in model_files), fixed_str, manual_matches_str,
threads_num, max_layer_distance, skip_str, out_dir, conf_args)
utils.execute_shell_command(java_cmd)
def main():
# Command line parser
parser = argparse.ArgumentParser(
description=
'Executes the block matching parameters testing application.')
parser.add_argument('--tile_files',
metavar='tile_files',
type=str,
nargs='+',
required=True,
help='the list of tile spec files to test')
parser.add_argument(
'-j',
'--jar_file',
type=str,
help=
'the jar file that includes the render (default: ../target/render-0.0.1-SNAPSHOT.jar)',
default='../target/render-0.0.1-SNAPSHOT.jar')
parser.add_argument(
'-c',
'--conf_file_name',
type=str,
help=
'the configuration file with the parameters for each step of the alignment process in json format (uses default parameters, if not supplied)',
default=None)
parser.add_argument('-t',
'--threads_num',
type=int,
help='the number of threads to use (default: 1)',
default=1)
args = parser.parse_args()
print "tile_files: {0}".format(args.tile_files)
block_matching_test_params(args.tile_files, args.jar_file, \
conf=utils.conf_args_from_file(args.conf_file_name, "MatchLayersByMaxPMCC"), threads_num=args.threads_num)
def match_multiple_pmcc(tiles_file,
index_pairs,
fixed_tiles,
jar,
out_fname,
conf_fname=None,
threads_num=None):
tiles_url = utils.path2url(os.path.abspath(tiles_file))
fixed_str = ""
if fixed_tiles != None:
fixed_str = "--fixedTiles {0}".format(" ".join(map(str, fixed_tiles)))
threads_str = ""
if threads_num != None:
threads_str = "--threads {0}".format(threads_num)
conf_args = utils.conf_args_from_file(conf_fname, 'MatchByMaxPMCC')
java_cmd = 'java -Xmx27g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.MatchByMaxPMCC --inputfile {1} {2} {3} {4} --targetPath {5} {6}'.format(
jar, tiles_url, fixed_str,
" ".join("--indices {}:{}".format(a, b) for a, b in index_pairs),
threads_str, out_fname, conf_args)
utils.execute_shell_command(java_cmd)