def render_tiles_2d(tiles_fname,
output_dir,
tile_size,
output_type,
jar_file,
output_pattern=None,
blend_type=None,
threads_num=None):
tiles_url = utils.path2url(tiles_fname)
threads_str = ""
if threads_num is not None:
threads_str = "--threads {}".format(threads_num)
blend_str = ""
if blend_type is not None:
blend_str = "--blendType {}".format(blend_type)
pattern_str = ""
if output_pattern is not None:
pattern_str = "--outputNamePattern {}".format(output_pattern)
java_cmd = 'java -Xmx32g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.RenderTiles --targetDir {1} --tileSize {2} \
{3} {4} --outputType {5} {6} --url {7}' .format(\
jar_file, output_dir, tile_size, threads_str, blend_str, output_type, pattern_str, tiles_url)
utils.execute_shell_command(java_cmd)
def normalize_coordinates(tile_fnames_or_dir, output_dir, jar_file):
all_files = []
for file_or_dir in tile_fnames_or_dir:
if not os.path.exists(file_or_dir):
print("{0} does not exist (file/directory), skipping".format(file_or_dir))
continue
if os.path.isdir(file_or_dir):
actual_dir_files = glob.glob(os.path.join(file_or_dir, '*.json'))
all_files.extend(actual_dir_files)
else:
all_files.append(file_or_dir)
if len(all_files) == 0:
print "No files for normalization found. Exiting."
return
print "Normalizing coordinates of {0} files".format(all_files)
files_urls = []
for file_name in all_files:
tiles_url = utils.path2url(file_name)
files_urls.append(tiles_url)
list_file = os.path.join(output_dir, "all_files.txt")
print "list_file", list_file
utils.write_list_to_file(list_file, files_urls)
list_file_url = utils.path2url(list_file)
java_cmd = 'java -Xmx3g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.NormalizeCoordinates --targetDir {1} {2}'.format(
jar_file, output_dir, list_file_url)
utils.execute_shell_command(java_cmd)
def create_meshes(tiles_fname, output_dir, jar_file, threads_num=4):
tiles_url = utils.path2url(os.path.abspath(tiles_fname))
# Compute the Sift features `for each tile in the tile spec file
java_cmd = 'java -Xmx32g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.SaveMesh --targetDir {1} --threads {2} --inputfile {3}'.format(\
jar_file, output_dir, threads_num, tiles_url)
utils.execute_shell_command(java_cmd)
def match_multiple_sift_features(tiles_file, features_file, index_pairs, jar,
out_fname, conf_args):
tiles_url = utils.path2url(os.path.abspath(tiles_file))
java_cmd = 'java -Xmx4g -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.MatchSiftFeatures --tilespecfile {1} --featurefile {2} {3} --targetPath {4} {5}'.format(
jar, tiles_url, features_file,
" ".join("--indices {}:{}".format(a, b) for a, b in index_pairs),
out_fname, conf_args)
utils.execute_shell_command(java_cmd)
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 block_matching_test_params(tile_files, jar_file, conf=None, threads_num=4):
#conf_args = utils.conf_args(conf, 'MatchLayersByMaxPMCC')
java_cmd = 'java -Xmx16g -XX:ParallelGCThreads=1 -cp "{0}" org.janelia.alignment.TestBlockMatchingParameters --tilespecFiles {1} \
--threads {2} {3}'.format(
jar_file, " ".join(utils.path2url(f) for f in tile_files), threads_num,
conf)
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 render_2d(tiles_fname, output_fname, width, jar_file, threads_num=None):
tiles_url = utils.path2url(tiles_fname)
threads_str = ""
if threads_num is not None:
threads_str = "--threads {}".format(threads_num)
width_str = "--width {}".format(width)
if width == -1:
width_str = "--fullImage"
java_cmd = 'java -Xmx32g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.Render --out {1} {2} \
{3} --hide --url {4}'.format(\
jar_file, output_fname, width_str, threads_str, tiles_url)
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 render_3d(tile_fnames_or_dir_fname,
output_dir,
from_layer,
to_layer,
scale,
from_x,
from_y,
to_x,
to_y,
jar_file,
threads_num=1):
list_file_url = utils.path2url(tile_fnames_or_dir_fname)
java_cmd = 'java -Xmx32g -XX:ParallelGCThreads=1 -cp "{0}" org.janelia.alignment.Render3D --targetDir {1} --scale {2} \
--threads {3} --fromLayer {4} --toLayer {5} --fromX {6} --fromY {7} --toX {8} --toY {9} --hide {10}' .format(\
jar_file, output_dir, scale, threads_num, from_layer, to_layer,
from_x, from_y, to_x, to_y, list_file_url)
utils.execute_shell_command(java_cmd)
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 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)
def update_bounding_box(tiles_fname, output_dir, jar_file, threads_num=1):
tiles_url = utils.path2url(tiles_fname)
java_cmd = 'java -Xmx9g -XX:ParallelGCThreads=1 -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.UpdateBoundingBox --threads {1} --targetDir {2} {3}'.format(\
jar_file, threads_num, output_dir, tiles_url)
utils.execute_shell_command(java_cmd)
def call_java_debug_match_pmcc(input_file, out_dir, jar_file):
input_url = utils.path2url(os.path.abspath(input_file))
java_cmd = 'java -Xmx4g -Djava.awt.headless=true -cp "{0}" org.janelia.alignment.DebugCorrespondence --inputfile {1} --targetDir {2}'.format(\
jar_file, input_url, out_dir)
utils.execute_shell_command(java_cmd)
