def prepare_annotation_files(slicing=None,
orientation=None,
directory=None,
postfix=None,
annotation_file=None,
reference_file=None,
distance_to_surface_file=None,
overwrite=False,
verbose=False):
"""Crop the annotation, reference and distance files to match the data.
Arguments
---------
slicing : tuple or None
The slice specification after reorienting.
orientation : tuple, str or None.
The orientation specification. Strings can be 'left' or 'right', for the
two hemispheres.
directory : str or None
The target directory. If None, use ClearMap resources folder.
postfix : str or None
Use this postfix for the cropped annotation file. If None and automatic
label is choosen.
annotation_file : str or None
The annotation file to use.
reference_file : str or None
The reference file to use.
distance_to_surface_file : str or None
The distance file to use.
overwrite : bool
If True, overwrite exisitng files.
Returns
-------
annotation_file : str
The cropped annotation file.
reference_file : str
The cropped reference file.
distance_to_surface_file : str
The distance cropped file.
"""
if annotation_file is None:
annotation_file = default_annotation_file
if reference_file is None:
reference_file = default_reference_file
if distance_to_surface_file is None:
distance_to_surface_file = default_distance_to_surface_file
files = [annotation_file, reference_file, distance_to_surface_file]
results = []
for f in files:
if f is not None:
fn = format_annotation_filename(f,
orientation=orientation,
slicing=slicing,
postfix=postfix,
directory=directory)
if verbose:
print('Preparing: %r' % fn)
if not overwrite and io.is_file(fn):
results.append(fn)
continue
if not io.is_file(f):
raise ValueError('Cannot find annotation file: %s' % f)
s = io.as_source(f)
if verbose:
print('Preparing: from source %r' % s)
data = np.array(s.array)
if not orientation is None:
#permute
per = res.orientation_to_permuation(orientation)
data = data.transpose(per)
#reverse axes
reslice = False
sl = [slice(None)] * data.ndim
for d, o in enumerate(orientation):
if o < 0:
sl[d] = slice(None, None, -1)
reslice = True
if reslice:
data = data[tuple(sl)]
if slicing is not None:
data = data[slicing]
io.write(fn, data)
results.append(fn)
else:
results.append(None)
return results
def info(self, tile_axes = None, check_extensions = True):
s = self.__str__() + '\n';
l = np.max([len(k) for k in self.file_type_to_name]);
l = '%' + '%d' % l + 's';
for k,v in self.file_type_to_name.items():
if len(te.Expression(v).tags) > 0:
if check_extensions:
files = self.file_list(k, extension='*');
extensions = [io.file_extension(f) for f in files];
extensions = np.unique(extensions);
#print(extensions)
else:
extensions = [self.extension(k)];
if len(extensions) == 0:
s += l % k + ': no file\n';
else:
kk = k;
for extension in extensions:
expression = te.Expression(self.filename(k, extension=extension));
tag_names = expression.tag_names();
if tile_axes is None:
tile_axes_ = tag_names;
else:
tile_axes_ = tile_axes;
for n in tile_axes_:
if not n in tag_names:
raise ValueError('The expression does not have the named pattern %s' % n);
for n in tag_names:
if not n in tile_axes_:
raise ValueError('The expression has the named pattern %s that is not in tile_axes=%r' % (n, tile_axes_));
#construct tiling
files = io.file_list(expression);
if len(files) > 0:
tile_positions = [expression.values(f) for f in files];
tile_positions = [tuple(tv[n] for n in tile_axes_) for tv in tile_positions];
tile_lower = tuple(np.min(tile_positions, axis = 0));
tile_upper = tuple(np.max(tile_positions, axis = 0));
tag_names = tuple(tag_names);
if kk is not None:
s += (l % kk) + ': '
kk = None;
else:
s += (l % '') + ' '
s+= ('%s {%d files, %r: %r -> %r}' % (expression.string()[len(self.directory)+1:], len(files), tag_names, tile_lower, tile_upper)) + '\n';
else:
fname = self.filename(k);
files = [];
if io.is_file(fname):
files += [fname];
fname = self.filename(k, postfix = '*');
files += io.file_list(fname);
if len(files) > 0:
files = [f[len(self.directory)+1:] for f in files]
s += l % k + ': ' + files[0] + '\n'
for f in files[1:]:
s += l % '' + ' ' + f + '\n'
else:
s += l % k + ': no file\n';
print(s);
def write(sink,
source,
slicing=None,
overwrite=True,
blocks=None,
processes=None,
verbose=False):
"""Write a large array to disk in parallel.
Arguments
---------
sink : str or Source
The sink on disk to write to.
source : array or Source
The data to write to disk.
slicing : slicing or None
Optional slicing for the sink to write to.
overwrite : bool
If True, create new file if the source specifications do not match.
blocks : int or None
Number of blocks to split array into for parallel processing.
processes : None or int
Number of processes, if None use number of cpus.
verbose : bool
Print info about the file to be loaded.
Returns
-------
sink : Source class
The sink to which the source was written.
"""
processes, timer, blocks = initialize_processing(processes=processes,
verbose=verbose,
function='write',
blocks=blocks,
return_blocks=True)
source, source_buffer, source_order = initialize_source(source,
as_1d=True,
return_order=True)
try:
sink = io.as_source(sink)
location = sink.location
except:
if isinstance(sink, str):
location = sink
sink = None
else:
raise ValueError(
'Sink is not a valid writable sink specification!')
if location is None:
raise ValueError('Sink is not a valid writable sink specification!')
if slicing is not None:
if not io.is_file(location):
raise ValueError(
'Cannot write a slice to a non-existent sink %s!' % location)
sink = slc.Slice(source=sink, slicing=slicing)
else:
if io.is_file(location):
mode = None
if (sink.shape != source.shape or sink.dtype != source.dtype
or sink.order != source_order):
if overwrite:
mode = 'w+'
else:
raise ValueError(
'Sink file %s exists but does not match source!')
sink_shape = source.shape
sink_dtype = source.dtype
sink_order = source.order
sink = None
else:
sink_shape = None
sink_dtype = None
sink_order = None
mode = None
sink = initialize_sink(sink=sink,
location=location,
shape=sink_shape,
dtype=sink_dtype,
order=sink_order,
mode=mode,
source=source,
return_buffer=False)
sink_order, sink_offset = sink.order, sink.offset
if sink_order not in ['C', 'F']:
raise NotImplementedError(
'Cannot read in parallel from non-contigous source!')
if (source_order != sink_order):
raise RuntimeError('Order of source %r and sink %r do not match!' %
(source_order, sink_order))
#print(source_buffer.shape, location, sink_offset, blocks, processes)
code.write(source_buffer,
location.encode(),
offset=sink_offset,
blocks=blocks,
processes=processes)
finalize_processing(verbose=verbose, function='write', timer=timer)
return sink
def skeletonize(source,
sink=None,
points=None,
method='PK12i',
steps=None,
in_place=False,
verbose=True,
**kwargs):
"""Skeletonize 3d binary arrays.
Arguments
---------
source : array or source
Binary image to skeletonize.
sink : sink specification
Optional sink.
points : array or None
Optional point list of the foreground points in the binary.
method : str
'PK12' or faster index version 'PK12i'.
steps : int or None
Number of maximal iteration steps. If None, maximal thinning.
in_place : bool
If True, the skeletonization is done directly on the input array.
Returns
-------
skeleton : Source
The skeletonized array.
"""
if verbose:
timer = tmr.Timer()
if not in_place and io.is_file(source):
binary_buffer = ap.read(source).as_buffer()
else:
binary, binary_buffer = ap.initialize_source(source)
if not in_place:
binary_buffer = np.array(binary_buffer)
if method == 'PK12':
result = PK12.skeletonize(binary_buffer,
points=points,
steps=steps,
verbose=verbose,
**kwargs)
elif method == 'PK12i':
result = PK12.skeletonize_index(binary_buffer,
points=points,
steps=steps,
verbose=verbose,
**kwargs)
else:
raise RuntimeError('Skeletonizaton method %r is not valid!' % method)
if verbose:
timer.print_elapsed_time(head='Skeletonization')
if sink is None:
sink = ap.io.as_source(result)
elif isinstance(sink, str):
sink = ap.write(sink, result)
else:
sink = io.write(sink, result)
return sink