def write(filename, source, header=None, **kwargs):
"""Write data into to raw/mhd file pair
Arguments
---------
filename : str
The file name of the raw/mhd file.
source : source specification
The source to write as mhd/raw file.
Returns
-------
filename : str
The filename of the mhd file.
"""
import ClearMap.IO.IO as io
fext = io.file_extension(filename)
if fext == "raw":
header_name = filename[:-3] + 'mhd'
raw_name = filename
elif fext == 'mhd':
header_name = filename
raw_name = filename[:-3] + 'raw'
else:
header_name = filename + '.mhd'
raw_name = filename + '.raw'
hdm_header = header_from_source(source, header=header)
write_header(header_name, hdm_header)
write_raw(raw_name, source)
return header_name
def write_color_palette(filename=None):
"""Creates a pal or lut file for imaris or imagej based on label colors of atlas.
Arguments
---------
filename : str
The name of the color palette file.
Returns
-------
filename : str
The name of the file to which the color palette was written.
"""
cm = color_map(alpha=False, as_int=True)
fext = io.file_extension(filename)
if fext == 'pal':
col.write_PAL(filename, cm)
elif fext == 'lut':
col.write_LUT(filename, cm)
else:
raise RuntimeError('color pallete format: %s not lut or pal' % fext)
return filename
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);