def _init_step_ids(self):
self._step_ids = OrderedDict()
for i, step in enumerate(self._steps):
step_id = step.name ##"%d_%s" % (i, step.name)
self._step_ids[step_id] = step
class Analysis(six.with_metaclass(AnalysisMetaClass, object)):
# XXX the metaclass automatically registers the Analysis class in the
# AnalysisFactory and intializes the param_template_map
def __init__(self, study):
self._init_steps()
self._init_step_ids()
self.study = study
self.pipeline = None
self.parameters = None
def _init_steps(self):
raise NotImplementedError("Analysis is an Abstract class.")
def _init_step_ids(self):
self._step_ids = OrderedDict()
for i, step in enumerate(self._steps):
step_id = step.name ##"%d_%s" % (i, step.name)
self._step_ids[step_id] = step
def step_from_id(self, step_id):
return self._step_ids.get(step_id)
def import_data(self, subject):
raise NotImplementedError("Analysis is an Abstract class. import_data must be redefined.")
def set_parameters(self, subject):
raise NotImplementedError("Analysis is an Abstract class. set_parameters must be redefined.")
def propagate_parameters(self):
raise NotImplementedError("Analysis is an Abstract class. propagate_parameter must be redefined.")
def list_input_parameters_with_existing_files(self):
raise NotImplementedError("Analysis is an Abstract class. list_input_parameters_with_existing_files must be redefined.")
def list_output_parameters_with_existing_files(self):
raise NotImplementedError("Analysis is an Abstract class. list_output_parameters_with_existing_files must be redefined.")
def has_some_results(self, step_ids=None):
raise NotImplementedError("Analysis is an Abstract class. has_some_results must be redefined.")
def has_all_results(self, step_ids=None):
raise NotImplementedError("Analysis is an Abstract class. has_all_results must be redefined.")
def existing_results(self, step_ids=None):
raise NotImplementedError("Analysis is an Abstract class. existing_results must be redefined.")
def clear_results(self, step_ids=None):
to_remove = self.existing_results(step_ids)
for filename in to_remove:
filenames = self._files_for_format(filename)
for f in filenames:
if os.path.isfile(f):
os.remove(f)
elif os.path.isdir(f):
shutil.rmtree(f)
def _files_for_format(self, filename):
ext_map = {
'ima': ['ima', 'dim'],
'img': ['img', 'hdr'],
'arg': ['arg', 'data'],
}
ext_pos = filename.rfind('.')
if ext_pos < 0:
return [filename, filename + '.minf']
ext = filename[ext_pos + 1:]
exts = ext_map.get(ext, [ext])
fname_base = filename[:ext_pos + 1]
return [fname_base + ext for ext in exts] + [filename + '.minf']
def convert_from_formats(self, old_volumes_format, old_meshes_format):
# TODO: use aims/somaio IO system for formats extensions
exts = [['.nii'], ['.nii.gz'], ['.img', '.hdr'], ['.ima', '.dim'],
['.dcm'], ['.mnc'],
['.gii'], ['.mesh'], ['.ply']]
vol_formats = ['.nii', '.nii.gz', '.img', '.ima', '.dcm', '.mnc']
mesh_formats = ['.gii', '.mesh', '.ply']
def _convert_data(old_name, new_name):
print('converting:', old_name, 'to:', new_name)
data = aims.read(old_name)
aims.write(data, new_name)
def _remove_data(name):
for fexts in exts:
for ext in fexts:
if name.endswith(ext):
basename = name[:-len(ext)]
real_exts = fexts + [fexts[0] + '.minf']
for cext in real_exts:
filename = basename + cext
if os.path.isdir(filename):
print('rmtree', filename)
shutil.rmtree(filename)
elif os.path.exists(filename):
print('rm', filename)
os.unlink(filename)
def _look_for_other_formats(value, new_value):
old_format = [fext[0] for fext in exts
if value.endswith(fext[0])]
if len(old_format) == 0:
return value
old_format = old_format[0]
if old_format in vol_formats:
dtype = 0
elif old_format in mesh_formats:
dtype = 1
else:
return value
typed_formats = [vol_formats, mesh_formats]
old_base = value[:-len(old_format)]
for fexts in exts:
if not fexts[0] in typed_formats[dtype]:
continue
if not isinstance(new_value, basestring) \
or not new_value.endswith(fexts[0]):
for ext in fexts:
new_old_value = old_base + ext
if not os.path.exists(new_old_value):
# not OK
break
else:
# found matching format
return old_base + fexts[0]
return value
print('convert analysis', self.subject, 'from formats:',
old_volumes_format, old_meshes_format, 'to:',
self.study.volumes_format, self.study.meshes_format)
#if old_volumes_format == self.study.volumes_format \
#and old_meshes_format == self.study.meshes_format:
#print(' nothing to do.')
#return
old_params = self.parameters
# force re-running FOM
self.set_parameters(self.subject)
todo = [(old_params, self.parameters)]
while todo:
old_dict, new_dict = todo.pop(0)
old_state = old_dict.get('state', {})
new_state = new_dict.get('state', {})
for key, value in six.iteritems(old_state):
if isinstance(value, basestring):
new_value = new_state.get(key)
if not os.path.exists(value) \
and (not isinstance(new_value, basestring)
or not os.path.exists(new_value)):
value = _look_for_other_formats(value, new_value)
if os.path.exists(value):
if new_value not in ('', None, traits.Undefined) \
and new_value != value:
_convert_data(value, new_value)
if new_value != value:
_remove_data(value)
old_nodes = old_dict.get('nodes', {})
new_nodes = new_dict.get('nodes', {})
if old_nodes:
todo += [(node, new_nodes.get(key, {}))
for key, node in six.iteritems(old_nodes)]