def __set_loaders_and_savers(self):
""" Get lists of loader and saver positions within the plugin list and
set the number of loaders.
:returns: loader index list and saver index list
:rtype: list(int(loader)), list(int(saver))
"""
from savu.plugins.loaders.base_loader import BaseLoader
from savu.plugins.savers.base_saver import BaseSaver
loader_idx = []
saver_idx = []
self.n_plugins = len(self.plugin_list)
for i in range(self.n_plugins):
bases = inspect.getmro(pu.load_class(self.plugin_list[i]['id']))
loader_list = [b for b in bases if b == BaseLoader]
saver_list = [b for b in bases if b == BaseSaver]
if loader_list:
loader_idx.append(i)
if saver_list:
saver_idx.append(i)
self.loader_idx = loader_idx
self.saver_idx = saver_idx
self.n_loaders = len(loader_idx)
self.n_savers = len(saver_idx)
def _set_parameters(self, args, kwargs, cls, cls_path, extras):
mod = '.'.join(cls_path.split('.')[:-1])
cls = cls_path.split('.')[-1]
func = pu.load_class(mod, cls).__init__
argspec = inspect.getargspec(func)
if len(argspec[0]) - 1 != len(args) + len(kwargs.keys()):
raise Exception('Incorrect number of input arguments mapped.')
data_lists = [
True if isinstance(a, list) and isinstance(a[0], int) else False
for a in args
]
# If there are multiple data objects this is incompatible with
# checkpointing.
ddict = {}
if args.count('self') > 2 or data_lists.count(True):
ddict = None
else:
ddict['args'] = args
ddict['kwargs'] = kwargs
ddict['cls'] = cls_path
ddict['extras'] = extras
return ddict
def _set_data_type(self, dObj, group, nxs_filename):
link = group.get(group.attrs['signal'], getlink=True)
if isinstance(link, h5py._hl.group.HardLink) and \
self.exp.meta_data.get('test_state') is True:
link.filename = nxs_filename
link.path = group.name + '/data'
fname = os.path.join(os.path.dirname(nxs_filename), link.filename)
dObj.backing_file = h5py.File(fname, 'r')
dObj.data = dObj.backing_file[link.path]
if 'data_type' not in group:
return
entry = group['data_type']
args = self._get_data(entry, 'args')
args = [args[''.join(['args', str(i)])] for i in range(len(args))]
args = [a if a != 'self' else dObj for a in args]
kwargs = self._get_data(entry, 'kwargs')
extras = self._get_data(entry, 'extras')
cls = str(self._get_data(entry, 'cls'))
cls_split = cls.split('.')
cls_inst = \
pu.load_class('.'.join(cls_split[:-1]), cls_name=cls_split[-1])
dObj.data = cls_inst(*args, **kwargs)
dObj.data._base_post_clone_updates(dObj.data, extras)
def _set_data_type(self, dObj, group, nxs_filename):
link = group.get(group.attrs['signal'], getlink=True)
if isinstance(link, h5py._hl.group.HardLink) and \
self.exp.meta_data.get('test_state') is True:
link.filename = nxs_filename
link.path = group.name + '/data'
fname = os.path.join(os.path.dirname(nxs_filename), link.filename)
dObj.backing_file = h5py.File(fname, 'r')
dObj.data = dObj.backing_file[link.path]
if 'data_type' not in group:
return
entry = group['data_type']
args = self._get_data(entry, 'args')
args = [args[''.join(['args', str(i)])] for i in range(len(args))]
args = [a if a != 'self' else dObj for a in args]
kwargs = self._get_data(entry, 'kwargs')
extras = self._get_data(entry, 'extras')
cls = str(self._get_data(entry, 'cls'))
cls_split = cls.split('.')
cls_inst = \
pu.load_class('.'.join(cls_split[:-1]), cls_name=cls_split[-1])
dObj.data = cls_inst(*args, **kwargs)
dObj.data._base_post_clone_updates(dObj.data, extras)
def __set_loaders_and_savers(self):
""" Get lists of loader and saver positions within the plugin list and
set the number of loaders.
:returns: loader index list and saver index list
:rtype: list(int(loader)), list(int(saver))
"""
from savu.plugins.loaders.base_loader import BaseLoader
from savu.plugins.savers.base_saver import BaseSaver
loader_idx = []
saver_idx = []
self.n_plugins = len(self.plugin_list)
for i in range(self.n_plugins):
pid = self.plugin_list[i]['id']
bases = inspect.getmro(pu.load_class(pid))
loader_list = [b for b in bases if b == BaseLoader]
saver_list = [b for b in bases if b == BaseSaver]
if loader_list:
loader_idx.append(i)
if saver_list:
saver_idx.append(i)
self.loader_idx = loader_idx
self.saver_idx = saver_idx
self.n_loaders = len(loader_idx)
self.n_savers = len(saver_idx)
def test_get_plugins_path_and_load(self):
savu_path = os.path.split(savu.__path__[0])[0]
plugin_path = os.path.join(savu_path, "plugin_examples")
os.environ["SAVU_PLUGINS_PATH"] = plugin_path
pu.get_plugins_paths()
plugin = pu.load_class("example_median_filter")()
self.assertEqual(plugin.name, "ExampleMedianFilter")
os.environ["SAVU_PLUGINS_PATH"] = ""
def _contains_gpu_processes(self):
""" Returns True if gpu processes exist in the process list. """
from savu.plugins.driver.gpu_plugin import GpuPlugin
for i in range(self.n_plugins):
bases = inspect.getmro(pu.load_class(self.plugin_list[i]['id']))
if GpuPlugin in bases:
return True
return False
def _contains_gpu_processes(self):
""" Returns True if gpu processes exist in the process list. """
from savu.plugins.driver.gpu_plugin import GpuPlugin
for i in range(self.n_plugins):
bases = inspect.getmro(pu.load_class(self.plugin_list[i]['id']))
if GpuPlugin in bases:
return True
return False
def create_next_instance(self, newObj):
dtype_dict = self.get_map_args()
if dtype_dict is None:
return None
args, kwargs, cls, extras = self._get_parameters(dtype_dict)
args = [newObj if isinstance(a, str) and a == 'self'
else a for a in args]
cls_split = cls.split('.')
mod = '.'.join(cls_split[:-1])
name = cls_split[-1]
cls_inst = pu.load_class(mod, cls_name=name)
newObj.data = cls_inst(*args, **kwargs)
self._base_post_clone_updates(newObj.data, extras)
def create_next_instance(self, newObj):
dtype_dict = self.get_map_args()
if dtype_dict is None:
return None
args, kwargs, cls, extras = self._get_parameters(dtype_dict)
args = [newObj if isinstance(a, str) and a == 'self'
else a for a in args]
cls_split = cls.split('.')
mod = '.'.join(cls_split[:-1])
name = cls_split[-1]
cls_inst = pu.load_class(mod, cls_name=name)
newObj.data = cls_inst(*args, **kwargs)
self._base_post_clone_updates(newObj.data, extras)
def _contains_gpu_processes(self):
""" Returns True if gpu processes exist in the process list. """
try:
from savu.plugins.driver.gpu_plugin import GpuPlugin
for i in range(self.n_plugins):
bases = inspect.getmro(pu.load_class(self.plugin_list[i]['id']))
if GpuPlugin in bases:
return True
except ImportError as ex:
if "pynvml" in ex.message:
logging.error('Error while importing GPU dependencies: %s',
ex.message)
else:
raise
return False
def _contains_gpu_processes(self):
""" Returns True if gpu processes exist in the process list. """
try:
from savu.plugins.driver.gpu_plugin import GpuPlugin
for i in range(self.n_plugins):
bases = inspect.getmro(pu.load_class(self.plugin_list[i]['id']))
if GpuPlugin in bases:
return True
except ImportError as ex:
if "pynvml" in ex.message:
logging.error('Error while importing GPU dependencies: %s',
ex.message)
else:
raise
return False
def set_plugin_list(options, pnames, *args):
args = args[0] if args else None
plugin_names = pnames if isinstance(pnames, list) else [pnames]
options['plugin_list'] = []
ID = [options['loader']]
data = [{}, {}] if not args else [args[0], args[-1]]
for i in range(len(plugin_names)):
ID.insert(i + 1, plugin_names[i])
plugin = pu.load_class(plugin_names[i])()
data_dict = set_data_dict(['tomo'], get_output_datasets(plugin))
data_dict = args[i + 1] if args else data_dict
data.insert(i + 1, data_dict)
for i in range(len(ID)):
name = \
''.join(x.capitalize() for x in (ID[i].split('.')[-1]).split('_'))
options['plugin_list'].append(set_plugin_entry(name, ID[i], data[i],
i))
def _add_missing_savers(self, exp):
""" Add savers for missing datasets. """
data_names = exp.index['in_data'].keys()
saved_data = []
for i in self._get_savers_index():
saved_data.append(self.plugin_list[i]['data']['in_datasets'])
saved_data = set([s for sub_list in saved_data for s in sub_list])
for name in [data for data in data_names if data not in saved_data]:
pos = exp.meta_data.get('nPlugin') + 1
exp.meta_data.set('nPlugin', pos)
process = {}
plugin = pu.load_class('savu.plugins.savers.hdf5_saver')()
plugin.parameters['in_datasets'] = [name]
process['name'] = plugin.name
process['id'] = plugin.__module__
process['pos'] = str(pos + 1)
process['data'] = plugin.parameters
process['active'] = True
process['desc'] = plugin.parameters_desc
self._add(pos + 1, process)
def _set_parameters(self, args, kwargs, cls, cls_path, extras):
mod = '.'.join(cls_path.split('.')[:-1])
cls = cls_path.split('.')[-1]
func = pu.load_class(mod, cls).__init__
argspec = inspect.getargspec(func)
if len(argspec[0])-1 != len(args) + len(kwargs.keys()):
raise Exception('Incorrect number of input arguments mapped.')
data_lists = [True if isinstance(a, list) and isinstance(a[0], int)
else False for a in args]
# If there are multiple data objects this is incompatible with
# checkpointing.
ddict = {}
if args.count('self') > 2 or data_lists.count(True):
ddict = None
else:
ddict['args'] = args
ddict['kwargs'] = kwargs
ddict['cls'] = cls_path
ddict['extras'] = extras
return ddict
def testGetPlugin(self):
mod = "savu.plugins.plugin"
plugin = pu.load_class(mod)()
self.assertEqual(plugin.__class__, test_plugin.Plugin,
"Failed to load the correct class")
self.assertRaises(NotImplementedError, plugin.process_frames, None)
def test_get_plugin_external_path(self):
savu_path = os.path.split(savu.__path__[0])[0]
mod = os.path.join(savu_path, "plugin_examples",
"example_median_filter.py")
plugin = pu.load_class(mod)()
self.assertEqual(plugin.name, "ExampleMedianFilter")
def testfind_args(self):
mod = "savu.plugins.filters.denoising.denoise_bregman_filter"
plugin = pu.load_class(mod)()
params = doc.find_args(plugin)
self.assertEqual(len(params['param']), 4)
def plugin_setup(self):
ppath = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
plugin = pu.load_class(ppath)()
return plugin
def test_load_plugin(self):
cu.populate_plugins()
plugin_path = pu.dawn_plugins[dawn_plugins.keys()[0]]['path2plugin']
inst = pu.load_class(plugin_path)()
sl = inst.__dict__['slice_list']
exp = inst.__dict__['exp']
