How to use the h5py.SoftLink function in h5py
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cctbx / cctbx_project / xfel / euxfel / agipd_cxigeom2nexus.py View on Github 
quad_slow = slow // self.n_quads
module_fast = quad_fast
module_slow = quad_slow // self.n_modules
asic_fast = module_fast
asic_slow = module_slow // self.n_asics
detector = instrument.create_group('ELE_D0')
detector.attrs['NX_class'] = 'NXdetector'
if 'mask' in h5py.File(self.params.cxi_file, 'r')['entry_1/data_1']:
detector.create_dataset('pixel_mask_applied', (1,), data=[True], dtype='uint32')
detector['pixel_mask'] = h5py.ExternalLink(self.params.cxi_file, "entry_1/data_1/mask")
array_name = 'ARRAY_D0'
alias = 'data'
data_name = 'data'
detector[alias] = h5py.SoftLink('/entry/data/%s'%data_name)
for quad in range(self.n_quads):
q_key = "q%d"%quad
q_name = 'AXIS_D0Q%d'%quad
quad_vector = self.hierarchy[q_key].local_origin.elems
self.create_vector(transformations, q_name, 0.0, depends_on='AXIS_D0', equipment='detector', equipment_component='detector_quad',transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset = quad_vector, offset_units = 'mm')
for module_num in range(self.n_modules):
m_key = "p%d"%((quad*self.n_modules)+module_num)
m_name = 'AXIS_D0Q%dM%d'%(quad, module_num)
module_vector = self.hierarchy[q_key][m_key].local_origin.elems
self.create_vector(transformations, m_name, 0.0, depends_on=q_name, equipment='detector', equipment_component='detector_module',transformation_type='rotation', units='degrees', vector=(0., 0., -1.), offset = module_vector, offset_units = 'mm')
for asic_num in range(self.n_asics):
a_key = "p%da%d"%((quad*self.n_modules)+module_num, asic_num)
a_name = 'AXIS_D0Q%dM%dA%d'%(quad, module_num, asic_num)
asic_vector = self.hierarchy[q_key][m_key][a_key]['local_origin'].elemsdef createSoftLink(self, parentUUID, linkPath, link_name):
self.initFile()
if self.readonly:
msg = "Unable to create link (Updates are not allowed)"
self.log.info(msg)
raise IOError(errno.EPERM, msg)
parentObj = self.getGroupObjByUuid(parentUUID)
if parentObj is None:
msg = "Unable to create link, parent UUID: " + parentUUID + " not found"
self.log.info(msg)
raise IOError(errno.ENXIO, msg)
if link_name in parentObj:
# link already exists
self.log.info("linkname already exists, deleting")
del parentObj[link_name] # delete old link
parentObj[link_name] = h5py.SoftLink(linkPath)
now = time.time()
self.setCreateTime(parentUUID, objType="link", name=link_name, timestamp=now)
self.setModifiedTime(parentUUID, objType="link", name=link_name, timestamp=now)
return Trueattrs = {}
if issubclass(class_, h5py.Dataset):
attrs = dict(self.obj.attrs)
if self.obj.shape == ():
attrs["shape"] = "scalar"
else:
attrs["shape"] = self.obj.shape
attrs["dtype"] = self.obj.dtype
if self.obj.shape == ():
attrs["value"] = self.obj.value
else:
attrs["value"] = "..."
elif isinstance(self.obj, h5py.ExternalLink):
attrs["linked path"] = self.obj.path
attrs["linked file"] = self.obj.filename
elif isinstance(self.obj, h5py.SoftLink):
attrs["linked path"] = self.obj.path
if len(attrs) > 0:
tooltip = htmlFromDict(attrs)
else:
tooltip = ""
return tooltip"""
if link_name not in h5f:
_logger.debug("Creating link " + link_name + " -> " + target_name)
elif overwrite_data:
_logger.warn("Overwriting " + link_name + " with link to" +
target_name)
del h5f[link_name]
else:
_logger.warn(link_name + " already exist. Can't create link to " +
target_name)
return None
if link_type == "hard":
h5f[link_name] = h5f[target_name]
elif link_type == "soft":
h5f[link_name] = h5py.SoftLink(target_name)
else:
raise ValueError("link_type must be 'hard' or 'soft'")
detector_1 = f['entry_1']['instrument_1']['detector_1']
sample_1 = f['entry_1']['sample_1']
geometry_1 = f['entry_1']['sample_1']['geometry_1']
# Add new data fields
f.create_dataset("cxi_version",data=140)
source_1 = instrument_1.create_group("source_1")
source_1.create_dataset("energy", data=photon_energy_J) # in J
detector_1.create_dataset("distance", data=det_distance)
detector_1.create_dataset("x_pixel_size", data=det_pixelsize)
detector_1.create_dataset("y_pixel_size", data=det_pixelsize)
detector_1["translation"] = h5py.SoftLink('/entry_1/sample_1/geometry_1/translation')
detector_1.create_dataset("corner_position", data=corner_position)
data_1 = entry_1.create_group("data_1")
data_1["data"] = h5py.SoftLink('/entry_1/instrument_1/detector_1/data')
data_1["translation"] = h5py.SoftLink('/entry_1/sample_1/geometry_1/translation')
# These are optional data that should be provided (if known)
# ----------------------------------------------------------
source_1.create_dataset("illumination", data=sim.get_illumination())
#detector_1.create_dataset("Fillumination_mask", data=illumination_intensities_mask)
#detector_1.create_dataset("solution", data=sim.obj)
#detector_1.create_dataset("initial_image",data=initial_image)
# Close CXI file and exit
f.close()if src_obj_id_hash in srcid_desobj_map:
des_obj = srcid_desobj_map[src_obj_id_hash]
logging.debug("creating hardlink to {}".format(des_obj.id.id))
gdes[title] = des_obj
else:
msg = "could not find map item to src id: {}".format(src_obj_id_hash)
logging.warn(msg)
if ctx["verbose"]:
print("WARNING: " + msg)
elif link_classname == "SoftLink":
msg = "creating SoftLink({}) with title: {}".format(lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
soft_link = h5py.SoftLink(lnk.path)
else:
soft_link = h5pyd.SoftLink(lnk.path)
gdes[title] = soft_link
elif link_classname == "ExternalLink":
msg = "creating ExternalLink({}, {}) with title: {}".format(lnk.filename, lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
ext_link = h5py.ExternalLink(lnk.filename, lnk.path)
else:
ext_link = h5pyd.ExternalLink(lnk.filename, lnk.path)
gdes[title] = ext_link
else:
msg = "Unexpected link type: {}".format(lnk.__class__.__name__)
logging.warning(msg)dim1.attrs["long_name"] = dim1_long_name
dim2.attrs["long_name"] = dim2_long_name
else:
# spectrum stack -> n_rows, n_columns, n_channels
dim0_long_name = "y"
dim1_long_name = "x"
dim2_long_name = "channels"
dim1 = map_.require_dataset(dim1_name,
shape=(data.shape[1],),
dtype=numpy.float32)
dim0 = map_.require_dataset(dim0_name,
shape=(data.shape[0],),
dtype=numpy.float32)
dim0[:] = xScale[0] + xScale[1] * len(dim0)
dim1[:] = yScale[0] + yScale[1] * len(dim1)
map_[dim2_name] = h5py.SoftLink(h5g["channels"].name)
dim2 = map_[dim2_name]
dim0.attrs["long_name"] = dim0_long_name
dim1.attrs["long_name"] = dim1_long_name
axes = [dim0_name, dim1_name, dim2_name]
map_.attrs["axes"] = numpy.array(axes, dtype=strdtype)
# set the default detector plot
att = "default"
if att not in h5g.attrs:
h5g.attrs[att] = u"map"
# should make use of standard HDF5 scales and labeling
# instead of (or in addition to) the NeXus approach?
USE_HDF5_SCALES = False
if USE_HDF5_SCALES:
dim0.make_scale(dim0_long_name):param h5py.Group data:
:param list(3-tuple) axes: name(str), value(None,h5py.Dataset,numpy.ndarray), attrs(dict)
:param bool append:
"""
raiseIsNotNxClass(data, u'NXdata')
if append:
newaxes = data.attrs.get('axes', [])
else:
newaxes = []
for name, value, attrs in axes:
if value is None:
pass # is or will be created elsewhere
elif isinstance(value, h5py.Dataset):
if value.parent != data:
data[name] = h5py.SoftLink(value.name)
elif isinstance(value, dict):
data.create_dataset(name, **value)
else:
data[name] = value
if attrs:
data[name].attrs.update(attrs)
newaxes.append(name)
if newaxes:
data.attrs['axes'] = asNxChar(newaxes)
updated(data)
