def _create_fit_datasets(self):
"""
Creates the HDF5 fit dataset. pycroscopy requires that the h5 group, guess dataset,
corresponding spectroscopic and position datasets be created and populated at this point.
This function will create the HDF5 dataset for the fit and link it to same ancillary datasets as the guess.
The fit dataset will NOT be populated here but will instead be populated using the __setData function
"""
if self._h5_guess is None or self.h5_results_grp is None:
warn('Need to guess before fitting!')
return
"""
Once the guess is complete, the last_pixel attribute will be set to complete for the group.
Once the fit is initiated, during the creation of the status dataset, this last_pixel
attribute will be used and it wil make the fit look like it was already complete. Which is not the case.
This is a problem of doing two processes within the same group.
Until all legacy is removed, we will simply reset the last_pixel attribute.
"""
self.h5_results_grp.attrs['last_pixel'] = 0
write_simple_attrs(self.h5_results_grp, self.parms_dict)
# Create the fit dataset as an empty dataset of the same size and dtype
# as the guess.
# Also automatically links in the ancillary datasets.
self._h5_fit = USIDataset(create_empty_dataset(self._h5_guess,
dtype=sho32,
dset_name='Fit'))
self._h5_fit.file.flush()
if self.verbose and self.mpi_rank == 0:
print('Finished creating Fit dataset')
def _write_results_chunk(self):
"""
Writes the labels and mean response to the h5 file
Returns
---------
h5_group : HDF5 Group reference
Reference to the group that contains the decomposition results
"""
h5_decomp_group = create_results_group(self.h5_main, self.process_name)
write_simple_attrs(h5_decomp_group, self.parms_dict)
write_simple_attrs(h5_decomp_group, {'n_components': self.__components.shape[0],
'n_samples': self.h5_main.shape[0], 'last_pixel': self.h5_main.shape[0]})
decomp_desc = Dimension('Endmember', 'a. u.', self.__components.shape[0])
# equivalent to V - compound / complex
h5_components = write_main_dataset(h5_decomp_group, self.__components, 'Components',
get_attr(self.h5_main, 'quantity')[0], 'a.u.', decomp_desc,
None,
h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals)
# equivalent of U - real
h5_projections = write_main_dataset(h5_decomp_group, np.float32(self.__projection), 'Projection', 'abundance',
'a.u.', None, decomp_desc, dtype=np.float32,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals)
# return the h5 group object
self.h5_results_grp = h5_decomp_group
return self.h5_results_grp
def _create_guess_datasets(self):
"""
Creates the h5 group, guess dataset, corresponding spectroscopic datasets and also
links the guess dataset to the spectroscopic datasets.
"""
h5_group = create_results_group(self.h5_main, 'SHO_Fit')
write_simple_attrs(h5_group, {'SHO_guess_method': "pycroscopy BESHO"})
h5_sho_inds, h5_sho_vals = write_reduced_spec_dsets(
h5_group, self.h5_main.h5_spec_inds, self.h5_main.h5_spec_vals,
self._fit_dim_name)
self.h5_guess = write_main_dataset(
h5_group, (self.h5_main.shape[0], self.num_udvs_steps),
'Guess',
'SHO',
'compound',
None,
None,
h5_pos_inds=self.h5_main.h5_pos_inds,
h5_pos_vals=self.h5_main.h5_pos_vals,
h5_spec_inds=h5_sho_inds,
h5_spec_vals=h5_sho_vals,
chunks=(1, self.num_udvs_steps),
dtype=sho32,
main_dset_attrs=self._parms_dict,
verbose=self._verbose)
write_simple_attrs(self.h5_guess, {
'SHO_guess_method': "pycroscopy BESHO",
'last_pixel': 0
})
copy_region_refs(self.h5_main, self.h5_guess)
def _translate_image_stack(self, meas_grp, gwy_data, obj, channels):
"""
Use this function to write data corresponding to a stack of scan images (most common)
Returns
-------
"""
current_channel = ''
# Iterate through each object in the gwy dataset
gwy_key = obj.split('/')
# Test whether a new channel needs to be created
# The 'filename' structure in the gwy file should not have a channel created hence the try/except block
try:
if int(gwy_key[1]) not in channels.keys():
current_channel = create_indexed_group(meas_grp, "Channel")
channels[int(gwy_key[1])] = current_channel
else:
current_channel = channels[int(gwy_key[1])]
except ValueError:
if obj.endswith('filename'):
pass
# The data structure of the gwy file will be used to create the main dataset in the h5 file
if obj.endswith('data'):
x_range = gwy_data[obj].get('xreal', 1.0)
x_vals = np.linspace(0, x_range, gwy_data[obj]['xres'])
# print('obj {}\nx_vals {}'.format(obj, x_vals))
y_range = gwy_data[obj].get('yreal', 1.0)
y_vals = np.linspace(0, y_range, gwy_data[obj]['yres'])
pos_desc = [Dimension('X',
gwy_data[obj]['si_unit_xy'].get('unitstr'),
x_vals),
Dimension('Y',
gwy_data[obj]['si_unit_xy'].get('unitstr'),
y_vals)]
# print(pos_desc)
spec_dim = gwy_data['/{}/data/title'.format(gwy_key[1])]
spec_desc = Dimension(spec_dim,
gwy_data[obj]['si_unit_z'].get('unitstr', 'arb. units'),
[0])
two_dim_image = gwy_data[obj]['data']
write_main_dataset(current_channel,
np.atleast_2d(np.reshape(two_dim_image,
len(pos_desc[0].values) * len(pos_desc[1].values))).transpose(),
'Raw_Data',
spec_dim,
gwy_data[obj]['si_unit_z'].get('unitstr'),
pos_desc, spec_desc)
# print('main dataset has been written')
# image data processing
elif obj.endswith('meta'):
meta = {}
write_simple_attrs(current_channel, meta, verbose=False)
return channels
def _translate_gsf(self, file_path, meas_grp):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gsf file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gsf.html
"""
# Read the data in from the specified file
gsf_meta, gsf_values = gsf_read(file_path)
# Write parameters where available specifically for sample_name
# data_type, comments and experiment_date to file-level parms
# Using pop, move some global parameters from gsf_meta to global_parms:
self.global_parms['data_type'] = 'Gwyddion_GSF'
self.global_parms['comments'] = gsf_meta.get('comment', '')
self.global_parms['experiment_date'] = gsf_meta.get('date', '')
# overwrite some parameters at the file level:
write_simple_attrs(meas_grp.parent, self.global_parms)
# Build the reference values for the ancillary position datasets:
# TODO: Remove information from parameters once it is used meaningfully where it needs to be.
# Here, it is no longer necessary to save XReal anymore so we will pop (remove) it from gsf_meta
x_offset = gsf_meta.get('XOffset', 0)
x_range = gsf_meta.get('XReal', 1.0)
# TODO: Use Numpy wherever possible instead of pure python
x_vals = np.linspace(0, x_range, gsf_meta.get('XRes')) + x_offset
y_offset = gsf_meta.get('YOffset', 0)
y_range = gsf_meta.get('YReal', 1.0)
y_vals = np.linspace(0, y_range, gsf_meta.get('YRes')) + y_offset
# Just define the ancillary position and spectral dimensions. Do not create datasets yet
pos_desc = [Dimension('X', gsf_meta.get('XYUnits', 'arb. units'), x_vals),
Dimension('Y', gsf_meta.get('XYUnits', 'arb. units'), y_vals)]
spec_desc = Dimension('Intensity', gsf_meta.get('ZUnits', 'arb. units'), [1])
"""
You only need to prepare the dimensions for positions and spectroscopic. You do not need to write the
ancillary datasets at this point. write_main_dataset will take care of that. You only need to use
write_ind_val_datasets() for the cases where you may need to reuse the datasets. See the tutorial online.
"""
# Create the channel-level group
chan_grp = create_indexed_group(meas_grp, 'Channel')
write_simple_attrs(chan_grp, gsf_meta)
# Create the main dataset (and the
two_dim_image = gsf_values
write_main_dataset(chan_grp,
np.atleast_2d(np.reshape(two_dim_image,
len(pos_desc[0].values) * len(pos_desc[1].values))).transpose(),
'Raw_Data', gsf_meta.get('Title', 'Unknown'), gsf_meta.get('ZUnits', 'arb. units'),
pos_desc, spec_desc)
def test_check_for_old_guess_incomplete(self):
self.fitter._fitter_name = 'Fitter'
# Set last_pixel to less than number of positions
write_simple_attrs(self.h5_guess, {'last_pixel': np.random.randint(self.h5_guess.shape[0]-1)})
partial, completed = self.fitter._check_for_old_guess()
self.assertEqual(USIDataset(partial[0]), self.h5_guess)
self.assertEqual(completed, [])
def test_check_for_old_guess_complete(self):
self.fitter._fitter_name = 'Fitter'
# Set last_pixel to number of positions
write_simple_attrs(self.h5_guess, {'last_pixel': self.h5_guess.shape[0]})
partial, completed = self.fitter._check_for_old_guess()
self.assertEqual(partial, [])
self.assertEqual(USIDataset(completed[0]), self.h5_guess)
def _write_results_chunk(self):
"""
Writes the labels and mean response to the h5 file
Returns
---------
h5_group : HDF5 Group reference
Reference to the group that contains the clustering results
"""
print('Writing clustering results to file.')
num_clusters = self.__mean_resp.shape[0]
h5_cluster_group = create_results_group(self.h5_main, self.process_name)
write_simple_attrs(h5_cluster_group, self.parms_dict)
h5_cluster_group.attrs['last_pixel'] = self.h5_main.shape[0]
h5_labels = write_main_dataset(h5_cluster_group, np.uint32(self.__labels.reshape([-1, 1])), 'Labels',
'Cluster ID', 'a. u.', None, Dimension('Cluster', 'ID', 1),
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals,
aux_spec_prefix='Cluster_', dtype=np.uint32)
if self.num_comps != self.h5_main.shape[1]:
'''
Setup the Spectroscopic Indices and Values for the Mean Response if we didn't use all components
Note that a sliced spectroscopic matrix may not be contiguous. Let's just lose the spectroscopic data
for now until a better method is figured out
'''
"""
if isinstance(self.data_slice[1], np.ndarray):
centroid_vals_mat = h5_centroids.h5_spec_vals[self.data_slice[1].tolist()]
else:
centroid_vals_mat = h5_centroids.h5_spec_vals[self.data_slice[1]]
ds_centroid_values.data[0, :] = centroid_vals_mat
"""
if isinstance(self.data_slice[1], np.ndarray):
vals_slice = self.data_slice[1].tolist()
else:
vals_slice = self.data_slice[1]
vals = self.h5_main.h5_spec_vals[:, vals_slice].squeeze()
new_spec = Dimension('Original_Spectral_Index', 'a.u.', vals)
h5_inds, h5_vals = write_ind_val_dsets(h5_cluster_group, new_spec, is_spectral=True)
else:
h5_inds = self.h5_main.h5_spec_inds
h5_vals = self.h5_main.h5_spec_vals
# For now, link centroids with default spectroscopic indices and values.
h5_centroids = write_main_dataset(h5_cluster_group, self.__mean_resp, 'Mean_Response',
get_attr(self.h5_main, 'quantity')[0], get_attr(self.h5_main, 'units')[0],
Dimension('Cluster', 'a. u.', np.arange(num_clusters)), None,
h5_spec_inds=h5_inds, aux_pos_prefix='Mean_Resp_Pos_',
h5_spec_vals=h5_vals)
return h5_cluster_group
def test_invalid_attrs_dict(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
with h5py.File(file_path, mode='w') as h5_f:
h5_group = h5_f.create_group('Blah')
with self.assertRaises(TypeError):
hdf_utils.write_simple_attrs(
h5_group, ['attrs', 1.234, 'should be dict',
np.arange(3)])
def _translate_force_map(self, h5_meas_grp):
"""
Reads the scan image + force map from the proprietary file and writes it to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# First lets write the image into the measurement group that has already been created:
image_parms = self.meta_data['Ciao image list']
quantity = image_parms.pop('Image Data_2')
image_mat = self._read_image_layer(image_parms)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(
h5_chan_grp,
np.reshape(image_mat, (-1, 1)),
'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity,
'a. u.',
[
Dimension('X', 'nm', image_parms['Samps/line']),
Dimension('Y', 'nm', image_parms['Number of lines'])
],
Dimension('single', 'a. u.', 1),
dtype=np.float32,
compression='gzip')
# Think about standardizing attributes for rows and columns
write_simple_attrs(h5_chan_grp, image_parms)
# Now work on the force map:
force_map_parms = self.meta_data['Ciao force image list']
quantity = force_map_parms.pop('Image Data_4')
force_map_vec = self._read_data_vector(force_map_parms)
tr_rt = [
int(item) for item in force_map_parms['Samps/line'].split(' ')
]
force_map_2d = force_map_vec.reshape(image_mat.size, np.sum(tr_rt))
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(
h5_chan_grp,
force_map_2d,
'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity,
'a. u.',
[
Dimension('X', 'nm', image_parms['Samps/line']),
Dimension('Y', 'nm', image_parms['Number of lines'])
],
Dimension('Z', 'nm', int(np.sum(tr_rt))),
dtype=np.float32,
compression='gzip')
# Think about standardizing attributes
write_simple_attrs(h5_chan_grp, force_map_parms)
def _translate_gwy(self, file_path, meas_grp):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gwy file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gwyfile-format.html
"""
# Need to build a set of channels to test against and a function-level variable to write to
channels = {}
# Read the data in from the specified file
gwy_data = gwyfile.load(file_path)
for obj in gwy_data:
gwy_key = obj.split('/')
try:
# if the second index of the gwy_key can be cast into an int then
# it needs to be processed either as an image or a graph
int(gwy_key[1])
if gwy_key[2] == 'graph':
# graph processing
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Graph'
channels = self._translate_graph(meas_grp, gwy_data, obj,
channels)
elif obj.endswith('data'):
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Image'
channels = self._translate_image_stack(
meas_grp, gwy_data, obj, channels)
else:
continue
except ValueError:
# if the second index of the gwy_key cannot be cast into an int
# then it needs to be processed wither as a spectra, volume or xyz
if gwy_key[1] == 'sps':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Spectra'
channels = self._translate_spectra(meas_grp, gwy_data, obj,
channels)
elif gwy_key[1] == 'brick':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Volume'
channels = self._translate_volume(meas_grp, gwy_data, obj,
channels)
elif gwy_key[1] == 'xyz':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'XYZ'
channels = self._translate_xyz(meas_grp, gwy_data, obj,
channels)
write_simple_attrs(meas_grp.parent, self.global_parms)
def test_none_ignored(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
with h5py.File(file_path, mode='w') as h5_f:
attrs = {'att_1': None}
hdf_utils.write_simple_attrs(h5_f, attrs)
self.assertTrue('att_1' not in h5_f.attrs.keys())
os.remove(file_path)
def _translate_gwy(self, file_path, meas_grp):
"""
Parameters
----------
file_path
meas_grp
For more information on the .gwy file format visit the link below -
http://gwyddion.net/documentation/user-guide-en/gwyfile-format.html
"""
# Need to build a set of channels to test against and a function-level variable to write to
channels = {}
# Read the data in from the specified file
gwy_data = gwyfile.load(file_path)
for obj in gwy_data:
gwy_key = obj.split('/')
try:
# if the second index of the gwy_key can be cast into an int then
# it needs to be processed either as an image or a graph
int(gwy_key[1])
if gwy_key[2] == 'graph':
# graph processing
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Graph'
channels = self._translate_graph(meas_grp, gwy_data,
obj, channels)
elif obj.endswith('data'):
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Image'
channels = self._translate_image_stack(meas_grp, gwy_data,
obj, channels)
else:
continue
except ValueError:
# if the second index of the gwy_key cannot be cast into an int
# then it needs to be processed wither as a spectra, volume or xyz
if gwy_key[1] == 'sps':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Spectra'
channels = self._translate_spectra(meas_grp, gwy_data,
obj, channels)
elif gwy_key[1] == 'brick':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'Volume'
channels = self._translate_volume(meas_grp, gwy_data,
obj, channels)
elif gwy_key[1] == 'xyz':
self.global_parms['data_type'] = 'GwyddionGWY_' + 'XYZ'
channels = self._translate_xyz(meas_grp, gwy_data,
obj, channels)
write_simple_attrs(meas_grp.parent, self.global_parms)
def _write_dset_attributes(h5_dset, attrs, print_log=False):
"""
Writes attributes to a h5py dataset
Parameters
----------
h5_dset : h5py.Dataset object
h5py dataset to which the attributes will be written to.
This function handles region references as well
attrs : dict
Dictionary containing the attributes as key-value pairs
print_log : bool, optional. Default=False
Whether or not to print debugging statements
"""
if not isinstance(attrs, dict):
HDFwriter.__safe_abort(h5_dset.file)
raise TypeError(
'attrs should be a dictionary but is instead of type '
'{}'.format(type(attrs)))
if not isinstance(h5_dset, h5py.Dataset):
raise TypeError(
'h5_dset should be a h5py Dataset object but is instead of type '
'{}. UNABLE to safely abort'.format(type(h5_dset)))
# First, set aside the complicated attribute(s)
attr_dict = attrs.copy()
labels_dict = attr_dict.pop('labels', None)
# Next, write the simple ones using a centralized function
write_simple_attrs(h5_dset,
attr_dict,
obj_type='dataset',
verbose=print_log)
if labels_dict is None:
if print_log:
print('Finished writing all attributes of dataset')
return
if isinstance(labels_dict, (tuple, list)):
# What if the labels dictionary is just a list of names? make a dictionary using the names
# This is the most that can be done.
labels_dict = attempt_reg_ref_build(h5_dset,
labels_dict,
verbose=print_log)
if len(labels_dict) == 0:
if print_log:
warn('No region references to write')
return
# Now, handle the region references attribute:
write_region_references(h5_dset, labels_dict, verbose=print_log)
def _translate_force_curve(self, h5_meas_grp):
"""
Reads the force curves from the proprietary file and writes them to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# since multiple channels will share the same position and spectroscopic dimensions, why not share them?
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(h5_meas_grp,
Dimension(
'single', 'a. u.',
1),
is_spectral=False)
# Find out the size of the force curves from the metadata:
layer_info = None
for class_name in self.meta_data.keys():
if 'Ciao force image list' in class_name:
layer_info = self.meta_data[class_name]
break
tr_rt = [int(item) for item in layer_info['Samps/line'].split(' ')]
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(
h5_meas_grp,
Dimension('Z', 'nm', int(np.sum(tr_rt))),
is_spectral=True)
for class_name in self.meta_data.keys():
if 'Ciao force image list' in class_name:
layer_info = self.meta_data[class_name]
quantity = layer_info.pop('Image Data_4')
data = self._read_data_vector(layer_info)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(
h5_chan_grp,
np.expand_dims(data, axis=0),
'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity,
'a. u.',
None,
None,
dtype=np.float32,
compression='gzip',
h5_pos_inds=h5_pos_inds,
h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds,
h5_spec_vals=h5_spec_vals)
# Think about standardizing attributes
write_simple_attrs(h5_chan_grp, layer_info)
def _translate_image_stack(self, h5_meas_grp):
"""
Reads the scan images from the proprietary file and writes them to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# since multiple channels will share the same position and spectroscopic dimensions, why not share them?
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(h5_meas_grp,
Dimension(
'single', 'a. u.',
1),
is_spectral=True)
# Find out the size of the force curves from the metadata:
layer_info = None
for class_name in self.meta_data.keys():
if 'Ciao image list' in class_name:
layer_info = self.meta_data[class_name]
break
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(h5_meas_grp, [
Dimension('X', 'nm', layer_info['Samps/line']),
Dimension('Y', 'nm', layer_info['Number of lines'])
],
is_spectral=False)
for class_name in self.meta_data.keys():
if 'Ciao image list' in class_name:
layer_info = self.meta_data[class_name]
quantity = layer_info.pop('Image Data_2')
data = self._read_image_layer(layer_info)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(
h5_chan_grp,
np.reshape(data, (-1, 1)),
'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity,
'a. u.',
None,
None,
dtype=np.float32,
compression='gzip',
h5_pos_inds=h5_pos_inds,
h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds,
h5_spec_vals=h5_spec_vals)
# Think about standardizing attributes for rows and columns
write_simple_attrs(h5_chan_grp, layer_info)
def _write_results_chunk(self):
"""
Writes the provided SVD results to file
Parameters
----------
"""
comp_dim = Dimension('Principal Component', 'a. u.', len(self.__s))
h5_svd_group = create_results_group(self.h5_main, self.process_name,
h5_parent_group=self._h5_target_group)
self.h5_results_grp = h5_svd_group
self._write_source_dset_provenance()
write_simple_attrs(h5_svd_group, self.parms_dict)
write_simple_attrs(h5_svd_group, {'svd_method': 'sklearn-randomized'})
h5_u = write_main_dataset(h5_svd_group, np.float32(self.__u), 'U', 'Abundance', 'a.u.', None, comp_dim,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals,
dtype=np.float32, chunks=calc_chunks(self.__u.shape, np.float32(0).itemsize))
# print(get_attr(self.h5_main, 'quantity')[0])
h5_v = write_main_dataset(h5_svd_group, self.__v, 'V', get_attr(self.h5_main, 'quantity')[0],
'a.u.', comp_dim, None, h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals,
chunks=calc_chunks(self.__v.shape, self.h5_main.dtype.itemsize))
# No point making this 1D dataset a main dataset
h5_s = h5_svd_group.create_dataset('S', data=np.float32(self.__s))
'''
Check h5_main for plot group references.
Copy them into V if they exist
'''
for key in self.h5_main.attrs.keys():
if '_Plot_Group' not in key:
continue
ref_inds = get_indices_for_region_ref(self.h5_main, self.h5_main.attrs[key], return_method='corners')
ref_inds = ref_inds.reshape([-1, 2, 2])
ref_inds[:, 1, 0] = h5_v.shape[0] - 1
svd_ref = create_region_reference(h5_v, ref_inds)
h5_v.attrs[key] = svd_ref
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_svd_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_svd_group.attrs['last_pixel'] = self.h5_main.shape[0]
def _create_group(h5_parent_group, micro_group, print_log=False):
"""
Creates a h5py.Group object from the provided VirtualGroup object under h5_new_group and writes all attributes
Parameters
----------
h5_parent_group : h5py.Group object
Parent group under which the new group object will be created
micro_group : VirtualGroup object
Definition for the new group
print_log : bool, optional. Default=False
Whether or not to print debugging statements
Returns
-------
h5_new_group : h5py.Group
The newly created group
"""
if not isinstance(micro_group, VirtualGroup):
HDFwriter.__safe_abort(h5_parent_group.file)
raise TypeError('micro_group should be a VirtualGroup object but is instead of type '
'{}'.format(type(micro_group)))
if not isinstance(h5_parent_group, h5py.Group):
raise TypeError('h5_parent_group should be a h5py.Group object but is instead of type '
'{}'.format(type(h5_parent_group)))
if micro_group.name == '':
HDFwriter.__safe_abort(h5_parent_group.file)
raise ValueError('VirtualGroup object with empty name will not be handled by this function')
# First complete the name of the group by adding the index suffix
if micro_group.indexed:
micro_group.name = assign_group_index(h5_parent_group, micro_group.name, verbose=print_log)
# Now, try to write the group
try:
h5_new_group = h5_parent_group.create_group(micro_group.name)
if print_log:
print('Created Group {}'.format(h5_new_group.name))
except ValueError:
h5_new_group = h5_parent_group[micro_group.name]
if print_log:
print('Found Group already exists {}'.format(h5_new_group.name))
except Exception:
HDFwriter.__safe_abort(h5_parent_group.file)
raise
# Write attributes
write_simple_attrs(h5_new_group, micro_group.attrs, 'group', verbose=print_log)
return h5_new_group
def test_np_array(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
with h5py.File(file_path, mode='w') as h5_f:
attrs = {'att_1': np.random.rand(4)}
hdf_utils.write_simple_attrs(h5_f, attrs)
for key, expected_val in attrs.items():
self.assertTrue(
np.all(hdf_utils.get_attr(h5_f, key) == expected_val))
os.remove(file_path)
def _write_results_chunk(self):
"""
Writes the provided SVD results to file
Parameters
----------
"""
comp_dim = Dimension('Principal Component', 'a. u.', len(self.__s))
h5_svd_group = create_results_group(self.h5_main, self.process_name)
self.h5_results_grp = h5_svd_group
write_simple_attrs(h5_svd_group, self.parms_dict)
write_simple_attrs(h5_svd_group, {'svd_method': 'sklearn-randomized'})
h5_u = write_main_dataset(h5_svd_group, np.float32(self.__u), 'U', 'Abundance', 'a.u.', None, comp_dim,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals,
dtype=np.float32, chunks=calc_chunks(self.__u.shape, np.float32(0).itemsize))
# print(get_attr(self.h5_main, 'quantity')[0])
h5_v = write_main_dataset(h5_svd_group, self.__v, 'V', get_attr(self.h5_main, 'quantity')[0],
'a.u.', comp_dim, None, h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals,
chunks=calc_chunks(self.__v.shape, self.h5_main.dtype.itemsize))
# No point making this 1D dataset a main dataset
h5_s = h5_svd_group.create_dataset('S', data=np.float32(self.__s))
'''
Check h5_main for plot group references.
Copy them into V if they exist
'''
for key in self.h5_main.attrs.keys():
if '_Plot_Group' not in key:
continue
ref_inds = get_indices_for_region_ref(self.h5_main, self.h5_main.attrs[key], return_method='corners')
ref_inds = ref_inds.reshape([-1, 2, 2])
ref_inds[:, 1, 0] = h5_v.shape[0] - 1
svd_ref = create_region_reference(h5_v, ref_inds)
h5_v.attrs[key] = svd_ref
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_svd_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_svd_group.attrs['last_pixel'] = self.h5_main.shape[0]
def _create_guess_datasets(self):
"""
Creates the h5 group, guess dataset, corresponding spectroscopic datasets and also
links the guess dataset to the spectroscopic datasets.
"""
self.h5_results_grp = create_results_group(
self.h5_main,
self.process_name,
h5_parent_group=self._h5_target_group)
write_simple_attrs(self.h5_results_grp, self.parms_dict)
# If writing to a new HDF5 file:
# Add back the data_type attribute - still being used in the visualizer
if self.h5_results_grp.file != self.h5_main.file:
write_simple_attrs(
self.h5_results_grp.file,
{'data_type': get_attr(self.h5_main.file, 'data_type')})
ret_vals = write_reduced_anc_dsets(self.h5_results_grp,
self.h5_main.h5_spec_inds,
self.h5_main.h5_spec_vals,
self._fit_dim_name,
verbose=self.verbose)
h5_sho_inds, h5_sho_vals = ret_vals
self._h5_guess = write_main_dataset(
self.h5_results_grp, (self.h5_main.shape[0], self.num_udvs_steps),
'Guess',
'SHO',
'compound',
None,
None,
h5_pos_inds=self.h5_main.h5_pos_inds,
h5_pos_vals=self.h5_main.h5_pos_vals,
h5_spec_inds=h5_sho_inds,
h5_spec_vals=h5_sho_vals,
chunks=(1, self.num_udvs_steps),
dtype=sho32,
main_dset_attrs=self.parms_dict,
verbose=self.verbose)
# Does not make sense to propagate region refs - nobody uses them
# copy_region_refs(self.h5_main, self._h5_guess)
self._h5_guess.file.flush()
if self.verbose and self.mpi_rank == 0:
print('Finished creating Guess dataset')
def _create_root_image(self, image_path):
"""
Create the Groups and Datasets for a single root image
Parameters
----------
image_path : str
Path to the image file
Returns
-------
None
"""
image, image_parms = read_dm3(image_path)
if image.ndim == 3:
image = np.sum(image, axis=0)
'''
Create the Measurement and Channel Groups to hold the
image Datasets
'''
meas_grp = create_indexed_group(self.h5_f, 'Measurement')
chan_grp = create_indexed_group(meas_grp, 'Channel')
'''
Set the Measurement Group attributes
'''
usize, vsize = image.shape
image_parms['image_size_u'] = usize
image_parms['image_size_v'] = vsize
image_parms['translator'] = 'OneView'
image_parms['num_pixels'] = image.size
write_simple_attrs(meas_grp, image_parms)
'''
Build Spectroscopic and Position dimensions
'''
spec_desc = Dimension('Image', 'a.u.', [1])
pos_desc = [Dimension('X', 'pixel', np.arange(image.shape[0])),
Dimension('Y', 'pixel', np.arange(image.shape[1]))]
h5_image = write_main_dataset(chan_grp, np.reshape(image, (-1, 1)), 'Raw_Data',
'Intensity', 'a.u.',
pos_desc, spec_desc)
self.root_image_list.append(h5_image)
def translate(self, file_path, *args, **kwargs):
# Two kinds of files:
# 1. Simple GSF files -> use metadata, data = gsf_read(file_path)
# 2. Native .gwy files -> use the gwyfile package
# I have a notebook that shows how such data can be read.
# Create the .h5 file from the input file
if not isinstance(file_path, (str, unicode)):
raise TypeError('file_path should be a string!')
if not (file_path.endswith('.gsf') or file_path.endswith('.gwy')):
# TODO: Gwyddion is weird, it doesn't append the file extension some times.
# In theory, you could identify the kind of file by looking at the header (line 38 in gsf_read()).
# Ideally the header check should be used instead of the extension check
raise ValueError('file_path must have a .gsf or .gwy extension!')
file_path = path.abspath(file_path)
folder_path, base_name = path.split(file_path)
base_name = base_name[:-4]
h5_path = path.join(folder_path, base_name + '.h5')
if path.exists(h5_path):
remove(h5_path)
self.h5_file = h5py.File(h5_path, 'w')
"""
Setup the global parameters
---------------------------
translator: Gywddion
data_type: depends on file type
GwyddionGSF_<gsf_meta['title']>
or
GwyddionGWY_<gwy_meta['title']>
"""
self.global_parms = generate_dummy_main_parms()
self.global_parms['translator'] = 'Gwyddion'
# Create the measurement group
meas_grp = create_indexed_group(self.h5_file, 'Measurement')
if file_path.endswith('.gsf'):
self._translate_gsf(file_path, meas_grp)
if file_path.endswith('gwy'):
self._translate_gwy(file_path, meas_grp)
write_simple_attrs(self.h5_file, self.global_parms)
return h5_path
def _create_root_image(self, image_path):
"""
Create the Groups and Datasets for a single root image
Parameters
----------
image_path : str
Path to the image file
Returns
-------
None
"""
image, image_parms = read_dm3(image_path)
if image.ndim == 3:
image = np.sum(image, axis=0)
'''
Create the Measurement and Channel Groups to hold the
image Datasets
'''
meas_grp = create_indexed_group(self.h5_f, 'Measurement')
chan_grp = create_indexed_group(meas_grp, 'Channel')
'''
Set the Measurement Group attributes
'''
usize, vsize = image.shape
image_parms['image_size_u'] = usize
image_parms['image_size_v'] = vsize
image_parms['translator'] = 'OneView'
image_parms['num_pixels'] = image.size
write_simple_attrs(meas_grp, image_parms)
'''
Build Spectroscopic and Position dimensions
'''
spec_desc = Dimension('Image', 'a.u.', [1])
pos_desc = [Dimension('X', 'pixel', np.arange(image.shape[0])),
Dimension('Y', 'pixel', np.arange(image.shape[1]))]
h5_image = write_main_dataset(chan_grp, np.reshape(image, (-1, 1)), 'Raw_Data',
'Intensity', 'a.u.',
pos_desc, spec_desc)
self.root_image_list.append(h5_image)
def _create_projection_datasets(self):
"""
Setup the Loop_Fit Group and the loop projection datasets
"""
# First grab the spectroscopic indices and values and position indices
self._sho_spec_inds = self.h5_main.h5_spec_inds
self._sho_spec_vals = self.h5_main.h5_spec_vals
self._sho_pos_inds = self.h5_main.h5_pos_inds
fit_dim_ind = self.h5_main.spec_dim_labels.index(self._fit_dim_name)
self._fit_spec_index = fit_dim_ind
self._fit_offset_index = 1 + fit_dim_ind
# Calculate the number of loops per position
cycle_start_inds = np.argwhere(self._sho_spec_inds[fit_dim_ind, :] == 0).flatten()
tot_cycles = cycle_start_inds.size
# Make the results group
self._h5_group = create_results_group(self.h5_main, 'Loop_Fit')
write_simple_attrs(self._h5_group, {'projection_method': 'pycroscopy BE loop model'})
# Write datasets
self.h5_projected_loops = create_empty_dataset(self.h5_main, np.float32, 'Projected_Loops',
h5_group=self._h5_group)
h5_loop_met_spec_inds, h5_loop_met_spec_vals = write_reduced_spec_dsets(self._h5_group, self._sho_spec_inds,
self._sho_spec_vals, self._fit_dim_name,
basename='Loop_Metrics')
self.h5_loop_metrics = write_main_dataset(self._h5_group, (self.h5_main.shape[0], tot_cycles), 'Loop_Metrics',
'Metrics', 'compound', None, None, dtype=loop_metrics32,
h5_pos_inds=self.h5_main.h5_pos_inds,
h5_pos_vals=self.h5_main.h5_pos_vals,
h5_spec_inds=h5_loop_met_spec_inds,
h5_spec_vals=h5_loop_met_spec_vals)
# Copy region reference:
copy_region_refs(self.h5_main, self.h5_projected_loops)
copy_region_refs(self.h5_main, self.h5_loop_metrics)
self.h5_main.file.flush()
self._met_spec_inds = self.h5_loop_metrics.h5_spec_inds
return
def _write_dset_attributes(h5_dset, attrs, print_log=False):
"""
Writes attributes to a h5py dataset
Parameters
----------
h5_dset : h5py.Dataset object
h5py dataset to which the attributes will be written to.
This function handles region references as well
attrs : dict
Dictionary containing the attributes as key-value pairs
print_log : bool, optional. Default=False
Whether or not to print debugging statements
"""
if not isinstance(attrs, dict):
HDFwriter.__safe_abort(h5_dset.file)
raise TypeError('attrs should be a dictionary but is instead of type '
'{}'.format(type(attrs)))
if not isinstance(h5_dset, h5py.Dataset):
raise TypeError('h5_dset should be a h5py Dataset object but is instead of type '
'{}. UNABLE to safely abort'.format(type(h5_dset)))
# First, set aside the complicated attribute(s)
attr_dict = attrs.copy()
labels_dict = attr_dict.pop('labels', None)
# Next, write the simple ones using a centralized function
write_simple_attrs(h5_dset, attr_dict, obj_type='dataset', verbose=print_log)
if labels_dict is None:
if print_log:
print('Finished writing all attributes of dataset')
return
if isinstance(labels_dict, (tuple, list)):
# What if the labels dictionary is just a list of names? make a dictionary using the names
# This is the most that can be done.
labels_dict = attempt_reg_ref_build(h5_dset, labels_dict, verbose=print_log)
if len(labels_dict) == 0:
if print_log:
warn('No region references to write')
return
# Now, handle the region references attribute:
write_region_references(h5_dset, labels_dict, verbose=print_log)
def _write_results_chunk(self):
"""
Writes the labels and mean response to the h5 file
Returns
---------
h5_group : HDF5 Group reference
Reference to the group that contains the decomposition results
"""
h5_decomp_group = create_results_group(self.h5_main, self.process_name,
h5_parent_group=self._h5_target_group)
self._write_source_dset_provenance()
write_simple_attrs(h5_decomp_group, self.parms_dict)
write_simple_attrs(h5_decomp_group, {'n_components': self.__components.shape[0],
'n_samples': self.h5_main.shape[0]})
decomp_desc = Dimension('Endmember', 'a. u.', self.__components.shape[0])
# equivalent to V - compound / complex
h5_components = write_main_dataset(h5_decomp_group, self.__components, 'Components',
get_attr(self.h5_main, 'quantity')[0], 'a.u.', decomp_desc,
None,
h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals)
# equivalent of U - real
h5_projections = write_main_dataset(h5_decomp_group, np.float32(self.__projection), 'Projection', 'abundance',
'a.u.', None, decomp_desc, dtype=np.float32,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals)
# return the h5 group object
self.h5_results_grp = h5_decomp_group
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_decomp_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_decomp_group.attrs['last_pixel'] = self.h5_main.shape[0]
return self.h5_results_grp
def _create_guess_datasets(self):
"""
Creates the h5 group, guess dataset, corresponding spectroscopic datasets and also
links the guess dataset to the spectroscopic datasets.
"""
h5_group = create_results_group(self.h5_main, 'SHO_Fit')
write_simple_attrs(h5_group, {'SHO_guess_method': "pycroscopy BESHO"})
h5_sho_inds, h5_sho_vals = write_reduced_spec_dsets(h5_group, self.h5_main.h5_spec_inds,
self.h5_main.h5_spec_vals, self._fit_dim_name)
self.h5_guess = write_main_dataset(h5_group, (self.h5_main.shape[0], self.num_udvs_steps), 'Guess', 'SHO',
'compound', None, None, h5_pos_inds=self.h5_main.h5_pos_inds,
h5_pos_vals=self.h5_main.h5_pos_vals, h5_spec_inds=h5_sho_inds,
h5_spec_vals=h5_sho_vals, chunks=(1, self.num_udvs_steps), dtype=sho32,
main_dset_attrs=self._parms_dict, verbose=self._verbose)
write_simple_attrs(self.h5_guess, {'SHO_guess_method': "pycroscopy BESHO", 'last_pixel': 0})
copy_region_refs(self.h5_main, self.h5_guess)
def _setupH5(self, image_parms):
"""
Setup the HDF5 file in which to store the data
Due to the structure of the ndata format, we can only create the Measurement and Channel groups here
Parameters
----------
image_parms : dict
Dictionary of parameters
Returns
-------
h5_main : h5py.Dataset
HDF5 Dataset that the images will be written into
h5_mean_spec : h5py.Dataset
HDF5 Dataset that the mean over all positions will be written
into
h5_ronch : h5py.Dataset
HDF5 Dateset that the mean over all Spectroscopic steps will be
written into
"""
root_parms = generate_dummy_main_parms()
root_parms['data_type'] = 'PtychographyData'
# Create the hdf5 data Group
write_simple_attrs(self.h5_f, root_parms)
h5_channels = list()
for meas_parms in image_parms:
# Create new measurement group for each set of parameters
meas_grp = create_indexed_group(self.h5_f, 'Measurement')
# Write the parameters as attributes of the group
write_simple_attrs(meas_grp, meas_parms)
chan_grp = create_indexed_group(meas_grp, 'Channel')
h5_channels.append(chan_grp)
self.h5_f.flush()
return h5_channels
def _setupH5(self, image_parms):
"""
Setup the HDF5 file in which to store the data
Due to the structure of the ndata format, we can only create the Measurement and Channel groups here
Parameters
----------
image_parms : dict
Dictionary of parameters
Returns
-------
h5_main : h5py.Dataset
HDF5 Dataset that the images will be written into
h5_mean_spec : h5py.Dataset
HDF5 Dataset that the mean over all positions will be written
into
h5_ronch : h5py.Dataset
HDF5 Dateset that the mean over all Spectroscopic steps will be
written into
"""
root_parms = dict()
root_parms['data_type'] = 'PtychographyData'
# Create the hdf5 data Group
write_simple_attrs(self.h5_f, root_parms)
h5_channels = list()
for meas_parms in image_parms:
# Create new measurement group for each set of parameters
meas_grp = create_indexed_group(self.h5_f, 'Measurement')
# Write the parameters as attributes of the group
write_simple_attrs(meas_grp, meas_parms)
chan_grp = create_indexed_group(meas_grp, 'Channel')
h5_channels.append(chan_grp)
self.h5_f.flush()
return h5_channels
def test_to_grp(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
with h5py.File(file_path, mode='w') as h5_f:
h5_group = h5_f.create_group('Blah')
attrs = {
'att_1': 'string_val',
'att_2': 1.234,
'att_3': [1, 2, 3.14, 4],
'att_4': ['s', 'tr', 'str_3']
}
hdf_utils.write_simple_attrs(h5_group, attrs)
for key, expected_val in attrs.items():
self.assertTrue(
np.all(hdf_utils.get_attr(h5_group, key) == expected_val))
os.remove(file_path)
def _create_fit_datasets(self):
"""
Creates the HDF5 fit dataset. pycroscopy requires that the h5 group, guess dataset,
corresponding spectroscopic and position datasets be created and populated at this point.
This function will create the HDF5 dataset for the fit and link it to same ancillary datasets as the guess.
The fit dataset will NOT be populated here but will instead be populated using the __setData function
"""
if self.h5_guess is None:
warn('Need to guess before fitting!')
return
if self.step_start_inds is None:
h5_spec_inds = self.h5_main.h5_spec_inds
self.step_start_inds = np.where(h5_spec_inds[0] == 0)[0]
if self.num_udvs_steps is None:
self.num_udvs_steps = len(self.step_start_inds)
if self.freq_vec is None:
self._get_frequency_vector()
h5_sho_grp = self.h5_guess.parent
write_simple_attrs(h5_sho_grp, {'SHO_fit_method': "pycroscopy BESHO"})
# Create the fit dataset as an empty dataset of the same size and dtype as the guess.
# Also automatically links in the ancillary datasets.
self.h5_fit = USIDataset(create_empty_dataset(self.h5_guess, dtype=sho32, dset_name='Fit'))
# This is necessary comparing against new runs to avoid re-computation + resuming partial computation
write_simple_attrs(self.h5_fit, self._parms_dict)
write_simple_attrs(self.h5_fit, {'SHO_fit_method': "pycroscopy BESHO", 'last_pixel': 0})
self.h5_fit.file.flush()
def _write_results_chunk(self):
"""
Writes the labels and mean response to the h5 file
Returns
---------
h5_group : HDF5 Group reference
Reference to the group that contains the decomposition results
"""
h5_decomp_group = create_results_group(self.h5_main, self.process_name)
write_simple_attrs(h5_decomp_group, self.parms_dict)
write_simple_attrs(h5_decomp_group, {'n_components': self.__components.shape[0],
'n_samples': self.h5_main.shape[0]})
decomp_desc = Dimension('Endmember', 'a. u.', self.__components.shape[0])
# equivalent to V - compound / complex
h5_components = write_main_dataset(h5_decomp_group, self.__components, 'Components',
get_attr(self.h5_main, 'quantity')[0], 'a.u.', decomp_desc,
None,
h5_spec_inds=self.h5_main.h5_spec_inds,
h5_spec_vals=self.h5_main.h5_spec_vals)
# equivalent of U - real
h5_projections = write_main_dataset(h5_decomp_group, np.float32(self.__projection), 'Projection', 'abundance',
'a.u.', None, decomp_desc, dtype=np.float32,
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals)
# return the h5 group object
self.h5_results_grp = h5_decomp_group
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_decomp_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_decomp_group.attrs['last_pixel'] = self.h5_main.shape[0]
return self.h5_results_grp
def _translate_image_stack(self, h5_meas_grp):
"""
Reads the scan images from the proprietary file and writes them to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# since multiple channels will share the same position and spectroscopic dimensions, why not share them?
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(h5_meas_grp, Dimension('single', 'a. u.', 1), is_spectral=True)
# Find out the size of the force curves from the metadata:
layer_info = None
for class_name in self.meta_data.keys():
if 'Ciao image list' in class_name:
layer_info = self.meta_data[class_name]
break
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(h5_meas_grp, [Dimension('X', 'nm', layer_info['Samps/line']),
Dimension('Y', 'nm',
layer_info['Number of lines'])],
is_spectral=False)
for class_name in self.meta_data.keys():
if 'Ciao image list' in class_name:
layer_info = self.meta_data[class_name]
quantity = layer_info.pop('Image Data_2')
data = self._read_image_layer(layer_info)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(h5_chan_grp, np.reshape(data, (-1, 1)), 'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity, 'a. u.',
None, None, dtype=np.float32, compression='gzip',
h5_pos_inds=h5_pos_inds, h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds, h5_spec_vals=h5_spec_vals)
# Think about standardizing attributes for rows and columns
write_simple_attrs(h5_chan_grp, layer_info)
def _translate_force_map(self, h5_meas_grp):
"""
Reads the scan image + force map from the proprietary file and writes it to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# First lets write the image into the measurement group that has already been created:
image_parms = self.meta_data['Ciao image list']
quantity = image_parms.pop('Image Data_2')
image_mat = self._read_image_layer(image_parms)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(h5_chan_grp, np.reshape(image_mat, (-1, 1)), 'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity, 'a. u.',
[Dimension('X', 'nm', image_parms['Samps/line']),
Dimension('Y', 'nm', image_parms['Number of lines'])],
Dimension('single', 'a. u.', 1), dtype=np.float32, compression='gzip')
# Think about standardizing attributes for rows and columns
write_simple_attrs(h5_chan_grp, image_parms)
# Now work on the force map:
force_map_parms = self.meta_data['Ciao force image list']
quantity = force_map_parms.pop('Image Data_4')
force_map_vec = self._read_data_vector(force_map_parms)
tr_rt = [int(item) for item in force_map_parms['Samps/line'].split(' ')]
force_map_2d = force_map_vec.reshape(image_mat.size, np.sum(tr_rt))
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(h5_chan_grp, force_map_2d, 'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity, 'a. u.',
[Dimension('X', 'nm', image_parms['Samps/line']),
Dimension('Y', 'nm', image_parms['Number of lines'])],
Dimension('Z', 'nm', int(np.sum(tr_rt))), dtype=np.float32, compression='gzip')
# Think about standardizing attributes
write_simple_attrs(h5_chan_grp, force_map_parms)
def test_to_dset(self):
file_path = 'test.h5'
data_utils.delete_existing_file(file_path)
with h5py.File(file_path, mode='w') as h5_f:
h5_dset = h5_f.create_dataset('Test', data=np.arange(3))
attrs = {
'att_1': 'string_val',
'att_2': 1.2345,
'att_3': [1, 2, 3, 4],
'att_4': ['str_1', 'str_2', 'str_3']
}
hdf_utils.write_simple_attrs(h5_dset, attrs)
self.assertEqual(len(h5_dset.attrs), len(attrs))
for key, expected_val in attrs.items():
self.assertTrue(
np.all(hdf_utils.get_attr(h5_dset, key) == expected_val))
os.remove(file_path)
def _create_guess_datasets(self):
"""
Creates the h5 group, guess dataset, corresponding spectroscopic datasets and also
links the guess dataset to the spectroscopic datasets.
"""
self.h5_results_grp = create_results_group(self.h5_main, self.process_name)
write_simple_attrs(self.h5_results_grp, self.parms_dict)
h5_sho_inds, h5_sho_vals = write_reduced_anc_dsets(self.h5_results_grp, self.h5_main.h5_spec_inds,
self.h5_main.h5_spec_vals, self._fit_dim_name)
self._h5_guess = write_main_dataset(self.h5_results_grp, (self.h5_main.shape[0], self.num_udvs_steps), 'Guess', 'SHO',
'compound', None, None, h5_pos_inds=self.h5_main.h5_pos_inds,
h5_pos_vals=self.h5_main.h5_pos_vals, h5_spec_inds=h5_sho_inds,
h5_spec_vals=h5_sho_vals, chunks=(1, self.num_udvs_steps), dtype=sho32,
main_dset_attrs=self.parms_dict, verbose=self.verbose)
copy_region_refs(self.h5_main, self._h5_guess)
self._h5_guess.file.flush()
if self.verbose and self.mpi_rank == 0:
print('Finished creating Guess dataset')
def _translate_force_curve(self, h5_meas_grp):
"""
Reads the force curves from the proprietary file and writes them to HDF5 datasets
Parameters
----------
h5_meas_grp : h5py.Group object
Reference to the measurement group
"""
# since multiple channels will share the same position and spectroscopic dimensions, why not share them?
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(h5_meas_grp, Dimension('single', 'a. u.', 1), is_spectral=False)
# Find out the size of the force curves from the metadata:
layer_info = None
for class_name in self.meta_data.keys():
if 'Ciao force image list' in class_name:
layer_info = self.meta_data[class_name]
break
tr_rt = [int(item) for item in layer_info['Samps/line'].split(' ')]
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(h5_meas_grp, Dimension('Z', 'nm', int(np.sum(tr_rt))),
is_spectral=True)
for class_name in self.meta_data.keys():
if 'Ciao force image list' in class_name:
layer_info = self.meta_data[class_name]
quantity = layer_info.pop('Image Data_4')
data = self._read_data_vector(layer_info)
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_main_dataset(h5_chan_grp, np.expand_dims(data, axis=0), 'Raw_Data',
# Quantity and Units needs to be fixed by someone who understands these files better
quantity, 'a. u.',
None, None, dtype=np.float32, compression='gzip',
h5_pos_inds=h5_pos_inds, h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds, h5_spec_vals=h5_spec_vals)
# Think about standardizing attributes
write_simple_attrs(h5_chan_grp, layer_info)
def _create_guess_datasets(self):
"""
Creates the HDF5 Guess dataset and links the it to the ancillary datasets.
"""
self.h5_guess = create_empty_dataset(self.h5_loop_metrics, loop_fit32, 'Guess')
write_simple_attrs(self._h5_group, {'guess method': 'pycroscopy statistical'})
# This is necessary comparing against new runs to avoid re-computation + resuming partial computation
write_simple_attrs(self.h5_guess, self._parms_dict)
write_simple_attrs(self.h5_guess, {'Loop_fit_method': "pycroscopy statistical", 'last_pixel': 0})
self.h5_main.file.flush()
def _create_fit_datasets(self):
"""
Creates the HDF5 Fit dataset and links the it to the ancillary datasets.
"""
if self.h5_guess is None:
warn('Need to guess before fitting!')
return
self.h5_fit = create_empty_dataset(self.h5_guess, loop_fit32, 'Fit')
write_simple_attrs(self._h5_group, {'fit method': 'pycroscopy functional'})
# This is necessary comparing against new runs to avoid re-computation + resuming partial computation
write_simple_attrs(self.h5_fit, self._parms_dict)
write_simple_attrs(self.h5_fit, {'Loop_fit_method': "pycroscopy functional", 'last_pixel': 0})
def _create_fit_datasets(self):
"""
Creates the HDF5 fit dataset. pycroscopy requires that the h5 group, guess dataset,
corresponding spectroscopic and position datasets be created and populated at this point.
This function will create the HDF5 dataset for the fit and link it to same ancillary datasets as the guess.
The fit dataset will NOT be populated here but will instead be populated using the __setData function
"""
if self.h5_guess is None:
warn('Need to guess before fitting!')
return
if self.step_start_inds is None:
h5_spec_inds = self.h5_main.h5_spec_inds
self.step_start_inds = np.where(h5_spec_inds[0] == 0)[0]
if self.num_udvs_steps is None:
self.num_udvs_steps = len(self.step_start_inds)
if self.freq_vec is None:
self._get_frequency_vector()
h5_sho_grp = self.h5_guess.parent
write_simple_attrs(h5_sho_grp, {'SHO_fit_method': "pycroscopy BESHO"})
# Create the fit dataset as an empty dataset of the same size and dtype as the guess.
# Also automatically links in the ancillary datasets.
self.h5_fit = USIDataset(
create_empty_dataset(self.h5_guess, dtype=sho32, dset_name='Fit'))
# This is necessary comparing against new runs to avoid re-computation + resuming partial computation
write_simple_attrs(self.h5_fit, self._parms_dict)
write_simple_attrs(self.h5_fit, {
'SHO_fit_method': "pycroscopy BESHO",
'last_pixel': 0
})
self.h5_fit.file.flush()
def translate(self, file_path):
"""
The main function that translates the provided file into a .h5 file
Parameters
----------
file_path : String / unicode
Absolute path of any file in the directory
Returns
-------
h5_path : String / unicode
Absolute path of the h5 file
"""
file_path = path.abspath(file_path)
# Figure out the basename of the data:
(basename, parm_paths, data_paths) = self._parse_file_path(file_path)
(folder_path, unused) = path.split(file_path)
h5_path = path.join(folder_path, basename+'.h5')
if path.exists(h5_path):
remove(h5_path)
# Load parameters from .mat file - 'BE_wave', 'FFT_BE_wave', 'total_cols', 'total_rows'
matread = loadmat(parm_paths['parm_mat'], variable_names=['BE_wave', 'FFT_BE_wave', 'total_cols', 'total_rows'])
be_wave = np.float32(np.squeeze(matread['BE_wave']))
# Need to take the complex conjugate if reading from a .mat file
# FFT_BE_wave = np.conjugate(np.complex64(np.squeeze(matread['FFT_BE_wave'])))
num_cols = int(matread['total_cols'][0][0])
expected_rows = int(matread['total_rows'][0][0])
self.points_per_pixel = len(be_wave)
# Load parameters from .txt file - 'BE_center_frequency_[Hz]', 'IO rate'
is_beps, parm_dict = parmsToDict(parm_paths['parm_txt'])
# Get file byte size:
# For now, assume that bigtime_00 always exists and is the main file
file_size = path.getsize(data_paths[0])
# Calculate actual number of lines since the first few lines may not be saved
self.num_rows = 1.0 * file_size / (4 * self.points_per_pixel * num_cols)
if self.num_rows % 1:
warn('Error - File has incomplete rows')
return None
else:
self.num_rows = int(self.num_rows)
samp_rate = parm_dict['IO_rate_[Hz]']
ex_freq_nominal = parm_dict['BE_center_frequency_[Hz]']
# method 1 for calculating the correct excitation frequency:
pixel_duration = 1.0 * self.points_per_pixel / samp_rate
num_periods = pixel_duration * ex_freq_nominal
ex_freq_correct = 1 / (pixel_duration / np.floor(num_periods))
# method 2 for calculating the exact excitation frequency:
"""
fft_ex_wfm = np.abs(np.fft.fftshift(np.fft.fft(be_wave)))
w_vec = np.linspace(-0.5 * samp_rate, 0.5 * samp_rate - 1.0*samp_rate / self.points_per_pixel,
self.points_per_pixel)
hot_bins = np.squeeze(np.argwhere(fft_ex_wfm > 1E+3))
ex_freq_correct = w_vec[hot_bins[-1]]
"""
# correcting the excitation frequency - will be VERY useful during analysis and filtering
parm_dict['BE_center_frequency_[Hz]'] = ex_freq_correct
# Some very basic information that can help the processing crew
parm_dict['num_bins'] = self.points_per_pixel
parm_dict['grid_num_rows'] = self.num_rows
parm_dict['data_type'] = 'G_mode_line'
if self.num_rows != expected_rows:
print('Note: {} of {} lines found in data file'.format(self.num_rows, expected_rows))
# Calculate number of points to read per line:
self.__bytes_per_row__ = int(file_size/self.num_rows)
# First finish writing all global parameters, create the file too:
h5_f = h5py.File(h5_path, 'w')
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'G_mode_line'
global_parms['translator'] = 'G_mode_line'
write_simple_attrs(h5_f, global_parms)
meas_grp = create_indexed_group(h5_f, 'Measurement')
write_simple_attrs(meas_grp, parm_dict)
pos_desc = Dimension('Y', 'm', np.arange(self.num_rows))
spec_desc = Dimension('Excitation', 'V', np.tile(VALUES_DTYPE(be_wave), num_cols))
first_dat = True
for key in data_paths.keys():
# Now that the file has been created, go over each raw data file:
# 1. write all ancillary data. Link data. 2. Write main data sequentially
""" We only allocate the space for the main data here.
This does NOT change with each file. The data written to it does.
The auxiliary datasets will not change with each raw data file since
only one excitation waveform is used"""
chan_grp = create_indexed_group(meas_grp, 'Channel')
if first_dat:
if len(data_paths) > 1:
# All positions and spectra are shared between channels
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(meas_grp, pos_desc, is_spectral=False)
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(meas_grp, spec_desc, is_spectral=True)
elif len(data_paths) == 1:
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(chan_grp, pos_desc, is_spectral=False)
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(chan_grp, spec_desc, is_spectral=True)
first_dat = False
else:
pass
h5_main = write_main_dataset(chan_grp, (self.num_rows, self.points_per_pixel * num_cols), 'Raw_Data',
'Deflection', 'V',
None, None,
h5_pos_inds=h5_pos_inds, h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds, h5_spec_vals=h5_spec_vals,
chunks=(1, self.points_per_pixel), dtype=np.float16)
# Now transfer scan data in the dat file to the h5 file:
self._read_data(data_paths[key], h5_main)
h5_f.close()
print('G-Line translation complete!')
return h5_path
def translate(self, parm_path):
"""
Basic method that translates .mat data files to a single .h5 file
Parameters
------------
parm_path : string / unicode
Absolute file path of the parameters .mat file.
Returns
----------
h5_path : string / unicode
Absolute path of the translated h5 file
"""
self.parm_path = path.abspath(parm_path)
(folder_path, file_name) = path.split(parm_path)
(file_name, base_name) = path.split(folder_path)
h5_path = path.join(folder_path, base_name + '.h5')
# Read parameters
parm_dict = readGmodeParms(parm_path)
# Add the w^2 specific parameters to this list
parm_data = loadmat(parm_path, squeeze_me=True, struct_as_record=True)
freq_sweep_parms = parm_data['freqSweepParms']
parm_dict['freq_sweep_delay'] = np.float(
freq_sweep_parms['delay'].item())
gen_sig = parm_data['genSig']
parm_dict['wfm_fix_d_fast'] = np.int32(gen_sig['restrictT'].item())
freq_array = np.float32(parm_data['freqArray'])
# prepare and write spectroscopic values
samp_rate = parm_dict['IO_down_samp_rate_[Hz]']
num_bins = int(parm_dict['wfm_n_cycles'] * parm_dict['wfm_p_slow'] *
samp_rate)
w_vec = np.arange(-0.5 * samp_rate, 0.5 * samp_rate,
np.float32(samp_rate / num_bins))
# There is most likely a more elegant solution to this but I don't have the time... Maybe np.meshgrid
spec_val_mat = np.zeros((len(freq_array) * num_bins, 2),
dtype=VALUES_DTYPE)
spec_val_mat[:, 0] = np.tile(w_vec, len(freq_array))
spec_val_mat[:, 1] = np.repeat(freq_array, num_bins)
spec_ind_mat = np.zeros((2, len(freq_array) * num_bins),
dtype=np.int32)
spec_ind_mat[0, :] = np.tile(np.arange(num_bins), len(freq_array))
spec_ind_mat[1, :] = np.repeat(np.arange(len(freq_array)), num_bins)
num_rows = parm_dict['grid_num_rows']
num_cols = parm_dict['grid_num_cols']
parm_dict['data_type'] = 'GmodeW2'
num_pix = num_rows * num_cols
global_parms = dict()
global_parms['grid_size_x'] = parm_dict['grid_num_cols']
global_parms['grid_size_y'] = parm_dict['grid_num_rows']
# assuming that the experiment was completed:
global_parms['current_position_x'] = parm_dict['grid_num_cols'] - 1
global_parms['current_position_y'] = parm_dict['grid_num_rows'] - 1
global_parms['data_type'] = parm_dict[
'data_type'] # self.__class__.__name__
global_parms['translator'] = 'W2'
# Now start creating datasets and populating:
if path.exists(h5_path):
remove(h5_path)
h5_f = h5py.File(h5_path, 'w')
write_simple_attrs(h5_f, global_parms)
meas_grp = create_indexed_group(h5_f, 'Measurement')
chan_grp = create_indexed_group(meas_grp, 'Channel')
write_simple_attrs(chan_grp, parm_dict)
pos_dims = [
Dimension('X', 'nm', num_rows),
Dimension('Y', 'nm', num_cols)
]
spec_dims = [
Dimension('Response Bin', 'a.u.', num_bins),
Dimension('Excitation Frequency ', 'Hz', len(freq_array))
]
# Minimize file size to the extent possible.
# DAQs are rated at 16 bit so float16 should be most appropriate.
# For some reason, compression is more effective on time series data
h5_main = write_main_dataset(chan_grp, (num_pix, num_bins),
'Raw_Data',
'Deflection',
'V',
pos_dims,
spec_dims,
chunks=(1, num_bins),
dtype=np.float32)
h5_ex_freqs = chan_grp.create_dataset('Excitation_Frequencies',
freq_array)
h5_bin_freq = chan_grp.create_dataset('Bin_Frequencies', w_vec)
# Now doing link_h5_objects_as_attrs:
link_h5_objects_as_attrs(h5_main, [h5_ex_freqs, h5_bin_freq])
# Now read the raw data files:
pos_ind = 0
for row_ind in range(1, num_rows + 1):
for col_ind in range(1, num_cols + 1):
file_path = path.join(
folder_path,
'fSweep_r' + str(row_ind) + '_c' + str(col_ind) + '.mat')
print('Working on row {} col {}'.format(row_ind, col_ind))
if path.exists(file_path):
# Load data file
pix_data = loadmat(file_path, squeeze_me=True)
pix_mat = pix_data['AI_mat']
# Take the inverse FFT on 2nd dimension
pix_mat = np.fft.ifft(np.fft.ifftshift(pix_mat, axes=1),
axis=1)
# Verified with Matlab - no conjugate required here.
pix_vec = pix_mat.transpose().reshape(pix_mat.size)
h5_main[pos_ind, :] = np.float32(pix_vec)
h5_f.flush() # flush from memory!
else:
print('File not found for: row {} col {}'.format(
row_ind, col_ind))
pos_ind += 1
if (100.0 * pos_ind / num_pix) % 10 == 0:
print('completed translating {} %'.format(
int(100 * pos_ind / num_pix)))
h5_f.close()
return h5_path
def translate(self, file_path, verbose=False, append_path='',
grp_name='Measurement', parm_encoding='utf-8'):
"""
Translates the provided file to .h5
Parameters
----------
file_path : String / unicode
Absolute path of the .ibw file
verbose : Boolean (Optional)
Whether or not to show print statements for debugging
append_path : string (Optional)
h5_file to add these data to, must be a path to the h5_file on disk
grp_name : string (Optional)
Change from default "Measurement" name to something specific
parm_encoding : str, optional
Codec to be used to decode the bytestrings into Python strings if needed.
Default 'utf-8'
Returns
-------
h5_path : String / unicode
Absolute path of the .h5 file
"""
file_path = path.abspath(file_path)
# Prepare the .h5 file:
folder_path, base_name = path.split(file_path)
base_name = base_name[:-4]
if not append_path:
h5_path = path.join(folder_path, base_name + '.h5')
if path.exists(h5_path):
remove(h5_path)
h5_file = h5py.File(h5_path, 'w')
else:
h5_path = append_path
if not path.exists(append_path):
raise Exception('File does not exist. Check pathname.')
h5_file = h5py.File(h5_path, 'r+')
# Load the ibw file first
ibw_obj = bw.load(file_path)
ibw_wave = ibw_obj.get('wave')
parm_dict = self._read_parms(ibw_wave, parm_encoding)
chan_labels, chan_units = self._get_chan_labels(ibw_wave, parm_encoding)
if verbose:
print('Channels and units found:')
print(chan_labels)
print(chan_units)
# Get the data to figure out if this is an image or a force curve
images = ibw_wave.get('wData')
if images.shape[-1] != len(chan_labels):
chan_labels = chan_labels[1:] # for layer 0 null set errors in older AR software
if images.ndim == 3: # Image stack
if verbose:
print('Found image stack of size {}'.format(images.shape))
type_suffix = 'Image'
num_rows = parm_dict['ScanLines']
num_cols = parm_dict['ScanPoints']
images = images.transpose(2, 1, 0) # now ordered as [chan, Y, X] image
images = np.reshape(images, (images.shape[0], -1, 1)) # 3D [chan, Y*X points,1]
pos_desc = [Dimension('X', 'm', np.linspace(0, parm_dict['FastScanSize'], num_cols)),
Dimension('Y', 'm', np.linspace(0, parm_dict['SlowScanSize'], num_rows))]
spec_desc = Dimension('arb', 'a.u.', [1])
else: # single force curve
if verbose:
print('Found force curve of size {}'.format(images.shape))
type_suffix = 'ForceCurve'
images = np.atleast_3d(images) # now [Z, chan, 1]
images = images.transpose((1, 2, 0)) # [chan ,1, Z] force curve
# The data generated above varies linearly. Override.
# For now, we'll shove the Z sensor data into the spectroscopic values.
# Find the channel that corresponds to either Z sensor or Raw:
try:
chan_ind = chan_labels.index('ZSnsr')
spec_data = VALUES_DTYPE(images[chan_ind]).squeeze()
except ValueError:
try:
chan_ind = chan_labels.index('Raw')
spec_data = VALUES_DTYPE(images[chan_ind]).squeeze()
except ValueError:
# We don't expect to come here. If we do, spectroscopic values remains as is
spec_data = np.arange(images.shape[2])
pos_desc = Dimension('X', 'm', [1])
spec_desc = Dimension('Z', 'm', spec_data)
# Create measurement group
meas_grp = create_indexed_group(h5_file, grp_name)
# Write file and measurement level parameters
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'IgorIBW_' + type_suffix
global_parms['translator'] = 'IgorIBW'
write_simple_attrs(h5_file, global_parms)
write_simple_attrs(meas_grp, parm_dict)
# Create Position and spectroscopic datasets
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(meas_grp, pos_desc, is_spectral=False)
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(meas_grp, spec_desc, is_spectral=True)
# Prepare the list of raw_data datasets
for chan_data, chan_name, chan_unit in zip(images, chan_labels, chan_units):
if verbose:
print('channel', chan_name)
print('unit', chan_unit)
chan_grp = create_indexed_group(meas_grp, 'Channel')
write_main_dataset(chan_grp, np.atleast_2d(chan_data), 'Raw_Data',
chan_name, chan_unit,
None, None,
h5_pos_inds=h5_pos_inds, h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds, h5_spec_vals=h5_spec_vals,
dtype=np.float32)
if verbose:
print('Finished preparing raw datasets')
h5_file.close()
return h5_path
def _create_group(h5_parent_group, micro_group, print_log=False):
"""
Creates a h5py.Group object from the provided VirtualGroup object under h5_new_group and writes all attributes
Parameters
----------
h5_parent_group : h5py.Group object
Parent group under which the new group object will be created
micro_group : VirtualGroup object
Definition for the new group
print_log : bool, optional. Default=False
Whether or not to print debugging statements
Returns
-------
h5_new_group : h5py.Group
The newly created group
"""
if not isinstance(micro_group, VirtualGroup):
HDFwriter.__safe_abort(h5_parent_group.file)
raise TypeError(
'micro_group should be a VirtualGroup object but is instead of type '
'{}'.format(type(micro_group)))
if not isinstance(h5_parent_group, h5py.Group):
raise TypeError(
'h5_parent_group should be a h5py.Group object but is instead of type '
'{}'.format(type(h5_parent_group)))
if micro_group.name == '':
HDFwriter.__safe_abort(h5_parent_group.file)
raise ValueError(
'VirtualGroup object with empty name will not be handled by this function'
)
# First complete the name of the group by adding the index suffix
if micro_group.indexed:
micro_group.name = assign_group_index(h5_parent_group,
micro_group.name,
verbose=print_log)
# Now, try to write the group
try:
h5_new_group = h5_parent_group.create_group(micro_group.name)
if print_log:
print('Created Group {}'.format(h5_new_group.name))
except ValueError:
h5_new_group = h5_parent_group[micro_group.name]
if print_log:
print('Found Group already exists {}'.format(
h5_new_group.name))
except Exception:
HDFwriter.__safe_abort(h5_parent_group.file)
raise
# Write attributes
write_simple_attrs(h5_new_group,
micro_group.attrs,
'group',
verbose=print_log)
return h5_new_group
def write(self, data, print_log=False):
"""
Writes data into the hdf5 file and assigns data attributes such as region references.
The tree structure is inferred from the AFMData Object.
Parameters
----------
data : Instance of MicroData
Tree structure describing the organization of the data
print_log : Boolean (Optional)
Whether or not to print all log statements - use for debugging purposes
Returns
-------
ref_list : List of HDF5dataset or HDF5Datagroup references
References to the objects written
"""
h5_file = self.file
h5_file.attrs['Pycroscopy version'] = version
# Checking if the data is a VirtualGroup object
if not isinstance(data, VirtualData):
raise TypeError(
'Input expected to be of type MicroData but is of type: {} \n'.
format(type(data)))
if isinstance(data, VirtualDataset):
# just want to write a single dataset:
try:
h5_parent = h5_file[data.parent]
except KeyError:
raise KeyError(
'Parent ({}) of provided VirtualDataset ({}) does not exist in the '
'file'.format(data.parent, data.name))
h5_dset = HDFwriter._create_dataset(h5_parent,
data,
print_log=print_log)
return [h5_dset]
assert isinstance(data, VirtualGroup) # just to avoid PEP8 warning
# Populating the tree structure recursively
ref_list = []
# Figuring out if the first item in VirtualGroup tree is file or group
if data.name == '' and data.parent == '/':
# For file we just write the attributes
write_simple_attrs(h5_file,
data.attrs,
obj_type='file',
verbose=print_log)
root = h5_file.name
ref_list.append(h5_file)
else:
# For a group we write it and its attributes
h5_grp = self._create_group(h5_file[data.parent],
data,
print_log=print_log)
root = h5_grp.name
ref_list.append(h5_grp)
# Recursive function
def __populate(child, parent):
"""
Recursive function to build the tree from the top down.
Parameters
----------
child : VirtualGroup object
tree to be written
parent : h5py.Group or h5py.File object
HDF5 object to build tree under
Returns
-------
ref_list : list
list of h5py.Dataset and h5py.Group objects created when populating the file
"""
# Update the parent attribute with the true path
child.parent = parent
h5_parent_group = h5_file[parent]
if isinstance(child, VirtualGroup):
h5_obj = HDFwriter._create_group(h5_parent_group,
child,
print_log=print_log)
# here we do the recursive function call
for ch in child.children:
__populate(ch, parent + '/' + child.name)
else:
h5_obj = HDFwriter._create_dataset(h5_parent_group,
child,
print_log=print_log)
ref_list.append(h5_obj)
return ref_list
# Recursive function is called at each stage beginning at the root
for curr_child in data.children:
__populate(curr_child, root)
if print_log:
print(
'Finished writing to h5 file.\n' +
'Right now you got yourself a fancy folder structure. \n' +
'Make sure you do some reference linking to take advantage of the full power of HDF5.'
)
return ref_list
def translate(self, data_filepath, out_filename, verbose=False, debug=False):
'''
The main function that translates the provided file into a .h5 file
Parameters
----------------
data_filepath : String / unicode
Absolute path of the data file
out_filename : String / unicode
Name for the new generated hdf5 file. The new file will be
saved in the same folder of the input file with
file name "out_filename".
NOTE: the .h5 extension is automatically added to "out_filename"
debug : Boolean (Optional. default is false)
Whether or not to print log statements
Returns
----------------
h5_path : String / unicode
Absolute path of the generated .h5 file
'''
self.debug = debug
# Open the datafile
try:
data_filepath = os.path.abspath(data_filepath)
ARh5_file = h5py.File(data_filepath, 'r')
except:
print('Unable to open the file', data_filepath)
raise
# Get info from the origin file like Notes and Segments
self.notes = ARh5_file.attrs['Note']
self.segments = ARh5_file['ForceMap']['Segments'] #shape: (X, Y, 4)
self.segments_name = list(ARh5_file['ForceMap'].attrs['Segments'])
self.map_size['X'] = ARh5_file['ForceMap']['Segments'].shape[0]
self.map_size['Y'] = ARh5_file['ForceMap']['Segments'].shape[1]
self.channels_name = list(ARh5_file['ForceMap'].attrs['Channels'])
try:
self.points_per_sec = np.float(self.note_value('ARDoIVPointsPerSec'))
except NameError:
self.points_per_sec = np.float(self.note_value('NumPtsPerSec'))
if self.debug:
print('Map size [X, Y]: ', self.map_size)
print('Channels names: ', self.channels_name)
# Only the extension 'Ext' segment can change size
# so we get the shortest one and we trim all the others
extension_idx = self.segments_name.index('Ext')
short_ext = np.amin(np.array(self.segments[:, :, extension_idx]))
longest_ext = np.amax(np.array(self.segments[:, :, extension_idx]))
difference = longest_ext - short_ext # this is a difference between integers
tot_length = (np.amax(self.segments) - difference) + 1
# +1 otherwise array(tot_length) will be of 1 position shorter
points_trimmed = np.array(self.segments[:, :, extension_idx]) - short_ext
if self.debug:
print('Data were trimmed in the extension segment of {} points'.format(difference))
# Open the output hdf5 file
folder_path = os.path.dirname(data_filepath)
h5_path = os.path.join(folder_path, out_filename + '.h5')
h5_file = h5py.File(h5_path, 'w')
# Create the measurement group
h5_meas_group = create_indexed_group(h5_file, 'Measurement')
# Create all channels and main datasets
# at this point the main dataset are just function of time
x_dim = np.linspace(0, np.float(self.note_value('FastScanSize')),
self.map_size['X'])
y_dim = np.linspace(0, np.float(self.note_value('FastScanSize')),
self.map_size['Y'])
z_dim = np.arange(tot_length) / np.float(self.points_per_sec)
pos_dims = [Dimension('Cols', 'm', x_dim),
Dimension('Rows', 'm', y_dim)]
spec_dims = [Dimension('Time', 's', z_dim)]
# This is quite time consuming, but on magnetic drive is limited from the disk, and therefore is not useful
# to parallelize these loops
for index, channel in enumerate(self.channels_name):
cur_chan = create_indexed_group(h5_meas_group, 'Channel')
main_dset = np.empty((self.map_size['X'], self.map_size['Y'], tot_length))
for column in np.arange(self.map_size['X']):
for row in np.arange(self.map_size['Y']):
AR_pos_string = str(column) + ':' + str(row)
seg_start = self.segments[column, row, extension_idx] - short_ext
main_dset[column, row, :] = ARh5_file['ForceMap'][AR_pos_string][index, seg_start:]
# Reshape with Fortran order to have the correct position indices
main_dset = np.reshape(main_dset, (-1, tot_length), order='F')
if index == 0:
first_main_dset = cur_chan
quant_unit = self.get_def_unit(channel)
h5_raw = write_main_dataset(cur_chan, # parent HDF5 group
main_dset, # 2D array of raw data
'Raw_'+channel, # Name of main dset
channel, # Physical quantity
self.get_def_unit(channel), # Unit
pos_dims, # position dimensions
spec_dims, #spectroscopy dimensions
)
else:
h5_raw = write_main_dataset(cur_chan, # parent HDF5 group
main_dset, # 2D array of raw data
'Raw_'+channel, # Name of main dset
channel, # Physical quantity
self.get_def_unit(channel), # Unit
pos_dims, # position dimensions
spec_dims, #spectroscopy dimensions
# Link Ancilliary dset to the first
h5_pos_inds=first_main_dset['Position_Indices'],
h5_pos_vals=first_main_dset['Position_Values'],
h5_spec_inds=first_main_dset['Spectroscopic_Indices'],
h5_spec_vals=first_main_dset['Spectroscopic_Values'],
)
# Make Channels with IMAGES.
# Position indices/values are the same of all other channels
# Spectroscopic indices/valus are they are just one single dimension
img_spec_dims = [Dimension('arb', 'a.u.', [1])]
for index, image in enumerate(ARh5_file['Image'].keys()):
main_dset = np.reshape(np.array(ARh5_file['Image'][image]), (-1,1), order='F')
cur_chan = create_indexed_group(h5_meas_group, 'Channel')
if index == 0:
first_image_dset = cur_chan
h5_raw = write_main_dataset(cur_chan, # parent HDF5 group
main_dset, # 2D array of image (shape: P*Q x 1)
'Img_'+image, # Name of main dset
image, # Physical quantity
self.get_def_unit(image), # Unit
pos_dims, # position dimensions
img_spec_dims, #spectroscopy dimensions
# Link Ancilliary dset to the first
h5_pos_inds=first_main_dset['Position_Indices'],
h5_pos_vals=first_main_dset['Position_Values'],
)
else:
h5_raw = write_main_dataset(cur_chan, # parent HDF5 group
main_dset, # 2D array of image (shape: P*Q x 1)
'Img_'+image, # Name of main dset
image, # Physical quantity
self.get_def_unit(image), # Unit
pos_dims, # position dimensions
img_spec_dims, #spectroscopy dimensions
# Link Ancilliary dset to the first
h5_pos_inds=first_main_dset['Position_Indices'],
h5_pos_vals=first_main_dset['Position_Values'],
h5_spec_inds=first_image_dset['Spectroscopic_Indices'],
h5_spec_vals=first_image_dset['Spectroscopic_Values'],
)
# Create the new segments that will be stored as attribute
new_segments = {}
for seg, name in enumerate(self.segments_name):
new_segments.update({name:self.segments[0,0,seg] - short_ext})
write_simple_attrs(h5_meas_group, {'Segments':new_segments,
'Points_trimmed':points_trimmed,
'Notes':self.notes})
write_simple_attrs(h5_file,
{'translator':'ARhdf5',
'instrument':'Asylum Research '+self.note_value('MicroscopeModel'),
'AR sftware version':self.note_value('Version')})
if self.debug:
print(print_tree(h5_file))
print('\n')
for key, val in get_attributes(h5_meas_group).items():
if key != 'Notes':
print('{} : {}'.format(key, val))
else:
print('{} : {}'.format(key, 'notes string too long to be written here.'))
# Clean up
ARh5_file.close()
h5_file.close()
self.translated = True
return h5_path
def translate(self, data_channels=None, verbose=False):
"""
Translate the data into a Pycroscopy compatible HDF5 file.
Parameters
----------
data_channels : (optional) list of str
Names of channels that will be read and stored in the file.
If not given, all channels in the file will be used.
verbose : (optional) Boolean
Whether or not to print statements
Returns
-------
h5_path : str
Filepath to the output HDF5 file.
"""
if self.parm_dict is None or self.data_dict is None:
self._read_data(self.data_path)
if data_channels is None:
print('No channels specified. All channels in file will be used.')
data_channels = self.parm_dict['channel_parms'].keys()
if verbose:
print('Using the following channels')
for channel in data_channels:
print(channel)
if os.path.exists(self.h5_path):
os.remove(self.h5_path)
h5_file = h5py.File(self.h5_path, 'w')
# Create measurement group and assign attributes
meas_grp = create_indexed_group(h5_file, 'Measurement')
write_simple_attrs(
meas_grp, self.parm_dict['meas_parms']
)
# Create datasets for positional and spectroscopic indices and values
spec_dim = self.data_dict['Spectroscopic Dimensions']
pos_dims = self.data_dict['Position Dimensions']
h5_pos_inds, h5_pos_vals = write_ind_val_dsets(meas_grp, pos_dims,
is_spectral=False)
h5_spec_inds, h5_spec_vals = write_ind_val_dsets(meas_grp, spec_dim,
is_spectral=True)
# Create the datasets for all the channels
num_points = h5_pos_inds.shape[0]
for data_channel in data_channels:
raw_data = self.data_dict[data_channel].reshape([num_points, -1])
chan_grp = create_indexed_group(meas_grp, 'Channel')
data_label = data_channel
data_unit = self.parm_dict['channel_parms'][data_channel]['Unit']
write_simple_attrs(
chan_grp, self.parm_dict['channel_parms'][data_channel]
)
write_main_dataset(chan_grp, raw_data, 'Raw_Data',
data_label, data_unit,
None, None,
h5_pos_inds=h5_pos_inds,
h5_pos_vals=h5_pos_vals,
h5_spec_inds=h5_spec_inds,
h5_spec_vals=h5_spec_vals)
h5_file.flush()
h5_file.close()
print('Nanonis translation complete.')
return self.h5_path
def translate(self, parm_path):
"""
The main function that translates the provided file into a .h5 file
Parameters
------------
parm_path : string / unicode
Absolute file path of the parameters .mat file.
Returns
----------
h5_path : string / unicode
Absolute path of the translated h5 file
"""
parm_path = path.abspath(parm_path)
parm_dict, excit_wfm = self._read_parms(parm_path)
self._parse_file_path(parm_path)
num_dat_files = len(self.file_list)
f = open(self.file_list[0], 'rb')
spectrogram_size, count_vals = self._parse_spectrogram_size(f)
print("Excitation waveform shape: ", excit_wfm.shape)
print("spectrogram size:", spectrogram_size)
num_pixels = parm_dict['grid_num_rows'] * parm_dict['grid_num_cols']
print('Number of pixels: ', num_pixels)
print('Count Values: ', count_vals)
if (num_pixels + 1) != count_vals:
print("Data size does not match number of pixels expected. Cannot continue")
#Find how many channels we have to make
num_ai_chans = num_dat_files // 2 # Division by 2 due to real/imaginary
# Now start creating datasets and populating:
#Start with getting an h5 file
h5_file = h5py.File(self.h5_path)
#First create a measurement group
h5_meas_group = create_indexed_group(h5_file, 'Measurement')
#Set up some parameters that will be written as attributes to this Measurement group
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'trKPFM'
global_parms['translator'] = 'trKPFM'
write_simple_attrs(h5_meas_group, global_parms)
write_simple_attrs(h5_meas_group, parm_dict)
#Now start building the position and spectroscopic dimension containers
#There's only one spectroscpoic dimension and two position dimensions
#The excit_wfm only has the DC values without any information on cycles, time, etc.
#What we really need is to add the time component. For every DC step there are some time steps.
num_time_steps = (spectrogram_size-5) //excit_wfm.size
#Let's repeat the excitation so that we get the full vector of same size as the spectrogram
#TODO: Check if this is the norm for this type of dataset
full_spect_val = np.copy(excit_wfm).repeat(num_time_steps)
spec_dims = Dimension('Bias', 'V', full_spect_val)
pos_dims = [Dimension('Cols', 'nm', parm_dict['grid_num_cols']),
Dimension('Rows', 'um', parm_dict['grid_num_rows'])]
self.raw_datasets = list()
for chan_index in range(num_ai_chans):
chan_grp = create_indexed_group(h5_meas_group,'Channel')
if chan_index == 0:
write_simple_attrs(chan_grp,{'Harmonic': 1})
else:
write_simple_attrs(chan_grp,{'Harmonic': 2})
h5_raw = write_main_dataset(chan_grp, # parent HDF5 group
(num_pixels, spectrogram_size - 5),
# shape of Main dataset
'Raw_Data', # Name of main dataset
'Deflection', # Physical quantity contained in Main dataset
'V', # Units for the physical quantity
pos_dims, # Position dimensions
spec_dims, # Spectroscopic dimensions
dtype=np.complex64, # data type / precision
compression='gzip',
chunks=(1, spectrogram_size - 5),
main_dset_attrs={'quantity': 'Complex'})
#h5_refs = hdf.write(chan_grp, print_log=False)
#h5_raw = get_h5_obj_refs(['Raw_Data'], h5_refs)[0]
#link_h5_objects_as_attrs(h5_raw, get_h5_obj_refs(aux_ds_names, h5_refs))
self.raw_datasets.append(h5_raw)
self.raw_datasets.append(h5_raw)
# Now that the N channels have been made, populate them with the actual data....
self._read_data(parm_dict, parm_path, spectrogram_size)
h5_file.file.close()
#hdf.close()
return self.h5_path
def _create_results_datasets(self):
"""
Creates all the datasets necessary for holding all parameters + data.
"""
self.h5_results_grp = create_results_group(self.h5_main, self.process_name)
self.parms_dict.update({'last_pixel': 0, 'algorithm': 'pycroscopy_SignalFilter'})
write_simple_attrs(self.h5_results_grp, self.parms_dict)
assert isinstance(self.h5_results_grp, h5py.Group)
if isinstance(self.composite_filter, np.ndarray):
h5_comp_filt = self.h5_results_grp.create_dataset('Composite_Filter',
data=np.float32(self.composite_filter))
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Finished creating the Composite_Filter dataset'.format(self.mpi_rank))
# First create the position datsets if the new indices are smaller...
if self.num_effective_pix != self.h5_main.shape[0]:
# TODO: Do this part correctly. See past solution:
"""
# need to make new position datasets by taking every n'th index / value:
new_pos_vals = np.atleast_2d(h5_pos_vals[slice(0, None, self.num_effective_pix), :])
pos_descriptor = []
for name, units, leng in zip(h5_pos_inds.attrs['labels'], h5_pos_inds.attrs['units'],
[int(np.unique(h5_pos_inds[:, dim_ind]).size / self.num_effective_pix)
for dim_ind in range(h5_pos_inds.shape[1])]):
pos_descriptor.append(Dimension(name, units, np.arange(leng)))
ds_pos_inds, ds_pos_vals = build_ind_val_dsets(pos_descriptor, is_spectral=False, verbose=self.verbose)
h5_pos_vals.data = np.atleast_2d(new_pos_vals) # The data generated above varies linearly. Override.
"""
h5_pos_inds_new, h5_pos_vals_new = write_ind_val_dsets(self.h5_results_grp,
Dimension('pixel', 'a.u.', self.num_effective_pix),
is_spectral=False, verbose=self.verbose and self.mpi_rank==0)
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Created the new position ancillary dataset'.format(self.mpi_rank))
else:
h5_pos_inds_new = self.h5_main.h5_pos_inds
h5_pos_vals_new = self.h5_main.h5_pos_vals
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Reusing source datasets position datasets'.format(self.mpi_rank))
if self.noise_threshold is not None:
self.h5_noise_floors = write_main_dataset(self.h5_results_grp, (self.num_effective_pix, 1), 'Noise_Floors',
'Noise', 'a.u.', None, Dimension('arb', '', [1]),
dtype=np.float32, aux_spec_prefix='Noise_Spec_',
h5_pos_inds=h5_pos_inds_new, h5_pos_vals=h5_pos_vals_new,
verbose=self.verbose and self.mpi_rank == 0)
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Finished creating the Noise_Floors dataset'.format(self.mpi_rank))
if self.write_filtered:
# Filtered data is identical to Main_Data in every way - just a duplicate
self.h5_filtered = create_empty_dataset(self.h5_main, self.h5_main.dtype, 'Filtered_Data',
h5_group=self.h5_results_grp)
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Finished creating the Filtered dataset'.format(self.mpi_rank))
self.hot_inds = None
if self.write_condensed:
self.hot_inds = np.where(self.composite_filter > 0)[0]
self.hot_inds = np.uint(self.hot_inds[int(0.5 * len(self.hot_inds)):]) # only need to keep half the data
condensed_spec = Dimension('hot_frequencies', '', int(0.5 * len(self.hot_inds)))
self.h5_condensed = write_main_dataset(self.h5_results_grp, (self.num_effective_pix, len(self.hot_inds)),
'Condensed_Data', 'Complex', 'a. u.', None, condensed_spec,
h5_pos_inds=h5_pos_inds_new, h5_pos_vals=h5_pos_vals_new,
dtype=np.complex, verbose=self.verbose and self.mpi_rank == 0)
if self.verbose and self.mpi_rank == 0:
print('Rank {} - Finished creating the Condensed dataset'.format(self.mpi_rank))
if self.mpi_size > 1:
self.mpi_comm.Barrier()
self.h5_main.file.flush()
def _setupH5(self, usize, vsize, data_type, scan_size_x, scan_size_y, image_parms):
"""
Setup the HDF5 file in which to store the data including creating
the Position and Spectroscopic datasets
Parameters
----------
usize : int
Number of pixel columns in the images
vsize : int
Number of pixel rows in the images
data_type : type
Data type to save image as
scan_size_x : int
Number of images in the x dimension
scan_size_y : int
Number of images in the y dimension
image_parms : dict
Dictionary of parameters
Returns
-------
h5_main : h5py.Dataset
HDF5 Dataset that the images will be written into
h5_mean_spec : h5py.Dataset
HDF5 Dataset that the mean over all positions will be written
into
h5_ronch : h5py.Dataset
HDF5 Dateset that the mean over all Spectroscopic steps will be
written into
"""
num_pixels = usize * vsize
num_files = scan_size_x * scan_size_y
root_parms = generate_dummy_main_parms()
root_parms['data_type'] = 'PtychographyData'
main_parms = {'num_images': num_files,
'image_size_u': usize,
'image_size_v': vsize,
'num_pixels': num_pixels,
'translator': 'Ptychography',
'scan_size_x': scan_size_x,
'scan_size_y': scan_size_y}
main_parms.update(image_parms)
# Create the hdf5 data Group
write_simple_attrs(self.h5_f, root_parms)
meas_grp = create_indexed_group(self.h5_f, 'Measurement')
write_simple_attrs(meas_grp, main_parms)
chan_grp = create_indexed_group(meas_grp, 'Channel')
# Build the Position and Spectroscopic Datasets
spec_desc = [Dimension('U', 'pixel', np.arange(usize)),
Dimension('V', 'pixel', np.arange(vsize))]
pos_desc = [Dimension('X', 'pixel', np.arange(scan_size_x)),
Dimension('Y', 'pixel', np.arange(scan_size_y))]
ds_chunking = calc_chunks([num_files, num_pixels],
data_type(0).itemsize,
unit_chunks=(1, num_pixels))
# Allocate space for Main_Data and Pixel averaged Data
h5_main = write_main_dataset(chan_grp, (num_files, num_pixels), 'Raw_Data',
'Intensity', 'a.u.',
pos_desc, spec_desc,
chunks=ds_chunking, dtype=data_type)
h5_ronch= chan_grp.create_dataset('Mean_Ronchigram', shape=[num_pixels], dtype=np.float32)
h5_mean_spec = chan_grp.create_dataset('Spectroscopic_Mean', shape=[num_files], dtype=np.float32)
self.h5_f.flush()
return h5_main, h5_mean_spec, h5_ronch
def translate(self, parm_path):
"""
The main function that translates the provided file into a .h5 file
Parameters
------------
parm_path : string / unicode
Absolute file path of the parameters .mat file.
Returns
----------
h5_path : string / unicode
Absolute path of the translated h5 file
"""
parm_path = path.abspath(parm_path)
parm_dict, excit_wfm = self._read_parms(parm_path)
folder_path, base_name = path.split(parm_path)
waste, base_name = path.split(folder_path)
# Until a better method is provided....
with h5py.File(path.join(folder_path, 'line_1.mat'), 'r') as h5_mat_line_1:
num_ai_chans = h5_mat_line_1['data'].shape[1]
h5_path = path.join(folder_path, base_name+'.h5')
if path.exists(h5_path):
remove(h5_path)
with h5py.File(h5_path) as h5_f:
h5_meas_grp = create_indexed_group(h5_f, 'Measurement')
global_parms = generate_dummy_main_parms()
global_parms.update({'data_type': 'gIV', 'translator': 'gIV'})
write_simple_attrs(h5_meas_grp, global_parms)
# Only prepare the instructions for the dimensions here
spec_dims = Dimension('Bias', 'V', excit_wfm)
pos_dims = Dimension('Y', 'm', np.linspace(0, parm_dict['grid_scan_height_[m]'],
parm_dict['grid_num_rows']))
self.raw_datasets = list()
for chan_index in range(num_ai_chans):
h5_chan_grp = create_indexed_group(h5_meas_grp, 'Channel')
write_simple_attrs(h5_chan_grp, parm_dict)
"""
Minimize file size to the extent possible.
DAQs are rated at 16 bit so float16 should be most appropriate.
For some reason, compression is effective only on time series data
"""
h5_raw = write_main_dataset(h5_chan_grp, (parm_dict['grid_num_rows'], excit_wfm.size), 'Raw_Data',
'Current',
'1E-{} A'.format(parm_dict['IO_amplifier_gain']), pos_dims, spec_dims,
dtype=np.float16, chunks=(1, excit_wfm.size), compression='gzip')
self.raw_datasets.append(h5_raw)
# Now that the N channels have been made, populate them with the actual data....
self._read_data(parm_dict, folder_path)
return h5_path
def _write_results_chunk(self):
"""
Writes the labels and mean response to the h5 file
Returns
---------
h5_group : HDF5 Group reference
Reference to the group that contains the clustering results
"""
print('Writing clustering results to file.')
num_clusters = self.__mean_resp.shape[0]
h5_cluster_group = create_results_group(self.h5_main, self.process_name)
write_simple_attrs(h5_cluster_group, self.parms_dict)
h5_labels = write_main_dataset(h5_cluster_group, np.uint32(self.__labels.reshape([-1, 1])), 'Labels',
'Cluster ID', 'a. u.', None, Dimension('Cluster', 'ID', 1),
h5_pos_inds=self.h5_main.h5_pos_inds, h5_pos_vals=self.h5_main.h5_pos_vals,
aux_spec_prefix='Cluster_', dtype=np.uint32)
if self.num_comps != self.h5_main.shape[1]:
'''
Setup the Spectroscopic Indices and Values for the Mean Response if we didn't use all components
Note that a sliced spectroscopic matrix may not be contiguous. Let's just lose the spectroscopic data
for now until a better method is figured out
'''
"""
if isinstance(self.data_slice[1], np.ndarray):
centroid_vals_mat = h5_centroids.h5_spec_vals[self.data_slice[1].tolist()]
else:
centroid_vals_mat = h5_centroids.h5_spec_vals[self.data_slice[1]]
ds_centroid_values.data[0, :] = centroid_vals_mat
"""
if isinstance(self.data_slice[1], np.ndarray):
vals_slice = self.data_slice[1].tolist()
else:
vals_slice = self.data_slice[1]
vals = self.h5_main.h5_spec_vals[:, vals_slice].squeeze()
new_spec = Dimension('Original_Spectral_Index', 'a.u.', vals)
h5_inds, h5_vals = write_ind_val_dsets(h5_cluster_group, new_spec, is_spectral=True)
else:
h5_inds = self.h5_main.h5_spec_inds
h5_vals = self.h5_main.h5_spec_vals
# For now, link centroids with default spectroscopic indices and values.
h5_centroids = write_main_dataset(h5_cluster_group, self.__mean_resp, 'Mean_Response',
get_attr(self.h5_main, 'quantity')[0], get_attr(self.h5_main, 'units')[0],
Dimension('Cluster', 'a. u.', np.arange(num_clusters)), None,
h5_spec_inds=h5_inds, aux_pos_prefix='Mean_Resp_Pos_',
h5_spec_vals=h5_vals)
# Marking completion:
self._status_dset_name = 'completed_positions'
self._h5_status_dset = h5_cluster_group.create_dataset(self._status_dset_name,
data=np.ones(self.h5_main.shape[0], dtype=np.uint8))
# keeping legacy option:
h5_cluster_group.attrs['last_pixel'] = self.h5_main.shape[0]
return h5_cluster_group
def translate(self,
file_path,
show_plots=True,
save_plots=True,
do_histogram=False):
"""
Basic method that translates .dat data file(s) to a single .h5 file
Inputs:
file_path -- Absolute file path for one of the data files.
It is assumed that this file is of the OLD data format.
Outputs:
Nothing
"""
file_path = path.abspath(file_path)
(folder_path, basename) = path.split(file_path)
(basename, path_dict) = self._parse_file_path(file_path)
h5_path = path.join(folder_path, basename + '.h5')
if path.exists(h5_path):
remove(h5_path)
self.h5_file = h5py.File(h5_path, 'w')
isBEPS = True
parm_dict = self.__getParmsFromOldMat(path_dict['old_mat_parms'])
ignored_plt_grps = ['in-field'
] # Here we assume that there is no in-field.
# If in-field data is captured then the translator would have to be modified.
# Technically, we could do away with this if statement, as isBEPS is always true for this translation
if isBEPS:
parm_dict['data_type'] = 'BEPSData'
std_expt = parm_dict[
'VS_mode'] != 'load user defined VS Wave from file'
if not std_expt:
warn(
'This translator does not handle user defined voltage spectroscopy'
)
return
spec_label = getSpectroscopicParmLabel(parm_dict['VS_mode'])
# Check file sizes:
if 'read_real' in path_dict.keys():
real_size = path.getsize(path_dict['read_real'])
imag_size = path.getsize(path_dict['read_imag'])
else:
real_size = path.getsize(path_dict['write_real'])
imag_size = path.getsize(path_dict['write_imag'])
if real_size != imag_size:
raise ValueError(
"Real and imaginary file sizes DON'T match!. Ending")
num_rows = int(parm_dict['grid_num_rows'])
num_cols = int(parm_dict['grid_num_cols'])
num_pix = num_rows * num_cols
tot_bins = real_size / (
num_pix * 4) # Finding bins by simple division of entire datasize
# Check for case where only a single pixel is missing.
check_bins = real_size / ((num_pix - 1) * 4)
if tot_bins % 1 and check_bins % 1:
warn('Aborting! Some parameter appears to have changed in-between')
return
elif not tot_bins % 1:
# Everything's ok
pass
elif not check_bins % 1:
tot_bins = check_bins
warn(
'Warning: A pixel seems to be missing from the data. File will be padded with zeros.'
)
tot_bins = int(tot_bins)
(bin_inds, bin_freqs, bin_FFT, ex_wfm,
dc_amp_vec) = self.__readOldMatBEvecs(path_dict['old_mat_parms'])
"""
Because this is the old data format and there is a discrepancy in the number of bins (they seem to be 2 less
than the actual number), we need to re-calculate it based on the available data. This is done below.
"""
band_width = parm_dict['BE_band_width_[Hz]'] * (
0.5 - parm_dict['BE_band_edge_trim'])
st_f = parm_dict['BE_center_frequency_[Hz]'] - band_width
en_f = parm_dict['BE_center_frequency_[Hz]'] + band_width
bin_freqs = np.linspace(st_f, en_f, len(bin_inds), dtype=np.float32)
# Forcing standardized datatypes:
bin_inds = np.int32(bin_inds)
bin_freqs = np.float32(bin_freqs)
bin_FFT = np.complex64(bin_FFT)
ex_wfm = np.float32(ex_wfm)
self.FFT_BE_wave = bin_FFT
(UDVS_labs, UDVS_units, UDVS_mat) = self.__buildUDVSTable(parm_dict)
# Remove the unused plot group columns before proceeding:
(UDVS_mat, UDVS_labs, UDVS_units) = trimUDVS(UDVS_mat, UDVS_labs,
UDVS_units,
ignored_plt_grps)
spec_inds = np.zeros(shape=(2, tot_bins), dtype=INDICES_DTYPE)
# Will assume that all excitation waveforms have same number of bins
# Here, the denominator is 2 because only out of field measruements. For IF + OF, should be 1
num_actual_udvs_steps = UDVS_mat.shape[0] / 2
bins_per_step = tot_bins / num_actual_udvs_steps
# Some more checks
if bins_per_step % 1:
warn('Non integer number of bins per step!')
return
else:
bins_per_step = int(bins_per_step)
num_actual_udvs_steps = int(num_actual_udvs_steps)
stind = 0
for step_index in range(UDVS_mat.shape[0]):
if UDVS_mat[step_index, 2] < 1E-3: # invalid AC amplitude
continue # skip
spec_inds[0, stind:stind + bins_per_step] = np.arange(
bins_per_step, dtype=INDICES_DTYPE) # Bin step
spec_inds[1, stind:stind + bins_per_step] = step_index * np.ones(
bins_per_step, dtype=INDICES_DTYPE) # UDVS step
stind += bins_per_step
del stind, step_index
# Some very basic information that can help the processing / analysis crew
parm_dict['num_bins'] = tot_bins
parm_dict['num_pix'] = num_pix
parm_dict['num_udvs_steps'] = num_actual_udvs_steps
global_parms = generate_dummy_main_parms()
global_parms['grid_size_x'] = parm_dict['grid_num_cols']
global_parms['grid_size_y'] = parm_dict['grid_num_rows']
global_parms['experiment_date'] = parm_dict['File_date_and_time']
# assuming that the experiment was completed:
global_parms['current_position_x'] = parm_dict['grid_num_cols'] - 1
global_parms['current_position_y'] = parm_dict['grid_num_rows'] - 1
global_parms['data_type'] = parm_dict[
'data_type'] # self.__class__.__name__
global_parms['translator'] = 'ODF'
write_simple_attrs(self.h5_file, global_parms)
# Create Measurement and Channel groups
meas_grp = create_indexed_group(self.h5_file, 'Measurement')
write_simple_attrs(meas_grp, parm_dict)
chan_grp = create_indexed_group(meas_grp, 'Channel')
chan_grp.attrs['Channel_Input'] = parm_dict['IO_Analog_Input_1']
# Create Auxilliary Datasets
h5_ex_wfm = chan_grp.create_dataset('Excitation_Waveform', data=ex_wfm)
udvs_slices = dict()
for col_ind, col_name in enumerate(UDVS_labs):
udvs_slices[col_name] = (slice(None), slice(col_ind, col_ind + 1))
h5_UDVS = chan_grp.create_dataset('UDVS',
data=UDVS_mat,
dtype=np.float32)
write_simple_attrs(h5_UDVS, {'labels': UDVS_labs, 'units': UDVS_units})
h5_bin_steps = chan_grp.create_dataset('Bin_Steps',
data=np.arange(bins_per_step,
dtype=np.uint32),
dtype=np.uint32)
# Need to add the Bin Waveform type - infer from UDVS
exec_bin_vec = self.signal_type * np.ones(len(bin_inds),
dtype=np.int32)
h5_wfm_typ = chan_grp.create_dataset('Bin_Wfm_Type',
data=exec_bin_vec,
dtype=np.int32)
h5_bin_inds = chan_grp.create_dataset('Bin_Indices',
data=bin_inds,
dtype=np.uint32)
h5_bin_freq = chan_grp.create_dataset('Bin_Frequencies',
data=bin_freqs,
dtype=np.float32)
h5_bin_FFT = chan_grp.create_dataset('Bin_FFT',
data=bin_FFT,
dtype=np.complex64)
# Noise floor should be of shape: (udvs_steps x 3 x positions)
h5_noise_floor = chan_grp.create_dataset(
'Noise_Floor',
shape=(num_pix, num_actual_udvs_steps),
dtype=nf32,
chunks=(1, num_actual_udvs_steps))
"""
ONLY ALLOCATING SPACE FOR MAIN DATA HERE!
Chunk by each UDVS step - this makes it easy / quick to:
1. read data for a single UDVS step from all pixels
2. read an entire / multiple pixels at a time
The only problem is that a typical UDVS step containing 50 steps occupies only 400 bytes.
This is smaller than the recommended chunk sizes of 10,000 - 999,999 bytes
meaning that the metadata would be very substantial.
This assumption is fine since we almost do not handle any user defined cases
"""
"""
New Method for chunking the Main_Data dataset. Chunking is now done in N-by-N squares of UDVS steps by pixels.
N is determined dinamically based on the dimensions of the dataset. Currently it is set such that individual
chunks are less than 10kB in size.
Chris Smith -- [email protected]
"""
pos_dims = [
Dimension('X', 'nm', num_cols),
Dimension('Y', 'nm', num_rows)
]
# Create Spectroscopic Values and Spectroscopic Values Labels datasets
spec_vals, spec_inds, spec_vals_labs, spec_vals_units, spec_vals_names = createSpecVals(
UDVS_mat, spec_inds, bin_freqs, exec_bin_vec, parm_dict, UDVS_labs,
UDVS_units)
spec_dims = list()
for row_ind, row_name in enumerate(spec_vals_labs):
spec_dims.append(
Dimension(row_name, spec_vals_units[row_ind],
spec_vals[row_ind]))
pixel_chunking = maxReadPixels(10240, num_pix * num_actual_udvs_steps,
bins_per_step,
np.dtype('complex64').itemsize)
chunking = np.floor(np.sqrt(pixel_chunking))
chunking = max(1, chunking)
chunking = min(num_actual_udvs_steps, num_pix, chunking)
self.h5_main = write_main_dataset(chan_grp, (num_pix, tot_bins),
'Raw_Data',
'Piezoresponse',
'V',
pos_dims,
spec_dims,
dtype=np.complex64,
chunks=(chunking,
chunking * bins_per_step),
compression='gzip')
self.mean_resp = np.zeros(shape=(self.ds_main.shape[1]),
dtype=np.complex64)
self.max_resp = np.zeros(shape=(self.ds_main.shape[0]),
dtype=np.float32)
self.min_resp = np.zeros(shape=(self.ds_main.shape[0]),
dtype=np.float32)
# Now read the raw data files:
self._read_data(path_dict['read_real'], path_dict['read_imag'],
parm_dict)
self.h5_file.flush()
generatePlotGroups(self.ds_main,
self.mean_resp,
folder_path,
basename,
self.max_resp,
self.min_resp,
max_mem_mb=self.max_ram,
spec_label=spec_label,
show_plots=show_plots,
save_plots=save_plots,
do_histogram=do_histogram)
self.h5_file.close()
return h5_path
def translate(self, file_path, *args, **kwargs):
"""
Translates a given Bruker / Veeco / Nanoscope AFM derived file to HDF5. Currently handles scans, force curves,
and force-distance maps
Note that this translator was written with a single example file for each modality and may be buggy.
Parameters
----------
file_path : str / unicode
path to data file
Returns
-------
h5_path : str / unicode
path to translated HDF5 file
"""
self.file_path = path.abspath(file_path)
self.meta_data, other_parms = self._extract_metadata()
# These files are weirdly named with extensions such as .001
h5_path = file_path.replace('.', '_') + '.h5'
if path.exists(h5_path):
remove(h5_path)
h5_file = h5py.File(h5_path, 'w')
type_suffixes = ['Image', 'Force_Curve', 'Force_Map']
# 0 - stack of scan images
# 1 - single force curve
# 2 - force map
force_count = 0
image_count = 0
for class_name in self.meta_data.keys():
if 'Ciao force image list' in class_name:
force_count += 1
elif 'Ciao image list' in class_name:
image_count += 1
data_type = 0
if force_count > 0:
if image_count > 0:
data_type = 2
else:
data_type = 1
global_parms = generate_dummy_main_parms()
global_parms['data_type'] = 'Bruker_AFM_' + type_suffixes[data_type]
global_parms['translator'] = 'Bruker_AFM'
write_simple_attrs(h5_file, global_parms)
# too many parameters. Making a dummy group just for the parameters.
h5_parms_grp = h5_file.create_group('Parameters')
# We currently have a dictionary of dictionaries. This needs to be flattened
flat_dict = dict()
for class_name, sub_dict in other_parms.items():
for key, val in sub_dict.items():
flat_dict[class_name + '_' + key] = val
write_simple_attrs(h5_parms_grp, flat_dict)
# Create measurement group
h5_meas_grp = create_indexed_group(h5_file, 'Measurement')
# Call the data specific translation function
trans_funcs = [self._translate_image_stack, self._translate_force_curve, self._translate_force_map]
trans_funcs[data_type](h5_meas_grp)
# wrap up and return path
h5_file.close()
return h5_path
