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Commit 9c449383 authored by Unknown's avatar Unknown
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Generalize BELoopModel 

Allow fitting against arbitrary dimension name.
parent 30e94481
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pycroscopy/analysis/be_loop_model.py
View file @ 9c449383
......@@ -80,12 +80,13 @@ class BELoopModel(Model):
self._current_pos_slice = slice(None)
self._current_sho_spec_slice = slice(None)
self._current_met_spec_slice = slice(None)
self._dc_offset_index = 0
self._fit_offset_index = 0
self._sho_all_but_forc_inds = None
self._sho_all_but_dc_forc_inds = None
self._met_all_but_forc_inds = None
self._current_forc = 0
self._maxDataChunk = 1
self._fit_dim = variables[0]
def _is_legal(self, h5_main, variables=['DC_Offset']):
"""
......@@ -105,26 +106,37 @@ class BELoopModel(Model):
Whether or not this dataset satisfies the necessary conditions for analysis
"""
if get_attr(h5_main.file, 'data_type') != 'BEPSData':
warn('Provided dataset does not appear to be a BEPS dataset')
return False
elif not h5_main.name.startswith('/Measurement_'):
warn('Provided dataset is not derived from a measurement group')
return False
file_data_type = get_attr(h5_main.file, 'data_type')
meas_grp_name = h5_main.name.split('/')
h5_meas_grp = h5_main.file[meas_grp_name[1]]
meas_data_type = get_attr(h5_meas_grp, 'data_type')
if get_attr(h5_meas_grp, 'VS_mode') not in ['DC modulation mode', 'current mode']:
warn('Provided dataset is not a DC modulation or current mode BEPS dataset')
return False
elif get_attr(h5_meas_grp, 'VS_cycle_fraction') != 'full':
warn('Provided dataset does not have full cycles')
return False
elif h5_main.dtype != sho32:
if h5_main.dtype != sho32:
warn('Provided dataset is not a SHO results dataset.')
return False
# This check is clunky but should account for case differences. If Python2 support is dropped, simplify with
# single check using casefold.
if not (meas_data_type.lower != file_data_type.lower or meas_data_type.upper != file_data_type.upper):
warn('Mismatch between file and Measurement group data types for the chosen dataset.')
print('File data type is {}. The data type for Measurement group {} is {}'.format(file_data_type,
h5_meas_grp.name,
meas_data_type))
return False
if file_data_type == 'BEPSData':
if get_attr(h5_meas_grp, 'VS_mode') not in ['DC modulation mode', 'current mode']:
warn('Provided dataset is not a DC modulation or current mode BEPS dataset')
return False
elif get_attr(h5_meas_grp, 'VS_cycle_fraction') != 'full':
warn('Provided dataset does not have full cycles')
return False
elif file_data_type == 'cKPFMData':
if get_attr(h5_meas_grp, 'VS_mode') != 'cKPFM':
warn('Provided dataset has an unsupported VS_mode.')
return False
return super(BELoopModel, self)._is_legal(h5_main, variables)
def _set_guess(self, h5_guess):
......@@ -148,9 +160,9 @@ class BELoopModel(Model):
'''
Find the Spectroscopic index for the DC_Offset
'''
dc_ind = np.argwhere(get_attr(self._sho_spec_vals, 'labels') == 'DC_Offset').squeeze()
self._dc_spec_index = dc_ind
self._dc_offset_index = 1 + dc_ind
fit_ind = np.argwhere(get_attr(self._sho_spec_vals, 'labels') == self._fit_dim).squeeze()
self._fit_spec_index = fit_ind
self._fit_offset_index = 1 + fit_ind
'''
Get the group and projection datasets
......@@ -236,12 +248,12 @@ class BELoopModel(Model):
'''
Do the projection and guess
'''
projected_loops_2d, loop_metrics_1d = self._project_loop_batch(self.dc_vec, np.transpose(loops_2d))
guessed_loops = self._guess_loops(self.dc_vec, projected_loops_2d)
projected_loops_2d, loop_metrics_1d = self._project_loop_batch(self.fit_dim_vec, np.transpose(loops_2d))
guessed_loops = self._guess_loops(self.fit_dim_vec, projected_loops_2d)
# Reshape back
if len(self._sho_all_but_forc_inds) != 1:
projected_loops_2d = self._reshape_projected_loops_for_h5(projected_loops_2d.T,
projected_loops_2d2 = self._reshape_projected_loops_for_h5(projected_loops_2d.T,
order_dc_offset_reverse,
nd_mat_shape_dc_first,
verbose=verbose)
......@@ -250,7 +262,7 @@ class BELoopModel(Model):
guessed_loops_2 = self._reshape_results_for_h5(guessed_loops, nd_mat_shape_dc_first, verbose=verbose)
# Store results
self.h5_projected_loops[self._start_pos:self._end_pos, self._current_sho_spec_slice] = projected_loops_2d
self.h5_projected_loops[self._start_pos:self._end_pos, self._current_sho_spec_slice] = projected_loops_2d2
self.h5_loop_metrics[self._start_pos:self._end_pos, self._current_met_spec_slice] = metrics_2d
self.h5_guess[self._start_pos:self._end_pos, self._current_met_spec_slice] = guessed_loops_2
......@@ -357,7 +369,7 @@ class BELoopModel(Model):
'''
Shift the loops and vdc vector
'''
shift_ind, vdc_shifted = self.shift_vdc(self.dc_vec)
shift_ind, vdc_shifted = self.shift_vdc(self.fit_dim_vec)
loops_2d_shifted = np.roll(loops_2d, shift_ind, axis=0).T
'''
......@@ -435,18 +447,18 @@ class BELoopModel(Model):
"""
# First grab the spectroscopic indices and values and position indices
self._sho_spec_inds = getAuxData(self.h5_main, auxDataName=['Spectroscopic_Indices'])[0]
self._sho_spec_vals = getAuxData(self.h5_main, auxDataName=['Spectroscopic_Values'])[0]
self._sho_pos_inds = getAuxData(self.h5_main, auxDataName=['Position_Indices'])[0]
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
dc_ind = np.argwhere(get_attr(self._sho_spec_vals, 'labels') == 'DC_Offset').squeeze()
not_dc = get_attr(self._sho_spec_vals, 'labels') != 'DC_Offset'
fit_dim_ind = self.h5_main.spec_dim_labels.index(self._fit_dim)
not_fit_dim = np.arange(len(self.h5_main.spec_dim_labels)) != fit_dim_ind
self._dc_spec_index = dc_ind
self._dc_offset_index = 1 + dc_ind
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[dc_ind, :] == 0).flatten()
cycle_start_inds = np.argwhere(self._sho_spec_inds[fit_dim_ind, :] == 0).flatten()
tot_cycles = cycle_start_inds.size
# Prepare containers for the dataets
......@@ -457,7 +469,7 @@ class BELoopModel(Model):
maxshape=(self.h5_main.shape[0], tot_cycles))
ds_loop_met_spec_inds, ds_loop_met_spec_vals = buildReducedSpec(self._sho_spec_inds, self._sho_spec_vals,
not_dc, cycle_start_inds,
not_fit_dim, cycle_start_inds,
basename='Loop_Metrics')
# name of the dataset being projected.
......@@ -517,12 +529,12 @@ class BELoopModel(Model):
"""
# Step 1: Find number of FORC cycles and repeats (if any), DC steps, and number of loops
# dc_offset_index = np.argwhere(self._sho_spec_inds.attrs['labels'] == 'DC_Offset').squeeze()
num_dc_steps = np.unique(self._sho_spec_inds[self._dc_spec_index, :]).size
num_dc_steps = np.unique(self._sho_spec_inds[self._fit_spec_index, :]).size
all_spec_dims = list(range(self._sho_spec_inds.shape[0]))
all_spec_dims.remove(self._dc_spec_index)
all_spec_dims.remove(self._fit_spec_index)
# Remove FORC_cycles
sho_spec_labels = get_attr(self._sho_spec_inds, 'labels')
sho_spec_labels = self.h5_main.spec_dim_labels
has_forcs = 'FORC' in sho_spec_labels or 'FORC_Cycle' in sho_spec_labels
if has_forcs:
forc_name = 'FORC' if 'FORC' in sho_spec_labels else 'FORC_Cycle'
......@@ -600,12 +612,12 @@ class BELoopModel(Model):
h5_pos=None,
h5_spec=self._sho_spec_inds[self._sho_all_but_forc_inds,
self._current_sho_spec_slice])
dim_names_orig = np.hstack(('Positions',
get_attr(self._sho_spec_inds, 'labels')[self._sho_all_but_forc_inds]))
if not success:
warn('Error - could not reshape provided raw data chunk...')
return None
dim_names_orig = np.hstack(('Positions', np.array(self.h5_main.spec_dim_labels)[self._sho_all_but_forc_inds]))
if verbose:
print('Shape of N dimensional dataset:', fit_nd.shape)
print('Dimensions of order:', dim_names_orig)
......@@ -614,10 +626,10 @@ class BELoopModel(Model):
# order_dc_offset_reverse = np.roll(range(fit_nd.ndim), self._dc_offset_index)
# step 5: Move the voltage dimension to the first dim
order_dc_outside_nd = [self._dc_offset_index] + list(range(self._dc_offset_index)) + \
list(range(self._dc_offset_index + 1, len(fit_nd.shape)))
order_dc_offset_reverse = list(range(1, self._dc_offset_index + 1)) + [0] + \
list(range(self._dc_offset_index + 1, len(fit_nd.shape)))
order_dc_outside_nd = [self._fit_offset_index] + list(range(self._fit_offset_index)) + \
list(range(self._fit_offset_index + 1, len(fit_nd.shape)))
order_dc_offset_reverse = list(range(1, self._fit_offset_index + 1)) + [0] + \
list(range(self._fit_offset_index + 1, len(fit_nd.shape)))
fit_nd2 = np.transpose(fit_nd, tuple(order_dc_outside_nd))
dim_names_dc_out = dim_names_orig[order_dc_outside_nd]
if verbose:
......@@ -736,33 +748,45 @@ class BELoopModel(Model):
DC offsets for the current FORC step
"""
spec_sort = get_sort_order(self._sho_spec_inds[self._sho_all_but_forc_inds, self._current_sho_spec_slice])
# get the size for each of these dimensions
spec_dims = get_dimensionality(self._sho_spec_inds[self._sho_all_but_forc_inds,
self._current_sho_spec_slice], spec_sort)
spec_dims = self.h5_main.spec_dim_sizes
# apply this knowledge to reshape the spectroscopic values
# remember to reshape such that the dimensions are arranged in reverse order (slow to fast)
spec_vals_nd = np.reshape(self._sho_spec_vals[self._sho_all_but_forc_inds, self._current_sho_spec_slice],
[-1] + spec_dims[::-1])
spec_vals_nd, success = reshape_to_Ndims(self._sho_spec_vals[self._sho_all_but_forc_inds,
self._current_sho_spec_slice],
h5_spec=self._sho_spec_inds[self._sho_all_but_forc_inds,
self._current_sho_spec_slice])
# This should result in a N+1 dimensional matrix where the first index contains the actual data
# the other dimensions are present to easily slice the data
spec_labels_sorted = np.hstack(('Dim', get_attr(self._sho_spec_inds, 'labels')[spec_sort[::-1]]))
spec_labels_sorted = np.hstack(('Dim', self.h5_main.spec_dim_labels))
if verbose:
print('Spectroscopic dimensions sorted by rate of change:')
print(spec_labels_sorted)
# slice the N dimensional dataset such that we only get the DC offset for default values of other dims
dc_pos = np.argwhere(spec_labels_sorted == 'DC_Offset')[0][0]
dc_slice = list()
for dim_ind in range(spec_labels_sorted.size):
if dim_ind == dc_pos:
dc_slice.append(slice(None))
fit_dim_pos = np.argwhere(spec_labels_sorted == self._fit_dim)[0][0]
# fit_dim_slice = list()
# for dim_ind in range(spec_labels_sorted.size):
# if dim_ind == fit_dim_pos:
# fit_dim_slice.append(slice(None))
# else:
# fit_dim_slice.append(slice(0, 1))
fit_dim_slice = [fit_dim_pos]
for idim, dim in enumerate(spec_labels_sorted[1:]):
if dim == self._fit_dim:
fit_dim_slice.append(slice(None))
fit_dim_slice[0] = idim
else:
dc_slice.append(slice(0, 1))
fit_dim_slice.append(slice(0, 1))
if verbose:
print('slice to extract Vdc:')
print(dc_slice)
print(fit_dim_slice)
self.dc_vec = np.squeeze(spec_vals_nd[tuple(dc_slice)])
self.fit_dim_vec = np.squeeze(spec_vals_nd[tuple(fit_dim_slice)])
return
......
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