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Commit e07fec58 authored by Unknown's avatar Unknown
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Update interactive sho and loop plotters to use generic bias dimension

parent 5be080eb
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Showing with 91 additions and 59 deletions
pycroscopy/viz/be_viz_utils.py
View file @ e07fec58
......@@ -328,8 +328,7 @@ def jupyter_visualize_beps_sho(h5_sho_dset, step_chan, resp_func=None, resp_labe
plt.show()
def update_sho_plots(sho_quantity, **kwargs):
step_ind = kwargs['Bias Step']
def update_sho_plots(sho_quantity, step_ind):
bias_slider.set_xdata((step_ind, step_ind))
spatial_map = sho_dset_collapsed[:, :, step_ind, 0][sho_quantity]
map_title = '{} - {}={}'.format(sho_quantity, step_chan, bias_mat[step_ind][0])
......@@ -368,10 +367,15 @@ def jupyter_visualize_beps_sho(h5_sho_dset, step_chan, resp_func=None, resp_labe
slider_dict = dict()
slider_dict['Bias Step'] = (0, bias_mat.shape[0] - 1, 1)
sho_quantity_picker = widgets.Dropdown(options=list(sho_dset_collapsed.dtype.names[:-1]),
description='SHO Quantity')
bias_step_picker = widgets.IntSlider(min=0, max=bias_mat.shape[0]-1, step=1,
description='Bias Step')
cid = img_map.figure.canvas.mpl_connect('button_press_event', pos_picker)
display(save_fig_filebox_button(fig, h5_sho_dset.file.filename))
widgets.interact(update_sho_plots, sho_quantity=list(sho_dset_collapsed.dtype.names[:-1]), **slider_dict)
widgets.interact(update_sho_plots, sho_quantity=sho_quantity_picker, step_ind=bias_step_picker)
def jupyter_visualize_be_spectrograms(h5_main, cmap=None):
"""
......@@ -619,14 +623,16 @@ def jupyter_visualize_beps_loops(h5_projected_loops, h5_loop_guess, h5_loop_fit,
# Also reshape the projected loops to Positions-DC_Step-Loop
final_loop_shape = pos_dims + [loop_spec_dims[spec_step_dim_ind]] + [-1]
proj_nd_3 = np.reshape(proj_nd, final_loop_shape)
proj_nd2 = np.moveaxis(proj_nd, spec_step_dim_ind+len(pos_dims), len(pos_dims))
proj_nd_3 = np.reshape(proj_nd2, final_loop_shape)
# Do the same for the guess and fit datasets
guess_3d = np.reshape(guess_nd, pos_dims + [-1])
fit_3d = np.reshape(fit_nd, pos_dims + [-1])
# Get the bias vector:
bias_vec = np.reshape(spec_nd[spec_step_dim_ind], final_loop_shape[len(pos_dims):])
spec_nd2 = np.moveaxis(spec_nd[spec_step_dim_ind], spec_step_dim_ind, 0)
bias_vec = np.reshape(spec_nd2, final_loop_shape[len(pos_dims):])
# Shift the bias vector and the loops by a quarter cycle
shift_ind = int(-1 * bias_vec.shape[0] / 4)
......@@ -719,6 +725,8 @@ def jupyter_visualize_beps_loops(h5_projected_loops, h5_loop_guess, h5_loop_fit,
crosshair.set_xdata(xdata)
crosshair.set_ydata(ydata)
loop_ind = loop_slider.value
proj_data = proj_nd_shifted[xdata, ydata, :, loop_ind]
bias_data = bias_shifted[:, loop_ind]
guess_data = loop_fit_function(bias_data, np.array(list(guess_3d[xdata, ydata, loop_ind])))
......@@ -756,9 +764,6 @@ def jupyter_visualize_parameter_maps(h5_loop_parameters, cmap=None, **kwargs):
h5_loop_parameters = PycroDataset(h5_loop_parameters)
# Get the position and spectroscopic datasets
h5_loop_pos_inds = h5_loop_parameters.h5_pos_inds
h5_loop_spec_vals = h5_loop_parameters.h5_pos_vals
pos_dims = h5_loop_parameters.pos_dim_sizes
num_cycles = h5_loop_parameters.shape[1]
......@@ -788,7 +793,7 @@ def jupyter_visualize_parameter_maps(h5_loop_parameters, cmap=None, **kwargs):
[pos_dims[0], pos_dims[1], -1])
fig.suptitle('Maps of Loop Parameter {}'.format(parameter_name))
# Loop over all axes
for icycle, ax_cycle in enumerate(axes):
for icycle, ax_cycle in enumerate(axes[:num_cycles]):
image = ax_cycle.get_images()[0]
image.set_data(parameter_map_stack[:, :, icycle])
image.set_clim(vmin=np.min(parameter_map_stack[:, :, icycle]),
......@@ -1054,7 +1059,8 @@ def jupyter_visualize_loop_sho_raw_comparison(h5_loop_parameters, cmap=None):
def plot_loop_sho_raw_comparison(h5_loop_parameters, selected_loop_parm=None, selected_loop_cycle=0,
selected_loop_pos=[0,0], selected_step=0, tick_font_size=14, cmap='viridis'):
selected_loop_pos=[0,0], selected_step=0, tick_font_size=14, cmap='viridis',
step_chan='DC_Offset'):
"""
Parameters
......@@ -1069,64 +1075,67 @@ def plot_loop_sho_raw_comparison(h5_loop_parameters, selected_loop_parm=None, se
The initial position to be plotted
selected_step : int
The initial bias step to be plotted
tick_font_size : 14
tick_font_size : int
Font size for the axes tick labels
cmap : str or matplotlib.colors.Colormap
Colormap to be used in plotting the parameter map
step_chan : str
Name of spectral dimension loops were fit over
Returns
-------
None
"""
if not isinstance(h5_loop_parameters, PycroDataset):
h5_loop_parameters = PycroDataset(h5_loop_parameters)
# Find the precursor datasets used to calculate these parameters
h5_loop_grp = h5_loop_parameters.parent
h5_loop_projections = h5_loop_grp['Projected_Loops']
h5_loop_fit = h5_loop_grp['Fit']
h5_loop_guess = h5_loop_grp['Guess']
h5_loop_projections = PycroDataset(h5_loop_grp['Projected_Loops'], sort_dims=False)
h5_loop_fit = PycroDataset(h5_loop_grp['Fit'], sort_dims=False)
h5_loop_guess = PycroDataset(h5_loop_grp['Guess'], sort_dims=False)
h5_sho_grp = h5_loop_grp.parent
h5_sho_fit = h5_sho_grp['Fit']
h5_sho_guess = h5_sho_grp['Guess']
h5_sho_fit = PycroDataset(h5_sho_grp['Fit'], sort_dims=False)
h5_sho_guess = PycroDataset(h5_sho_grp['Guess'], sort_dims=False)
h5_main = get_source_dataset(h5_sho_grp)
h5_main.toggle_sorting()
# Now get the needed ancillary datasets for each main dataset
h5_pos_inds = getAuxData(h5_loop_parameters, 'Position_Indices')[0]
h5_pos_vals = getAuxData(h5_loop_parameters, 'Position_Values')[0]
pos_order = get_sort_order(np.transpose(h5_pos_inds))
pos_dims = get_dimensionality(np.transpose(h5_pos_inds), pos_order)
pos_labs = get_attr(h5_pos_inds, 'labels')
pos_dims = h5_loop_parameters.pos_dim_sizes
pos_labs = h5_loop_parameters.pos_dim_labels
h5_loop_spec_inds = getAuxData(h5_loop_parameters, 'Spectroscopic_Indices')[0]
h5_loop_spec_vals = getAuxData(h5_loop_parameters, 'Spectroscopic_Values')[0]
loop_spec_order = get_sort_order(h5_loop_spec_inds)
loop_spec_dims = get_dimensionality(h5_loop_spec_inds, loop_spec_order)
loop_spec_labs = get_attr(h5_loop_spec_inds, 'labels')
# h5_loop_spec_inds = h5_loop_parameters.h5_spec_inds
h5_loop_spec_vals = h5_loop_parameters.h5_spec_vals
# loop_spec_order = get_sort_order(h5_loop_spec_inds)
loop_spec_dims = h5_loop_parameters.spec_dim_sizes
loop_spec_labs = h5_loop_parameters.spec_dim_labels
h5_sho_spec_inds = getAuxData(h5_sho_fit, 'Spectroscopic_Indices')[0]
h5_sho_spec_vals = getAuxData(h5_sho_fit, 'Spectroscopic_Values')[0]
sho_spec_order = get_sort_order(h5_sho_spec_inds)
sho_spec_dims = get_dimensionality(h5_sho_spec_inds, sho_spec_order)
sho_spec_labs = get_attr(h5_sho_spec_inds, 'labels')
h5_sho_spec_inds = h5_sho_fit.h5_spec_inds
h5_sho_spec_vals = h5_sho_fit.h5_spec_vals
# sho_spec_order = get_sort_order(h5_sho_spec_inds)
sho_spec_dims = h5_sho_fit.spec_dim_sizes
sho_spec_labs = h5_sho_fit.spec_dim_labels
h5_main_spec_inds = getAuxData(h5_main, 'Spectroscopic_Indices')[0]
h5_main_spec_vals = getAuxData(h5_main, 'Spectroscopic_Values')[0]
main_spec_order = get_sort_order(h5_main_spec_inds)
main_spec_dims = get_dimensionality(h5_main_spec_inds, main_spec_order)
main_spec_labs = get_attr(h5_main_spec_inds, 'labels')
h5_main_spec_inds = h5_main.h5_spec_inds
h5_main_spec_vals = h5_main.h5_spec_vals
# main_spec_order = get_sort_order(h5_main_spec_inds)
main_spec_dims = h5_main.spec_dim_sizes
main_spec_labs = h5_main.spec_dim_labels
'''
Select the initial plotting slices
'''
loop_parameter_names = h5_loop_parameters.dtype.names
loop_num_cycles = h5_loop_parameters.shape[1]
loop_parameter_spec_labs = get_attr(h5_loop_spec_vals, 'labels')
sho_bias_dim = np.argwhere(sho_spec_labs[sho_spec_order] == 'DC_Offset').squeeze()
# loop_parameter_spec_labs = h5_loop_parameters.spec_dim_labels
sho_bias_dim = np.argwhere(np.array(sho_spec_labs) == step_chan).squeeze()
steps_per_loop = sho_spec_dims[sho_bias_dim]
main_bias_dim = np.argwhere(main_spec_labs[main_spec_order] == 'DC_Offset').squeeze()
main_freq_dim = np.argwhere(main_spec_labs[main_spec_order] == 'Frequency').squeeze()
main_bias_dim = np.argwhere(np.array(main_spec_labs) == step_chan).squeeze()
main_freq_dim = np.argwhere(np.array(main_spec_labs) == 'Frequency').squeeze()
if selected_loop_parm is None:
selected_loop_parm = loop_parameter_names[0]
......@@ -1135,7 +1144,7 @@ def plot_loop_sho_raw_comparison(h5_loop_parameters, selected_loop_parm=None, se
'''
Get the bias vector to be plotted against
'''
loop_bias_vec = h5_sho_spec_vals[get_attr(h5_sho_spec_vals, 'DC_Offset')].squeeze()
loop_bias_vec = h5_sho_spec_vals[get_attr(h5_sho_spec_vals, step_chan)].squeeze()
shift_ind = int(-1 * steps_per_loop / 4)
loop_bias_vec = loop_bias_vec.reshape(sho_spec_dims[::-1])
loop_bias_vec = np.moveaxis(loop_bias_vec, len(loop_bias_vec.shape)-sho_bias_dim-1, 0)
......@@ -1159,53 +1168,76 @@ def plot_loop_sho_raw_comparison(h5_loop_parameters, selected_loop_parm=None, se
# Also create the title string for the map
loop_map_title = list()
for label in loop_parameter_spec_labs:
for label in loop_spec_labs:
val = h5_loop_spec_vals[get_attr(h5_loop_spec_vals, label)].squeeze()[selected_loop_cycle]
loop_map_title.append('{}: {}'.format(label, val))
loop_map_title.append('{}: {}'.format(label, val))
loop_map_title = ' - '.join(loop_map_title)
return loop_parameter_map, loop_map_title
def _get_loops(selected_loop_cycle, selected_loop_pos):
selected_loop_ndims = np.unravel_index(selected_loop_cycle, loop_spec_dims, order='F')
selected_loop_ndims = np.unravel_index(selected_loop_cycle, loop_spec_dims[::-1], order='F')
# Now build the loop plot for the selected position in the loop map
selected_loop_bias_vec = loop_bias_vec[:, selected_loop_cycle]
pos_ind = np.ravel_multi_index(selected_loop_pos, pos_dims)
loop_proj_vec = h5_loop_projections[pos_ind].reshape(sho_spec_dims[::-1])
loop_proj_vec = np.moveaxis(loop_proj_vec, len(sho_spec_dims)-sho_bias_dim-1, -1)[selected_loop_ndims]
loop_proj_vec = np.roll(loop_proj_vec, shift_ind)
slice_dict = dict()
for pos_dim, dim_ind in zip(pos_labs, selected_loop_pos):
slice_dict[pos_dim] = [dim_ind]
for spec_dim, dim_ind in zip(loop_spec_labs, selected_loop_ndims):
slice_dict[spec_dim] = [dim_ind]
loop_proj_vec, _ = h5_loop_projections.slice(False, slice_dict)
loop_proj_vec2 = np.roll(loop_proj_vec.squeeze(), shift_ind)
loop_guess_slice, _ = h5_loop_guess.slice(True, slice_dict)
loop_fit_slice, _ = h5_loop_fit.slice(True, slice_dict)
# loop_proj_vec = h5_loop_projections[pos_ind].reshape(sho_spec_dims[::-1])
# loop_proj_vec2 = np.rollaxis(loop_proj_vec,
# len(sho_spec_dims)-sho_bias_dim-1,
# len(sho_spec_dims))[selected_loop_ndims]
# loop_proj_vec3 = np.roll(loop_proj_vec2, shift_ind)
loop_guess_vec = loop_fit_function(selected_loop_bias_vec,
h5_loop_guess[pos_ind, selected_loop_cycle].tolist())
loop_guess_slice.squeeze().tolist())
loop_fit_vec = loop_fit_function(selected_loop_bias_vec,
h5_loop_fit[pos_ind, selected_loop_cycle].tolist())
loop_fit_slice.squeeze().tolist())
return selected_loop_bias_vec, loop_proj_vec, loop_guess_vec, loop_fit_vec
return selected_loop_bias_vec, loop_proj_vec2, loop_guess_vec, loop_fit_vec
def _get_sho(selected_loop_pos, selected_step, selected_loop_cycle):
selected_loop_ndims = np.unravel_index(selected_loop_cycle, loop_spec_dims, order='F')
selected_loop_ndims = np.unravel_index(selected_loop_cycle, loop_spec_dims[::-1], order='F')
# get the SHO Guess and Fit and Raw Data for the selected position, cycle, and step
pos_ind = np.ravel_multi_index(selected_loop_pos, pos_dims)
# Get the frequency vector for the selected step
w_vec = np.moveaxis(full_w_vec, main_freq_dim, -1)[selected_step][selected_loop_ndims]
w_vec = np.rollaxis(full_w_vec, main_freq_dim, len(main_spec_dims)) # Move frequency to the end
w_vec2 = np.rollaxis(w_vec, main_bias_dim-1, 0)[selected_step][selected_loop_ndims[::-1]]
# Get the slice of the sho guess and fit
sho_guess = h5_sho_guess[pos_ind].reshape(sho_spec_dims[::-1])
sho_guess = np.moveaxis(sho_guess, len(sho_spec_dims)-sho_bias_dim-1, -1)[selected_loop_ndims][selected_step]
sho_guess = SHOfunc(sho_guess, w_vec)
sho_guess = np.rollaxis(sho_guess,
len(sho_spec_dims)-sho_bias_dim-1,
len(sho_spec_dims))[selected_loop_ndims][selected_step]
sho_guess = SHOfunc(sho_guess, w_vec2)
sho_fit = h5_sho_fit[pos_ind].reshape(sho_spec_dims[::-1])
sho_fit = np.moveaxis(sho_fit, len(sho_spec_dims)-sho_bias_dim-1, -1)[selected_loop_ndims][selected_step]
sho_fit = SHOfunc(sho_fit, w_vec)
sho_fit = np.rollaxis(sho_fit,
len(sho_spec_dims)-sho_bias_dim-1,
len(sho_spec_dims))[selected_loop_ndims][selected_step]
sho_fit = SHOfunc(sho_fit, w_vec2)
# Get the slice of the Raw Data
raw_data_vec, _ = reshape_to_Ndims(np.atleast_2d(h5_main[pos_ind]), h5_spec=h5_main_spec_inds)
raw_data_vec = np.moveaxis(raw_data_vec.squeeze(),
main_freq_dim, -1)[selected_step][selected_loop_ndims]
# Move freqency dimension to the end
raw_data_vec2 = np.rollaxis(raw_data_vec.squeeze(), main_freq_dim, len(main_spec_dims))
# Now move the bias dimension to the front
raw_data_vec3 = np.rollaxis(raw_data_vec2, main_bias_dim-1, 0)[selected_step][selected_loop_ndims[::-1]]
return w_vec, sho_guess, sho_fit, raw_data_vec
return w_vec2, sho_guess, sho_fit, raw_data_vec3
'''
Get the starting values
......
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