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series_plotter.py
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series_plotter.py
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import os
import io
import zipfile
import copy
import numpy as np
import ipywidgets as ipw
from IPython.display import display, clear_output, HTML
import matplotlib
import matplotlib.pyplot as plt
from apps.scanning_probe import igor
colormaps = ['seismic', 'gist_heat']
def remove_from_tuple(tup, index):
tmp_list = list(tup)
del tmp_list[index]
return tuple(tmp_list)
def make_plot(fig, ax, data, extent, title=None, title_size=None, center0=False, vmin=None, vmax=None, cmap='gist_heat', noadd=False):
if center0:
data_amax = np.max(np.abs(data))
im = ax.imshow(data.T, origin='lower', cmap=cmap, interpolation='bicubic', extent=extent, vmin=-data_amax, vmax=data_amax)
else:
im = ax.imshow(data.T, origin='lower', cmap=cmap, interpolation='bicubic', extent=extent, vmin=vmin, vmax=vmax)
if noadd:
ax.set_xticks([])
ax.set_yticks([])
else:
ax.set_xlabel(r"x ($\AA$)")
ax.set_ylabel(r"y ($\AA$)")
#if 1e-3 < np.max(data) < 1e3:
# cb = fig.colorbar(im, ax=ax)
#else:
# cb = fig.colorbar(im, ax=ax, format=FormatScalarFormatter("%.1f"))
cb = fig.colorbar(im, ax=ax)
cb.formatter.set_powerlimits((-2, 2))
cb.update_ticks()
ax.set_title(title, loc='left')
if title_size:
ax.title.set_fontsize(title_size)
ax.axis('scaled')
def make_series_label(info, i_spin=None):
if info['type'] == 'const-height sts':
label = 'ch-sts fwhm=%.2f h=%.1f' % (info['fwhm'], info['height'])
elif info['type'] == 'const-height stm':
label = 'ch-stm fwhm=%.2f h=%.1f' % (info['fwhm'], info['height'])
elif info['type'] == 'const-isovalue sts':
label = 'cc-sts fwhm=%.2f isov=%.0e' % (info['fwhm'], info['isovalue'])
elif info['type'] == 'const-isovalue stm':
label = 'cc-stm fwhm=%.2f isov=%.0e' % (info['fwhm'], info['isovalue'])
elif info['type'] == 'const-height orbital':
label = 'ch-orb h=%.1f' % info['height']
elif info['type'] == 'const-height orbital^2':
label = 'ch-orb^2 h=%.1f' % info['height']
elif info['type'] == 'const-isovalue orbital^2':
label = 'cc-orb^2 isov=%.0e' % info['isovalue']
elif info['type'] == 'const-height orbital sts':
label = 'ch-orb^2 h=%.1f' % info['height']
elif info['type'] == 'const-isovalue orbital sts':
label = 'cc-orb^2 isov=%.0e' % info['isovalue']
else:
print("No support for: " + str(info))
if i_spin is not None:
label += ", s%d" % i_spin
return label
def make_orb_label(index, homo_index):
i_rel_homo = index - homo_index
if i_rel_homo < 0:
hl_label = "HOMO%+d" % i_rel_homo
elif i_rel_homo == 0:
hl_label = "HOMO"
elif i_rel_homo == 1:
hl_label = "LUMO"
else:
hl_label = "LUMO%+d" % (i_rel_homo-1)
return "MO %d, " % index + hl_label
class SeriesPlotter():
def __init__(self, select_indexes_function, zip_prepend):
self.series = {}
self.extent = None
self.figure_xy_ratio = None
self.wc_pk = None
self.zip_prepend = zip_prepend
self.select_indexes_function = select_indexes_function
### -------------------------------------------
### Selector
self.elem_list = []
self.selections_vbox = ipw.VBox([])
self.add_row_btn = ipw.Button(description='Add series row', disabled=True)
self.add_row_btn.on_click(lambda b: self.add_selection_row())
style = {'description_width': '80px'}
layout = {'width': '40%'}
self.selector_widget = ipw.VBox([self.add_row_btn, self.selections_vbox])
### -------------------------------------------
### Plotter
self.plot_btn = ipw.Button(description='Plot', disabled=True)
self.plot_btn.on_click(self.plot_series)
self.clear_btn = ipw.Button(description='Clear', disabled=True)
self.clear_btn.on_click(self.full_clear)
self.plot_output = ipw.VBox()
### -------------------------------------------
self.fig_y = 4
### -------------------------------------------
### Creating a zip
self.zip_btn = ipw.Button(description='Image zip', disabled=True)
self.zip_btn.on_click(self.create_zip_link)
self.zip_progress = ipw.FloatProgress(
value=0,
min=0,
max=1.0,
description='progress:',
bar_style='info',
orientation='horizontal'
)
self.link_out = ipw.Output()
def add_series_collection(self, general_info, series_info, series_data):
# self.series : "series_label": (data_series, series_info, general_info)
for info, data in zip(series_info, series_data):
spin = general_info.get('spin')
series_label = make_series_label(info, i_spin=spin)
self.series[series_label] = (data, info, general_info)
if info['type'] == 'const-height orbital':
sq_info = copy.deepcopy(info)
sq_info['type'] = 'const-height orbital^2'
sq_data = copy.deepcopy(data) ** 2
series_label = make_series_label(sq_info, i_spin=spin)
self.series[series_label] = (sq_data, sq_info, general_info)
x_arr = general_info['x_arr'] * 0.529177
y_arr = general_info['y_arr'] * 0.529177
self.extent = [np.min(x_arr), np.max(x_arr), np.min(y_arr), np.max(y_arr)]
self.figure_xy_ratio = (np.max(x_arr)-np.min(x_arr)) / (np.max(y_arr)-np.min(y_arr))
def setup_added_collections(self, wc_pk):
self.add_selection_row()
self.add_row_btn.disabled=False
self.plot_btn.disabled=False
self.clear_btn.disabled=False
self.zip_btn.disabled = False
self.wc_pk = wc_pk
def add_selection_row(self):
drop_full_series = ipw.Dropdown(description="series", options=sorted(self.series.keys(), reverse=True),
style = {'description_width': 'auto'})
drop_cmap = ipw.Dropdown(description="colormap", options=colormaps,
style = {'description_width': 'auto'})
sym_check = ipw.Checkbox(
value=False,
description='sym. zero',
disabled=False,
style = {'description_width': 'auto'},
layout=ipw.Layout(width='auto')
)
norm_check = ipw.Checkbox(
value=False,
description='normalize',
disabled=False,
style = {'description_width': 'auto'},
layout=ipw.Layout(width='auto')
)
rm_btn = ipw.Button(description='x', layout=ipw.Layout(width='30px'))
rm_btn.on_click(lambda b: self.remove_line_row(b))
elements = [drop_full_series, drop_cmap, sym_check, norm_check, rm_btn]
element_widths = ['280px', '210px', '120px', '120px', '35px']
boxed_row = ipw.HBox([ipw.HBox([row_el], layout=ipw.Layout(border='0.1px solid', width=row_w)) for row_el, row_w in zip(elements, element_widths)])
self.elem_list.append(elements)
self.selections_vbox.children += (boxed_row, )
def remove_line_row(self, b):
rm_btn_list = [elem[4] for elem in self.elem_list]
rm_index = rm_btn_list.index(b)
del self.elem_list[rm_index]
self.selections_vbox.children = remove_from_tuple(self.selections_vbox.children, rm_index)
def plot_series(self, b):
fig_y_in_px = 0.8*self.fig_y*matplotlib.rcParams['figure.dpi']
num_series = len(self.elem_list)
box_layout = ipw.Layout(overflow_x='scroll',
border='3px solid black',
width='100%',
height='%dpx' % (fig_y_in_px*num_series + 70),
display='inline-flex',
flex_flow='column wrap',
align_items='flex-start')
plot_hbox = ipw.Box(layout=box_layout)
self.plot_output.children += (plot_hbox, )
plot_hbox.children = ()
index_list = self.select_indexes_function()
for i in index_list:
plot_out = ipw.Output()
plot_hbox.children += (plot_out, )
with plot_out:
fig = plt.figure(figsize=(self.fig_y*self.figure_xy_ratio, self.fig_y*num_series))
for i_ser in range(num_series):
series_label = self.elem_list[i_ser][0].value
cmap = self.elem_list[i_ser][1].value
sym_check = self.elem_list[i_ser][2].value
norm_check = self.elem_list[i_ser][3].value
# ---------------------------------------------------------
# Retrieve the series data
data, info, general_info = self.series[series_label]
energy = general_info['energies'][i]
# Build labels, title and file name
orb_indexes = general_info.get('orb_indexes')
homo = general_info.get('homo')
mo_label = None
if orb_indexes is not None:
mo_label = make_orb_label(orb_indexes[i], homo)
title = '%s\n' % series_label
if mo_label is not None:
title += mo_label + ' '
title += 'E=%.2f eV' % energy
# ---------------------------------------------------------
# Is normalization enabled ?
vmin = None
vmax = None
if norm_check:
vmin = np.min(data[index_list, :, :])
vmax = np.max(data[index_list, :, :])
# ---------------------------------------------------------
# Make the plot
ax = plt.subplot(num_series, 1, i_ser+1)
make_plot(fig, ax, data[i, :, :], center0=sym_check, vmin=vmin, vmax=vmax,
extent=self.extent, title=title, cmap=cmap, noadd=True)
plt.show()
def create_zip_link(self, b):
self.zip_btn.disabled = True
filename = "%s_pk%d.zip" % (self.zip_prepend, self.wc_pk)
zip_buffer = io.BytesIO()
with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED, False) as zip_file:
self.data_to_zip(zip_file)
os.makedirs("tmp", exist_ok=True)
with open('tmp/'+filename, 'wb') as f:
f.write(zip_buffer.getvalue())
with self.link_out:
display(HTML('<a href="tmp/%s" target="_blank">download zip</a>' % filename))
def data_to_zip(self, zip_file):
index_list = self.select_indexes_function()
num_series = len(self.elem_list)
total_pics = len(index_list) * num_series
for i in index_list:
for i_ser in range(num_series):
series_label = self.elem_list[i_ser][0].value
cmap = self.elem_list[i_ser][1].value
sym_check = self.elem_list[i_ser][2].value
norm_check = self.elem_list[i_ser][3].value
# ---------------------------------------------------------
# Retrieve the series data
data, info, general_info = self.series[series_label]
energy = general_info['energies'][i]
# Build labels, title and file name
orb_indexes = general_info.get('orb_indexes')
homo = general_info.get('homo')
mo_label = None
if orb_indexes is not None:
mo_label = make_orb_label(orb_indexes[i], homo)
title = '%s\n' % series_label
if mo_label is not None:
title += mo_label + ' '
title += 'E=%.2f eV' % energy
plot_name = series_label.lower().replace(" ", '_').replace("=", '').replace('^', '').replace(',', '')
if mo_label is not None:
plot_name += "_mo%03d_e%.2f" % (orb_indexes[i], energy)
else:
plot_name += "_%03d_e%.2f" % (i, energy)
# ---------------------------------------------------------
# Is normalization enabled ?
vmin = None
vmax = None
if norm_check:
vmin = np.min(data[index_list, :, :])
vmax = np.max(data[index_list, :, :])
# ---------------------------------------------------
# Add the png to zip
fig = plt.figure(figsize=(self.fig_y*self.figure_xy_ratio, self.fig_y))
ax = plt.gca()
make_plot(fig, ax, data[i, :, :], center0=sym_check, vmin=vmin, vmax=vmax,
extent=self.extent, title=title, cmap=cmap, noadd=False)
imgdata = io.BytesIO()
fig.savefig(imgdata, format='png', dpi=200, bbox_inches='tight')
zip_file.writestr(plot_name+".png", imgdata.getvalue())
plt.close()
# ---------------------------------------------------
# Add txt data to the zip
header = "xlim=(%.2f, %.2f), ylim=(%.2f, %.2f)" % (self.extent[0], self.extent[1],
self.extent[2], self.extent[3])
txtdata = io.BytesIO()
np.savetxt(txtdata, data[i, :, :], header=header, fmt="%.3e")
zip_file.writestr("txt/"+plot_name+".txt", txtdata.getvalue())
# ---------------------------------------------------
# ---------------------------------------------------
# Add IGOR format to zip
igorwave = igor.Wave2d(
data=data[i, :, :],
xmin=self.extent[0],
xmax=self.extent[1],
xlabel='x [Angstroms]',
ymin=self.extent[2],
ymax=self.extent[3],
ylabel='y [Angstroms]',
name="'%s'" % plot_name,
)
zip_file.writestr("itx/"+plot_name+".itx", str(igorwave))
# ---------------------------------------------------
self.zip_progress.value += 1.0/float(total_pics-1)
def full_clear(self, b):
self.plot_output.children = ()