Add plot functionality for single diffractograms
This commit is contained in:
rasmusvt
parent
d6734184cc
commit
2b1b9b0d9b
3 changed files with 363 additions and 22 deletions
|
|
@ -275,8 +275,8 @@ def prettify_gc_plot(fig, ax, options=None):
|
||||||
|
|
||||||
# Otherwise apply user input
|
# Otherwise apply user input
|
||||||
else:
|
else:
|
||||||
major_xtick = options['yticks'][0]
|
major_ytick = options['yticks'][0]
|
||||||
minor_xtick = options['yticks'][1]
|
minor_ytick = options['yticks'][1]
|
||||||
|
|
||||||
|
|
||||||
# Apply values
|
# Apply values
|
||||||
|
|
|
||||||
|
|
@ -90,25 +90,7 @@ def integrate_1d(calibrant, bins, path=None, image=None, options=None):
|
||||||
return open_1d_data(filename)
|
return open_1d_data(filename)
|
||||||
|
|
||||||
|
|
||||||
def open_1d_data(path, options=None):
|
|
||||||
|
|
||||||
with open(path, 'r') as f:
|
|
||||||
position = 0
|
|
||||||
|
|
||||||
current_line = f.readline()
|
|
||||||
|
|
||||||
while current_line[0] == '#':
|
|
||||||
position = f.tell()
|
|
||||||
current_line = f.readline()
|
|
||||||
|
|
||||||
f.seek(position)
|
|
||||||
|
|
||||||
df = pd.read_csv(f, header=None, delim_whitespace=True)
|
|
||||||
|
|
||||||
df.columns = ['2th', 'I']
|
|
||||||
|
|
||||||
|
|
||||||
return df
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -165,7 +147,7 @@ def view_integrator(calibrant):
|
||||||
def read_brml(path, options=None):
|
def read_brml(path, options=None):
|
||||||
|
|
||||||
|
|
||||||
required_options = ['extract_folder']
|
required_options = ['extract_folder', 'save_folder']
|
||||||
default_options = {
|
default_options = {
|
||||||
'extract_folder': 'temp',
|
'extract_folder': 'temp',
|
||||||
'save_folder': None
|
'save_folder': None
|
||||||
|
|
@ -240,8 +222,42 @@ def read_brml(path, options=None):
|
||||||
return diffractogram
|
return diffractogram
|
||||||
|
|
||||||
|
|
||||||
|
def read_diffractogram(path, options=None):
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
with open(path, 'r') as f:
|
||||||
|
position = 0
|
||||||
|
|
||||||
|
current_line = f.readline()
|
||||||
|
|
||||||
|
while current_line[0] == '#':
|
||||||
|
position = f.tell()
|
||||||
|
current_line = f.readline()
|
||||||
|
|
||||||
|
f.seek(position)
|
||||||
|
|
||||||
|
diffractogram = pd.read_csv(f, header=None, delim_whitespace=True)
|
||||||
|
|
||||||
|
diffractogram.columns = ['2th', 'I']
|
||||||
|
|
||||||
|
|
||||||
|
return diffractogram
|
||||||
|
|
||||||
|
|
||||||
|
def read_data(path, kind, options=None):
|
||||||
|
|
||||||
|
if kind == 'beamline':
|
||||||
|
diffractogram = read_diffractogram(path, options=options)
|
||||||
|
|
||||||
|
elif kind == 'recx':
|
||||||
|
diffractogram = read_brml(path, options=options)
|
||||||
|
|
||||||
|
elif kind == 'image':
|
||||||
|
diffractogram = get_image_array(path)
|
||||||
|
|
||||||
|
|
||||||
|
return diffractogram
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,2 +1,327 @@
|
||||||
import matplotlib.pyplot as plt
|
import matplotlib.pyplot as plt
|
||||||
import numpy
|
from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
|
||||||
|
|
||||||
|
import pandas as pd
|
||||||
|
import numpy as np
|
||||||
|
import math
|
||||||
|
|
||||||
|
import beamtime.xrd as xrd
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def plot_diffractogram(path, kind, options=None):
|
||||||
|
|
||||||
|
# Prepare plot, and read and process data
|
||||||
|
fig, ax = prepare_diffractogram_plot(options=options)
|
||||||
|
diffractogram = xrd.io.read_data(path=path, kind=kind, options=options)
|
||||||
|
|
||||||
|
|
||||||
|
# Update options
|
||||||
|
required_options = ['x_vals', 'y_vals', 'scatter']
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
default_options = {
|
||||||
|
'x_vals': '2th',
|
||||||
|
'y_vals': 'I',
|
||||||
|
'scatter': False
|
||||||
|
}
|
||||||
|
|
||||||
|
options = update_options(options=options, required_options=required_options, default_options=default_options)
|
||||||
|
|
||||||
|
if options['scatter']:
|
||||||
|
diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, kind='scatter')
|
||||||
|
|
||||||
|
else:
|
||||||
|
diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fig, ax = prettify_diffractogram_plot(fig=fig, ax=ax, options=options)
|
||||||
|
|
||||||
|
|
||||||
|
return diffractogram, fig, ax
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def prepare_diffractogram_plot(options=None):
|
||||||
|
# First take care of the options for plotting - set any values not specified to the default values
|
||||||
|
required_options = ['columns', 'width', 'height', 'format', 'dpi', 'facecolor']
|
||||||
|
default_options = {'columns': 1, 'width': 14, 'format': 'golden_ratio', 'dpi': None, 'facecolor': 'w'}
|
||||||
|
|
||||||
|
|
||||||
|
# Define the required sizes
|
||||||
|
required_sizes = ['lines', 'axes']
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# If none are set at all, just pass the default_options
|
||||||
|
if not options:
|
||||||
|
options = default_options
|
||||||
|
options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
|
||||||
|
options['figsize'] = (options['width'], options['height'])
|
||||||
|
|
||||||
|
|
||||||
|
# Define default sizes
|
||||||
|
default_sizes = {
|
||||||
|
'lines': 3*options['columns'],
|
||||||
|
'axes': 3*options['columns']
|
||||||
|
}
|
||||||
|
|
||||||
|
# Initialise dictionary if it doesn't exist
|
||||||
|
if not 'sizes' in options.keys():
|
||||||
|
options['sizes'] = {}
|
||||||
|
|
||||||
|
|
||||||
|
# Update dictionary with default values where none is supplied
|
||||||
|
for size in required_sizes:
|
||||||
|
if size not in options['sizes']:
|
||||||
|
options['sizes'][size] = default_sizes[size]
|
||||||
|
|
||||||
|
|
||||||
|
# If options is passed, go through to fill out the rest.
|
||||||
|
else:
|
||||||
|
# Start by setting the width:
|
||||||
|
if 'width' not in options.keys():
|
||||||
|
options['width'] = default_options['width']
|
||||||
|
|
||||||
|
# Then set height - check options for format. If not given, set the height to the width scaled by the golden ratio - if the format is square, set the same. This should possibly allow for the tweaking of custom ratios later.
|
||||||
|
if 'height' not in options.keys():
|
||||||
|
if 'format' not in options.keys():
|
||||||
|
options['height'] = options['width'] * (math.sqrt(5) - 1) / 2
|
||||||
|
elif options['format'] == 'square':
|
||||||
|
options['height'] = options['width']
|
||||||
|
|
||||||
|
options['figsize'] = (options['width'], options['height'])
|
||||||
|
|
||||||
|
# After height and width are set, go through the rest of the options to make sure that all the required options are filled
|
||||||
|
for option in required_options:
|
||||||
|
if option not in options.keys():
|
||||||
|
options[option] = default_options[option]
|
||||||
|
|
||||||
|
fig, ax = plt.subplots(figsize=(options['figsize']), dpi=options['dpi'], facecolor=options['facecolor'])
|
||||||
|
|
||||||
|
|
||||||
|
plt.rc('lines', linewidth=options['sizes']['lines'])
|
||||||
|
plt.rc('axes', linewidth=options['sizes']['axes'])
|
||||||
|
|
||||||
|
return fig, ax
|
||||||
|
|
||||||
|
def prettify_diffractogram_plot(fig, ax, options=None):
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
######################### UPDATE OPTIONS #########################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
# Define the required options
|
||||||
|
required_options = [
|
||||||
|
'columns',
|
||||||
|
'xticks', 'yticks',
|
||||||
|
'units',
|
||||||
|
'show_major_ticks', 'show_minor_ticks', 'show_tick_labels',
|
||||||
|
'xlim', 'ylim',
|
||||||
|
'hide_x_axis', 'hide_y_axis',
|
||||||
|
'positions',
|
||||||
|
'xlabel', 'ylabel',
|
||||||
|
'sizes',
|
||||||
|
'title'
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
# Define the default options
|
||||||
|
default_options = {
|
||||||
|
'columns': 1,
|
||||||
|
'xticks': [10, 5], 'yticks': [10000, 5000],
|
||||||
|
'units': {'2th': '$^o$', 'I': 'arb. u.'},
|
||||||
|
'show_major_ticks': [True, False, True, False], 'show_minor_ticks': [True, False, True, False], 'show_tick_labels': [True, False, False, False],
|
||||||
|
'xlim': None,'ylim': None,
|
||||||
|
'hide_x_axis': False, 'hide_y_axis': False,
|
||||||
|
'positions': {'xaxis': 'bottom', 'yaxis': 'left'},
|
||||||
|
'xlabel': None, 'ylabel': None,
|
||||||
|
'sizes': None,
|
||||||
|
'title': None
|
||||||
|
}
|
||||||
|
|
||||||
|
options = update_options(options, required_options, default_options)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
########################## DEFINE SIZES ##########################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
# Define the required sizes
|
||||||
|
required_sizes = [
|
||||||
|
'labels',
|
||||||
|
'legend',
|
||||||
|
'title',
|
||||||
|
'line', 'axes',
|
||||||
|
'tick_labels',
|
||||||
|
'major_ticks', 'minor_ticks']
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# Define default sizes
|
||||||
|
default_sizes = {
|
||||||
|
'labels': 30*options['columns'],
|
||||||
|
'legend': 30*options['columns'],
|
||||||
|
'title': 30*options['columns'],
|
||||||
|
'line': 3*options['columns'],
|
||||||
|
'axes': 3*options['columns'],
|
||||||
|
'tick_labels': 30*options['columns'],
|
||||||
|
'major_ticks': 20*options['columns'],
|
||||||
|
'minor_ticks': 10*options['columns']
|
||||||
|
}
|
||||||
|
|
||||||
|
# Initialise dictionary if it doesn't exist
|
||||||
|
if not options['sizes']:
|
||||||
|
options['sizes'] = {}
|
||||||
|
|
||||||
|
|
||||||
|
# Update dictionary with default values where none is supplied
|
||||||
|
for size in required_sizes:
|
||||||
|
if size not in options['sizes']:
|
||||||
|
options['sizes'][size] = default_sizes[size]
|
||||||
|
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
########################## AXIS LABELS ###########################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
|
||||||
|
if not options['xlabel']:
|
||||||
|
options['xlabel'] = prettify_labels(options['x_vals']) + ' [{}]'.format(options['units'][options['x_vals']])
|
||||||
|
|
||||||
|
else:
|
||||||
|
options['xlabel'] = options['xlabel'] + ' [{}]'.format(options['units'][options['x_vals']])
|
||||||
|
|
||||||
|
|
||||||
|
if not options['ylabel']:
|
||||||
|
options['ylabel'] = prettify_labels(options['y_vals']) + ' [{}]'.format(options['units'][options['y_vals']])
|
||||||
|
|
||||||
|
else:
|
||||||
|
options['ylabel'] = options['ylabel'] + ' [{}]'.format(options['units'][options['y_vals']])
|
||||||
|
|
||||||
|
ax.set_xlabel(options['xlabel'], size=options['sizes']['labels'])
|
||||||
|
ax.set_ylabel(options['ylabel'], size=options['sizes']['labels'])
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
###################### TICK MARKS & LABELS #######################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
ax.tick_params(
|
||||||
|
direction='in',
|
||||||
|
which='major',
|
||||||
|
bottom=options['show_major_ticks'][0], labelbottom=options['show_tick_labels'][0],
|
||||||
|
left=options['show_major_ticks'][1], labelleft=options['show_tick_labels'][1],
|
||||||
|
top=options['show_major_ticks'][2], labeltop=options['show_tick_labels'][2],
|
||||||
|
right=options['show_major_ticks'][3], labelright=options['show_tick_labels'][3],
|
||||||
|
length=options['sizes']['major_ticks'],
|
||||||
|
width=options['sizes']['axes'])
|
||||||
|
|
||||||
|
|
||||||
|
ax.tick_params(direction='in', which='minor', bottom=options['show_minor_ticks'][0], left=options['show_minor_ticks'][1], top=options['show_minor_ticks'][2], right=options['show_minor_ticks'][3], length=options['sizes']['minor_ticks'], width=options['sizes']['axes'])
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
if options['positions']['yaxis'] == 'right':
|
||||||
|
ax.yaxis.set_label_position("right")
|
||||||
|
ax.yaxis.tick_right()
|
||||||
|
|
||||||
|
|
||||||
|
if options['hide_x_axis']:
|
||||||
|
ax.axes.xaxis.set_visible(False)
|
||||||
|
|
||||||
|
if options['hide_y_axis']:
|
||||||
|
ax.axes.yaxis.set_visible(False)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# Otherwise apply user input
|
||||||
|
if options['xticks']:
|
||||||
|
major_xtick = options['xticks'][0]
|
||||||
|
minor_xtick = options['xticks'][1]
|
||||||
|
|
||||||
|
|
||||||
|
if options['yticks']:
|
||||||
|
|
||||||
|
major_ytick = options['yticks'][0]
|
||||||
|
minor_ytick = options['yticks'][1]
|
||||||
|
|
||||||
|
|
||||||
|
# Apply values
|
||||||
|
ax.xaxis.set_major_locator(MultipleLocator(major_xtick))
|
||||||
|
ax.xaxis.set_minor_locator(MultipleLocator(minor_xtick))
|
||||||
|
|
||||||
|
ax.yaxis.set_major_locator(MultipleLocator(major_ytick))
|
||||||
|
ax.yaxis.set_minor_locator(MultipleLocator(minor_ytick))
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# SET FONTSIZE OF TICK LABELS
|
||||||
|
|
||||||
|
plt.xticks(fontsize=options['sizes']['tick_labels'])
|
||||||
|
plt.yticks(fontsize=options['sizes']['tick_labels'])
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
########################## AXES LIMITS ###########################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
if options['xlim']:
|
||||||
|
plt.xlim(options['xlim'])
|
||||||
|
|
||||||
|
if options['ylim']:
|
||||||
|
plt.ylim(options['ylim'])
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
############################# TITLE ##############################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
if options['title']:
|
||||||
|
ax.set_title(options['title'], size=options['sizes']['title'])
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
############################# LEGEND #############################
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
if ax.get_legend():
|
||||||
|
ax.get_legend().remove()
|
||||||
|
|
||||||
|
return fig, ax
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def prettify_labels(label):
|
||||||
|
|
||||||
|
labels_dict = {
|
||||||
|
'2th': '2$\\theta$',
|
||||||
|
'I': 'Intensity'
|
||||||
|
}
|
||||||
|
|
||||||
|
return labels_dict[label]
|
||||||
|
|
||||||
|
#def plot_diffractograms():
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#def plot_heatmap():
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def update_options(options, required_options, default_options):
|
||||||
|
|
||||||
|
if not options:
|
||||||
|
options = default_options
|
||||||
|
|
||||||
|
else:
|
||||||
|
for option in required_options:
|
||||||
|
if option not in options.keys():
|
||||||
|
options[option] = default_options[option]
|
||||||
|
|
||||||
|
return options
|
||||||
Loading…
Add table
Add a link
Reference in a new issue