rasmus/nafuma
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Allow rescaling ylim with interactive diff plot

Browse source
This commit is contained in:
rasmusvt 2022-04-05 16:12:19 +02:00
parent c0449f2e18
commit 876e0f8d3d
2 changed files with 122 additions and 50 deletions
Download patch file Download diff file Expand all files Collapse all files

11
beamtime/xrd/io.py
View file

@ -358,9 +358,18 @@ def read_data(data, options={}, index=0):
def apply_offset(diffractogram, wavelength, index, options): def apply_offset(diffractogram, wavelength, index, options):
options['current_offset_y'] = options['offset_y'] if 'current_offset_y' not in options.keys():
options['current_offset_y'] = options['offset_y']
else:
if options['current_offset_y'] != options['offset_y']:
options['offset_change'] = True
options['current_offset_y'] = options['offset_y']
options['current_offset_x'] = options['offset_x'] options['current_offset_x'] = options['offset_x']
#Apply offset along y-axis #Apply offset along y-axis
diffractogram['I'] = diffractogram['I_org'] # Reset intensities diffractogram['I'] = diffractogram['I_org'] # Reset intensities

161
beamtime/xrd/plot.py
View file

@ -20,7 +20,7 @@ def plot_diffractogram(data, options={}):
data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)''' data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
# Update options # Update options
required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', 'offset_change',
'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active'] 'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
default_options = { default_options = {
@ -33,6 +33,7 @@ def plot_diffractogram(data, options={}):
'offset': True, 'offset': True,
'offset_x': 0, 'offset_x': 0,
'offset_y': 1, 'offset_y': 1,
'offset_change': False,
'line': True, # whether or not to plot diffractogram as a line plot 'line': True, # whether or not to plot diffractogram as a line plot
'scatter': False, # whether or not to plot individual data points 'scatter': False, # whether or not to plot individual data points
'reflections_plot': False, # whether to plot reflections as a plot 'reflections_plot': False, # whether to plot reflections as a plot
@ -53,6 +54,7 @@ def plot_diffractogram(data, options={}):
default_options['offset_y'] = 0.05 default_options['offset_y'] = 0.05
options = aux.update_options(options=options, required_options=required_options, default_options=default_options) options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
options['current_offset_y'] = options['offset_y']
# Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms # Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
if not isinstance(data['path'], list): if not isinstance(data['path'], list):
@ -174,7 +176,8 @@ def plot_diffractogram(data, options={}):
if options['interactive_session_active']: if options['interactive_session_active']:
update_widgets(options=options) options['current_y_offset'] = options['widget'].kwargs['offset_y']
update_widgets(data=data, options=options)
@ -213,7 +216,7 @@ def generate_heatmap(data, options={}):
ndatapoints = len(data['diffractogram'][0]['2th']) ndatapoints = len(data['diffractogram'][0]['2th'])
xlims = [0, ndatapoints] xlims = [0, ndatapoints, 0, ndatapoints] # 0: xmin, 1: xmax, 2: xmin_start, 3: xmax_start
xticks = {} xticks = {}
xticklabels = {} xticklabels = {}
@ -279,13 +282,18 @@ def determine_grid_layout(options):
def plot_diffractogram_interactive(data, options): def plot_diffractogram_interactive(data, options):
xminmax = {'2th': [None, None], '2th_cuka': [None, None], '2th_moka': [None, None], 'd': [None, None], '1/d': [None, None], 'q': [None, None], 'q2': [None, None], 'q4': [None, None], 'heatmap': [None, None], 'start': [None, None, None, None]} # Format here is xminmax[0]: xmin, xminmax[1]: xmax, xminmax[2]: xmin_start, xminmax[3]: xmax_start, where "_start" denotes starting value of the slider
yminmax = {'diff': [None, None, None, None], 'heatmap': [None, None], 'start': [None, None, None, None]} xminmax = { '2th': [None, None, None, None], '2th_cuka': [None, None, None, None], '2th_moka': [None, None, None, None],
'd': [None, None, None, None], '1/d': [None, None, None, None],
'q': [None, None, None, None], 'q2': [None, None, None, None], 'q4': [None, None, None, None],
'heatmap': [None, None, None, None], 'start': [None, None, None, None]}
yminmax = { 'diff': [None, None, None, None], 'heatmap': [None, None, None, None], 'start': [None, None, None, None]}
update_xminmax(xminmax=xminmax, data=data, options=options) update_xminmax(xminmax=xminmax, data=data, options=options)
update_yminmax(yminmax=yminmax, data=data, options=options) update_yminmax(yminmax=yminmax, data=data, options=options)
options['xminmax'], options['yminmax'] = xminmax, yminmax
# Get start values for ylim slider based on choice (FIXME This can be impleneted into update_yminmax). Can also make a 'start' item that stores the start values, instead of having 4 items in 'diff' as it is now. # Get start values for ylim slider based on choice (FIXME This can be impleneted into update_yminmax). Can also make a 'start' item that stores the start values, instead of having 4 items in 'diff' as it is now.
if options['heatmap']: if options['heatmap']:
@ -337,8 +345,8 @@ def plot_diffractogram_interactive(data, options):
x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q2', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'), x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q2', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
xlim=options['widgets']['xlim']['w'], xlim=options['widgets']['xlim']['w'],
ylim=options['widgets']['ylim']['w'], ylim=options['widgets']['ylim']['w'],
offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01), offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01, description='offset_y'),
offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01) offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01, description='offset_x')
) )
else: else:
@ -348,6 +356,8 @@ def plot_diffractogram_interactive(data, options):
xlim=options['widgets']['xlim']['w']) xlim=options['widgets']['xlim']['w'])
options['widget'] = w
display(w) display(w)
@ -357,7 +367,9 @@ def update_xminmax(xminmax, data, options={}):
Input: Input:
minmax (dict): contains ''' minmax (dict): contains '''
xminmax['2th'] = [None, None, None, None]
for index, diffractogram in enumerate(data['diffractogram']): for index, diffractogram in enumerate(data['diffractogram']):
if not xminmax['2th'][0] or diffractogram['2th'].min() < xminmax['2th'][0]: if not xminmax['2th'][0] or diffractogram['2th'].min() < xminmax['2th'][0]:
xminmax['2th'][0] = diffractogram['2th'].min() xminmax['2th'][0] = diffractogram['2th'].min()
min_index = index min_index = index
@ -366,23 +378,43 @@ def update_xminmax(xminmax, data, options={}):
xminmax['2th'][1] = diffractogram['2th'].max() xminmax['2th'][1] = diffractogram['2th'].max()
max_index = index max_index = index
xminmax['2th_cuka'][0], xminmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(), data['diffractogram'][max_index]['2th_cuka'].max()
xminmax['2th_moka'][0], xminmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(), data['diffractogram'][max_index]['2th_moka'].max() xminmax['2th'][2], xminmax['2th'][3] = xminmax['2th'][0], xminmax['2th'][1]
xminmax['d'][0], xminmax['d'][1] = data['diffractogram'][max_index]['d'].min(), data['diffractogram'][min_index]['d'].max() # swapped, intended
xminmax['1/d'][0], xminmax['1/d'][1] = data['diffractogram'][min_index]['1/d'].min(), data['diffractogram'][max_index]['1/d'].max() xminmax['2th_cuka'][0], xminmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(), data['diffractogram'][max_index]['2th_cuka'].max()
xminmax['q'][0], xminmax['q'][1] = data['diffractogram'][min_index]['q'].min(), data['diffractogram'][max_index]['q'].max() xminmax['2th_cuka'][2], xminmax['2th_cuka'][3] = xminmax['2th_cuka'][0], xminmax['2th_cuka'][1]
xminmax['q2'][0], xminmax['q2'][1] = data['diffractogram'][min_index]['q2'].min(), data['diffractogram'][max_index]['q2'].max()
xminmax['q4'][0], xminmax['q4'][1] = data['diffractogram'][min_index]['q4'].min(), data['diffractogram'][max_index]['q4'].max() xminmax['2th_moka'][0], xminmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(), data['diffractogram'][max_index]['2th_moka'].max()
xminmax['heatmap'] = options['heatmap_xlim'] xminmax['2th_moka'][2], xminmax['2th_moka'][3] = xminmax['2th_moka'][0], xminmax['2th_moka'][1]
xminmax['d'][0], xminmax['d'][1] = data['diffractogram'][max_index]['d'].min(), data['diffractogram'][min_index]['d'].max() # swapped, intended
xminmax['d'][2], xminmax['d'][3] = xminmax['d'][0], xminmax['d'][1]
xminmax['1/d'][0], xminmax['1/d'][1] = data['diffractogram'][min_index]['1/d'].min(), data['diffractogram'][max_index]['1/d'].max()
xminmax['1/d'][2], xminmax['1/d'][3] = xminmax['1/d'][0], xminmax['1/d'][1]
xminmax['q'][0], xminmax['q'][1] = data['diffractogram'][min_index]['q'].min(), data['diffractogram'][max_index]['q'].max()
xminmax['q'][2], xminmax['q'][3] = xminmax['q'][0], xminmax['q'][1]
xminmax['q2'][0], xminmax['q2'][1] = data['diffractogram'][min_index]['q2'].min(), data['diffractogram'][max_index]['q2'].max()
xminmax['q2'][2], xminmax['q2'][3] = xminmax['q2'][0], xminmax['q2'][1]
xminmax['q4'][0], xminmax['q4'][1] = data['diffractogram'][min_index]['q4'].min(), data['diffractogram'][max_index]['q4'].max()
xminmax['q4'][2], xminmax['q4'][3] = xminmax['q4'][0], xminmax['q4'][1]
xminmax['heatmap'] = options['heatmap_xlim'] # This value is set in the generate_heatmap()-function
xminmax['start'][0], xminmax['start'][1] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1] xminmax['start'][0], xminmax['start'][1] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1]
xminmax['start'][2], xminmax['start'][3] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1] xminmax['start'][2], xminmax['start'][3] = xminmax[options['x_vals']][2], xminmax[options['x_vals']][3]
def update_yminmax(yminmax: dict, data, options={}): def update_yminmax(yminmax: dict, data: dict, options={}) -> None:
for index, diffractogram in enumerate(data['diffractogram']): yminmax['diff'] = [None, None, None, None]
# Go through diffractograms and find the minimum and maximum intensity values
for diffractogram in data['diffractogram']:
if not yminmax['diff'][0] or (yminmax['diff'][0] > (diffractogram['I'].min())): if not yminmax['diff'][0] or (yminmax['diff'][0] > (diffractogram['I'].min())):
yminmax['diff'][0] = diffractogram['I'].min() yminmax['diff'][0] = diffractogram['I'].min()
@ -399,8 +431,9 @@ def update_yminmax(yminmax: dict, data, options={}):
yminmax['diff'][1] = yminmax['diff'][1]*5 yminmax['diff'][1] = yminmax['diff'][1]*5
yminmax['heatmap'][0] = 0 # Set start values to the edges of the dataset
yminmax['heatmap'][1] = data['heatmap'].shape[0] yminmax['heatmap'][0], yminmax['heatmap'][1] = 0, data['heatmap'].shape[0]
yminmax['heatmap'][2], yminmax['heatmap'][3] = yminmax['heatmap'][0], yminmax['heatmap'][1]
if options['heatmap']: if options['heatmap']:
@ -413,59 +446,89 @@ def update_yminmax(yminmax: dict, data, options={}):
yminmax['start'][2], yminmax['start'][3] = yminmax['diff'][2], yminmax['diff'][3] yminmax['start'][2], yminmax['start'][3] = yminmax['diff'][2], yminmax['diff'][3]
def update_defaults(widget: dict, minmax: dict) -> None:
''' Updates the default x- or y-limits of a given widget. Refer to plot_diffractogram_interactive() to see the form of the widget that is passed in. An update of the min/max-values is done just prior to calling this function.
Changes dictionaries in place.
Input:
widget (dict): A dictionary containing the widget itself (widget['w']) and all its default-values (e.g. widget['2th_default'])
minmax (dict): A dictionary containing min and max values, as well as min_start and max_start values. (e.g. minmax['2th'] is a list with four elements: [xmin, xmax, xmin_start, xmax_start])
Output:
None.'''
for name, attr in widget.items():
if name.endswith('default'):
attr['min'] = minmax[name.replace('_default', '')][0]
attr['max'] = minmax[name.replace('_default', '')][1]
attr['value'] = [minmax[name.replace('_default', '')][2], minmax[name.replace('_default', '')][3]]
def update_widgets(options): def update_widgets(data, options):
for widget, attr in options['widgets'].items():
if widget == 'xlim': for widget_name, widget in options['widgets'].items():
if options['heatmap'] and (attr['state'] != 'heatmap'): # Make changes to xlim-widget
setattr(attr['w'], 'min', attr['heatmap_default']['min']) if widget_name == 'xlim':
setattr(attr['w'], 'max', attr['heatmap_default']['max']) # First update the min and max values
setattr(attr['w'], 'value', attr['heatmap_default']['value']) update_xminmax(xminmax=options['xminmax'], data=data, options=options)
setattr(attr['w'], 'step', attr['heatmap_default']['step']) update_defaults(widget=widget, minmax=options['xminmax'])
attr['state'] = 'heatmap' if options['heatmap'] and (widget['state'] != 'heatmap'):
setattr(widget['w'], 'min', widget['heatmap_default']['min'])
setattr(widget['w'], 'max', widget['heatmap_default']['max'])
setattr(widget['w'], 'value', widget['heatmap_default']['value'])
setattr(widget['w'], 'step', widget['heatmap_default']['step'])
widget['state'] = 'heatmap'
elif not options['heatmap'] and (attr['state'] != options['x_vals']): elif not options['heatmap'] and (widget['state'] != options['x_vals']):
for arg in attr[f'{options["x_vals"]}_default']: # Then loop through all attributes in the widget and change to current mode.
for arg in widget[f'{options["x_vals"]}_default']:
# If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first # If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first
if arg == 'min': if arg == 'min':
if attr[f'{options["x_vals"]}_default']['min'] > getattr(attr['w'], 'max'): if widget[f'{options["x_vals"]}_default']['min'] > getattr(widget['w'], 'max'):
setattr(attr['w'], 'max', attr[f'{options["x_vals"]}_default']['max']) setattr(widget['w'], 'max', widget[f'{options["x_vals"]}_default']['max'])
elif arg == 'max': elif arg == 'max':
if attr[f'{options["x_vals"]}_default']['max'] < getattr(attr['w'], 'min'): if widget[f'{options["x_vals"]}_default']['max'] < getattr(widget['w'], 'min'):
setattr(attr['w'], 'min', attr[f'{options["x_vals"]}_default']['min']) setattr(widget['w'], 'min', widget[f'{options["x_vals"]}_default']['min'])
setattr(attr['w'], arg, attr[f'{options["x_vals"]}_default'][arg]) setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
attr['state'] = options['x_vals'] widget['state'] = options['x_vals']
elif widget == 'ylim': # Make changes to ylim-widget
state = 'heatmap' if options['heatmap'] else 'diff' elif widget_name == 'ylim':
update_yminmax(yminmax=options['yminmax'], data=data, options=options)
update_defaults(widget=widget, minmax=options['yminmax'])
state = 'heatmap' if options['heatmap'] else 'diff'
if attr['state'] != state: if widget['state'] != state or options['offset_change']:
for arg in attr[f'{state}_default']: for arg in widget[f'{state}_default']:
# If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first # If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first
if arg == 'min': if arg == 'min':
if attr[f'{state}_default']['min'] > getattr(attr['w'], 'max'): if widget[f'{state}_default']['min'] > getattr(widget['w'], 'max'):
setattr(attr['w'], 'max', attr[f'{state}_default']['max']) setattr(widget['w'], 'max', widget[f'{state}_default']['max'])
elif arg == 'max': elif arg == 'max':
if attr[f'{state}_default']['max'] < getattr(attr['w'], 'min'): if widget[f'{state}_default']['max'] < getattr(widget['w'], 'min'):
setattr(attr['w'], 'min', attr[f'{state}_default']['min']) setattr(widget['w'], 'min', widget[f'{state}_default']['min'])
setattr(attr['w'], arg, attr[f'{state}_default'][arg]) setattr(widget['w'], arg, widget[f'{state}_default'][arg])
attr['state'] = state options['offset_change'] = False
widget['state'] = state