class Plot():
"""This class is used to generate the figures for the plots."""
def __init__(self):
""" Description of init """
# Create the option parser for the command line options
usage = (
'usage: %prog [options]\n\n'
'All options are strings. Boolean options are true when they \n'
'contains a certain specific keywords, which is written in \n'
'the option description in parantheses.')
parser = OptionParser(usage=usage)
# Add the options to the option parser
parser.add_option('-a',
'--type',
help='Type string from '
'graphsettings.xml')
parser.add_option('-b', '--idlist', help='List of id\'s to plot')
parser.add_option('-c',
'--from_d',
help='From timestamp, format: '
'YYYY-MM-DD HH:MM')
parser.add_option('-d',
'--to_d',
help='To timestamp, format: '
'YYYY-MM-DD HH:MM')
parser.add_option('-e', '--xmin', help='X-min for zoom')
parser.add_option('-f', '--xmax', help='X-max for zoom')
parser.add_option('-g', '--ymin', help='Y-min for zoom')
parser.add_option('-i', '--ymax', help='Y-max for zoom')
parser.add_option('-j',
'--offset',
help='List of offsets for the '
'graphs (for plots that goes on a log scale and has '
'negative values)')
parser.add_option(
'-k',
'--as_function_of_t',
help='Plot the graphs as '
'a function of temperature (boolean \'checked\'=True)')
parser.add_option('-l',
'--logscale',
help='Use a log for the right '
'axis (boolean \'checked\'=True)')
parser.add_option('-m',
'--shift_temp_unit',
help='Change between K '
'and C when values are plotted as a function of '
'temperature (boolean \'checked\'=True)')
parser.add_option('-n',
'--flip_x',
help='Exchange min and max for the '
'x-axis (boolean \'checked\'=True)')
parser.add_option('-o',
'--shift_be_ke',
help='Shift between binding '
'energy and kinetic energy for XPS plots (boolean '
'\'checked\'=True)')
# -p is availabel from previous options
parser.add_option(
'-q',
'--image_format',
help='Image format for the '
'figure exports, given as the figure extension. Can '
'be svg, eps, ps, pdf and default. Default means use '
'the one in graphsettings.xml or internal deaault.')
parser.add_option('-r',
'--small_plot',
help='Produce a small plot '
'(boolean \'checked\'=1)')
# Parse the options
(options, args) = parser.parse_args()
### Process options - all options are given as string, and they need to
### be converted into other data types
# Convert idlist
self.idlist = [
int(element) for element in options.idlist.split(',')[1:]
]
# Turn the offset 'key:value,' pair string into a dictionary
self.offsets = dict([[int(offset.split(':')[0]),
offset.split(':')[1]]
for offset in options.offset.split(',')[1:]])
# Gather from and to in a fictionary
self.from_to = {'from': options.from_d, 'to': options.to_d}
# Turn several options into booleans
self.as_function_of_t = True if options.as_function_of_t ==\
'checked' else False
self.shift_temp_unit = True if options.shift_temp_unit ==\
'checked' else False
self.logscale = True if options.logscale == 'checked' else False
self.flip_x = True if options.flip_x == 'checked' else False
self.shift_be_ke = True if options.shift_be_ke == 'checked' else False
self.small_plot = True if options.small_plot == '1' else False
### Create database backend object
self.db = dataBaseBackend(typed=options.type,
from_to=self.from_to,
id_list=self.idlist,
offsets=self.offsets,
as_function_of_t=self.as_function_of_t,
shift_temp_unit=self.shift_temp_unit,
shift_be_ke=self.shift_be_ke)
### Ask self.db for a measurement count
measurement_count = self.db.get_data_count()
# Set the image format to standard, overwite with gs value and again
# options value if i exits
if options.image_format:
if options.image_format == 'default':
if self.db.global_settings.has_key('image_format'):
self.image_format = self.db.global_settings['image_format']
else:
self.image_format = 'png'
else:
self.image_format = options.image_format
else:
self.image_format = 'png'
# Create a hash from the measurement_count, options and
#self.db.global_settings
hash = hashlib.md5()
hash.update(
str(options) + str(self.db.global_settings) +
str(measurement_count))
# self.namehash is unique for this plot and will form the filename
self.namehash = ('/var/www/cinfdata/figures/' + hash.hexdigest() +
'.' + self.image_format)
# For use in other methods
self.options = options
# object to give first good color, and then random colors
self.c = Color()
self.left_color = 'black'
self.right_color = 'black'
def main(self):
if os.path.exists(self.namehash) and False:
print self.namehash
else:
# Call a bunch of functions
self._init_plot()
self._plot()
if self.left_color != 'black':
if self.right_color != 'black':
self.c.color_axis(self.ax1, self.ax2, self.left_color,
self.right_color)
else:
self.c.color_axis(self.ax1, None, self.left_color, None)
self._legend()
self._zoom_and_flip()
self._transform_and_label_axis()
if not self.small_plot:
self._title()
self._grids()
self._save()
def _init_plot(self):
### Apply settings
# Small plots
if self.small_plot:
# Apply default settings
plt.rcParams.update({
'figure.figsize': [4.5, 3.0],
'ytick.labelsize': 'x-small',
'xtick.labelsize': 'x-small',
'legend.fontsize': 'x-small'
})
# Overwrite with values from graphsettings
plt.rcParams.update(self.db.global_settings['rcparams_small'])
else:
plt.rcParams.update({
'figure.figsize': [9.0, 6.0],
'axes.titlesize': '24',
'legend.fontsize': 'small'
})
plt.rcParams.update(self.db.global_settings['rcparams_regular'])
self.fig = plt.figure(1)
self.ax1 = self.fig.add_subplot(111)
self.ax2 = None
# Decide on the y axis type
self.gs = self.db.global_settings
if self.logscale:
self.ax1.set_yscale('log')
elif self.gs['default_yscale'] == 'log':
self.ax1.set_yscale('log')
def _plot(self):
# Make plot
data_in_plot = False
for data in self.db.get_data():
if len(data['data']) > 0:
data_in_plot = data_in_plot or True
# Speciel case for barplots
if self.db.global_settings.has_key('default_style') and\
self.db.global_settings['default_style'] == 'barplot':
self.ax1.bar(data['data'][:, 0],
data['data'][:, 1],
color=self.c.get_color())
# Normal graph styles
else:
# If the graph go on the right side of the plot
if data['info']['on_the_right']:
# Initialise secondary plot if it isn't already
if not self.ax2:
self._init_second_y_axis()
# If info has a color (i.e. it is given in gs ordering)
if data['info'].has_key('color'):
# Set the color for the graph and axis
color = data['info']['color']
self.right_color = data['info']['color']
else:
# Else get a new color from self.c
color = self.c.get_color()
# Make the actual plot
self.ax2.plot(data['data'][:, 0],
data['data'][:, 1],
color=color,
label=self._legend_item(data) + '(R)')
# If the graph does not go on the right side of the plot
else:
# If info has a color (i.e. it is given in gs ordering)
if data['info'].has_key('color'):
# Set the color for the graph and axis
color = data['info']['color']
self.left_color = data['info']['color']
else:
# Else get a new color from self.c
color = self.c.get_color()
# Make the actual plot
self.ax1.plot(data['data'][:, 0],
data['data'][:, 1],
color=color,
label=self._legend_item(data))
# If no data has been been put on the graph at all, explain why there
# is none
if not data_in_plot:
y = 0.00032 if self.logscale or self.gs[
'default_yscale'] == 'log' else 0.5
self.ax1.text(0.5,
y,
'No data',
horizontalalignment='center',
verticalalignment='center',
color='red',
size=60)
def _legend(self):
if self.db.global_settings['default_xscale'] != 'dat':
ax1_legends = self.ax1.get_legend_handles_labels()
if self.ax2:
ax2_legends = self.ax2.get_legend_handles_labels()
for color, text in zip(ax2_legends[0], ax2_legends[1]):
ax1_legends[0].append(color)
ax1_legends[1].append(text)
# loc for locations, 0 means 'best'. Why that isn't deafult I
# have no idea
self.ax1.legend(ax1_legends[0], ax1_legends[1], loc=0)
def _zoom_and_flip(self):
# Now we are done with the plotting, change axis if necessary
# Get current axis limits
self.axis = self.ax1.axis()
if self.options.xmin != self.options.xmax:
self.axis = (float(self.options.xmin), float(self.options.xmax)) +\
self.axis[2:4]
if self.options.ymin != self.options.ymax:
self.axis = self.axis[0:2] + (float(
self.options.ymin), float(self.options.ymax))
if self.flip_x:
self.axis = (self.axis[1], self.axis[0]) + self.axis[2:4]
self.ax1.axis(self.axis)
def _transform_and_label_axis(self):
""" Transform X-AXIS axis and label it """
# If it is a date plot
if self.db.global_settings['default_xscale'] == 'dat':
# Turn the x-axis into timemarks
# IMPLEMENT add something to TimeMarks initialisation to take care
# or morning_pressure
markformat = '%H:%M' if self.small_plot else '%b-%d %H:%M'
timemarks = TimeMarks(self.axis[0],
self.axis[1],
markformat=markformat)
(old_tick_labels, new_tick_labels) = timemarks.get_time_marks()
self.ax1.set_xticks(old_tick_labels)
self.bbox_xlabels = self.ax1.\
set_xticklabels(new_tick_labels, rotation=25,
horizontalalignment='right')
# Make a little extra room for the rotated x marks
#self.fig.subplots_adjust(bottom=0.12)
elif self.options.type == 'masstime':
gs_temp_unit = self.gs['temperature_unit']
other_temp_unit = 'C' if gs_temp_unit == 'K' else 'K'
cur_temp_unit = other_temp_unit if self.shift_temp_unit else\
gs_temp_unit
if self.as_function_of_t and not self.small_plot:
self.ax1.set_xlabel(self.gs['t_xlabel'] + cur_temp_unit)
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
elif self.options.type == 'xps':
if self.shift_be_ke and not self.small_plot:
self.ax1.set_xlabel(self.gs['alt_xlabel'])
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
# Label Y-axis
if not self.small_plot:
self.ax1.set_ylabel(self.gs['ylabel'], color=self.left_color)
if self.ax2:
self.ax2.set_ylabel(self.gs['right_ylabel'],
color=self.right_color)
def _title(self):
""" TITLE """
# Set the title and raise it a bit
if self.as_function_of_t:
self.bbox_title = self.ax1.set_title(self.gs['t_title'], y=1.03)
else:
self.bbox_title = self.ax1.set_title(self.gs['title'], y=1.03)
def _grids(self):
# GRIDS
self.ax1.grid(b=True, which='major')
#plt.xscale('linear')
#plt.xticks(range(0,100,10))
#plt.x_minor_ticks(range(0,100,10))
#plt.grid(b='on', which='minor')
#plt.grid(b='on', which='major')
def _save(self):
## Filesave
# Save
self.fig.savefig(self.namehash, bbox_inches='tight', pad_inches=0.03)
# This is the magical line that plot.php opens
# For the script to work this has to be the only print statement
print self.namehash
### Here start the small helper functions that are called from the main flow
def _init_second_y_axis(self):
self.ax2 = self.ax1.twinx()
if self.db.global_settings['right_yscale'] == 'log':
self.ax2.set_yscale('log')
def _legend_item(self, data):
if self.db.global_settings['default_xscale'] == 'dat':
return ''
elif data['gs'].has_key('legend_field_name') and\
data['info'][data['gs']['legend_field_name']]:
return data['info']['mass_label'] + '-' + str(data['info']['id'])
else:
return str(data['info']['id'])
class Plot():
"""This class is used to generate the figures for the plots."""
def __init__(self):
""" Description of init """
# Create the option parser for the command line options
usage = ('usage: %prog [options]\n\n'
'All options are strings. Boolean options are true when they \n'
'contains a certain specific keywords, which is written in \n'
'the option description in parantheses.')
parser = OptionParser(usage=usage)
# Add the options to the option parser
parser.add_option('-a', '--type', help='Type string from '
'graphsettings.xml')
parser.add_option('-b', '--idlist', help='List of id\'s to plot')
parser.add_option('-c', '--from_d', help='From timestamp, format: '
'YYYY-MM-DD HH:MM')
parser.add_option('-d', '--to_d', help='To timestamp, format: '
'YYYY-MM-DD HH:MM')
parser.add_option('-e', '--xmin', help='X-min for zoom')
parser.add_option('-f', '--xmax', help='X-max for zoom')
parser.add_option('-g', '--ymin', help='Y-min for zoom')
parser.add_option('-i', '--ymax', help='Y-max for zoom')
parser.add_option('-j', '--offset', help='List of offsets for the '
'graphs (for plots that goes on a log scale and has '
'negative values)')
parser.add_option('-k', '--as_function_of_t', help='Plot the graphs as '
'a function of temperature (boolean \'checked\'=True)')
parser.add_option('-l', '--logscale', help='Use a log for the right '
'axis (boolean \'checked\'=True)')
parser.add_option('-m', '--shift_temp_unit', help='Change between K '
'and C when values are plotted as a function of '
'temperature (boolean \'checked\'=True)')
parser.add_option('-n', '--flip_x', help='Exchange min and max for the '
'x-axis (boolean \'checked\'=True)')
parser.add_option('-o', '--shift_be_ke', help='Shift between binding '
'energy and kinetic energy for XPS plots (boolean '
'\'checked\'=True)')
# -p is availabel from previous options
parser.add_option('-q', '--image_format', help='Image format for the '
'figure exports, given as the figure extension. Can '
'be svg, eps, ps, pdf and default. Default means use '
'the one in graphsettings.xml or internal deaault.')
parser.add_option('-r', '--small_plot', help='Produce a small plot '
'(boolean \'checked\'=1)')
# Parse the options
(options, args) = parser.parse_args()
### Process options - all options are given as string, and they need to
### be converted into other data types
# Convert idlist
self.idlist = [int(element) for element in options.idlist.split(',')[1:]]
# Turn the offset 'key:value,' pair string into a dictionary
self.offsets = dict([[int(offset.split(':')[0]), offset.split(':')[1]]
for offset in options.offset.split(',')[1:]])
# Gather from and to in a fictionary
self.from_to = {'from':options.from_d, 'to':options.to_d}
# Turn several options into booleans
self.as_function_of_t = True if options.as_function_of_t ==\
'checked' else False
self.shift_temp_unit = True if options.shift_temp_unit ==\
'checked' else False
self.logscale = True if options.logscale == 'checked' else False
self.flip_x = True if options.flip_x == 'checked' else False
self.shift_be_ke = True if options.shift_be_ke == 'checked' else False
self.small_plot = True if options.small_plot == '1' else False
### Create database backend object
self.db = dataBaseBackend(typed=options.type, from_to=self.from_to,
id_list=self.idlist, offsets=self.offsets,
as_function_of_t=self.as_function_of_t,
shift_temp_unit=self.shift_temp_unit,
shift_be_ke=self.shift_be_ke)
### Ask self.db for a measurement count
measurement_count = self.db.get_data_count()
# Set the image format to standard, overwite with gs value and again
# options value if i exits
if options.image_format:
if options.image_format == 'default':
if self.db.global_settings.has_key('image_format'):
self.image_format = self.db.global_settings['image_format']
else:
self.image_format = 'png'
else:
self.image_format = options.image_format
else:
self.image_format = 'png'
# Create a hash from the measurement_count, options and
#self.db.global_settings
hash = hashlib.md5()
hash.update(str(options) + str(self.db.global_settings) +
str(measurement_count))
# self.namehash is unique for this plot and will form the filename
self.namehash = ('/var/www/cinfdata/figures/' + hash.hexdigest() + '.' +
self.image_format)
# For use in other methods
self.options = options
# object to give first good color, and then random colors
self.c = Color()
self.left_color = 'black'
self.right_color = 'black'
def main(self):
if os.path.exists(self.namehash) and False:
print self.namehash
else:
# Call a bunch of functions
self._init_plot()
self._plot()
if self.left_color != 'black':
if self.right_color != 'black':
self.c.color_axis(self.ax1, self.ax2, self.left_color, self.right_color)
else:
self.c.color_axis(self.ax1, None, self.left_color, None)
self._legend()
self._zoom_and_flip()
self._transform_and_label_axis()
if not self.small_plot:
self._title()
self._grids()
self._save()
def _init_plot(self):
### Apply settings
# Small plots
if self.small_plot:
# Apply default settings
plt.rcParams.update({'figure.figsize':[4.5, 3.0],
'ytick.labelsize':'x-small',
'xtick.labelsize':'x-small',
'legend.fontsize':'x-small'})
# Overwrite with values from graphsettings
plt.rcParams.update(self.db.global_settings['rcparams_small'])
else:
plt.rcParams.update({'figure.figsize':[9.0, 6.0],
'axes.titlesize':'24',
'legend.fontsize':'small'})
plt.rcParams.update(self.db.global_settings['rcparams_regular'])
self.fig = plt.figure(1)
self.ax1 = self.fig.add_subplot(111)
self.ax2 = None
# Decide on the y axis type
self.gs = self.db.global_settings
if self.logscale:
self.ax1.set_yscale('log')
elif self.gs['default_yscale'] == 'log':
self.ax1.set_yscale('log')
def _plot(self):
# Make plot
data_in_plot = False
for data in self.db.get_data():
if len(data['data']) > 0:
data_in_plot = data_in_plot or True
# Speciel case for barplots
if self.db.global_settings.has_key('default_style') and\
self.db.global_settings['default_style'] == 'barplot':
self.ax1.bar(data['data'][:,0], data['data'][:,1],
color=self.c.get_color())
# Normal graph styles
else:
# If the graph go on the right side of the plot
if data['info']['on_the_right']:
# Initialise secondary plot if it isn't already
if not self.ax2:
self._init_second_y_axis()
# If info has a color (i.e. it is given in gs ordering)
if data['info'].has_key('color'):
# Set the color for the graph and axis
color = data['info']['color']
if 'overview' in self.options.type:
self.right_color = data['info']['color']
else:
# Else get a new color from self.c
color = self.c.get_color()
# Make the actual plot
self.ax2.plot(data['data'][:,0], data['data'][:,1],
color=color,
label=self._legend_item(data)+'(R)')
# If the graph does not go on the right side of the plot
else:
# If info has a color (i.e. it is given in gs ordering)
if data['info'].has_key('color'):
# Set the color for the graph and axis
color = data['info']['color']
if 'overview' in self.options.type:
self.left_color = data['info']['color']
else:
# Else get a new color from self.c
color = self.c.get_color()
# Make the actual plot
self.ax1.plot(data['data'][:,0], data['data'][:,1],
color=color,
label=self._legend_item(data))
# If no data has been been put on the graph at all, explain why there
# is none
if not data_in_plot:
y = 0.00032 if self.logscale or self.gs['default_yscale'] == 'log' else 0.5
self.ax1.text(0.5, y, 'No data', horizontalalignment='center',
verticalalignment='center', color='red', size=60)
def _legend(self):
if self.db.global_settings['default_xscale'] != 'dat':
ax1_legends = self.ax1.get_legend_handles_labels()
if self.ax2:
ax2_legends = self.ax2.get_legend_handles_labels()
for color, text in zip(ax2_legends[0], ax2_legends[1]):
ax1_legends[0].append(color)
ax1_legends[1].append(text)
# loc for locations, 0 means 'best'. Why that isn't deafult I
# have no idea
self.ax1.legend(ax1_legends[0], ax1_legends[1], loc=0)
def _zoom_and_flip(self):
# Now we are done with the plotting, change axis if necessary
# Get current axis limits
self.axis = self.ax1.axis()
if self.options.xmin != self.options.xmax:
self.axis = (float(self.options.xmin), float(self.options.xmax)) +\
self.axis[2:4]
if self.options.ymin != self.options.ymax:
self.axis = self.axis[0:2] + (float(self.options.ymin),
float(self.options.ymax))
if self.flip_x:
self.axis = (self.axis[1], self.axis[0]) + self.axis[2:4]
self.ax1.axis(self.axis)
def _transform_and_label_axis(self):
""" Transform X-AXIS axis and label it """
# If it is a date plot
if self.db.global_settings['default_xscale'] == 'dat':
# Turn the x-axis into timemarks
# IMPLEMENT add something to TimeMarks initialisation to take care
# or morning_pressure
markformat = '%H:%M' if self.small_plot else '%b-%d %H:%M'
timemarks = TimeMarks(self.axis[0], self.axis[1],
markformat=markformat)
(old_tick_labels, new_tick_labels) = timemarks.get_time_marks()
self.ax1.set_xticks(old_tick_labels)
self.bbox_xlabels = self.ax1.\
set_xticklabels(new_tick_labels, rotation=25,
horizontalalignment='right')
# Make a little extra room for the rotated x marks
#self.fig.subplots_adjust(bottom=0.12)
elif self.options.type == 'masstime':
gs_temp_unit = self.gs['temperature_unit']
other_temp_unit = 'C' if gs_temp_unit == 'K' else 'K'
cur_temp_unit = other_temp_unit if self.shift_temp_unit else\
gs_temp_unit
if self.as_function_of_t and not self.small_plot:
self.ax1.set_xlabel(self.gs['t_xlabel'] + cur_temp_unit)
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
elif self.options.type == 'xps':
if self.shift_be_ke and not self.small_plot:
self.ax1.set_xlabel(self.gs['alt_xlabel'])
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
elif not self.small_plot:
self.ax1.set_xlabel(self.gs['xlabel'])
# Label Y-axis
if not self.small_plot:
self.ax1.set_ylabel(self.gs['ylabel'], color=self.left_color)
if self.ax2:
self.ax2.set_ylabel(self.gs['right_ylabel'], color=self.right_color)
def _title(self):
""" TITLE """
# Set the title and raise it a bit
if self.as_function_of_t:
self.bbox_title = self.ax1.set_title(
self.gs['t_title'], y=1.03)
else:
self.bbox_title = self.ax1.set_title(
self.gs['title'], y=1.03)
def _grids(self):
# GRIDS
self.ax1.grid(b=True, which = 'major')
#plt.xscale('linear')
#plt.xticks(range(0,100,10))
#plt.x_minor_ticks(range(0,100,10))
#plt.grid(b='on', which='minor')
#plt.grid(b='on', which='major')
def _save(self):
## Filesave
# Save
self.fig.savefig(self.namehash, bbox_inches='tight', pad_inches=0.03)
# This is the magical line that plot.php opens
# For the script to work this has to be the only print statement
print self.namehash
### Here start the small helper functions that are called from the main flow
def _init_second_y_axis(self):
self.ax2 = self.ax1.twinx()
if self.db.global_settings['right_yscale'] == 'log':
self.ax2.set_yscale('log')
def _legend_item(self, data):
if self.db.global_settings['default_xscale'] == 'dat':
return ''
elif data['gs'].has_key('legend_field_name') and\
data['info'][data['gs']['legend_field_name']]:
return data['info']['mass_label'] + '-' + str(data['info']['id'])
else:
return str(data['info']['id'])
