def run_real(self):
"""Runs the main application"""
# Get the type of the curve to be plotted
try:
self.curve_class = CurveFactory.find_class_by_name(self.options.curve_type)
except ValueError:
self.parser.error("Unsupported curve type: %s" % self.options.curve_type)
self.process_input_files()
self.run_tests()
def add_parser_options(self):
"""Creates the command line parser object for the application"""
super(AUCCalculatorApplication, self).add_parser_options()
parser = self.parser
parser.add_option("-t", "--curve-type", dest="curve_types",
metavar="TYPE", choices=CurveFactory.get_curve_names(),
action="append", default=[],
help="sets the TYPE of the curve to be plotted "
"(roc, pr, ac, sespe or croc). May be specified "
"multiple times.")
def add_parser_options(self):
"""Creates the command line parser object for the application"""
super(AUCCalculatorApplication, self).add_parser_options()
parser = self.parser
parser.add_option("-t",
"--curve-type",
dest="curve_types",
metavar="TYPE",
choices=CurveFactory.get_curve_names(),
action="append",
default=[],
help="sets the TYPE of the curve to be plotted "
"(roc, pr, ac, sespe or croc). May be specified "
"multiple times.")
def run_real(self):
"""Runs the main application"""
# If no curve type was given, assume a ROC curve
if not self.options.curve_types:
self.options.curve_types = ["roc"]
# Get the types of the curves to be plotted
curve_classes = []
for name in self.options.curve_types:
try:
curve_classes.append(CurveFactory.find_class_by_name(name))
except ValueError:
self.parser.error("Unknown curve type: %s" % name)
self.process_input_files()
for curve_class in curve_classes:
self.print_scores_for_curve(curve_class)
def run_real(self):
"""Runs the main application"""
# If no curve type was given, assume a ROC curve
if not self.options.curve_types:
self.options.curve_types = ["roc"]
# Get the types of the curves to be plotted
curve_classes = []
for name in self.options.curve_types:
try:
curve_classes.append(CurveFactory.find_class_by_name(name))
except ValueError:
self.parser.error("Unknown curve type: %s" % name)
self.process_input_files()
for curve_class in curve_classes:
self.print_scores_for_curve(curve_class)
def add_parser_options(self):
"""Creates the command line parser object for the application"""
super(ROCPlotterApplication, self).add_parser_options()
parser = self.parser
parser.add_option("-t", "--curve-type", dest="curve_types",
metavar="TYPE", choices=CurveFactory.get_curve_names(),
action="append", default=[],
help="sets the TYPE of the curve to be plotted "
"(roc, pr, ac, sespe or croc). May be specified "
"multiple times.")
parser.add_option("-l", "--log-scale", dest="log_scale",
metavar="AXES",
help="use logarithmic scale on the given AXES. "
"Valid values: none, x, y and xy",
choices=["none", "x", "y", "xy"], default="none")
parser.add_option("-o", "--output", dest="output", metavar="FILE",
help="saves the plot to the given FILE instead of showing it",
default=None)
parser.add_option("-s", "--size", dest="size", metavar="WIDTHxHEIGHT",
help="sets the size of the figure to WIDTHxHEIGHT, where "
"WIDTH and HEIGHT are measures in inches. You may "
"specify alternative measures (cm or mm) by adding "
"them as a suffix; e.g., \"6cmx4cm\" or \"6cm x 4cm\"",
default=None)
parser.add_option("--dpi", dest="dpi", metavar="DPI",
type=float, default=72.0,
help="specifies the dpi value (dots per inch) when "
"converting pixels to inches and vice versa "
"in figure and font size calculations. "
"Default: %default")
parser.add_option("--font-size", dest="font_size", metavar="SIZE",
type=float, default=None,
help="overrides the font size to be used on figures, "
"in points (pt).")
parser.add_option("--show-auc", dest="show_auc", action="store_true",
default=False, help="shows the AUC scores in the legend")
parser.add_option("--no-resampling", dest="resampling", action="store_false",
default=True, help="don't resample curves before "
"plotting and AUC calculation")
def run_real(self):
"""Runs the main application"""
import matplotlib
# Do we need headless mode for matplotlib?
if self.options.output:
matplotlib.use("agg")
# If no curve type was given, assume a ROC curve
if not self.options.curve_types:
self.options.curve_types = ["roc"]
# Set up the font size
if self.options.font_size is not None:
for param in ['font.size', 'legend.fontsize']:
matplotlib.rcParams[param] = self.options.font_size
# Get the types of the curves to be plotted
curve_classes = []
for name in self.options.curve_types:
try:
curve_classes.append(CurveFactory.find_class_by_name(name))
except ValueError:
self.parser.error("Unknown curve type: %s" % name)
# Do we have multiple curve types? If so, we need PDF output
pp = None
if len(curve_classes) > 1:
if not self.options.output or \
not self.options.output.endswith(".pdf"):
self.parser.error("multiple curves can only be plotted to PDF")
try:
from matplotlib.backends.backend_pdf import PdfPages
except ImportError:
self.parser.error("Matplotlib is too old and does not have "
"multi-page PDF support yet. Please upgrade it to "
"Matplotlib 0.99 or later")
pp = PdfPages(self.options.output)
def figure_saver(figure):
pp.savefig(figure, bbox_inches="tight")
elif self.options.output:
# Figure with a single plot will be created
def figure_saver(figure):
self.log.info("Saving plot to %s..." % self.options.output)
figure.savefig(self.options.output, bbox_inches="tight")
else:
# Figure will be shown on screen
def figure_saver(figure):
import matplotlib.pyplot as plt
plt.show()
self.process_input_files()
self.log.info("Plotting results...")
for curve_class in curve_classes:
fig = self.get_figure_for_curves(curve_class)
figure_saver(fig)
# For multi-page output, we have to close it explicitly
if pp is not None:
pp.close()
def add_parser_options(self):
"""Creates the command line parser object for the application"""
super(ROCPlotterApplication, self).add_parser_options()
parser = self.parser
parser.add_option("-t",
"--curve-type",
dest="curve_types",
metavar="TYPE",
choices=CurveFactory.get_curve_names(),
action="append",
default=[],
help="sets the TYPE of the curve to be plotted "
"(roc, pr, ac, sespe or croc). May be specified "
"multiple times.")
parser.add_option("-l",
"--log-scale",
dest="log_scale",
metavar="AXES",
help="use logarithmic scale on the given AXES. "
"Valid values: none, x, y and xy",
choices=["none", "x", "y", "xy"],
default="none")
parser.add_option(
"-o",
"--output",
dest="output",
metavar="FILE",
help="saves the plot to the given FILE instead of showing it",
default=None)
parser.add_option(
"-s",
"--size",
dest="size",
metavar="WIDTHxHEIGHT",
help="sets the size of the figure to WIDTHxHEIGHT, where "
"WIDTH and HEIGHT are measures in inches. You may "
"specify alternative measures (cm or mm) by adding "
"them as a suffix; e.g., \"6cmx4cm\" or \"6cm x 4cm\"",
default=None)
parser.add_option("--dpi",
dest="dpi",
metavar="DPI",
type=float,
default=72.0,
help="specifies the dpi value (dots per inch) when "
"converting pixels to inches and vice versa "
"in figure and font size calculations. "
"Default: %default")
parser.add_option(
"--font-size",
dest="font_size",
metavar="SIZE",
type=float,
default=None,
help="overrides the font size to be used on figures, "
"in points (pt).")
parser.add_option("--show-auc",
dest="show_auc",
action="store_true",
default=False,
help="shows the AUC scores in the legend")
parser.add_option("--no-resampling",
dest="resampling",
action="store_false",
default=True,
help="don't resample curves before "
"plotting and AUC calculation")
def run_real(self):
"""Runs the main application"""
import matplotlib
# Do we need headless mode for matplotlib?
if self.options.output:
matplotlib.use("agg")
# If no curve type was given, assume a ROC curve
if not self.options.curve_types:
self.options.curve_types = ["roc"]
# Set up the font size
if self.options.font_size is not None:
for param in ['font.size', 'legend.fontsize']:
matplotlib.rcParams[param] = self.options.font_size
# Get the types of the curves to be plotted
curve_classes = []
for name in self.options.curve_types:
try:
curve_classes.append(CurveFactory.find_class_by_name(name))
except ValueError:
self.parser.error("Unknown curve type: %s" % name)
# Do we have multiple curve types? If so, we need PDF output
pp = None
if len(curve_classes) > 1:
if not self.options.output or \
not self.options.output.endswith(".pdf"):
self.parser.error("multiple curves can only be plotted to PDF")
try:
from matplotlib.backends.backend_pdf import PdfPages
except ImportError:
self.parser.error(
"Matplotlib is too old and does not have "
"multi-page PDF support yet. Please upgrade it to "
"Matplotlib 0.99 or later")
pp = PdfPages(self.options.output)
def figure_saver(figure):
pp.savefig(figure, bbox_inches="tight")
elif self.options.output:
# Figure with a single plot will be created
def figure_saver(figure):
self.log.info("Saving plot to %s..." % self.options.output)
figure.savefig(self.options.output, bbox_inches="tight")
else:
# Figure will be shown on screen
def figure_saver(figure):
import matplotlib.pyplot as plt
plt.show()
self.process_input_files()
self.log.info("Plotting results...")
for curve_class in curve_classes:
fig = self.get_figure_for_curves(curve_class)
figure_saver(fig)
# For multi-page output, we have to close it explicitly
if pp is not None:
pp.close()
