#!/usr/bin/env python3.8
# (c) Massachusetts Institute of Technology 2015-2018
# (c) Brian Teague 2018-2022
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
cytoflowgui.workflow.operations.channel_stat
--------------------------------------------
"""
import numpy as np
import scipy.stats
from traits.api import (Str, Callable, Property, Any, List, provides, observe)
import cytoflow.utility as util
from cytoflow import ChannelStatisticOp
from cytoflowgui.workflow.serialization import camel_registry, traits_repr
from .operation_base import IWorkflowOperation, WorkflowOperation
from ..subset import ISubset
mean_95ci = lambda x: util.ci(x, np.mean, boots = 100)
geomean_95ci = lambda x: util.ci(x, util.geom_mean, boots = 100)
summary_functions = {"Mean" : np.mean,
"Geom.Mean" : util.geom_mean,
"Median" : np.median,
"Count" : len,
"Std.Dev" : np.std,
"Geom.SD" : util.geom_sd_range,
"SEM" : scipy.stats.sem,
"Geom.SEM" : util.geom_sem_range,
"Mean 95% CI" : mean_95ci,
"Geom.Mean 95% CI" : geomean_95ci
}
fill = {"Mean" : 0,
"Geom.Mean" : 0,
"Median" : 0,
"Count" : 0,
"Std.Dev" : 0,
"Geom.SD" : (0,0),
"SEM" : 0,
"Geom.SEM" : (0,0),
"Mean 95% CI" : 0,
"Geom.Mean 95% CI" : 0
}
ChannelStatisticOp.__repr__ = traits_repr
[docs]@provides(IWorkflowOperation)
class ChannelStatisticWorkflowOp(WorkflowOperation, ChannelStatisticOp):
# operation traits
name = Str(apply = True)
channel = Str(apply = True)
statistic_name = Str(apply = True)
by = List(Str, apply = True)
# override the base class's "subset" with one that is dynamically generated /
# updated from subset_list
subset = Property(Str, observe = "subset_list.items.str")
subset_list = List(ISubset, apply = True)
# functions aren't picklable, so make this one transient
# and send the name instead
function = Callable(transient = True)
# automatically pick a good fill
fill = Property(Any, observe = 'statistic_name', transient = True)
# MAGIC - returns the value of the 'fill' property
def _get_fill(self):
if self.statistic_name:
return fill[self.statistic_name]
else:
return 0
# bits to support the subset editor
@observe('subset_list:items.str')
def _on_subset_changed(self, _):
self.changed = 'subset_list'
# MAGIC - returns the value of the "subset" Property, above
def _get_subset(self):
return " and ".join([subset.str for subset in self.subset_list if subset.str])
[docs] def apply(self, experiment):
if not self.statistic_name:
raise util.CytoflowOpError("Summary function isn't set")
self.function = summary_functions[self.statistic_name]
return ChannelStatisticOp.apply(self, experiment)
[docs] def clear_estimate(self):
# no-op
return
[docs] def get_notebook_code(self, idx):
op = ChannelStatisticOp()
op.copy_traits(self, op.copyable_trait_names())
fn_import = {"Mean" : "from numpy import mean",
"Median" : "from numpy import median",
"Geom.Mean" : None,
"Count" : None,
"Std.Dev" : "from numpy import std",
"Geom.SD" : None,
"SEM" : "from scipy.stats import sem",
"Geom.SEM" : None,
"Mean 95% CI" : "from numpy import mean",
"Geom.Mean 95% CI" : None
}
fn_name = {"Mean" : "mean",
"Median" : "median",
"Geom.Mean" : "geom_mean",
"Count" : "len",
"Std.Dev" : "std",
"Geom.SD" : "geom_sd_range",
"SEM" : "sem",
"Geom.SEM" : "geom_sem_range",
"Mean 95% CI" : "lambda x: ci(x, mean, boots = 100)",
"Geom.Mean 95% CI" : "lambda x: ci(x, geom_mean, boots = 100)"
}
op.function = summary_functions[self.statistic_name]
try:
# this doesn't work for builtins like "len"
op.function.__name__ = fn_name[self.statistic_name]
except AttributeError:
pass
return "\n{import_statement}\nop_{idx} = {repr}\n\nex_{idx} = op_{idx}.apply(ex_{prev_idx})"\
.format(import_statement = (fn_import[self.statistic_name]
if fn_import[self.statistic_name] is not None
else ""),
repr = repr(op),
idx = idx,
prev_idx = idx - 1)
### Serialization
@camel_registry.dumper(ChannelStatisticWorkflowOp, 'channel-statistic', version = 1)
def _dump(op):
return dict(name = op.name,
channel = op.channel,
statistic_name = op.statistic_name,
by = op.by,
subset_list = op.subset_list)
@camel_registry.loader('channel-statistic', version = 1)
def _load(data, version):
return ChannelStatisticWorkflowOp(**data)