/
publication_bias_wizards.py
214 lines (156 loc) · 7.78 KB
/
publication_bias_wizards.py
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################################################################################
#
# George Dietz
# CEBM@Brown
#
# My policy for the wizards is that they should know nothing about the various
# selections that are made on the pages (store nothing internally)
# rather the selections are stored in the pages themselves and are retrieved
# with accessor functions through the wizard
#
################################################################################
from PyQt4 import QtCore, QtGui
from PyQt4.Qt import *
from ome_globals import *
#import python_to_R
from common_wizard_pages.choose_effect_size_page import ChooseEffectSizePage
from common_wizard_pages.data_location_page import DataLocationPage
from common_wizard_pages.refine_studies_page import RefineStudiesPage
from common_wizard_pages.methods_and_parameters_page import MethodsAndParametersPage
from common_wizard_pages.summary_page import SummaryPage
from common_wizard_pages.failsafe_page import FailsafeWizardPage
from common_wizard_pages.funnel_page import FunnelPage
(Page_ChooseEffectSize, Page_DataLocation, Page_RefineStudies,
Page_MethodsAndParameters, Page_Summary, Page_Failsafe,
Page_FunnelParameters) = range(7)
class AbstractPublicationBiasWizard(QtGui.QWizard):
def __init__(self, model, parent=None):
super(AbstractPublicationBiasWizard, self).__init__(parent)
self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True)
self.model = model
self.last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type
# Initialize pages that we will need to access later
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
self.setWizardStyle(QWizard.ClassicStyle)
QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
def _change_size(self, pageid):
print("changing size")
self.adjustSize()
def nextId(self):
raise NotImplementedError("Not implemented")
#### Getters
# Data location
def get_data_location(self):
return self.data_location_page.get_data_locations()
# Refine Studies page
def get_included_studies_in_proper_order(self):
all_studies = self.model.get_studies_in_current_order()
included_studies = self.refine_studies_page.get_included_studies()
included_studies_in_order = [study for study in all_studies if study in included_studies]
return included_studies_in_order
def save_selections(self): # returns a bool
# Should the selections be saved?
return self.summary_page.save_selections()
class FailsafeWizard(AbstractPublicationBiasWizard):
def __init__(self, model, parent=None):
AbstractPublicationBiasWizard.__init__(self, model=model, parent=parent)
self.setWindowTitle("Failsafe Analysis")
# Add custom pages
self.data_location_page.set_show_raw_data(False)
self.failsafe_page = FailsafeWizardPage(previous_parameters=self.model.get_last_failsafe_parameters())
self.setPage(Page_Failsafe, self.failsafe_page)
self.setStartId(Page_DataLocation)
def nextId(self):
page_id = self.currentId()
return self.next_id_helper(page_id)
def next_id_helper(self, page_id):
if page_id == Page_DataLocation:
return Page_RefineStudies
if page_id == Page_RefineStudies:
return Page_Failsafe
elif page_id == Page_Failsafe:
return Page_Summary
elif page_id == Page_Summary:
return -1
### Getters ###
# Failsafe page
def get_failsafe_parameters(self):
# parameters for failsafe calculation
return self.failsafe_page.get_parameters()
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
return wizard_summary(wizard=self, next_id_helper=self.next_id_helper,
summary_page_id=Page_Summary,
analysis_label="Failsafe Analysis")
class FunnelWizard(AbstractPublicationBiasWizard):
def __init__(self, model, meta_f_str=None, parent=None):
AbstractPublicationBiasWizard.__init__(self, model=model, parent=parent)
##### Add custom pages ####
# Effect Size Page
self.choose_effect_size_page = ChooseEffectSizePage(
add_generic_effect=True,
data_type=self.last_analysis['data_type'],
metric=self.last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
# Methods and parameters apge
self.methods_and_params_page_instance = MethodsAndParametersPage(
model=model, meta_f_str=meta_f_str,
disable_forest_plot_tab=True, funnel_mode=True)
self.setPage(Page_MethodsAndParameters, self.methods_and_params_page_instance)
# Funnel page
self.funnel_params_page = FunnelPage(old_funnel_params=self.model.get_funnel_params())
self.setPage(Page_FunnelParameters, self.funnel_params_page)
self.setStartId(Page_ChooseEffectSize)
def nextId(self):
page_id = self.currentId()
return self.next_id_helper(page_id)
def next_id_helper(self, page_id):
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_MethodsAndParameters
elif page_id == Page_MethodsAndParameters:
return Page_FunnelParameters
elif page_id == Page_FunnelParameters:
return Page_Summary
elif page_id == Page_Summary:
return -1
### Getters ####
# Effect Size Page
def get_data_type_and_metric(self):
''' returns tuple (data_type, metric) '''
return self.choose_effect_size_page.get_data_type_and_metric()
# Methods and parameters page
def get_plot_params(self):
return self.methods_and_params_page_instance.get_plot_params()
def get_current_method(self):
return self.methods_and_params_page_instance.get_current_method()
def get_current_method_pretty_name(self):
return self.methods_and_params_page_instance.get_current_method_pretty_name()
def get_modified_meta_f_str(self):
return self.methods_and_params_page_instance.get_modified_meta_f_str()
# Funnel page
def get_funnel_parameters(self):
return self.funnel_params_page.get_parameters()
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
return wizard_summary(wizard=self, next_id_helper=self.next_id_helper,
summary_page_id=Page_Summary,
analysis_label="Funnelplot Analysis")
# if __name__ == '__main__':
# import sys
#
# app = QtGui.QApplication(sys.argv)
# wizard = MetaAnalysisWizard(parent=None)
# wizard.show()
# sys.exit(app.exec_())