def actionSBFit(formFields):
global textFormat
fn = getDataFile(formFields)
oc = ocUtils("SB")
global globalOcInstance
globalOcInstance = oc
if not textFormat:
print '<pre>'
oc.initFromCommandLine(["", fn])
if not textFormat:
print '</pre>'
oc.setDataFile(formFields["datafilename"])
handleGraphOptions(oc, formFields)
#functionFlag = formFields.get("functionvalues", "")
#if functionFlag:
#oc.setValuesAreFunctions(1)
if not formFields.has_key("data") or not formFields.has_key("model"):
actionNone(formFields, "Missing form fields")
os.remove(fn)
return
skipNominalFlag = formFields.get("skipnominal", "")
if skipNominalFlag:
oc.setSkipNominal(1)
maybeSkipResiduals(formFields, oc)
maybeSkipIVIs(formFields, oc)
target = formFields["negativeDVforConfusion"] if formFields.has_key(
"negativeDVforConfusion") else ""
onlyGfx = formFields.has_key("onlyGfx")
processSBFit(fn, formFields["model"], target, oc, onlyGfx)
os.remove(fn)
def computeBestModel(filename):
oc = ocUtils("VB")
global globalOcInstance
globalOcInstance = oc
oc.initFromCommandLine(["occam", filename])
oc.setDataFile(filename)
oc.setAction("search")
# Hardcoded settings (for now):
oc.setSortDir("descending")
oc.setSearchSortDir("descending") # try to maximize dBIC or dAIC.
oc.setRefModel("bottom") # Always uses bottom as reference.
# Parameters from the web form
oc.sortName = search["sort by"]
oc.setSearchLevels(int(search["levels"]))
oc.setSearchWidth(int(search["width"]))
oc.setSearchFilter(search["type"])
[i, d] = search["direction"].split(" ")
oc.searchDir = d
oc.setStartModel(i)
return oc.findBestModel()
def actionSearch(formFields):
global textFormat
fn = getDataFile(formFields)
man = "VB"
oc = ocUtils(man)
global globalOcInstance
globalOcInstance = oc
if not textFormat:
print '<pre>'
oc.initFromCommandLine(["", fn])
if not textFormat:
print '</pre>'
oc.setDataFile(formFields["datafilename"])
# unused error? this should get caught by getDataFile() above
if not formFields.has_key("data"):
actionForm(form, "Missing form fields")
print "missing data"
return
#textFormat = formFields.get("format", "")
if textFormat:
oc.setReportSeparator(ocUtils.COMMASEP)
else:
oc.setReportSeparator(ocUtils.HTMLFORMAT)
oc.setSortDir(formFields.get("sortdir", ""))
levels = formFields.get("searchlevels")
if levels and levels > 0:
oc.setSearchLevels(levels)
width = formFields.get("searchwidth")
if width and width > 0:
oc.setSearchWidth(width)
reportSort = formFields.get("sortreportby", "")
searchSort = formFields.get("sortby", "")
inverseFlag = formFields.get("inversenotation", "")
if inverseFlag:
oc.setUseInverseNotation(1)
skipNominalFlag = formFields.get("skipnominal", "")
if skipNominalFlag:
oc.setSkipNominal(1)
functionFlag = formFields.get("functionvalues", "")
if functionFlag:
oc.setValuesAreFunctions(1)
oc.setStartModel(formFields.get("model", "default"))
refModel = formFields.get("refmodel", "default")
#specificRefModel = ""
#if refModel == "specific" and formFields.has_key("specificrefmodel"):
# refModel = formFields["specificrefmodel"]
#specificRefModel = refModel
if refModel == "starting":
refModel = oc.getStartModel()
oc.setRefModel(refModel)
oc.searchDir = formFields.get("searchdir", "default")
oc.setSearchSortDir(formFields.get("searchsortdir", ""))
oc.setSearchFilter(formFields.get("searchtype", "all"))
oc.setAlphaThreshold(formFields.get("alpha-threshold", "0.05"))
oc.setAction("search")
## INTENTIONALLY COMMENTED OUT CODE IN THIS MULTILINE STRING!!!
## This code handles the backpropagation-based evaluation,
## but it is not currently used (and the HTML forms do not define "evalmode"
## so it will crash!!)
disabledBPCode = """
if formFields["evalmode"] == "bp":
reportvars = "Level$I, bp_t, bp_h, ddf, bp_lr, bp_alpha, bp_information"
oc.setNoIPF(true)
if reportSort == "information": reportSort = "bp_information"
elif reportSort == "alpha": reportSort = "bp_alpha"
if searchSort == "information": searchSort = "bp_information"
elif searchSort == "alpha": searchSort = "bp_alpha"
if oc.isDirected():
reportvars += ", bp_cond_pct_dh"
reportvars += ", bp_aic, bp_bic"
"""
if False: pass
else:
reportvars = "Level$I"
if formFields.get("show_h", ""):
reportvars += ", h"
reportvars += ", ddf"
if formFields.get("show_dlr", ""):
reportvars += ", lr"
if formFields.get(
"show_alpha",
"") or searchSort == "alpha" or reportSort == "alpha":
reportvars += ", alpha"
reportvars += ", information"
if oc.isDirected():
if formFields.get("show_pct_dh", ""):
reportvars += ", cond_pct_dh"
if formFields.get("show_aic",
"") or searchSort == "aic" or reportSort == "aic":
reportvars += ", aic"
if formFields.get("show_bic",
"") or searchSort == "bic" or reportSort == "bic":
reportvars += ", bic"
if formFields.get("show_incr_a", ""):
reportvars += ", incr_alpha, prog_id"
## INTENTIONALLY COMMENTED OUT CODE IN THIS MULTILINE STRING!!!
## This code handles the backpropagation-based evaluation,
## but it is not currently used (and the HTML forms do not define "evalmode"
## so it will crash!!)
disabledBPCode = """
if formFields.get("show_bp", "") and formFields["evalmode"] <> "bp":
reportvars += ", bp_t"
"""
if oc.isDirected():
if formFields.get("show_pct", "") or formFields.get(
"show_pct_cover", ""
) or searchSort == "pct_correct_data" or reportSort == "pct_correct_data":
reportvars += ", pct_correct_data"
if formFields.get("show_pct_cover", ""):
reportvars += ", pct_coverage"
if oc.hasTestData():
reportvars += ", pct_correct_test"
if formFields.get("show_pct_miss", ""):
reportvars += ", pct_missed_test"
oc.setReportSortName(reportSort)
oc.sortName = searchSort
oc.setReportVariables(reportvars)
if textFormat:
oc.doAction(printOptions)
else:
print "<hr><p>"
print '<div class="data">'
oc.doAction(printOptions)
print "</div>"
os.remove(fn)
0]
sys.exit()
if len(sys.argv) >= 4:
swidth = sys.argv[2]
slevels = sys.argv[3]
else:
swidth = 3
slevels = 7
if len(sys.argv) >= 5:
filter = sys.argv[4]
else:
filter = "loopless"
util = ocUtils("SB") # create a variable-based manager
t1 = time.time()
util.initFromCommandLine(sys.argv[0:2]) # initialize with the data file
#------------- Main script ---------------
# This script sets various options on a ocUtils object, and then runs the desired action.
# ocUtils is a convenience wrapper around the basic occam3 objects, and it sets appropriate
# defaults if you don't set every option.
# For settings which require model attribute names, the allowed values include:
# h, t, df, ddf, loops [1=loops, 0=no loops]
# information, unexplained, ipf_iterations, lr, alpha, beta, level, aic, bic
# cond_h, cond_dh, cond_pct_dh, cond_df, cond_ddf, p2, p2_alpha, p2_beta
# (Note that the Pearson statistics aren't computed by default because they are expensive.)
# To force a particular attribute to be printed as an integer, append "$I" to the name (e.g., Level$I)
# p2 -- computed by default because they are expensive
# p2_alpha
# p2_alpha
# p2_beta
# p2_beta
# To force a particular attribute to be printed as an integer,
# append "$I" to the name (e.g., Level$I)
#-------------------------------------------------
# create an ocUtils object. This is a convenience wrapper which can
# handle Occam2 files and options
# See the source file for other options which can be set
util = ocUtils()
util.initFromCommandLine(sys.argv)
# set desired options which aren't in the data file, or override them
# here.
# set separator between report fields.
# 1=tab, 2=comma, 3=space fill, 4=HTML
util.setReportSeparator(3)
# set report names, from the list above. If omitted, the list is set
# based on whether the ref model is top or bottom. List is separated
# by commas, and provided as a single text string
# for ref=top, this is a good list:
#util.setReportVars("Level$I, h, ddf, lr, alpha, information")
# for ref=bottom, use something like this:
#import pdb
import os, sys
#sys.path.append("/www")
import occam
import time
from ocutils import ocUtils
if len(sys.argv) < 3:
print 'Incorrect parameters.'
print 'Usage: %s datafile model' % sys.argv[0]
sys.exit()
oc = ocUtils("VB")
t1 = time.time()
oc.initFromCommandLine(sys.argv[0:2]) # initialize with the data file
oc.setFitModel(sys.argv[2])
oc.setAction("fit")
oc.setReportSeparator(3)
oc.setSkipNominal(1)
oc.setDDFMethod(1)
#oc.setDefaultFitModel("IV:CD")
t2 = time.time()
oc.doAction(1)
t3 = time.time()
# distribution of this software for license terms.
import pdb
import os, sys
sys.path.append("/www")
import occam
import time
from ocutils import ocUtils
if len(sys.argv) < 3:
print 'Incorrect parameters.'
print 'Usage: %s datafile model' % sys.argv[0]
sys.exit()
oc = ocUtils("SB")
t1 = time.time()
oc.initFromCommandLine(sys.argv[0:2]) # initialize with the data file
oc.setFitModel(sys.argv[2])
oc.setAction("SBfit")
oc.setReportSeparator(3)
#oc.setDDFMethod(1)
t2 = time.time()
oc.doAction(0)
t3 = time.time()
print "start: %8f" % (t2 - t1)
print "fit: %8f" % (t3 - t2)