def saveResults(meta, resultPath, results, extras, bestIndex, analyze, hiddenResults=None, hiddenDetails=None, databaseCGI=None, reclassify=False, details=True):
if extras == None:
print "No detailed information for cross-validation"
return
if not os.path.exists(os.path.dirname(resultPath)):
os.makedirs(os.path.dirname(resultPath))
meta = result.getMeta(meta)
# Add general results
meta["results"] = {"best":results[bestIndex], "all":results}
if hiddenResults != None:
meta["results"]["hidden"] = hiddenResults
# Insert detailed results
if details:
featureByIndex = result.getFeaturesByIndex(meta)
if hiddenDetails != None:
saveDetails(meta, hiddenDetails.get("predictions", None), hiddenDetails.get("importances", None), "hidden", featureByIndex, reclassify=reclassify)
fold = 0
for extra in extras:
saveDetails(meta, extra.get("predictions", None), extra.get("importances", None), fold, featureByIndex, reclassify=reclassify)
fold += 1
else:
if "examples" in meta:
del meta["examples"]
if "features" in meta:
del meta["features"]
# Analyze results
if analyze:
print "Analyzing results"
meta = gene.analyze.analyze(meta, databaseCGI)
# Save results
if resultPath != None:
result.saveMeta(meta, resultPath)
def saveDetails(meta, predictions, importances, fold, featureByIndex=None, reclassify=False):
if featureByIndex == None:
featureByIndex = result.getFeaturesByIndex(meta)
if predictions != None:
for index in predictions:
if fold == "hidden":
example = result.getExampleFromSet(meta, index, "hidden")
else:
example = result.getExampleFromSet(meta, index, "train")
if reclassify and ("classification" in example):
del example["classification"]
if "classification" in example:
raise Exception("Example " + str(index) + " has already been classified " + str([fold, str(example)]))
result.setValue(example, "prediction", predictions[index], "classification")
result.setValue(example, "fold", fold, "classification")
if importances != None:
for i in range(len(importances)):
if importances[i] != 0:
feature = result.getFeature(meta, i, featureByIndex)
if fold != "hidden":
result.setValue(feature, fold, importances[i], "importances")
#if "sort" not in feature:
# result.setValue(feature, "sort", 0)
else:
result.setValue(feature, "hidden-importance", importances[i])
result.setValue(feature, "sort", importances[i])
def saveResults(meta, resultPath, perfs, selected):
if not os.path.exists(os.path.dirname(resultPath)):
os.makedirs(os.path.dirname(resultPath))
meta = result.getMeta(meta)
featureByIndex = result.getFeaturesByIndex(meta)
for foldIndex in range(len(selected)):
ranks = selected[foldIndex]
for featureRank in range(len(ranks)):
featureIndex = ranks[featureRank]
feature = result.getFeature(meta, featureIndex, featureByIndex)
result.setValue(feature, foldIndex, featureRank, "ranks")
result.setValue(feature, "sort", -sum(feature["ranks"].values()) / len(feature["ranks"]))
result.saveMeta(meta, resultPath)