def wellIndex(dataSet):
wellColumns = data.columnsDump(dataSet, data.systemObjectColumns)
wTs = wellTypes(dataSet)
if len(wTs) > 0:
annotationMap = wellAnnotations(dataSet)['Type']
typeToPopID = {tp: i + 3 for i, tp in enumerate(wTs)} # Well type IDs start at 3, see src/model.ts -> Population
cfg = configuration('CellMorph')
columnCnt = len(cfg.columns)
rowCnt = len(cfg.rows)
def convertTag(wellTag):
plate, column, row = [int(part) for part in wellTag.split("_")]
return plate * columnCnt * rowCnt + column * rowCnt + row
annotationDict = {convertTag(tag): typeToPopID[wT[0]] for tag, wT in annotationMap.iteritems()}
annotationArr = np.array([annotationDict[i] for i in range(len(annotationDict))], np.int)
objectAbsWell = wellColumns['plate'] * columnCnt * rowCnt + wellColumns['column'] * rowCnt + wellColumns['row']
wellColumns['type'] = annotationArr[objectAbsWell.values]
else:
wellColumns['type'] = np.nan
return wellColumns
def columns(dataSet, columns):
cols = list(columns)
return data.columnsDump(dataSet, cols)