outputShapefile= os.path.splitext(inRaster)[0] + "_thr" + str(i) + "_" + str(minHa).replace('.','p') + "ha.shp"
whereClause = '"Area_ha" >=' + minHa
waterSql = '"Value" > 0 AND "Value" <=' + int(i)
# Process: Con (needs spatial analyst license)
outCon = Con(inRaster, 1, 0 , waterSql)
outCon.save("outCon")
arcpy.AddMessage("Open flood extent map is created (raster)")
# Process: Focal Statistics (5x5 Mode)
outFocalStats = FocalStatistics(outCon, "Rectangle 5 5 CELL", "MAJORITY", "DATA")
outFocalStats.save("outFocalStats")
arcpy.AddMessage("Image is filtered")
# Process: Convert Raster to Polygon
arcpy.RasterToPolygon_conversion(outFocalStats, "Raster2poly.shp", "NO_SIMPLIFY", "")
arcpy.AddMessage("Converted to vector")
# Process: Select Gridcode >0
arcpy.Select_analysis("Raster2poly.shp", "Raster2polyCode0.shp", "GRIDCODE >0")
# Process: Add Field to Calculate Area
arcpy.AddField_management("Raster2polyCode0.shp", "Area_ha", "FLOAT", "", "", "", "", "NON_NULLABLE", "NON_REQUIRED", "")
# Process: Calculate Field: Area in Ha
arcpy.CalculateField_management("Raster2polyCode0.shp", "Area_ha", "!Shape!.area/10000", "PYTHON_9.3", "")
arcpy.AddMessage("Area calculated (ha) for flooded polygons")
# Process: Select min polygon size
arcpy.Select_analysis("Raster2polyCode0.shp", outputShapefile, whereClause)
arcpy.AddMessage("Applying the minimum hectare size")
# Process: Delete intermediate files
arcpy.Delete_management("outCon", "")
arcpy.Delete_management("outFocalStats", "")
arcpy.Delete_management("Raster2poly.shp", "")
arcpy.Delete_management("Raster2polyCode0.shp", "")
arcpy.AddMessage("Intermediate files deleted")
edit your original post and throw the script within code blocks (the # symbol in the html editor)