Module Import alias Import alias Import alias Import alias ImportFrom alias Import alias Import alias identifier ImportFrom alias ImportFrom alias identifier Import alias Import alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad FunctionDef arguments args NameParam defaults body Expr Str With Call NameLoad NameLoad Str NameStore body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Return NameLoad decorator_list FunctionDef arguments args NameParam defaults NameLoad body Assign NameStore BinOpAdd IfExp NameLoad ListLoad BinOpMod Str NameLoad ListLoad ListLoad Call AttributeLoad NameLoad attr Str Call AttributeLoad NameLoad attr Str Call AttributeLoad NameLoad attr Return Call AttributeLoad NameLoad attr keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body If UnaryOpNot NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd Str NameLoad Expr Call AttributeLoad NameLoad attr Num orelse Expr Call AttributeLoad NameLoad attr NameLoad decorator_list Import alias ClassDef bases NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam NameParam defaults body Return Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str BinOpAdd Call NameLoad NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body If CompareIs AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr Return AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Pass decorator_list AttributeLoad NameLoad attr FunctionDef arguments args NameParam defaults body Expr Str Return ListComp NameLoad comprehension TupleStore NameStore NameStore Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return ListComp NameLoad comprehension TupleStore NameStore NameStore Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr UnaryOpNot NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore Dict For NameStore Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad Str attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Slice Num Expr Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad ListLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore NameLoad For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad If CompareEq Call NameLoad NameLoad Num body Continue Assign NameStore Call AttributeLoad NameLoad attr NameLoad If CompareIs NameLoad NameLoad body Assign NameStore NameLoad orelse AugAssignBitAnd NameStore NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Pass decorator_list AttributeLoad NameLoad attr FunctionDef arguments args NameParam defaults body Expr Str Pass decorator_list AttributeLoad NameLoad attr FunctionDef arguments args NameParam NameParam defaults body Expr Str Pass decorator_list AttributeLoad NameLoad attr FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Index Num If CompareEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr BinOpMod Str Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr orelse Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad For TupleStore NameStore TupleStore NameStore NameStore Call NameLoad Call Call NameLoad Str Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad If CompareEq NameLoad Num body Expr Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad If BoolOpAnd NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Continue Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults Str body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad NameLoad attr TupleLoad Num Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Return Call AttributeLoad NameLoad attr TupleLoad Num Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return AttributeLoad AttributeLoad NameLoad attr attr decorator_list NameLoad decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults Str body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assert CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assert Call AttributeLoad NameLoad attr CompareGt NameLoad Num Return BinOpDiv BinOpSub NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore BinOpMult Call AttributeLoad NameLoad attr TupleLoad Num NameLoad AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad ExtSlice Slice Index NameLoad Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad ExtSlice Slice Index NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad NameLoad attr TupleLoad Num Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Return CompareNotEq SubscriptLoad NameLoad Index Num Num decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam defaults Str body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore BinOpMult Call AttributeLoad NameLoad attr TupleLoad Num NameLoad AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr BinOpDiv Num Num For NameStore Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad ExtSlice Slice Index NameLoad Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad NameLoad Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad Call AttributeLoad NameLoad attr BinOpDiv Call AttributeLoad NameLoad attr BinOpSub SubscriptLoad NameLoad ExtSlice Slice Index NameLoad NameLoad NameLoad Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults Str Num Num body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assert CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad ExtSlice Slice Index AttributeLoad NameLoad attr Assign NameStore BinOpSub SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assert Call AttributeLoad NameLoad attr CompareGt NameLoad Num Return BinOpDiv BinOpSub NameLoad SubscriptLoad NameLoad Index Num NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore BinOpMult Call AttributeLoad NameLoad attr TupleLoad Num NameLoad AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad Call NameLoad SubscriptLoad NameLoad ExtSlice Slice Index NameLoad AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index TupleLoad Num NameLoad Call NameLoad SubscriptLoad NameLoad ExtSlice Slice Index NameLoad AttributeLoad NameLoad attr Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad NameLoad attr TupleLoad Num Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Return CompareNotEq SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num decorator_list decorator_list Assign NameStore Call NameLoad GeneratorExp TupleLoad AttributeLoad NameLoad attr NameLoad comprehension NameStore ListLoad NameLoad NameLoad NameLoad NameLoad If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore NameStore NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad ImportFrom alias Assign NameStore Call NameLoad NameLoad Assign NameStore Call SubscriptLoad NameLoad Index AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad
N/A N/A sys N/A os N/A logging N/A json optparse OptionParser N/A progressbar N/A numpy np scipy.stats.stats scoreatpercentile scipy.stats norm Gaussian N/A cpa N/A cpa.dbconnect N/A cpa.util N/A logger N/A N/A logging getLogger __name__ np_load N/A N/A filename N/A N/A N/A Work around bug in numpy that causes file handles to be left open. N/A N/A open filename rb f N/A N/A x N/A N/A np load f N/A N/A N/A f close N/A x N/A make_progress_bar N/A N/A text N/A None N/A N/A widgets N/A N/A text N/A N/A %s:  text N/A N/A N/A N/A progressbar Percentage N/A N/A progressbar Bar N/A N/A progressbar ETA N/A N/A N/A progressbar ProgressBar widgets widgets N/A _check_directory N/A N/A dir resume N/A N/A N/A N/A N/A N/A os path exists dir N/A N/A N/A resume N/A N/A N/A N/A logger error N/A Directory exists already (remove or use -r):  dir N/A N/A N/A sys exit 1 N/A N/A N/A N/A os makedirs dir N/A N/A abc BaseNormalization N/A object N/A N/A __metaclass__ N/A abc ABCMeta N/A _cached_colmask None __init__ N/A N/A self cache param_dir N/A N/A N/A N/A self cache cache N/A N/A self dir N/A N/A N/A os path join N/A cache cache_dir param_dir N/A N/A self _colmask_filename N/A N/A N/A os path join N/A self dir colmask.npy N/A _params_filename N/A N/A self plate N/A N/A N/A N/A N/A N/A os path join N/A self dir params N/A N/A unicode plate .npy N/A _colmask N/A N/A self N/A N/A N/A N/A N/A self _cached_colmask None N/A N/A N/A self _cached_colmask N/A np_load N/A self _colmask_filename N/A N/A self _cached_colmask N/A property normalize N/A N/A self plate data N/A N/A N/A N/A N/A abc abstractmethod colnames N/A N/A self N/A N/A N/A Return the names of the columns returned by normalize() N/A N/A col N/A N/A col keep N/A zip N/A N/A self cache colnames N/A self _colmask keep N/A property colnames_excluded N/A N/A self N/A N/A N/A Return the names of the columns excluded by normalize() N/A N/A col N/A N/A col keep N/A zip N/A N/A self cache colnames N/A self _colmask N/A keep N/A property _create_cache N/A N/A self predicate resume N/A False N/A N/A N/A N/A self _create_cache_params predicate resume N/A N/A N/A self _create_cache_colmask predicate N/A _get_controls N/A N/A self predicate N/A N/A N/A Return a dictionary mapping plate names to lists of control wells N/A plates_and_images N/A N/A row N/A N/A N/A cpa db execute N/A select distinct %s, %s from %s where %s N/A N/A N/A cpa properties plate_id N/A N/A ,  join N/A N/A N/A cpa dbconnect image_key_columns N/A N/A cpa properties image_table predicate N/A N/A plate N/A row N/A 0 N/A imKey N/A tuple N/A row N/A 1 N/A N/A N/A N/A N/A plates_and_images setdefault plate N/A append imKey N/A plates_and_images N/A _create_cache_colmask N/A N/A self predicate N/A N/A N/A colmask None N/A N/A plate imKeys N/A N/A N/A N/A self _get_controls predicate items N/A N/A params N/A np_load N/A N/A self _params_filename plate N/A N/A N/A len params 0 N/A N/A N/A nonzero N/A N/A self _check_param_zero params N/A N/A colmask None N/A N/A colmask nonzero N/A N/A colmask nonzero N/A N/A N/A np save N/A self _colmask_filename colmask N/A _compute_params N/A N/A self features N/A N/A N/A N/A N/A abc abstractmethod _null_param N/A N/A self N/A N/A N/A 
        Return a value that corresponds to a null value for the normalization
        parameter.
         N/A N/A N/A abc abstractproperty _check_param_zero N/A N/A self params N/A N/A N/A 
        Return a boolean vector of length = len(colmask), where an element is 
        True iff the normalization for the corresponding variable can be 
        calculated. E.g. scale == 0.
         N/A N/A N/A abc abstractproperty _create_cache_params_1 N/A N/A self plate imKeys filename N/A N/A N/A features N/A N/A N/A N/A self cache load imKeys N/A 0 N/A N/A N/A len features 0 N/A N/A N/A N/A logger warning N/A No DMSO features for plate %s N/A str plate N/A params N/A self _null_param N/A N/A params N/A N/A self _compute_params features N/A N/A N/A np save filename params N/A _create_cache_params N/A N/A self predicate resume N/A False N/A N/A controls N/A N/A self _get_controls predicate N/A N/A i N/A plate imKeys N/A enumerate N/A N/A make_progress_bar Params N/A N/A controls items N/A N/A filename N/A N/A self _params_filename plate N/A N/A i 0 N/A N/A N/A _check_directory N/A N/A N/A os path dirname filename resume N/A N/A resume N/A N/A N/A os path exists filename N/A N/A N/A N/A N/A self _create_cache_params_1 plate imKeys filename N/A N/A DummyNormalization N/A BaseNormalization N/A __init__ N/A N/A self cache param_dir N/A dummy N/A N/A N/A N/A N/A super DummyNormalization self __init__ cache param_dir N/A normalize N/A N/A self plate data N/A N/A N/A data N/A _null_param N/A N/A self N/A N/A N/A N/A N/A np zeros N/A 0 N/A len N/A N/A self cache colnames N/A _check_param_zero N/A N/A self params N/A N/A N/A False N/A _compute_params N/A N/A self features N/A N/A N/A N/A N/A np zeros N/A 0 N/A len features N/A colnames N/A N/A self N/A N/A N/A N/A N/A self cache colnames N/A property N/A StdNormalization N/A BaseNormalization N/A __init__ N/A N/A self cache param_dir N/A std N/A N/A N/A N/A N/A super StdNormalization self __init__ cache param_dir N/A normalize N/A N/A self plate data N/A N/A N/A params N/A np_load N/A N/A self _params_filename plate N/A N/A N/A N/A data shape N/A 1 N/A N/A params shape N/A 1 N/A data N/A data N/A N/A N/A N/A self _colmask N/A params N/A params N/A N/A N/A N/A self _colmask N/A shift N/A params N/A 0 N/A scale N/A params N/A 1 N/A N/A N/A np all N/A scale 0 N/A N/A N/A data shift scale N/A _compute_params N/A N/A self features N/A N/A N/A m N/A N/A features shape N/A 1 N/A params N/A N/A N/A np ones N/A 2 m N/A np nan N/A j N/A xrange m N/A N/A N/A params N/A N/A 0 j N/A N/A np mean N/A features N/A N/A N/A j N/A N/A params N/A N/A 1 j N/A N/A np std N/A features N/A N/A N/A j N/A params N/A _null_param N/A N/A self N/A N/A N/A N/A N/A np zeros N/A 0 N/A len N/A N/A self cache colnames N/A _check_param_zero N/A N/A self params N/A N/A N/A N/A N/A params N/A 1 0 N/A N/A RobustStdNormalization N/A StdNormalization N/A __init__ N/A N/A self cache param_dir N/A robust_std N/A N/A N/A N/A N/A super RobustStdNormalization self __init__ cache param_dir N/A _compute_params N/A N/A self features N/A N/A N/A m N/A N/A features shape N/A 1 N/A params N/A N/A N/A np ones N/A 2 m N/A np nan N/A c N/A N/A Gaussian ppf N/A 3 4.0 N/A j N/A xrange m N/A N/A d N/A N/A np median N/A features N/A N/A N/A j N/A N/A params N/A N/A 0 j d N/A N/A params N/A N/A 1 j N/A N/A np median N/A N/A N/A np fabs N/A N/A features N/A N/A N/A j d c N/A params N/A N/A RobustLinearNormalization N/A BaseNormalization N/A __init__ N/A N/A self cache param_dir lower_q upper_q N/A robust_linear 1 99 N/A N/A N/A N/A N/A super RobustLinearNormalization self __init__ cache param_dir N/A N/A self lower_q lower_q N/A N/A self upper_q upper_q N/A normalize N/A N/A self plate data N/A N/A N/A percentiles N/A np_load N/A N/A self _params_filename plate N/A N/A N/A N/A data shape N/A 1 N/A N/A percentiles shape N/A 1 N/A data N/A data N/A N/A N/A N/A self _colmask N/A percentiles N/A percentiles N/A N/A N/A N/A self _colmask N/A divisor N/A N/A percentiles N/A 1 N/A percentiles N/A 0 N/A N/A N/A np all N/A divisor 0 N/A N/A N/A data N/A percentiles N/A 0 divisor N/A _compute_params N/A N/A self features N/A N/A N/A m N/A N/A features shape N/A 1 N/A percentiles N/A N/A N/A np ones N/A 2 m N/A np nan N/A j N/A xrange m N/A N/A N/A percentiles N/A N/A 0 j N/A scoreatpercentile N/A features N/A N/A N/A j N/A self lower_q N/A N/A percentiles N/A N/A 1 j N/A scoreatpercentile N/A features N/A N/A N/A j N/A self upper_q N/A percentiles N/A _null_param N/A N/A self N/A N/A N/A N/A N/A np zeros N/A 0 N/A len N/A N/A self cache colnames N/A _check_param_zero N/A N/A self params N/A N/A N/A N/A N/A params N/A 1 N/A params N/A 0 N/A N/A N/A normalizations N/A dict N/A N/A N/A c __name__ c N/A c N/A RobustLinearNormalization RobustStdNormalization StdNormalization DummyNormalization N/A N/A __name__ __main__ N/A N/A N/A N/A logging basicConfig level N/A logging INFO N/A parser N/A OptionParser usage: %prog [-r] [-m method] PROPERTIES-FILE CACHE-DIR PREDICATE N/A N/A N/A parser add_option -m --method dest method action store default RobustStdNormalization help method N/A N/A options args N/A N/A parser parse_args N/A N/A N/A len args 3 N/A N/A N/A N/A parser error Incorrect number of arguments N/A N/A properties_file cache_dir predicate args N/A N/A N/A N/A cpa properties LoadFile properties_file cpa.profiling.cache Cache N/A cache N/A Cache cache_dir N/A normalizer N/A N/A normalizations N/A N/A options method cache N/A N/A N/A normalizer _create_cache predicate