"""Basic function to preprocess tabular data before assembling it in a `DataLoaders`. Docs: https://docs.fast.ai/tabular.core.html.md""" # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/40_tabular.core.ipynb. # %% auto #0 __all__ = ['make_date', 'add_datepart', 'add_elapsed_times', 'cont_cat_split', 'df_shrink_dtypes', 'df_shrink', 'Tabular', 'TabularPandas', 'TabularProc', 'Categorify', 'FillStrategy', 'FillMissing', 'ReadTabBatch', 'show_batch', 'TabDataLoader', 'TabWeightedDL'] # %% ../../nbs/40_tabular.core.ipynb #7bf25495 from ..torch_basics import * from ..data.all import * # %% ../../nbs/40_tabular.core.ipynb #2638ab5a pd.set_option('mode.chained_assignment','raise') # %% ../../nbs/40_tabular.core.ipynb #0bbabf95 def make_date(df, date_field): "Make sure `df[date_field]` is of the right date type." field_dtype = df[date_field].dtype if isinstance(field_dtype, pd.core.dtypes.dtypes.DatetimeTZDtype): field_dtype = np.datetime64 if not isinstance(field_dtype, np.dtype) or not np.issubdtype(field_dtype, np.datetime64): df[date_field] = pd.to_datetime(df[date_field]) # %% ../../nbs/40_tabular.core.ipynb #2731eac6 def add_datepart(df, field_name, prefix=None, drop=True, time=False): "Helper function that adds columns relevant to a date in the column `field_name` of `df`." make_date(df, field_name) field = df[field_name] prefix = ifnone(prefix, re.sub('[Dd]ate$', '', field_name)) attr = ['Year', 'Month', 'Week', 'Day', 'Dayofweek', 'Dayofyear', 'Is_month_end', 'Is_month_start', 'Is_quarter_end', 'Is_quarter_start', 'Is_year_end', 'Is_year_start'] if time: attr = attr + ['Hour', 'Minute', 'Second'] # Pandas removed `dt.week` in v1.1.10 week = field.dt.isocalendar().week.astype(field.dt.day.dtype) if hasattr(field.dt, 'isocalendar') else field.dt.week for n in attr: df[prefix + n] = getattr(field.dt, n.lower()) if n != 'Week' else week mask = ~field.isna() df[prefix + 'Elapsed'] = np.where(mask,field.values.astype(np.int64) // 10 ** 9,np.nan) if drop: df.drop(field_name, axis=1, inplace=True) return df # %% ../../nbs/40_tabular.core.ipynb #4d78de59 def _get_elapsed(df,field_names, date_field, base_field, prefix): for f in field_names: day1 = np.timedelta64(1, 'D') last_date,last_base,res = np.datetime64(),None,[] for b,v,d in zip(df[base_field].values, df[f].values, df[date_field].values): if last_base is None or b != last_base: last_date,last_base = np.datetime64(),b if v: last_date = d res.append(((d-last_date).astype('timedelta64[D]') / day1)) df[prefix + f] = res return df # %% ../../nbs/40_tabular.core.ipynb #e3901ffe def add_elapsed_times(df, field_names, date_field, base_field): "Add in `df` for each event in `field_names` the elapsed time according to `date_field` grouped by `base_field`" field_names = list(L(field_names)) #Make sure date_field is a date and base_field a bool df[field_names] = df[field_names].astype('bool') make_date(df, date_field) work_df = df[field_names + [date_field, base_field]] work_df = work_df.sort_values([base_field, date_field]) work_df = _get_elapsed(work_df, field_names, date_field, base_field, 'After') work_df = work_df.sort_values([base_field, date_field], ascending=[True, False]) work_df = _get_elapsed(work_df, field_names, date_field, base_field, 'Before') for a in ['After' + f for f in field_names] + ['Before' + f for f in field_names]: work_df[a] = work_df[a].fillna(0).astype(int) for a,s in zip([True, False], ['_bw', '_fw']): work_df = work_df.set_index(date_field) tmp = (work_df[[base_field] + field_names].sort_index(ascending=a) .groupby(base_field).rolling(7, min_periods=1).sum()) if base_field in tmp: tmp.drop(base_field, axis=1,inplace=True) tmp.reset_index(inplace=True) work_df.reset_index(inplace=True) work_df = work_df.merge(tmp, 'left', [date_field, base_field], suffixes=['', s]) work_df.drop(field_names, axis=1, inplace=True) return df.merge(work_df, 'left', [date_field, base_field]) # %% ../../nbs/40_tabular.core.ipynb #6086b66b def cont_cat_split(df, max_card=20, dep_var=None): "Helper function that returns column names of cont and cat variables from given `df`." cont_names, cat_names = [], [] for label in df: if label in L(dep_var): continue if ((pd.api.types.is_integer_dtype(df[label].dtype) and df[label].unique().shape[0] > max_card) or pd.api.types.is_float_dtype(df[label].dtype)): cont_names.append(label) else: cat_names.append(label) return cont_names, cat_names # %% ../../nbs/40_tabular.core.ipynb #9a3b6c97 def df_shrink_dtypes(df, skip=[], obj2cat=True, int2uint=False): "Return any possible smaller data types for DataFrame columns. Allows `object`->`category`, `int`->`uint`, and exclusion." # 1: Build column filter and typemap excl_types, skip = {'category','datetime64[ns]','bool'}, set(skip) typemap = {'int' : [(np.dtype(x), np.iinfo(x).min, np.iinfo(x).max) for x in (np.int8, np.int16, np.int32, np.int64)], 'uint' : [(np.dtype(x), np.iinfo(x).min, np.iinfo(x).max) for x in (np.uint8, np.uint16, np.uint32, np.uint64)], 'float' : [(np.dtype(x), np.finfo(x).min, np.finfo(x).max) for x in (np.float32, np.float64, np.longdouble)] } if obj2cat: typemap['object'] = typemap['str'] = 'category' else: excl_types.update({'object', 'str'}) new_dtypes = {} exclude = lambda dt: dt[1].name not in excl_types and dt[0] not in skip for c, old_t in filter(exclude, df.dtypes.items()): t = next((v for k,v in typemap.items() if old_t.name.startswith(k)), None) if isinstance(t, list): # Find the smallest type that fits if int2uint and t==typemap['int'] and df[c].min() >= 0: t=typemap['uint'] new_t = next((r[0] for r in t if r[1]<=df[c].min() and r[2]>=df[c].max()), None) if new_t and new_t == old_t: new_t = None else: new_t = t if isinstance(t, str) else None if new_t: new_dtypes[c] = new_t return new_dtypes # %% ../../nbs/40_tabular.core.ipynb #a97f5143 def df_shrink(df, skip=[], obj2cat=True, int2uint=False): "Reduce DataFrame memory usage, by casting to smaller types returned by `df_shrink_dtypes()`." dt = df_shrink_dtypes(df, skip, obj2cat=obj2cat, int2uint=int2uint) return df.astype(dt) # %% ../../nbs/40_tabular.core.ipynb #d3046984 class _TabIloc: "Get/set rows by iloc and cols by name" def __init__(self,to): self.to = to def __getitem__(self, idxs): df = self.to.items if isinstance(idxs,tuple): rows,cols = idxs cols = df.columns.isin(cols) if is_listy(cols) else df.columns.get_loc(cols) else: rows,cols = idxs,slice(None) return self.to.new(df.iloc[rows, cols]) # %% ../../nbs/40_tabular.core.ipynb #498b3f92 class Tabular(CollBase, GetAttr, FilteredBase): "A `DataFrame` wrapper that knows which cols are cont/cat/y, and returns rows in `__getitem__`" _default,with_cont='procs',True def __init__(self, df, procs=None, cat_names=None, cont_names=None, y_names=None, y_block=None, splits=None, do_setup=True, device=None, inplace=False, reduce_memory=True): if inplace and splits is not None and pd.options.mode.chained_assignment is not None: warn("Using inplace with splits will trigger a pandas error. Set `pd.options.mode.chained_assignment=None` to avoid it.") if not inplace: df = df.copy() if reduce_memory: df = df_shrink(df) if splits is not None: df = df.iloc[sum(splits, [])] self.dataloaders = delegates(self._dl_type.__init__)(self.dataloaders) super().__init__(df) self.y_names,self.device = L(y_names),device if y_block is None and self.y_names: # Make ys categorical if they're not numeric ys = df[self.y_names] if len(ys.select_dtypes(include='number').columns)!=len(ys.columns): y_block = CategoryBlock() else: y_block = RegressionBlock() if y_block is not None and do_setup: if callable(y_block): y_block = y_block() procs = L(procs) + y_block.type_tfms self.cat_names,self.cont_names,self.procs = L(cat_names),L(cont_names),Pipeline(procs) self.split = len(df) if splits is None else len(splits[0]) if do_setup: self.setup() def new(self, df, inplace=False): return type(self)(df, do_setup=False, reduce_memory=False, y_block=TransformBlock(), inplace=inplace, **attrdict(self, 'procs','cat_names','cont_names','y_names', 'device')) def subset(self, i): return self.new(self.items[slice(0,self.split) if i==0 else slice(self.split,len(self))]) def copy(self): self.items = self.items.copy(); return self def decode(self): return self.procs.decode(self) def decode_row(self, row): return self.new(pd.DataFrame(row).T).decode().items.iloc[0] def show(self, max_n=10, **kwargs): display_df(self.new(self.all_cols[:max_n]).decode().items) def setup(self): self.procs.setup(self) def process(self): self.procs(self) def loc(self): return self.items.loc def iloc(self): return _TabIloc(self) def targ(self): return self.items[self.y_names] def x_names (self): return self.cat_names + self.cont_names def n_subsets(self): return 2 def y(self): return self[self.y_names[0]] def new_empty(self): return self.new(pd.DataFrame({}, columns=self.items.columns)) def to_device(self, d=None): self.device = d return self def all_col_names (self): ys = [n for n in self.y_names if n in self.items.columns] return self.x_names + self.y_names if len(ys) == len(self.y_names) else self.x_names properties(Tabular,'loc','iloc','targ','all_col_names','n_subsets','x_names','y') # %% ../../nbs/40_tabular.core.ipynb #e23698c9 class TabularPandas(Tabular): "A `Tabular` object with transforms" def transform(self, cols, f, all_col=True): if not all_col: cols = [c for c in cols if c in self.items.columns] if len(cols) > 0: self[cols] = self[cols].transform(f) # %% ../../nbs/40_tabular.core.ipynb #efdb998b def _add_prop(cls, nm): @property def f(o): return o[list(getattr(o,nm+'_names'))] @f.setter def fset(o, v): o[getattr(o,nm+'_names')] = v setattr(cls, nm+'s', f) setattr(cls, nm+'s', fset) _add_prop(Tabular, 'cat') _add_prop(Tabular, 'cont') _add_prop(Tabular, 'y') _add_prop(Tabular, 'x') _add_prop(Tabular, 'all_col') # %% ../../nbs/40_tabular.core.ipynb #5c7cd5ef class TabularProc(InplaceTransform): "Base class to write a non-lazy tabular processor for dataframes" def setup(self, items=None, train_setup=False): #TODO: properly deal with train_setup super().setup(getattr(items,'train',items), train_setup=False) # Procs are called as soon as data is available return self(items.items if isinstance(items,Datasets) else items) @property def name(self): return f"{super().name} -- {getattr(self,'__stored_args__',{})}" # %% ../../nbs/40_tabular.core.ipynb #87389d74 def _apply_cats (voc, add, c): if not (hasattr(c, 'dtype') and isinstance(c.dtype, CategoricalDtype)): return pd.Categorical(c, categories=voc[c.name][add:]).codes+add return c.cat.codes+add #if is_categorical_dtype(c) else c.map(voc[c.name].o2i) def _decode_cats(voc, c): return c.map(dict(enumerate(voc[c.name].items))) # %% ../../nbs/40_tabular.core.ipynb #958b9760 class Categorify(TabularProc): "Transform the categorical variables to something similar to `pd.Categorical`" order = 1 def setups(self, to): store_attr(classes={n:CategoryMap(to.iloc[:,n].items, add_na=(n in to.cat_names)) for n in to.cat_names}, but='to') def encodes(self, to): to.transform(to.cat_names, partial(_apply_cats, self.classes, 1)) def decodes(self, to): to.transform(to.cat_names, partial(_decode_cats, self.classes)) def __getitem__(self,k): return self.classes[k] # %% ../../nbs/40_tabular.core.ipynb #1a858dde @Categorize def setups(self, to:Tabular): if len(to.y_names) > 0: if self.vocab is None: self.vocab = CategoryMap(getattr(to, 'train', to).iloc[:,to.y_names[0]].items, strict=True) else: self.vocab = CategoryMap(self.vocab, sort=False, add_na=self.add_na) self.c = len(self.vocab) return self(to) @Categorize def encodes(self, to:Tabular): to.transform(to.y_names, partial(_apply_cats, {n: self.vocab for n in to.y_names}, 0), all_col=False) return to @Categorize def decodes(self, to:Tabular): to.transform(to.y_names, partial(_decode_cats, {n: self.vocab for n in to.y_names}), all_col=False) return to # %% ../../nbs/40_tabular.core.ipynb #c786be37 @Normalize def setups(self, to:Tabular): store_attr(but='to', means=dict(getattr(to, 'train', to).conts.mean()), stds=dict(getattr(to, 'train', to).conts.std(ddof=0)+1e-7)) return self(to) @Normalize def encodes(self, to:Tabular): to.conts = (to.conts-self.means) / self.stds return to @Normalize def decodes(self, to:Tabular): to.conts = (to.conts*self.stds ) + self.means return to # %% ../../nbs/40_tabular.core.ipynb #76a90230 class FillStrategy: "Namespace containing the various filling strategies." def median (c,fill): return c.median() def constant(c,fill): return fill def mode (c,fill): return c.dropna().value_counts().idxmax() # %% ../../nbs/40_tabular.core.ipynb #e67b4128 class FillMissing(TabularProc): "Fill the missing values in continuous columns." def __init__(self, fill_strategy=FillStrategy.median, add_col=True, fill_vals=None): if fill_vals is None: fill_vals = defaultdict(int) store_attr() def setups(self, to): missing = pd.isnull(to.conts).any() store_attr(but='to', na_dict={n:self.fill_strategy(to[n], self.fill_vals[n]) for n in missing[missing].keys()}) self.fill_strategy = self.fill_strategy.__name__ def encodes(self, to): missing = pd.isnull(to.conts) for n in missing.any()[missing.any()].keys(): assert n in self.na_dict, f"nan values in `{n}` but not in setup training set" for n in self.na_dict.keys(): to[n] = to[n].fillna(self.na_dict[n]) if self.add_col: to.loc[:,n+'_na'] = missing[n] if n+'_na' not in to.cat_names: to.cat_names.append(n+'_na') # %% ../../nbs/40_tabular.core.ipynb #9be310e6 def _maybe_expand(o): return o[:,None] if o.ndim==1 else o # %% ../../nbs/40_tabular.core.ipynb #774acf79 class ReadTabBatch(ItemTransform): "Transform `TabularPandas` values into a `Tensor` with the ability to decode" def __init__(self, to): self.to = to.new_empty() def encodes(self, to): if not to.with_cont: res = (tensor(to.cats).long(),) else: res = (tensor(to.cats).long(),tensor(to.conts).float()) ys = [n for n in to.y_names if n in to.items.columns] if len(ys) == len(to.y_names): res = res + (tensor(to.targ),) if to.device is not None: res = to_device(res, to.device) return res def decodes(self, o): o = [_maybe_expand(o_) for o_ in to_np(o) if o_.size != 0] vals = np.concatenate(o, axis=1) try: df = pd.DataFrame(vals, columns=self.to.all_col_names) except: df = pd.DataFrame(vals, columns=self.to.x_names) to = self.to.new(df) return to # %% ../../nbs/40_tabular.core.ipynb #063a6e8e @dispatch def show_batch(x: Tabular, y, its, max_n=10, ctxs=None): x.show() # %% ../../nbs/40_tabular.core.ipynb #bcf9ce05 @delegates() class TabDataLoader(TfmdDL): "A transformed `DataLoader` for Tabular data" def __init__(self, dataset, bs=16, shuffle=False, after_batch=None, num_workers=0, **kwargs): if after_batch is None: after_batch = L(TransformBlock().batch_tfms)+ReadTabBatch(dataset) super().__init__(dataset, bs=bs, shuffle=shuffle, after_batch=after_batch, num_workers=num_workers, **kwargs) def create_item(self, s): return self.dataset.iloc[s or 0] def create_batch(self, b): return self.dataset.iloc[b] def do_item(self, s): return 0 if s is None else s TabularPandas._dl_type = TabDataLoader # %% ../../nbs/40_tabular.core.ipynb #253b8d64 @delegates() class TabWeightedDL(TabDataLoader): "A transformed `DataLoader` for Tabular Weighted data" def __init__(self, dataset, bs=16, wgts=None, shuffle=False, after_batch=None, num_workers=0, **kwargs): wgts = np.array([1.]*len(dataset) if wgts is None else wgts) self.wgts = wgts / wgts.sum() super().__init__(dataset, bs=bs, shuffle=shuffle, after_batch=after_batch, num_workers=num_workers, **kwargs) self.idxs = self.get_idxs() def get_idxs(self): if self.n == 0: return [] if not self.shuffle: return super().get_idxs() return list(np.random.choice(self.n, self.n, p=self.wgts)) TabularPandas._dl_type = TabWeightedDL # %% ../../nbs/40_tabular.core.ipynb #67f710b2 @EncodedMultiCategorize def setups(self, to:Tabular): self.c = len(self.vocab) return self(to) @EncodedMultiCategorize def encodes(self, to:Tabular): return to @EncodedMultiCategorize def decodes(self, to:Tabular): to.transform(to.y_names, lambda c: c==1) return to # %% ../../nbs/40_tabular.core.ipynb #d6b3e995 @RegressionSetup def setups(self, to:Tabular): if self.c is not None: return self.c = len(to.y_names) return to @RegressionSetup def encodes(self, to:Tabular): return to @RegressionSetup def decodes(self, to:Tabular): return to