Source file owl_dataframe.ml
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# 1 "src/base/misc/owl_dataframe.ml"
open Owl_types
type elt =
| Bool of bool
| Int of int
| Float of float
| String of string
| Any
type series =
| Bool_Series of bool array
| Int_Series of int array
| Float_Series of float array
| String_Series of string array
| Any_Series
type t =
{ mutable data : series array
;
mutable head : (string, int) Hashtbl.t
;
mutable used : int
;
mutable size : int
}
let unpack_bool = function
| Bool x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_int = function
| Int x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_float = function
| Float x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_string = function
| String x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_bool_series = function
| Bool_Series x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_int_series = function
| Int_Series x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_float_series = function
| Float_Series x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let unpack_string_series = function
| String_Series x -> x
| _ -> raise Owl_exception.NOT_SUPPORTED
let pack_bool x = Bool x
let pack_int x = Int x
let pack_float x = Float x
let pack_string x = String x
let pack_bool_series x = Bool_Series x
let pack_int_series x = Int_Series x
let pack_float_series x = Float_Series x
let pack_string_series x = String_Series x
let allocate_space data =
Array.(
map
(function
| Bool_Series c -> Bool_Series (append c (copy c))
| Int_Series c -> Int_Series (append c (copy c))
| Float_Series c -> Float_Series (append c (copy c))
| String_Series c -> String_Series (append c (copy c))
| Any_Series -> Any_Series)
data)
let set_elt_in_series x i = function
| Bool a -> (unpack_bool_series x).(i) <- a
| Int a -> (unpack_int_series x).(i) <- a
| Float a -> (unpack_float_series x).(i) <- a
| String a -> (unpack_string_series x).(i) <- a
| Any -> ()
let get_elt_in_series x i =
match x with
| Bool_Series c -> Bool c.(i)
| Int_Series c -> Int c.(i)
| Float_Series c -> Float c.(i)
| String_Series c -> String c.(i)
| Any_Series -> Any
let init_series n = function
| Bool a -> Bool_Series (Array.make n a)
| Int a -> Int_Series (Array.make n a)
| Float a -> Float_Series (Array.make n a)
| String a -> String_Series (Array.make n a)
| Any -> Any_Series
let resize_series n = function
| Bool_Series c -> Bool_Series (Owl_utils_array.resize ~head:true true n c)
| Int_Series c -> Int_Series (Owl_utils_array.resize ~head:true 0 n c)
| Float_Series c -> Float_Series (Owl_utils_array.resize ~head:true 0. n c)
| String_Series c -> String_Series (Owl_utils_array.resize ~head:true "" n c)
| Any_Series -> Any_Series
let append_series x y =
match x, y with
| Bool_Series x, Bool_Series y -> Bool_Series (Array.append x y)
| Int_Series x, Int_Series y -> Int_Series (Array.append x y)
| Float_Series x, Float_Series y -> Float_Series (Array.append x y)
| String_Series x, String_Series y -> String_Series (Array.append x y)
| Any_Series, Any_Series -> Any_Series
| _ -> failwith "append_series: unsupported type"
let length_series = function
| Bool_Series c -> Array.length c
| Int_Series c -> Array.length c
| Float_Series c -> Array.length c
| String_Series c -> Array.length c
| Any_Series -> 0
let slice_series slice = function
| Bool_Series c -> Bool_Series (Owl_utils_array.get_slice slice c)
| Int_Series c -> Int_Series (Owl_utils_array.get_slice slice c)
| Float_Series c -> Float_Series (Owl_utils_array.get_slice slice c)
| String_Series c -> String_Series (Owl_utils_array.get_slice slice c)
| Any_Series -> Any_Series
let argsort_series = function
| Bool_Series c -> Owl_utils_array.argsort ~cmp:Stdlib.compare c
| Int_Series c -> Owl_utils_array.argsort ~cmp:Stdlib.compare c
| Float_Series c -> Owl_utils_array.argsort ~cmp:Stdlib.compare c
| String_Series c -> Owl_utils_array.argsort ~cmp:Stdlib.compare c
| Any_Series -> [||]
let min_series = function
| Bool_Series c -> Owl_utils_array.min_i ~cmp:Stdlib.compare c
| Int_Series c -> Owl_utils_array.min_i ~cmp:Stdlib.compare c
| Float_Series c -> Owl_utils_array.min_i ~cmp:Stdlib.compare c
| String_Series c -> Owl_utils_array.min_i ~cmp:Stdlib.compare c
| Any_Series -> -1
let max_series = function
| Bool_Series c -> Owl_utils_array.max_i ~cmp:Stdlib.compare c
| Int_Series c -> Owl_utils_array.max_i ~cmp:Stdlib.compare c
| Float_Series c -> Owl_utils_array.max_i ~cmp:Stdlib.compare c
| String_Series c -> Owl_utils_array.max_i ~cmp:Stdlib.compare c
| Any_Series -> -1
let remove_ith_elt i = function
| Bool_Series c -> Bool_Series (Owl_utils_array.remove c i)
| Int_Series c -> Int_Series (Owl_utils_array.remove c i)
| Float_Series c -> Float_Series (Owl_utils_array.remove c i)
| String_Series c -> String_Series (Owl_utils_array.remove c i)
| Any_Series -> Any_Series
let insert_ith_elt i e = function
| Bool_Series c -> Bool_Series (Owl_utils_array.insert c [| unpack_bool e |] i)
| Int_Series c -> Int_Series (Owl_utils_array.insert c [| unpack_int e |] i)
| Float_Series c -> Float_Series (Owl_utils_array.insert c [| unpack_float e |] i)
| String_Series c -> String_Series (Owl_utils_array.insert c [| unpack_string e |] i)
| Any_Series -> Any_Series
let get_ith_elt i = function
| Bool_Series c -> Bool c.(i)
| Int_Series c -> Int c.(i)
| Float_Series c -> Float c.(i)
| String_Series c -> String c.(i)
| Any_Series -> Any
let elt_to_str = function
| Bool a -> string_of_bool a
| Int a -> string_of_int a
| Float a -> string_of_float a
| String a -> a
| Any -> ""
let series_type_to_str = function
| Bool_Series _c -> "b"
| Int_Series _c -> "i"
| Float_Series _c -> "f"
| String_Series _c -> "s"
| Any_Series -> "a"
let str_to_elt_fun = function
| "b" -> fun a -> Bool (bool_of_string a)
| "i" -> fun a -> Int (int_of_string a)
| "f" -> fun a -> if a = "" then Float nan else Float (float_of_string a)
| "s" -> fun a -> String a
| _ -> failwith "str_to_elt_fun: unsupported type"
let elt_array_to_series typ x =
match typ with
| Bool_Series _ -> pack_bool_series (Array.map unpack_bool x)
| Int_Series _ -> pack_int_series (Array.map unpack_int x)
| Float_Series _ -> pack_float_series (Array.map unpack_float x)
| String_Series _ -> pack_string_series (Array.map unpack_string x)
| Any_Series -> Any_Series
let make ?data head_names =
let col_num = Array.length head_names in
let head = Hashtbl.create 64 in
Array.iteri
(fun i s ->
assert (Hashtbl.mem head s = false);
Hashtbl.add head s i)
head_names;
let data =
match data with
| Some a -> a
| None -> Array.make col_num Any_Series
in
assert (Array.length data = col_num);
let size = if col_num = 0 then 0 else length_series data.(0) in
let used = size in
Array.iter (fun c -> assert (length_series c = size)) data;
{ data; head; used; size }
let col_num x = Array.length x.data
let row_num x = x.used
let shape x = row_num x, col_num x
let numel x = row_num x * col_num x
let types x = Array.map series_type_to_str x.data
let append_row x row =
assert (col_num x = Array.length row);
if x.size = 0
then (
let n = 16 in
x.data <- Array.map (init_series n) row;
x.size <- n;
x.used <- 1)
else (
if x.used = x.size
then (
x.data <- allocate_space x.data;
x.size <- length_series x.data.(0));
Array.iteri (fun i a -> set_elt_in_series x.data.(i) x.used a) row;
x.used <- x.used + 1)
let append_col x col head =
let m, n = shape x in
assert (m = length_series col);
let col = resize_series x.size col in
Hashtbl.add x.head head n;
x.data <- Array.append x.data [| col |]
let get_heads x =
let kv = Hashtbl.fold (fun k v acc -> Array.append acc [| k, v |]) x.head [||] in
Array.sort (fun a b -> snd a - snd b) kv;
Array.map fst kv
let set_heads x head_names =
assert (Array.length head_names = Array.length x.data);
let head = Hashtbl.create 64 in
Array.iteri
(fun i s ->
assert (Hashtbl.mem head s = false);
Hashtbl.add head s i)
head_names;
x.head <- head
let remove_row x i =
let i = Owl_utils_ndarray.adjust_index i (row_num x) in
let new_data = Array.map (fun s -> remove_ith_elt i s) x.data in
x.data <- new_data;
x.used <- x.used - 1;
x.size <- x.size - 1
let remove_col x j =
let j = Owl_utils_ndarray.adjust_index j (col_num x) in
x.data <- Owl_utils_array.filteri (fun i _ -> i <> j) x.data;
let new_head = Owl_utils_array.filteri (fun i _ -> i <> j) (get_heads x) in
set_heads x new_head
let insert_row x i row =
let i = Owl_utils_ndarray.adjust_index i (row_num x) in
if x.size = 0
then (
let n = 16 in
x.data <- Array.map (init_series n) row;
x.size <- n;
x.used <- 1)
else (
if x.used = x.size
then (
x.data <- allocate_space x.data;
x.size <- length_series x.data.(0));
let new_data = Array.mapi (fun j s -> insert_ith_elt i row.(j) s) x.data in
x.data <- new_data;
x.used <- x.used + 1;
x.size <- x.size + 1)
let insert_col x j col_head col =
let j = Owl_utils_ndarray.adjust_index j (col_num x) in
let new_data = Owl_utils_array.insert x.data [| col |] j in
x.data <- new_data;
let new_head = Owl_utils_array.insert (get_heads x) [| col_head |] j in
set_heads x new_head
let id_to_head x i = (get_heads x).(i)
let head_to_id x name = Hashtbl.find x.head name
let get_row x i = Array.map (fun y -> get_elt_in_series y i) x.data
let get_col x j =
match x.data.(j) with
| Bool_Series c -> Bool_Series (Array.sub c 0 x.used)
| Int_Series c -> Int_Series (Array.sub c 0 x.used)
| Float_Series c -> Float_Series (Array.sub c 0 x.used)
| String_Series c -> String_Series (Array.sub c 0 x.used)
| Any_Series -> Any_Series
let get_rows x idx = Array.map (get_row x) idx
let get_cols x idx = Array.map (get_col x) idx
let _get_row_assoc _x _idx =
raise (Owl_exception.NOT_IMPLEMENTED "owl_dataframe._get_row_assoc")
let get_col_by_name x name =
let j = Hashtbl.find x.head name in
get_col x j
let get_cols_by_name x names = Array.map (get_col_by_name x) names
let get x i j =
match x.data.(j) with
| Bool_Series c -> Bool c.(i)
| Int_Series c -> Int c.(i)
| Float_Series c -> Float c.(i)
| String_Series c -> String c.(i)
| Any_Series -> Any
let set x i j a =
match x.data.(j) with
| Bool_Series c -> c.(i) <- unpack_bool a
| Int_Series c -> c.(i) <- unpack_int a
| Float_Series c -> c.(i) <- unpack_float a
| String_Series c -> c.(i) <- unpack_string a
| Any_Series -> ()
let get_by_name x i name =
let j = Hashtbl.find x.head name in
get x i j
let set_by_name x i name a =
let j = Hashtbl.find x.head name in
set x i j a
let to_cols x = x.data
let to_rows x =
let stack = Owl_utils.Stack.make () in
let m = row_num x in
for i = 0 to m - 1 do
Owl_utils.Stack.push stack (get_row x i)
done;
Owl_utils.Stack.to_array stack
let copy x =
let head = Hashtbl.copy x.head in
let used = x.used in
let size = x.size in
let data =
Array.map
(function
| Bool_Series c -> Bool_Series (Array.copy c)
| Int_Series c -> Int_Series (Array.copy c)
| Float_Series c -> Float_Series (Array.copy c)
| String_Series c -> String_Series (Array.copy c)
| Any_Series -> Any_Series)
x.data
in
{ data; head; used; size }
let copy_struct x =
let head = Hashtbl.copy x.head in
let used = 0 in
let size = 0 in
let data =
Array.map
(function
| Bool_Series _c -> Bool_Series [||]
| Int_Series _c -> Int_Series [||]
| Float_Series _c -> Float_Series [||]
| String_Series _c -> String_Series [||]
| Any_Series -> Any_Series)
x.data
in
{ data; head; used; size }
let reset x =
x.used <- 0;
x.size <- 0;
x.data
<- Array.map
(function
| Bool_Series _c -> Bool_Series [||]
| Int_Series _c -> Int_Series [||]
| Float_Series _c -> Float_Series [||]
| String_Series _c -> String_Series [||]
| Any_Series -> Any_Series)
x.data
let concat_horizontal x y =
assert (row_num x = row_num y);
let head = Hashtbl.copy x.head in
let col_num_x = col_num x in
Hashtbl.iter (fun k v -> Hashtbl.add head k (v + col_num_x)) y.head;
let col_num_y = col_num y in
let data = Array.make (col_num_x + col_num_y) Any_Series in
let size = max x.size y.size in
for i = 0 to col_num_x - 1 do
data.(i) <- resize_series size x.data.(i)
done;
for i = 0 to col_num_y - 1 do
data.(col_num_x + i) <- resize_series size y.data.(i)
done;
{ data; head; used = x.used; size }
let concat_vertical x y =
assert (col_num x = col_num y);
let head = Hashtbl.copy x.head in
let used = x.used + y.used in
let data = Array.make (col_num x) Any_Series in
for i = 0 to col_num x - 1 do
let sx = get_col x i in
let j = id_to_head x i |> head_to_id y in
let sy = get_col y j in
data.(i) <- append_series sx sy
done;
{ data; head; used; size = used }
let iteri_row f x =
let m = row_num x in
for i = 0 to m - 1 do
f i (get_row x i)
done
let iter_row f x = iteri_row (fun _ row -> f row) x
let mapi_row f x =
let head = Hashtbl.copy x.head in
let used = 0 in
let size = 0 in
let data = Array.map (fun _ -> Any_Series) x.data in
let y = { data; head; used; size } in
iteri_row (fun i row -> append_row y (f i row)) x;
y
let map_row f x = mapi_row (fun _ row -> f row) x
let filteri_row f x =
let head = Hashtbl.copy x.head in
let used = 0 in
let size = 0 in
let data = Array.map (fun _ -> Any_Series) x.data in
let y = { data; head; used; size } in
iteri_row (fun i row -> if f i row = true then append_row y row) x;
y
let filter_row f x = filteri_row (fun _ row -> f row) x
let filter_mapi_row f x =
let head = Hashtbl.copy x.head in
let used = 0 in
let size = 0 in
let data = Array.map (fun _ -> Any_Series) x.data in
let y = { data; head; used; size } in
iteri_row
(fun i row ->
match f i row with
| Some r -> append_row y r
| None -> ())
x;
y
let filter_map_row f x = filter_mapi_row (fun _ row -> f row) x
let get_slice slice x =
let slice = Array.(map of_list (of_list slice)) |> Array.map (fun s -> R_ s) in
let shp_x = [| row_num x; col_num x |] in
let _tmp0 = Owl_base_slicing.check_slice_definition slice shp_x in
let slice =
Array.map
(function
| R_ s -> s
| _ -> failwith "get_slice: unsupported")
_tmp0
in
let name = Owl_utils_array.get_slice slice.(1) (get_heads x) in
let data =
Array.map (head_to_id x) name |> get_cols x |> Array.map (slice_series slice.(0))
in
let used = length_series data.(0) in
let head = Hashtbl.create (Array.length name) in
Array.iteri (fun i s -> Hashtbl.add head s i) name;
{ data; head; used; size = used }
let _set_slice _x = raise (Owl_exception.NOT_IMPLEMENTED "owl_dataframe._set_slice")
let get_slice_by_name slice x =
let row_slice = Array.of_list (fst slice) in
let col_slice = Array.of_list (snd slice) in
let shp_x = [| row_num x; col_num x |] in
let refmt = Owl_base_slicing.check_slice_definition [| R_ row_slice |] shp_x in
let row_slice =
(function
| R_ s -> s
| _ -> failwith "get_slice: unsupported")
refmt.(0)
in
let col_slice = if Array.length col_slice = 0 then get_heads x else col_slice in
let data = Array.map (slice_series row_slice) (get_cols_by_name x col_slice) in
let used = length_series data.(0) in
let head = Hashtbl.create (Array.length col_slice) in
Array.iteri (fun i s -> Hashtbl.add head s i) col_slice;
{ data; head; used; size = used }
let _set_slice_by_name _x =
raise (Owl_exception.NOT_IMPLEMENTED "owl_dataframe._set_slice_by_name")
let head n x =
let m = row_num x in
assert (n > 0 && n <= m);
get_slice [ [ 0; n - 1 ]; [] ] x
let tail n x =
let m = row_num x in
assert (n > 0 && n <= m);
get_slice [ [ -n; -1 ]; [] ] x
let min_i x head =
let series = get_col_by_name x head in
min_series series
let max_i x head =
let series = get_col_by_name x head in
max_series series
let sort ?(inc = true) x head =
let series = get_col_by_name x head in
let indices = argsort_series series in
if inc = false then Owl_utils_array.reverse indices;
let y = copy_struct x in
Array.iter (fun i -> get_row x i |> append_row y) indices;
y
let unique x head =
let series = get_col_by_name x head in
let s_size = length_series series in
let h_size = max 64 (s_size / 2) in
let htbl = Hashtbl.create h_size in
let stack = Owl_utils_stack.make () in
for i = 0 to s_size - 1 do
let k = get_ith_elt i series in
if Hashtbl.mem htbl k = false
then (
Hashtbl.add htbl k None;
Owl_utils_stack.push stack k)
done;
let elt_array = Owl_utils_stack.to_array stack in
elt_array_to_series series elt_array
let _join ?on ?how x =
let on =
match on with
| Some a -> head_to_id x a
| None -> 0
in
let how =
match how with
| Some a -> a
| None -> `Inner
in
on, how
let guess_separator lines =
let sep = [| ','; ' '; '\t'; ';'; ':'; '|' |] in
let tmp =
Array.map
(fun c ->
let l = String.split_on_char c lines.(0) in
c, List.length l)
sep
in
Array.sort (fun a b -> snd b - snd a) tmp;
let sep = Array.map fst tmp in
let not_sep = ref true in
let sep_idx = ref 0 in
while !not_sep = true do
let c = sep.(!sep_idx) in
let n = String.split_on_char c lines.(0) |> List.length in
(try
Array.iter
(fun line ->
let m = String.split_on_char c line |> List.length in
if m <> n then raise Owl_exception.FOUND)
lines;
not_sep := false
with
| _exn -> ());
if !not_sep = true then sep_idx := !sep_idx + 1
done;
if !not_sep = false then sep.(!sep_idx) else ','
let guess_types sep lines =
let typ = [| "b"; "i"; "f" |] in
let num_lines = Array.length lines in
assert (num_lines > 1);
let num_cols = lines.(0) |> String.trim |> String.split_on_char sep |> List.length in
let stacks = Array.init num_cols (fun _ -> Owl_utils_stack.make ()) in
Array.iteri
(fun i line ->
if i > 0
then
String.trim line
|> String.split_on_char sep
|> List.iteri (fun i c -> Owl_utils_stack.push stacks.(i) c))
lines;
let cols = Array.map Owl_utils_stack.to_array stacks in
Array.mapi
(fun _i col ->
let guess_typ = ref "s" in
(try
Array.iter
(fun col_typ ->
let typ_fun = str_to_elt_fun col_typ in
let wrong_guess = ref false in
(try
Array.iter
(fun x ->
let y = String.trim x in
typ_fun y |> ignore)
col
with
| _exn -> wrong_guess := true);
if !wrong_guess = false
then (
guess_typ := col_typ;
raise Owl_exception.FOUND))
typ
with
| _exn -> ());
!guess_typ)
cols
let of_csv ?sep ?head ?types fname =
let lines = Owl_io.head 100 fname in
let sep =
match sep with
| Some a -> a
| None -> guess_separator lines
in
let head_i = 0 in
let head_names =
match head with
| Some a -> a
| None -> Owl_io.csv_head ~sep head_i fname
in
let types =
match types with
| Some a -> a
| None -> guess_types sep lines
in
assert (Array.length head_names = Array.length types);
let convert_f = Array.map str_to_elt_fun types in
let dataframe = make head_names in
let dropped_line = ref 0 in
Owl_io.read_csv_proc
~sep
(fun i line ->
try
if i <> head_i
then (
let row = Array.map2 (fun f a -> f a) convert_f line in
append_row dataframe row)
with
| _exn ->
dropped_line := !dropped_line + 1;
Owl_log.warn "of_csv: fail to parse line#%i @ %s" i fname)
fname;
if !dropped_line > 0 then Owl_log.warn "%i lines have been dropped." !dropped_line;
dataframe
let to_csv ?sep x fname =
let m, n = shape x in
let csv = Array.make_matrix (m + 1) n "" in
csv.(0) <- get_heads x;
for i = 0 to m - 1 do
for j = 0 to n - 1 do
csv.(i + 1).(j) <- elt_to_str (get x i j)
done
done;
Owl_io.write_csv ?sep csv fname
let ( .%() ) x idx = get_by_name x (fst idx) (snd idx)
let ( .%()<- ) x idx a = set_by_name x (fst idx) (snd idx) a
let ( .?() ) x f = filter_row f x
let ( .?()<- ) x f g = filter_map_row (fun r -> if f r = true then Some (g r) else None) x
let ( .$() ) x slice = get_slice_by_name slice x
let[@warning "-32"] ( .$()<- ) _x _idx _a =
raise (Owl_exception.NOT_IMPLEMENTED "owl_dataframe.( .$( )<- )")