c

16 files changed, 122 insertions, 2 deletions

diff --git a/algorithms/dune b/algorithms/dune
index 90f35b8..069a29e 100644
--- a/algorithms/dune
+++ b/algorithms/dune
@@ -1,6 +1,6 @@
 (library
  (inline_tests)
  (name algorithms_lib)
- (libraries core owl progress genetics_lib utils_lib structures_lib)
+ (libraries core owl  genetics_lib utils_lib structures_lib)
  (preprocess
   (pps ppx_inline_test ppx_jane)))
diff --git a/app/spectral_classification/src/classification.ml b/app/spectral_classification/src/classification.ml
new file mode 100644
index 0000000..e401e57
--- /dev/null
+++ b/app/spectral_classification/src/classification.ml
@@ -0,0 +1,7 @@
+open! Core
+open Owl
+
+type t = Mat.mat
+
+let create values = Mat.of_array values 1 (Array.length values)
+let sexp_of_t t = Mat.to_array t |> Array.sexp_of_t Float.sexp_of_t
diff --git a/app/spectral_classification/src/classification.mli b/app/spectral_classification/src/classification.mli
new file mode 100644
index 0000000..02a60b2
--- /dev/null
+++ b/app/spectral_classification/src/classification.mli
@@ -0,0 +1,5 @@
+open! Core
+
+type t [@@deriving sexp_of]
+
+val create : float array -> t
diff --git a/app/spectral_classification/src/classification_rules.ml b/app/spectral_classification/src/classification_rules.ml
new file mode 100644
index 0000000..aebf5a8
--- /dev/null
+++ b/app/spectral_classification/src/classification_rules.ml
@@ -0,0 +1,12 @@
+open! Core
+open Owl
+
+type t = Mat.mat
+
+let create values ~length ~number = Mat.of_array values number length
+
+let sexp_of_t t =
+  let n, _ = Mat.shape t in
+  let l = List.init n ~f:(fun i -> Mat.row t i |> Mat.to_array |> Array.to_list) in
+  List.sexp_of_t (List.sexp_of_t Float.sexp_of_t) l
+;;
diff --git a/app/spectral_classification/src/classification_rules.mli b/app/spectral_classification/src/classification_rules.mli
new file mode 100644
index 0000000..9b11f0d
--- /dev/null
+++ b/app/spectral_classification/src/classification_rules.mli
@@ -0,0 +1,10 @@
+open! Core
+open Genetics_lib
+
+type t [@@deriving sexp_of]
+
+(** This might throw if this isn't a nonempty matrix (i.e. each array have the same size. )*)
+val create : float array -> length:int -> number:int -> t
+
+(** Throws if chromosome length is different than the number of classifiers. *)
+val classify : t -> Chromosome.t -> Classification.t
diff --git a/app/spectral_classification/src/dune b/app/spectral_classification/src/dune
new file mode 100644
index 0000000..3a2958e
--- /dev/null
+++ b/app/spectral_classification/src/dune
@@ -0,0 +1,6 @@
+(library
+ (inline_tests)
+ (name spectral_classification_lib)
+ (libraries core owl owl-plplot curl utils_lib structures_lib algorithms_lib)
+ (preprocess
+  (pps ppx_inline_test ppx_jane)))
diff --git a/app/spectral_classification/src/main.ml b/app/spectral_classification/src/main.ml
new file mode 100644
index 0000000..3ad2609
--- /dev/null
+++ b/app/spectral_classification/src/main.ml
@@ -0,0 +1 @@
+open! Core
diff --git a/app/spectral_classification/src/main.mli b/app/spectral_classification/src/main.mli
new file mode 100644
index 0000000..ac8385a
--- /dev/null
+++ b/app/spectral_classification/src/main.mli
@@ -0,0 +1,3 @@
+open! Core
+
+(* val command : Command.t *)
diff --git a/app/spectral_classification/src/parser.ml b/app/spectral_classification/src/parser.ml
new file mode 100644
index 0000000..c24c8df
--- /dev/null
+++ b/app/spectral_classification/src/parser.ml
@@ -0,0 +1,34 @@
+open! Core
+
+let parse_line line =
+  let is_good_str str =
+    if String.is_empty str
+    then false
+    else if String.length str = 1 && Char.is_whitespace (String.get str 0)
+    then false
+    else true
+  in
+  String.split_lines line
+  |> String.concat
+  |> String.split ~on:' '
+  |> List.filter ~f:is_good_str
+  |> List.map ~f:Float.of_string
+;;
+
+let%expect_test "parse_line" =
+  print_s [%sexp (parse_line "   0. 124    0.231e32   \n 123.    \n\n\t " : float list)];
+  [%expect{| (0 124 2.31E+31 123) |}]
+;;
+
+let load_classification_rules filename =
+  let lines = In_channel.read_lines filename in
+  let number = List.length lines
+  and values = List.concat_map lines ~f:parse_line in
+  let length = List.length values / number in
+  Classification_rules.create (Array.of_list values) ~length ~number
+;;
+
+let load_classification filename =
+  let line = In_channel.read_all filename in
+  parse_line line |> Array.of_list |> Classification.create
+;;
diff --git a/app/spectral_classification/src/parser.mli b/app/spectral_classification/src/parser.mli
new file mode 100644
index 0000000..18538f4
--- /dev/null
+++ b/app/spectral_classification/src/parser.mli
@@ -0,0 +1,4 @@
+open! Core
+
+val load_classification_rules : Filename.t -> Classification_rules.t
+val load_classification : Filename.t -> Classification.t
diff --git a/app/spectral_classification/src/spectral_classification.ml b/app/spectral_classification/src/spectral_classification.ml
new file mode 100644
index 0000000..a5a59ad
--- /dev/null
+++ b/app/spectral_classification/src/spectral_classification.ml
@@ -0,0 +1 @@
+module Main = Main
diff --git a/app/spectral_classification/test/classification_rules.txt b/app/spectral_classification/test/classification_rules.txt
new file mode 100644
index 0000000..f817a48
--- /dev/null
+++ b/app/spectral_classification/test/classification_rules.txt
@@ -0,0 +1,4 @@
+ 1.0000000e+000 2.0000000e+000 3.0000000e+000
+  1.0000000e+000  1.0000000e+000  1.0000000e+0000
+ 1.0124300e+000 1.0300000e+000 4.0000000e+000
+ 1.0052310e+000 7.0000000e+000 5.0000000e+000
diff --git a/app/spectral_classification/test/dune b/app/spectral_classification/test/dune
new file mode 100644
index 0000000..f3ad6ad
--- /dev/null
+++ b/app/spectral_classification/test/dune
@@ -0,0 +1,15 @@
+(library
+ (inline_tests
+  (deps classification_rules.txt image_expert.txt))
+ (name spectral_classification_test)
+ (libraries
+  core
+  owl
+  owl-plplot
+  curl
+  spectral_classification_lib
+  utils_lib
+  structures_lib
+  algorithms_lib)
+ (preprocess
+  (pps ppx_inline_test ppx_jane)))
diff --git a/app/spectral_classification/test/image_expert.txt b/app/spectral_classification/test/image_expert.txt
new file mode 100644
index 0000000..05b17b8
--- /dev/null
+++ b/app/spectral_classification/test/image_expert.txt
@@ -0,0 +1 @@
+  7.0000000e+000  4.0000000e+000    4.0000000e+000  4.0000000e+000
diff --git a/app/spectral_classification/test/test.ml b/app/spectral_classification/test/test.ml
new file mode 100644
index 0000000..ef83c9d
--- /dev/null
+++ b/app/spectral_classification/test/test.ml
@@ -0,0 +1,16 @@
+open! Core
+open Spectral_classification_lib
+
+let%expect_test "load_classification_rules" =
+  let classification_rules =
+    Parser.load_classification_rules "classification_rules.txt"
+  in
+  print_s [%sexp (classification_rules : Classification_rules.t)];
+  [%expect {| ((1 2 3) (1 1 1) (1.01243 1.03 4) (1.005231 7 5)) |}]
+;;
+
+let%expect_test "load_classification" =
+  let classification = Parser.load_classification "image_expert.txt" in
+  print_s [%sexp (classification : Classification.t)];
+  [%expect {| (7 4 4 4) |}]
+;;
diff --git a/dune b/dune
index f5aa205..0c5bf09 100644
--- a/dune
+++ b/dune
@@ -1,5 +1,6 @@
 (env
- (dev)
+ (dev
+  (ocamlopt_flags (:standard)))
  (release
   (ocamlopt_flags
    (:standard -O3))))