/
data.clj
269 lines (233 loc) · 9 KB
/
data.clj
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
(ns tech.libs.smile.data
(:require [tech.v2.datatype :as dtype]
[tech.v2.datatype.protocols :as dtype-proto]
[tech.v2.datatype.typecast :as typecast]
[tech.v2.datatype.datetime :as dtype-dt]
[tech.v2.datatype.casting :as casting]
[tech.ml.dataset.impl.dataset :as ds-impl]
[tech.ml.dataset.column :as ds-col]
[tech.ml.dataset.string-table :as str-table]
[clojure.set :as set])
(:import [tech.ml.dataset.impl.dataset Dataset]
[smile.data DataFrame DataFrameImpl DataFrameFactory]
[java.time.format DateTimeFormatter]
[java.time LocalDate LocalTime LocalDateTime]
[smile.math.matrix Matrix]
[smile.data.type StructType StructField DataType DataType$ID DataTypes]
[smile.data.vector BaseVector Vector BooleanVector ByteVector ShortVector
IntVector LongVector FloatVector DoubleVector StringVector
BooleanVectorImpl ByteVectorImpl ShortVectorImpl
IntVectorImpl LongVectorImpl FloatVectorImpl DoubleVectorImpl
StringVectorImpl VectorImpl
VectorFactory]
[smile.data.measure NominalScale DiscreteMeasure]
[org.roaringbitmap RoaringBitmap]
[java.util Collection List ArrayList]
[java.io Writer]))
(set! *warn-on-reflection* true)
(def datatype->smile-map
{:boolean DataTypes/BooleanType
:int8 DataTypes/ByteType
:character DataTypes/CharType
:int16 DataTypes/ShortType
:int32 DataTypes/IntegerType
:int64 DataTypes/LongType
:float32 DataTypes/FloatType
:float64 DataTypes/DoubleType
:decimal DataTypes/DecimalType
:string DataTypes/StringType
:local-date DataTypes/DateType
:local-time DataTypes/TimeType
:local-date-time DataTypes/DateTimeType
:packed-local-date DataTypes/DateType
:packed-local-time DataTypes/TimeType
:packed-local-date-time DataTypes/DateTimeType
:object DataTypes/ObjectType})
(def smile->datatype-map
(-> (set/map-invert datatype->smile-map)
(assoc DataTypes/DateType :local-date
DataTypes/TimeType :local-time
DataTypes/DateTimeType :local-date-time)))
(defn datatype->smile
^DataType [dtype]
(when dtype
(get datatype->smile-map dtype DataTypes/ObjectType)))
(defn colname->str
^String [cname]
(cond
(string? cname) cname
(keyword? cname) (name cname)
(symbol? cname) (name cname)
:else
(str cname)))
(defn smile-struct-field
^StructField [name dtype]
(StructField. (colname->str name)
(datatype->smile dtype)))
(defn column->field
^StructField [col]
(smile-struct-field (ds-col/column-name col)
(dtype/get-datatype col)))
(defn datatype->smile-vec-type
"Datatype has to be a compile time constant"
[datatype]
(case (casting/safe-flatten datatype)
:boolean 'BooleanVector
:int8 'ByteVector
:int16 'ShortVector
:int32 'IntVector
:int64 'LongVector
:float32 'FloatVector
:float64 'DoubleVector
:string 'StringVector
:object 'Vector))
(defn datatype->smile-vec-impl-type
"Datatype has to be a compile time constant"
[datatype]
(case (casting/safe-flatten datatype)
:boolean 'BooleanVectorImpl
:int8 'ByteVectorImpl
:int16 'ShortVectorImpl
:int32 'IntVectorImpl
:int64 'LongVectorImpl
:float32 'FloatVectorImpl
:float64 'DoubleVectorImpl
:string 'StringVectorImpl
'VectorImpl))
(defn column->smile
^BaseVector [col]
(let [col-base-dtype (dtype/get-datatype col)
col-data (if (dtype-dt/packed-datatype? col-base-dtype)
(dtype-dt/unpack col)
col)
col-dtype (dtype/get-datatype col-data)
col-ary (if-let [col-ary (dtype/->array col-data)]
col-ary
(dtype/make-container :java-array col-dtype col-data))
field (column->field col)]
(case (casting/safe-flatten col-dtype)
:boolean (VectorFactory/booleanVector field ^booleans col-ary)
:int8 (VectorFactory/byteVector field ^bytes col-ary)
:int16 (VectorFactory/shortVector field ^shorts col-ary)
:int32 (VectorFactory/intVector field ^ints col-ary)
:int64 (VectorFactory/longVector field ^longs col-ary)
:float32 (VectorFactory/floatVector field ^floats col-ary)
:float64 (VectorFactory/doubleVector field ^doubles col-ary)
:string (VectorFactory/stringVector field ^"[Ljava.lang.String;" col-ary)
(VectorFactory/genericVector field col-ary))))
(defn dataset->dataframe
"Convert a dataset to a smile.data DataFrame"
^DataFrame [ds]
(if (instance? DataFrame ds)
ds
(DataFrameFactory/construct ^"[Lsmile.data.vector.BaseVector;"
(into-array BaseVector (map column->smile ds)))))
(defmacro construct-primitive-smile-vec
[datatype name data]
(case datatype
:boolean `(BooleanVectorImpl. ~name (typecast/as-boolean-array ~data))
:int8 `(ByteVectorImpl. ~name (typecast/as-byte-array ~data))
:int16 `(ShortVectorImpl. ~name (typecast/as-short-array ~data))
:int32 `(IntVectorImpl. ~name (typecast/as-int-array ~data))
:int64 `(LongVectorImpl. ~name (typecast/as-long-array ~data))
:float32 `(FloatVectorImpl. ~name (typecast/as-float-array ~data))
:float64 `(DoubleVectorImpl. ~name (typecast/as-double-array ~data))))
(extend-type BaseVector
dtype-proto/PDatatype
(get-datatype [v]
(if-let [retval (get smile->datatype-map (.type v))]
retval
:object))
dtype-proto/PCountable
(ecount [v] (long (.size v))))
(defmacro extend-primitive-vec
[datatype]
`(extend-type ~(datatype->smile-vec-impl-type datatype)
dtype-proto/PDatatype
(get-datatype [v#] ~datatype)
dtype-proto/PToArray
(->sub-array [v#]
{:java-array (.array v#)
:offset 0
:length (dtype/ecount (.array v#))})
(->array-copy [v#]
(dtype/clone (.array v#)))
dtype-proto/PToNioBuffer
(convertible-to-nio-buffer? [v#] true)
(->buffer-backing-store [v#]
(dtype-proto/->buffer-backing-store (.array v#)))
dtype-proto/PBuffer
(sub-buffer [v# offset# length#]
(dtype-proto/sub-buffer (.array v#) offset# length#))
dtype-proto/PClone
(clone [v#]
(construct-primitive-smile-vec
~datatype (StructField. (.name v#) (.type v#) (.measure v#))
(dtype/clone (.array v#))))
dtype-proto/PToReader
(convertible-to-reader? [v#] true)
(->reader [v# options#] (dtype-proto/->reader (.array v#) options#))
dtype-proto/PToWriter
(convertible-to-writer? [v#] true)
(->writer [v# options#] (dtype-proto/->writer (.array v#) options#))))
(extend-primitive-vec :boolean)
(extend-primitive-vec :int8)
(extend-primitive-vec :int16)
(extend-primitive-vec :int32)
(extend-primitive-vec :int64)
(extend-primitive-vec :float32)
(extend-primitive-vec :float64)
(extend-type VectorImpl
dtype-proto/PToArray
(->sub-array [v]
{:java-array (.array v)
:offset 0
:length (dtype/ecount (.array v))})
(->array-copy [v]
(dtype/clone (.array v)))
dtype-proto/PBuffer
(sub-buffer [v offset length]
(dtype-proto/sub-buffer (.array v) offset length))
dtype-proto/PClone
(clone [v]
(let [new-field (StructField. (.name v) (.type v) (.measure v))]
(if (= :string (dtype/get-datatype v))
(StringVectorImpl. new-field ^"[Ljava.lang.String;" (dtype/clone (.array v)))
(VectorImpl. new-field (.array v)))))
dtype-proto/PToReader
(convertible-to-reader? [v] true)
(->reader [v options] (dtype-proto/->reader (.array v) options))
dtype-proto/PToWriter
(convertible-to-writer? [v#] true)
(->writer [v options] (dtype-proto/->writer (.array v) options)))
(defn dataframe->dataset
([df {:keys [unify-strings?]
:or {unify-strings? true}
:as options}]
(->> df
(map (fn [^BaseVector smile-vec]
{:name (.name smile-vec)
:data
(if (and unify-strings?
(= :string (dtype/get-datatype smile-vec)))
(let [col-rdr (dtype/->reader smile-vec)
str-rdr (dtype/object-reader
(dtype/ecount col-rdr)
#(let [read-val (col-rdr %)]
(cond
(string? read-val)
read-val
(nil? read-val)
""
:else
(throw (Exception.
(format "Value not a string: %s"
read-val))))))]
(str-table/string-table-from-strings str-rdr))
smile-vec)}))
(ds-impl/new-dataset options {:name "_unnamed"})))
([df]
(dataframe->dataset df {})))
(defmethod print-method DataFrameImpl
[dataset w]
(.write ^Writer w (.toString ^Object dataset)))