/
tablesaw.clj
441 lines (358 loc) · 14.7 KB
/
tablesaw.clj
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(ns tech.libs.tablesaw
(:require [tech.libs.tablesaw.tablesaw-column :as dtype-tbl]
[tech.ml.protocols.column :as col-proto]
[tech.v2.datatype :as dtype]
[tech.v2.datatype.base :as dtype-base]
[tech.v2.datatype.protocols :as dtype-proto]
[tech.v2.datatype.pprint :as dtype-pp]
[clojure.set :as c-set]
[tech.ml.dataset.seq-of-maps :as ds-seq-of-maps]
[tech.ml.dataset.generic-columnar-dataset :as columnar-dataset]
[tech.io :as io]
[clojure.data.csv :as csv])
(:import [tech.tablesaw.api Table ColumnType
NumericColumn DoubleColumn
StringColumn BooleanColumn]
[tech.tablesaw.columns Column]
[tech.tablesaw.io.csv CsvReadOptions
CsvReadOptions$Builder]
[tech.tablesaw.io Source]
[java.util UUID]
[java.io InputStream BufferedInputStream
ByteArrayInputStream]
[org.apache.commons.math3.stat.descriptive.moment Skewness]
[tech.tablesaw.io ColumnTypeDetector ReadOptions ReadOptions$Builder]
[tech.v2.datatype ObjectReader]))
(set! *warn-on-reflection* true)
(set! *unchecked-math* :warn-on-boxed)
(defn- create-table-from-column-seq
[^Table table col-seq]
(Table/create (.name table) (into-array Column col-seq)))
(defn- column->metadata
[^Column col]
(merge {:name (.name col)}
(when (= :string (dtype/get-datatype col))
{:categorical? true})))
(declare make-column)
(deftype TablesawColumn [^Column col metadata cache]
col-proto/PIsColumn
(is-column? [this] true)
col-proto/PColumn
(column-name [this] (or (:name metadata) (.name col)))
(set-name [this colname]
(TablesawColumn. col (assoc metadata :name colname) {}))
(supported-stats [this] (col-proto/supported-stats col))
(metadata [this] (merge metadata
{:name (col-proto/column-name this)
:size (dtype/ecount col)
:datatype (dtype/get-datatype col)}))
(set-metadata [this data-map]
(TablesawColumn. col data-map cache))
(cache [this] cache)
(set-cache [this cache-map]
(TablesawColumn. col metadata cache-map))
(missing [this] (col-proto/missing col))
(unique [this] (col-proto/unique col))
(stats [this stats-set]
(when-not (instance? NumericColumn col)
(throw (ex-info "Stats aren't available on non-numeric columns"
{:column-type (dtype/get-datatype col)
:column-name (col-proto/column-name this)
:column-java-type (type col)})))
(let [stats-set (set (if-not (seq stats-set)
dtype-tbl/available-stats
stats-set))
existing (->> stats-set
(map (fn [skey]
(when-let [cached (get metadata skey)]
[skey cached])))
(remove nil?)
(into {}))
missing-stats (c-set/difference stats-set (set (keys existing)))]
(merge existing
(col-proto/stats col missing-stats))))
(correlation [this other-column correlation-type]
(col-proto/correlation col
(.col ^TablesawColumn other-column)
correlation-type))
(column-values [this] (col-proto/column-values col))
(is-missing? [this idx] (col-proto/is-missing? col idx))
(select [this idx-seq] (make-column (col-proto/select col idx-seq) metadata {}))
(empty-column [this datatype elem-count metadata]
(dtype-proto/make-container :tablesaw-column datatype elem-count
(assoc (select-keys metadata [:name])
:empty? true)))
(new-column [this datatype elem-count-or-values metadata]
(dtype-proto/make-container :tablesaw-column datatype
elem-count-or-values metadata))
(clone [this]
(dtype-proto/make-container :tablesaw-column
(dtype/get-datatype this)
(col-proto/column-values this)
metadata))
(to-double-array [this error-missing?]
(col-proto/to-double-array col error-missing?))
dtype-proto/PDatatype
(get-datatype [this] (dtype-base/get-datatype col))
dtype-proto/PCopyRawData
(copy-raw->item! [raw-data ary-target target-offset options]
(dtype-proto/copy-raw->item! col ary-target target-offset options))
dtype-proto/PPrototype
(from-prototype [src datatype shape]
(col-proto/new-column src datatype (first shape) (select-keys [:name] metadata)))
dtype-proto/PToNioBuffer
(convertible-to-nio-buffer? [item]
(dtype-proto/convertible-to-nio-buffer? col))
(->buffer-backing-store [item]
(dtype-proto/as-nio-buffer col))
dtype-proto/PToList
(convertible-to-fastutil-list? [item]
(dtype-proto/convertible-to-fastutil-list? col))
(->list-backing-store [item]
(dtype-proto/as-list col))
dtype-proto/PToReader
(convertible-to-reader? [item] true)
(->reader [item options]
(dtype-proto/->reader col options))
dtype-proto/PToWriter
(convertible-to-writer? [item] true)
(->writer [item options]
(dtype-proto/->writer col options))
dtype-proto/PToIterable
(convertible-to-iterable? [item] true)
(->iterable [item options]
(dtype-proto/->reader col options))
dtype-proto/PToMutable
(convertible-to-mutable? [item] true)
(->mutable [item options]
(dtype-proto/->mutable col options))
dtype-proto/PBuffer
(sub-buffer [item offset length]
(TablesawColumn.
(dtype-proto/sub-buffer col offset length)
metadata {}))
dtype-proto/PToArray
(->sub-array [src] (dtype-proto/->sub-array col))
(->array-copy [src] (dtype-proto/->array-copy col))
dtype-proto/PCountable
(ecount [item] (dtype-proto/ecount col))
ObjectReader
(lsize [item] (long (dtype-proto/ecount col)))
(read [item idx]
(.get col idx))
Object
(toString [item]
(let [n-items (dtype/ecount item)
format-str (if (> n-items 20)
"#tablesaw-column<%s>%s\n%s\n[%s...]"
"#tablesaw-column<%s>%s\n%s\n[%s]")]
(format format-str
(name (dtype/get-datatype item))
[n-items]
(col-proto/column-name item)
(-> (dtype/->reader item)
(dtype-proto/sub-buffer 0 (min 20 n-items))
(dtype-pp/print-reader-data))))))
(defmethod print-method TablesawColumn
[col ^java.io.Writer w]
(.write w (.toString ^Object col)))
(defn make-column
[datatype-col metadata & [cache]]
(if (instance? TablesawColumn datatype-col)
(throw (ex-info "Nested" {})))
(TablesawColumn. datatype-col metadata cache))
(defmethod dtype-proto/make-container :tablesaw-column
[_container-type datatype elem-count-or-seq
{:keys [empty?] :as options}]
(when (and empty?
(not (number? elem-count-or-seq)))
(throw (ex-info "Empty columns must have colsize argument." {})))
(->
(if empty?
(dtype-tbl/make-empty-column datatype elem-count-or-seq options)
(dtype-tbl/make-column datatype elem-count-or-seq options))
(make-column options {})))
(defn autodetect-csv-separator
[^BufferedInputStream input-stream & options]
(.mark input-stream 1000)
(let [byte-data (byte-array 1000)
num-read (.read input-stream byte-data)
_ (.reset input-stream)]
(apply io/autodetect-csv-separator (ByteArrayInputStream. byte-data 0 num-read)
options)))
(defmulti keyword->tablesaw-column-type
(fn [col-type-kwd]
col-type-kwd))
(defmethod keyword->tablesaw-column-type :default
[col-type-kwd]
(if (instance? ColumnType col-type-kwd)
col-type-kwd
(case col-type-kwd
:int16 ColumnType/SHORT
:int32 ColumnType/INTEGER
:int64 ColumnType/LONG
:float32 ColumnType/FLOAT
:float64 ColumnType/DOUBLE
:boolean ColumnType/BOOLEAN
:string ColumnType/STRING)))
(defn to-minimal-csv-seq
"Read a smaller csv up to a given character limit."
[^BufferedInputStream input-stream options]
;;Need enough bytes that we can reliably autodetect a lot of files.
(let [num-bytes (long (or (:autodetect-max-bytes options)
65536))
_ (.mark input-stream num-bytes)
byte-data (byte-array num-bytes)
bytes-read (.read input-stream byte-data)
_ (.reset input-stream)
;;the last line must be incomplete
csv-seq (-> (ByteArrayInputStream. byte-data 0 bytes-read)
(io/reader)
(csv/read-csv :separator (:separator options)))]
;;deal with last line exception
(loop [cleaned-seq []
csv-seq csv-seq]
(let [next-line
(try
(first csv-seq)
(catch Throwable _e
nil))]
(if-not next-line
cleaned-seq
(recur (conj cleaned-seq next-line)
(rest csv-seq)))))))
(defn autodetect-column-types
[^BufferedInputStream input-stream column-type-detect-fn options]
(->> (to-minimal-csv-seq input-stream options)
(column-type-detect-fn)
(map keyword->tablesaw-column-type)
(into-array ColumnType)))
(defn extended-column-types
[]
(let [rdr-type ReadOptions
target-field (.getDeclaredField rdr-type "EXTENDED_TYPES")
_ (.setAccessible target-field true)]
(.get target-field nil)))
(defn construct-read-options
^ReadOptions []
(let [ctor (.getDeclaredConstructor ReadOptions$Builder (make-array Class 0))
_ (.setAccessible ctor true)
builder (.newInstance ctor (make-array Object 0))
build-method (.getDeclaredMethod ^Class (type builder)
"build" (make-array Class 0))]
(.setAccessible build-method true)
(.invoke build-method builder (make-array Object 0))))
(defn tablesaw-detect-column-types
[^BufferedInputStream input-stream options]
(let [read-options (construct-read-options)
detector (ColumnTypeDetector. ^Java.util.List (extended-column-types))
^java.lang.Iterable iterable
(->> (to-minimal-csv-seq input-stream options)
;;drop column names
(rest)
(map #(into-array String %)))]
(.detectColumnTypes detector
(.iterator iterable)
read-options)))
(defn ^CsvReadOptions$Builder
->csv-builder [path & options]
(let [^BufferedInputStream input-stream (apply io/buffered-input-stream
path options)
separator (apply autodetect-csv-separator input-stream options)
opt-map (assoc (apply hash-map options) :separator separator)
;;We have to detect all of the column types here.
column-types (if-let [coltypes (:column-types opt-map)]
(map keyword->tablesaw-column-type coltypes)
(if-let [col-fn (:column-type-fn opt-map)]
(autodetect-column-types input-stream col-fn opt-map)
(tablesaw-detect-column-types input-stream opt-map)))]
(cond-> (CsvReadOptions/builder input-stream)
true
(.separator separator)
true
(.header (boolean (if (nil? (:header? opt-map))
true
(:header? opt-map))))
column-types
(.columnTypes
(into-array ColumnType
^"[Ltech.tablesaw.api.ColumnType;"
column-types)))))
(defn tablesaw-columns->tablesaw-dataset
[table-name columns]
(columnar-dataset/make-dataset
table-name
(if (or (sequential? columns)
(instance? java.util.List columns))
(->> columns
(mapv #(make-column % (column->metadata %))))
(->> columns
(mapv (fn [[col-name col]]
(make-column col (assoc (column->metadata col)
:name col-name))))))
{}))
(defn ->tablesaw-dataset
[^Table table]
(tablesaw-columns->tablesaw-dataset (.name table) (.columns table)))
(defn path->tablesaw-dataset
[path & options]
(let [input (if (and (string? path)
(.endsWith ^String path ".gz"))
(io/gzip-input-stream path)
path)]
(-> (Table/read)
(.csv ^CsvReadOptions$Builder (apply ->csv-builder input options))
->tablesaw-dataset)))
(defn col-dtype-cast
[data-val dtype]
(if (= dtype
:string)
(if (or (keyword? data-val)
(symbol? data-val))
(name data-val)
(str data-val))
(dtype/cast data-val dtype)))
(defn map-seq->tablesaw-dataset
"Scan a sequence of maps and produce a tablesaw dataset."
[map-seq-dataset {:keys [column-definitions
table-name]
:or {table-name "_unnamed"}
:as options}]
(let [column-definitions
(if column-definitions
column-definitions
(ds-seq-of-maps/autoscan-map-seq map-seq-dataset options))
;;force the dataset here as knowing the count helps
column-map (->> column-definitions
(map (fn [{colname :name
datatype :datatype}]
(let [datatype (if (= datatype :keyword)
:string
datatype)]
[colname
(dtype-tbl/make-empty-column
datatype 0 {:name colname})])))
(into {}))
_ (->> map-seq-dataset
(map-indexed
(fn [idx item-row]
(doseq [[item-name item-val] item-row]
(let [^Column col (get column-map item-name)
missing (- (int idx) (.size col))]
(dotimes [_idx missing]
(.appendMissing col))
(if-not (nil? item-val)
(.append col (col-dtype-cast
item-val (dtype/get-datatype col)))
(.appendMissing col))))))
(dorun))
column-seq (vals column-map)
max-ecount (long (if (seq column-seq)
(apply max (map dtype/ecount column-seq))
0))]
;;Ensure all columns are same length
(doseq [^Column col column-seq]
(let [missing-count (- max-ecount (.size col))]
(dotimes [_idx missing-count]
(.appendMissing col))))
(tablesaw-columns->tablesaw-dataset table-name column-map)))