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@7of9

ADDA | TensorFlow > TFRecordsへのIntField-Y格納と試し読み v0.1 > 3次元のinput node

Last updated at Posted at 2017-07-09
動作環境
GeForce GTX 1070 (8GB)
ASRock Z170M Pro4S [Intel Z170chipset]
Ubuntu 16.04 LTS desktop amd64
TensorFlow v1.1.0
cuDNN v5.1 for Linux
CUDA v8.0
Python 3.5.2
IPython 6.0.0 -- An enhanced Interactive Python.
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
GNU bash, version 4.3.48(1)-release (x86_64-pc-linux-gnu)

関連: ADDA > convertToInputcsv_170422.py > TensorFlow用のファイル(input.csv)に変換 > v0.1
関連: TensorFlow / ADDA > 線形方程式の初期値用データの学習 > 学習コード:v0.4 (Exr, Exi, Eyr, Eyi, Ezr, Eziの全学習)

概要

This article is related to ADDA (light scattering simulator based on the discrete dipole approximation).

ADDAの計算で重要となるのが、X,Y,Z方向の電場の値。ランダムな初期値を用いると計算が遅く、最終の解に近い初期値を用いると計算が早くなることは経験済。

supercomputerで計算した最終解を元にDeep learningで学習を行い、その結果を通常のPCで用いる。そうすることで、通常のPC上での計算を高速化し、Communityとしての計算資源の効率利用を目論んでいる。

X,Y,Z方向の電場の値をTensorFlowで学習させようとしている。

X,Y,Zの３次元入力データに対しての学習は以下で実施した。
http://qiita.com/7of9/items/6c5959c786851bce3e76
これを５次元に拡張できないか検討中。

TFRecordsを使うのが良いように思う。

code

対象ファイル

以下のような形式のファイル

$ head IntField-Y
x y z |E|^2 Ex.r Ex.i Ey.r Ey.i Ez.r Ez.i
-0.2362099733 -1.653469813 -5.905249332 0.3808724401 -0.01643908869 0.005065047872 0.5364061341 0.2932420721 0.03475441278 -0.07514132662
0.2362099733 -1.653469813 -5.905249332 0.3808724401 0.01643908869 -0.005065047872 0.5364061341 0.2932420721 0.03475441278 -0.07514132662
-1.181049866 -1.181049866 -5.905249332 0.4643931372 -0.06216652936 0.02425352236 0.6162560583 0.2767004228 0.02440613753 -0.05486267928
-0.7086299199 -1.181049866 -5.905249332 0.3684482195 -0.07402580779 0.006390743272 0.5140943697 0.3061227037 0.02715301914 -0.06470039038
-0.2362099733 -1.181049866 -5.905249332 0.4059533367 -0.03451368538 -0.002394051725 0.5213408941 0.3571248095 0.03088293921 -0.06684457553
0.2362099733 -1.181049866 -5.905249332 0.4059533367 0.03451368538 0.002394051725 0.5213408941 0.3571248095 0.03088293921 -0.06684457553
0.7086299199 -1.181049866 -5.905249332 0.3684482195 0.07402580779 -0.006390743272 0.5140943697 0.3061227037 0.02715301914 -0.06470039038
1.181049866 -1.181049866 -5.905249332 0.4643931372 0.06216652936 -0.02425352236 0.6162560583 0.2767004228 0.02440613753 -0.05486267928
-1.181049866 -0.7086299199 -5.905249332 0.5691917417 -0.06618972606 0.005431362716 0.6710482671 0.3357264532 0.01676364612 -0.03849823498
...

TFRecords保存 v0.1

toTFRecords_InitFieldY_170709.py
import numpy as np
import tensorflow as tf

"""
v0.1 Jul. 09, 2017
   - save as [TFRecords] format
      + add convert_to_raw()
      + add [OUT_FILE]
      + add _int64_feature()
      + add _bytes_feature()
=== branched to [IntFieldY_to_TFRecords_170709.py] ===
v0.1 Apr. 22, 2017 (convertToInputcsv_170422.py)
   - read 'IntField' then output for TensorFlow
"""

# on
#   Ubuntu 16.04 LTS
#   TensorFlow v1.1
#   Python 3.5.2

# codingrule: PEP8


def _bytes_feature(value):
    return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))


def _int64_feature(value):
    return tf.train.Feature(int64_list=tf.train.Int64List(value=[value]))


def convert_to_raw(orgval):
    wrk_org = np.array(orgval, dtype=np.float32)
    wrk_raw = wrk_org.tostring()
    return wrk_raw

OUT_FILE = 'IntField-Y_170709.tfrecords'
data = np.genfromtxt('IntField-Y', delimiter=' ')

xpos, ypos, zpos = data[1:, 0], data[1:, 1], data[1:, 2]  # dipole location
E2 = data[1:, 3]
Exr, Exi = data[1:, 4], data[1:, 5]  # real and imaginary part of Ex
Eyr, Eyi = data[1:, 6], data[1:, 7]  # real and imaginary part of Ey
Ezr, Ezi = data[1:, 8], data[1:, 9]  # real and imaginary part of Ez

list = zip(xpos, ypos, zpos, Exr, Exi, Eyr, Eyi, Ezr, Ezi)

with tf.python_io.TFRecordWriter(OUT_FILE) as tf_writer:
    for tpl in list:
        xpos, ypos, zpos = tpl[0:3]
        exr, exi, eyr, eyi, ezr, ezi = tpl[3:9]
        # for debug
        print("%s, %s, %s, %s, %s, %s, %s, %s, %s" % tpl)
        #
        example = tf.train.Example(features=tf.train.Features(feature={
            'xpos_raw': _bytes_feature(convert_to_raw(xpos)),
            'ypos_raw': _bytes_feature(convert_to_raw(ypos)),
            'zpos_raw': _bytes_feature(convert_to_raw(zpos)),
            'exr_raw': _bytes_feature(convert_to_raw(exr)),
            'exi_raw': _bytes_feature(convert_to_raw(exi)),
            'eyr_raw': _bytes_feature(convert_to_raw(eyr)),
            'eyi_raw': _bytes_feature(convert_to_raw(eyi)),
            'ezr_raw': _bytes_feature(convert_to_raw(ezr)),
            'ezi_raw': _bytes_feature(convert_to_raw(ezi))
            }))
        tf_writer.write(example.SerializeToString())

試し読み v0.1

toTFRecords_InitFieldY_170709.pyにて保存したファイルが正しいかを確認するためのコード。

fromTFRecords_InitFieldY_170709.py
import numpy as np
import tensorflow as tf

"""
v0.1 Jul. 09, 2017
  - read position and Ex, Ey, Ez
     + add get_feature_float32()
"""

# on
#   Ubuntu 16.04 LTS
#   TensorFlow v1.1
#   Python 3.5.2

# codingrule: PEP8


def get_feature_float32(example, feature_name):
    wrk_raw = (example.features.feature[feature_name]
               .bytes_list
               .value[0])
    wrk_1d = np.fromstring(wrk_raw, dtype=np.float32)
    wrk_org = wrk_1d.reshape([1, -1])
    return wrk_org

INP_FILE = 'IntField-Y_170709.tfrecords'

record_iterator = tf.python_io.tf_record_iterator(path=INP_FILE)
for record in record_iterator:
    example = tf.train.Example()
    example.ParseFromString(record)

    xpos_org = get_feature_float32(example, 'xpos_raw')
    ypos_org = get_feature_float32(example, 'ypos_raw')
    zpos_org = get_feature_float32(example, 'zpos_raw')
    exr_org = get_feature_float32(example, 'exr_raw')
    exi_org = get_feature_float32(example, 'exi_raw')
    eyr_org = get_feature_float32(example, 'eyr_raw')
    eyi_org = get_feature_float32(example, 'eyi_raw')
    ezr_org = get_feature_float32(example, 'ezr_raw')
    ezi_org = get_feature_float32(example, 'ezi_raw')

    list_pos = *xpos_org, *ypos_org, *zpos_org
    list_e = *exr_org, *exi_org, *eyr_org, *eyi_org, *ezr_org, *ezi_org

    print(*list_pos, *list_e)

実行

$ python3 toTFRecords_InitFieldY_170709.py > out.170709_1100.org 
$ head out.170709_1100.org 
-0.2362099733, -1.653469813, -5.905249332, -0.01643908869, 0.005065047872, 0.5364061341, 0.2932420721, 0.03475441278, -0.07514132662
0.2362099733, -1.653469813, -5.905249332, 0.01643908869, -0.005065047872, 0.5364061341, 0.2932420721, 0.03475441278, -0.07514132662
-1.181049866, -1.181049866, -5.905249332, -0.06216652936, 0.02425352236, 0.6162560583, 0.2767004228, 0.02440613753, -0.05486267928
-0.7086299199, -1.181049866, -5.905249332, -0.07402580779, 0.006390743272, 0.5140943697, 0.3061227037, 0.02715301914, -0.06470039038
-0.2362099733, -1.181049866, -5.905249332, -0.03451368538, -0.002394051725, 0.5213408941, 0.3571248095, 0.03088293921, -0.06684457553
0.2362099733, -1.181049866, -5.905249332, 0.03451368538, 0.002394051725, 0.5213408941, 0.3571248095, 0.03088293921, -0.06684457553
0.7086299199, -1.181049866, -5.905249332, 0.07402580779, -0.006390743272, 0.5140943697, 0.3061227037, 0.02715301914, -0.06470039038
1.181049866, -1.181049866, -5.905249332, 0.06216652936, -0.02425352236, 0.6162560583, 0.2767004228, 0.02440613753, -0.05486267928
-1.181049866, -0.7086299199, -5.905249332, -0.06618972606, 0.005431362716, 0.6710482671, 0.3357264532, 0.01676364612, -0.03849823498
-0.7086299199, -0.7086299199, -5.905249332, -0.04588795234, 0.004803621663, 0.5436149295, 0.3728649763, 0.02019377811, -0.04343718622

$ python3 fromTFRecords_InitFieldY_170709.py  | head
[-0.23620997] [-1.6534698] [-5.90524912] [-0.01643909] [ 0.00506505] [ 0.53640616] [ 0.29324207] [ 0.03475441] [-0.07514133]
[ 0.23620997] [-1.6534698] [-5.90524912] [ 0.01643909] [-0.00506505] [ 0.53640616] [ 0.29324207] [ 0.03475441] [-0.07514133]
[-1.18104982] [-1.18104982] [-5.90524912] [-0.06216653] [ 0.02425352] [ 0.61625606] [ 0.27670044] [ 0.02440614] [-0.05486268]
[-0.70862991] [-1.18104982] [-5.90524912] [-0.07402581] [ 0.00639074] [ 0.51409435] [ 0.30612269] [ 0.02715302] [-0.06470039]
[-0.23620997] [-1.18104982] [-5.90524912] [-0.03451369] [-0.00239405] [ 0.52134091] [ 0.35712481] [ 0.03088294] [-0.06684458]
[ 0.23620997] [-1.18104982] [-5.90524912] [ 0.03451369] [ 0.00239405] [ 0.52134091] [ 0.35712481] [ 0.03088294] [-0.06684458]
[ 0.70862991] [-1.18104982] [-5.90524912] [ 0.07402581] [-0.00639074] [ 0.51409435] [ 0.30612269] [ 0.02715302] [-0.06470039]
[ 1.18104982] [-1.18104982] [-5.90524912] [ 0.06216653] [-0.02425352] [ 0.61625606] [ 0.27670044] [ 0.02440614] [-0.05486268]
[-1.18104982] [-0.70862991] [-5.90524912] [-0.06618973] [ 0.00543136] [ 0.67104828] [ 0.33572644] [ 0.01676365] [-0.03849823]
[-0.70862991] [-0.70862991] [-5.90524912] [-0.04588795] [ 0.00480362] [ 0.54361492] [ 0.37286496] [ 0.02019378] [-0.04343719]
Traceback (most recent call last):
  File "fromTFRecords_InitFieldY_170709.py", line 46, in <module>
    print(*list_pos, *list_e)
BrokenPipeError: [Errno 32] Broken pipe

うまくいっているようだ。

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