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JoyboyWangJoyboyWang
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‎graphBuild/run.py‎

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#!/usr/bin/env python3
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# encoding = utf-8
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import os
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import sys
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import numpy as np
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from sklearn.neighbors import KDTree
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import shutil
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import random
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import json
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import time
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dirname = os.path.dirname(__file__)
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sys.path.append(os.path.join(dirname, ".."))
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from thesne.sne_config import SNEConfig
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sys.path.append(os.path.join(dirname, "../dataGen/"))
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import dg_utils
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# read point sets and configuration from file.
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def ReadPointSets(filepath, norm_data):
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_points = []
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_labels = []
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_dim = 0
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_pts_size = 0
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_flag = False
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with open(filepath, 'r', encoding='utf-8') as f:
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lines = f.readlines()
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_pts_size = len(lines)
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for line in lines:
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items = line.split()
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_point = []
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for item in items[:-1]:
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_point.append(float(item))
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if not _flag:
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_dim += 1
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_flag = True
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_points.append(_point)
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# label
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_labels.append(items[-1])
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p = np.array(_points)
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if norm_data == True:
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min_p = np.min(p)
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max_p = np.max(p)
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p = (p - min_p) / (max_p - min_p)
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return p, np.array(_labels), _pts_size, _dim
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def sav_graph(filepath, points, labels, k_closest_count):
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tree = KDTree(points)
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dists, indices = tree.query(points,
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k=k_closest_count + 1) # 一口气对所有points构建knn
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with open(filepath, 'w') as file: # 打开新文件fm_{0}.txt
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# first write in the number of nodes
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file.write(str(points.shape[0]) + "\n") # 写入当前点
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for i in range(points.shape[0]):
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file.write(str(i) + "\t") # 写入当前点
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count = 0
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for t in range(indices[i].shape[0]):
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if indices[i][t] == i: # 是否包含自身
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continue
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if count == k_closest_count: # 只写入Indices中前k-1个点
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break
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# write incient point and corresponding distance
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file.write(str(indices[i][t]) + "\t" + str(dists[i][t]) + "\t")
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count += 1
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file.write('\n')
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if __name__ == '__main__':
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argv = sys.argv
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assert (len(argv) == 2)
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config_path = argv[1] #"../../config/config_0.json"
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start = time.perf_counter()
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with open(config_path, 'r') as f:
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config_json = json.loads(f.read())
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config = SNEConfig(config_json)
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input_dir = config.input_dir
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graph_path = config.graph_dir
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dg_utils.ClearDir(graph_path)
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k_closest_count = config.k_closest_count #min(3*perplexity, pts_size) # K近邻的个数+1（虽然是K=4，但由于包含自身，实际为K-1邻近）
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raw_files = []
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for filename in os.listdir(input_dir):
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raw_file = os.path.join(input_dir, filename)
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(file, ext) = os.path.splitext(raw_file)
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if ext == ".txt":
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raw_files.append(raw_file)
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# size_dims = []
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for filepath in raw_files:
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data_id = dg_utils.GetGraphIDFromPath(filepath)
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print("当前处理: " + str(data_id) + " Graph")
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cur_points, labels, pts_size, dim = ReadPointSets(filepath,
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norm_data=True)
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print((pts_size, dim))
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sav_graph(os.path.join(graph_path, "g_{}.txt".format(data_id)),
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cur_points, labels, k_closest_count) # 打开新文件fm_{1}.txt
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elapsed = (time.perf_counter() - start)
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print("Total time for building knn graph:", elapsed)

‎graphSim/.gitignore‎

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# This file is used to ignore files which are generated
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# ----------------------------------------------------------------------------
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*~
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*.autosave
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*.a
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*.core
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*.moc
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*.o
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*.obj
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*.orig
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*.rej
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*.so
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*.so.*
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*_pch.h.cpp
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*_resource.rc
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*.qm
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.#*
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*.*#
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core
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!core/
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tags
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.DS_Store
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.directory
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*.debug
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Makefile*
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*.prl
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*.app
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moc_*.cpp
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ui_*.h
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qrc_*.cpp
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Thumbs.db
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*.res
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*.rc
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/.qmake.cache
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/.qmake.stash
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# qtcreator generated files
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*.pro.user*
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# xemacs temporary files
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*.flc
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# Vim temporary files
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.*.swp
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# Visual Studio generated files
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*.ib_pdb_index
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*.idb
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*.ilk
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*.pdb
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*.sln
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*.suo
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*.vcproj
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*vcproj.*.*.user
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*.ncb
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*.sdf
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*.opensdf
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*.vcxproj
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*vcxproj.*
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# MinGW generated files
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*.Debug
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*.Release
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# Python byte code
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*.pyc
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# Binaries
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# --------
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*.dll
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*.exe
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‎graphSim/build-graphSim-Desktop_Qt_5_13_1_clang_64bit-Debug/.qmake.stash‎

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QMAKE_MAC_SDK.macosx.Path = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk
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QMAKE_MAC_SDK.macosx.PlatformPath = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform
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QMAKE_MAC_SDK.macosx.SDKVersion = 11.1
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_CC = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_CXX = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_FIX_RPATH = \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool \
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-id
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_AR = \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar \
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cq
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_RANLIB = \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib \
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-s
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_LINK = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_LINK_SHLIB = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_ACTOOL = /Applications/Xcode.app/Contents/Developer/usr/bin/actool
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_LINK_C = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
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QMAKE_MAC_SDK.macx-clang.macosx.QMAKE_LINK_C_SHLIB = /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
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QMAKE_CXX.QT_COMPILER_STDCXX = 199711L
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QMAKE_CXX.QMAKE_APPLE_CC = 6000
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QMAKE_CXX.QMAKE_APPLE_CLANG_MAJOR_VERSION = 12
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QMAKE_CXX.QMAKE_APPLE_CLANG_MINOR_VERSION = 0
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QMAKE_CXX.QMAKE_APPLE_CLANG_PATCH_VERSION = 0
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QMAKE_CXX.QMAKE_GCC_MAJOR_VERSION = 4
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QMAKE_CXX.QMAKE_GCC_MINOR_VERSION = 2
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QMAKE_CXX.QMAKE_GCC_PATCH_VERSION = 1
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QMAKE_CXX.COMPILER_MACROS = \
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QT_COMPILER_STDCXX \
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QMAKE_APPLE_CC \
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QMAKE_APPLE_CLANG_MAJOR_VERSION \
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QMAKE_APPLE_CLANG_MINOR_VERSION \
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QMAKE_APPLE_CLANG_PATCH_VERSION \
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QMAKE_GCC_MAJOR_VERSION \
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QMAKE_GCC_MINOR_VERSION \
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QMAKE_GCC_PATCH_VERSION
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QMAKE_CXX.INCDIRS = \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1 \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include \
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/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/include \
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
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QMAKE_CXX.LIBDIRS = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk/usr/lib
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QMAKE_XCODE_DEVELOPER_PATH = /Applications/Xcode.app/Contents/Developer
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QMAKE_XCODE_VERSION = 12.3

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