From 493ce5439af6a008ff170f4bca0ee7031e32231b Mon Sep 17 00:00:00 2001 From: "Suren A. Chilingaryan" Date: Thu, 13 Dec 2018 06:13:04 +0100 Subject: Windows port (unsuccessful as the external part does not running on Windows due to multiple reasons) --- docker-compose.win.yml | 23 +++++ external/install.bat | 11 +++ external/run.bat | 20 ++++ external/win/stdint.h | 247 +++++++++++++++++++++++++++++++++++++++++++++++++ win/prepare.bat | 7 ++ win/run.bat | 2 + 6 files changed, 310 insertions(+) create mode 100644 docker-compose.win.yml create mode 100644 external/install.bat create mode 100644 external/run.bat create mode 100644 external/win/stdint.h create mode 100644 win/prepare.bat create mode 100644 win/run.bat diff --git a/docker-compose.win.yml b/docker-compose.win.yml new file mode 100644 index 0000000..f5b673c --- /dev/null +++ b/docker-compose.win.yml @@ -0,0 +1,23 @@ +version: '2.4' + +services: + redis: + ports: + - 127.0.0.1:6379:6379 + mysql: + ports: + - 127.0.0.1:3306:3306 + biomedisa: + runtime: "" + build: + context: ./biomedisa + args: + TENSORFLOW_DEVICE: cpu + TENSORFLOW_APPEND: + volumes: + - ${BIOMEDISA_HOST_SRC_PATH}:/biomedisa + - ${BIOMEDISA_HOST_SRC_PATH}:${BIOMEDISA_HOST_SRC_PATH} + django: + volumes: + - ${BIOMEDISA_HOST_SRC_PATH}:/biomedisa + - ${BIOMEDISA_HOST_SRC_PATH}:${BIOMEDISA_HOST_SRC_PATH} diff --git a/external/install.bat b/external/install.bat new file mode 100644 index 0000000..7784b87 --- /dev/null +++ b/external/install.bat @@ -0,0 +1,11 @@ +python -m pip install --user --upgrade pip +pip install --user "pycuda-2018.1+cuda92148-cp27-cp27m-win_amd64.whl" +pip install --user MySQL_python-1.2.5-cp27-none-win_amd64.whl + +pip --no-cache-dir install --user setuptools==39.1.0 numpy==1.14.5 tifffile==0.14.0 SimpleParse==2.1.1 redis==2.10.6 rq==0.12 +pip --no-cache-dir install --user weave scikit-image opencv-python h5py pydicom Pillow django mpi4py pycuda + +REM Needs fixing, doesn't work with recent versions of RQ +REM pip install --user git+https://github.com/michaelbrooks/rq-win.git#egg=rq-win + +COPY stdint.h "C:\Users\csa\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\include" diff --git a/external/run.bat b/external/run.bat new file mode 100644 index 0000000..47f5dd1 --- /dev/null +++ b/external/run.bat @@ -0,0 +1,20 @@ +REM No grep in batch, but Powershell supports it. We can convert script to powershell +REM path=$(cat ../.env | grep -oP 'BIOMEDISA_HOST_SRC_PATH=\K.*') + +SET BIOMEDISA_PATH=C:/Users/csa/biomedisa/ +SET PYTHON_PATH="C:\Users\csa\AppData\Roaming\Python\Scripts" + +SET PATH=%PATH%;%PYTHON_PATH%; +SET PYTHONPATH=%BIOMEDISA_PATH%;%PYTHONPATH% +SET DJANGO_SETTINGS_MODULE=biomedisa.settings +SET BIOMEDISA_SRC_PATH="%BIOMEDISA_PATH%" +SET MYSQL_HOST=127.0.0.1 +SET REDIS_HOST="localhost" + +REM RQ is not working on Windows due to absent (clone). RQ-win project doesn't work with current version of RQ (but probably easy to fix) +REM cd "%BIOMEDISA_PATH%" || exit -1 +REM %PYTHON_PATH%\rqworker -w rq_win.WindowsWorker -u http://localhost first_queue + +REM This fails since different paths are written to MySQL database from the containers.... +REM cd biomedisa_features/random_walk +REM python rw_main.py C:\Users\csa\biomedisa\media\images\tumor.tif C:\Users\csa\biomedisa\media\images\labels.tumor.tif diff --git a/external/win/stdint.h b/external/win/stdint.h new file mode 100644 index 0000000..d02608a --- /dev/null +++ b/external/win/stdint.h @@ -0,0 +1,247 @@ +// ISO C9x compliant stdint.h for Microsoft Visual Studio +// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124 +// +// Copyright (c) 2006-2008 Alexander Chemeris +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// 1. Redistributions of source code must retain the above copyright notice, +// this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. The name of the author may be used to endorse or promote products +// derived from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED +// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +/////////////////////////////////////////////////////////////////////////////// + +#ifndef _MSC_VER // [ +#error "Use this header only with Microsoft Visual C++ compilers!" +#endif // _MSC_VER ] + +#ifndef _MSC_STDINT_H_ // [ +#define _MSC_STDINT_H_ + +#if _MSC_VER > 1000 +#pragma once +#endif + +#include + +// For Visual Studio 6 in C++ mode and for many Visual Studio versions when +// compiling for ARM we should wrap include with 'extern "C++" {}' +// or compiler give many errors like this: +// error C2733: second C linkage of overloaded function 'wmemchr' not allowed +#ifdef __cplusplus +extern "C" { +#endif +# include +#ifdef __cplusplus +} +#endif + +// Define _W64 macros to mark types changing their size, like intptr_t. +#ifndef _W64 +# if !defined(__midl) && (defined(_X86_) || defined(_M_IX86)) && _MSC_VER >= 1300 +# define _W64 __w64 +# else +# define _W64 +# endif +#endif + + +// 7.18.1 Integer types + +// 7.18.1.1 Exact-width integer types + +// Visual Studio 6 and Embedded Visual C++ 4 doesn't +// realize that, e.g. char has the same size as __int8 +// so we give up on __intX for them. +#if (_MSC_VER < 1300) + typedef signed char int8_t; + typedef signed short int16_t; + typedef signed int int32_t; + typedef unsigned char uint8_t; + typedef unsigned short uint16_t; + typedef unsigned int uint32_t; +#else + typedef signed __int8 int8_t; + typedef signed __int16 int16_t; + typedef signed __int32 int32_t; + typedef unsigned __int8 uint8_t; + typedef unsigned __int16 uint16_t; + typedef unsigned __int32 uint32_t; +#endif +typedef signed __int64 int64_t; +typedef unsigned __int64 uint64_t; + + +// 7.18.1.2 Minimum-width integer types +typedef int8_t int_least8_t; +typedef int16_t int_least16_t; +typedef int32_t int_least32_t; +typedef int64_t int_least64_t; +typedef uint8_t uint_least8_t; +typedef uint16_t uint_least16_t; +typedef uint32_t uint_least32_t; +typedef uint64_t uint_least64_t; + +// 7.18.1.3 Fastest minimum-width integer types +typedef int8_t int_fast8_t; +typedef int16_t int_fast16_t; +typedef int32_t int_fast32_t; +typedef int64_t int_fast64_t; +typedef uint8_t uint_fast8_t; +typedef uint16_t uint_fast16_t; +typedef uint32_t uint_fast32_t; +typedef uint64_t uint_fast64_t; + +// 7.18.1.4 Integer types capable of holding object pointers +#ifdef _WIN64 // [ + typedef signed __int64 intptr_t; + typedef unsigned __int64 uintptr_t; +#else // _WIN64 ][ + typedef _W64 signed int intptr_t; + typedef _W64 unsigned int uintptr_t; +#endif // _WIN64 ] + +// 7.18.1.5 Greatest-width integer types +typedef int64_t intmax_t; +typedef uint64_t uintmax_t; + + +// 7.18.2 Limits of specified-width integer types + +#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259 + +// 7.18.2.1 Limits of exact-width integer types +#define INT8_MIN ((int8_t)_I8_MIN) +#define INT8_MAX _I8_MAX +#define INT16_MIN ((int16_t)_I16_MIN) +#define INT16_MAX _I16_MAX +#define INT32_MIN ((int32_t)_I32_MIN) +#define INT32_MAX _I32_MAX +#define INT64_MIN ((int64_t)_I64_MIN) +#define INT64_MAX _I64_MAX +#define UINT8_MAX _UI8_MAX +#define UINT16_MAX _UI16_MAX +#define UINT32_MAX _UI32_MAX +#define UINT64_MAX _UI64_MAX + +// 7.18.2.2 Limits of minimum-width integer types +#define INT_LEAST8_MIN INT8_MIN +#define INT_LEAST8_MAX INT8_MAX +#define INT_LEAST16_MIN INT16_MIN +#define INT_LEAST16_MAX INT16_MAX +#define INT_LEAST32_MIN INT32_MIN +#define INT_LEAST32_MAX INT32_MAX +#define INT_LEAST64_MIN INT64_MIN +#define INT_LEAST64_MAX INT64_MAX +#define UINT_LEAST8_MAX UINT8_MAX +#define UINT_LEAST16_MAX UINT16_MAX +#define UINT_LEAST32_MAX UINT32_MAX +#define UINT_LEAST64_MAX UINT64_MAX + +// 7.18.2.3 Limits of fastest minimum-width integer types +#define INT_FAST8_MIN INT8_MIN +#define INT_FAST8_MAX INT8_MAX +#define INT_FAST16_MIN INT16_MIN +#define INT_FAST16_MAX INT16_MAX +#define INT_FAST32_MIN INT32_MIN +#define INT_FAST32_MAX INT32_MAX +#define INT_FAST64_MIN INT64_MIN +#define INT_FAST64_MAX INT64_MAX +#define UINT_FAST8_MAX UINT8_MAX +#define UINT_FAST16_MAX UINT16_MAX +#define UINT_FAST32_MAX UINT32_MAX +#define UINT_FAST64_MAX UINT64_MAX + +// 7.18.2.4 Limits of integer types capable of holding object pointers +#ifdef _WIN64 // [ +# define INTPTR_MIN INT64_MIN +# define INTPTR_MAX INT64_MAX +# define UINTPTR_MAX UINT64_MAX +#else // _WIN64 ][ +# define INTPTR_MIN INT32_MIN +# define INTPTR_MAX INT32_MAX +# define UINTPTR_MAX UINT32_MAX +#endif // _WIN64 ] + +// 7.18.2.5 Limits of greatest-width integer types +#define INTMAX_MIN INT64_MIN +#define INTMAX_MAX INT64_MAX +#define UINTMAX_MAX UINT64_MAX + +// 7.18.3 Limits of other integer types + +#ifdef _WIN64 // [ +# define PTRDIFF_MIN _I64_MIN +# define PTRDIFF_MAX _I64_MAX +#else // _WIN64 ][ +# define PTRDIFF_MIN _I32_MIN +# define PTRDIFF_MAX _I32_MAX +#endif // _WIN64 ] + +#define SIG_ATOMIC_MIN INT_MIN +#define SIG_ATOMIC_MAX INT_MAX + +#ifndef SIZE_MAX // [ +# ifdef _WIN64 // [ +# define SIZE_MAX _UI64_MAX +# else // _WIN64 ][ +# define SIZE_MAX _UI32_MAX +# endif // _WIN64 ] +#endif // SIZE_MAX ] + +// WCHAR_MIN and WCHAR_MAX are also defined in +#ifndef WCHAR_MIN // [ +# define WCHAR_MIN 0 +#endif // WCHAR_MIN ] +#ifndef WCHAR_MAX // [ +# define WCHAR_MAX _UI16_MAX +#endif // WCHAR_MAX ] + +#define WINT_MIN 0 +#define WINT_MAX _UI16_MAX + +#endif // __STDC_LIMIT_MACROS ] + + +// 7.18.4 Limits of other integer types + +#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260 + +// 7.18.4.1 Macros for minimum-width integer constants + +#define INT8_C(val) val##i8 +#define INT16_C(val) val##i16 +#define INT32_C(val) val##i32 +#define INT64_C(val) val##i64 + +#define UINT8_C(val) val##ui8 +#define UINT16_C(val) val##ui16 +#define UINT32_C(val) val##ui32 +#define UINT64_C(val) val##ui64 + +// 7.18.4.2 Macros for greatest-width integer constants +#define INTMAX_C INT64_C +#define UINTMAX_C UINT64_C + +#endif // __STDC_CONSTANT_MACROS ] + + +#endif // _MSC_STDINT_H_ ] diff --git a/win/prepare.bat b/win/prepare.bat new file mode 100644 index 0000000..a4000b9 --- /dev/null +++ b/win/prepare.bat @@ -0,0 +1,7 @@ +REM Enable Shared Drivers in Docker Configuration +REM Local driver does not work on windows, volumes should be specified inside services +REM The path C:\Users\... should look like: +REM BIOMEDISA_HOST_SRC_PATH=/C/Users/csa/biomedisa +cd .. +docker-compose -p biomedisa -f docker-compose.yml -f docker-compose.win.yml build +docker-compose -p biomedisa -f docker-compose.yml -f docker-compose.win.yml run --rm django /run-bootstrap.sh diff --git a/win/run.bat b/win/run.bat new file mode 100644 index 0000000..60a3b28 --- /dev/null +++ b/win/run.bat @@ -0,0 +1,2 @@ +cd .. +docker-compose -p biomedisa -f docker-compose.yml -f docker-compose.cpu.yml up -- cgit v1.2.1