Windows port (unsuccessful as the external part does not running on Windows due to multiple reasons)HEADmaster

6 files changed, 310 insertions, 0 deletions

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 <limits.h>
+
+// For Visual Studio 6 in C++ mode and for many Visual Studio versions when
+// compiling for ARM we should wrap <wchar.h> 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 <wchar.h>
+#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 <wchar.h>
+#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