Every time I run the airway segmentation test the test fails because of an access violation. Below is the last part of the output before it crashes. Looks like it gets up to the point where it's checking the local convention for the decimal point and then the surface extraction?

My computer has 2 NVIDIA cards: a Tesla C2075 and a Quaddrro K2200.

For instance, when executing the viewer, I get the following message on the console:

INFO: Creating new QApp
INFO: Loaded configuration file: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/build/fast_configuration.txt
INFO: Test data path: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/data//
INFO: Kernel source path: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/source/FAST/
INFO: Kernel binary path: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/build/kernel_binaries/
INFO: Documentation path: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/doc/
INFO: Pipeline path: /Users/norman/workspace/dev/misc/fast-medimg/fast-git/pipelines/
INFO: Creating new GL context for computation thread
INFO: QApp already exists..
INFO: Device manager initialize..
INFO: Initial GL context: 0x7fb83b84dc00
INFO: Initial GL share group: 0x7fb83cf00000
INFO: Found 1 OpenCL platforms.
INFO: 1 platforms selected for inspection.
INFO: Platform 0: Apple
INFO: This platform has 0 available devices in total
INFO: Looking for GPU devices only.
INFO: 1 selected.
INFO: Inspecting device 0 with the name Iris Pro
INFO: Initial GL context: 0x7fb83b84dc00
INFO: Initial GL share group: 0x7fb83cf00000
INFO: Device has OpenGL interop capability
INFO: The device was accepted.
INFO: A device-platform mismatch was detected.
INFO: The platform Apple was selected as the best platform.
INFO: A total of 1 devices were selected for the context from this platform:
/Users/norman/workspace/dev/misc/fast-medimg/fast-git/pipelines/cardiac_view_classification.fpl
/Users/norman/workspace/dev/misc/fast-medimg/fast-git/pipelines/dnn_left_ventricle_segmentation.fpl
/Users/norman/workspace/dev/misc/fast-medimg/fast-git/pipelines/image_renderer.fpl
asd
Finished viewer setup
[1]    59485 segmentation fault  ./bin/viewer

The crash report looks the following. Any ideas? All apps seem to crash for fast::View::initializeGL()

Process:               viewer [59485]
Path:                  /Users/USER/*/viewer
Identifier:            viewer
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        zsh [59397]
Responsible:           iTerm2 [364]
User ID:               501

Date/Time:             2017-11-08 16:45:25.050 +0100
OS Version:            Mac OS X 10.11.6 (15G1510)
Report Version:        11
Anonymous UUID:        D1CF50F7-2886-8A51-8DAD-F32E4E57B5F6

Sleep/Wake UUID:       57489E58-DB26-4643-A2A7-1AA259E59714

Time Awake Since Boot: 520000 seconds
Time Since Wake:       6100 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000090

VM Regions Near 0x90:
--> 
    __TEXT                 0000000107e4a000-0000000107e5a000 [   64K] r-x/rwx SM=COW  /Users/USER/*

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libFAST.dylib                 	0x0000000107fc6450 fast::View::initializeGL() + 688
1   org.qt-project.QtOpenGL       	0x000000010811b1c6 QGLWidget::glInit() + 54
2   org.qt-project.QtOpenGL       	0x000000010811add5 QGLWidget::resizeEvent(QResizeEvent*) + 85
3   org.qt-project.QtWidgets      	0x00000001081caec1 QWidget::event(QEvent*) + 2193
4   org.qt-project.QtWidgets      	0x000000010818aedd QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
5   org.qt-project.QtWidgets      	0x000000010818d822 QApplication::notify(QObject*, QEvent*) + 5906
6   libFAST.dylib                 	0x0000000107fc0dc5 fast::FASTApplication::notify(QObject*, QEvent*) + 21
7   org.qt-project.QtCore         	0x0000000108ff2aa4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
8   org.qt-project.QtWidgets      	0x00000001081c39a3 QWidgetPrivate::sendPendingMoveAndResizeEvents(bool, bool) + 275
9   org.qt-project.QtWidgets      	0x00000001081c964a QWidgetPrivate::show_helper() + 42
10  org.qt-project.QtWidgets      	0x00000001081ca3bc QWidget::setVisible(bool) + 956
11  org.qt-project.QtWidgets      	0x00000001081c99b3 QWidgetPrivate::showChildren(bool) + 275
12  org.qt-project.QtWidgets      	0x00000001081c966c QWidgetPrivate::show_helper() + 76
13  org.qt-project.QtWidgets      	0x00000001081ca3bc QWidget::setVisible(bool) + 956
14  libFAST.dylib                 	0x0000000107fc0019 fast::Window::start() + 169
15  viewer                        	0x0000000107e4e199 main + 41
16  libdyld.dylib                 	0x00007fff9454a5ad start + 1

Thread 1:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 2:: Dispatch queue: com.apple.libdispatch-manager
0   libsystem_kernel.dylib        	0x00007fff95e87efa kevent_qos + 10
1   libdispatch.dylib             	0x00007fff8bbeb165 _dispatch_mgr_invoke + 216
2   libdispatch.dylib             	0x00007fff8bbeadcd _dispatch_mgr_thread + 52

Thread 3:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 4:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 5:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 6:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 7:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 8:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 9:
0   libsystem_kernel.dylib        	0x00007fff95e875e2 __workq_kernreturn + 10
1   libsystem_pthread.dylib       	0x00007fff97332578 _pthread_wqthread + 1283
2   libsystem_pthread.dylib       	0x00007fff97330341 start_wqthread + 13

Thread 10:

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x00007fb83b853508  rcx: 0x0000000000000002  rdx: 0x0000000000000000
  rdi: 0x0000000000000001  rsi: 0x00007fb83b853508  rbp: 0x00007fff57db4a40  rsp: 0x00007fff57db4130
   r8: 0x0000000000000006   r9: 0x00000000ffffff00  r10: 0x0000000108d2a401  r11: 0x0000000108b9e750
  r12: 0x00007fb83b853200  r13: 0x9c00cd0040e7b4e7  r14: 0x00007fb83ad3eae0  r15: 0x00007fb83afce410
  rip: 0x0000000107fc6450  rfl: 0x0000000000010206  cr2: 0x0000000000000090
  
Logical CPU:     0
Error Code:      0x00000004
Trap Number:     14


Binary Images:
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       0x10ee0a000 -        0x10ee0afe7 +cl_kernels (???) <A83289D6-464A-4B57-AA52-F947E8C216AB> cl_kernels
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    0x7fff9a692000 -     0x7fff9b2bbff7  com.apple.AppKit (6.9 - 1404.47) <F3411F6E-DD87-34D0-8C68-C69B2205E41D> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
    0x7fff9b491000 -     0x7fff9b4bafff  libsystem_info.dylib (477.50.4) <FAA9226D-64DE-3769-A6D8-6CABA4B7FF4D> /usr/lib/system/libsystem_info.dylib
    0x7fff9b4bb000 -     0x7fff9b4c0ff3  libunwind.dylib (35.3) <F6EB48E5-4D12-359A-AB54-C937FBBE9043> /usr/lib/system/libunwind.dylib
    0x7fff9b4c1000 -     0x7fff9b4ccfff  com.apple.CrashReporterSupport (10.11 - 718) <05892B57-F2CD-3C84-B984-0417F6B361DB> /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Versions/A/CrashReporterSupport
    0x7fff9b54b000 -     0x7fff9b55bfff  libbsm.0.dylib (34) <7E14504C-A8B0-3574-B6EB-5D5FABC72926> /usr/lib/libbsm.0.dylib
    0x7fff9b55c000 -     0x7fff9b561fff  com.apple.TCC (1.0 - 1) <F5EEB2D3-9517-3975-97BE-22CB8E11B8A3> /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
    0x7fff9b562000 -     0x7fff9b56bfff  com.apple.icloud.FindMyDevice (1.0 - 1) <B9C741F2-6FAC-3BA7-B6E0-9A910C6E8D4E> /System/Library/PrivateFrameworks/FindMyDevice.framework/Versions/A/FindMyDevice
    0x7fff9b605000 -     0x7fff9b670ff7  com.apple.framework.CoreWLAN (11.0 - 1101.20) <3B35C543-7FCE-333F-80C1-432FA41DDCDE> /System/Library/Frameworks/CoreWLAN.framework/Versions/A/CoreWLAN
    0x7fff9b693000 -     0x7fff9b707ff7  com.apple.Heimdal (4.0 - 2.0) <5D365381-8B5E-3259-8867-FC4A7D307BDE> /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
    0x7fff9b771000 -     0x7fff9ba56ffb  com.apple.CoreServices.CarbonCore (1136.2 - 1136.2) <2DBAFC9A-6CD6-351D-B1F4-87D81AA6D640> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
    0x7fff9bb0e000 -     0x7fff9bb9bdd7  com.apple.AppleJPEG (1.0 - 1) <BF7EDBDB-A52D-37F7-BDE4-EAD49310D7A9> /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
    0x7fff9bb9c000 -     0x7fff9bbaefff  libsasl2.2.dylib (209) <11C7D200-0CA5-30F4-A19A-178CA81D48FE> /usr/lib/libsasl2.2.dylib
    0x7fff9bbc0000 -     0x7fff9bbc2ff7  com.apple.securityhi (9.0 - 55006) <AC151C58-A7AD-3ECF-B15D-5E09FF94FC23> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
    0x7fff9bbc3000 -     0x7fff9bbc5fff  libCVMSPluginSupport.dylib (12.1) <20BA72AF-C7C5-3551-8F59-E1AED5FC69F0> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
    0x7fff9bbc6000 -     0x7fff9bbc8fff  libCGXType.A.dylib (970) <A931200A-B248-39EF-8A8B-311D881BE372> /System/Library/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.dylib
    0x7fff9bbc9000 -     0x7fff9bbcafff  com.apple.TrustEvaluationAgent (2.0 - 25) <0239494E-FEFE-39BC-9FC7-E251BA5128F1> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
    0x7fff9bc2f000 -     0x7fff9bc31fff  com.apple.loginsupport (1.0 - 1) <9B2F5F9B-ED38-313F-B798-D2B667BCD6B5> /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
    0x7fff9bd96000 -     0x7fff9bdc7fff  com.apple.GSS (4.0 - 2.0) <B490333A-3B3E-397A-AD75-68846E9A9140> /System/Library/Frameworks/GSS.framework/Versions/A/GSS
    0x7fff9be78000 -     0x7fff9c1ccfff  com.apple.Foundation (6.9 - 1259.22) <C83D734C-6885-3549-80FE-70DEB04318D5> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
    0x7fff9c203000 -     0x7fff9c261fff  com.apple.CoreServices.OSServices (728.13 - 728.13) <477EA3F9-D13E-3D83-ABAD-4DC7DB134CF0> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
    0x7fff9c262000 -     0x7fff9c65efff  libLAPACK.dylib (1162.2) <987E42B0-5108-3065-87F0-9DF7616A8A06> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
    0x7fff9c67c000 -     0x7fff9c762ff7  libcrypto.0.9.8.dylib (59.60.1) <D68067AD-D1E0-3196-9796-51BE9B969C8E> /usr/lib/libcrypto.0.9.8.dylib
    0x7fff9c933000 -     0x7fff9c935ffb  libutil.dylib (43) <4C9BFE8B-563B-3EEA-A323-8F4F14E0A46C> /usr/lib/libutil.dylib
    0x7fff9c93c000 -     0x7fff9caa3fff  libBLAS.dylib (1162.2) <A1398FE0-39D2-33EA-9A0F-B2644EEA29A0> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    0x7fff9caa4000 -     0x7fff9cc30ff7  libGLProgrammability.dylib (12.1) <6D4C193C-5F7B-3E82-81D9-D14D25BBD962> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
    0x7fff9cd6b000 -     0x7fff9cd8ffff  com.apple.MultitouchSupport.framework (304.12 - 304.12) <598A8689-E97E-3C8D-AACD-8A0EB1956CA6> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
    0x7fff9cd90000 -     0x7fff9cd95ff7  libheimdal-asn1.dylib (453.40.10) <981DE40B-FA16-36F7-BE92-8C8A115D6CD9> /usr/lib/libheimdal-asn1.dylib
    0x7fff9cdec000 -     0x7fff9cefaff3  com.apple.desktopservices (1.10.3 - 1.10.3) <3A6906D4-C0B8-30D1-B589-0466E5E42B69> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
    0x7fff9d039000 -     0x7fff9d10fffb  com.apple.DiskImagesFramework (10.11.4 - 417.4) <FB30D069-648F-3FB2-AA55-FC603606C49E> /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
    0x7fff9d161000 -     0x7fff9d1d8feb  libcorecrypto.dylib (335.50.1) <B5C05FD7-A540-345A-87BF-8E41848A3C17> /usr/lib/system/libcorecrypto.dylib
    0x7fff9d1d9000 -     0x7fff9d247ff7  com.apple.ApplicationServices.ATS (377 - 394.4) <CB64C2B7-828A-3C4C-8F3C-72B78630CD94> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
    0x7fff9d940000 -     0x7fff9d947ff7  libcompiler_rt.dylib (62) <A13ECF69-F59F-38AE-8609-7B731450FBCD> /usr/lib/system/libcompiler_rt.dylib
    0x7fff9d948000 -     0x7fff9d950fff  com.apple.CoreServices.FSEvents (1223.10.1 - 1223.10.1) <7F5B7A23-BC1D-3FA9-A9B8-D534F1E1979A> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
    0x7fff9d951000 -     0x7fff9d952fff  libsystem_blocks.dylib (65) <1244D9D5-F6AA-35BB-B307-86851C24B8E5> /usr/lib/system/libsystem_blocks.dylib
    0x7fff9d953000 -     0x7fff9d97cfff  com.apple.ProtectedCloudStorage (1.0 - 1) <7436B2B3-943A-3500-B099-80F133B3E002> /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
    0x7fff9d9ae000 -     0x7fff9d9f3ff7  com.apple.coreservices.SharedFileList (24.4 - 24.5) <1D2AD77B-778F-3253-A295-3D0A32A8121C> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
    0x7fff9dbdb000 -     0x7fff9dbdffff  libGIF.dylib (1461) <161A59BF-6311-3542-A89F-E96AFC76C536> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
    0x7fff9dbe7000 -     0x7fff9dc2cff3  libFontRegistry.dylib (155.2) <A70DD497-35F3-34DA-9C19-F4B90080E961> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
    0x7fff9dc2d000 -     0x7fff9dc80ff7  libc++.1.dylib (120.1) <8FC3D139-8055-3498-9AC5-6467CB7F4D14> /usr/lib/libc++.1.dylib
    0x7fff9dc81000 -     0x7fff9dc83ff7  libquarantine.dylib (80) <B3B7B630-9012-3DA3-9458-5C009625E606> /usr/lib/system/libquarantine.dylib
    0x7fff9dc84000 -     0x7fff9dc93ffb  com.apple.LangAnalysis (1.7.0 - 1.7.0) <18D21123-A3E7-3851-974A-08E5D4540475> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
    0x7fff9ddb1000 -     0x7fff9ddb1fff  com.apple.ApplicationServices (48 - 48) <ADD57D3A-142F-3EF5-BFD8-EACD82164884> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
    0x7fff9ddb2000 -     0x7fff9dddbffb  libRIP.A.dylib (970) <BA17C96B-83CC-3835-8AFD-CB5A69D3D26F> /System/Library/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
    0x7fff9dddc000 -     0x7fff9de96fff  com.apple.DiscRecording (9.0.1 - 9010.4.3) <540853B2-B123-3560-8023-C92EE229051A> /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording
    0x7fff9de97000 -     0x7fff9de98ff3  com.apple.print.framework.Print (10.0 - 266) <3E85F70C-D7D4-34E1-B88A-C1F503F99CDA> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
    0x7fff9def3000 -     0x7fff9defcff3  libsystem_notify.dylib (150.40.1) <D48BDE34-0F7E-34CA-A0FF-C578E39987CC> /usr/lib/system/libsystem_notify.dylib
    0x7fff9defd000 -     0x7fff9dfecff7  libxml2.2.dylib (29.13) <1C510151-06AE-322B-A725-79C91EF79E1C> /usr/lib/libxml2.2.dylib
    0x7fff9e850000 -     0x7fff9ea71ff7  com.apple.CoreImage (11.4.0 - 366.4.20) <7721BA55-A10E-3425-8392-C5D7C510EAAB> /System/Library/Frameworks/CoreImage.framework/Versions/A/CoreImage
    0x7fff9eaf6000 -     0x7fff9eb18fff  com.apple.IconServices (68.1 - 68.1) <CDEEDBE6-F53B-3BA1-82D4-23BCA3DD8949> /System/Library/PrivateFrameworks/IconServices.framework/Versions/A/IconServices
    0x7fff9eb67000 -     0x7fff9eba1ff7  com.apple.DebugSymbols (132 - 132) <23A42C53-B941-3871-9EE2-4C87A46005B5> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
    0x7fff9ebbc000 -     0x7fff9ebc1ff7  libmacho.dylib (875.1) <318264FA-58F1-39D8-8285-1F6254EE410E> /usr/lib/system/libmacho.dylib
    0x7fff9ebc2000 -     0x7fff9ed68ff7  com.apple.audio.toolbox.AudioToolbox (1.13 - 1.13) <370E95BC-956C-3962-86CC-0A14CF6A0389> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
    0x7fff9eecd000 -     0x7fff9effaff3  com.apple.CoreText (352.0 - 494.13) <143887ED-1AB1-3C62-AC65-4F13E26B6D7C> /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
    0x7fff9effb000 -     0x7fff9f01ffff  libJPEG.dylib (1461) <97CF2E14-E83D-3C30-9678-26DD1A9467C2> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
    0x7fff9f020000 -     0x7fff9f07efff  com.apple.SystemConfiguration (1.14 - 1.14) <ACAEDA14-FAA0-3F14-B476-DE492A52D383> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
    0x7fff9f08c000 -     0x7fff9f09ffff  com.apple.CoreBluetooth (1.0 - 1) <E54CA9A2-A5C6-30C5-9D6E-8472DBA9371E> /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth
    0x7fff9f0a0000 -     0x7fff9f0efff7  com.apple.opencl (2.7.0 - 2.7.0) <DAEC71D4-E0E7-3E24-BB44-C977A798C575> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
    0x7fff9f150000 -     0x7fff9f5c6fff  com.apple.CoreFoundation (6.9 - 1259.11) <B8056BE3-151B-3003-91C9-6720CF04937B> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
    0x7fff9fa15000 -     0x7fff9fab9fff  com.apple.Bluetooth (4.4.6 - 4.4.6f1) <FFD72A25-3213-3857-9B4F-DD674F0078F0> /System/Library/Frameworks/IOBluetooth.framework/Versions/A/IOBluetooth
    0x7fff9faba000 -     0x7fff9fc38fff  com.apple.UIFoundation (1.0 - 436.1) <AABB5267-E7B7-3D75-B051-E665BDA8DEF4> /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
    0x7fff9fc8a000 -     0x7fff9fcdffff  com.apple.AE (701 - 701) <AD492742-F884-386B-A450-FAC281B9FFA4> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
    0x7fff9fce0000 -     0x7fffa0f29ff3  com.apple.CoreGraphics (1.600.0 - 960.7) <FFB90E5E-F8FA-326C-8EF2-F809F9A58830> /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
    0x7fffa0f66000 -     0x7fffa0f91ffb  libarchive.2.dylib (33.20.2.1.1) <BC764A1E-573A-3D95-A3CC-1758935ADC56> /usr/lib/libarchive.2.dylib
    0x7fffa1041000 -     0x7fffa1043fff  com.apple.EFILogin (2.0 - 2) <38150198-DD7F-3C73-BCAA-C74BB376393A> /System/Library/PrivateFrameworks/EFILogin.framework/Versions/A/EFILogin
    0x7fffa117b000 -     0x7fffa117cfff  liblangid.dylib (122) <9CC4F0D1-5C51-3B69-BC8F-EE3A51FD0822> /usr/lib/liblangid.dylib
    0x7fffa117d000 -     0x7fffa117dfff  com.apple.CoreServices (728.13 - 728.13) <CFE3EE73-A3F5-3824-9210-0790C07120F3> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
    0x7fffa117e000 -     0x7fffa11cffff  com.apple.audio.CoreAudio (4.3.0 - 4.3.0) <EA7D4F3B-062B-3C81-A98C-C89264D00D48> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
    0x7fffa11d0000 -     0x7fffa1277fff  com.apple.LanguageModeling (1.0 - 1) <58C18A47-BDE7-3CBE-81C0-797029D170A1> /System/Library/PrivateFrameworks/LanguageModeling.framework/Versions/A/LanguageModeling
    0x7fffa16bf000 -     0x7fffa16c8ff7  com.apple.CommonAuth (4.0 - 2.0) <4B8673E1-3697-3FE2-8D30-AC7AC5D4F8BF> /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
    0x7fffa16c9000 -     0x7fffa16e0ff7  libsystem_coretls.dylib (83.40.5) <C90DAE38-4082-381C-A185-2A6A8B677628> /usr/lib/system/libsystem_coretls.dylib
    0x7fffa16e4000 -     0x7fffa16f2fff  com.apple.opengl (12.1.0 - 12.1.0) <12EBDE6A-2F44-3429-8337-2BB36870BFD8> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
    0x7fffa1700000 -     0x7fffa173afff  com.apple.QD (3.12 - 302) <0FE53180-2895-3D14-A1E7-F82DE1D106E1> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
    0x7fffa1744000 -     0x7fffa1744fff  libmetal_timestamp.dylib (600.0.44.2) <DEEA1127-7A5D-3EF2-A4B2-AE125CBA5DB5> /System/Library/PrivateFrameworks/GPUCompiler.framework/libmetal_timestamp.dylib
    0x7fffa17b6000 -     0x7fffa17c1fff  libkxld.dylib (3248.60.11.5.3) <B6A73C46-FEF3-390A-A816-89F1D35B3D53> /usr/lib/system/libkxld.dylib
    0x7fffa17c2000 -     0x7fffa1828ff7  libsystem_network.dylib (583.50.1) <B52DAB73-92DC-3DA7-B9F4-B899D66445C1> /usr/lib/system/libsystem_network.dylib
    0x7fffa19be000 -     0x7fffa19e0ff7  com.apple.Sharing (442.13.6 - 442.13.6) <DDD2811C-6ECB-32F2-8EE1-69BF9657B4A8> /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
    0x7fffa19e7000 -     0x7fffa19ebfff  libcache.dylib (75) <9548AAE9-2AB7-3525-9ECE-A2A7C4688447> /usr/lib/system/libcache.dylib
    0x7fffa19ec000 -     0x7fffa19eefff  libsystem_coreservices.dylib (19.2) <1B3F5AFC-FFCD-3ECB-8B9A-5538366FB20D> /usr/lib/system/libsystem_coreservices.dylib
    0x7fffa19ef000 -     0x7fffa1a0eff7  com.apple.framework.Apple80211 (11.0 - 1121.34.2) <90477FAE-B835-3931-80FB-FDFF02B21D9D> /System/Library/PrivateFrameworks/Apple80211.framework/Versions/A/Apple80211
    0x7fffa1a13000 -     0x7fffa1a15ff7  libsystem_configuration.dylib (802.40.13) <3DEB7DF9-6804-37E1-BC83-0166882FF0FF> /usr/lib/system/libsystem_configuration.dylib
    0x7fffa1a9c000 -     0x7fffa1aa0fff  libpam.2.dylib (20) <CFCD19BD-87BC-3F2B-BB1C-4C23E8E55F1A> /usr/lib/libpam.2.dylib
    0x7fffa1b77000 -     0x7fffa1b88ff7  libsystem_trace.dylib (201.10.3) <E9311C03-9E61-3B13-AF3F-A64956FFF269> /usr/lib/system/libsystem_trace.dylib
    0x7fffa1b89000 -     0x7fffa1e7efff  com.apple.HIToolbox (2.1.1 - 807.2) <36413C45-36AF-34EF-9C0E-F18B31D1E565> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 1
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 20166361
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=253.2M resident=0K(0%) swapped_out_or_unallocated=253.2M(100%)
Writable regions: Total=188.0M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=188.0M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate.framework               128K        2 
Activity Tracing                  2048K        2 
CG backing stores                 1328K        5 
CG image                           296K        6 
CG shared images                   464K       13 
CoreAnimation                       40K        7 
CoreUI image data                  376K        4 
CoreUI image file                  192K        4 
Dispatch continuations            16.0M        2 
IOKit                             14.5M       21 
Kernel Alloc Once                    8K        3 
MALLOC                           124.0M       31 
MALLOC guard page                   32K        7 
OpenCL                               8K        2 
STACK GUARD                       56.0M       11 
Stack                             12.1M       11 
Stack (reserved)                   520K        2         reserved VM address space (unallocated)
Stack Guard                          4K        2 
VM_ALLOCATE                        304K        8 
__DATA                            18.8M      238 
__GLSLBUILTINS                    2588K        2 
__IMAGE                            528K        2 
__LINKEDIT                        98.5M       33 
__TEXT                           154.8M      241 
__UNICODE                          552K        2 
mapped file                      984.2M      123 
shared memory                     16.8M       13 
===========                     =======  ======= 
TOTAL                              1.5G      770 
TOTAL, minus reserved VM space     1.5G      770 

Model: MacBookPro11,4, BootROM MBP114.0172.B16, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.29f24
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453120
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453120
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x152), Broadcom BCM43xx 1.0 (7.21.95.175.1a6)
Bluetooth: Version 4.4.6f1 17910, 3 services, 27 devices, 1 incoming serial ports
Network Service: Thunderbolt Ethernet, Ethernet, en5
PCI Card: Apple 57762-A0, Ethernet Controller, [email protected],0,0
Serial ATA Device: APPLE SSD SM1024G, 1 TB
USB Device: USB 3.0 Bus
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1
Thunderbolt Device: Thunderbolt to Gigabit Ethernet Adapter, Apple Inc., 3, 5.5

In CMake, if you don't set the FAST_TEST_DATA_DIR, by default the data is downloaded to the source directory under data/.

By default, the configuration file doesn't have a data directory set because the FAST_TEST_DATA_DIR variable is empty:

# from CMakeList.txt, line 170
# If test data dir has been set by user, write it to config file
if(NOT FAST_TEST_DATA_DIR STREQUAL "")
    # Remove any existing "
    string(REPLACE "\"" "" FAST_TEST_DATA_DIR ${FAST_TEST_DATA_DIR})
    message("-- FAST test data directory set to: \"${FAST_TEST_DATA_DIR}\"")
    set(CONFIG_TEST_DATA_PATH "TestDataPath = ${FAST_TEST_DATA_DIR}/")
endif()

When reading the configuration file during the tests, the data path defaults to a directory named data in the build directory.

The same is true of the KernelSourcePath (see lines 71-80 of Config.cpp).

void loadConfiguration() {
    if (mConfigurationLoaded)
    	    return;

    // Set default paths
    mTestDataPath = getPath() + "../data/";
    mKernelSourcePath = getPath() + "../source/FAST/";
    mKernelBinaryPath = getPath() + "kernel_binaries/";
    mDocumentationPath = getPath() + "../doc/";
    mPipelinePath = getPath() + "../pipelines/";
    //....
}

The simple fix is to set the KernelSourcePath to a default value and to set the FAST_TEST_DATA_DIR variable to the default value if the user doesn't set it explicitly.

Describe the bug When running a simple pw-classification pipeline, using runPipeline, I observed that the predictions were off-by-one. Both horizontally and vertically.

To Reproduce The FPL file and corresponding model and WSI can be downloaded from this URL: https://drive.google.com/drive/folders/1jeovs5hco5U2wPrTHXiWghwiaugP6F6L?usp=sharing

Simply update the paths and run using runPipeline.

To make it easier to debug, I would disable heatmap interpolation (that is useInterpolation = false in FP). I have not started doing heatmap stuff with runPipeline yet in FP by default, and therefore not noticed that this was not possible to set this using an Attribute with Pipelines. Simply add option for Attribute here (setInterpolation method already exists): https://github.com/smistad/FAST/blob/e47eb8bb75dbb5f4a9983471d261edd09b5250cf/source/FAST/Visualization/HeatmapRenderer/HeatmapRenderer.cpp#L16

Otherwise I can make a PR for that.

System:

• Bug found using Windows 10
• Both NVIDIA and Intel OpenCL vendors were tested and produced the same bug

Expected behavior One-to-one correspondence between WSI and heatmap, aligned in a way that makes sense.

Screenshots

Disclaimer The newest commit of FAST was not used for doing the tests, but rather an older release (probably a month old). If it works for you I can try updating FAST and redoing the tests.

1. Added fix to ensure that import/export of low and high-res images are being properly exported in C++.
2. Added small fix for RGB/BGR switch in ImageExporter. 3. Added option to set attributes through text pipelines for a selection of classes. 4. Added method to set the tissue acceptance threshold (which was hard-coded to 0.5). 5. Lowered the image pyramidal plane size threshold to accept lower image planes in the stitcher, which were relevant in a study. I left a comment in the code if we want to switch back and compare in the future. 6. Also did some minor refactoring to keep the code more consistent on a selection of files.

Tested this using FastPathology on Ubuntu, both through C++ and runPipeline. Both worked fine.

(1) The bug was found comparing the specific classes against HDF5TensorExporter/HDF5TensorImporter, which seemed to work great. Using these two scripts as reference I noticed some minor differences.

I found that adding setModified(true) was quite important. I'm not really sure why not just using mIsModified=true did not work. Perhaps there was something I forgot to add to the header. Now there are occasions where I am using both setModified(true) AND mIsModified=true, where the latter is then probably redundant? Perhaps it is easier for you to say what is correct, so I just left it like this for you to evaluate.

I am also assuming that there should be an override for the execute method if the parent class has an execute method already. I noticed that this was done for the HDF5TensorExporter, and not the specific scripts I was working with. However, in this case it did not really seem to matter.

(2) I noticed that when creating thumbnail images from WSIs, that the exported images had swapped RGB channels. I proposed a simple fix that I have used earlier, but perhaps there is a more elegant solution. This should reproduce the bug: auto importer = WholeSlideImageImporter::New(); importer->setFilename(path_to_wsi); auto currImage = importer->updateAndGetOutputData();

auto access = currImage->getAccess(ACCESS_READ); auto input = access->getLevelAsImage(currImage->getNrOfLevels() - 1)

auto exporter = ImageExporter::New(); exporter->setFilename(path_to_output.png); exporter->setInputData(input); exporter->update();

(5) Perhaps this threshold should even be a hyperparameter one could set? But for now, I just manually lowered them. Did not notice any real difference using runPipeline and FastPathology on Ubuntu, for A05.svs and a larger 40x WSI from a local cohort. But perhaps overall runtime of high-res models will be slower? Right? But perhaps this is okay for now?

Let me know if there are any requests.

could this part "2. Read IR Generated by ModelOptimizer (.xml and .bin files)" be put into a new virtual function just for loading model and weights from memory buffers?

virtual void readNetwork(CNNNetReader network_reader);

default implementation could be something like void OpenVINOEngine::readNetwork(CNNNetReader network_reader) { auto input_model = getFilename(); if(!fileExists(input_model)) throw FileNotFoundException(input_model); network_reader.ReadNetwork(fileNameToString(input_model)); network_reader.ReadWeights(fileNameToString(input_model).substr(0, input_model.size() - 4) + ".bin"); }

https://docs.openvinotoolkit.org/latest/_docs_IE_DG_protecting_model_guide.html

Hello: when I build in win,there is an error error C2664 “void std::_Ptr_base<_Ty>::_Reset0(_Ty (*),std::_Ref_count_base *)”: can not change “uchar ”to“unsigned char ()[]” error occured in FAST memory.cpp line 695

Hello there,

I have realised that libFAST.so contains no SOVERSION. This can be set within CMAKE itself to be set during build time. The SOVERSION can then be incremented / bumped whenever there is a change with ABI. Could start with a SOVERSION of 0. Would it be possible if you could add this?

The SOVERSION is important within packaging and the debian ecosystem with regards to ABI backwards compat and a plethora of other things.

Thanks, Shayan

I tried adding update(0) in VTKImageExporter.cpp and VTKImageImporter.cpp, which fixed one error but there was another error I couldn't figure out.

10%] Building CXX object CMakeFiles/FAST.dir/source/FAST/Exporters/VTKImageExporter.cpp.o
[ 11%] Building CXX object CMakeFiles/FAST.dir/source/FAST/Exporters/VTKMeshExporter.cpp.o
/build/fast/FAST/source/FAST/Exporters/VTKImageExporter.cpp: In member function ‘virtual int fast::VTKImageExporter::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*)’:
/build/fast/FAST/source/FAST/Exporters/VTKImageExporter.cpp:53:12: error: no matching function for call to ‘fast::VTKImageExporter::update()’
     update(); // Run FAST pipeline
            ^
In file included from /build/fast/FAST/source/FAST/Exporters/VTKImageExporter.hpp:5:0,
                 from /build/fast/FAST/source/FAST/Exporters/VTKImageExporter.cpp:1:
/build/fast/FAST/source/FAST/ProcessObject.hpp:28:14: note: candidate: void fast::ProcessObject::update(uint64_t, fast::StreamingMode)
         void update(uint64_t timestep, StreamingMode streamingMode = STREAMING_MODE_PROCESS_ALL_FRAMES);
              ^
/build/fast/FAST/source/FAST/ProcessObject.hpp:28:14: note:   candidate expects 2 arguments, 0 provided
/build/fast/FAST/source/FAST/Exporters/VTKMeshExporter.cpp: In member function ‘virtual int fast::VTKMeshExporter::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*)’:
/build/fast/FAST/source/FAST/Exporters/VTKMeshExporter.cpp:30:12: error: no matching function for call to ‘fast::VTKMeshExporter::update()’
     update(); // Run FAST pipeline
            ^
In file included from /build/fast/FAST/source/FAST/Exporters/VTKMeshExporter.hpp:5:0,
                 from /build/fast/FAST/source/FAST/Exporters/VTKMeshExporter.cpp:1:
/build/fast/FAST/source/FAST/ProcessObject.hpp:28:14: note: candidate: void fast::ProcessObject::update(uint64_t, fast::StreamingMode)
         void update(uint64_t timestep, StreamingMode streamingMode = STREAMING_MODE_PROCESS_ALL_FRAMES);
              ^
/build/fast/FAST/source/FAST/ProcessObject.hpp:28:14: note:   candidate expects 2 arguments, 0 provided
CMakeFiles/FAST.dir/build.make:1048: recipe for target 'CMakeFiles/FAST.dir/source/FAST/Exporters/VTKImageExporter.cpp.o' failed
make[2]: *** [CMakeFiles/FAST.dir/source/FAST/Exporters/VTKImageExporter.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
CMakeFiles/FAST.dir/build.make:1061: recipe for target 'CMakeFiles/FAST.dir/source/FAST/Exporters/VTKMeshExporter.cpp.o' failed
make[2]: *** [CMakeFiles/FAST.dir/source/FAST/Exporters/VTKMeshExporter.cpp.o] Error 1
CMakeFiles/Makefile2:69: recipe for target 'CMakeFiles/FAST.dir/all' failed
make[1]: *** [CMakeFiles/FAST.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

Couldn't figure this one out

[ 62%] Building CXX object CMakeFiles/testFAST.dir/source/FAST/Importers/Tests/VTKImageImporterTests.cpp.o
In file included from /build/fast/FAST/source/FAST/Importers/VTKImageImporter.hpp:4:0,
                 from /build/fast/FAST/source/FAST/Importers/Tests/VTKImageImporterTests.cpp:2:
/build/fast/FAST/source/FAST/ProcessObject.hpp: In function ‘void ____C_A_T_C_H____T_E_S_T____10()’:
/build/fast/FAST/source/FAST/ProcessObject.hpp:170:21: error: ‘fast::DataObject::pointer fast::ProcessObject::getOutputData(uint) [with DataType = fast::Image; fast::DataObject::pointer = fast::SharedPointer<fast::DataObject>; uint = unsigned int]’ is protected
 DataObject::pointer ProcessObject::getOutputData(uint portID) {
                     ^
/build/fast/FAST/source/FAST/Importers/Tests/VTKImageImporterTests.cpp:13:63: error: within this context
     Image::pointer fastImage = importer->getOutputData<Image>();
                                                               ^
In file included from /build/fast/FAST/source/FAST/Importers/VTKImageImporter.hpp:4:0,
                 from /build/fast/FAST/source/FAST/Importers/Tests/VTKImageImporterTests.cpp:2:
/build/fast/FAST/source/FAST/ProcessObject.hpp:170:21: error: ‘fast::DataObject::pointer fast::ProcessObject::getOutputData(uint) [with DataType = fast::Image; fast::DataObject::pointer = fast::SharedPointer<fast::DataObject>; uint = unsigned int]’ is protected
 DataObject::pointer ProcessObject::getOutputData(uint portID) {
                     ^
/build/fast/FAST/source/FAST/Importers/Tests/VTKImageImporterTests.cpp:23:70: error: within this context
     Image::pointer importedImage = vtkImporter->getOutputData<Image>();
                                                                      ^
CMakeFiles/testFAST.dir/build.make:400: recipe for target 'CMakeFiles/testFAST.dir/source/FAST/Importers/Tests/VTKImageImporterTests.cpp.o' failed
make[2]: *** [CMakeFiles/testFAST.dir/source/FAST/Importers/Tests/VTKImageImporterTests.cpp.o] Error 1
CMakeFiles/Makefile2:180: recipe for target 'CMakeFiles/testFAST.dir/all' failed
make[1]: *** [CMakeFiles/testFAST.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

Changed from for loop to a stl algorithm to find min and max of the input coordinates of a bounding box. This may also result in a small optimization.

I should also note that I tested this by running the BoundingBoxRendererTests and it passed.

Describe the bug

My code is :

#include "FAST/Importers/ImageFileImporter.hpp" #include "FAST/Visualization/ImageRenderer/ImageRenderer.hpp" #include "FAST/Visualization/SegmentationRenderer/SegmentationRenderer.hpp" #include "FAST/Visualization/SimpleWindow.hpp" #include "FAST/Algorithms/GradientVectorFlow/EulerGradientVectorFlow.hpp" #include "FAST/Algorithms/GradientVectorFlow/MultigridGradientVectorFlow.hpp"

using namespace fast;

int main() { auto importer = ImageFileImporter::create("d:\1.jpg"); auto gvf = MultigridGradientVectorFlow::create()->connect(importer); auto imageRenderer = ImageRenderer::create()->connect(importer); auto segmentationRenderer = SegmentationRenderer::create()->connect(gvf); auto window = SimpleWindow2D::create()->connect({ imageRenderer, segmentationRenderer }); #ifdef FAST_CONTINUOUS_INTEGRATION // This will automatically close the window after 5 seconds, used for CI testing window->setTimeout(5 * 1000); #endif window->run(); return 0; }

The source code can be compiled, but it will run into errors!

To Reproduce The source code can be compiled, but it will run into errors.Run will throw an exception.

virtual bool notify(QObject *receiver, QEvent *event) { try { return QApplication::notify(receiver, event); } catch(Exception &e) { Reporter::error() << "FAST exception caught in Qt event handler " << e.what() << Reporter::end(); throw e;

System:

• OS and version: [e.g. Windows 10]
• GPU and OpenCL vendor (NVIDIA, Intel)

Expected behavior Can you give an example to correctly use EulerGradientVectorFlow and MultigridGradientVectorFlow?

Screenshots If applicable, add screenshots to help explain your problem.

Hi, @smistad , @andreped , I'd like to report a vulnerability issue in pyfast_4.3.0.

Dependency Graph between Python and Shared Libraries

Issue Description

As shown in the above dependency graph(here shows part of the dependency graph, which depends on vulnerable shared libraries), pyfast_4.3.0 directly or transitively depends on 81 C libraries (.so). However, I noticed that some C libraries are vulnerable, containing the following CVEs: libdcmdata.so.13, libdcmimgle.so.13, liboflog.so.13 and libofstd.so.13from C project dcmtk(version:3.6.2) exposed 1 vulnerabilities: CVE-2019-1010228 libgdk_pixbuf-2.0.so.0 from C project gdk-pixbuf(version:2.36.11) exposed 4 vulnerabilities: CVE-2021-20240, CVE-2017-6313, CVE-2017-6312, CVE-2017-6314 libhdf5.so.103 and libhdf5_cpp.so.103 from C project hdf5(version:1.10.6) exposed 4 vulnerabilities: CVE-2020-10811, CVE-2020-10812, CVE-2020-10810, CVE-2020-10809 libicudata.so.60 and libicuuc.so.60 from C project icu(version:60.2) exposed 1 vulnerabilities: CVE-2020-21913 libjpeg.so.8from C project libjpeg-turbo(version:1.5.2) exposed 2 vulnerabilities: CVE-2018-14498, CVE-2017-15232 libopenjp2.so.7 from C project openjpeg2(version:2.3.0) exposed 8 vulnerabilities: CVE-2020-6851, CVE-2020-27824, CVE-2020-27823, CVE-2018-18088, CVE-2018-14423, CVE-2018-6616, CVE-2018-5785, CVE-2017-17480 libxml2.so.2 from C project libxml2(version:2.9.4) exposed 22 vulnerabilities: CVE-2016-4658, CVE-2016-1838, CVE-2021-3541, CVE-2021-3537, CVE-2021-3518, CVE-2021-3517,CVE-2019-19956, CVE-2018-14404, CVE-2017-18258, CVE-2017-5130, CVE-2017-15412, CVE-2017-7375, CVE-2017-7376, CVE-2017-9050, CVE-2017-9047, CVE-2017-9048, CVE-2017-9049, CVE-2017-8872, CVE-2017-5969, CVE-2016-9318, CVE-2017-16931, CVE-2017-16932

Furthermore, the vulnerable methods in the vulnerable shared libraries can be actually invoked by Python code. For instance, the following call chain can reach the vulnerable method(C code) H5AC_unpin_entry() in file H5AC.c reported by CVE-2020-10810.

call chain-----
H5Literate_by_name()->H5G_iterate()->H5G__obj_iterate()->H5G__dense_iterate()->H5HF_open()->H5HF_close()->H5HF_space_close()->H5FS_close()->H5FS_decr()->H5AC_unpin_entry()

Suggested Vulnerability Patch Versions

dcmtk has fixed the vulnerabilities in versions >=3.6.4 gdk-pixbuf has fixed the vulnerabilities in versions >=2.42.0 hdf5 has fixed the vulnerabilities in versions >=1.12.1 libjpeg-turbo has fixed the vulnerabilities in versions >=2.0.0 icu has fixed the vulnerabilities in versions >=67-1 openjpeg2 has fixed the vulnerabilities in versions >=2.4.0 libxml2 has fixed the vulnerabilities in versions >=2.9.11

Python build tools cannot report vulnerable C libraries, which may induce potential security issues to many downstream Python projects. As a popular python package (pyfast has 2,048 downloads per month), could you please upgrade the above shared libraries to their patch versions?

Thanks for your help~ Best regards, MikeWazowski

Describe the bug I installed FAST on MacOS12.2.1 (21D62) but I can’t run this https://fast.eriksmistad.no/scan_convert_iq_data_8py-example.html example

Please do not use issues for questions. Use the gitter chat for questions and discussions: https://gitter.im/smistad/FAST

To Reproduce

1. install homebrew /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
2. install required package brew install openslide libomp
3. In Anaconda pip install pyfast
4. In pycharm run the code provided in this example import fast import numpy as np import matplotlib.pyplot as plt

Create some fake IQ beamspace data

iq_data = fast.Image.createFromArray(np.random.normal(size=(512,512,2)).astype(np.float32))

Add some geometric data used for scan conversion

iq_data.setFrameData('isPolar', 'true') iq_data.setFrameData('startRadius', '0') iq_data.setFrameData('stopRadius', '0.12') iq_data.setFrameData('startTheta', '-0.785398') # Start and stop angle in radians iq_data.setFrameData('stopTheta', '0.785398') iq_data.setFrameData('depthSpacing', '0.000235') iq_data.setFrameData('azimuthSpacing', '0.003074')

Create processing & visualization chain

envelope = fast.EnvelopeAndLogCompressor.create()
.connect(iq_data)

scan_convert = fast.ScanConverter.create()
.connect(envelope)

renderer = fast.ImageRenderer.create()
.connect(scan_convert)

fast.SimpleWindow2D.create()
.connect(renderer)
.run()

Visualize output of scan converter with matplotlib instead of FAST:

plt.imshow(np.asarray(scan_convert.runAndGetOutputData())[..., 0], cmap='gray') plt.show()

System:

• MacBooks Pro 2019. MacOS12.2.1 (21D62)
• Radeon Pro Vega 20 4 GB
• Intel UHD Graphics 630 1536 MB

Expected behavior fake IQ data will show up Screenshots Error message from pycharm qt.qpa.window: <QNSWindow: 0x7fac7d9f6bb0; contentView=<QNSView: 0x7fac7d9f68f0; QCocoaWindow(0x6000031a5810, window=QWidgetWindow(0x6000022ed380, name="QGLWidgetClassWindow"))>> has active key-value observers (KVO)! These will stop working now that the window is recreated, and will result in exceptions when the observers are removed. Break in QCocoaWindow::recreateWindowIfNeeded to debug.

There are numerous scenarios where it might be of interest to apply a concatenation, especially of images/segmentations. I found that in the FlowNetwork script there is a PO called ImagesToSequence, which seems to do a concatenation along the "time" axis: https://github.com/smistad/FAST/blob/5b88fcc1d24fdf6f458f0876cd75890c25784e85/source/FAST/Algorithms/NeuralNetwork/FlowNetwork.cpp#L53

However, there is not an option to set which axis to concatenate along. It should also be easy to concatenate multiple elements simultaneously, similarly as done in numpy: output = np.concatenate([x1, x2, ...], axis=k)

https://github.com/smistad/FAST/blob/2a8aa0ba76cd4096db78a8ae482a3effbea96351/source/FAST/Algorithms/NeuralNetwork/InferenceEngines/CMakeLists.txt#L56

if(WIN32)
    target_link_libraries(InferenceEngineOpenVINO FAST optimized inference_engine.lib debug inference_engined.lib)
else()
   target_link_libraries(InferenceEngineOpenVINO FAST libinference_engine.so)
endif()

In addition the cmake/ExternalOpenVINO.cmake must be changed locally to build and install Debug version of OpenVINO. Found no way so far to setup cmake for automatic for this....

    BUILD_COMMAND
        ${CMAKE_COMMAND} --build . --config Debug --target inference_engine COMMAND
        ${CMAKE_COMMAND} --build . --config Debug --target clDNNPlugin COMMAND
        ${CMAKE_COMMAND} --build . --config Debug --target myriadPlugin COMMAND
        ${CMAKE_COMMAND} --build . --config Debug --target MKLDNNPlugin
    INSTALL_COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/inference_engined.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/inference_engined.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/clDNNPlugind.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/MKLDNNPlugind.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/myriadPlugind.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/ngraphd.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/bin/intel64/Debug/plugins.xml ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/inference-engine/temp/tbb/bin/tbb.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/ COMMAND
        ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/inference-engine/include/ ${FAST_EXTERNAL_INSTALL_DIR}/include/openvino/
    )

Her kommer pull-requesten av oppgave-koden! Er det noe problemer med den kan dere også hente koden på git: rubenfagerli/Fast branch: Us3Dhybrid

Den kan sikkert være ganske vanskelig å merge direkte, da det er kode hentet fra Mehdis renderer-branch osv.. Trolig lettere å bruke de relevante filene og bygge det rundt dem til nyeste versjon.

Algoritmefilene ligger i: FAST/Algorithms/UsReconstruction/Us3Dhybrid/ Us3Dhybrid.cpp er algoritme-filen, mens kernelene er splittet opp i flere filer.

I hovedsak er us3Dhybrid.cl kernel for hybrid-accumulering, både med vanlig compounding og "alpha"-blending. Gaussian og linear er kompilerings-options "USE_GAUSSIAN_WEIGHT".

us3Dpnn.cl gjør både akkumulering og normalizering (med local hole filling)

normalizeVolume.cl er normalisering kernel for hybrid.

Ellers er det så vidt jeg husker overskuddsfiler, brukt i testing etc.

Eksempelfilen ligger i : FAST/Examples/UltrasoundReconstruction/Us3Dhybrid/ Og heter RunUs3Dhybrid.cpp Denne kan se på for å se hvordan algoritmen kjøres. Main metoden kjører enten en performance test, eller en(/et sett med) rekonstruksjon. Det er den første/øverste void runAlgorithmAndExportImage(...) funksjonen som er gjeldende.

Filene kan være litt kaotiske og med noen overflødige funksjoner, men bare start fra execute(), constructor og main() metodene så skal det være ganske greit. Og se på eksempelet for å se alle variablene som bør settes. Er det noen andre spørsmål, bare spør. -Ruben