sintefmedtek / custusx Goto Github PK

Hello! I have several GBs of .mhd and .zraw files from 2017.

I'm trying to load a single one into CustusX but I'm getting this error:

[13:20] Workflow change to [Patient Data]
[13:20] Layout 0 changed to 3D ACS
[13:20] Startup Load [C:/Users/lRaulMN/Patients/Laboratory/pacientePrueba.cx3] as recent patient
[13:20] Set Active Patient: C:/Users/lRaulMN/Patients/Laboratory/pacientePrueba.cx3
[13:20] DatabaseDirectory set to: C:/Users/lRaulMN/CustusX_settings/profiles/Laboratory/settings/DICOMDatabase
[13:20] Open Database C:/Users/lRaulMN/CustusX_settings/profiles/Laboratory/settings/DICOMDatabase/ctkDICOM.sql, open= 1
[13:20] Saved patient C:/Users/lRaulMN/Patients/Laboratory/Prueba.cx3
[13:20] Set Active Patient: C:/Users/lRaulMN/Patients/Laboratory/Prueba.cx3
[13:20] Saved patient C:/Users/lRaulMN/Patients/Laboratory/Prueba.cx3
[13:20] Importing data...
[13:20] MetaImage: Read: Cannot open data file
[13:20] Load of data [C:/Users/lRaulMN/Desktop/Prueba.mhd] failed with message:
ERROR: In D:\b\b\CX-TB-BW\VTK\VTK\IO\Image\vtkMetaImageReader.cxx, line 237
vtkMetaImageReader (0000021F6A526CC0): MetaImage cannot read data from file.


[13:20] Failed to load file: [C:/Users/lRaulMN/Desktop/Prueba.mhd]
[13:20] Error with data file: C:/Users/lRaulMN/Desktop/Prueba.mhd Import canceled.

This is the .mhd file:

ObjectType = Image
NDims = 2
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = True
CompressedDataSize = 319794
CenterOfRotation = 0 0
ElementSpacing = 0.271 0.271
DimSize = 820 616
AnatomicalOrientation = ??
ElementNumberOfChannels = 3
ElementSize = 0.271 0.271
ElementType = MET_UCHAR
TransformMatrix =  6.12323e-17 -1 -6.12323e-17 1.22465e-16 -6.12323e-17 1 -1 -6.12323e-17 1.22465e-16
Offset =  -2.72141e-14 111.11 48.238
Modality = US
ImageType3 = US-Acq_2_20170621T145520_Sonix
ElementDataFile = Prueba.zraw

Any ideas? The "Kaisa.mhd" from the tutorial works fine.

Hello,I am building up this project.And we met some troubles：after we compiled the code and
ran the executable “CustusX”，it crashed（SegmentFault）。I have no idea about how to handle this..

here is the GDB LOG：

(gdb) bt
#0 0x00007f7c114aef68 in ?? ()
from /home/bme305/Qt5.5.1/5.5/gcc_64/lib/libQt5Core.so.5
#1 0x00007f7c112f6b4c in QString::toUtf8_helper(QString const&) ()
from /home/bme305/Qt5.5.1/5.5/gcc_64/lib/libQt5Core.so.5
#2 0x0000000000a43fde in QString::toUtf8() const & ()
#3 0x0000000000a4402b in QString::toStdStringabi:cxx11 const ()
#4 0x0000000000d5e7c8 in operator<<(std::ostream&, QString const&) ()
#5 0x0000000000d62810 in cx::operator<<(std::ostream&, cx::MESSAGE_LEVEL const&) ()
#6 0x0000000000ab6779 in bool boost::detail::lexical_istream_limited_src<char, std::char_traits, true, 2ul>::shl_input_streamable<cx::MESSAGE_LEVEL const>(cx::MESSAGE_LEVEL const&) ()
#7 0x0000000000ab6527 in bool boost::detail::lexical_istream_limited_src<char, std::char_traits, true, 2ul>::operator<< cx::MESSAGE_LEVEL(cx::MESSAGE_LEVEL const&) ()
#8 0x0000000000ab60ca in boost::detail::lexical_converter_impl<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, cx::MESSAGE_LEVEL>::try_convert(cx::MESSAGE_LEVEL const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >&) ()
#9 0x0000000000ab59c8 in bool boost::conversion::detail::try_lexical_convert<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, cx::MESSAGE_LEVEL>(cx::MESSAGE_LEVEL const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >&) ()
---Type to continue, or q to quit---
#10 0x0000000000ab538c in std::__cxx11::basic_string<char, std::char_traits, std::allocator > boost::lexical_cast<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, cx::MESSAGE_LEVEL>(cx::MESSAGE_LEVEL const&) ()
#11 0x0000000000ab463d in std::__cxx11::basic_string<char, std::char_traits, std::allocator > string_castcx::MESSAGE_LEVEL(cx::MESSAGE_LEVEL const&) ()
#12 0x0000000000ab3966 in QString qstring_castcx::MESSAGE_LEVEL(cx::MESSAGE_LEVEL const&) ()
#13 0x0000000000d7a293 in cx::Message::getPrintableMessage() const ()
#14 0x0000000000cee49d in cx::Reporter::sendMessage(cx::Message) ()
#15 0x0000000000d7922f in cx::MessageLogger::~MessageLogger() ()
#16 0x0000000000b7c5ad in cx::PluginFrameworkManager::handlePluginException(QString const&, ctkException const&) ()
#17 0x0000000000b7baf1 in cx::PluginFrameworkManager::install(QString const&)
()
#18 0x0000000000b7a797 in cx::PluginFrameworkManager::loadState() ()
#19 0x0000000000b76202 in cx::LogicManager::initializeServices() ()
#20 0x0000000000b76019 in cx::LogicManager::initialize(boost::shared_ptrcx::ApplicationComponent) ()
#21 0x0000000000a1e1c1 in main ()

MY OS is Ubuntu16.04，LTS;
QT version：5.5.1
cmake log：

-- 'BeforeCMAKE_CXX_FLAGS'

-- 'CX_CMAKE_CXX_FLAGS'

-- 'AfterCMAKE_CXX_FLAGS'

-- DirDefs:

-- The Ninja was used.

-- Setting CX_SYSTEM_BASE_NAME=[CustusX]

-- Setting CX_SYSTEM_DEFAULT_APPLICATION=[CustusX]

fatal: 没有标签准确匹配 '7f1def756e5d44370192c35f3ee7ae6cb3cd65f9'

-- CustusX Alpha Version: 2019.04.11-dev+develop.7f1d

-----------------CX_INSTALL_ROOT_DIR: CustusX

-----------------CX_INSTALL_BINARY_DIR: CustusX/bin

-----------------CX_INSTALL_CONFIG_DIR: CustusX/config

-----------------CX_BUNDLE_NAME: CustusX

-- Boost version: 1.58.0

-- Trying to find DCMTK expecting DCMTKConfig.cmake

-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok

-- Generated: /home/bme305/dev/cx/CX/build_Release/source/plugins/DGraphInput-alldep-withext.txt

-- Checking to see if CXX compiler accepts flag -fvisibility=hidden

-- Checking to see if CXX compiler accepts flag -fvisibility=hidden - yes

-- Generating master Catch exe.

-- Adding tests from:

-- cxtestResource

-- cxtestResourceUsReconstructionTypes

-- cxtestResourceVisualization

-- cxtestOpenIGTLinkUtilities

-- cxtestUtilities

-- cxtestResourceWidgets

-- cxtestGrabber

-- cxtestFilter

-- cxtestLogicManager

-- cxtestGui

-- cxtest_org_custusx_core_patientmodel

-- cxtest_org_custusx_core_view

-- cxtest_org_custusx_core_tracking

-- cxtest_org_custusx_core_tracking_igstk

-- cxtest_org_custusx_core_openigtlink3

-- cxtest_org_custusx_core_video

-- cxtest_org_custusx_core_filemanager

-- cxtest_org_custusx_dicom

-- cxtest_org_custusx_usreconstruction_vnncl

-- cxtest_org_custusx_usreconstruction_pnn

-- cxtest_org_custusx_registration

-- cxtest_org_custusx_registration_method_manual

-- cxtest_org_custusx_registration_method_landmark

-- cxtest_org_custusx_registration_method_bronchoscopy

-- cxtest_org_custusx_registration_method_centerline

-- cxtest_org_custusx_registration_method_commandline

-- cxtest_org_custusx_usreconstruction

-- cxtest_org_custusx_acquisition

-- cxtest_org_custusx_calibration

-- cxtest_org_custusx_help

-- cxtest_org_custusx_filter_accusurf

-- cxtest_org_custusx_ceetron

-- cxtest_org_custusx_filter_airwaysfromcenterline

-- Qt5 plugin directory:/home/bme305/Qt5.5.1/5.5/gcc_64/plugins

-- QT_PLUGINS_DIR: /home/bme305/Qt5.5.1/5.5/gcc_64/plugins

-- QT_LIBS_DIR: /home/bme305/Qt5.5.1/5.5/gcc_64/lib

-- PATTERN=CustusX/bin/*.so

-- PATTERN=CustusX/bin/plugins/*.so

--

Configuration for CustusX 2019.04.11-dev+develop.7f1d

Build Settings:



	System Base Name: CustusX



	Built on system: Linux-4.15.0-43-generic  x86_64



	Build type: 



	Shared Libraries: 



	Coverage: OFF



	Dev docs: OFF



	User docs: ON







Libraries:



	Qt Version 5.5.1



	VTK Version: 7.1.0



	ITK Version: 4.12.0



	CTK Version: 0.1.0



	OpenCV Version: 3.3.0



	CMake Version: 3.12.0



	IGSTK Version: 5.2.0



	OpenIGTLink Version: 3.1.0



	Boost Version: 1.58.0



	OpenCL Version: 



	OpenGL Version:  3.0 Mesa 18.0.5







	Eigen Version: 3.3.5







	OpenCL Utility Library: OFF







Plugins:



	org.custusx.acquisition ON



	org.custusx.calibration ON



	org.custusx.ceetron ON



	org.custusx.core.filemanager ON



	org.custusx.core.openigtlink3 ON



	org.custusx.core.patientmodel ON



	org.custusx.core.state ON



	org.custusx.core.tracking ON



	org.custusx.core.tracking.system.igstk ON



	org.custusx.core.video ON



	org.custusx.core.view ON



	org.custusx.dicom ON



	org.custusx.example OFF



	org.custusx.filter.accusurf ON



	org.custusx.filter.airways OFF



	org.custusx.filter.airwaysfromcenterline ON



	org.custusx.filter.routetotarget ON



	org.custusx.help ON



	org.custusx.registration ON



	org.custusx.registration.gui ON



	org.custusx.registration.method.bronchoscopy ON



	org.custusx.registration.method.centerline ON



	org.custusx.registration.method.commandline ON



	org.custusx.registration.method.landmark ON



	org.custusx.registration.method.manual ON



	org.custusx.registration.method.plate ON



	org.custusx.registration.method.pointcloud ON



	org.custusx.registration.method.vessel ON



	org.custusx.training ON



	org.custusx.usreconstruction ON



	org.custusx.usreconstruction.pnn ON



	org.custusx.usreconstruction.vnncl ON



	org.custusx.virtualbronchoscopy ON



	org.custusx.webserver OFF

-- **** Generating user qthelp documentation...

-- **** Generating user html documentation...

-- Configuring done

CMake Warning (dev) in source/plugins/org.custusx.dicom/CMakeLists.txt:

Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link

interface. Run "cmake --help-policy CMP0022" for policy details. Use the

cmake_policy command to set the policy and suppress this warning.

Target "org_custusx_dicom" has an INTERFACE_LINK_LIBRARIES property which

differs from its LINK_INTERFACE_LIBRARIES properties.

INTERFACE_LINK_LIBRARIES:

CTKPluginFramework;cxGUIExtenderService;cxResourceWidgets;cxResource;CTKDICOMWidgets;CTKDICOMCore;cxPluginUtilities;cxResourceVisualization;Qt5::Core;dl;Qt5::Widgets;Qt5::Xml;Qt5::OpenGL;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmpstat.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmpstat.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmsr.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmsr.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmtls.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmtls.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmqrdb.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmqrdb.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmnet.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmnet.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmjpeg.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmjpeg.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimage.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimage.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimgle.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimgle.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmdata.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmdata.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/liboflog.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/liboflog.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libofstd.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libofstd.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg12.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg12.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg16.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg16.so>;$<$<NOT:$<CONFIG:DEBUG>>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg8.so>;$<$<CONFIG:DEBUG>:/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg8.so>;-lpthread;Qt5::Sql;Qt5::Gui;vtkCommonCore;vtkCommonDataModel;vtkCommonSystem;vtkIOImage;vtkInteractionStyle;vtkRenderingAnnotation;vtkRenderingCore;vtkRenderingOpenGL2;vtkRenderingFreeType;Qt5::Sql;Qt5::Concurrent

LINK_INTERFACE_LIBRARIES:
CTKPluginFramework;cxGUIExtenderService;cxResourceWidgets;cxResource;CTKDICOMWidgets;CTKDICOMCore;cxPluginUtilities;cxResourceVisualization;Qt5::Core;dl;Qt5::Widgets;Qt5::Xml;Qt5::OpenGL;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmpstat.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmsr.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmtls.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmqrdb.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmnet.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmjpeg.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimage.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmimgle.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libdcmdata.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/liboflog.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libofstd.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg12.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg16.so;/home/bme305/dev/cx/CTK/build_Release/DCMTK-build/lib/libijg8.so;-lpthread;Qt5::Sql;Qt5::Gui;vtkCommonCore;vtkCommonDataModel;vtkCommonSystem;vtkIOImage;vtkInteractionStyle;vtkRenderingAnnotation;vtkRenderingCore;vtkRenderingOpenGL2;vtkRenderingFreeType;Qt5::Sql;Qt5::Concurrent

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /home/bme305/dev/cx/CX/build_Release

If you need more information，please let me know，we sincerely ask you for help，thanks！

This officially opens the issue tracker. Welcome!

Dear SINTEF developers,

In the documentation of the PNN algorithm, the following is written down: "If the voxel already has a value, different approaches are possible: Taking the average, taking the maximum, taking the most recent value, or taking the first value."

However, in CustusX 18.04 in the tab Acquisition>Reconstruction I can select the algorithm "pnn" but there is no option between the different approaches as stated in the documentation.
I found in this GitHub that the algorithm used the maximum value as default, but I could not recognize any code for selecting an approach.

Is there a bug in my CustusX 18.04 or am I missing something?

Hi developers,

I tried to use CustusX to display video from a UVC endscopy optical fiber camera, but it didn't work. The Cheese can't detect the camera either. However, when I used the command "guvcview /dev/video0", it works well. My ubuntu version is 20.04. And I used the nightly build version of CustusX.

When I typed "lsubs", it shows:
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 003 Device 003: ID 13d3:3563 IMC Networks Wireless_Device
Bus 003 Device 002: ID 27c6:521d Shenzhen Goodix Technology Co.,Ltd. FingerPrint
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 001 Device 004: ID 0b05:19b6 ASUSTek Computer, Inc. N-KEY Device
Bus 001 Device 010: ID 046d:c092 Logitech, Inc. G102 LIGHTSYNC Gaming Mouse
Bus 001 Device 020: ID 5357:3001 Suwaytech Inc SWT USB2.0 Camera
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

We can see "Bus 001 Device 020: ID 5357:3001 Suwaytech Inc SWT USB2.0 Camera" the camera is detected normally.

Then I typed "dmesg", the terminal shows:
[ 844.285468] usb 1-1: new high-speed USB device number 17 using xhci_hcd
[ 844.451837] usb 1-1: New USB device found, idVendor=5357, idProduct=3001, bcdDevice= 1.00
[ 844.451848] usb 1-1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[ 844.451851] usb 1-1: Product: SWT USB2.0 Camera
[ 844.451854] usb 1-1: Manufacturer: Suwaytech Inc
[ 844.451856] usb 1-1: SerialNumber: 30M46A0000000101
[ 844.456852] usb 1-1: Found UVC 1.00 device SWT USB2.0 Camera (5357:3001)

However, when I start Cheese or CustusX, both of them don't detect the camera.

I tried to plugin another normal webcam, both Cheese and CustusX can detect it.
Therefore, I typed "dmesg", the terminal shows:
[ 835.905232] usb 1-1: new high-speed USB device number 16 using xhci_hcd
[ 836.274243] usb 1-1: New USB device found, idVendor=046d, idProduct=0825, bcdDevice= 0.12
[ 836.274253] usb 1-1: New USB device strings: Mfr=0, Product=0, SerialNumber=2
[ 836.274257] usb 1-1: SerialNumber: 4A29AF60
[ 836.293500] usb 1-1: Found UVC 1.00 device (046d:0825)
[ 836.408453] input: UVC Camera (046d:0825) as /devices/pci0000:00/0000:00:08.1/0000:04:00.3/usb1/1-1/1-1:1.0/input/input41

The last line [ 836.408453] input: UVC Camera (046d:0825) as /devices/pci0000:00/0000:00:08.1/0000:04:00.3/usb1/1-1/1-1:1.0/input/input41 is missing when I pluggined the endscopy optical fiber camera, so I am guessing this is where the problem is.

Does someone else have the same issue?

Shu