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help > Issue with with Vaa3D plugin LCM_boost
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Feb 27, 2019 02:02 PM | Zhen Guan
Issue with with Vaa3D plugin LCM_boost
Dear Zhi,
I would like to report an error in Vaa3d. The vaa3d is downloaded from https://web.bii.a-star.edu.sg/vaa3d/ and the version is Linux (v3.200): Ubuntu 14.04+ 64bit.
The input file is of format .nii.gz which is the result of applying 3d U-Net on 3D image and itself is a 3d image as well.
I first type ./vaa3d in Ubuntu Terminal to call vaa3d and then use plugin data_IO/NIFTI_file_reader/Import ANALYZE image files to import images for view. It works fine and I could also view the input image in 3d view.
Next, I run plugin neuron tracing/LCM_boost/LCM_boost(some method). However, it returns error on all LCM_boost plugins and with an error message.
I also tried sudo ./vaa3d in the Terminal to do the same thing and now it pops a different error message.
My Ubuntu version is here:
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.2 LTS
Release: 18.04
Codename: bionic
Regards,
Guan Zhen
--------------------------
Here is the error message by executing ./vaa3d
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ ./vaa3d
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x22ce9f30
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x233fbd00)
size hint=1177 1141 min size hint=1177 1024
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x233fbd00)
V3d_PluginLoader setImage: 0x233fbd00 0x7ffe2ed776e0
MainWindow setImage now: XFormWidget(0x233fbd00) 0x7ffe2ed776e0
[0x7f13f077f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x233fbd00) / 0x233fbd00
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x233fbd00) / 0x233fbd00
done with runPluginInterface2_1().
already run! done status=1
V3dR_MainWindow::V3dR_MainWindow =====================================
"3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_GLWidget::V3dR_GLWidget ========================================
V3dR_MainWindow::connectSignal with V3dR_GLWidget
V3dR_GLWidget::initializeGL
GLformat: (version = 0x307f) (samples double-buffer stereo plane overlay = 4 1 0 0 0)
GLformat: (r g b a = 8 8 8 -1) + (depth stencil accum = 24 8 -1)
V3dR_GLWidget::choiceRenderer
Renderer::Renderer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Renderer_gl1::Renderer_gl1
OpenGL 2.0 (or higher) is available!
[OK] OpenGL Shading Language is available!
Renderer_gl2::Renderer_gl2
V3dR_GLWidget::settingRenderer
V3dR_GLWidget::preparingRenderer
Renderer_gl1::cleanData
Renderer_gl1::setupData
Down-sampling to 512x512x256
data4dp = 0x7f13f077f010 (start 0x0x0_0_0, size 512x512x241_1_1)
rgbaBuf = 0x7f13b4eff010 (512x512x241_1_1)
data box in original image space @ (0 0 0)--(511 511 240)
data4dp_to_rgba3d ............................................... cost time = 1.8 sec
Renderer_gl2::initialize (2)
Renderer_gl1::initialize (1)
Renderer::initialize (0)
Renderer_gl1::cleanObj
Renderer_gl1::loadObj
Renderer_gl1::cleanVol
Renderer_gl2::cleanStreamBuffer
Renderer_gl1::loadVol
" ARB_texture_non_power_of_two supported "
" ARB_texture_compression supported "
" EXT_texture3D (or OpenGL 2.0) supported "
" texture stream (need PBO and GLSL) supported "
" GLSL (and OpenGL 2.0) supported "
setupStack start --- try (compress 3d npt stream shader = 1 0 0 0 1)
sampleScale = 1x1x1 sampledImage = 512x512x241 fillTexture = 512x512x256
Renderer_gl1::loadVol() - creating data structures for managing 2D texture slice set
setupStack: id & buffer ....................... cost time = 0.001 sec
Calling setupStackTexture() from Renderer_gl1::subloadTex()
Renderer_gl2::setupStackTexture() start
Renderer_gl1::setupStackTexture() start
texture: real = 512x512x241 fill = 512x512x256
subloadTex [0]: (compress 3d npt stream shader = 1 0 0 0 1) ...... cost time = 9.255 sec
tex_stream_buffer = false
BoundingBox surface (1 1 1)--(-1 -1 -1)
BoundingBox default (0 0 0)--(512 512 241)
Renderer_gl2::cleanShader
Renderer_gl2::loadShader
+++++++++ shader for Surface Object
Load shader: ":/shader/obj_fragment.txt"
Load shader: ":/shader/lighting.txt"
Load shader: ":/shader/color_vertex.txt"
Load shader: ":/shader/lighting.txt"
+++++++++ shader for Volume texture2D
Load shader: ":/shader/tex_fragment.txt"
+++++++++ shader for Volume texture3D
Load shader: ":/shader/tex_fragment.txt"
+++++++++ GLSL shader setup finished.
Renderer_gl2::initColormap
V3dR_GLWidget::customEvent( ? )
( QEvent_InitControlValue )
V3dR_MainWindow::initControlValue
GL texture compression supported, enable texture compression function
GL shading language supported, enable volume colormap function
V3dR_GLWidget::customEvent( ? )
( QEvent_OpenFiles )
Renderer_gl1::loadObjectListFromFile
V3dR_GLWidget::updateTool (surfaceDlg=0x0) (colormapDlg=0x0)
V3dR_GLWidget::customEvent( ? )
( QEvent_Ready )
-------------------------------------------------------------- Ready
frontSlice: real = 512^2 fill = 512^2
"V3dR_MainWindow::changeEvent, ActivationChange-> 3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_GLWidget::updateTool (surfaceDlg=0x0) (colormapDlg=0x0)
hello before processHit
hello after processHit
V3dR_MainWindow::closeEvent, glWidget = 0x234eb7a0
Renderer_gl2::~Renderer_gl2
Renderer_gl2::cleanShader
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
Renderer_gl2::cleanStreamBuffer
Renderer_gl1::~Renderer_gl1
Renderer_gl1::cleanVol
Renderer_gl1::cleanObj
Renderer_gl1::cleanData
Renderer::~Renderer <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
V3dR_GLWidget::~V3dR_GLWidget =======================================
"3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_MainWindow::~V3dR_MainWindow ====================================
runPluginInterface2_1 ... 0x232978c0
/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii
The current input file has the suffix [nii]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...
size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
Fail to open file for reading.
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
Fail to open file for reading.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.
The current input file has the suffix [nii]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...
size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
Fail to open file for reading.
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
Fail to open file for reading.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.
Could not open the vaa3d raw file
Initialise
.....................................................
x1 and x2 is 0 -1
.....................................................
y1 and y2 is 0 -1
.....................................................
z1 and z2 is 0 -1
offset is 0
offset is 0
offset is 0
OpenCV Error: Assertion failed (s >= 0) in setSize, file /local1/Downloads/opencv-3.0.0/modules/core/src/matrix.cpp, line 293
The plugin fails to run [LCM_boost(MultiScale Ehancement based)]. Check your plugin code please.
done with runPluginInterface2_1().
already run! done status=1
--------------------------------
Here is the error message by executing sudo ./vaa3d
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ sudo ./vaa3d
[sudo] password for guanz:
[./vaa3d]
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/LCM_boost/libLCM_boost.so: (libopencv_core.so.3.0: cannot open shared object file: No such file or directory) ): "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/LCM_boost/libLCM_boost.so"
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x23315c70
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x23d0eb30)
size hint=1177 1141 min size hint=1177 1010
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x23d0eb30)
V3d_PluginLoader setImage: 0x23d0eb30 0x7ffd876c9610
MainWindow setImage now: XFormWidget(0x23d0eb30) 0x7ffd876c9610
[0x7f5c6c77f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x23d0eb30) / 0x23d0eb30
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x23d0eb30) / 0x23d0eb30
done with runPluginInterface2_1().
already run! done status=1
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
I would like to report an error in Vaa3d. The vaa3d is downloaded from https://web.bii.a-star.edu.sg/vaa3d/ and the version is Linux (v3.200): Ubuntu 14.04+ 64bit.
The input file is of format .nii.gz which is the result of applying 3d U-Net on 3D image and itself is a 3d image as well.
I first type ./vaa3d in Ubuntu Terminal to call vaa3d and then use plugin data_IO/NIFTI_file_reader/Import ANALYZE image files to import images for view. It works fine and I could also view the input image in 3d view.
Next, I run plugin neuron tracing/LCM_boost/LCM_boost(some method). However, it returns error on all LCM_boost plugins and with an error message.
I also tried sudo ./vaa3d in the Terminal to do the same thing and now it pops a different error message.
My Ubuntu version is here:
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.2 LTS
Release: 18.04
Codename: bionic
Regards,
Guan Zhen
--------------------------
Here is the error message by executing ./vaa3d
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ ./vaa3d
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x22ce9f30
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x233fbd00)
size hint=1177 1141 min size hint=1177 1024
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x233fbd00)
V3d_PluginLoader setImage: 0x233fbd00 0x7ffe2ed776e0
MainWindow setImage now: XFormWidget(0x233fbd00) 0x7ffe2ed776e0
[0x7f13f077f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x233fbd00) / 0x233fbd00
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x233fbd00) / 0x233fbd00
done with runPluginInterface2_1().
already run! done status=1
V3dR_MainWindow::V3dR_MainWindow =====================================
"3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_GLWidget::V3dR_GLWidget ========================================
V3dR_MainWindow::connectSignal with V3dR_GLWidget
V3dR_GLWidget::initializeGL
GLformat: (version = 0x307f) (samples double-buffer stereo plane overlay = 4 1 0 0 0)
GLformat: (r g b a = 8 8 8 -1) + (depth stencil accum = 24 8 -1)
V3dR_GLWidget::choiceRenderer
Renderer::Renderer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Renderer_gl1::Renderer_gl1
OpenGL 2.0 (or higher) is available!
[OK] OpenGL Shading Language is available!
Renderer_gl2::Renderer_gl2
V3dR_GLWidget::settingRenderer
V3dR_GLWidget::preparingRenderer
Renderer_gl1::cleanData
Renderer_gl1::setupData
Down-sampling to 512x512x256
data4dp = 0x7f13f077f010 (start 0x0x0_0_0, size 512x512x241_1_1)
rgbaBuf = 0x7f13b4eff010 (512x512x241_1_1)
data box in original image space @ (0 0 0)--(511 511 240)
data4dp_to_rgba3d ............................................... cost time = 1.8 sec
Renderer_gl2::initialize (2)
Renderer_gl1::initialize (1)
Renderer::initialize (0)
Renderer_gl1::cleanObj
Renderer_gl1::loadObj
Renderer_gl1::cleanVol
Renderer_gl2::cleanStreamBuffer
Renderer_gl1::loadVol
" ARB_texture_non_power_of_two supported "
" ARB_texture_compression supported "
" EXT_texture3D (or OpenGL 2.0) supported "
" texture stream (need PBO and GLSL) supported "
" GLSL (and OpenGL 2.0) supported "
setupStack start --- try (compress 3d npt stream shader = 1 0 0 0 1)
sampleScale = 1x1x1 sampledImage = 512x512x241 fillTexture = 512x512x256
Renderer_gl1::loadVol() - creating data structures for managing 2D texture slice set
setupStack: id & buffer ....................... cost time = 0.001 sec
Calling setupStackTexture() from Renderer_gl1::subloadTex()
Renderer_gl2::setupStackTexture() start
Renderer_gl1::setupStackTexture() start
texture: real = 512x512x241 fill = 512x512x256
subloadTex [0]: (compress 3d npt stream shader = 1 0 0 0 1) ...... cost time = 9.255 sec
tex_stream_buffer = false
BoundingBox surface (1 1 1)--(-1 -1 -1)
BoundingBox default (0 0 0)--(512 512 241)
Renderer_gl2::cleanShader
Renderer_gl2::loadShader
+++++++++ shader for Surface Object
Load shader: ":/shader/obj_fragment.txt"
Load shader: ":/shader/lighting.txt"
Load shader: ":/shader/color_vertex.txt"
Load shader: ":/shader/lighting.txt"
+++++++++ shader for Volume texture2D
Load shader: ":/shader/tex_fragment.txt"
+++++++++ shader for Volume texture3D
Load shader: ":/shader/tex_fragment.txt"
+++++++++ GLSL shader setup finished.
Renderer_gl2::initColormap
V3dR_GLWidget::customEvent( ? )
( QEvent_InitControlValue )
V3dR_MainWindow::initControlValue
GL texture compression supported, enable texture compression function
GL shading language supported, enable volume colormap function
V3dR_GLWidget::customEvent( ? )
( QEvent_OpenFiles )
Renderer_gl1::loadObjectListFromFile
V3dR_GLWidget::updateTool (surfaceDlg=0x0) (colormapDlg=0x0)
V3dR_GLWidget::customEvent( ? )
( QEvent_Ready )
-------------------------------------------------------------- Ready
frontSlice: real = 512^2 fill = 512^2
"V3dR_MainWindow::changeEvent, ActivationChange-> 3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_GLWidget::updateTool (surfaceDlg=0x0) (colormapDlg=0x0)
hello before processHit
hello after processHit
V3dR_MainWindow::closeEvent, glWidget = 0x234eb7a0
Renderer_gl2::~Renderer_gl2
Renderer_gl2::cleanShader
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
GL Error #1282(invalid operation) in File ../3drenderer/glsl_r.cpp at line: 281
Renderer_gl2::cleanStreamBuffer
Renderer_gl1::~Renderer_gl1
Renderer_gl1::cleanVol
Renderer_gl1::cleanObj
Renderer_gl1::cleanData
Renderer::~Renderer <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
V3dR_GLWidget::~V3dR_GLWidget =======================================
"3D View [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii]"
V3dR_MainWindow::~V3dR_MainWindow ====================================
runPluginInterface2_1 ... 0x232978c0
/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii
The current input file has the suffix [nii]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...
size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
Fail to open file for reading.
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
Fail to open file for reading.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.
The current input file has the suffix [nii]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...
size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
Fail to open file for reading.
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
Fail to open file for reading.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.
Could not open the vaa3d raw file
Initialise
.....................................................
x1 and x2 is 0 -1
.....................................................
y1 and y2 is 0 -1
.....................................................
z1 and z2 is 0 -1
offset is 0
offset is 0
offset is 0
OpenCV Error: Assertion failed (s >= 0) in setSize, file /local1/Downloads/opencv-3.0.0/modules/core/src/matrix.cpp, line 293
The plugin fails to run [LCM_boost(MultiScale Ehancement based)]. Check your plugin code please.
done with runPluginInterface2_1().
already run! done status=1
--------------------------------
Here is the error message by executing sudo ./vaa3d
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ sudo ./vaa3d
[sudo] password for guanz:
[./vaa3d]
Searching in ./plugins ......
Fail instantiation( Cannot load library /home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/LCM_boost/libLCM_boost.so: (libopencv_core.so.3.0: cannot open shared object file: No such file or directory) ): "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/plugins/neuron_tracing/LCM_boost/libLCM_boost.so"
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x23315c70
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x23d0eb30)
size hint=1177 1141 min size hint=1177 1010
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x23d0eb30)
V3d_PluginLoader setImage: 0x23d0eb30 0x7ffd876c9610
MainWindow setImage now: XFormWidget(0x23d0eb30) 0x7ffd876c9610
[0x7f5c6c77f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x23d0eb30) / 0x23d0eb30
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x23d0eb30) / 0x23d0eb30
done with runPluginInterface2_1().
already run! done status=1
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
ERROR in Vaa3D_PluginLoader::runPlugin: loader->instance()
Feb 27, 2019 05:02 PM | Zhi Zhou
RE: Issue with with Vaa3D plugin LCM_boost
command line usage does not support nii.gz image format at this
moment. Please save the image as v3draw/raw format first, and use
3draw/raw format as your input image to run plugins from command
line. Thanks.
Feb 28, 2019 01:02 PM | Zhen Guan
RE: Issue with with Vaa3D plugin LCM_boost
Dear Zhi,
Thanks for your reply. I encountered another problem while converting .nii.gz file to v3draw. What I did is to use plugin data_IO/convert_and_load_with_bioinformats/convert to .v3draw and import to do the conversion. Please refer the details below.
-------------------------
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ ./vaa3d
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x23135900
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x2381f1f0)
size hint=1177 1141 min size hint=1177 1024
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x2381f1f0)
V3d_PluginLoader setImage: 0x2381f1f0 0x7ffcafdcc2a0
MainWindow setImage now: XFormWidget(0x2381f1f0) 0x7ffcafdcc2a0
[0x7fb23477f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x2381f1f0) / 0x2381f1f0
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x2381f1f0) / 0x2381f1f0
done with runPluginInterface2_1().
already run! done status=1
runPluginInterface2_1 ... 0x2312f010
Convert to .v3draw with Bioformats and importinput file name = [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz]
intermediate folder name = [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test]
"/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/bioformats_tools/bfconvert" "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz" "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/Feb08_P2013_seg.nii.v3draw"
/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz
NiftiReader initializing /home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz
Exception in thread "main" java.lang.NullPointerException
at loci.formats.in.NiftiReader.initFile(NiftiReader.java:216)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.formats.ImageReader.setId(ImageReader.java:757)
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:338)
at loci.formats.tools.ImageConverter.main(ImageConverter.java:681)
It seems there is some difficulty to generate the intermediate file. You may need to choose a different folder to try again.
Thanks for your reply. I encountered another problem while converting .nii.gz file to v3draw. What I did is to use plugin data_IO/convert_and_load_with_bioinformats/convert to .v3draw and import to do the conversion. Please refer the details below.
-------------------------
guanz@administrator-System-Product-Name:~/Desktop/Vaa3D_Ubuntu_64bit_v3.200$ ./vaa3d
[./vaa3d]
QGtkStyle was unable to detect the current GTK+ theme.
Searching in ./plugins ......
Searching ./plugins done.
Starting Vaa3D version checker...
http://home.penglab.com/proj/vaa3d/curre...
Process obtained version info.
remote version=[3.2] current version=[3.2]
Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now.
runPluginInterface2_1 ... 0x23135900
The pixel map size is 400 300 (for invalid imagedata)
The pixel map size is 200 300 (for invalid imagedata)
The pixel map size is 400 200 (for invalid imagedata)
cur layout=0
MainWindow::createMdiChild *** workspace->windowList: () += XFormWidget(0x2381f1f0)
size hint=1177 1141 min size hint=1177 1024
XFormWidget::setCurrentFileName: "new_image"
MainWindow newImageWindow: "new_image"
V3d_PluginLoader newImageWindow: XFormWidget(0x2381f1f0)
V3d_PluginLoader setImage: 0x2381f1f0 0x7ffcafdcc2a0
MainWindow setImage now: XFormWidget(0x2381f1f0) 0x7ffcafdcc2a0
[0x7fb23477f010]
now in the function setImageData() line=4871.
channel 0 min=[0] max=[8]
set the color map max=8
ChannelTable::linkXFormWidgetChannel CDim=1
CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 CTU_3 CTU_1 CTU_2 CTU_1 CTU_2 CTU_3 succeed in setting up image data.
XFormWidget::setCurrentFileName: "new_image_processed"
XFormWidget::setCurrentFileName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
MainWindow setImageName: "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii"
V3d_PluginLoader setImageName: XFormWidget(0x2381f1f0) / 0x2381f1f0
CTU_3 CTU_1 CTU_2 V3d_PluginLoader updateImageWindow: XFormWidget(0x2381f1f0) / 0x2381f1f0
done with runPluginInterface2_1().
already run! done status=1
runPluginInterface2_1 ... 0x2312f010
Convert to .v3draw with Bioformats and importinput file name = [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz]
intermediate folder name = [/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test]
"/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/bioformats_tools/bfconvert" "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz" "/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/Feb08_P2013_seg.nii.v3draw"
/home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz
NiftiReader initializing /home/guanz/Desktop/Vaa3D_Ubuntu_64bit_v3.200/DATA/CT_lumen_test/test1_8vote_unform_sample/Feb08_P2013_seg.nii.gz
Exception in thread "main" java.lang.NullPointerException
at loci.formats.in.NiftiReader.initFile(NiftiReader.java:216)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.formats.ImageReader.setId(ImageReader.java:757)
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:338)
at loci.formats.tools.ImageConverter.main(ImageConverter.java:681)
It seems there is some difficulty to generate the intermediate file. You may need to choose a different folder to try again.
Mar 1, 2019 12:03 AM | Zhen Guan
RE: Issue with with Vaa3D plugin LCM_boost
Originally posted by Zhi Zhou:
Dear Zhi,
Thanks for your reply. I encountered another problem while converting .nii.gz file to v3draw. What I did is to use plugin data_IO/convert_and_load_with_bioinformats/convert to .v3draw and import to do the conversion.
command line usage does not support nii.gz image
format at this moment. Please save the image as v3draw/raw format
first, and use 3draw/raw format as your input image to run plugins
from command line. Thanks.
Dear Zhi,
Thanks for your reply. I encountered another problem while converting .nii.gz file to v3draw. What I did is to use plugin data_IO/convert_and_load_with_bioinformats/convert to .v3draw and import to do the conversion.
Mar 1, 2019 01:03 AM | Zhi Zhou
RE: Issue with with Vaa3D plugin LCM_boost
convert_and_load_with_bioinformats plugin may
not work.
Mar 1, 2019 02:03 AM | Zhi Zhou
RE: Issue with with Vaa3D plugin LCM_boost
convert_and_load_with_bioinformats plugin may not work. You'e
better still use NIFTI_file_reader plugin to read nii.gz file.
Otherwise, you may have to use third-party software(e.g. Fiji)
to save the image as v3draw/tif format and the open it in
Vaa3D.
Mar 5, 2019 01:03 AM | Zhen Guan
RE: Issue with with Vaa3D plugin LCM_boost
Originally posted by Zhi Zhou:
Dear Zhi,
I have convert the images to .v3draw format and encounter an error "fail to call base tracer". Since LCM_Boost is an additional step after the base segmentation, I would like to know if I need to run the base segmentation on the original image first, for instance multi-scale enhancement, and then run LCM_Boost(based on multi-scale enhancement) on both the original image and the confidence map.What I has done is to drag both the confidence map and the original image (both are of .v3draw format) into vaa3d and then run one of the LCM_Boost plugins.
convert_and_load_with_bioinformats plugin
may not work. You'e better still use NIFTI_file_reader plugin to
read nii.gz file. Otherwise, you may have to use third-party
software(e.g. Fiji) to save the image as v3draw/tif format and
the open it in Vaa3D.
Dear Zhi,
I have convert the images to .v3draw format and encounter an error "fail to call base tracer". Since LCM_Boost is an additional step after the base segmentation, I would like to know if I need to run the base segmentation on the original image first, for instance multi-scale enhancement, and then run LCM_Boost(based on multi-scale enhancement) on both the original image and the confidence map.What I has done is to drag both the confidence map and the original image (both are of .v3draw format) into vaa3d and then run one of the LCM_Boost plugins.
Mar 5, 2019 02:03 AM | Zhi Zhou
RE: Issue with with Vaa3D plugin LCM_boost
As far as I know, you should get results directly by
running LCM_boost plugin. Please contact the developer Lin Gu
for more detailed information.