Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

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Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

joao santinha
Hi all,

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 
I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:
 
"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.
Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

Is this known? Is there a way to solve this issue?

Kind regards,
Joao 




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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Csaba Pinter-2

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Andrey Fedorov-2
In reply to this post by joao santinha
Have you tried following the message, and create a DICOM database in a new location? (first click the ">>" button in DICOM Browser, then click the button to the right from "LocalDatabase:" and select a new folder)

Inline image 1

On Mon, Feb 13, 2017 at 10:14 AM, joao santinha <[hidden email]> wrote:
Hi all,

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 
I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:
 
"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.
Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

Is this known? Is there a way to solve this issue?

Kind regards,
Joao 




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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

joao santinha
In reply to this post by joao santinha
Hi Csaba and Andrey,

Yes I have tried and I get exactly the same error but for the new folder.

I am sending you also the terminal output that has more information.

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open


Thank you,

Joao


On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 



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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Csaba Pinter-2
In reply to this post by joao santinha

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Andrey Fedorov-2
And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

You are sure you used the proper qmake while building Slicer, right?

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

joao santinha
In reply to this post by Csaba Pinter-2
Hi Andrey and Csaba,

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 
I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.


And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501


Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C



Time Awake Since Boot: 600000 seconds


System Integrity Protection: enabled


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


Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY


Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 


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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1


Thanks in advance,

Joao


On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:
And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

You are sure you used the proper qmake while building Slicer, right?

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Csaba Pinter-2
In reply to this post by Csaba Pinter-2

Great news, thanks for the update!

So you rebuilt Slicer from scratch with the proper cmake? Do you know which change fixed it?

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 04:14
To: Andrey Fedorov <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Andrey and Csaba,

 

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 

I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.

 

And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501

 

Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C

 

 

Time Awake Since Boot: 600000 seconds

 

System Integrity Protection: enabled

 

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

 

Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY

 

Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 

 

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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1

 

Thanks in advance,

Joao

 

On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:

And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

 

You are sure you used the proper qmake while building Slicer, right?

 

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

 

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

joao santinha
In reply to this post by Csaba Pinter-2
Hi Csaba,

Yes, the problem was that I had multiple qmake's on my system and cmake picked the wrong version. After correcting that, I am able to import DICOM files but I get a crash (report on my last email) when I try to load it. 

Thanks,
Joao

On Tue, Feb 14, 2017 at 1:30 PM, Csaba Pinter <[hidden email]> wrote:

Great news, thanks for the update!

So you rebuilt Slicer from scratch with the proper cmake? Do you know which change fixed it?

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 04:14
To: Andrey Fedorov <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Andrey and Csaba,

 

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 

I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.

 

And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501

 

Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C

 

 

Time Awake Since Boot: 600000 seconds

 

System Integrity Protection: enabled

 

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

 

Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY

 

Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 

 

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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1

 

Thanks in advance,

Joao

 

On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:

And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

 

You are sure you used the proper qmake while building Slicer, right?

 

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

 

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Andras Lasso-2

It seems to be a debug assertion, probably because the image is not a fully valid DICOM data set. Is the image loaded correctly if you build Slicer in Release mode? How the image is created? Can you share the image so that we can investigate the crash (make sure there is no patient identifiable information in it)?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: February 14, 2017 9:10
To: Csaba Pinter <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba,

 

Yes, the problem was that I had multiple qmake's on my system and cmake picked the wrong version. After correcting that, I am able to import DICOM files but I get a crash (report on my last email) when I try to load it. 

 

Thanks,

Joao

 

On Tue, Feb 14, 2017 at 1:30 PM, Csaba Pinter <[hidden email]> wrote:

Great news, thanks for the update!

So you rebuilt Slicer from scratch with the proper cmake? Do you know which change fixed it?

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 04:14
To: Andrey Fedorov <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Andrey and Csaba,

 

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 

I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.

 

And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501

 

Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C

 

 

Time Awake Since Boot: 600000 seconds

 

System Integrity Protection: enabled

 

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

 

Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY

 

Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 

 

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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1

 

Thanks in advance,

Joao

 

On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:

And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

 

You are sure you used the proper qmake while building Slicer, right?

 

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

 

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

Csaba Pinter-2
In reply to this post by Csaba Pinter-2

OK so it wasn’t the ini file, I was just checking.

 

Sorry, I somehow missed the part about the crash.

Indeed, if you could share an anonymized dataset we can investigate it.

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 09:10
To: Csaba Pinter <[hidden email]>
Cc: Andrey Fedorov <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba,

 

Yes, the problem was that I had multiple qmake's on my system and cmake picked the wrong version. After correcting that, I am able to import DICOM files but I get a crash (report on my last email) when I try to load it. 

 

Thanks,

Joao

 

On Tue, Feb 14, 2017 at 1:30 PM, Csaba Pinter <[hidden email]> wrote:

Great news, thanks for the update!

So you rebuilt Slicer from scratch with the proper cmake? Do you know which change fixed it?

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 04:14
To: Andrey Fedorov <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Andrey and Csaba,

 

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 

I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.

 

And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501

 

Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C

 

 

Time Awake Since Boot: 600000 seconds

 

System Integrity Protection: enabled

 

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

 

Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY

 

Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 

 

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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1

 

Thanks in advance,

Joao

 

On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:

And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

 

You are sure you used the proper qmake while building Slicer, right?

 

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

 

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

joao santinha
In reply to this post by Csaba Pinter-2
Hi all,

Building Slicer in Release mode solves the issue and the image is loaded correctly! 

I will send the anonymized dataset to your email as soon as possible. 

Thanks for your help!!!
Joao

On Tue, Feb 14, 2017 at 2:39 PM, Csaba Pinter <[hidden email]> wrote:

OK so it wasn’t the ini file, I was just checking.

 

Sorry, I somehow missed the part about the crash.

Indeed, if you could share an anonymized dataset we can investigate it.

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 09:10
To: Csaba Pinter <[hidden email]>
Cc: Andrey Fedorov <[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba,

 

Yes, the problem was that I had multiple qmake's on my system and cmake picked the wrong version. After correcting that, I am able to import DICOM files but I get a crash (report on my last email) when I try to load it. 

 

Thanks,

Joao

 

On Tue, Feb 14, 2017 at 1:30 PM, Csaba Pinter <[hidden email]> wrote:

Great news, thanks for the update!

So you rebuilt Slicer from scratch with the proper cmake? Do you know which change fixed it?

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Tuesday, February 14, 2017 04:14
To: Andrey Fedorov <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Andrey and Csaba,

 

In fact, the qmake version picked automatically by cmake was incorrect. I changed it and deleted the file ~/.config/www.na-mic.org/Slicer.ini and now I don't have that error anymore. 

I am able to open the DICOM Browser without the error and import the DICOM files from directories but when I try to load an imported series I get a crash. Here is the terminal output:

Number of loaded modules: 144 

Switch to module:  "Welcome" 

2017-02-14 08:53:55.442 Slicer[14449:4513183] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

error: [/Users/jsantinha/CODE/Slicer-SuperBuild/Slicer-build/bin/Slicer.app/Contents/MacOS/./Slicer] exit abnormally - Report the problem.

 

And here is part of the crash report:

Process:               Slicer [14449]

Path:                  /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer

Identifier:            ???

Version:               ??? (4.7.0-2017-02-08)

Code Type:             X86-64 (Native)

Parent Process:        ??? [14448]

Responsible:           Slicer [14449]

User ID:               501

 

Date/Time:             2017-02-14 08:54:23.082 +0000

OS Version:            Mac OS X 10.12.3 (16D32)

Report Version:        12

Anonymous UUID:        9B54E0DE-A10C-3B91-4B4A-B4484968642C

 

 

Time Awake Since Boot: 600000 seconds

 

System Integrity Protection: enabled

 

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

 

Exception Type:        EXC_CRASH (SIGABRT)

Exception Codes:       0x0000000000000000, 0x0000000000000000

Exception Note:        EXC_CORPSE_NOTIFY

 

Application Specific Information:

Assertion failed: (GetVR().Compatible( de.GetVR() ) || de.GetVR() == VR::INVALID), function SetFromDataElement, file /Users/jsantinha/CODE/Slicer-Superbuild/ITKv4/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmAttribute.h, line 445.

 

 

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

0   libsystem_kernel.dylib        0x00007fffc5c43dd6 __pthread_kill + 10

1   libsystem_pthread.dylib       0x00007fffc5d2f787 pthread_kill + 90

2   libsystem_c.dylib             0x00007fffc5ba9420 abort + 129

3   libsystem_c.dylib             0x00007fffc5b70893 __assert_rtn + 320

4   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b66c84 gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataElement(gdcm::DataElement const&) + 388 (gdcmAttribute.h:445)

5   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b5a84e gdcm::Attribute<(unsigned short)40, (unsigned short)8464, 8, 1>::SetFromDataSet(gdcm::DataSet const&) + 158 (gdcmAttribute.h:470)

6   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b59aaf gdcm::PixmapReader::ReadImageInternal(gdcm::MediaStorage const&, bool) + 49727 (gdcmPixmapReader.cxx:1063)

7   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b4d862 gdcm::PixmapReader::ReadImage(gdcm::MediaStorage const&) + 34 (gdcmPixmapReader.cxx:602)

8   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a299 gdcm::ImageReader::ReadImage(gdcm::MediaStorage const&) + 57 (gdcmImageReader.cxx:59)

9   libitkgdcmMSFF-4.11.1.dylib   0x0000000118b423e0 gdcm::PixmapReader::Read() + 384 (gdcmPixmapReader.cxx:89)

10  libitkgdcmMSFF-4.11.1.dylib   0x0000000118b6a255 gdcm::ImageReader::Read() + 21 (gdcmImageReader.cxx:54)

11  libITKIOGDCM-4.11.1.dylib     0x00000001188a2da9 itk::GDCMImageIO::CanReadFile(char const*) + 1865 (itkGDCMImageIO.cxx:169)

12  libvtkITK.dylib               0x0000000112cfaaed vtkITKArchetypeImageSeriesReader::RequestInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 6029 (vtkITKArchetypeImageSeriesReader.cxx:231)

13  libvtkCommon-7.1.1.dylib      0x0000000124b214e5 vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 213 (vtkImageAlgorithm.cxx:109)

14  libvtkCommon-7.1.1.dylib      0x0000000124b0b264 vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 164 (vtkExecutive.cxx:775)

15  libvtkCommon-7.1.1.dylib      0x0000000124affcf2 vtkDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 130 (vtkDemandDrivenPipeline.cxx:479)

16  libvtkCommon-7.1.1.dylib      0x0000000124b468d0 vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 80 (vtkStreamingDemandDrivenPipeline.cxx:452)

17  libvtkCommon-7.1.1.dylib      0x0000000124afefa2 vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 866 (vtkDemandDrivenPipeline.cxx:237)

18  libvtkCommon-7.1.1.dylib      0x0000000124b45839 vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 3161 (vtkStreamingDemandDrivenPipeline.cxx:353)

19  libvtkCommon-7.1.1.dylib      0x0000000124aff723 vtkDemandDrivenPipeline::UpdateInformation() + 307 (vtkDemandDrivenPipeline.cxx:403)

20  libvtkCommon-7.1.1.dylib      0x0000000124b45927 vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 39 (vtkStreamingDemandDrivenPipeline.cxx:372)

21  libvtkCommon-7.1.1.dylib      0x0000000124b458f6 vtkStreamingDemandDrivenPipeline::Update(int) + 38 (vtkStreamingDemandDrivenPipeline.cxx:365)

22  libvtkCommon-7.1.1.dylib      0x0000000124aece22 vtkAlgorithm::Update(int) + 50 (vtkAlgorithm.cxx:1457)

23  libvtkCommon-7.1.1.dylib      0x0000000124aecde6 vtkAlgorithm::Update() + 70 (vtkAlgorithm.cxx:1451)

24  libMRMLCore.dylib             0x00000001122d50af vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode*) + 6079 (vtkMRMLVolumeArchetypeStorageNode.cxx:348)

25  libMRMLCore.dylib             0x0000000112123e70 vtkMRMLStorageNode::ReadData(vtkMRMLNode*, bool) + 2992 (vtkMRMLStorageNode.cxx:1185)

26  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cef4ad vtkSlicerVolumesLogic::AddArchetypeVolume(std::__1::list<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int), std::__1::allocator<ArchetypeVolumeNodeSet (*)(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, vtkMRMLScene*, int)> > const&, char const*, char const*, int, vtkStringArray*) + 4669 (vtkSlicerVolumesLogic.cxx:700)

27  libvtkSlicerVolumesModuleLogic.dylib 0x0000000137cf0769 vtkSlicerVolumesLogic::AddArchetypeScalarVolume(char const*, char const*, int, vtkStringArray*) + 313 (vtkSlicerVolumesLogic.cxx:618)

28  libvtkSlicerVolumesModuleLogicPythonD.dylib 0x000000013db3975a PyvtkSlicerVolumesLogic_AddArchetypeScalarVolume(_object*, _object*) + 298 (vtkSlicerVolumesLogicPython.cxx:465)

29  libpython2.7.dylib            0x000000011c7803dc PyEval_EvalFrameEx + 14876 (ceval.c:4350)

30  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

31  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

32  libpython2.7.dylib            0x000000011c783d51 fast_function + 369 (ceval.c:4436)

33  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

34  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

35  libpython2.7.dylib            0x000000011c783c56 fast_function + 118 (ceval.c:4450)

36  libpython2.7.dylib            0x000000011c77fb55 PyEval_EvalFrameEx + 12693 (ceval.c:4371)

37  libpython2.7.dylib            0x000000011c77c65d PyEval_EvalCodeEx + 1997 (ceval.c:3582)

38  libpython2.7.dylib            0x000000011c71feab function_call + 363 (funcobject.c:526)

39  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

40  libpython2.7.dylib            0x000000011c703955 instancemethod_call + 325 (classobject.c:2602)

41  libpython2.7.dylib            0x000000011c6f7804 PyObject_Call + 100 (abstract.c:2546)

42  libpython2.7.dylib            0x000000011c7836d5 PyEval_CallObjectWithKeywords + 165 (ceval.c:4219)

43  libPythonQt.dylib             0x000000010f41e602 PythonQtSignalTarget::call(_object*, PythonQtMethodInfo const*, void**, bool) + 594 (PythonQtSignalReceiver.cpp:124)

44  libPythonQt.dylib             0x000000010f41e353 PythonQtSignalTarget::call(void**) const + 67 (PythonQtSignalReceiver.cpp:55)

45  libPythonQt.dylib             0x000000010f41f5cd PythonQtSignalReceiver::qt_metacall(QMetaObject::Call, int, void**) + 253 (PythonQtSignalReceiver.cpp:263)

46  QtCore                        0x000000011e422fca QMetaObject::activate(QObject*, QMetaObject const*, int, void**) + 1516

47  QtGui                         0x000000011dbf6202 QAbstractButton::clicked(bool) + 64

48  QtGui                         0x000000011d9b996e QAbstractButtonPrivate::emitClicked() + 52

49  QtGui                         0x000000011d9b9870 QAbstractButtonPrivate::click() + 196

50  QtGui                         0x000000011d9ba20a QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 88

51  libPythonQt.dylib             0x000000010f746487 PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent*) + 535 (com_trolltech_qt_gui6.cpp:10859)

52  QtGui                         0x000000011d70055b QWidget::event(QEvent*) + 1895

53  QtGui                         0x000000011d9ba116 QAbstractButton::event(QEvent*) + 160

54  libPythonQt.dylib             0x000000010f743670 PythonQtShell_QPushButton::event(QEvent*) + 688 (com_trolltech_qt_gui6.cpp:10451)

55  QtGui                         0x000000011d6c11ac QApplicationPrivate::notify_helper(QObject*, QEvent*) + 194

56  QtGui                         0x000000011d6c273a QApplication::notify(QObject*, QEvent*) + 1016

57  libqSlicerBaseQTGUI.dylib     0x000000010b6ea97f qSlicerApplication::notify(QObject*, QEvent*) + 63 (qSlicerApplication.cxx:384)

58  QtCore                        0x000000011e40eaf0 QCoreApplication::notifyInternal(QObject*, QEvent*) + 118

59  QtGui                         0x000000011d6c1a86 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) + 416

60  QtGui                         0x000000011d6794c7 qt_mac_handleMouseEvent(NSEvent*, QEvent::Type, Qt::MouseButton, QWidget*, bool) + 977

61  com.apple.AppKit              0x00007fffae9dfc92 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 1544

62  com.apple.AppKit              0x00007fffae9df2be -[NSWindow(NSEventRouting) sendEvent:] + 541

63  QtGui                         0x000000011d67178f -[QCocoaWindow sendEvent:] + 113

64  com.apple.AppKit              0x00007fffae867bf5 -[NSApplication(NSEvent) sendEvent:] + 1145

65  QtGui                         0x000000011d675c00 -[QNSApplication sendEvent:] + 97

66  com.apple.AppKit              0x00007fffae0e3f81 -[NSApplication run] + 1002

67  QtGui                         0x000000011d67e11b QEventDispatcherMac::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 1725

68  QtCore                        0x000000011e40bfc5 QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 77

69  QtCore                        0x000000011e40c13f QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 365

70  QtCore                        0x000000011e40ef4a QCoreApplication::exec() + 200

71                                0x000000010b2f25bd (anonymous namespace)::SlicerAppMain(int, char**) + 6829 (Main.cxx:243)

72                                0x000000010b2f0b02 main + 34 (Main.cxx:277)

73  libdyld.dylib                 0x00007fffc5b15255 start + 1

 

Thanks in advance,

Joao

 

On Mon, Feb 13, 2017 at 3:56 PM, Andrey Fedorov <[hidden email]> wrote:

And on Mac your ini file will be in  ~/.config/www.na-mic.org/Slicer.ini

 

You are sure you used the proper qmake while building Slicer, right?

 

It often happens there are multiple qmake's available on the system, and an incorrect one could be picked up by cmake. You can check it by going back to cmake and checking qmake location.

 

On Mon, Feb 13, 2017 at 10:53 AM, Csaba Pinter <[hidden email]> wrote:

Please double-check that the folder that you specify can be written without admin rights.

 

If you made sure of that and the error still occurs, I’d ty deleting the Slicer.ini file here

c:\Users\jsantinha\AppData\Roaming\NA-MIC\

 

csaba

 

From: joao santinha [mailto:[hidden email]]
Sent: Monday, February 13, 2017 10:44
To: Csaba Pinter <[hidden email]>; [hidden email]
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi Csaba and Andrey,

 

Yes I have tried and I get exactly the same error but for the new folder.

 

I am sending you also the terminal output that has more information.

 

Number of loaded modules: 138 

Switch to module:  "Welcome" 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleButton'; defaulting to base class 'QWidget'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

"QFormBuilder was unable to create a custom widget of the class 'ctkCollapsibleGroupBox'; defaulting to base class 'QGroupBox'." 

2017-02-13 15:35:10.821 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

Switch to module:  "DICOM" 

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

" DROP TABLE IF EXISTS 'SchemaInfo' ;" 

 

QSqlQuery::exec: database not open

There was an error during execution of the statement:  " DROP TABLE IF EXISTS 'SchemaInfo' ;" 

Error message:  "Driver not loaded Driver not loaded" 

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlQuery::exec: database not open

SQL failed

 Bad SQL: 

Error text: Driver not loaded Driver not loaded

QSqlDatabase: QSQLITE driver not loaded

QSqlDatabase: available drivers: 

QSqlDatabasePrivate::addDatabase: duplicate connection name 'SLICER', old connection removed.

The database file path "/Users/jsantinha/CODE/NewDatabaseFolder/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser.

2017-02-13 15:35:15.789 Slicer[18159:3424607] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

QSqlQuery::prepare: database not open

 

Thank you,

Joao

 

On Mon, Feb 13, 2017 at 3:29 PM, Csaba Pinter <[hidden email]> wrote:

Hi Joao,

 

Have you tried what the error message suggests?

“Please pick a different database directory using the LocalDatabase button in the DICOM Browser”

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of joao santinha
Sent: Monday, February 13, 2017 10:15
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Built Slicer Error DICOM Module - The database file path "ctkDICOM.sql" cannot be opened.

 

Hi all,

 

I have Slicer installed on my Mac, but I wanted to build it and run it from the source code. 

I followed the instruction provided in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions and chose the revision corresponding to Slicer 4.6.2.

 

When I launch Slicer and press the button to open the DICOM Module for loading DICOM datasets, I get an popup alert with the following message:

 

"The database file path "/Users/jsantinha/CODE/SlicerDatabase/ctkDICOM.sql" cannot be opened.

Please pick a different database directory using the LocalDatabase button in the DICOM Browser."

 

If I press ok, then I try to use the "Import" function and select DICOM studies but I get 0 New Patients, 0 New Studies, 0 New Series, 0 New Instances.

 

I thought it could be related to the fact that I had Slicer installed already and so I removed the installed version and re-build it but I get the same error.

 

Is this known? Is there a way to solve this issue?

 

Kind regards,

Joao 

 

 

 

 


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