[vtkusers] Problem with Data in VTK

Fri Sep 22 23:54:11 EDT 2017

Hi,   Thanks so much again for the reply. But manually removing MD5 does not work. That's actually I just wanted to clarify. It helps me to know which files I should use. Like for the medical program, I tried to do that just by removing MD5 name from the file. But I get the following errors:
ERROR: In C:\VTK\VTK-8.0.1\IO\Image\vtkVolume16Reader.cxx, line 400
vtkVolume16Reader (0393A228): Error reading raw pgm data!
My question just how to get the clean data as we used to get in the early versions of VTK. Any suggestion will be highly appreciated

    On Wednesday, September 20, 2017 6:47 AM, David E DeMarle <dave.demarle at kitware.com> wrote:

 Your options are:1) manually move/rename the md5 files one by one (I don't recommend this)2) build vtk and let cmake rename/move the files automatically (not too hard)3) download and use the zipped up package of 8.0.1 data files I created with 1 and posted in my last email (very very easy):
   https://data.kitware.com/api/ v1/file/ 59c1aeec8d777f7d33e9d4f8/ download

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
On Tue, Sep 19, 2017 at 11:08 PM, Jennifer Lee <lee_jennifer_82 at yahoo.com> wrote:

Hello,    Thanks so much for taking time to work on this.  I didn't build using VTK_DATA. I found that there are some MD5 files related to data files in the following directory: C:\VTK\VTK-8.0.1\Testing\Data.
Suppose if I want to run Tcl files in Medical directory, I have MD5 files as follows:
C:\VTK\VTK-8.0.1\Testing\Data\ headsq\quarter.1.md5C:\VTK\VTK-8.0.1\Testing\Data\ headsq\quarter.2.md5C:\VTK\VTK-8.0.1\Testing\Data\ headsq\quarter.3.md5C:\VTK\VTK-8.0.1\Testing\Data\ headsq\quarter.3.md5:::
How to work with these MD5 files if I don't configure with VTK_DATA  in CMake.Thanks again in advance.
Regards,Jennifer

    On Tuesday, September 19, 2017 5:02 PM, David E DeMarle <dave.demarle at kitware.com> wrote:

 Sorry for the frustration Jennifer.
This is what I've done for demonstration.download VTK-8.0.1.zip to c:\tmp\foodownload VTKData-8.0.1.zip into to c:\tmp\foounzip bothc:\tmp\foo now contains VTK-8.0.1c:\tmp\foo\VTK-8.0.1 contains CMakeLists.txt, a bunch of other source code files, and a .ExternalData directory with all those md5's under it.
In a vs2013 x64 native tools command prompt (from visual studio community) I:
make a build directory "c:\tmp\foo\build" and cd into it
I run cmake -G Ninja ..\VTK-8.0.1 and let cmake configure the build files.Then I run ninja to compile from the command line (presumably I could have skipped -G Ninja above and then used visual studio ide intead but that's slower). 
The build starts off with a whole bunch of lines like this:C:\tmp\foo\build>nmake
[1/6225] Generating C:/tmp/foo/build/ExternalData/ Testing/Data/ex-blow_5/ex- blow_5_1_2.vtu
-- Found object: "C:/tmp/foo/VTK-8.0.1/. ExternalData/MD5/ 84001730339b29750bee19f1b4af52 ef"
[2/6225] Generating C:/tmp/foo/build/ExternalData/ Testing/Data/ex-blow_5/ex- blow_5_0_6.vtu
-- Found object: "C:/tmp/foo/VTK-8.0.1/. ExternalData/MD5/ 3a5df717510b2b8f59e5c16dc91ff0 67"
[3/6225] Generating -- Found object: ...
Meaning that it is making those links we spoke about to the md5 files. If I had skipped download unzip of VTKData-8.0.1.zip it would have instead downloaded each of the files instead of finding them.
When it is done, VTK_DATA_ROOT should be c:/tmp/foo/build/ExternalData/ Testing in my case as that is where the files end up.
To make it simpleer I've pushed a zipped up copy of what I've made above to:https://data.kitware.com/api/ v1/file/ 59c1aeec8d777f7d33e9d4f8/ download

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
On Sat, Sep 16, 2017 at 12:43 PM, Jennifer Lee <lee_jennifer_82 at yahoo.com> wrote:

Hi,   I don't have any ExternalData/Testing file. I'm using VTK. Could you let me know what I'm missing? All I've is some MD5 data under the following directory:C:\VTK\VTK-8.0.1\ Testing\Data.  When I downloaded VTKData, it looks all encrypted as follows:
  00b6935d399b80e4f9edc1414a4c36 3f00ba7d9399c914edb4a6faa0b10ae7 e500d2efba0581fb7d436bcc45a9aced cb
   I really don't understand what I am missing and how to solve the problem.  Any help will be highly appreciated. I used VTK in 2013. I never encountered this problem. That time I could use the data directly. And I just needed to set VTK_DATA_ROOT. I'm confused with MD5 files and encrypted VTKData. I just need to know how I can find the original data.  Any clarification will be highly appreciated. 
Regards,Jennifer 

    On Friday, September 15, 2017 11:03 AM, Shawn Waldon <shawn.waldon at kitware.com> wrote:

 Hi Jennifer,

Try looking inside ExternalData/Testing inside your ParaView build directory.  This folder should contain the data files with their original filenames rather than the MD5s (or symlinks/shortcuts to the data to save disk space but should work the same).

HTH,
Shawn

On Fri, Sep 15, 2017 at 1:47 PM, Jennifer Lee via vtkusers <vtkusers at vtk.org> wrote:

Hi,   I've the following directory: C:\VTK\VTK-8.0.1\Testing\ External;  This contains the following two files: CMakeLists and CMakeConfig.cmake.

   I don't have any C:\VTK\VTK-8.0.1\ExternalData\ Testing.    I've also attached some screenshots of some directories just if you need for further clarification.
   I really don't understand  what I'm missing and why it should be so complication to work with current data. Any help will be highly appreciated.
Regards,Jennifer 

 On Thursday, September 14, 2017 3:20 PM, David E DeMarle <dave.demarle at kitware.com> wrote:

 What is in C:\VTK\VTK-8.0.1\ ExternalData\Testing?

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
On Thu, Sep 14, 2017 at 5:22 PM, Jennifer Lee <lee_jennifer_82 at yahoo.com> wrote:

Hi,   Thanks for the reply. I downloaded the data and set the VTK_DATA_ROOT to C:\VTK\VTKData.    Actually that's what I used to do before. I never built VTKData project. How to do that? I believe the source will be C:\VTK\VTKData; but which one will be the build directory?   Please let  me know.   I've built the VTK project with BUILD_TESTING on. This generated data to the following directory:  
  C:\VTK\VTK-8.0.1\Testing\Data\ headsq. But these are all MD5 files and if VTK_DATA_ROOT is pointed there, it can't find these files.
   Any clarification will be highly appreciated. 

Regards,Jennifer

    On Wednesday, September 13, 2017 11:15 PM, Jon Haitz Legarreta <jhlegarreta at vicomtech.org> wrote:

 Hi Jennifer,
what does your C:\VTK\VTKData directory contain? Have you built the VTKData project? You must build that project so that the actual testing data files are retrieved.

HTH,
JON HAITZ

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On 14 September 2017 at 07:58, Jennifer Lee via vtkusers <vtkusers at vtk.org> wrote:

Hello,     Still I could notmake it work. Setting VTK_DATA_ROOT to ‘C:\VTK\VTK-8.0.1\ ExternalData\Testing’didn’t work for me. It can’t find the data.  I have separate source and build: Source is : C:\VTK\VTK-8.0.1Build is: C:\VTK\VTK-binData is: C:\VTK\VTKData  As I also built with TESTING_ON; so, I’ve MD5 files underTesting directory. C:\VTK\VTK-8.0.1\Testing. I tried to run the tcl script Medical1.tcl. If I set the  data root to ‘C:\VTK\VTK-8.0.1\Testing’, itcan’t find the data (I think because these are MD5 files). If I set the dataroot to C:\VTK\VTKData, it also does not work. I need help to fix the problem.Thanks! Regards,Jennifer 

    On Wednesday, September 13, 2017 7:58 AM, David E DeMarle <dave.demarle at kitware.com> wrote:

 On Wed, Sep 13, 2017 at 2:12 AM, Jennifer Lee <lee_jennifer_82 at yahoo.com> wrote:

Hello,   Thanks so much for the reply. 
Please ignore my poor knowledge. I’m really having troublein understanding. 

No worries, this confuses lots of people including me. 

I’ve data in the following directory:
C:\VTK\VTKData-8.0.1\VTK-8.0. 1\.ExternalData\MD5. Now, thefiles look like something below: 
00b6935d399b80e4f9edc1414a4c36 3f00ba7d9399c914edb4a6faa0b10ae7 e500d2efba0581fb7d436bcc45a9aced cb00d49b1746f315992fac476892c681 ae::::I really don’t understand what they mean. It seems tome  these are some encrypted names whichneed to be decrypted. I don’t know how to do that.

These are checksums of the real data files. Cmake and git know that they have to download a different file whenever the data file's checksum doesn't agree with the above. 
I built with TESTING_ON, now data are available in the “Testing”directory too. Suppose I’d like to run the Medical examples. Now, data isavailable in the following directory:

C:\VTK\VTK-8.0.1\Testing\Data\ headsq
With VTK_DATA_ROOT set to C:\VTK\VTK-8.0.1\Testing
But these are all MD5 files. So the following line of thecode does not find the data:
v16 SetFilePrefix "$VTK_DATA_ROOT/Data/headsq/ quarter".
Please help me how to make things work. If I've missed any step, please let me know.Thanks in advance.

Where is you build directory? I highly recommend always keeping your VTK source directory and your VTK build directory separate.
Assuming you've built VTK in C:\VTK\VTK-8.0.1, try setting VTK_DATA_ROOT to C:\VTK\VTK-8.0.1\ExternalData\ Testing. This is where the data file links are. The real data files are elsewhere in files with MD5 names, but for all intents and purposes the data link files that refer to them work as if they were the read data files.

Regards,Jennifer

    On Tuesday, September 12, 2017 9:32 AM, David E DeMarle <dave.demarle at kitware.com> wrote:

 We changed the structure of regression test data in 6.1 to allow developers to make proposed changes to code and data concurrently and ensure that the continuous integration test machines do not fail when they run new tests on old data.
The net result is that a VTK build tree has test data files that are actually symbolic links to the md5 files which live elsewhere. You can generally open and use the symbolic links exactly as you would a normal data file. If you turn on testing in your build, cmake will try to download each one of the files. Alternatively you can untar the source and data packages for a release in the same directory and the default build setup will use them and avoid downloading anything else.

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
On Sat, Sep 9, 2017 at 7:43 PM, Jennifer Lee via vtkusers <vtkusers at vtk.org> wrote:

  Hello,     I used VTK in 2013. After that, I installed VTK after more than 4 years. I found some changes in Data in the latest version. How to make those MD5 files work? Please let me know. I didn't find much documentation. I'm really having problem with this.     Thanks in advance!
Regards,Jennifer.
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