I have the following script that I am writing which in the end is going to generate one of our DREAM3D style hdf5 files. I have a self compiled hdf5 1.8.10-patch 1 on an OS X 10.6.8 system. here is the script
#!/bin/bash
# This script will attempt to convert ascii text files into a .dream3d file
# We assume that the h5import program is in the current path
# First we need the dimensions, resolution and origin of the voxel data
HDF5_INSTALL="/Users/Shared/Toolkits/hdf5-1.8.10"
PATH=$PATH:$HDF5_INSTALL/bin
When I run the script I get the following error:
[mjackson@Ferb:Desktop]$ ./AsciiToDream3D.sh
Unknown keyword in configuration file: /tmp/dims.config
Error in processing the configuration file: /tmp/dims.config.
Program aborted.
I followed one of the examples given in the help for h5import. Any idea what h5import is complaining about? Also as a usage note, it would be nice if the error message actually output which keyword h5import had an issue with. Would help the debugging a lot.
1.8.10 h5import can now use h5dump output files, would that work?
Allen
···
On Thursday, February 28, 2013 11:38:02 AM Michael Jackson wrote:
I have the following script that I am writing which in the end is going to
generate one of our DREAM3D style hdf5 files. I have a self compiled hdf5
1.8.10-patch 1 on an OS X 10.6.8 system. here is the script
#!/bin/bash
# This script will attempt to convert ascii text files into a .dream3d file
# We assume that the h5import program is in the current path
# First we need the dimensions, resolution and origin of the voxel data
HDF5_INSTALL="/Users/Shared/Toolkits/hdf5-1.8.10"
PATH=$PATH:$HDF5_INSTALL/bin
When I run the script I get the following error:
[mjackson@Ferb:Desktop]$ ./AsciiToDream3D.sh
Unknown keyword in configuration file: /tmp/dims.config
Error in processing the configuration file: /tmp/dims.config.
Program aborted.
I followed one of the examples given in the help for h5import. Any idea what
h5import is complaining about? Also as a usage note, it would be nice if
the error message actually output which keyword h5import had an issue with.
Would help the debugging a lot.
Thanks
___________________________________________________________
Mike Jackson Principal Software Engineer
BlueQuartz Software Dayton, Ohio mike.jackson@bluequartz.netwww.bluequartz.net
1.8.10 h5import can now use h5dump output files, would that work?
Allen
On Thursday, February 28, 2013 11:38:02 AM Michael Jackson wrote:
I have the following script that I am writing which in the end is going to
generate one of our DREAM3D style hdf5 files. I have a self compiled hdf5
1.8.10-patch 1 on an OS X 10.6.8 system. here is the script
#!/bin/bash
# This script will attempt to convert ascii text files into a .dream3d file
# We assume that the h5import program is in the current path
# First we need the dimensions, resolution and origin of the voxel data
HDF5_INSTALL="/Users/Shared/Toolkits/hdf5-1.8.10"
PATH=$PATH:$HDF5_INSTALL/bin
When I run the script I get the following error:
[mjackson@Ferb:Desktop]$ ./AsciiToDream3D.sh
Unknown keyword in configuration file: /tmp/dims.config
Error in processing the configuration file: /tmp/dims.config.
Program aborted.
I followed one of the examples given in the help for h5import. Any idea what
h5import is complaining about? Also as a usage note, it would be nice if
the error message actually output which keyword h5import had an issue with.
Would help the debugging a lot.
Thanks
___________________________________________________________
Mike Jackson Principal Software Engineer
BlueQuartz Software Dayton, Ohio mike.jackson@bluequartz.netwww.bluequartz.net
Yes that is the basic idea, check the h5import help and the tools reference
manual web page for the details. I think you may need another switch to get
enough info in the header.
Allen
···
On Thursday, February 28, 2013 03:28:57 PM Michael Jackson wrote:
On Feb 28, 2013, at 3:05 PM, Allen D Byrne wrote:
> 1.8.10 h5import can now use h5dump output files, would that work?
>
> Allen
>
> On Thursday, February 28, 2013 11:38:02 AM Michael Jackson wrote:
>> I have the following script that I am writing which in the end is going
>> to
>> generate one of our DREAM3D style hdf5 files. I have a self compiled hdf5
>> 1.8.10-patch 1 on an OS X 10.6.8 system. here is the script
>>
>> #!/bin/bash
>> # This script will attempt to convert ascii text files into a .dream3d
>> file
>> # We assume that the h5import program is in the current path
>>
>> # First we need the dimensions, resolution and origin of the voxel data
>> HDF5_INSTALL="/Users/Shared/Toolkits/hdf5-1.8.10"
>> PATH=$PATH:$HDF5_INSTALL/bin
>>
>> dimsFile="/tmp/dims.txt"
>> echo "25 50 10" > $dimsFile
>> dimsConfig="/tmp/dims.config"
>> echo "PATH VoxelDataContainer DIMENSIONS" > $dimsConfig
>> echo "INPUT-CLASS TEXTIN" >> $dimsConfig
>> echo "RANK 1" >> $dimsConfig
>> echo "DIMENSION-SIZES 3" >> $dimsConfig
>> echo "OUTPUT-CLASS IN" >> $dimsConfig
>> echo "OUTPUT-SIZE 64" >> $dimsConfig
>> echo "OUTPUT-ARCHITECTURE IEEE" >> $dimsConfig
>> echo "OUTPUT-BYTE-ORDER LE" >> $dimsConfig
>>
>> resFile="/tmp/res.txt"
>> echo "1.0 0.75 0.25" > $resFile
>> resConfig="/tmp/res.config"
>> echo "PATH VoxelDataContainer SPACING" > $resConfig
>> echo "INPUT-CLASS TEXTFP" >> $resConfig
>> echo "RANK 1" >> $resConfig
>> echo "DIMENSION-SIZES 3" >> $resConfig
>> echo "OUTPUT-CLASS FP" >> $resConfig
>> echo "OUTPUT-SIZE 32" >> $resConfig
>> echo "OUTPUT-ARCHITECTURE IEEE" >> $resConfig
>> echo "OUTPUT-BYTE-ORDER LE" >> $resConfig
>>
>> orgFile="/tmp/origin.txt"
>> echo "0 0 0" > $orgFile
>> orgConfig="/tmp/origin.config"
>> echo "PATH VoxelDataContainer ORIGIN" > $orgConfig
>> echo "INPUT-CLASS TEXTFP" >> $orgConfig
>> echo "RANK 1" >> $orgConfig
>> echo "DIMENSION-SIZES 3" >> $orgConfig
>> echo "OUTPUT-CLASS FP" >> $orgConfig
>> echo "OUTPUT-SIZE 32" >> $orgConfig
>> echo "OUTPUT-ARCHITECTURE IEEE" >> $orgConfig
>> echo "OUTPUT-BYTE-ORDER LE" >> $orgConfig
>>
>> h5import $dimsFile -config $dimsConfig $resFile -config $resConfig
>> $orgFile -config $orgConfig -outfile /tmp/out.dream3d
>>
>> When I run the script I get the following error:
>> [mjackson@Ferb:Desktop]$ ./AsciiToDream3D.sh
>> Unknown keyword in configuration file: /tmp/dims.config
>> Error in processing the configuration file: /tmp/dims.config.
>> Program aborted.
>>
>> I followed one of the examples given in the help for h5import. Any idea
>> what h5import is complaining about? Also as a usage note, it would be
>> nice if the error message actually output which keyword h5import had an
>> issue with. Would help the debugging a lot.
>>
>> Thanks
>> ___________________________________________________________
>> Mike Jackson Principal Software Engineer
>> BlueQuartz Software Dayton, Ohio
>> mike.jackson@bluequartz.netwww.bluequartz.net
>>
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum@hdfgroup.org
>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
