[Insight-users] MetaImage: absolute path in ElementDataFile not working
Florian Pierron
F.Pierron at exeter.ac.uk
Tue May 13 18:57:39 EDT 2008
Hi Luis,
Sorry for the misunderstanding: yes I was speaking about the
ElementDataFile field inside the .mhd / header file.
The thing is that I don't necessary have the write access on the folder
containing the raw image. That's the reason why I need an absolute path...
To give you the full picture of the problem, I need to read really
really really really big data (300 GB) and resample / crop them on
import. I tried to use the UseStreamedReadingOn on the RawImageIO and
UseStreamingOn on the ImageFileReader followed by a
RegionOfInterestImageFilter and ShrinkImageFilter. But I couldn't get
the streaming work on the RawImageIO. After reading some posts on the
mailing list, it seems that the MetaImageIO is the only streamable
reader. So I created a temporary .mhd file and the streaming seems to
work like a charm now :-). That is simply amazing, thanks for this good
piece of code!
Regards,
Florian
PS: I think the patch I provided to allow absolute path in the
ElementDataFile of an .mha file is quite useful for the reason mentioned
above. Moreover
if the ElementDataFile field is NOT an absolute path, it will work as
before and append the header path to the ElementDataFile. But if the
ElementDataFile field is an absolute path, it will NOT append the header
path. But at the end, you are the one who decides ;-)
On 13/05/2008 22:52, Luis Ibanez wrote:
>
> Hi Florian,
>
> I just confirmed that in Windows XP with
> my Visual Studio 7.1 build I can successfully
> run the following command:
>
> Insight/bin/release/ImageReadWrite.exe
> "C:/cygwin/home/ibanez/data/One Space/brainweb165a10f17.mha"
> output.mhd
>
>
> (in a single line).
>
>
> This seems to indicate that MetaImage (at least in this
> platform) can read both Absolute paths and paths with
> a space on them.
>
>
> Also, all tests that are run in the Dashboard use absolute
> paths. This is because CMake expands/resolve all paths to
> absolute when generated the test command line in the
> ADD_TEST() statement.
>
>
> -----
>
>
> In any case, I just realize what the problem is,
> Sorry that I didn't get it in the first email.
>
>
> Your header file MyData.mhd contains:
>
> ElementDataFile = C:\Program Files\Data\MyData.raw
>
> It should just be:
>
> ElementDataFile = MyData.raw
>
>
> The MetaImage library takes care of appending to
> the raw file the path of the .mhd file.
>
> Otherwise you couldn't ever move your files from
> one directory to another. You simply need to keep
> the two files (.mhd and .raw) together in the same
> directory.
>
>
>
>
>
> Thanks
>
>
> Luis
>
>
> -------------------------
> Florian Pierron wrote:
>> Hi Luis,
>>
>> Sorry to take so much of your time, but it's still not working for me
>> (without spaces in the path).
>>
>> The patch that I described previously by changing the condition on
>> the variable 'usePath' seems to fix the problem. Are you sure
>> MetaImage supports absolute path in the ElementDataFile field?
>>
>> Regards,
>> Florian
>>
>>
>> On 13/05/2008 17:30, Luis Ibanez wrote:
>>
>>>
>>> Hi Florian,
>>>
>>> Thanks for sending our files.
>>>
>>> I'm not sure that MetaImage can manage
>>> filenames that have spaces in the path....
>>>
>>>
>>> Your file is located at:
>>>
>>> "C:\Program Files\Data\MyData.raw"
>>>
>>>
>>> Just to double check,
>>> Please do the following
>>>
>>> Move your .mhd and .raw files to a directory
>>> without spaces. Something like:
>>>
>>> C:\itktest\MyData.mhd
>>> C:\itktest\MyData.raw
>>>
>>>
>>> Try to read them from that location,
>>> and let us know what you find.
>>>
>>> If you can read the files then we
>>> should probably fill a bug report
>>> regarding filenames with spaces
>>> and the MetaImage library.
>>>
>>>
>>> Thanks
>>>
>>>
>>> Luis
>>>
>>>
>>> -----------------------
>>> Florian Pierron wrote:
>>>
>>>> Hi Luis,
>>>>
>>>> Thanks for your quick reply.
>>>>
>>>> I am using VC2005 to compile the code. I don't see anything
>>>> obviously wrong with the path, it is:
>>>> ElementDataFile = C:\Program Files\Data\MyData.raw
>>>>
>>>> I have attached the .mha file and the .raw image. Let me know if
>>>> you can load it.
>>>>
>>>> Regards,
>>>> Florian
>>>>
>>>> ***********************
>>>> ObjectType = Image
>>>> NDims = 2
>>>> DimSize = 50 50
>>>> ElementByteOrderMSB = False
>>>> ElementNumberOfChannels = 1
>>>> ElementType = MET_UCHAR
>>>> ElementDataFile = C:\Program Files\Data\MyData.raw
>>>> ***********************
>>>>
>>>>
>>>> On 12/05/2008 14:50, Luis Ibanez wrote:
>>>>
>>>>>
>>>>> Hi Florian,
>>>>>
>>>>> Could you please post the *exact* absolute path that you were using
>>>>> when you encounter this problem ?
>>>>>
>>>>> We are able to read files with absolute path without any problem.
>>>>> It is therefore likely that there is something special about the
>>>>> path that you were using.
>>>>>
>>>>> Also, please let us know what platform are you using.
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>>
>>>>> Luis
>>>>>
>>>>>
>>>>> ---------------------
>>>>> Florian Pierron wrote:
>>>>>
>>>>>> Dear ITK developer team,
>>>>>>
>>>>>> I noticed that having an absolute path in the ElementDataFile is
>>>>>> not supported in ITK 3.4.0. I don't know if there is a good
>>>>>> reason for that or if it's just by mistake but it seems that
>>>>>> there is an easy fix to that (if I am not wrong...). I have
>>>>>> changed the following lines in \Utilities\MetaIO\metaImage.cxx:
>>>>>>
>>>>>> - usePath = MET_GetFilePath(_headerName, pathName)
>>>>>>
>>>>>> by
>>>>>>
>>>>>> + usePath = !MET_GetFilePath(elementDataFileName.c_str(),
>>>>>> pathName) &&
>>>>>> + MET_GetFilePath(_headerName, pathName);
>>>>>>
>>>>>> So that usePath (which determines in fact if the path to the
>>>>>> header / meta file should be append to the elementDataFileName)
>>>>>> is used only if the elementDataFileName is not an absolute path
>>>>>> and if there is a path for the header / meta file.
>>>>>>
>>>>>> Find attached the patch file.
>>>>>>
>>>>>> Regards,
>>>>>> Florian
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> ### Eclipse Workspace Patch 1.0
>>>>>> #P ITK_3_4_0
>>>>>> Index: Utilities/MetaIO/metaImage.cxx
>>>>>> ===================================================================
>>>>>> RCS file: /cvsroot/Insight/Insight/Utilities/MetaIO/metaImage.cxx,v
>>>>>> retrieving revision 1.76
>>>>>> diff -u -r1.76 metaImage.cxx
>>>>>> --- Utilities/MetaIO/metaImage.cxx 12 Sep 2007 11:46:05
>>>>>> -0000 1.76
>>>>>> +++ Utilities/MetaIO/metaImage.cxx 12 May 2008 10:53:09 -0000
>>>>>> @@ -3,7 +3,7 @@
>>>>>> Program: MetaIO
>>>>>> Module: $RCSfile: metaImage.cxx,v $
>>>>>> Language: C++
>>>>>> - Date: $Date: 2007-09-12 11:46:05 $
>>>>>> + Date: $Date: 2007/09/12 11:46:05 $
>>>>>> Version: $Revision: 1.76 $
>>>>>>
>>>>>> Copyright (c) Insight Software Consortium. All rights reserved.
>>>>>> @@ -1118,10 +1118,6 @@
>>>>>> return false;
>>>>>> }
>>>>>>
>>>>>> - bool usePath;
>>>>>> - char pathName[255];
>>>>>> - usePath = MET_GetFilePath(_headerName, pathName);
>>>>>> -
>>>>>> char* buf = new char[8001];
>>>>>> inputStream.read(buf,8000);
>>>>>> unsigned long fileSize = inputStream.gcount();
>>>>>> @@ -1139,6 +1135,10 @@
>>>>>>
>>>>>> std::string elementDataFileName =
>>>>>> M_GetTagValue(header,"ElementDataFile");
>>>>>>
>>>>>> + char pathName[255];
>>>>>> + bool usePath = !MET_GetFilePath(elementDataFileName.c_str(),
>>>>>> pathName) && + MET_GetFilePath(_headerName,
>>>>>> pathName);
>>>>>> +
>>>>>> char* fName = new char[512];
>>>>>>
>>>>>> if(!strcmp("Local", elementDataFileName.c_str()) || @@
>>>>>> -1375,10 +1375,10 @@
>>>>>> }
>>>>>>
>>>>>> int i, j;
>>>>>> - bool usePath;
>>>>>> char pathName[255];
>>>>>> char fName[255];
>>>>>> - usePath = MET_GetFilePath(m_FileName, pathName);
>>>>>> + bool usePath = !MET_GetFilePath(m_ElementDataFileName,
>>>>>> pathName) && + MET_GetFilePath(m_FileName,
>>>>>> pathName);
>>>>>>
>>>>>> if(!strcmp("Local", m_ElementDataFileName) ||
>>>>>> !strcmp("LOCAL", m_ElementDataFileName) ||
>>>>>> @@ -1620,7 +1620,8 @@
>>>>>> }
>>>>>>
>>>>>> char pathName[255];
>>>>>> - bool usePath = MET_GetFilePath(m_FileName, pathName);
>>>>>> + bool usePath = !MET_GetFilePath(m_ElementDataFileName,
>>>>>> pathName) && + MET_GetFilePath(m_FileName,
>>>>>> pathName);
>>>>>> if(usePath)
>>>>>> {
>>>>>> char elementPathName[255];
>>>>>> @@ -2240,7 +2241,8 @@
>>>>>> {
>>>>>> char dataFileName[255];
>>>>>> char pathName[255];
>>>>>> - bool usePath = MET_GetFilePath(m_FileName, pathName);
>>>>>> + bool usePath = !MET_GetFilePath(m_ElementDataFileName,
>>>>>> pathName) && + MET_GetFilePath(m_FileName,
>>>>>> pathName);
>>>>>> if(usePath)
>>>>>> {
>>>>>> sprintf(dataFileName, "%s%s", pathName,
>>>>>> m_ElementDataFileName);
>>>>>> @@ -2471,10 +2473,10 @@
>>>>>> m_Quantity *= (_indexMax[i] - _indexMin[i] + 1);
>>>>>> }
>>>>>>
>>>>>> - bool usePath;
>>>>>> char pathName[255];
>>>>>> char fName[255];
>>>>>> - usePath = MET_GetFilePath(m_FileName, pathName);
>>>>>> + bool usePath = !MET_GetFilePath(m_ElementDataFileName,
>>>>>> pathName) && + MET_GetFilePath(m_FileName,
>>>>>> pathName);
>>>>>>
>>>>>> if(!strcmp("Local", m_ElementDataFileName) ||
>>>>>> !strcmp("LOCAL", m_ElementDataFileName) ||
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Insight-users mailing list
>>>>>> Insight-users at itk.org
>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> ObjectType = Image
>>>> NDims = 2
>>>> DimSize = 50 50
>>>> ElementByteOrderMSB = False
>>>> ElementNumberOfChannels = 1
>>>> ElementType = MET_UCHAR
>>>> ElementDataFile = C:\Program Files\Data\MyData.raw
>>>
>>>
>>
>
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