(0009662)
Rupert Brooks (reporter)
2007-11-10 11:57

The thisbreaksreader.mnc file is not experimental data - it is intentionally a file of all zeros. It is the structure of this file that somehow breaks the reader. The data contents are meaningless.

Sorry for any confusion this may have caused. Not enough coffee for me apparently.

-rb

(0010527)
Rupert Brooks (reporter)
2008-02-16 13:30

I have noticed another strange property of this class. I am not sure whether this is a bug, or a feature. The class will reorder the dimensions of the incoming file so that the axis that varies the most in Z, is the third axis, the one that varies the most in Y is the second and so forth.

I found this a very unnatural behavior - i have a number of ultrasound slices to import, at varying locations in space. Some come in with dimensions 1x240x320, some come in as 240x320x1, some come in as 320x240x1. They are all ordered identically in the incoming file.

This is a designed behavior, not an accident. It is explicitly done in the function
void MINC2ImageIO::XYZFromDirectionCosines(midimhandle_t *hdims, int *dim_indices, int *numberOfComponents)
in itkMINC2ImageIO.cxx

I think a more logical behavior would be to either read them in in the order they are in the MINC file, or to assign zspace, yspace, xspace in minc to Z,Y,X in ITK.

(0014471)
Steve Robbins (developer)
2009-01-07 01:29

Over the recent holiday, I wrote more test cases and tried modifying MINC2ImageIO to get them passing. Along the way I discovered that it fails completely for 2D images and that Read() doesn't pay attention to the ImageIORegion as it should.

I'm attaching the test cases (written using Googletest) even though they are a long way from complete, in the hope that someone else will help complete them.

Using these tests I started a rewrite of MINC2ImageIO, which also remains unfinished (but does past the test suite so far). Write me if you want the code.

(0014494)
Luis Ibanez (manager)
2009-01-09 03:53

We are reviewing the support for Streaming in the ImageFileWriter, and along with it, the behavior expected for the ImageIORegion. We will like to see your modifications to the MINC2ImageIO.

(0014550)
Steve Robbins (developer)
2009-01-14 01:40

Luis: I put my tests and code into a GIT repository; you can retrieve it using "git clone git://github.com/smr99/itk-mincimageio.git" [^]

(0014551)
Steve Robbins (developer)
2009-01-14 01:46

Further to the git repository: you can also obtain the fails in tar or zip format using the "Download" button on this page: http://github.com/smr99/itk-mincimageio/tree/master [^]

(0022973)
Luis Ibanez (manager)
2010-11-07 01:14

Steve,
Is this still an issue ?

Should we use the MINC2ImageIO from your Git repository in order to update the class in ITKv4 ?

(0022986)
Steve Robbins (developer)
2010-11-07 01:19

Luis,

I have not touched this since January, 2009. I assume what I wrote then still holds. I think the unit tests improved coverage, but my fixes were just the beginning. This class needs a whole lot of attention before I'd trust it with my data.

Issue History
Date Modified	Username	Field	Change
2007-11-10 11:45	Rupert Brooks	New Issue
2007-11-10 11:45	Rupert Brooks	File Added: testmincio.zip
2007-11-10 11:57	Rupert Brooks	Note Added: 0009662
2008-01-23 10:44	Luis Ibanez	Status	new => assigned
2008-01-23 10:44	Luis Ibanez	Assigned To	=> Andinet
2008-02-16 13:30	Rupert Brooks	Note Added: 0010527
2009-01-07 01:29	Steve Robbins	Note Added: 0014471
2009-01-07 01:30	Steve Robbins	File Added: testmincio-smr.tar.gz
2009-01-09 03:51	Luis Ibanez	Assigned To	Andinet => Luis Ibanez
2009-01-09 03:53	Luis Ibanez	Note Added: 0014494
2009-01-14 01:40	Steve Robbins	Note Added: 0014550
2009-01-14 01:46	Steve Robbins	Note Added: 0014551
2010-11-07 01:14	Luis Ibanez	Note Added: 0022973
2010-11-07 01:19	Steve Robbins	Note Added: 0022986

Notes
(0009662) Rupert Brooks (reporter) 2007-11-10 11:57	The thisbreaksreader.mnc file is not experimental data - it is intentionally a file of all zeros. It is the structure of this file that somehow breaks the reader. The data contents are meaningless. Sorry for any confusion this may have caused. Not enough coffee for me apparently. -rb

(0010527) Rupert Brooks (reporter) 2008-02-16 13:30	I have noticed another strange property of this class. I am not sure whether this is a bug, or a feature. The class will reorder the dimensions of the incoming file so that the axis that varies the most in Z, is the third axis, the one that varies the most in Y is the second and so forth. I found this a very unnatural behavior - i have a number of ultrasound slices to import, at varying locations in space. Some come in with dimensions 1x240x320, some come in as 240x320x1, some come in as 320x240x1. They are all ordered identically in the incoming file. This is a designed behavior, not an accident. It is explicitly done in the function void MINC2ImageIO::XYZFromDirectionCosines(midimhandle_t hdims, int dim_indices, int *numberOfComponents) in itkMINC2ImageIO.cxx I think a more logical behavior would be to either read them in in the order they are in the MINC file, or to assign zspace, yspace, xspace in minc to Z,Y,X in ITK.

(0014471) Steve Robbins (developer) 2009-01-07 01:29	Over the recent holiday, I wrote more test cases and tried modifying MINC2ImageIO to get them passing. Along the way I discovered that it fails completely for 2D images and that Read() doesn't pay attention to the ImageIORegion as it should. I'm attaching the test cases (written using Googletest) even though they are a long way from complete, in the hope that someone else will help complete them. Using these tests I started a rewrite of MINC2ImageIO, which also remains unfinished (but does past the test suite so far). Write me if you want the code.

(0014494) Luis Ibanez (manager) 2009-01-09 03:53	We are reviewing the support for Streaming in the ImageFileWriter, and along with it, the behavior expected for the ImageIORegion. We will like to see your modifications to the MINC2ImageIO.

(0014550) Steve Robbins (developer) 2009-01-14 01:40	Luis: I put my tests and code into a GIT repository; you can retrieve it using "git clone git://github.com/smr99/itk-mincimageio.git" [^]

(0014551) Steve Robbins (developer) 2009-01-14 01:46	Further to the git repository: you can also obtain the fails in tar or zip format using the "Download" button on this page: http://github.com/smr99/itk-mincimageio/tree/master [^]

(0022973) Luis Ibanez (manager) 2010-11-07 01:14	Steve, Is this still an issue ? Should we use the MINC2ImageIO from your Git repository in order to update the class in ITKv4 ?

(0022986) Steve Robbins (developer) 2010-11-07 01:19	Luis, I have not touched this since January, 2009. I assume what I wrote then still holds. I think the unit tests improved coverage, but my fixes were just the beginning. This class needs a whole lot of attention before I'd trust it with my data.

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