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Computational biology and medical image processing scripts and programs
Once it is committed, add solveSOR to CMAKE build system as a mex function
Original issue reported on code.google.com by [email protected]
on 14 Jan 2015 at 12:25
Insert a spatial check when slices are ordered, such that the slices are
ordered in space rather then by selection.
Original issue reported on code.google.com by [email protected]
on 28 Jan 2015 at 10:07
What steps will reproduce the problem?
1. For example, rotate 90º to one side an image foo.mha with rotate3DImage
What is the expected output? What do you see instead?
Assume that foo.mha has resolution [sx, sy, sz].
The new image will have resolution [sx, sy, sz] too, but this means that in
fact the image content resolution has changed.
If the image has been rotated, now the resolution should be e.g. [sy, sx, sz].
Original issue reported on code.google.com by [email protected]
on 4 Mar 2010 at 3:49
Convert mex TV into normal matlab format.
Original issue reported on code.google.com by [email protected]
on 26 Nov 2014 at 10:15
1) Line
% Reformats nD-arrayed 2D image data for display as 2D montage.
should be changed to
% imagesc_nD Reformats nD-arrayed 2D image data for display as 2D montage.
2) Line "% IM_IN = nD data where first two dimensions correspond to a 2D
image. 3rd to nth dimension are arrays of" is too long. This makes "help
imagesc_nD" difficult to read. Matlab has smart justify to cut lines to a
maximum length.
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:05
Look for a way to merge changes made by Tasos and by Chris to dicomdir code.
To be discussed with Tasos on Tuesday.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 11:12
Decide on one of my functions to commit, ensure header etc in Gerardus format,
commit it.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 11:55
I think that property may be missing in some of the files, which translates
into bad EOLs when opening with notepad.exe in Windows
Original issue reported on code.google.com by [email protected]
on 19 Mar 2012 at 7:56
Missing:
copyright, licence, subversion properties (Rev, Date and native), checking input/output arguments.
Format problems:
function names must start with lower case.
matlab/CardiacToolbox/ImgCrossProduct.m
matlab/CardiacToolbox/ImgDotProduct.m
matlab/CardiacToolbox/ImgNormalise.m
matlab/CardiacToolbox/IsImgNormalised.m
matlab/CardiacToolbox/conv_hull_3D.m
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:20
Code that was mentioned in 6th Gerardus meeting to be committed.
Original issue reported on code.google.com by [email protected]
on 27 Jan 2015 at 4:07
Just do it
Original issue reported on code.google.com by [email protected]
on 26 Nov 2014 at 10:50
B-splines in ITK - elastix use an underlying grid, but elastix doesn't return
the location of the grid points. For illustration purposes, it would be useful
to have a Matlab function that computes those points.
The details of how the grid is computed are here:
elastix\trunkpublic\src\Common\Transforms\itkGridScheduleComputer
Original issue reported on code.google.com by [email protected]
on 13 Nov 2014 at 8:27
We have to meet
Original issue reported on code.google.com by [email protected]
on 10 Dec 2014 at 12:04
ChangeLog forgotten
Is CardiacToolbox the appropriate toolbox?
Isn't this the same as A*x?
Original issue reported on code.google.com by [email protected]
on 10 Dec 2014 at 11:19
Move code in personal script "histology_alone_mouse.m" to a function in the
repository.
Original issue reported on code.google.com by [email protected]
on 4 Nov 2014 at 9:11
shell-scripts/batch_process_subject.sh
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:49
Which image causes the new version reference frame code to crash?
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 11:58
We have to make papers reproducible. Code for papers gets developed in
private-gerardus, and when they are published, move to public gerardus.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 9:50
When you run the program extractVoxelCoordinatesFromSegmentationMask with
the -i flag, i.e. the output is formatted as voxel indices instead of real
world coordinates, the x- and y-coordinates are swapped.
A 3D volume voxel with indices
index[0], index[1], index[2]
maps to real world coordinates as
f(index[1]), f(index[0]), f(index[2])
That is, you need to swap index[0] and index[1].
Original issue reported on code.google.com by [email protected]
on 11 Sep 2009 at 1:32
Can be replaced by:
cross(A, B, 4)
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 11:13
I will submit the cmr42 contour reader to gerardus.
Added as an issue to keep me accountable :p
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 11:59
Ramon and I had a quick chat about the licencing nature of the project. The
project is currently licenced under the GPL with the main copyright holder
stated as the University of Oxford.
I was thinking that perhaps a more substantial discussion would be useful on
this topic, and it's something that should be addressed relatively early,
before we commit to substantial amounts of code / contributions. Ramon
encouraged me to post this as an 'issue' here.
Points to address would be:
* Is the current licence the best for the project
* Does it address the academic nature of the project (for instance, it does not
force or encourage people to cite the project or the individual author or
associated papers when using / modifying the code).
* What is the legal situation with the university being the main copyright
holder? Should the project has its own autonomous copyright? Do individual
authors / contributors have a say / rights over their work? Does submitting to
the project 'lock' a contributor out of their rights to that code?
* What is the legal position with using third-party code? For example, if we're
using a tool which has been modified from matlab's fileexchange, does this
affect us as a project? (see:
http://wiki.octave.org/FAQ#Why_can.27t_I_use_code_from_File_Exchange_in_Octave.3
F_It.27s_released_under_a_BSD_license.21 )
I would be keen to have a better idea about these issues before committing
substantially to the project; particularly the points about citeability and
code ownership.
Let me know your thoughts :)
Original issue reported on code.google.com by [email protected]
on 24 Oct 2014 at 2:20
Create small DICOM dataset that can be used as a test Dataset. ( Load DIMCOM
and vizualize it).
If public domain images, the dataset will go in public Gerardus. If images from
Biomedia Oxford clinical images, then the dataset will go into private
Gerardus.
path: matlab/test/data/dcm
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:22
It would simplify the scripts that we use for the local coordinate system work
if they used the scimat format.
Original issue reported on code.google.com by [email protected]
on 28 Jan 2015 at 12:19
Great work. Just a small thing. The help header does not contain the syntax(es)
of the function.
E.g. for function foo(), you would have
% Y = FOO(X)
%
% X is a scalar between 0 and 1.
%
% Y is the square value of X.
See for example
https://code.google.com/p/gerardus/source/browse/trunk/matlab/PointsToolbox/plot
_dmatrix.m
Original issue reported on code.google.com by [email protected]
on 25 Nov 2014 at 10:34
Add dicom read tools, available from MATLAB file exchange.
Upload my edits to this code with added functionality.
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:21
Possibly create a toolbox for all the DT code that is not cardiac-specific. e.g
Darryl's dt2image, fit_dt & then Jo's work (yet to be committed).
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 12:15
Ben to check his functions work with new DICOM read function added by Chris
Original issue reported on code.google.com by [email protected]
on 14 Jan 2015 at 12:01
Install TortoiseSVN.
Check out Gerardus to your hard drive.
Original issue reported on code.google.com by [email protected]
on 10 Dec 2014 at 11:15
HISTOLOGY_BLOCKFACE_REG Register deformed histology volume to blockface.
Original issue reported on code.google.com by [email protected]
on 4 Nov 2014 at 9:09
Currently, our CMake build system finds the installed Matlab version by running
something like "matlab -version". However, this is a bit slow, and requires to
be connected to the Uni VPN for Matlab installs that depend on the central
licence server.
So is there a way of finding out the version without having to run matlab?
Original issue reported on code.google.com by [email protected]
on 10 Feb 2015 at 10:52
TV filters should be added to Gerardus.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 10:57
If the m4 library is not installed, CMake will do the configuration step
("cmake ..") without problem, but then the build ("make") will fail when
compiling the GMP library.
If you look into the GMP compilation log, you see that the problem is that m4
is missing, but this may be a bit esoteric for most users.
The desired behaviour would be that cmake detects that m4 (or any other
dependency) is missing, and give a clear error at the configuration stage.
This is something that happens at least with the linux build, not sure whether
this is also a problem in Windows or MacOS X.
Original issue reported on code.google.com by [email protected]
on 16 Jan 2015 at 3:35
Code already written, just needs the help and copyright headers.
Original issue reported on code.google.com by [email protected]
on 14 Jan 2015 at 12:25
when calling the function
ImOut = itk_imfilter('advess',scimatIn,1,6,6,5);
I get an image with only minor edge effects different to the original. When
using a pure C++ itk implementation I get a much changed image.
link to images: https://www.dropbox.com/s/53xxj2vq5iggv47/AdvessImages.zip?dl=0
Original issue reported on code.google.com by [email protected]
on 28 Jan 2015 at 3:28
Attachments:
Darryl has added a MEX function
FiltersToolbox/forward_TV_mex.cpp
Ramon to integrate in the CMake build system.
Original issue reported on code.google.com by [email protected]
on 23 Nov 2014 at 12:16
Why isn't there a CMakeLists.txt file in matlab/PointsToolbox?
Original issue reported on code.google.com by [email protected]
on 19 Mar 2012 at 7:52
Look for functions that can be contributed.
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:08
Revision: 1659
Good work, Ben, although as a minor issue, the commit has kind of broken the
function ;). I have left notes directly on the code with the fixes that need to
be done. Your should be able to see them here:
https://code.google.com/p/gerardus/source/browse/trunk/matlab/FiltersToolbox/sci
mat_crop.m
Please have a look, try to fix it, and let me know if you need help.
Original issue reported on code.google.com by [email protected]
on 27 Jan 2015 at 11:13
Create sanity check function for loaded dicom data
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:22
Format from gmsh to Chaste
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:00
Visualization functions for DICOM struct
make any visualization functions consistent with DICOM struct format generated
for cine
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 1:25
private-gerardus:
matlab/CardiacToolbox/local_reference_frame
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:30
In matlab/CardiacToolbox/local_reference_frame.m:
% [rv, cv, lv, sf] = local_reference_frame(mask, 'first', 50);
%
%
% Author: Darryl McClymont <[email protected]>
should be
% [rv, cv, lv, sf] = local_reference_frame(mask, 'first', 50);
% Author: Darryl McClymont <[email protected]>
Otherwise, when you run "help local_reference_frame" in Matlab you get the
whole licence block.
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:22
surface_param:
XY plane:
'xy': Simple projection on XY.
'pca': Projection on main PCA plane.
'isomap': Isomap (with Dijkstra's shortest path).
'cmdsmap': MDS mapping, global neighbourhood, classical
MDS.
'lmdscale': MDS mapping, local neighbourhood, local MDS.
Unit sphere:
'sphproj': Simple projection on sphere around centroid.
'cald': CALD method by Shen & Makedon 2006.
'smdscale': Spherical extension of lmdscale.
tri_sphparam:
'cmdscale': Classical Multidimensional Scaling (MDS).
'smacof': Unconstrained SMACOF, followed by projection of points on
sphere.
'consmacof-global': Constrained SMACOF with untangling of all
vertices simulataneously (too slow except for small
problems).
'consmacof-local': Constrained SMACOF with local untangling of
connected vertices. If the algorithm cannot find a way to
untangle a local component, it leaves its vertices
untouched. This method is parallelized. To take advantage
of multiple threads, before running this function:
% activate pool of workers
matlabpool
% select number of parallel threads
myCluster = parcluster();
myCluster.NumWorkers = 6;
Original issue reported on code.google.com by [email protected]
on 10 Oct 2014 at 8:18
Syntax missing in help header for FORWARD_TV
Original issue reported on code.google.com by [email protected]
on 26 Nov 2014 at 10:06
No sufolders inside of toolboxes.
https://code.google.com/p/gerardus/source/browse/#svn%2Ftrunk%2Fmatlab%2FCardiac
Toolbox%2FgetCMR42Contours%253Fstate%253Dclosed
And getCMR42Contours is derivative from a third party toolbox too.
This should go in the ThirdPartyToolbox, in a subfolder with the toolbox name,
e.g. ThirdPartyToolbox/BlahBlahToolbox.
First, the original third party code is added and commited.
Then, you apply your changes, and add near their copyright/licence snippet
something along the lines of
% This is a derivative work of the original BlahBlah toolbox.
% Author: Tasos <[email protected]>
% Version: 0.1.0
% $Date$
% $Rev$
%
% Summary of changes:
%
% * modified GUI to select several files at the same time.
% * change of colours.
The script add_gerardus_path.m will pick up the new
ThirdPartyToolbox/BlahBlahToolbox folder and add it to the path, anyway.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 12:37
We have been discussing how to generate documentation for the functions in the
project.
It has to be automatic. E.g. we write a doc_foo.m script for function foo.m,
with examples on how to use it. This doc_foo.m generates some images too. Then,
we run something like Matlab Publisher (as suggested by Tasos), and this
produces XML, HTML or Wiki code, that can automatically be commited to
gerardus/wiki/.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 10:33
1) Whitespaces missing, function name in help header must be equal to actual
function name, and end with full stop:
"%DT_TO_IMAGE Inverses the transform in fit_DT"
to
"% DT_to_image Inverses the transform in fit_DT."
https://code.google.com/p/gerardus/source/browse/trunk/matlab/CardiacToolbox/DT_
to_image.m#2
2) Isn't it "Inverts" instead of "Inverses"?
3) Matlab tends to call this kind of function "dt2image.m" instead of
"DT_to_image.m" (e.g. ind2sub, sph2cart, etc.). And generally, we want lower
case for the beginning of function names.
Original issue reported on code.google.com by [email protected]
on 29 Oct 2014 at 12:48
Ask Adam to join
Original issue reported on code.google.com by [email protected]
on 5 Nov 2014 at 10:42
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