Extract submatrix from ROI

[Vincent Le Saux]

Hi all,

I'm using guiqwt and guidata to build a simple software dedicated to the
processing of infrared images (succession of images) and it is pretty easy
with guidata and guiqwt (thanks Pierre!). One of my main concern is to
analyze specific areas of various form and to perform mean operation over
these zones in order to get a scalar. So, I need:
- to draw the specific forms I need on the image -> No problem thanks
to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific forms,
i.e. the list of pixels that are contained in the form -> I didn't find
such tools in the source code (the cross_section tools can be easily
adapted for the rectangle shape, but for the other forms, I'm stucked!).

So my question is: is it possible to extract easily and automatically the
submatrix from a ROI defined by the various tool shape (may be with a
mask??)? The idea would be to get directly this information while creating
the object (and to update automatically the informations when we change the
form).

Any ideas?

Thank you.

Cheers,

Vincent

[Vincent Le Saux]

Hi all,

For those who are interested in, I found a solution (that works, but needs
one additional specific module included in python(x,y)). I get the
informations from the form (using for example the get_points() method) and
then use the skimage.draw module that do exactly what I want.

Pierre, is it planned to add such a tool in guiqwt (or guiplot later)? To
my opinion, it is very useful feature...

Cheers,

Vincent

Post by Vincent Le Saux
Hi all,
I'm using guiqwt and guidata to build a simple software dedicated to the
processing of infrared images (succession of images) and it is pretty easy
with guidata and guiqwt (thanks Pierre!). One of my main concern is to
analyze specific areas of various form and to perform mean operation over
- to draw the specific forms I need on the image -> No problem thanks
to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific forms,
i.e. the list of pixels that are contained in the form -> I didn't find
such tools in the source code (the cross_section tools can be easily
adapted for the rectangle shape, but for the other forms, I'm stucked!).
So my question is: is it possible to extract easily and automatically the
submatrix from a ROI defined by the various tool shape (may be with a
mask??)? The idea would be to get directly this information while creating
the object (and to update automatically the informations when we change the
form).
Any ideas?
Thank you.
Cheers,
Vincent

[Stefan Reinsberg]

This sounds very interesting. Can you provide some further details? Or
maybe some code snippets?
Cheers, Stefan

Post by Vincent Le Saux
Hi all,
For those who are interested in, I found a solution (that works, but needs
one additional specific module included in python(x,y)). I get the
informations from the form (using for example the get_points() method) and
then use the skimage.draw module that do exactly what I want.
Pierre, is it planned to add such a tool in guiqwt (or guiplot later)? To
my opinion, it is very useful feature...
Cheers,
Vincent

Post by Vincent Le Saux
Hi all,
I'm using guiqwt and guidata to build a simple software dedicated to the
processing of infrared images (succession of images) and it is pretty easy
with guidata and guiqwt (thanks Pierre!). One of my main concern is to
analyze specific areas of various form and to perform mean operation over
- to draw the specific forms I need on the image -> No problem thanks
to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific forms,
i.e. the list of pixels that are contained in the form -> I didn't find
such tools in the source code (the cross_section tools can be easily
adapted for the rectangle shape, but for the other forms, I'm stucked!).
So my question is: is it possible to extract easily and automatically the
submatrix from a ROI defined by the various tool shape (may be with a
mask??)? The idea would be to get directly this information while creating
the object (and to update automatically the informations when we change the
form).
Any ideas?
Thank you.
Cheers,
Vincent

[Vincent Le Saux]

In haste,


imagewidget = ImageWidget(xlabel="x [pixels]",ylabel="y [pixels]")
...
item = make.image(...)
# to get the item list (panel)
listitems = imagewidget.panels['itemlist']
# to get an item (here, the first one, supposing a form has already been
created and is placed on the top of the list)
form = listitems.listwidget.items[0]
# to get the characteristic points
points = form.get_points()
... # then it is very easy to use the skimage.draw module (see for example
:
http://scikits-image.org/docs/dev/auto_examples/plot_shapes.html#example-plot-shapes-py)

If you have any further questions (or if you want a complete example), feel
free to ask!

Cheers,

Vincent

Post by Stefan Reinsberg
This sounds very interesting. Can you provide some further details? Or
maybe some code snippets?
Cheers, Stefan

Post by Vincent Le Saux
Hi all,
For those who are interested in, I found a solution (that works, but
needs one additional specific module included in python(x,y)). I get the
informations from the form (using for example the get_points() method) and
then use the skimage.draw module that do exactly what I want.
Pierre, is it planned to add such a tool in guiqwt (or guiplot later)? To
my opinion, it is very useful feature...
Cheers,
Vincent

Post by Vincent Le Saux
Hi all,
I'm using guiqwt and guidata to build a simple software dedicated to the
processing of infrared images (succession of images) and it is pretty easy
with guidata and guiqwt (thanks Pierre!). One of my main concern is to
analyze specific areas of various form and to perform mean operation over
- to draw the specific forms I need on the image -> No problem
thanks to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific forms,
i.e. the list of pixels that are contained in the form -> I didn't find
such tools in the source code (the cross_section tools can be easily
adapted for the rectangle shape, but for the other forms, I'm stucked!).
So my question is: is it possible to extract easily and automatically
the submatrix from a ROI defined by the various tool shape (may be with a
mask??)? The idea would be to get directly this information while creating
the object (and to update automatically the informations when we change the
form).
Any ideas?
Thank you.
Cheers,
Vincent

[Stefan Reinsberg]

Thanks Vincent, Let me try this out and if I do stumble I'll come back
with more questions. Cheers, Stefan

[Samuel Garcia]

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Hi,
I did something similar sometimes ago with that function:

from matplotlib.nxutils import points_inside_poly

You give a list of pixel and get a list a bool, and you can create a
image mask of bool.

I do not known if there is something similar in guiqwt.
Certainly yes.

Samuel

Post by Vincent Le Saux
Hi all,
I'm using guiqwt and guidata to build a simple software dedicated to
the processing of infrared images (succession of images) and it is
pretty easy with guidata and guiqwt (thanks Pierre!). One of my main
concern is to analyze specific areas of various form and to perform
- to draw the specific forms I need on the image -> No problem
thanks to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific
forms, i.e. the list of pixels that are contained in the form -> I
didn't find such tools in the source code (the cross_section tools can
be easily adapted for the rectangle shape, but for the other forms,
I'm stucked!).
So my question is: is it possible to extract easily and automatically
the submatrix from a ROI defined by the various tool shape (may be
with a mask??)? The idea would be to get directly this information
while creating the object (and to update automatically the
informations when we change the form).
Any ideas?
Thank you.
Cheers,
Vincent

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Lyon Neuroscience
CNRS - UMR5292 - INSERM U1028 - Universite Claude Bernard LYON 1
Equipe R et D
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
Tél : [phone]
Fax : [phone]
http://olfac.univ-lyon1.fr/unite/equipe-07/
http://neuralensemble.org/trac/OpenElectrophy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Pierre Raybaut]

Thank you all for these interesting comments.
I may add such features to guiqwt in the near future.

For now the only supported similar features are:
* extract array from a rectangle shape:
http://code.google.com/p/guiqwt/source/browse/guiqwt/image.py#1484
* mask rectangular/circular areas on an array:
http://code.google.com/p/guiqwt/source/browse/guiqwt/tests/image_masked.py

Cheers,
-Pierre

Post by Samuel Garcia
Hi,
from matplotlib.nxutils import points_inside_poly
You give a list of pixel and get a list a bool, and you can create a
image mask of bool.
I do not known if there is something similar in guiqwt.
Certainly yes.
Samuel

Post by Vincent Le Saux
Hi all,
I'm using guiqwt and guidata to build a simple software dedicated to
the processing of infrared images (succession of images) and it is
pretty easy with guidata and guiqwt (thanks Pierre!). One of my main
concern is to analyze specific areas of various form and to perform
- to draw the specific forms I need on the image -> No problem
thanks to the polygone, rectangle, circle and freeform tools ;
- to extract the submatrices contained within these specific
forms, i.e. the list of pixels that are contained in the form -> I
didn't find such tools in the source code (the cross_section tools can
be easily adapted for the rectangle shape, but for the other forms,
I'm stucked!).
So my question is: is it possible to extract easily and automatically
the submatrix from a ROI defined by the various tool shape (may be
with a mask??)? The idea would be to get directly this information
while creating the object (and to update automatically the
informations when we change the form).
Any ideas?
Thank you.
Cheers,
Vincent

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Samuel Garcia
Lyon Neuroscience
CNRS - UMR5292 - INSERM U1028 - Universite Claude Bernard LYON 1
Equipe R et D
50, avenue Tony Garnier
69366 LYON Cedex 07
FRANCE
Tél : [phone]
Fax : [phone]
http://olfac.univ-lyon1.fr/unite/equipe-07/
http://neuralensemble.org/trac/OpenElectrophy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~