uwrapc missing output images

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DaveWatts

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Mar 1, 2011, 10:16:26 AM3/1/11
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Hi,

there are some hard coded paths in the example uwrapc.conf files (e.g.
in the ring directory), but more importantly there are no
diffraction.png output, initial_guess.png and initial_support.png
images output by the program. It is not possible to check your final
reconstruction (the only images output by the program are
autocorrelation.png and patterson_support.png).

Cheers

David Watts

Filipe Maia

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Mar 1, 2011, 1:09:25 PM3/1/11
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Hi,

Yes I know that uwrapc.conf has hard paths. It's not possible at the moment to have relative paths to the configuration file location.
What tutorial are you following? I think the png files were removed some versions ago and now only .h5 files are output.
The two left over png should also be removed.
You can convert the h5 to png using image_to_png. You can actually convert to some other formats like tiff, vtk, and even xplor density maps using the same program.

Cheers,
Filipe

DaveWatts

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Mar 2, 2011, 9:47:34 AM3/2/11
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Hi,

I am following the Hawk User manual version 1.01 (Alpha), at the
bottom of page 3 the manual mentions these images which I am now able
to convert after updating the software. Is it possible to convert the
jet colourmapped images to greyscale using the program?

Thanks

David

On Mar 1, 7:09 pm, Filipe Maia <filipe.c.m...@gmail.com> wrote:
> Hi,
>
> Yes I know that uwrapc.conf has hard paths. It's not possible at the moment
> to have relative paths to the configuration file location.
> What tutorial are you following? I think the png files were removed some
> versions ago and now only .h5 files are output.
> The two left over png should also be removed.
> You can convert the h5 to png using image_to_png. You can actually convert
> to some other formats like tiff, vtk, and even xplor density maps using the
> same program.
>
> Cheers,
> Filipe
>
> On Tue, Mar 1, 2011 at 07:16, DaveWatts
> <david.terence.wa...@googlemail.com>wrote:

Filipe Maia

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Mar 2, 2011, 2:11:59 PM3/2/11
to cx...@googlegroups.com
I think it's not currently possible to save pngs with grayscale.
You can view them using the graphical interface in grayscale but not save as png.
If you want something similar you can try to save as tiff files.
This will create 32bit floating point tiff files that can be opened in programs such as ImageJ.
The tiff also has the advantage that it will keep all the information (of non complex images), while the png is only useful for display purposes.
You can create tiff files with image_to_png. image_to_png in the beginning only converted to pngs but nowadays it converts between formats depending in the file extension.
It's not possible to convert png to tiff though, because there's information loss while creating the png files.

Cheers,
Filipe

DaveWatts

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Mar 3, 2011, 7:03:17 AM3/3/11
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When I performed

image_to_png real_space-0009999.h5 out.tiff

The tiff file was in greyscale but the greyscale values are so
oversaturated that a binary black and white image is observed. The
tiff file must be in a strange format as it is not opened correctly in
gimp and I had to use the ImageMagick Display program.

The diffraction image file in the database is also an example of this

http://www.cxidb.org/id-1.html
Diffraction Pattern: cxidb-1.tiff (TIFF format)

image_to_png real_space-0009999.h5 out.png works better but a jet
color mapped image is produced, I have managed to convert to greyscale
this image (using the octave jet(256) command to provide a mapping
look up table. My converted image looks ok, but I am not sure on the
exact colour mapping of the jet colour space that you use.

Cheers

David

On Mar 2, 8:11 pm, Filipe Maia <filipe.c.m...@gmail.com> wrote:
> I think it's not currently possible to save pngs with grayscale.
> You can view them using the graphical interface in grayscale but not save as
> png.
> If you want something similar you can try to save as tiff files.
> This will create 32bit floating point tiff files that can be opened in
> programs such as ImageJ.
> The tiff also has the advantage that it will keep all the information (of
> non complex images), while the png is only useful for display purposes.
> You can create tiff files with image_to_png. image_to_png in
> the beginning only converted to pngs but nowadays it converts between
> formats depending in the file extension.
> It's not possible to convert png to tiff though, because there's information
> loss while creating the png files.
>
> Cheers,
> Filipe
>
> On Wed, Mar 2, 2011 at 06:47, DaveWatts
> <david.terence.wa...@googlemail.com>wrote:

DaveWatts

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Mar 3, 2011, 7:04:39 AM3/3/11
to cxidb
Sorry, I overlooked the part of your email that said that the files
are 32 bit, I will try again with ImageJ

Cheers

David

On Mar 2, 8:11 pm, Filipe Maia <filipe.c.m...@gmail.com> wrote:
> I think it's not currently possible to save pngs with grayscale.
> You can view them using the graphical interface in grayscale but not save as
> png.
> If you want something similar you can try to save as tiff files.
> This will create 32bit floating point tiff files that can be opened in
> programs such as ImageJ.
> The tiff also has the advantage that it will keep all the information (of
> non complex images), while the png is only useful for display purposes.
> You can create tiff files with image_to_png. image_to_png in
> the beginning only converted to pngs but nowadays it converts between
> formats depending in the file extension.
> It's not possible to convert png to tiff though, because there's information
> loss while creating the png files.
>
> Cheers,
> Filipe
>
> On Wed, Mar 2, 2011 at 06:47, DaveWatts
> <david.terence.wa...@googlemail.com>wrote:
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