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Thread-Topic: [Tiff] Using photon lists rather than rasters
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From: "Terry L. Sprout" <Terry.Sprout@Agile-Automation.com>
To: "TIFF" <tiff@lists.maptools.org>
Subject: Re: [Tiff] Using photon lists rather than rasters
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I appreciate your comments. After more thought, I think I will take your
suggestion and at least convert the image to a 1-bit/sample image (I
will have to experiment on the time it takes to compress further).
Another scheme we will use to save disk space is to integrate multiple
images into a single image. This will create a longer exposure (seconds
or minutes per image) and the bandwidth will be decreased significantly.
Then I can include the integrated image along with a list of all the
photons used to create the image. Scientists can still take the photon
lists and create more images at different exposure times as they wish.
This scheme will allow any TIFF reader to display the image and it
allows others that understand the photon lists to do more as desired.

=20

=20

Terry L. Sprout

(510) 324-5501

w7-32

=20

From: tiff-bounces@lists.maptools.org
[mailto:tiff-bounces@lists.maptools.org] On Behalf Of Chris Cox
Sent: Wednesday, July 27, 2011 5:45 PM
To: TIFF
Subject: Re: [Tiff] Using photon lists rather than rasters

=20

It's still not an image.

You really should use another format more appropriate to your data.

Chris



On 7/27/11 5:31 PM, "Terry L. Sprout"
<Terry.Sprout@Agile-Automation.com> wrote:

The 1 bit/sample idea would work if the coordinates were not sub-pixel
resolution and if there was only one time-point of photons in the list.
Another issue I have is the time it will take to perform the
compression. Some cameras I deal with today acquire 1000 ips and we are
moving into > 20,000 ips. It's difficult enough writing the original
image; compression will be worse.
=20
I understand your concerns regarding undocumented custom compression
types. After all, what is the point of using a standard file format if
most readers cannot display the image.
=20
What if I publish the compression scheme?
=20


Terry L. Sprout
(510) 324-5501
w7-32
=20

From: tiff-bounces@lists.maptools.org
[mailto:tiff-bounces@lists.maptools.org] On Behalf Of Chris Cox
Sent: Wednesday, July 27, 2011 5:01 PM
To: TIFF
Subject: Re: [Tiff] Using photon lists rather than rasters


Tagged Image File Format.

I would rather not see a TIFF "image" that is not an image and is not
readable by other software.
TIFF already gets too much abuse with undocumented custom compression
types that render the files useless.

In this case you are creating a vector display list, for which there are
more appropriate types.

Personally, I'd just apply a better predictor to improve compression and
keep the image data.  If all you need are locations/centroids of photon
hits - you could easily convert the image to a 1 bit/sample
representation and compress that.


Chris
=20


On 7/27/11 3:51 PM, "Terry L. Sprout"
<Terry.Sprout@Agile-Automation.com> wrote:
Ryan Wong wrote the following message and accidently sent it directly to
my email:
=20
***************************
Hello Terry,=20

TIFF is a raster image format, not a vector image format. Inside a TIFF
file, each page must contain exactly one raster image. It can contain
vector annotations in metadata, but viewers are not required to render
it. It will most likely be ignored by most TIFF viewers that do not
understand it. A TIFF page can contain thumbnail images, which, like any
other metadata, can be ignored by viewers that do not support it.

No matter how hard you try, no current software would be able to decode
from your photons list. Even far into the future, mainstream software do
not have a need to support "photon lists", but they will happily render
the raster image part of a processed TIFF file.

My suggestion is to store the coordinates as a metadata tag, which
accompanies with the original (unprocessed) image file. TIFF metadata
tags can store arbitrary byte data and do not have size limits (unless
going into the gigabytes range). This is the recommended way of storing
your coordinates data. And yes, floating point (32-bit, 64-bit and all
IEEE-approved ones) are supported in metadata.

Viewers that do not understand your photons list will simply ignore it,
and will still display the unprocessed image. Similar to the way EXIF
can be added as an optional part of any TIFF file.

If you do not take this approach, I don't think your proposal will be
accepted by the larger TIFF community at all. In particular,
modifications to NewSubFileType, proposals to support a StripByteCount
of zero, will be shot down immediately.

Thanks,
rwong_002@hotmail.com <mailto:rwong_002@hotmail.com>=20
=20
Disclaimer: The opinions expressed here are the views of the writer(s)
and do not necessarily reflect the views and opinions of the writers'
employer(s). Neither the writer(s), nor the writers' employers, make any
claim as to the accuracy of the opinions expressed here.
***************************



Hello Ryan,
=20
Thank you for your comments.
=20
Including the original image doesn't help since one purpose is to create
smaller files so the drive doesn't fill up so fast. My software can
currently fill up a hard drive at 240 MB/s. Some people are using a
camera that outputs very sparse photons (maybe 100 photons from a 300 KB
image 120 times per second) and they only want to know where the photons
are located. They can then playback the photon list and create images
with different exposures. The original image will consume over 600 KB
per image (they're 2 bytes per pixel) or 73 MB/s; or 4.8 GB/m; or 262
GB/h. In contrast, the photon list will only consume about 400 bytes per
image; or 48 KB/s; or 2.9 MB/m; or 173 MB/h. That's a very good
compression ratio.
=20
I've decided to treat the coordinate list as a new compression type,
since that's basically what it is. When my new compression type is used
(34927), my new coordinate list tag (51098) must be used as well. The
coordinate list tag is a pointer to a linked list of IFDs that will
contain a list of pixel coordinates along with a list of intensity
values (and a timestamp). TIFF readers that don't understand the
compression type should ignore the image. I don't really expect most
people that provide TIFF readers to add this capability, but they can if
they want to view the images. The scientists that use this data will add
this capability because it helps them in their analysis.
=20


Terry L. Sprout
(510) 324-5501
w7-32
=20


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<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I appreciate your comments. After more thought, I think I =
will
take your suggestion and at least convert the image to a 1-bit/sample =
image (I
will have to experiment on the time it takes to compress further). =
Another
scheme we will use to save disk space is to integrate multiple images =
into a
single image. This will create a longer exposure (seconds or minutes per =
image)
and the bandwidth will be decreased significantly. Then I can include =
the
integrated image along with a list of all the photons used to create the =
image.
Scientists can still take the photon lists and create more images at =
different
exposure times as they wish. This scheme will allow any TIFF reader to =
display
the image and it allows others that understand the photon lists to do =
more as
desired.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Terry L. Sprout<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>(510) 324-5501<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>w7-32<o:p></o:p></span></p>

</div>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
tiff-bounces@lists.maptools.org [mailto:tiff-bounces@lists.maptools.org] =
<b>On
Behalf Of </b>Chris Cox<br>
<b>Sent:</b> Wednesday, July 27, 2011 5:45 PM<br>
<b>To:</b> TIFF<br>
<b>Subject:</b> Re: [Tiff] Using photon lists rather than =
rasters<o:p></o:p></span></p>

</div>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><span =
style=3D'font-size:10.0pt;
font-family:"Myriad Pro","serif"'>It&#8217;s still not an image.<br>
<br>
You really should use another format more appropriate to your data.<br>
<br>
Chris<br>
<br>
<br>
<br>
On 7/27/11 5:31 PM, &quot;Terry L. Sprout&quot; &lt;<a
href=3D"Terry.Sprout@Agile-Automation.com">Terry.Sprout@Agile-Automation.=
com</a>&gt;
wrote:</span><o:p></o:p></p>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><span =
style=3D'font-size:11.0pt;
font-family:"Myriad Pro","serif"'>The 1 bit/sample idea would work if =
the
coordinates were not sub-pixel resolution and if there was only one =
time-point
of photons in the list. Another issue I have is the time it will take to
perform the compression. Some cameras I deal with today acquire 1000 ips =
and we
are moving into &gt; 20,000 ips. It&#8217;s difficult enough writing the
original image; compression will be worse.<br>
&nbsp;<br>
I understand your concerns regarding undocumented custom compression =
types.
After all, what is the point of using a standard file format if most =
readers
cannot display the image.<br>
&nbsp;<br>
What if I publish the compression scheme?<br>
&nbsp;<br>
</span><span style=3D'font-size:10.0pt;font-family:"Myriad =
Pro","serif"'><br>
</span><span style=3D'font-size:11.0pt;font-family:"Myriad =
Pro","serif"'><br>
Terry L. Sprout<br>
(510) 324-5501<br>
w7-32<br>
&nbsp;<br>
</span><span style=3D'font-size:10.0pt;font-family:"Myriad =
Pro","serif"'><br>
<b>From:</b> <a =
href=3D"tiff-bounces@lists.maptools.org">tiff-bounces@lists.maptools.org<=
/a>
[<a =
href=3D"mailto:tiff-bounces@lists.maptools.org">mailto:tiff-bounces@lists=
.maptools.org</a>]
<b>On Behalf Of </b>Chris Cox<br>
<b>Sent:</b> Wednesday, July 27, 2011 5:01 PM<br>
<b>To:</b> TIFF<br>
<b>Subject:</b> Re: [Tiff] Using photon lists rather than rasters<br>
</span><br>
<span style=3D'font-size:10.0pt;font-family:"Myriad Pro","serif"'><br>
Tagged Image File Format.<br>
<br>
I would rather not see a TIFF &#8220;image&#8221; that is not an image =
and is
not readable by other software.<br>
TIFF already gets too much abuse with undocumented custom compression =
types
that render the files useless.<br>
<br>
In this case you are creating a vector display list, for which there are =
more
appropriate types.<br>
<br>
Personally, I&#8217;d just apply a better predictor to improve =
compression and
keep the image data. &nbsp;If all you need are locations/centroids of =
photon
hits &#8211; you could easily convert the image to a 1 bit/sample
representation and compress that.<br>
<br>
<br>
Chris<br>
&nbsp;<br>
<br>
<br>
On 7/27/11 3:51 PM, &quot;Terry L. Sprout&quot; &lt;<a
href=3D"Terry.Sprout@Agile-Automation.com">Terry.Sprout@Agile-Automation.=
com</a>&gt;
wrote:<br>
</span><span style=3D'font-size:11.0pt;font-family:"Myriad =
Pro","serif"'>Ryan
Wong wrote the following message and accidently sent it directly to my =
email:<br>
&nbsp;<br>
***************************<br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>Hello Terry, =
<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>TIFF is a raster =
image
format, not a vector image format. Inside a TIFF file, each page must =
contain
exactly one raster image. It can contain vector annotations in metadata, =
but
viewers are not required to render it. It will most likely be ignored by =
most
TIFF viewers that do not understand it. A TIFF page can contain =
thumbnail
images, which, like any other metadata, can be ignored by viewers that =
do not
support it.<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>No matter how =
hard you
try, no current software would be able to decode from your photons list. =
Even
far into the future, mainstream software do not have a need to support
&#8220;photon lists&#8221;, but they will happily render the raster =
image part
of a processed TIFF file.<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>My suggestion is =
to store
the coordinates as a metadata tag, which accompanies with the original
(unprocessed) image file. TIFF metadata tags can store arbitrary byte =
data and
do not have size limits (unless going into the gigabytes range). This is =
the
recommended way of storing your coordinates data. And yes, floating =
point
(32-bit, 64-bit and all IEEE-approved ones) are supported in =
metadata.<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>Viewers that do =
not
understand your photons list will simply ignore it, and will still =
display the
unprocessed image. Similar to the way EXIF can be added as an optional =
part of
any TIFF file.<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>If you do not =
take this
approach, I don&#8217;t think your proposal will be accepted by the =
larger TIFF
community at all. In particular, modifications to NewSubFileType, =
proposals to
support a StripByteCount of zero, will be shot down immediately.<br>
</span><span style=3D'color:#1F497D'><br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>Thanks,<br>
<span style=3D'color:#1F497D'><a =
href=3D"rwong_002@hotmail.com">rwong_002@hotmail.com</a></span></span><sp=
an
style=3D'color:#1F497D'> &lt;<a =
href=3D"mailto:rwong_002@hotmail.com">mailto:rwong_002@hotmail.com</a>&gt=
;
<br>
&nbsp;<br>
</span><span style=3D'font-family:"Myriad Pro","serif"'>Disclaimer: The =
opinions
expressed here are the views of the writer(s) and do not necessarily =
reflect
the views and opinions of the writers&#8217; employer(s). Neither the
writer(s), nor the writers&#8217; employers, make any claim as to the =
accuracy
of the opinions expressed here.<br>
</span><span style=3D'font-size:11.0pt;font-family:"Myriad =
Pro","serif"'>***************************<br>
</span><span style=3D'font-size:10.0pt;font-family:"Myriad =
Pro","serif"'><br>
<br>
<br>
</span><span style=3D'font-size:11.0pt;font-family:"Myriad =
Pro","serif"'>Hello
Ryan,<br>
&nbsp;<br>
Thank you for your comments.<br>
&nbsp;<br>
Including the original image doesn&#8217;t help since one purpose is to =
create
smaller files so the drive doesn&#8217;t fill up so fast. My software =
can
currently fill up a hard drive at 240 MB/s. Some people are using a =
camera that
outputs very sparse photons (maybe 100 photons from a 300 KB image 120 =
times
per second) and they only want to know where the photons are located. =
They can
then playback the photon list and create images with different =
exposures. The
original image will consume over 600 KB per image (they&#8217;re 2 bytes =
per
pixel) or 73 MB/s; or 4.8 GB/m; or 262 GB/h. In contrast, the photon =
list will
only consume about 400 bytes per image; or 48 KB/s; or 2.9 MB/m; or 173 =
MB/h.
That&#8217;s a very good compression ratio.<br>
&nbsp;<br>
I&#8217;ve decided to treat the coordinate list as a new compression =
type,
since that&#8217;s basically what it is. When my new compression type is =
used
(34927), my new coordinate list tag (51098) must be used as well. The
coordinate list tag is a pointer to a linked list of IFDs that will =
contain a
list of pixel coordinates along with a list of intensity values (and a
timestamp). TIFF readers that don&#8217;t understand the compression =
type
should ignore the image. I don&#8217;t really expect most people that =
provide
TIFF readers to add this capability, but they can if they want to view =
the
images. The scientists that use this data will add this capability =
because it
helps them in their analysis.<br>
&nbsp;<br>
</span><span style=3D'font-size:10.0pt;font-family:"Myriad =
Pro","serif"'><br>
</span><span style=3D'font-size:11.0pt;font-family:"Myriad =
Pro","serif"'><br>
Terry L. Sprout<br>
(510) 324-5501<br>
w7-32<br>
&nbsp;</span><o:p></o:p></p>

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