Posted by
Michael Schmid on
Apr 19, 2011; 8:22am
URL: http://imagej.273.s1.nabble.com/Importing-data-from-ascii-format-tp3684915p3684916.html
Hi Dave,
if you want to import your data in ImageJ as raw, don't write ASCII.
Instead write bytes, without any delimiters in between, and use 8-bit
raw import in ImageJ.
If your software can't do that, if it can only write strings (text),
no raw bytes, then you should convert the pixel values to characters
by some function that gets the ascii character from the character
code, and use the pixel value as character code.
Conversion to text won't work if your software uses the 0 byte as
string terminator (many C programs do). Also, beware of software
translating higher values (>127) to Unicode with more than 1 byte.
What you currently do: ImageJ reads the ascii code for each pixel. If
you read bytes, the pixels written as "0" will be read as character
code 48 (0x30 hex), "1" will become 49, and "9" becomes 57. You would
have to write a colon ":" for 58, a semicolon ";" for 59, etc.
For exporting as unsigned short int, simply convert your image to "16-
bit". Save As>Raw Data should do the job, but you have to try whether
you need little or big endian format. You can set this in
Edit>Options>Input/Output, "Save tiff&raw in Intel byte order"
Michael
________________________________________________________________
On 18 Apr 2011, at 16:30, DavidOxley2 wrote:
> Dear all,
> I have found similar questions to mine, but nothing quite the same.
> I have
> very little experience with ImageJ and could not find an answer to my
> question in the documentation and thought this may be a place to
> start. If I
> am in the wrong place, please let me know.
> I have two questions:
>
> 1) problem importing ascii numbers
> I am trying to transfer some data from one software tool to
> another, where
> the second requires a 3Dimage file in binary format (unsigned short
> integers) as its input.
> I have a 3D voxel space of 100x100x100 voxels, which I essentially
> have full
> control over and can (in theory) write to any format I want (or imageJ
> needs). ImageJ was recommended to me as being able to load in ascii
> data and
> write out the 3D image file.
> I have reduced my voxel map to a very simple case of a straight
> line for
> debugging purposes. So I export my voxel space into a list of 1
> million
> decimals either 0 or 9:
> 0
> 0
> 0
> (...)
> 9
> (...)
> 0
>
> If I load this into imageJ using File>Import>Raw data.. and set up the
> formatting (100pixelsx100pixelsx100slices), then I can see my line
> where I
> expect it to be. However if I replace the 9's with 10's, the image
> seems to
> become a mess and I dont see my line anymore. I am guessing I need
> to add
> some space delimiter. I have tried 0,0,0 and 0 "\t" 0 etc, but cant
> find
> what is correct.
> If anyone can advise me how best to change my format, this will be
> very
> helpful.
>
> 2) Saving the imported data to 3D image
> Let's say I go back to the 9's and I can see my data no problem.
> Then I want
> to save it, I have been advised to save it as raw data, unsigned
> short int
> in binary format. But using File>Save As> Raw data , seems to just
> give me a
> list of integers again, when I need a binary option. Does this exist
> somewhere?
>
> These feel like basic questions to me, but I could not find what I
> wanted in
> the user guide. Perhaps someone can also recommend further
> documentation.
>
> Many thanks in advance,
>
>
> Dave
>
>
> --
> View this message in context:
http://imagej.588099.n2.nabble.com/
> Importing-data-from-ascii-format-tp6283855p6283855.html
> Sent from the ImageJ mailing list archive at Nabble.com.