Posted by
Dr. Harald von der Osten on
Dec 09, 2010; 7:24pm
URL: http://imagej.273.s1.nabble.com/FFT-Bandpass-Filter-How-to-exclude-particles-or-other-foreground-objects-tp3686219p3686223.html
Hi Adrian,
thnaks a lot for your help.
Unfortunately, TextReader says:
"Line 2 is not the same lenght as the first line"... and Fiji is killed.
The beginning of the data file is:
P2
8001 960
255
#
148
150
155
155
155
160
165
165
165
163
165
165
:
and so on. Hmmm...
Best wishes,
Harald
Zitat von Adrian Daerr <
[hidden email]>:
> Hello Harald,
>
>> how can I import an ascii file consisting out of nearly 5 million z
>> values in one row.
>
> Supposing that your z values are separated only by whitespace (spaces,
> tabs, newlines), it should suffice to prepend (using a text editor for
> example) the following lines to your file:
>
> P2
> <width> <height>
> <maxval>
>
> where <width> and <height> are your x and y dimensions, and <maxval> is
> the maximum z value (must be smaller or equal 65535; in your case 255 ?).
> The resulting image should be read by ImageJ as a portable gray map
> (pgm) image.
>
> Below is the manual page for the pnm/pgm format copied from a Linux box.
>
> cheers
> Adrian
>
> NAME
> pgm - portable graymap file format
>
>
> DESCRIPTION
> The PGM format is a lowest common denominator grayscale file format.
> It is designed to be extremely easy to learn and write programs for.
> (It's so simple that most people will simply reverse engineer it
> because it's easier than reading this specification).
>
> A PGM image represents a grayscale graphic image. There are many
> psueudo-PGM formats in use where everything is as specified herein
> except for the meaning of individual pixel values. For most purposes,
> a PGM image can just be thought of an array of arbitrary integers, and
> all the programs in the world that think they're processing a grayscale
> image can easily be tricked into processing something else.
>
> One official variant of PGM is the transparency mask. A transparency
> mask in Netpbm is represented by a PGM image, except that in place of
> pixel intensities, there are opaqueness values. See below.
>
>
> The format definition is as follows.
>
> A PGM file consists of a sequence of one or more PGM images. There are
> no data, delimiters, or padding before, after, or between images.
>
> Each PGM image consists of the following:
>
> - A "magic number" for identifying the file type. A pgm image's magic
> number is the two characters "P5".
>
> - Whitespace (blanks, TABs, CRs, LFs).
>
> - A width, formatted as ASCII characters in decimal.
>
> - Whitespace.
>
> - A height, again in ASCII decimal.
>
> - Whitespace.
>
> - The maximum gray value (Maxval), again in ASCII decimal. Must be
> less than 65536.
>
> - Newline or other single whitespace character.
>
> - A raster of Width * Height gray values, proceeding through the image
> in normal English reading order. Each gray value is a number from 0
> through Maxval, with 0 being black and Maxval being white. Each gray
> value is represented in pure binary by either 1 or 2 bytes. If the
> Maxval is less than 256, it is 1 byte. Otherwise, it is 2 bytes.
> The most significant byte is first.
>
> - Each gray value is a number proportional to the intensity of the
> pixel, adjusted by the CIE Rec. 709 gamma transfer function. (That
> transfer function specifies a gamma number of 2.2 and has a linear
> section for small intensities). A value of zero is therefore black.
> A value of Maxval represents CIE D65 white and the most intense value
> in the image and any other image to which the image might be com?
> pared.
>
> - Note that a common variation on the PGM format is to have the gray
> value be "linear," i.e. as specified above except without the gamma
> adjustment. pnmgamma takes such a PGM variant as input and produces
> a true PGM as output.
>
> - In the transparency mask variation on PGM, the value represents
> opaqueness. It is proportional to the fraction of intensity of a
> pixel that would show in place of an underlying pixel, with the same
> gamma transfer function mentioned above applied. So what normally
> means white represents total opaqueness and what normally means black
> represents total transparency. In between, you would compute the
> intensity of a composite pixel of an "under" and "over" pixel as
> under * (1-(alpha/alpha_maxval)) + over * (alpha/alpha_maxval).<
>
> - Characters from a "#" to the next end-of-line, before the maxval
> line, are comments and are ignored.
>
> Note that you can use pnmdepth To convert between a the format with 1
> byte per gray value and the one with 2 bytes per gray value.
>
> There is actually another version of the PGM format that is fairly
> rare: "plain" PGM format. The format above, which generally considered
>
> the normal one, is known as the "raw" PGM format. See pbm(5) for some
> commentary on how plain and raw formats relate to one another.
>
> The difference in the plain format is:
>
> - There is exactly one image in a file.
>
> - The magic number is P2 instead of P5.
>
> - Each pixel in the raster is represented as an ASCII decimal number
> (of arbitrary size).
>
> - Each pixel in the raster has white space before and after it. There
> must be at least one character of white space between any two pixels,
> but there is no maximum.
>
> - No line should be longer than 70 characters.
>
> Here is an example of a small graymap in this format:
> P2
> # feep.pgm
> 24 7
> 15
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 3 3 3 3 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 15 15 15 0
> 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 15 0
> 0 3 3 3 0 0 0 7 7 7 0 0 0 11 11 11 0 0 0 15 15 15 15 0
> 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 0 0
> 0 3 0 0 0 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>
> Programs that read this format should be as lenient as possible,
> accepting anything that looks remotely like a graymap.
>
>
> COMPATIBILITY
> Before April 2000, a raw format PGM file could not have a maxval
> greater than 255. Hence, it could not have more than one byte per sam?
> ple. Old programs may depend on this.
>
> Before July 2000, there could be at most one image in a PGM file. As a
> result, most tools to process PGM files ignore (and don't read) any
> data after the first image.
>
> AUTHOR
> Copyright (C) 1989, 1991 by Jef Poskanzer.
>