Re: Import -> Text Image
Posted by Adrian Daerr-2 on Dec 09, 2010; 4:43pm
URL: http://imagej.273.s1.nabble.com/FFT-Bandpass-Filter-How-to-exclude-particles-or-other-foreground-objects-tp3686219p3686222.html
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.