The Biaram Programs
Biaram is a collection of 141 separate programs for doing specific image processes such as deconvolution, image rotation, colour separation, etc. Each is a pre-compiled executable for MS Windows 9x/2000/NT/XP.
User's Manual
Download the second edition of the Biaram User's Manual (February 2008, 562 Kb PDF file).
Referencing
If you use any of these programs to generate results which you later publish, please reference the use of that program as follows (taking care to replace PROGRAM_NAME with the actual program name and replace ## with the actual version number):
Tadrous PJ. PROGRAM_NAME (Biaram image processing software) version ##, 2008, URL http://www.bialith.com
List of Programs
Alignlist
Version:
2.62. Linked to BiaQIm (Registration)
Use
alignlist together with autoreg and geomlist to automatically
register (align) a list of images. Alignlist takes in a text file
list of image names and calls autoreg repeatedly for each image in
the list in a manner specified by you. The result is another text
file which is a list of transform parameters for aligning each image
in the list. Geomlist performs the actual transformations.
Areflect
Version:
1.1. Linked to BiaQIm (Instant process)
Performs
my variant of anti-reflective image boundary treatment. See also
DeconLS, Bcontinue, Bcontmirr and Bmerge, Areflect3d.
Areflect3d
Version:
1.0.
Performs
my variant of anti-reflective image boundary treatment on image
stacks (i.e. 3D images). See also Areflect.
Autoreg
Version:
2.62. Linked to BiaQIm (Registration)
Use
autoreg alone or together with alignlist (v2.62) and geomlist (v2.62)
to automatically register a pair or a list of images. Autoreg takes
in two images and searches for the best registration parameters. The
output is either a text file containing the registration parameters
(rotation, x,y translation and x,y, scaling) and / or actual
transformation of the second image (to fit the first) according to
these parameters. The text file may be appended to form a transform
list suitable for input into geomlist. Pre-processing with Fourier
filtering and convolutions are in-built as are all the image warping
(transformation) routines and RGB / HSV channel separation for
registration of full colour images. Registration may be performed to
sub-pixel accuracy. There is a choice of matching algorithms
including the entropy-based normalised mutual information method. See
also Comreg, Tfmcombi.
Bcontinue
Version:
1.0.
Bcontinue
extends an image by continuing the grey levels at the boundaries for
<dim> number of pixels in all directions. See also Areflect,
Bcontmirr and Bmerge.
Bcontmirr
Version:
1.0.
BcontMirr
extends an image by reflecting the grey levels at the boundaries for
<dim> number of pixels in all directions. See also Areflect,
Bcontinue and Bmerge.
Bgcorr
Version:
2.0. Linked to BiaQIm (Enhancement)
Bgcorr
performs background (shading) correction on an image given the image
and an image of the plain background which contains the shading or
defects. It is a 1-step divisional procedure where the background
image is first treated to eliminate problems with divide-by-zero. An
optional Gaussian smoothing step for the background image is also
part of the pre-treatment. Use Bgcorr when you only have one or two
images to correct. If you want to correct many images, it is more
time-efficient to use Bgprep and Divbg. See also Listbgcorr
Bgprep
Version:
2.0. Linked to BiaQIm (Enhancement)
Use
Bgprep in conjunction with Divbg to perform divisional background
(shading) correction to a list of images. This is most conveniently
done as a batch process via BiaQIm. If many images are to be
corrected by one background image, the background image is prepared
for divisional correction by running Bgprep on it. Bgprep eliminates
any zeros and offers the option of performing a Gaussian smoothing
step. The prepared background image can then be used in the program
Divbg to perform the divisional correction with the input image.
Bmerge
Version:
1.1.
Bmerge
merges one image with another with a smooth cosine weighted
transition, over a rectangular band starting at <dim1>,<dim1>
and ending at <dim2>,<dim2>. See also Areflect, Bcontinue
and Bcontmirr.
Bmptoc
Version:
1.0. Linked to BiaQIm (Conversions)
Bmptoc
converts a 24bpp BMP image into its red, green and blue components.
See RgbtoBMP and Ppmtorgb.
Bmptohsv
Version:
1.0. Linked to BiaQIm (Conversions)
Bmptohsv
splits a 24bpp BMP image into its Hue, Saturation and Value
(intensity) components. See Hsvtorgb.
BmptoPNG
Version:
1.0.
This
converts 8bpp or 24bpp BMP images into the PNG format with full alpha
(opacity) support. Use this program on its own or via the FATCAM
graphical interface to build semitransparent 3D models in VRML from
serial sections. See also: FATCAM, zBMPtovrml, zslice, zgeom,
zstdise, zstretch, zsubsample.
Border
Version:
1.1. Linked to BiaQIm (Geometric)
Border
sets an external or internal border (or an internal rectangular 'box'
region) in an image to a given value. An external border extends the
dimensions of the image. There are a number of variant modes of
operation. See also Ewin and Enlarge.
Camber
Version:
2.0.
Camber reduces the intensity of pixels at the
boundaries of an image according to a PSF and can perform the inverse
operation. It may be useful as a pre-process for certain types of
deconvolution. See also Convolve, Deconvolve and the Decon** series
of programs.
CCDcalib
Version:
1.0. Linked to BiaQIm (Image Arithmetic)
Use
CCDcalib to perform photometric calibration of CCD images.
Ceilevel
Version:
1.0.
Ceilevel
generates a grey level scaling image of coefficients. When
multiplied, pixel-by-pixel, with the input image the scaling image
makes the output a constant value (= the ceiling). See also Formula.
Cepstrate
Version:
2.0. Linked to BiaQIm (PSF Estimation)
Cepstrate
allows you to generate an average power cepstrum of an image
(typically used to estimate the PSF as part of a blind deconvolution
procedure). See also Mkwin.
Circulate
Version:
1.0.
Circulate
takes in a 1D signal and makes it into a circularly symmetric 2D
image by using this signal as the radius profile and sweeping it
through 360 degrees using bilinear interpolation. See also
Symmetricise.
Cmdlist
Version:
1.0 - Released: 20/08/2002 - (Download size: 69.7 Kb) - Linked to
BiaQIm: No
Cmdlist
takes in a text file which is a list of commands and passes these,
one at a time, to the system command processor for execution. It is
an alternative way to do batch processing when ordinary .bat files
can't cope. See also MkBatch
Colreg
Version:
1.0.
Colreg
performs correction for chromatic aberrations in 24bpp images by
performing sub-pixel registration of the red, green and blue
components. The program requires the following Biaram programs for
full functionality: Autoreg, BMPtoc and RGBtoBMP (which see).
Combine
Version:
1.0.
Combines
two images according to some weighted basis function that may be
derived from or independent of the image intensity / colour values.
See also Formula, Leveljoin, Levelsplit, Zintegral and Stdise.
Comrc
Version:
1.0.
comrc
calculates the centre of 'mass' of an image (the 'mass' being the
pixel values - of the whole image or under an optional mask). The
output is the row and col position of the centre of mass which are
appended to the <out_textfile>. See also Comreg.
Comreg
Version:
1.0.
comreg
registers two images by calculating (or reading in from a text file)
the centre of 'mass' (CoM) of the index image (= image1) then
calculating the CoM of the image to be registered (= image2) then
outputting the x,y shifts that will make image2 have the same CoM as
the index image (and optionally shifting image2 by that amount. In
suitable images this gives sub-pixel shift registration MUCH faster
than using autoreg. 'Suitable' images are those that contain similar
features, similarly distributed and away from the boundaries of the
field and in a zero-valued background. No scale differences (in size
or grey levels) or rotation differences should exist. Examples
include astronomical scenes where no objects run off the boundaries
of the field in any of the images. See also Comrc and Autoreg.
Conved
Version:
1.1. Linked to BiaQIm (Edge Detection)
Use
conved to perform convolutional edge detection. There is a choice of
operators: Sobel, Prewitt, Robinson, Kirsch, Laplace or inverse
Laplace. See also Gened.
Convolve
Version:
2.0. Linked to BiaQIm (Filters)
Convolve
allows you to perform general convolution in spatial of Fourier
domain with a kernel of your choosing and in 1D, 2D or 3D. See also
Deconvolve, Conved and Camber.
ConvolVP
Version:
1.0.
ConvolVP
performs general spatially-variant PSF convolution in the spatial
domain with Fourier-type boundary treatment. See also DeconVP.
Cxcoeff
Version:
1.0.
Cxcoeff
multiples the real and imaginary parts of a complex array
(pixel-by-pixel) by coefficients supplied as two raw doubles arrays
(one for real and one for imaginary). See also Cxconj &
Cxformula.
Cxconj
Version:
1.0 - Released: 26/12/2004 - (Download size: 68 Kb) - Linked to
BiaQIm: No
Cxconj
computes the complex conjugate of the input image. See also Cxcoeff &
Cxformula.
Cxformula
Version:
1.0. Linked to BiaQIm (Image Arithmetic)
Cxformula
performs complex arithmetic between two complex arrays (of doubles).
See also Formula, Cxconj, Cxcoeff, Singleop and Setpix.
Cxsep
Version:
1.0. Linked to BiaQIm (Conversions)
Cxsep
splits a complex array (of doubles) into its real and imaginary
components. See also Cxsynth & Synthcx.
Cxsynth
Version:
1.0.
Cxsynth
takes two raw doubles arrays and knits them into a complex array. See
also Cxsep & Synthcx.
Cxwavgen
Version:
2.0.
Cxwavgen
lets you create a complex array with one real and one complex value
(all others zero). If back-DFTed the result is a pure 2D sinusoid.
See also Cxsep, Cxsynth and Synthcx.
Cxweight
Version:
1.0.
Cxweight
multiplies the real and imaginary components of a complex array,
pixel-by-pixel with two raw doubles arrays (one for real and one for
imaginary). If the raw doubles arrays are in diffraction pattern
order you should set the <cyclic?> argument to 1. See also the
other programs in the ‘Cx’ series.
Cyclise
Version:
2.0. Linked to BiaQIm (Geometric)
Cyclise
performs image cyclisation (converts the image into the form of a
cyclic matrix) in 1D, 2D or 3D. Both forward and reverse
transformations are supported. See also Fourier, Convolve and the
'Cx...' series of programs.
Decimate
Version:
1.0.
Decimate
chops an image up into (possibly overlapping) square sub-images of
dimensions <block_dim> x
<block_dim>. The top left corner of the first sub-image will
start at [0,0] of the input image and this start point will increment
by <stepsize> columns until it cant go any further to the
right, then by <stepsize> rows starting at the left again (i.e.
a raster scan in <stepsize> steps).
DeconBL
Version:
1.0.
DeconBL
performs iterative blind image deconvolution by the Biggs-Lucy
algorithm. See also DeconIB, DeconMB and DeconNR.
DeconCN
Version:
1.0.
DeconCN
performs image deconvolution using my variant of the Hogbom CLEAN
algorithm. See also Deconvolve.
DeconIB
Version:
1.0.
DeconBL
performs iterative blind image deconvolution by the Ayers &
Dainty algorithm. See also DeconBL, DeconMB and DeconNR.
DeconLS
Version:
2.0. Linked to BiaQIm (Deconvolution)
DeconLS
performs image deconvolution in 1D, 2D or 3D using either the 1-step
least squares method (with adjustable gamma) or the Weiner filter
(either simplified or full Weiner filtration may be performed
depending on the available amount of prior information about the
noise). See also Deconvolve and WeinSNR.
DeconMB
Version:
1.0.
DeconBL
performs iterative blind image deconvolution by a multi-frame
algorithm. See also DeconBL, DeconIB and DeconNR.
DeconME
Version:
2.0. Linked to BiaQIm (Deconvolution)
DeconME
performs image deconvolution in 1D, 2D or 3D using the Maximum
Entropy method as implemented in the MaxEnt algorithms of Jan Myrheim
and Haavard Rue (New Algorithms for Maximum Entropy Image
Restoration, Computer Vision, graphics and Image Processing:
Graphical Models and Image Processing; 54(3):223-238, May
1992) which they released under the terms of the GNU General Public
Licence. See also Deconvolve.
DeconNN
Version:
1.1.
DeconNN
performs 3-dimensional image restoration (sometimes considered
'deconvolution') using the Nearest-neighbours algorithm. This
technique is one method used in the art of optical sectioning
microscopy.
DeconNR
Version:
1.1.
DeconNR
performs blind deconvolution using the Non-negativity And Support
constrained Recursive Inverse Filtering (NAS-RIF) method of Kundur
(see IEEE Tran Signal Proc. (1998); 46(2):375-390) with
the option of Ong enhancement (see IEEE Trans Image Proc
(1999); 8(7):988-992). See also DeconBL, DeconIB and DeconMB.
Deconvovle
Version:
2.0. Linked to BiaQIm (Deconvolution)
Deconvolve
performs iterative deconvolution in 1D, 2D or 3D using a variety of
algorithms (Lucy-Richardson, Landweber, maximum entropy of Gull and
Daniell, Van Cittert and super-resolution). This is non-blind
deconvolution. See also the Deon** series of programs and see
Convolve.
DeconVP
Version:
1.0.
This
performs spatially variant PSF deconvolution via a spatial domain
Landweber iterative method. See also ConvolVP.
Digest
Version:
1.0.
This is a
utility which allows you to split up large files (of any type, not
necessarily related to images) into smaller chunks. This is useful if
you want to spread a large file over many storage media (e.g.
diskettes) or split up a large file to make it easier for people to
download over the Internet. The program also provides the means to
reconstitute the chunks into the original file.
Divbg
Version:
1.0. Linked to BiaQIm (Enhancement)
Use Divbg
in conjunction with Bgprep to perform divisional background (shading)
correction to a list of images. This is most conveniently done as a
batch process via BiaQIm. Divbg divides the input image with a
co-efficient image derived by preparing a background image via
Bgprep. See also Singleop and Formula.
Dtvfilt1d
Version:
1.0.
This is a
digital TV filter implemented for 1D signals. See: Dtvfilter for more
details. See also Conv1d.
Dtvfilter
Version:
2.0. Linked to BiaQIm (Enhancement)
Dtvfilter
performs de-noising by the method of digital Total Variation
filtering described in Tony F. Chan, Stanley Osher, and Jianhong
Shen, IEEE Trans. Image Proc.10(2):231-241 February 2001. In Jan.
2003 this download was extended to include batch-processing enhanced
versions of the program.
Enlarge
Version:
2.0. Linked to BiaQIm (Geometric)
Enlarge
doubles the dimensions of an image using Fourier transform
interpolation. Any size or dimensions image may be used as input
(i.e. not restricted to powers of 2). See also Halve, Scale and
Border.
Ewin
Version:
1.0. Linked to BiaQIm (Geometric)
Ewin
extracts a sub-window from an image and outputs this sub-window as a
separate image. See also Border.
Extend
Version:
1.1. Linked to BiaQIm (Geometric)
Extend
performs reflective image extension according to the algorithm of
Aghdasi F & Ward RK in IEEE Transactions on Image Processing
(1996); 5(4):611-618. This dramatically reduces image boundary
artefacts in frequency domain image restorations / manipulations. See
also Mkwin.
Exterlace
Version:
1.0. Linked to BiaQIm (Enhancement)
Exterlace
perform precision de-interlacing of video stills. Un-like similar
'tools' offered in certain photo re-touching packages, exterlace
offers a choice of precision behaviours for quantitative analysis
such as deconvolution or super-resolution reconstruction. You may
extract the odd and even frames as two half-sized images, two
full-sized images with alternate lines blank or two full-sized images
with alternate lines interpolated to produce two properly registered
frames. These may be averaged within the program to produce a single
full-sized frame. Other options are also available.
Extractval
Version:
2.0.
Use this
to extract all pixels of a certain value from an image into another
image. See also Levelsplit and Formula.
Formula
Version:
1.2. Linked to BiaQIm (Image Arithmetic)
Formula
performs arithmetic between two images. Each image is first
pre-multiplied by user specified coefficients (which may be set to
1.0 for no effect). Operations available are the usual addition,
subtraction, multiplication and division as well as some others:
power (image1 raised to the power of image2), root (the image2th root
of image1) and atan2 (arctangent of the ratio of the two images). See
also Cxformula, Singleop, Combine, Extractval, Ceilevel and Setpix.
Fourier
Version:
2.0. Linked to BiaQIm (Transforms)
Fourier
performs a general Fourier transform on images of any dimensions (not
just powers of 2) and in 1D, 2D or 3D. See also Mkwin, Symmetricise.
Genav
Version:
1.1. Linked to BiaQIm (Enhancement)
Genav is
a general image list averaging program. It outputs one image from a
list of many images. The output image is the average of all the
inputs. This program has a number of options such as whether to
produce a mean or median average and whether to use single pixels or
neighbourhood weighted values. It also can output a variance image
which may be used e.g. as input to maximum entropy deconvolution with
pixel-depended noise variance estimation. See also Groupav.
Gened
Version:
1.1. Linked to BiaQIm (Edge Detection)
Gened is
a general implementation of my powerful edge detector. See: Tadrous
PJ, 'A Simple and Sensitive Method for Directional Edge Detection in
Noisy Images', Pattern Recognition 1995; 28(10):1575-1586. See also
Conved.
Geomlist
Version:
2.62. Linked to BiaQIm (Registration)
Use
geomlist together with autoreg and alignlist to automatically
register (align) a list of images. Alignlist takes in a text file
list of image names and calls autoreg repeatedly for each image in
the list in a manner specified by you. The result is another text
file which is a list of transform parameters for aligning each image
in the list. Geomlist performs the actual transformations according
to this list of transform parameters. See also Geomrts, Tfmcombi.
Geomrts
Version:
1.2.
Use
Geomrts to perform a rotation, translation and scaling (RTS)
transform to a single image. You can use it to apply RTS transform
information output by Autoreg to an image which was not originally
used in the registration process (useful if you want to align two
stacks of images to each other where the images within in each stack
are already registered). See also Autoreg and Geomlist.
Groupav
Version:
1.0.
Use
Groupav to perform multi-image mean averaging in groups. The input is
a list of images and the idea is to average N images at a time from
the input list where N is the group size. The first N images in the
input list contribute to the first averaged output image, the next N
to the second, etc. See also Genav.
Halve
Version:
1.1. Linked to BiaQIm (Geometric)
Halve
halves the size of an image by 2x2 pixel binning (averaging). See
also Enlarge and Scale.
Hequalise
Version:
1.0. Linked to BiaQIm (Enhancement)
Use
Hequalise to perform histogram equalisation (HE) by either the usual
Full Frame method (FFHE), the powerful Local Area method (LAHE) or
the even more powerful Adaptive Neighbourhood method (ANHE). See
Paranjape RB, Morrow WM and Rangayyan RM. "Adaptive-Neighbourhood
Histogram Equalization for Image Enhancement", CVGIP: Graphical
Models and Image Processing (1992); 54(3):259-267.
Hsvtorgb
Version:
1.0. Linked to BiaQIm (Conversions)
Hsvtorgb
takes in a triplet set of images (hue, saturation and value) and
converts them into either one 24bpp BMP image or three 8bpp images
(red, green and blue components). See Bmptohsv.
Impulse
Version:
1.0 - Released: 29/12/2005 - (Download size: 286Kb) - Linked to
BiaQIm: No
Use this
to modify a single pixel in an image. See also Setpix, Mkplain,
Mkrect, Mkdisc and Mkdotgrid.
Integral
Version:
1.0 - Released: 27/12/2004 - (Download size: 70 Kb) - Linked to
BiaQIm: No
Use this
to get an integral value for all pixels in an image (also gives the
mean, variance and SD). See also Stats.
Invert
Version:
1.0. Linked to BiaQIm (Binary)
Although
linked to the Binary process menu of BiaQIm, Invert can be used as a
stand-alone program to invert (the pixel values of) images of other
data types including raw floating point and double precision arrays,
FITS files 8bpp grey level and 24bpp BMP files. See also Singleop and
Formula.
Jhist
Version:
1.0.
Jhist
takes in two images and generates a joint histogram as well as
entropic measurements including the normalised mutual information Y.
See Studholm C. et al. in Pattern Recognition 32(1999):71-86.
Kime
Version:
1.0.
Kime
performs minimal error thresholding of an image according to the
algorithm of J. Kittler & J. Illingworth (Pattern Recognition
19(1):41-47 1986). The image histogram is scanned from a
lower_p_tile to an upper_p_tile specified by the user. Colour images
are also supported. See also Extractval.
Labav
Version:
1.0. Linked to BiaQIm (Enhancement)
Labav
performs statistics on pixels within defined regions of a single
image. The regions are defined by a labelled mask. A further
exclusion mask can be used to define a homogenous background field.
Statistics available are mean, median, SD, variance and interquartile
range (IQR). The histogram bin size for the calculations is
user-definable. Labav can be useful for quantitative analysis of very
noisy images and is superior to the main alternative method (binning)
in that spatial information content can be utilised fully. See also
Stats.
Leveljoin
Version:
1.0.
Leveljoin
combines two images according to: image1 += (level - image2) at each
pixel. See also Levelsplit, Combine and Zintegral.
Levelsplit
Version:
1.0.
Levesplit
separates an image into two images - one containing all pixels above
a certain intensity and the other all those below it. The second
image is then grey-level inverted. See also Leveljoin and Formula.
Listbgcorr
Version:
1.0.
This
provides for an efficient method of background shading correction of
a list of many images. It requires Bgcorr for full functionality. See
also Bgcorr.
Listceiling
Version:
1.0.
Use this
to perform a ceiling operation on a list of files. See also Ceiling.
Listphotobleach
Version:
1.0.
This
requires the program 'photobleach' to work. It is the list version of
photobleach (q.v.) and should be used when you have measurements to
make on a whole stack of images rather than just one or two.
Listremove
Version:
1.0.
This
allows you to delete a whole list of images (or any files) from your
hard disc at once - there is no 'undo' facility.
Listwdenoise
Version:
1.0. Linked to BiaQIm (Enhance)
This is
the list version of Wdenoise (q.v.) and requires Wdenoise to be
installed in order to work. Listwdenoise is also required by BiaQIm
for full functionality of the Enhance menu options. An alternative
version with some enhancements for batch processing was added to the
distribution in Jan 2003.
Mkball
Version:
1.0.
Mkball
generates a 3D ball which may be used (e.g.) as a PSF or synthetic
object for 3D (de)convolution. See also Mksphere.
Mkbatch
Version:
1.0.
Mkbatch
allows you to create a batch file (to run under MSDOS) for the
purposes of batch processing of images. See also Cmdlist.
Mkbessel
Version:
1.0. Linked to BiaQIm (PSF Estimation)
Mkbessel
generates a 2D discretised Bessel function of the first order, first
kind. It may be used for convolution / deconvolution experiments. See
also Mkgauss, Mkdisc, Mksinc.
Mkdisc
Version:
1.0. Linked to BiaQIm (PSF Estimation)
Mkdisc
generates a discretised disc function which may be used for
de-convolution experiments. See also Impulse. See also Mkgauss,
Mkrect, Mkbessel.
Mkdotgrid
Version:
1.0.
Generates
a grid of pixel dots. See also Mklinegrid and Impulse.
Mkgauss
Version:
1.1. Linked to BiaQIm (PSF Estimation)
Mkgauss
generates a 2D discretised Gaussian approximation function which may
be used for de-convolution experiments. See also Mkdisc, Mkbessel,
Mkgeom.
Mkgeom
Version:
1.0.
Mkgeom
generates a 2D discretised function where the pixel values change in
a geometrical progression from the centre. It may be used to generate
test PSFs. See also Mkdisc, Mkbessel, Mkgauss.
Mklinegrid
Version:
1.0.
Generates
a grid of pixel lines. See also Mkdotgrid.
Mklsif
Version:
2.0.
Generates
a complex inverse filter based on the least squares algorithm. See
also DeconLS and DeconNR.
Mkplain
Version:
1.0.
Generates
a plain images where all pixels are of the same (user-defined) value.
See also Impulse.
Mkrect
Version:
1.0.
Generates
a rectangular object. See also Impulse, Mkdisc, Mkgeom.
Mkring
Version:
1.0.
Generates
an image of a ring of variable diameter and thickness. See also
Mkdisc, Mksphere.
Mksinc
Version:
1.0. Linked to BiaQIm (PSF Estimation)
Mksinc
generates both 1D and 2D discretised sinc functions which may be used
for deconvolution experiments. See also Mkbessel, Mkgauss, Mkdisc.
Mksphere
Version:
1.0.
Generates
a 3D hollow shell of variable radius and thickness. See also Mkball,
Mkring.
Mkwin
Version:
1.1. Linked to BiaQIm (Instant process)
Mkwin
generates 2D data windowing functions: Hann, Bartlett and Welch.
These are raw arrays of doubles which can be used to pre-multiply
images (using the Biaram program formula) before performing Fourier
transforms or deconvolution to lessen boundary artefacts. Can be
especially useful when calculating power spectra or cepstra. See also
Fourier, Formula, Cepstrate and Extend.
Mlogic
Version:
1.0. Linked to BiaQIm (Binary)
Mlogic
takes in two 8bpp BMP files whose pixel values are either 0 or 255.
It then combines them by means of binary operators.
Montage
Version:
1.0.
Montage
reads in a sequence of images whose names are listed in a text file.
It then stitches them together into a horizontal strip single
composite image with <gap> pixels between each image and the
gap pixels being of colour <val> <valG> <valB>.
Normalise
Version:
1.0.
Normalises
an image so that its integral value equals 1.0.
Photobleach
Version:
1.1.
Use
Photobleach to quantify the amount of photobleaching that has
occurred in a fluorescence system by comparing a before and after
image. See also Listphotobleach.
Ppmtorgb
Version:
2.0. Linked to BiaQIm (Conversions)
Ppmtorgb
splits a P6 24bpp PPM image into three 8bpp images (red, green and
blue components). Version 2.0 can also handle 48bpp PPM images (this
feature is not linked to BiaQIm). See also Bmptoc and RgbtoBMP.
PSNR
Version:
1.0.
PSNR
measures the Peak Signal to Noise Ratio and the root mean square
error of an image (given a reference image). It also outputs a
difference image. See also Stats.
Ptilehgm
Version:
1.0.
This
calculates and outputs the pixel value of an image corresponding to
the desired percentile and also generates a histogram to a
user-specified number of bins. See also Stats.
Qrmsep
Version:
1.0. Linked to BiaQIm (Binary)
QRMsep
extracts either or both of the two masks contained in a qrm file or
the labelled imaged contained therein. A qrm file is a custom
BiaQIm-related file format (qrm stands for QI Rich Mask) which can be
generated by BiaQIm to store not only the masks and labelled image
but also the distance transform, boundary data and measurement
information on objects. The current version of qrmsep only addresses
the masks or labelled image and not the other information.
Rankfilt
Version:
1.0. Linked to BiaQIm (Filter)
A rank
filter is a general form of the more familiar median filter. In a
median filter the rank is 50.0%. This general rank filter allows any
percentile rank to be used. This can effect a grey-level (or colour)
erosion or dilation. You can also have arbitrarily-shaped local
windows to allow custom rank filters (e.g. a line- or
corner-preserving median filter)
RgbtoBMP
Version:
1.1. Linked to BiaQIm (Conversions)
RgbtoBMP
recombines three 8bpp images (representing the red, green and blue
components) into one 24bpp BMP image. See Bmptoc.
Rotate
Version:
1.2. Linked to BiaQIm (Geometric)
Rotate
rotates an image. Fractional (non-integer) and negative angles are
supported and the centre of rotation may be arbitrarily chosen or
central. Angles may be interpreted in degrees or radians. Bilinear
interpolation is used. See also Trishear, Sincshear, Rotate180,
Rotate90.
Rotate180
Version:
1.0. Linked to BiaQIm (Geometric)
Rotates
an image through 180 degrees. See also Rotate.
Rotate90
Version:
1.0. Linked to BiaQIm (Geometric)
Rotates
an image through 90 degrees in clockwise or anticlockwise direction.
See also Rotate.
Scale
Version:
1.2. Linked to BiaQIm (Geometric)
Scale
performs independent x,y scaling of an image including the option of
using fractional and negative scales (a scale of -1.0 is equivalent
to a 'flip' operation. The flip algorithm is improved in v1.1). Cubic
interpolation is used. See also Halve and Enlarge.
Setpix
Version:
1.1. Linked to BiaQIm (Image Arithmetic)
Setpix
allows you to set a specific pixel's value to a value of your choice.
An optional mask may be specified in which case all pixels under the
mask will be set rather that a single pixel. See also Impulse.
Setpixlist
Version:
1.0.
setpixlist
sets the value of pixel [row,col] in an image using a list of images
as input and a text file containing a list of row,col values - one
pair for each image in the list. The text file contains the row
number followed by a tab or space then the col number followed by a
newline.
Shift3d
Version:
1.0.
Shift3d
takes in a 3D image (as a stack of 2D images listed in an ASCII list
file) and shifts the volume in x, y and z by trilinear interpolation.
The input data type may be any of the standard types. The <cyclic>
argument must be 1 or 0.
Shiftim
Version:
1.2. Linked to BiaQIm (Geometric)
Shiftim
performs independent x,y, translation of an image to sub-pixel
accuracy using linear interpolation. See also Sincshift.
Sincshear
Version:
1.1. Linked to BiaQIm (Geometric)
Sincshear
performs independent x,y shear warpings using sinc interpolation,
Upto three shears can be performed at once such that tri-shear
rotation can be carried out. A special option is included which lets
you use Sincshear as a one-step rotation program - you supply the
rotation angle and the shears are automatically calculated to achieve
this rotation. See also Trishear and Rotate.
Sincshift
Version:
1.1. Linked to BiaQIm (Geometric)
Sincshift
performs independent x,y translation to sub-pixel accuracy using sinc
interpolation. See also Shiftim.
Singleop
Version:
1.3. Linked to BiaQIm (Image Arithmetic)
Singleop
allows a range of mathematical operations to be performed on a single
image. These include addition, multiplication, subtraction and
division by a constant, exponential, logarithmic and power operations
(e.g. raising the image to a constant power or raising a constant
number to the power of the image), finding a difference map (from the
mean), clipping, linear transforms, integration, averaging and other
statistical operations and forward and inverse trigonometric
transforms. See also Setpix, Invert, Divbg, Formula and Cxformula.
Sortlist
Version:
1.0.
Sortlist
reads in a list of images and outputs them in order of the value of
some measure of the images properties e.g. in descending order of
entropy (the image with the most entropy at the top of the list).
Entropy is the only measure implemented in v1.0, other measures to
follow in later versions.
Stats
Version:
1.2.
Stats
takes in an image and produces two tsv files. One containing an image
histogram and the other a series of image statistics: range, mean,
min, max, inter-quartile-range, median, 25th and 75th percentile, SD,
variance and sample size. Like many other Biaram programs this one
can also be restricted to specific regions of the image if a
concurrent mask file is supplied. Version 1.1 has an important bug
fixed that affected percentile calculations. See also Zstats,
Integral, Ptilehgm, Jhist and Labav.
Stdise
Version:
1.0.
This is
analogous to Zstdise (q.v.) but is designed for just 2 images. See
also Formula and Combine.
Subshift
Version:
1.2. Linked to BiaQIm (Geometric)
Subshift
performs independent x,y, translation to sub-pixel accuracy using
cubic interpolation. See also Shiftim and Sincshift.
Symmetricise
Version:
1.0. Linked to BiaQIm (Instant process)
Symmetricise
makes an image symmetric by replacing values about the midline with
the average or repeats of themselves. All the standard input data
types are accepted with the exception of true colour BMP. There are
two intended uses for this program. One is to symmetricise a recorded
PSF which is supposed to be symmetric but is corrupted by noise. The
other is in the generation of a Fourier mask for manual Fourier
editing. See also Circulate and Fourier.
Synthcx
Version:
2.0. Linked to BiaQIm (Conversions)
Synthcx
synthesizes a single complex array (of doubles) from two input arrays
(real and imaginary components). The component inputs may be raw
arrays of doubles or (unlike Cxsynth) ASCII lists. See also Cxsep and
Cxsynth.
Tfmcombi
Version:
1.0.
TfmCombi
combines the geometric transform parameters in two transform lists
into one transform list. Each transform list (such as that generated
by Autoreg) is an ASCII list of numbers, the numbers on each line
specify - in this order - the rotation (degrees), y-translation,
x-translation (pixels), x-scale and y-scale (as proportions) for the
image. The first of the two lists to be combined must have no scaling
(i.e. both x-scale and y-scale must be 1.0) in this version. The
resulting combine transform list can be used to transform a set of
images with just one rotation, translation and scaling operation to
give the same effect as if the image was transformed by the RTS of
the first transform list followed by the RTS of the second. This is
useful if you perform registration in two stages to refine &
simplify the registration process. See also Autoreg, Geomlist.
Timecmd
Version:
1.2.
Use
Timecmd to see how long a command line task takes (including any of
the image processes listed here).
Trishear
Version:
1.4. Linked to BiaQIm (Geometric)
Trishear
performs independent x,y shear warpings using cubic interpolation,
Upto three shears can be performed at once such that tri-shear
rotation can be carried out. A special option is included which lets
you use Sincshear as a one-step rotation program - you supply the
rotation angle and the shears are automatically calculated to achieve
this rotation. See also Sincshear and Rotate
Txtod
Version:
1.0.
Use Txtod
to convert an ASCII file of numbers into a raw doubles array. See
also Synthcx, Xtotxt and Xtox.
Txtract
Version:
1.1.
Use
Txtract to extract columns or lines from an ASCII file of numbers.
See also Xtotxt and Txtod.
Watrous
Version:
1.0. Linked to BiaQIm (Transforms)
This
program performs a forward wavelet transform via the 'a trous'
algorithm described in Pantin E and Starck JL. Deconvolution of
astronomical images using the multiscale maximum entropy method.
Astron. Astrophys. Suppl. Ser.118:575-585 (1996). See also Zintegral
(performs the back-transform).
Wdenoise
Version:
1.1. Linked to BiaQIm (Enhancement)