gen_imaps

PURPOSE

gen_imaps generates intensity maps for a set of images that are partially overlapping.   One can then give these intensity maps to apply_map in order to produce a composite image where intensity variations in the original images do not produce obvious stitching artifacts.

TYPICAL USAGE

gen_imaps -image_list images.lst    \
-images images/ \
-masks masks/ \
-map_list maps.lst \
-maps maps/ \
-output imaps/

COMMAND LINE OPTIONS

-image_list images.lst

specifies the file that lists the images in the set.  This file contains just a list of image names, one per line.  Empty lines or lines beginning with '#' are ignored.

 -images directory/

specifies the directory where the images are stored.

-level output_imap_level

specifies the level of resolution of the output maps.  This is expressed as the base-2 logarithm of the pixel distance between map points (in both x and y diimensions).  For example, a value of 6 would indicate that the maps should have a grid point every 64 pixels in x and y.  The default value is 6.

-map_list maps.lst

specifies the maps that define the overlaps within the image set.  The map list file contains the names (one per line) of all maps relating one image to another.  The format of each line in this file is:

image_name0  image_name1  map_name  [ weight ]

These components are as follows:

image_name0 - the first image that the map refers to

image_name1 - the second image that the map refers to (the reference image)

map_name - the name given to the map.  This will be used to construct the filename in the maps directory.  Often the map_name is formed as some combination of the image names that it refers to.

weight - an optional weight factor to multiply all the inter-image spring constants by for springs generated from this map. This can be used to make some maps more important than others.  If omitted, this defaults to 1.

 -maps directory/

specifies the directory where the maps are stored.

-masks directory/

specifies the directory where the image masks are stored.   It is necessary to have the gen_imaps program use image masks if not all the pixels of the images contain valid image content.  See the section on image masks in the CONCEPTS page of AlignTK for more details.

-output directory/

specifies the directory where output intensity maps will be saved.

 

 

 

Copyright © 2020 National Center for Multiscale Modeling of Biological Systems. All Rights Reserved.