1 WAM examples at a glance

1.1 WAM programs with graphical interface

Program Name	Purpose	Details
wam_series	A GUI program using Windows Forms to get input from the user and apply a number of WAM operations.	Allows the user to selectively apply a number of WAM operations to a series of images. Includes options for different input and output formats, cutting a sub-area, median filtering, two kinds of overlays, converting to BYTE, remapping, calculating statistics, doing color stretch for the output files.
wam_match	Finds matches between in situ measurements and a series of satellite images	Creates a CSV text file with match-up statistics of a DX x DY window image statistics corresponding to in situ measurements.
wam_statist	Calculates statistics of masked areas for a series of images	Using a list of images, an image with masked areas or list of stations calculate statistics for the series of images. Output is a CSV file ready for importing into MS Excel.

1.2 Command-line WAM programs

Program Name	Purpose	Details
test_cut_hdf	Shows how to create a series of images of a selected sub-area, and save as JPEGs, GIFs or HDFs	Example shows how to read all matching HDF files in a folder, cut out a predefined sub-area, stretch the color scale, save each in different formats.
test_coastwatch_composite	Show how to create composites of a series of CoastWatch images	Reads all matching CoastWatch files in a folder, calculates composites, calculates the maximum pixel composite, the average pixel composite and the count image, stretches the color scales, saves each.
test_bandratio	Shows how to calculate a new image using a band ratio algorithm	Reads all matching pairs of image files in HDF (e.g. of 443 and 520 nm bands) in a folder, applies a band ratio algorithm, saves the calculated image as a float HDF, converts to a BYTE image using CHL scaling, stretches colors, saves as a JPEG.
wam_anomaly	Calculates anomalies relative to the mean monthly annual cycle	Reads all matching images, calculates and saves the mean annual images, then calculates and saves the anomalies relative to the monthly means
wam_band_ratio	Calculates a series of new images using a combination of images and a band ratio algorithm. Includes OC4v4 and SPGANT algorithms.	Reads all matching sets of radiance images (e.g. SeaWiFS 443, 490, 510, 555 nm Lwn bands), applies a band ratio algorithm, and saves the calculated image as a log-scaled Byte image in HDF.
wam_filter	Apply a filter, e.g. Median filter, to a series of images, save the results	Reads all matching HDF files in a folder, cuts out a predefined sub-area, applies the Median filter, and saves each as a JPEG.
wam_reduce	Reduces a series of HDF images	Reads all matching HDF files in a folder, reduces the size by a predefined times using a selected reduction type, saves each as HDF.
wam_remap2	Remap a series of (MODIS) images, possibly with external geo-referencing to a target projection	Reads all matching HDF files, picks a selected SDS, guesses the respective geo-referencing file, maps each to the target projection, saves the remapped image as HDF.
wam_remap_lla	Remap a series of images with external latitude/longitude array (LLA)to a target projection	Reads a list of 2 filenames (file with image and the file with LLA), picks a SDS, remaps to the target projection and saves in selected folder together with typical timing attributes.
wam_attribute	Print the value of an HDF attribute from a series of HDF files	Reads all matching HDF files in a folder, extracts the value of an integer attribute (e.g. “Start Day”), and prints the file name and the attribute value.
wam_pp	Calculate Primary Production according to the Behrenfeld-Falkowski model	Calculates primary production for a selected set of CHLO, PAR and SST images, saves as HDF.
run_pp	Calculate Behrenfeld-Falkowski primary production for a series of images	Reads a list of CHLO, PAR and SST images, calculates images of Behrenfeld-Falkowski primary production, saves as HDF.
test_statist	Calculate statistics of a rectangular area	Reads a specified image as HDF, calculates statistics for a specified rectangular area, prints to the screen and saves in a text file.
wam_statist_sta	Extract pixel values of a series of points (stations), calculate statistics for 3 x 3 pixel areas around the stations for a series of images	Reads a list of stations (specified by longitude, latitude, name) and a list of images; calculates statistics for 3x3 pixel areas centered at the station, saves statistics and pixel values in a comma separated text file.
wam_statist_grid	Calculate statistics for latitude/longitude grid for a series of images	Reads a series of images; calculates statistics for a lat/lon grid, saves statistics.
sortmasks	Sort the statistics of masked areas by area instead of by image	Sorts the statistics by mask number of a text file created by wam_statist. The output file sorted.csv is ready to be imported into a spreadsheet like MS Excel.
wam_integ_mask	Calculate integrals of a series of specified irregular areas (masks) of a series of images	Reads a mask image that specifies up to 255 different irregular areas (masks), calculates total integral (pixel value x pixel area) for a list of images from a list file, saves totals for all the images and all the masks in a comma separated text file.
wam_integ_lat	Calculate integrals of a series of 255 latitudinal areas (masks) excluding land and creates a time series of integrals	Reads a land mask image to separate missing pixels due to clouds from land. Automatically generates 255 masks according to latitude, calculates statistics and integrals (pixel value x pixel area) for a list of images from a list file, saves totals for all the images and all the masks in a comma separated text file.
addmasks	Adds integrals and statistics of masked areas from wam_integ_lat	Adds the integrals of selected range of (latitudinal) masks of a text file created by wam_integ_lat. The output file addmasks.csv is ready to be imported into a spreadsheet like MS Excel.
wam_poc	Calculates POC images from a series of nLw555 images according to Stramski et al. (1999).	A complex example that uses one set of images (nLw555) to calculate another set of images (POC).
wam_ratio	Calculates ratio images from two series of images	An example that reads two series of images, calculates pixel by pixel ratio, saves as HDF
wam_ratio_list	Calculates a series of ratio images from a series of image pairs using a list	In contrast to the previous example, gets the image names from a list file. Remaps the second image to the first. This example is used to calculate the ratio of a MODIS image to that of a SeaWiFS image.
wam_ratio_list_ef	Calculates a series of export flux images using input images of primary production, SST and Chl.	Uses Edward Laws’ algorithm to calculate export flux of primary production. Reads a list file with 3 filenames on each line.
wam_histo_mask	Calculates a series of histograms for a specified rectangle	Reads a mask, a list of file filenames, calculates and saves histograms of a rectangle.
wam_range_area_mask	Calculates total areas of for a range of values for a masked area	Reads a mask and calculates the total areas within the mask of a series of images, corresponding to a range of values. It assumes that the images are in the global equal angle projection.
wam_screen_modis	Using a quality flag image, screens, i.e. keeps only the high-quality pixels while replacing others with zeros	Screens Level-3 MODIS (SST or chl) images, converts to Byte with, respectively, SST-Pathfinder or Log-Chl scaling.
wam_screen_pf	Screens AVHRR Pathfinder version 5 files, keeps only the best quality pixels	Uses both SST and quality images, makes all SST pixels with quality flags less than 7 zero, converts to Byte with SST-Pathfinder scaling.
wam_to_hdf	Converts all matching plain raster images in a directory to HDF while adding attributes.	Is useful for creating HDF files from plain raster files. Using filenames as clues for time it tries to add attributes like “Start Year”, “Start Day” that are needed for time series analysis.
wam_composite, wam_composite2	Create an average composite and a count image of a series of HDF images	Reads HDF files listed in a list file, calculates a mean composite and a count image from all valid pixels, saves as HDF files. For SeaWiFS SMI files adjusts the attributes so that the start and end periods correspond to the first and last images, respectively.
wam_composite_quikscat	Creates composites of ascending and descending orbits of Level-3 QuikSCAT data	Reads all Level-3 QuikSCAT files in the folder, calculates the mean composite of ascending and descending orbits, saves as HDF files
wam_remap_annotate	A specific example to remap a series of images to a target projection, overlay an annotation layer with stations, color bar, grid, etc. This can be done more easily with wam_series.	First reads an HDF image in a target projection that has also the features to be overlaid, such as stations, color bar, etc., then reads all matching HDF images in a folder, maps each to the target projection, overlays the overlay image, saves the results in various forms (HDF, JPEG, BMP, etc.).
wam_rgb	Simple example for creating series of RGB composite images	Reads all matching image files from a folder, calculates RGB images from selected bands.
wam_rgb_modis	Creates accurately co-registered true-color RGB composites from MODIS Level-1B data	Creates true-color RGB images, at 1 km, 500 m or 250 m, does accurate band co-registration, optionally maps to a target projection.
zoom_modis_lat_lon	Interpolates 1-km MODIS latitude-longitude array to 250-m resolution	Reads all matching MOD03 or MYD03 files and interpolates the latitude and longitude arrays to 250 m. IT IS VERY SLOW! An optimized version is in development!
wam_turbidity	Calculates turbidity index from MODIS bands1 and 2, maps to a target projection	Reads a crefl-produced HDF file produced with bands 1 and 2, MOD03 geo-referencing file, saves as HDF and as JPEG.