addLandmark() - "Add LM" add temporary landmarks to landmark list
If exist in both I1 and I2 images into permanent landmarks
and indicate in images push landmark.
addUniqueSpotToSpotList() - add spot if it is unique to the spot list
else just update the spot measurement but keep the spot number if
it is an existing spot if +- 1 pixel in xC and/or yC
captureBackgroundValue() - capture the values under the mask of the
selected image if it is left or right and assign it to the
background pixel value for the current image.
captureMeasCWvalue() - capture the pixel values under the
computing window of the selected image if it is left or right and
assign it to the measurement pixel value for the current image.
captureMeasValue() - capture the pixel values under the mask of the
selected image if it is left or right and assign it to the
measurement pixel value for the current image.
close() - close this popup and reset flags if needed
[TODO] If they edited the calibration and peak calibration table,
and they did not save the calibration (i.e.
close() - close this popup and reset flags if needed
[TODO] If they edited the calibration and peak calibration table,
and they did not save the calibration (i.e.
createFlkUserPairsMenuTree() - create the paired FlkUser menu tree
from analyzing the Images/* directories and setup the database of
pairs of user directory images
createFlkUserSingleMenuTree() - create the single image
FlkUser menu tree from analyzing the Images/* directories and
setup the database of user directory single images
data type from sampleModel.getDataType()
The types are defined as DataBuffer.TYPE_xxxx where xxxx
is (BYTE, DOUBLE, FLOAT, INT, SHORT, UNDEFINED, USHORT)
Do spot measurement adding it to the spotList, protein lookup for that
spot, and popup current access server Web page in one operation when
the user clicks on a spot in an active image.
extrapolateNDwedgeMap() - extrapolate the maxNDsteps ND wedge peaks
in ndWedgeODvalues[0:maxNDsteps-1] with corresponding gray values
ndWedgeGrayValues[0:maxNDsteps-1] into a piecewise linear
mapGrayToOD[0:maxGray] array.
extrapolateNDwedgeMap() - extrapolate the maxNDsteps ND wedge peaks
in ndWedgeODvalues[0:maxNDsteps-1] with corresponding gray values
ndWedgeGrayValues[0:maxNDsteps-1] into a piecewise linear
mapGrayToOD[0:maxGray] array.
fitWarpLSQ() - weighted LSQ spatial transform w/ orthogonal polynomials
Based on algorithm described by Ardeshir Goshtasby in "Image
resgistration by local approximation methods", Image and Vision
computing, Vold 6, No.
FlkUser contains methods to maintain the internal FlkUserDB
database created by analyzing the user's image directories they have
placed in the Images/ folder.
getBaseFlkPropertiesStr() - add generate tab-delim base Flicker
properties State string to the string buffer
The format is tab-delimited (name \t value \n) with one entry/line.
getFullCalFilePath() - compute the .cal file from the qualified imageFile
If there is a subdirectory before the baseFile, then strip out the
directory name and add it before the actual base file.
Get the peaks from the circular mask measurement spot list using
the mean circle measurement grayscale values not corrected
for background (since we do not know what background is).
inheritNDwedgeODvalues() - if current calibration does NOT have ND wedge
OD values, but the paired gel DOES, then inherit its OD wedge values
and units to avoid having to type it.
interpolatePoints() - interpolate (xOld,yOld) to (xNew,yNew) into list
of x,y coordinates of maximum size maxN which are pushed onto the
bnd[] point list.
itemStateChanged() - handle item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and CheckboxMenuItems.
lookupProtIDandNameToSpotList() - if the gel is clickable and the user
enabled the clickable DB checkbox, then search the clickableCGIbaseURL
protein database for all spots in the spot list and for those
that have matches, update the Spot.id and Spot.name.
mapRelXYtoImage() - map (x,y) Mouse in current canvas to (xImg,yImg)
as well as updating the parent.(xImg,yImg) values
which are RELATIVE to the current image.
mapSPIDtoPIRURL() - if using a PIR server database AND we
have either looked up the Swiss-Prot ID for the spot, then
map the dataURL to the PRI site by adding the SP ID to the
currentPRIbaseURL.
mapXYtoAffineIdx() - Compute Affine transform (x',y') idx from f(x,y)
where idx is the index of the pixel in the input image to be used for
the output image.
popupSpotEditBoth() - popup a spot editing function to let you
edit two selected (putatively paired) spots together
Edit the data in 3 columns with the field name on the left column
the left image data in the middle column and the right image data in
the right column.
readCalibrationFile() - read the image calibration from the
"cal/{image file base}.cal" file
or
"cal/{image subdirectory}-DIR-{image file base}.cal" file.
rgb2gray() - convert color image to NTSC gray value image
using NTSC transform gray= red*0.33 + green*0.50 + blue*0.17
NOTE: don't apply this transform more than once or it will
have bogus results.
rmvSpotListFile() - clear the .spt file from the spt/ directory
by moving the spt/.spt file into spt/.spt.bkup
andclearing the .bkup file if it previously existed first.
setDefaultGrayscaleIndexColorMap() - set the RGB IndexColorMap from
(r,g,b) maps
Note: see Hacking Java, pg 90 on cycling color palette
[TODO] Update the display...
setNDwedgeTable() - set ND step wedge calibration set of
(grayscale,OD) wedge values, # of steps and max grayvalue
[CHECK] we may want to copy the data to fixed size
arrays [0:MAX_ND_STEPS-1].
setUseLogFlag() - flag to set the log flag
This is used if the data has more than 8-bits of grayscale
so the data is transformed by the log over the range of
255*log(10**nBits-1) to 0
warpLSQ() - weighted LSQ spatial transform with orthogonal polynomials
Based on algorithm described by Ardeshir Goshtasby in "Image
resgistration by local approximation methods", Image and Vision
computing, Vold 6, No.