CmpSpots.Cmpglb
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java.lang.Object
public class Cmpglb
Class Cmpglb is the base class that specifies global variables used by all of the other CmpSpots 2D spot pairing classes.
This code was derived and refactored from GELLAB-II cmpgl2 C language files and the Open2Dprot CmpSpots program Java files.
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.
| Field Summary | |
|---|---|
static DbAccession |
acc
|
static java.lang.String |
accDatabaseFile
full path Accession database file is xmlDir+accFile |
static java.lang.String |
accFile
Accession database file without the path. |
static int |
accFormatMode
Accession DB file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static int |
AP
Ambiguous Pair - CmpSpots generated label |
static java.lang.String |
applicationName
name of the application |
static java.lang.String[] |
argsV
Total command list arg list originally set fro main(args) |
static CmpAssign |
asgn
|
static java.lang.String |
banner
The full version data banner with todays date |
static java.lang.String |
bannerTitle
The short version data banner for popup titles |
static java.lang.String |
baseImageFileNameRsample
Base file name is the original Rsample input image file without the directory and without the file extension. |
static java.lang.String |
baseImageFileNameSample
Base file name is the original sample input image file without the directory and without the file extension. |
static java.lang.String |
batchDir
Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/ |
static java.lang.String |
cacheDir
Cache database directory {projDir}/cache/ |
static java.lang.String |
cmpspotsURL
Hardwired Open2Dprot server connection Switch to S.F. |
static boolean |
commutativeLMSswitch
The parsed of Command line switches |
static boolean |
CONSOLE_FLAG
|
static int |
CP
Composite Sample Database spot pair. |
static CmpSpots |
cs
instance of the main class |
static CmpData |
data
|
static java.lang.String |
DATE
CVS Version date |
static DbLM |
dbLM
Landmark part of the database |
static DbSample |
dbRsample
Rsample SSF state parameters read from files . |
static DbSample |
dbSample
Sample SSF state parameters read from files. |
static int |
DBUG_ALL_SSF_SPOTS
Debug code: print all SSF spots for both samples |
static boolean |
DBUG_APPEND
Debugging append text flag |
static int |
DBUG_ASSIGN_CODES
Debug code: Assign the pairing codes |
static int |
DBUG_ASSIGN_SSF_TO_LMS
Debug code: Assign the SSF spots to the landmark sets |
static int |
DBUG_COMPUTE_RADII
Debug code: compute the landmark sets 1/2 radii |
static boolean |
DBUG_CONSOLE
Debugging console text flag |
static int |
DBUG_DUMP_LM_SET_SPOTS
Debug code: dumpLMsetSpots() |
static int |
DBUG_DUMP_PREFACE_EPILOGUE
Debug code: dumpSPFpreface() and dumpStatisticsToSPFfile |
static int |
DBUG_DUMP_SPF
Debug code: dump the SPF data into the xml/ SPF file |
static int |
DBUG_FIND_LMS_IN_SSFS
Debug code: find landmarks in the SSF spot lists |
static int |
DBUG_FREE_0200000
Debug code: -free- |
static int |
DBUG_FREE_04000
Debug code: -free- |
static int |
DBUG_INITIAL_SPOT_PAIRING
Debug code: initialSpotPairing() and convolveG1G2() |
static int |
DBUG_PRINT_AT
Debug code: printAt() debugging |
static int |
DBUG_PRINT_FULL_NODE_INFO
Debug code: print full spot node info |
static int |
DBUG_PRINT_LMS_SET_SPOTS
Debug code: cvtLMsetSpotsToStr |
static int |
DBUG_PRINT_LMS_SPOT_MAPPING
Debug code: - print landmark DB and corresponding spot mapping |
static int |
DBUG_READ_LANDMARKS
Debug code: readLandmarks() |
static int |
DBUG_READ_SSF_DATA
Debug code: readSSFdata() |
static int |
DBUG_SECONDARY_PAIRING
Debug code: secondarySpotPairing() |
static int |
DBUG_SPECIFIC_SPOTS
Debug code: debug specific (hardwired) list of spots |
static int |
DBUG_SWITCH_ANALYSIS
Debug code: analyze command line switches |
static boolean |
DBUG_SWITCHES
Debugging switches |
static int |
dBugBits
-debug:bits |
static java.lang.String |
dbugBitsHelpStr
Debug bit options help for error messages |
static int[] |
dBugLMsetList
List of landmark set names to be debugged specified by -debug:bits,LMset#1,#2,...,#n (not letter). |
static boolean |
debugSwitch
The parsed of Command line switches |
static boolean |
defaultSwitch
The parsed of Command line switches |
static java.lang.String[] |
demoFileList
List of demo/ files downloadable from the server |
static boolean |
demoSwitch
The parsed of Command line switches |
static java.lang.String[] |
docFileList
List of documentation files downloadable from the server |
static boolean |
dtdSwitch
The parsed of Command line switches |
static int |
EP
Extrapolated Pair - by database program [FUTURE] |
static java.lang.String |
fileSeparator
File separator: Property("file.separator") |
static FileIO |
fio
|
static float |
fourSqrtPi
Constant 4*sqrt(PI) constant used in computing spot volume |
static int |
GS
Garbage Spot - generated by database or editing programs [FUTURE] |
static CmpIni |
ini
|
static java.lang.String |
inPixFileRsample
original Rsample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static java.lang.String |
inPixFileSample
original Sample input image file with full path and .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static boolean |
inputFormatSwitch
The parsed of Command line switches |
static boolean |
isCsamplePrimeSwitch
The parsed of Command line switches |
static java.lang.String[] |
jarFileList
List of program .jar files downloadable from the server |
static java.lang.String[] |
jarLibrFileList
List of library .jar files downloadable from the server |
static java.lang.String |
landmarkDatabaseFile
full path Landmark database file is xmlDir+lmsFile |
static boolean |
latchLandmarkSpotSwitch
The parsed of Command line switches |
static java.lang.String[] |
legalImageFileExtens
List of legal sample image file extensions |
static int |
LM
LandMark spot [could be virtual landmark] - by database program [FUTURE] |
static java.awt.Color |
LMSETCOLOR
|
static java.lang.String |
lmsFile
Landmark database file without the path. |
static int |
lmsFormatMode
Landmark DB file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static int |
MAX_LM_LATCH_THR
MAX distance to use to latch a landmark DB (x,y) value to a SSF (x,y) spot value if the -latchLMS is set |
static float |
maxLatchDist
Max distance to latch a landmark to its closest spot if any. |
static boolean |
nbrAltLMSSwitch
The parsed of Command line switches |
static int |
nDbugLMsetList
size of dBugLMsetList[]. |
static boolean |
NEVER
NEVER and CONSOLE_FLAG - debugging variables - must not be final! |
static int |
nlmDB
# landmarks read from landmark database file |
static int |
nSwitches
the number of Command line switches |
static int |
OPTBKGROUND
Shift background grayscale away from 0 so graphics show up better... |
static java.lang.String |
osName
name of this operating system: Property("os.name") |
static CmpPair |
pair
|
static CmpPairSecondary |
pair2ndary
|
static ParamHash |
paramH
|
static PixReader |
pix
|
static char[] |
pix1
Rsample or G1 source sample image |
static char[] |
pix2
Sample or G2 source sample image |
static java.lang.String |
pixFileExtn
Output images are either ".gif" or ".jpg" [TODO] change this to .jpg with JPEG writer. |
static int |
PP
Possible Pair - CmpSpots generated label |
static java.lang.String |
ppxDir
Original sample images directory {projDir}/ppx/ |
static CmpReportPopup |
pra
generic popup report |
static java.lang.String |
projDir
Project directory that is either userDir, specified by -projDir:{path}, or extracted from the input file path it the image is in a "/ppx/" subdirectory. |
static boolean |
projDirSwitch
The parsed of Command line switches |
static java.lang.String |
propertiesFile
Current startup properties file containing default switches if it exists. |
static boolean |
propertiesFileSwitch
The parsed of Command line switches |
static DbPairSamples |
ps
|
(package private) static boolean |
PUBLISH
NOTE: overide the following debugging options if publishing on net. |
static java.lang.String |
rdbmsDir
RDBMS database directory {projDir}/rdbms/ |
static java.lang.String |
REVISION
CVS Revision |
static Roi |
rRoiDbug
Rsample debug computing window used with -cwRdbug: |
static boolean |
rRoiDbugSwitch
The parsed of Command line switches |
static int |
RSAMPLE
The index for the Rsample (Reference Sample) |
static java.lang.String |
rsampleName
Name of Rsample G1 which includes the file extension but not the full path. |
static boolean |
rsampleSwitch
The parsed of Command line switches |
static int |
SAMPLE
The index for the Sample to be paired with the Rsample |
static java.lang.String |
sampleName
Name of Sample G2 which includes the file extension but not the full path. |
static boolean |
sampleSwitch
The parsed of Command line switches |
static boolean |
secondaryPairingSwitch
The parsed of Command line switches |
static java.lang.String |
simplePixFileRsample
Simple Rsample original Rsample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static java.lang.String |
simplePixFileSample
Simple original Sample input image file with .tif, .tiff, .jpg, .gif or .ppx file extensions. |
static Sort |
sort
|
static int |
SP
Sure Pair - CmpSpots generated label |
static int |
spfFormatMode
SPF output file modes: Allowed: IO_FORMAT_FULL, IO_FORMAT_GELLAB, IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static boolean |
spfFormatSwitch
The parsed of Command line switches |
static java.lang.String |
spfOutputFile
full xml/ SPF (Sample Pairs File) output file name |
static java.lang.String |
spfOutputPrefaceFile
full tab-delim PREFACE xml/ CmpSpot (Sample Pairs File) full path |
static java.awt.Color |
SPOTBOXCOLOR
|
static Roi |
sRoiDbug
Sample debug computing window used with -cwSdbug: |
static boolean |
sRoiDbugSwitch
The parsed of Command line switches |
static java.lang.String |
ssfFileRsample
SSF input file for G1 sample (i.e., Rsample) |
static java.lang.String |
ssfFileSample
SSF input file for G2 sample (i.e., Sample) |
static int |
ssfFormatMode
SSF input file modes: Allowed: IO_FORMAT_TAB_DELIM, IO_FORMAT_XML |
static java.lang.String |
ssfInputEpilogueFileRsample
full tab-delim G1 EPILOGUE xml/Rsample SSF full path |
static java.lang.String |
ssfInputEpilogueFileSample
full tab-delim G2 EPILOGUE xml/Sample SSFfull path |
static java.lang.String |
ssfInputFileRsample
xml/ Rsample G1 SSF File full path |
static java.lang.String |
ssfInputFileSample
xml/ Sample G2 SSF full path |
static java.lang.String |
ssfInputPrefaceFileRsample
full tab-delim G1 PREFACE xml/Rsample SSF full path |
static java.lang.String |
ssfInputPrefaceFileSample
full tab-delim G2 PREFACE xml/Sample SSF full path |
static long |
startTime
starting time in epoch msec time |
static java.lang.String[] |
sw
Command line + CmpSpots.properties state switches |
(package private) static boolean[] |
switchOptCBvalue
The switchOptcCBvalue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. |
(package private) static java.lang.String[] |
switchOptData
The switchOptData[0:(2*nData)-1] is used by the Report Popup that in turn may call PopupOptions. |
(package private) static java.lang.String[] |
switchOptValue
The switchOptValue[0:nData-1] is used by the Report Popup that in turn may call PopupOptions. |
static boolean |
thrPPswitch
The parsed of Command line switches |
static boolean |
thrSPswitch
The parsed of Command line switches |
static boolean |
timerSwitch
The parsed of Command line switches |
static java.lang.String |
tmpDir
Tmp images directory {projDir}/tmp/ |
static boolean |
updateSwitch
The parsed of Command line switches |
static int |
US
Unresolved Spot - CmpSpots generated label |
static boolean |
usageSwitch
The parsed of Command line switches |
(package private) static boolean |
USE_DEMO_DATA
Use the demo data by enabling the -demo flag and data. |
static boolean |
useAccFileSwitch
The parsed of Command line switches |
static boolean |
useHistGUISwitch
The parsed of Command line switches |
static boolean |
useLmsFileSwitch
The parsed of Command line switches |
static boolean |
usePercentDensitySwitch
The parsed of Command line switches |
static boolean |
usePopupGUISwitch
The parsed of Command line switches |
static java.lang.String |
userDir
current User directory: getProperty("user.dir")+fileSeparator |
static Util |
util
instance of utility class |
static java.lang.String |
VERSION
Manually define Version number |
static java.lang.String |
xmlDir
Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files. |
| Constructor Summary | |
|---|---|
Cmpglb()
|
|
| Method Summary | |
|---|---|
static int |
get2D(char[] pix,
int pixWidth,
int x,
int y)
get2D() - get the pixel at pix(x,y) computed at (y+pixWidth+x) |
static int |
get2D(int[] pix,
int pixWidth,
int x,
int y)
get2D() - get the pixel at pix(x,y) computed at (y+pixWidth+x) |
static void |
initGlb()
initGlb() - intialize any resources that must be set upon startup [TODO] Could move some of the above static defs here... |
static void |
resetGlb()
resetGlb() - reset any resources that must be reset for the next run of the program. |
static int |
set2D(char[] pix,
int pixWidth,
int x,
int y,
int g)
set2D() - save the pixel value g at pix(x,y) computed at (y+pixWidth+x) |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
|---|
public static CmpSpots cs
public static final java.lang.String applicationName
static boolean PUBLISH
static boolean USE_DEMO_DATA
public static final boolean DBUG_APPEND
public static boolean DBUG_SWITCHES
public static final boolean DBUG_CONSOLE
public static java.lang.String DATE
public static java.lang.String REVISION
public static java.lang.String VERSION
public static boolean NEVER
public static boolean CONSOLE_FLAG
public static final java.lang.String cmpspotsURL
public static java.lang.String[] jarFileList
public static java.lang.String[] jarLibrFileList
public static java.lang.String[] docFileList
public static java.lang.String[] demoFileList
public static final int MAX_LM_LATCH_THR
public static final int US
public static final int SP
public static final int PP
public static final int AP
public static final int EP
public static final int CP
public static final int GS
public static final int LM
public static final int DBUG_ASSIGN_CODES
public static final int DBUG_ASSIGN_SSF_TO_LMS
public static final int DBUG_COMPUTE_RADII
public static final int DBUG_DUMP_SPF
public static final int DBUG_FIND_LMS_IN_SSFS
public static final int DBUG_SWITCH_ANALYSIS
public static final int DBUG_INITIAL_SPOT_PAIRING
public static final int DBUG_PRINT_LMS_SPOT_MAPPING
public static final int DBUG_PRINT_AT
public static final int DBUG_PRINT_LMS_SET_SPOTS
public static final int DBUG_FREE_04000
public static final int DBUG_ALL_SSF_SPOTS
public static final int DBUG_READ_SSF_DATA
public static final int DBUG_READ_LANDMARKS
public static final int DBUG_SECONDARY_PAIRING
public static final int DBUG_FREE_0200000
public static final int DBUG_DUMP_LM_SET_SPOTS
public static final int DBUG_DUMP_PREFACE_EPILOGUE
public static final int DBUG_PRINT_FULL_NODE_INFO
public static final int DBUG_SPECIFIC_SPOTS
public static final java.lang.String dbugBitsHelpStr
public static final int OPTBKGROUND
public static final java.awt.Color LMSETCOLOR
public static final java.awt.Color SPOTBOXCOLOR
public static final int RSAMPLE
public static final int SAMPLE
public static int spfFormatMode
public static int ssfFormatMode
public static int accFormatMode
public static int lmsFormatMode
public static DbAccession acc
public static CmpAssign asgn
public static CmpData data
public static FileIO fio
public static CmpPair pair
public static CmpPairSecondary pair2ndary
public static CmpIni ini
public static DbPairSamples ps
public static ParamHash paramH
public static PixReader pix
public static Sort sort
public static Util util
public static CmpReportPopup pra
public static DbSample dbRsample
public static DbSample dbSample
public static DbLM dbLM
public static java.lang.String bannerTitle
public static java.lang.String banner
public static java.lang.String rsampleName
public static java.lang.String sampleName
public static final java.lang.String[] legalImageFileExtens
public static java.lang.String accDatabaseFile
public static java.lang.String accFile
public static java.lang.String landmarkDatabaseFile
public static java.lang.String lmsFile
public static java.lang.String ssfFileRsample
public static java.lang.String ssfFileSample
public static java.lang.String spfOutputFile
public static java.lang.String spfOutputPrefaceFile
public static java.lang.String propertiesFile
public static java.lang.String pixFileExtn
public static java.lang.String simplePixFileRsample
public static java.lang.String simplePixFileSample
public static java.lang.String inPixFileRsample
public static java.lang.String inPixFileSample
public static java.lang.String baseImageFileNameRsample
public static java.lang.String baseImageFileNameSample
public static java.lang.String ssfInputFileRsample
public static java.lang.String ssfInputPrefaceFileRsample
public static java.lang.String ssfInputEpilogueFileRsample
public static java.lang.String ssfInputFileSample
public static java.lang.String ssfInputPrefaceFileSample
public static java.lang.String ssfInputEpilogueFileSample
public static java.lang.String osName
public static java.lang.String fileSeparator
public static java.lang.String userDir
public static java.lang.String projDir
public static java.lang.String batchDir
public static java.lang.String cacheDir
public static java.lang.String ppxDir
public static java.lang.String rdbmsDir
public static java.lang.String tmpDir
public static java.lang.String xmlDir
public static java.lang.String[] argsV
public static java.lang.String[] sw
public static int nSwitches
public static boolean useAccFileSwitch
public static boolean nbrAltLMSSwitch
public static boolean isCsamplePrimeSwitch
public static boolean commutativeLMSswitch
public static boolean sRoiDbugSwitch
public static boolean rRoiDbugSwitch
public static boolean debugSwitch
public static boolean defaultSwitch
public static boolean demoSwitch
public static boolean dtdSwitch
public static boolean spfFormatSwitch
public static boolean usePopupGUISwitch
public static boolean useHistGUISwitch
public static boolean inputFormatSwitch
public static boolean useLmsFileSwitch
public static boolean latchLandmarkSpotSwitch
public static boolean usePercentDensitySwitch
public static boolean projDirSwitch
public static boolean propertiesFileSwitch
public static boolean rsampleSwitch
public static boolean sampleSwitch
public static boolean secondaryPairingSwitch
public static boolean thrSPswitch
public static boolean thrPPswitch
public static boolean timerSwitch
public static boolean updateSwitch
public static boolean usageSwitch
public static int dBugBits
public static int[] dBugLMsetList
public static int nDbugLMsetList
public static Roi rRoiDbug
public static Roi sRoiDbug
public static float fourSqrtPi
public static float maxLatchDist
public static int nlmDB
public static long startTime
public static char[] pix1
public static char[] pix2
static java.lang.String[] switchOptData
static boolean[] switchOptCBvalue
static java.lang.String[] switchOptValue
| Constructor Detail |
|---|
public Cmpglb()
| Method Detail |
|---|
public static void initGlb()
public static void resetGlb()
public static final int get2D(int[] pix,
int pixWidth,
int x,
int y)
pix - is the image bufferpixWidth - is width of imagex - of pixely - of pixel
public static final int get2D(char[] pix,
int pixWidth,
int x,
int y)
pix - is the image bufferpixWidth - is width of imagex - of pixely - of pixel
public static final int set2D(char[] pix,
int pixWidth,
int x,
int y,
int g)
pix - is the image bufferpixWidth - is width of imagex - of pixely - of pixelg - is new int value to save
|
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