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Elphel
imagej-elphel
Commits
f8cffed4
Commit
f8cffed4
authored
Sep 06, 2014
by
Andrey Filippov
Browse files
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Plain Diff
Added suggestions for manual screws (handling motors out of range)
parent
3fa095d3
Changes
3
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3 changed files
with
142 additions
and
13 deletions
+142
-13
Aberration_Calibration.java
src/main/java/Aberration_Calibration.java
+65
-2
FocusingField.java
src/main/java/FocusingField.java
+63
-3
LensAdjustment.java
src/main/java/LensAdjustment.java
+14
-8
No files found.
src/main/java/Aberration_Calibration.java
View file @
f8cffed4
...
@@ -4544,6 +4544,12 @@ if (MORE_BUTTONS) {
...
@@ -4544,6 +4544,12 @@ if (MORE_BUTTONS) {
return
;
return
;
}
}
}
}
// Just for old focal distance calculation
MOTORS
.
focusingHistory
.
optimalMotorPosition
(
// recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS
,
MOTORS
.
getMicronsPerStep
(),
//double micronsPerStep,
DEBUG_LEVEL
);
while
(
adjustFocusTiltLMA
());
while
(
adjustFocusTiltLMA
());
return
;
return
;
}
}
...
@@ -8698,10 +8704,12 @@ if (MORE_BUTTONS) {
...
@@ -8698,10 +8704,12 @@ if (MORE_BUTTONS) {
/* ===== Other methods ==================================================== */
/* ===== Other methods ==================================================== */
public
boolean
adjustFocusTiltLMA
(){
public
boolean
adjustFocusTiltLMA
(){
// just for reporting distance old way
// just for reporting distance old way
/*
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
MOTORS.focusingHistory.optimalMotorPosition( // recalculate calibration to estimate current distance from center PSF
FOCUS_MEASUREMENT_PARAMETERS,
FOCUS_MEASUREMENT_PARAMETERS,
MOTORS.getMicronsPerStep(), //double micronsPerStep,
MOTORS.getMicronsPerStep(), //double micronsPerStep,
DEBUG_LEVEL);
DEBUG_LEVEL);
*/
// No-move measure, add to history
// No-move measure, add to history
moveAndMaybeProbe
(
moveAndMaybeProbe
(
true
,
// just move, not probe
true
,
// just move, not probe
...
@@ -8724,7 +8732,7 @@ if (MORE_BUTTONS) {
...
@@ -8724,7 +8732,7 @@ if (MORE_BUTTONS) {
//get measurement
//get measurement
FocusingField
.
FocusingFieldMeasurement
fFMeasurement
=
MOTORS
.
getThisFFMeasurement
(
FOCUSING_FIELD
);
FocusingField
.
FocusingFieldMeasurement
fFMeasurement
=
MOTORS
.
getThisFFMeasurement
(
FOCUSING_FIELD
);
// calculate z, tx, ty, m1,m2,m3
// calculate z, tx, ty, m1,m2,m3
double
[]
zTxTyM1M2M3
=
FOCUSING_FIELD
.
adjustLMA
(
fFMeasurement
);
double
[]
zTxTyM1M2M3
=
FOCUSING_FIELD
.
adjustLMA
(
fFMeasurement
,
false
);
// show dialog: Apply, re-calculate, exit
// show dialog: Apply, re-calculate, exit
int
[]
currentMotors
=
fFMeasurement
.
motors
;
int
[]
currentMotors
=
fFMeasurement
.
motors
;
int
[]
newMotors
=
currentMotors
.
clone
();
int
[]
newMotors
=
currentMotors
.
clone
();
...
@@ -8738,15 +8746,47 @@ if (MORE_BUTTONS) {
...
@@ -8738,15 +8746,47 @@ if (MORE_BUTTONS) {
zTxTy
[
2
]=
zTxTyM1M2M3
[
2
];
zTxTy
[
2
]=
zTxTyM1M2M3
[
2
];
}
}
double
[]
targetTilts
={
0.0
,
0.0
};
double
[]
targetTilts
={
0.0
,
0.0
};
double
[]
manualScrewsCW
=
null
;
if
(
zTxTyM1M2M3
!=
null
){
manualScrewsCW
=
FOCUSING_FIELD
.
fieldFitting
.
mechanicalFocusingModel
.
getManualScrews
(
zTxTy
[
0
]-
FOCUSING_FIELD
.
targetRelFocalShift
,
//double zErr, // positive - away from lens
zTxTy
[
1
]-
targetTilts
[
0
],
// double tXErr,// positive - 1,2 away from lens, 3 - to the lens
zTxTy
[
2
]-
targetTilts
[
1
]);
// double tYErr);
}
double
scaleMovement
=
1.0
;
// calculate automatically - reduce when close
double
scaleMovement
=
1.0
;
// calculate automatically - reduce when close
boolean
parallelMove
=
false
;
if
(
MASTER_DEBUG_LEVEL
>
0
){
System
.
out
.
println
(
"----- Focus/tilt measurement results -----"
);
System
.
out
.
println
(
"Relative focal shift "
+
IJ
.
d2s
(
zTxTy
[
0
],
3
)+
" um ("
+
IJ
.
d2s
(
FOCUSING_FIELD
.
targetRelFocalShift
,
3
)+
"um)"
);
System
.
out
.
println
(
"Horizontal tilt "
+
IJ
.
d2s
(
zTxTy
[
1
],
3
)+
" um/mm ("
+
IJ
.
d2s
(
targetTilts
[
0
],
3
)+
"um/mm)"
);
System
.
out
.
println
(
"Vertical tilt "
+
IJ
.
d2s
(
zTxTy
[
2
],
3
)+
" um/mm ("
+
IJ
.
d2s
(
targetTilts
[
1
],
3
)+
"um/mm)"
);
for
(
int
i
=
0
;
i
<
newMotors
.
length
;
i
++){
System
.
out
.
println
(
"Suggested for motor "
+(
i
+
1
)+
" "
+
newMotors
[
i
]+
" ("
+
currentMotors
[
i
]+
")"
);
}
if
(
manualScrewsCW
!=
null
)
for
(
int
i
=
0
;
i
<
manualScrewsCW
.
length
;
i
++){
if
(
manualScrewsCW
[
i
]>=
0
)
System
.
out
.
println
(
"Suggested rotation for screw # "
+(
i
+
1
)+
" "
+
IJ
.
d2s
(
manualScrewsCW
[
i
],
3
)+
" (CW)"
);
else
System
.
out
.
println
(
"Suggested rotation for screw # "
+(
i
+
1
)+
" "
+
IJ
.
d2s
(
manualScrewsCW
[
i
],
3
)+
" (CCW)"
);
}
System
.
out
.
println
(
"----- end of Focus/tilt measurement results -----"
);
}
GenericDialog
gd
=
new
GenericDialog
(
"Adjusting focus/tilt"
);
GenericDialog
gd
=
new
GenericDialog
(
"Adjusting focus/tilt"
);
if
(
zTxTyM1M2M3
==
null
){
gd
.
addMessage
(
"**** Failed to determine focus/tilt, probably too far out of focus. ****"
);
gd
.
addMessage
(
"**** You may cancel the command and try \"Auto pre-focus\" first. ****"
);
}
gd
.
addNumericField
(
"Target focus (relative to best composirte)"
,
FOCUSING_FIELD
.
targetRelFocalShift
,
2
,
5
,
"um ("
+
IJ
.
d2s
(
zTxTy
[
0
],
3
)+
")"
);
gd
.
addNumericField
(
"Target focus (relative to best composirte)"
,
FOCUSING_FIELD
.
targetRelFocalShift
,
2
,
5
,
"um ("
+
IJ
.
d2s
(
zTxTy
[
0
],
3
)+
")"
);
gd
.
addNumericField
(
"Target horizontal tilt (normally 0)"
,
targetTilts
[
0
],
2
,
5
,
"um/mm ("
+
IJ
.
d2s
(
zTxTy
[
1
],
3
)+
")"
);
gd
.
addNumericField
(
"Target horizontal tilt (normally 0)"
,
targetTilts
[
0
],
2
,
5
,
"um/mm ("
+
IJ
.
d2s
(
zTxTy
[
1
],
3
)+
")"
);
gd
.
addNumericField
(
"Target vertical tilt (normally 0)"
,
targetTilts
[
1
],
2
,
5
,
"um/mm ("
+
IJ
.
d2s
(
zTxTy
[
2
],
3
)+
")"
);
gd
.
addNumericField
(
"Target vertical tilt (normally 0)"
,
targetTilts
[
1
],
2
,
5
,
"um/mm ("
+
IJ
.
d2s
(
zTxTy
[
2
],
3
)+
")"
);
gd
.
addNumericField
(
"Motor 1"
,
newMotors
[
0
],
0
,
5
,
"steps ("
+
currentMotors
[
0
]+
")"
);
gd
.
addNumericField
(
"Motor 1"
,
newMotors
[
0
],
0
,
5
,
"steps ("
+
currentMotors
[
0
]+
")"
);
gd
.
addNumericField
(
"Motor 2"
,
newMotors
[
1
],
0
,
5
,
"steps ("
+
currentMotors
[
1
]+
")"
);
gd
.
addNumericField
(
"Motor 2"
,
newMotors
[
1
],
0
,
5
,
"steps ("
+
currentMotors
[
1
]+
")"
);
gd
.
addNumericField
(
"Motor 3"
,
newMotors
[
2
],
0
,
5
,
"steps ("
+
currentMotors
[
2
]+
")"
);
gd
.
addNumericField
(
"Motor 3"
,
newMotors
[
2
],
0
,
5
,
"steps ("
+
currentMotors
[
2
]+
")"
);
gd
.
addMessage
(
"Suggested rotation of the top screws, use if motor positions are out of limits - outside of +/-25,000"
);
if
(
manualScrewsCW
!=
null
)
for
(
int
i
=
0
;
i
<
manualScrewsCW
.
length
;
i
++){
if
(
manualScrewsCW
[
i
]>=
0
)
gd
.
addMessage
(
"Screw # "
+(
i
+
1
)+
" "
+
IJ
.
d2s
(
manualScrewsCW
[
i
],
3
)+
" (CW)"
);
else
gd
.
addMessage
(
"Screw # "
+(
i
+
1
)+
" "
+
IJ
.
d2s
(
manualScrewsCW
[
i
],
3
)+
" (CCW)"
);
}
gd
.
addNumericField
(
"Scale movement"
,
scaleMovement
,
3
,
5
,
"x"
);
gd
.
addNumericField
(
"Scale movement"
,
scaleMovement
,
3
,
5
,
"x"
);
gd
.
addCheckbox
(
"Recalculate and apply parallel move only"
,
parallelMove
);
// should be false after manual movement
gd
.
addCheckbox
(
"Filter samples/channels by Z"
,
FOCUSING_FIELD
.
filterZ
);
// should be false after manual movement
gd
.
addCheckbox
(
"Filter samples/channels by Z"
,
FOCUSING_FIELD
.
filterZ
);
// should be false after manual movement
gd
.
addCheckbox
(
"Filter by value (leave lower than maximal fwhm used in focal scan mode)"
,
FOCUSING_FIELD
.
filterByScanValue
);
gd
.
addCheckbox
(
"Filter by value (leave lower than maximal fwhm used in focal scan mode)"
,
FOCUSING_FIELD
.
filterByScanValue
);
...
@@ -8773,7 +8813,7 @@ if (MORE_BUTTONS) {
...
@@ -8773,7 +8813,7 @@ if (MORE_BUTTONS) {
newMotors
[
1
]=
(
int
)
gd
.
getNextNumber
();
newMotors
[
1
]=
(
int
)
gd
.
getNextNumber
();
newMotors
[
2
]=
(
int
)
gd
.
getNextNumber
();
newMotors
[
2
]=
(
int
)
gd
.
getNextNumber
();
scaleMovement
=
gd
.
getNextNumber
();
scaleMovement
=
gd
.
getNextNumber
();
parallelMove
=
gd
.
getNextBoolean
();
FOCUSING_FIELD
.
filterZ
=
gd
.
getNextBoolean
();
FOCUSING_FIELD
.
filterZ
=
gd
.
getNextBoolean
();
FOCUSING_FIELD
.
filterByScanValue
=
gd
.
getNextBoolean
();
FOCUSING_FIELD
.
filterByScanValue
=
gd
.
getNextBoolean
();
FOCUSING_FIELD
.
filterByValueScale
=
gd
.
getNextNumber
();
FOCUSING_FIELD
.
filterByValueScale
=
gd
.
getNextNumber
();
...
@@ -8789,6 +8829,18 @@ if (MORE_BUTTONS) {
...
@@ -8789,6 +8829,18 @@ if (MORE_BUTTONS) {
MASTER_DEBUG_LEVEL
=(
int
)
gd
.
getNextNumber
();
MASTER_DEBUG_LEVEL
=(
int
)
gd
.
getNextNumber
();
DEBUG_LEVEL
=
MASTER_DEBUG_LEVEL
;
DEBUG_LEVEL
=
MASTER_DEBUG_LEVEL
;
FOCUSING_FIELD
.
setDebugLevel
(
DEBUG_LEVEL
);
FOCUSING_FIELD
.
setDebugLevel
(
DEBUG_LEVEL
);
if
(
parallelMove
){
// ignore/recalculate newMotors data
zTxTyM1M2M3
=
FOCUSING_FIELD
.
adjustLMA
(
fFMeasurement
,
true
);
// recalculate with parallel move only
newMotors
=
currentMotors
.
clone
();
if
(
zTxTyM1M2M3
!=
null
){
newMotors
[
0
]=(
int
)
Math
.
round
(
zTxTyM1M2M3
[
3
]);
newMotors
[
1
]=(
int
)
Math
.
round
(
zTxTyM1M2M3
[
4
]);
newMotors
[
2
]=(
int
)
Math
.
round
(
zTxTyM1M2M3
[
5
]);
}
System
.
out
.
println
(
"Parallel move position for motor 1 "
+
newMotors
[
0
]+
" ("
+
currentMotors
[
0
]+
")"
);
System
.
out
.
println
(
"Parallel move position for motor 2 "
+
newMotors
[
1
]+
" ("
+
currentMotors
[
1
]+
")"
);
System
.
out
.
println
(
"Parallel move position for motor 3 "
+
newMotors
[
2
]+
" ("
+
currentMotors
[
2
]+
")"
);
}
// Scale motor movement
// Scale motor movement
newMotors
[
0
]=
currentMotors
[
0
]+((
int
)
Math
.
round
((
newMotors
[
0
]-
currentMotors
[
0
])*
scaleMovement
));
newMotors
[
0
]=
currentMotors
[
0
]+((
int
)
Math
.
round
((
newMotors
[
0
]-
currentMotors
[
0
])*
scaleMovement
));
...
@@ -10042,6 +10094,7 @@ if (MORE_BUTTONS) {
...
@@ -10042,6 +10094,7 @@ if (MORE_BUTTONS) {
return
null
;
return
null
;
}
}
if
(
allOK
)
{
if
(
allOK
)
{
if
(
focusMeasurementParameters
.
scanMeasureLast
)
{
allOK
&=
moveAndMaybeProbe
(
allOK
&=
moveAndMaybeProbe
(
true
,
true
,
centerMotorPos
,
// null OK
centerMotorPos
,
// null OK
...
@@ -10060,6 +10113,16 @@ if (MORE_BUTTONS) {
...
@@ -10060,6 +10113,16 @@ if (MORE_BUTTONS) {
updateStatus
,
updateStatus
,
debugLevel
,
debugLevel
,
loopDebugLevel
);
loopDebugLevel
);
}
else
{
// just move, no measuring
System
.
out
.
println
(
"Returning motors to initial position at "
+
IJ
.
d2s
(
0.000000001
*(
System
.
nanoTime
()-
startTime
),
3
));
focusingMotors
.
moveElphel10364Motors
(
// return to last direct scan position
true
,
//boolean wait,
centerMotorPos
,
0.0
,
//double sleep,
true
,
//boolean showStatus,
""
,
//String message,
false
);
//focusMeasurementParameters.compensateHysteresis); //boolean hysteresis)
}
}
}
if
(
debugLevel
>
0
)
System
.
out
.
println
(
"Scanning focus in the center, number of steps="
+
focusMeasurementParameters
.
scanNumber
+
if
(
debugLevel
>
0
)
System
.
out
.
println
(
"Scanning focus in the center, number of steps="
+
focusMeasurementParameters
.
scanNumber
+
...
...
src/main/java/FocusingField.java
View file @
f8cffed4
...
@@ -4255,6 +4255,7 @@ public boolean LevenbergMarquardt(
...
@@ -4255,6 +4255,7 @@ public boolean LevenbergMarquardt(
}
}
}
}
double
[]
dmz
=
getAdjustedMotors
(
double
[]
dmz
=
getAdjustedMotors
(
null
,
// double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift
+
best_qb_corr
[
0
],
targetRelFocalShift
+
best_qb_corr
[
0
],
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltY
,
targetTiltY
,
...
@@ -4263,6 +4264,7 @@ public boolean LevenbergMarquardt(
...
@@ -4263,6 +4264,7 @@ public boolean LevenbergMarquardt(
System
.
out
.
println
(
"Suggested motor linearized positions: "
+
IJ
.
d2s
(
dmz
[
0
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
1
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
2
],
2
));
System
.
out
.
println
(
"Suggested motor linearized positions: "
+
IJ
.
d2s
(
dmz
[
0
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
1
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
2
],
2
));
}
}
double
[]
dm
=
getAdjustedMotors
(
double
[]
dm
=
getAdjustedMotors
(
null
,
// double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift
+
best_qb_corr
[
0
],
targetRelFocalShift
+
best_qb_corr
[
0
],
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltY
,
targetTiltY
,
...
@@ -4312,6 +4314,7 @@ public boolean LevenbergMarquardt(
...
@@ -4312,6 +4314,7 @@ public boolean LevenbergMarquardt(
}
}
}
}
double
[]
dmz
=
getAdjustedMotors
(
double
[]
dmz
=
getAdjustedMotors
(
null
,
// double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift
+
best_qb_corr
[
0
],
targetRelFocalShift
+
best_qb_corr
[
0
],
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltY
,
targetTiltY
,
...
@@ -4320,6 +4323,7 @@ public boolean LevenbergMarquardt(
...
@@ -4320,6 +4323,7 @@ public boolean LevenbergMarquardt(
System
.
out
.
println
(
"Suggested motor linearized positions: "
+
IJ
.
d2s
(
dmz
[
0
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
1
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
2
],
2
));
System
.
out
.
println
(
"Suggested motor linearized positions: "
+
IJ
.
d2s
(
dmz
[
0
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
1
],
2
)+
":"
+
IJ
.
d2s
(
dmz
[
2
],
2
));
}
}
double
[]
dm
=
getAdjustedMotors
(
double
[]
dm
=
getAdjustedMotors
(
null
,
// double [] zM0, // current linearized motors (or null for full adjustment)
targetRelFocalShift
+
best_qb_corr
[
0
],
targetRelFocalShift
+
best_qb_corr
[
0
],
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltX
,
// for testing, normally should be 0 um/mm
targetTiltY
,
targetTiltY
,
...
@@ -4369,7 +4373,9 @@ public boolean LevenbergMarquardt(
...
@@ -4369,7 +4373,9 @@ public boolean LevenbergMarquardt(
}
}
//,
//,
public
double
[]
adjustLMA
(
FocusingFieldMeasurement
measurement
){
public
double
[]
adjustLMA
(
FocusingFieldMeasurement
measurement
,
boolean
parallelMove
){
if
(!
testMeasurement
(
if
(!
testMeasurement
(
measurement
,
measurement
,
zMin
,
//+best_qb_corr[0],
zMin
,
//+best_qb_corr[0],
...
@@ -4390,7 +4396,13 @@ public boolean LevenbergMarquardt(
...
@@ -4390,7 +4396,13 @@ public boolean LevenbergMarquardt(
result
[
0
]=
zTilts
[
0
]-
best_qb_corr
[
0
];
result
[
0
]=
zTilts
[
0
]-
best_qb_corr
[
0
];
result
[
1
]=
zTilts
[
1
];
result
[
1
]=
zTilts
[
1
];
result
[
2
]=
zTilts
[
2
];
result
[
2
]=
zTilts
[
2
];
double
[]
zm
=
null
;
if
(
parallelMove
){
zm
=
new
double
[
3
];
for
(
int
i
=
0
;
i
<
zm
.
length
;
i
++)
zm
[
i
]=
fieldFitting
.
mechanicalFocusingModel
.
mToZm
(
measurement
.
motors
[
i
],
i
);
}
double
[]
dm
=
getAdjustedMotors
(
double
[]
dm
=
getAdjustedMotors
(
zm
,
targetRelFocalShift
+
best_qb_corr
[
0
],
targetRelFocalShift
+
best_qb_corr
[
0
],
0.0
,
// targetTiltX, // for testing, normally should be 0 um/mm
0.0
,
// targetTiltX, // for testing, normally should be 0 um/mm
0.0
,
// targetTiltY,
0.0
,
// targetTiltY,
...
@@ -4426,11 +4438,13 @@ public boolean LevenbergMarquardt(
...
@@ -4426,11 +4438,13 @@ public boolean LevenbergMarquardt(
}
}
public
double
[]
getAdjustedMotors
(
public
double
[]
getAdjustedMotors
(
double
[]
zM0
,
// current linearized motors (or null for full adjustment)
double
targetRelFocalShift
,
double
targetRelFocalShift
,
double
targetTiltX
,
// for testing, normally should be 0 um/mm
double
targetTiltX
,
// for testing, normally should be 0 um/mm
double
targetTiltY
,
// for testing, normally should be 0 um/mm
double
targetTiltY
,
// for testing, normally should be 0 um/mm
boolean
motorSteps
){
boolean
motorSteps
){
double
[]
zM
=
fieldFitting
.
mechanicalFocusingModel
.
getZM
(
double
[]
zM
=
fieldFitting
.
mechanicalFocusingModel
.
getZM
(
zM0
,
currentPX0
,
//fieldFitting.getCenterXY()[0],
currentPX0
,
//fieldFitting.getCenterXY()[0],
currentPY0
,
//fieldFitting.getCenterXY()[1],
currentPY0
,
//fieldFitting.getCenterXY()[1],
targetRelFocalShift
,
targetRelFocalShift
,
...
@@ -4516,7 +4530,7 @@ public boolean LevenbergMarquardt(
...
@@ -4516,7 +4530,7 @@ public boolean LevenbergMarquardt(
break
;
break
;
}
}
if
(!
changedEnable
)
{
if
(!
changedEnable
)
{
if
(
debugLevel
>
0
)
System
.
out
.
println
(
"No filter c
hnage, finished in "
+(
n
+
1
)+
" steps"
);
if
(
debugLevel
>
0
)
System
.
out
.
println
(
"No filter c
nange, finished in "
+(
n
+
1
)+
" step"
+((
n
==
0
)?
""
:
"s"
)
);
return
true
;
return
true
;
}
else
{
}
else
{
if
((
was2PrevEnable
!=
null
)
&&
(
prevEnable
!=
null
)
&&
(
was2PrevEnable
.
length
==
prevEnable
.
length
)){
if
((
was2PrevEnable
!=
null
)
&&
(
prevEnable
!=
null
)
&&
(
was2PrevEnable
.
length
==
prevEnable
.
length
)){
...
@@ -4541,7 +4555,7 @@ public boolean LevenbergMarquardt(
...
@@ -4541,7 +4555,7 @@ public boolean LevenbergMarquardt(
private
double
[]
pXY
=
null
;
private
double
[]
pXY
=
null
;
private
boolean
[]
centerSelect
=
null
;
private
boolean
[]
centerSelect
=
null
;
private
boolean
[]
centerSelectDefault
={
true
,
true
};
private
boolean
[]
centerSelectDefault
={
true
,
true
};
p
rivate
MechanicalFocusingModel
mechanicalFocusingModel
;
p
ublic
MechanicalFocusingModel
mechanicalFocusingModel
;
private
CurvatureModel
[]
curvatureModel
=
new
CurvatureModel
[
6
];
// 3 colors, sagittal+tangential each
private
CurvatureModel
[]
curvatureModel
=
new
CurvatureModel
[
6
];
// 3 colors, sagittal+tangential each
private
boolean
[]
channelSelect
=
null
;
private
boolean
[]
channelSelect
=
null
;
private
boolean
[]
mechanicalSelect
=
null
;
private
boolean
[]
mechanicalSelect
=
null
;
...
@@ -6609,9 +6623,44 @@ public boolean LevenbergMarquardt(
...
@@ -6609,9 +6623,44 @@ public boolean LevenbergMarquardt(
}
}
return
m
;
return
m
;
}
}
/**
* Calculate manual screw adjustments for focus/tilt to reduce amount of motor travel (when it is out of limits)
* @param zErr current focal distance error in microns, positive - away from lens
* @param tXErr current horizontal tilt in microns/mm , positive - 1,2 away from lens, 3 - to the lens
* @param tYErr current vertical tilt in microns/mm , positive - 2 away from lens, 1 - to the lens
* @return array of optimal CW rotations of each screw (1.0 == 360 deg)
* Screw locations:
* 5 2
* 3 +
* 4 1
* + - center
* 1,2 M2x0.4 set screws (push)
* 3 - M2x0.4 socket screw (push)
* 4 - M2x0.4 socket screw (pull)
* 5 - M2.5x0.45 screw (pull)
*/
public
double
[]
getManualScrews
(
double
zErr
,
// positive - away from lens
double
tXErr
,
// positive - 1,2 away from lens, 3 - to the lens
double
tYErr
){
// positive - 2 away from lens
double
[][]
screws
={
// right, down, thread pitch (pull)
{
20.5
,
17.5
,
-
0.4
},
{
20.5
,-
17.5
,
-
0.4
},
{-
20.5
,
0.0
,
-
0.4
},
{
0.0
,
17.5
,
0.4
},
{
0.0
,-
17.5
,
0.45
}};
double
[]
moveDownUm
=
new
double
[
screws
.
length
];
double
[]
turnCW
=
new
double
[
screws
.
length
];
for
(
int
i
=
0
;
i
<
screws
.
length
;
i
++){
moveDownUm
[
i
]=
zErr
+
screws
[
i
][
0
]*
tXErr
+
screws
[
i
][
1
]*
tYErr
;
turnCW
[
i
]=
0.001
*
moveDownUm
[
i
]/
screws
[
i
][
2
];
}
return
turnCW
;
}
/**
/**
* Calculate three linearized values of motor positions for current parameters, target center focal shift and tilt
* Calculate three linearized values of motor positions for current parameters, target center focal shift and tilt
* @param zM0 current linearized position (for parallel adjustment) or null for full adjustment
* @param px lens center X (pixels)
* @param px lens center X (pixels)
* @param py lens center Y (pixels)
* @param py lens center Y (pixels)
* @param targetZ target focal shift uin the center, microns, positive - away
* @param targetZ target focal shift uin the center, microns, positive - away
...
@@ -6620,6 +6669,7 @@ public boolean LevenbergMarquardt(
...
@@ -6620,6 +6669,7 @@ public boolean LevenbergMarquardt(
* @return array of 3 linearized motor positions (microns)
* @return array of 3 linearized motor positions (microns)
*/
*/
public
double
[]
getZM
(
public
double
[]
getZM
(
double
[]
zMCurrent
,
// current linearized motors (or null for full adjustment)
double
px
,
double
px
,
double
py
,
double
py
,
double
targetZ
,
double
targetZ
,
...
@@ -6627,6 +6677,16 @@ public boolean LevenbergMarquardt(
...
@@ -6627,6 +6677,16 @@ public boolean LevenbergMarquardt(
double
targetTy
){
double
targetTy
){
double
dx
=
PIXEL_SIZE
*(
px
-
getValue
(
MECH_PAR
.
mpX0
));
double
dx
=
PIXEL_SIZE
*(
px
-
getValue
(
MECH_PAR
.
mpX0
));
double
dy
=
PIXEL_SIZE
*(
py
-
getValue
(
MECH_PAR
.
mpY0
));
double
dy
=
PIXEL_SIZE
*(
py
-
getValue
(
MECH_PAR
.
mpY0
));
if
(
zMCurrent
!=
null
){
// 0.25* zM1+ 0.25* zM2+ 0.5 * zM3 = targetZ-getValue(MECH_PAR.z0);
// 0.25* (zM1+dzM)+ 0.25* (zM2+dzM)+ 0.5 * (zM3+dzM) = targetZ-getValue(MECH_PAR.z0);
// 0.25* (dzM+ 0.25* dzM+ 0.5 * dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
// dzM = targetZ-getValue(MECH_PAR.z0) - (0.25* zM1+ 0.25* zM2+ 0.5 * zM3 );
double
dZM
=
targetZ
-
getValue
(
MECH_PAR
.
z0
)-(
0.25
*
zMCurrent
[
0
]+
0.25
*
zMCurrent
[
1
]+
0.5
*
zMCurrent
[
2
]);
double
[]
zM
=
zMCurrent
.
clone
();
for
(
int
i
=
0
;
i
<
zM
.
length
;
i
++)
zM
[
i
]+=
dZM
;
return
zM
;
}
// double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
// double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
// double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
// double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
// double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//!
// double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//!
...
...
src/main/java/LensAdjustment.java
View file @
f8cffed4
...
@@ -305,6 +305,7 @@ public class LensAdjustment {
...
@@ -305,6 +305,7 @@ public class LensAdjustment {
public
boolean
scanTiltEnable
=
true
;
// enable scanning tilt
public
boolean
scanTiltEnable
=
true
;
// enable scanning tilt
public
boolean
scanTiltReverse
=
false
;
// enable scanning tilt in both directions
public
boolean
scanTiltReverse
=
false
;
// enable scanning tilt in both directions
public
boolean
scanMeasureLast
=
false
;
// Calculate PSF after last move (to original position)
public
int
scanTiltRangeX
=
14336
;
// 4 periods
public
int
scanTiltRangeX
=
14336
;
// 4 periods
public
int
scanTiltRangeY
=
14336
;
// 4 periods
public
int
scanTiltRangeY
=
14336
;
// 4 periods
public
int
scanTiltStepsX
=
24
;
public
int
scanTiltStepsX
=
24
;
...
@@ -520,6 +521,7 @@ public class LensAdjustment {
...
@@ -520,6 +521,7 @@ public class LensAdjustment {
boolean
scanTiltEnable
,
//=true; // enable scanning tilt
boolean
scanTiltEnable
,
//=true; // enable scanning tilt
boolean
scanTiltReverse
,
boolean
scanTiltReverse
,
boolean
scanMeasureLast
,
int
scanTiltRangeX
,
//=14336; // 4 periods
int
scanTiltRangeX
,
//=14336; // 4 periods
int
scanTiltRangeY
,
//=14336; // 4 periods
int
scanTiltRangeY
,
//=14336; // 4 periods
int
scanTiltStepsX
,
//=24;
int
scanTiltStepsX
,
//=24;
...
@@ -663,6 +665,7 @@ public class LensAdjustment {
...
@@ -663,6 +665,7 @@ public class LensAdjustment {
this
.
scanTiltEnable
=
scanTiltEnable
;
//=true; // enable scanning tilt
this
.
scanTiltEnable
=
scanTiltEnable
;
//=true; // enable scanning tilt
this
.
scanTiltReverse
=
scanTiltReverse
;
this
.
scanTiltReverse
=
scanTiltReverse
;
this
.
scanMeasureLast
=
scanMeasureLast
;
this
.
scanTiltRangeX
=
scanTiltRangeX
;
//, //=14336; // 4 periods
this
.
scanTiltRangeX
=
scanTiltRangeX
;
//, //=14336; // 4 periods
this
.
scanTiltRangeY
=
scanTiltRangeY
;
//, //=14336; // 4 periods
this
.
scanTiltRangeY
=
scanTiltRangeY
;
//, //=14336; // 4 periods
this
.
scanTiltStepsX
=
scanTiltStepsX
;
//=24;
this
.
scanTiltStepsX
=
scanTiltStepsX
;
//=24;
...
@@ -807,6 +810,7 @@ public class LensAdjustment {
...
@@ -807,6 +810,7 @@ public class LensAdjustment {
this
.
scanTiltEnable
,
// enable scanning tilt
this
.
scanTiltEnable
,
// enable scanning tilt
this
.
scanTiltReverse
,
this
.
scanTiltReverse
,
this
.
scanMeasureLast
,
this
.
scanTiltRangeX
,
// 4 periods
this
.
scanTiltRangeX
,
// 4 periods
this
.
scanTiltRangeY
,
// 4 periods
this
.
scanTiltRangeY
,
// 4 periods
this
.
scanTiltStepsX
,
this
.
scanTiltStepsX
,
...
@@ -952,24 +956,18 @@ public class LensAdjustment {
...
@@ -952,24 +956,18 @@ public class LensAdjustment {
properties
.
setProperty
(
prefix
+
"scanStep"
,
this
.
scanStep
+
""
);
properties
.
setProperty
(
prefix
+
"scanStep"
,
this
.
scanStep
+
""
);
properties
.
setProperty
(
prefix
+
"scanNumber"
,
this
.
scanNumber
+
""
);
properties
.
setProperty
(
prefix
+
"scanNumber"
,
this
.
scanNumber
+
""
);
properties
.
setProperty
(
prefix
+
"scanNumberNegative"
,
this
.
scanNumberNegative
+
""
);
properties
.
setProperty
(
prefix
+
"scanNumberNegative"
,
this
.
scanNumberNegative
+
""
);
properties
.
setProperty
(
prefix
+
"scanHysteresis"
,
this
.
scanHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"scanHysteresis"
,
this
.
scanHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"scanHysteresisNumber"
,
this
.
scanHysteresisNumber
+
""
);
properties
.
setProperty
(
prefix
+
"scanHysteresisNumber"
,
this
.
scanHysteresisNumber
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltEnable"
,
this
.
scanTiltEnable
+
""
);
// enable scanning tilt
properties
.
setProperty
(
prefix
+
"scanTiltEnable"
,
this
.
scanTiltEnable
+
""
);
// enable scanning tilt
properties
.
setProperty
(
prefix
+
"scanTiltReverse"
,
this
.
scanTiltReverse
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltReverse"
,
this
.
scanTiltReverse
+
""
);
properties
.
setProperty
(
prefix
+
"scanMeasureLast"
,
this
.
scanMeasureLast
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltRangeX"
,
this
.
scanTiltRangeX
+
""
);
// 4 periods
properties
.
setProperty
(
prefix
+
"scanTiltRangeX"
,
this
.
scanTiltRangeX
+
""
);
// 4 periods
properties
.
setProperty
(
prefix
+
"scanTiltRangeY"
,
this
.
scanTiltRangeY
+
""
);
// 4 periods
properties
.
setProperty
(
prefix
+
"scanTiltRangeY"
,
this
.
scanTiltRangeY
+
""
);
// 4 periods
properties
.
setProperty
(
prefix
+
"scanTiltStepsX"
,
this
.
scanTiltStepsX
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltStepsX"
,
this
.
scanTiltStepsX
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltStepsY"
,
this
.
scanTiltStepsY
+
""
);
properties
.
setProperty
(
prefix
+
"scanTiltStepsY"
,
this
.
scanTiltStepsY
+
""
);
properties
.
setProperty
(
prefix
+
"motorHysteresis"
,
this
.
motorHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"motorHysteresis"
,
this
.
motorHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"measuredHysteresis"
,
this
.
measuredHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"measuredHysteresis"
,
this
.
measuredHysteresis
+
""
);
properties
.
setProperty
(
prefix
+
"motorCalm"
,
this
.
motorCalm
+
""
);
properties
.
setProperty
(
prefix
+
"motorCalm"
,
this
.
motorCalm
+
""
);
properties
.
setProperty
(
prefix
+
"linearReductionRatio"
,
this
.
linearReductionRatio
+
""
);
properties
.
setProperty
(
prefix
+
"linearReductionRatio"
,
this
.
linearReductionRatio
+
""
);
properties
.
setProperty
(
prefix
+
"motorDebug"
,
this
.
motorDebug
+
""
);
properties
.
setProperty
(
prefix
+
"motorDebug"
,
this
.
motorDebug
+
""
);
properties
.
setProperty
(
prefix
+
"lensDistanceNumPoints"
,
this
.
lensDistanceNumPoints
+
""
);
properties
.
setProperty
(
prefix
+
"lensDistanceNumPoints"
,
this
.
lensDistanceNumPoints
+
""
);
...
@@ -1217,6 +1215,9 @@ public class LensAdjustment {
...
@@ -1217,6 +1215,9 @@ public class LensAdjustment {
this
.
scanTiltReverse
=
Boolean
.
parseBoolean
(
properties
.
getProperty
(
prefix
+
"scanTiltReverse"
));
this
.
scanTiltReverse
=
Boolean
.
parseBoolean
(
properties
.
getProperty
(
prefix
+
"scanTiltReverse"
));
if
(
properties
.
getProperty
(
prefix
+
"scanMeasureLast"
)!=
null
)
this
.
scanMeasureLast
=
Boolean
.
parseBoolean
(
properties
.
getProperty
(
prefix
+
"scanMeasureLast"
));
if
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeX"
)!=
null
)
if
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeX"
)!=
null
)
this
.
scanTiltRangeX
=
Integer
.
parseInt
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeX"
));
this
.
scanTiltRangeX
=
Integer
.
parseInt
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeX"
));
if
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeY"
)!=
null
)
if
(
properties
.
getProperty
(
prefix
+
"scanTiltRangeY"
)!=
null
)
...
@@ -1364,7 +1365,7 @@ public class LensAdjustment {
...
@@ -1364,7 +1365,7 @@ public class LensAdjustment {
gd
.
addCheckbox
(
"Scan for tilt measurement (approximately preserving center)"
,
this
.
scanTiltEnable
);
gd
.
addCheckbox
(
"Scan for tilt measurement (approximately preserving center)"
,
this
.
scanTiltEnable
);
gd
.
addCheckbox
(
"Scan for tilt measurement in both directions"
,
this
.
scanTiltReverse
);
gd
.
addCheckbox
(
"Scan for tilt measurement in both directions"
,
this
.
scanTiltReverse
);
gd
.
addCheckbox
(
"Calculate PSF after returning to the initial position"
,
this
.
scanMeasureLast
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in X-direction"
,
this
.
scanTiltRangeX
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in X-direction"
,
this
.
scanTiltRangeX
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in Y-direction"
,
this
.
scanTiltRangeY
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in Y-direction"
,
this
.
scanTiltRangeY
,
0
,
7
,
"motors steps"
);
...
@@ -1386,6 +1387,8 @@ public class LensAdjustment {
...
@@ -1386,6 +1387,8 @@ public class LensAdjustment {
this
.
scanTiltEnable
=
gd
.
getNextBoolean
();
this
.
scanTiltEnable
=
gd
.
getNextBoolean
();
this
.
scanTiltReverse
=
gd
.
getNextBoolean
();
this
.
scanTiltReverse
=
gd
.
getNextBoolean
();
this
.
scanMeasureLast
=
gd
.
getNextBoolean
();
this
.
scanTiltRangeX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeY
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeY
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltStepsX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltStepsX
=
(
int
)
gd
.
getNextNumber
();
...
@@ -1518,6 +1521,8 @@ public class LensAdjustment {
...
@@ -1518,6 +1521,8 @@ public class LensAdjustment {
gd
.
addCheckbox
(
"Scan for tilt measurement (approximately preserving center)"
,
this
.
scanTiltEnable
);
gd
.
addCheckbox
(
"Scan for tilt measurement (approximately preserving center)"
,
this
.
scanTiltEnable
);
gd
.
addCheckbox
(
"Scan for tilt measurement in both directions"
,
this
.
scanTiltReverse
);
gd
.
addCheckbox
(
"Scan for tilt measurement in both directions"
,
this
.
scanTiltReverse
);
gd
.
addCheckbox
(
"Calculate PSF after returning to the initial position"
,
this
.
scanMeasureLast
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in X-direction"
,
this
.
scanTiltRangeX
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in X-direction"
,
this
.
scanTiltRangeX
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in Y-direction"
,
this
.
scanTiltRangeY
,
0
,
7
,
"motors steps"
);
gd
.
addNumericField
(
"Full range of scanning motors tilting in Y-direction"
,
this
.
scanTiltRangeY
,
0
,
7
,
"motors steps"
);
...
@@ -1684,6 +1689,7 @@ public class LensAdjustment {
...
@@ -1684,6 +1689,7 @@ public class LensAdjustment {
this
.
scanTiltEnable
=
gd
.
getNextBoolean
();
this
.
scanTiltEnable
=
gd
.
getNextBoolean
();
this
.
scanTiltReverse
=
gd
.
getNextBoolean
();
this
.
scanTiltReverse
=
gd
.
getNextBoolean
();
this
.
scanMeasureLast
=
gd
.
getNextBoolean
();
this
.
scanTiltRangeX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeY
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltRangeY
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltStepsX
=
(
int
)
gd
.
getNextNumber
();
this
.
scanTiltStepsX
=
(
int
)
gd
.
getNextNumber
();
...
...
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