Skip to content

Commit

Permalink
Merge pull request #267 from bls337/main
Browse files Browse the repository at this point in the history 
remove commented code
  • Loading branch information
@bls337
bls337 authored Apr 18, 2024
2 parents f2f69cc + dd72767 commit 296a098
Show file tree
Hide file tree
Showing 2 changed files with 2 additions and 150 deletions.
150 changes: 1 addition & 149 deletions src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -116,155 +116,7 @@ public boolean prepareControllerForAcquisitionOffsetOnly(
return true;
}

// /**
// * Sets all the controller's properties according to volume settings
// * and otherwise gets controller all ready for acquisition
// * (except for final trigger).
// *
// * @param settings
// * @param channelOffset
// * @return false if there was some error that should abort acquisition
// */
// public boolean prepareControllerForAcquisition(
// final DefaultAcquisitionSettingsDISPIM settings,
// final double channelOffset) {
// // turn off beam and scan on both sides (they are turned off by SPIM state machine anyway)
// // also ensures that properties match reality at end of acquisition
// // SPIM state machine restores position of beam at end of SPIM state machine, now it
// // will be restored to blanking position
// scanner_.setBeamOn(false);
// //scanner2_.setBeamOn(false);
// scanner_.sa().setModeX(SingleAxis.Mode.DISABLED);
// //scanner2_.sa().setModeX(SingleAxis.Mode.DISABLED);
//
// final int numViews = settings.volumeSettings().numViews();
// final int firstView = settings.volumeSettings().firstView();
//
// // set up controller with appropriate SPIM parameters for each active side
// // some of these things only need to be done once if the same micro-mirror
// // card is used (as is typical) but keeping code universal to handle
// // case where MM devices reside on different controller cards
// // Note: firstView starts counting from 1...n views
// if (numViews > 1 || firstView == 1) {
// final boolean success = prepareControllerForAcquisitionSide(settings, 1, channelOffset, false);
// if (!success) {
// return false;
// }
// }
// if (numViews > 1 || firstView != 1) {
// final boolean success = prepareControllerForAcquisitionSide(settings, 2, channelOffset, false);
// if (!success) {
// return false;
// }
// }
//
// if (settings.isUsingStageScanning()
// && settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED) {
// if (numViews != 2) {
// studio_.logs().showError("Interleaved stage scan only possible for 2-sided acquisition.");
// return false;
// }
// if (settings.cameraMode() == CameraMode.OVERLAP) {
// studio_.logs().showError("Interleaved stage scan not compatible with overlap camera mode");
// return false;
// }
// }
//
// // make sure set to use TTL signal from backplane in case PLOGIC_LASER is set to PLogicMode different from diSPIM shutter
// plcCamera_.setPreset(12);
// plcLaser_.setPreset(12);
//
// // make sure shutter is set to the PLOGIC_LASER device
// try {
// core_.setShutterDevice(plcLaser_.getDeviceName());
// } catch (Exception e) {
// studio_.logs().showError("could not set shutter to " + plcLaser_.getDeviceName());
// }
//
// if (settings.isUsingStageScanning()) {
// // scanning with ASI stage
// // algorithm is as follows:
// // use the # of slices and slice spacing that the user specifies
// // because the XY stage is 45 degrees from the objectives have to move it sqrt(2) * slice step size
// // for now use the current X position as the start of acquisition and always start in positive X direction
// // for now always do serpentine scan with 2 passes at the same Y location, one pass each direction over the sample
// // => total scan distance = # slices * slice step size * sqrt(2)
// // scan start position = current X position
// // scan stop position = scan start position + total distance
// // slow axis start = current Y position
// // slow axis stop = current Y position
// // X motor speed = slice step size * sqrt(2) / slice duration
// // number of scans = number of sides (1 or 2)
// // scan mode = serpentine for 2-sided non-interleaved, raster otherwise (need to revisit for 2D stage scanning)
// // X acceleration time = use whatever current setting is
// // scan settling time = delay before side
//
// double actualMotorSpeed;
//
// // figure out the speed we should be going according to slice period, slice spacing, geometry, etc.
// final double requestedMotorSpeed = computeScanSpeed(settings, scanner_.getSPIMNumScansPerSlice()); // in mm/sec
//
// final boolean isInterleaved = (settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED);
//
// final float maxSpeed = xyStage_.getMaxSpeedX();
// if (requestedMotorSpeed > maxSpeed * 0.8) {
// // trying to go near max speed smooth scanning will be compromised
// studio_.logs().showError("Required stage speed is too fast, please reduce step size or increase sample exposure.");
// return false;
// }
// if (requestedMotorSpeed < maxSpeed / 2000) {
// // 1/2000 of the max speed is approximate place where smooth scanning breaks down (speed quantum is ~1/12000 max speed);
// // this also prevents setting to 0 which the controller rejects
// studio_.logs().showError("Required stage speed is too slow, please increase step size or decrease sample exposure.");
// return false;
// }
// xyStage_.setSpeedX(requestedMotorSpeed);
//
// // ask for the actual speed to calculate the actual step size
// actualMotorSpeed = xyStage_.getSpeedXUm() / 1000;
//
// // set the acceleration to a reasonable value for the (usually very slow) scan speed
// xyStage_.setAccelerationX(computeScanAcceleration(actualMotorSpeed,
// xyStage_.getMaxSpeedX(), settings.scanSettings().scanAccelerationFactor()));
//
// int numLines = settings.volumeSettings().numViews();
// if (isInterleaved) {
// numLines = 1; // assure in acquisition code that we can't have single-sided interleaved
// }
// numLines *= ((double) settings.numChannels() / computeScanChannelsPerPass(settings));
// xyStage_.setScanNumLines(numLines);
//
// final boolean isStageScan2Sided = (settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN) && settings.volumeSettings().numViews() == 2;
// xyStage_.setScanPattern(isStageScan2Sided ? ASIXYStage.ScanPattern.SERPENTINE : ASIXYStage.ScanPattern.RASTER);
//
// if (xyStage_.getAxisPolarityX() != ASIXYStage.AxisPolarity.NORMAL) {
// studio_.logs().showError(
// "Stage scanning requires X axis polarity set to " + ASIXYStage.AxisPolarity.NORMAL);
// return false;
// }
//
// if (settings.isUsingMultiplePositions()) {
// // use current position as center position for stage scanning
// // multi-position situation is handled in position-switching code instead
// Point2D.Double p = xyStage_.getXYPosition();
// // TODO: error if getXYPosition fails (return null?)
// // TODO: prepareStageScanForAcquisition(p.x, p.y, settings.getSPIMMode())
// prepareStageScanForAcquisition(p.x, p.y, settings);
// }
// } else {
// scanDistance_ = 0;
// }
//
// // sets PLogic "acquisition running" flag
// plcCamera_.setPreset(3);
// plcLaser_.setPreset(3);
//
// studio_.logs().logMessage("Finished preparing controller for acquisition with offset " + channelOffset +
// " with mode " + settings.acquisitionMode() + " and settings:\n" + settings);
// return true;
// }

public boolean prepareControllerForAcquisitionSCAPE(
public boolean prepareControllerForAcquisition(
final DefaultAcquisitionSettingsSCAPE settings,
final double channelOffset) {
// turn off beam and scan on both sides (they are turned off by SPIM state machine anyway)
Expand Down
2 changes: 1 addition & 1 deletion ...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -811,7 +811,7 @@ private boolean doHardwareCalculations(PLogicSCAPE plc) {
}

double extraChannelOffset = 0.0;
plc.prepareControllerForAcquisitionSCAPE(acqSettings_, extraChannelOffset);
plc.prepareControllerForAcquisition(acqSettings_, extraChannelOffset);
return true;
}

Expand Down

0 comments on commit 296a098

Please sign in to comment.