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block transferToServer if a crop is happening
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*.pyc | ||
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btpytools.egg-info/ | ||
build/ | ||
dist/ |
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tests/data/cropping_taking_place/acqLog_SM_1099839.txt
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main: {borderPixSize: 4.0, medFiltRawImage: 5.0, doTiledMerge: true, tiledMergeThresh: 1.05, | ||
defaultThreshSD: 7.0, reCalcThreshSD_threshold: 10.0, rescaleTo: 50.0} | ||
mainBin: {removeNoise: true, medFiltBW: 5.0, primaryShape: disk, primaryFiltSize: 50.0, | ||
expansionShape: square, doExpansion: true, expansionSize: 600.0} | ||
mainGetBB: {minSizeInSqMicrons: 15000.0} | ||
clipper: {doExtension: true, edgeThreshMicrons: 350.0, growROIbyMicrons: 450.0} | ||
mergeO: {mergeThresh: 1.3} | ||
stackStr: {rollingThreshold: true, nImages: 5.0} | ||
autoThresh: {skipMergeNROIThresh: 10.0, doBinaryExpansion: false, minThreshold: 2.0, | ||
maxThreshold: 12.0, allowMaxExtensionIfFewThreshLeft: true, decreaseThresholdBy: 0.9} |
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...place/downsampled_stacks/025_micron/ds_SM_1099839_210521_171144_25_25_ch02_chan_2_red.txt
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Downsampling SM_1099839 | ||
Acquired on: 2021/05/21 17:11:43 | ||
Downsampled: 08-Jun-2021 17:29:28 | ||
downsample file name: downsampled_stacks/025_micron/ds_SM_1099839_210521_171144_25_25_ch02_chan_2_red.tif | ||
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---log--- | ||
Begining to downsample: | ||
x/y: 10.953 | ||
z: 3.968 | ||
Loading and down-sampling x/y by 10.953 | ||
Rescaling in z by 3.9683 | ||
Done |
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...ace/downsampled_stacks/025_micron/ds_SM_1099839_210521_171144_25_25_ch03_chan_3_green.txt
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Downsampling SM_1099839 | ||
Acquired on: 2021/05/21 17:11:43 | ||
Downsampled: 08-Jun-2021 17:31:39 | ||
downsample file name: downsampled_stacks/025_micron/ds_SM_1099839_210521_171144_25_25_ch03_chan_3_green.tif | ||
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---log--- | ||
Begining to downsample: | ||
x/y: 10.953 | ||
z: 3.968 | ||
Loading and down-sampling x/y by 10.953 | ||
Rescaling in z by 3.9683 | ||
Done |
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...place/downsampled_stacks/050_micron/ds_SM_1099839_210521_171144_50_50_ch02_chan_2_red.txt
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Downsampling SM_1099839 | ||
Acquired on: 2021/05/21 17:11:43 | ||
Downsampled: 08-Jun-2021 17:31:39 | ||
downsample file name: downsampled_stacks/050_micron/ds_SM_1099839_210521_171144_50_50_ch02_chan_2_red.tif | ||
Rescaled 25 micron volume by 0.50 to write a 50 micron volume |
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...ace/downsampled_stacks/050_micron/ds_SM_1099839_210521_171144_50_50_ch03_chan_3_green.txt
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Downsampling SM_1099839 | ||
Acquired on: 2021/05/21 17:11:43 | ||
Downsampled: 08-Jun-2021 17:33:47 | ||
downsample file name: downsampled_stacks/050_micron/ds_SM_1099839_210521_171144_50_50_ch03_chan_3_green.tif | ||
Rescaled 25 micron volume by 0.50 to write a 50 micron volume |
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tests/data/cropping_taking_place/recipe_SM_1099839_210521_171144.yml
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Acquisition: {acqStartTime: '2021/05/21 17:11:43'} | ||
sample: {ID: XY_1099839, objectiveName: nikon 16x} | ||
mosaic: | ||
sectionStartNum: 1.0 | ||
numSections: 208.0 | ||
cuttingSpeed: 0.4 | ||
cutSize: 16.0 | ||
sliceThickness: 0.05 | ||
numOverlapZPlanes: 0.0 | ||
numOpticalPlanes: 8.0 | ||
overlapProportion: 0.1 | ||
sampleSize: {X: 8.18, Y: 12.79} | ||
scanmode: 'tiled: auto-ROI' | ||
tilesToRemove: -1.0 | ||
CuttingStartPoint: {X: 33.00001, Y: 0.0} | ||
FrontLeft: {X: 18.42387, Y: 11.11418} | ||
StitchingParameters: | ||
VoxelSize: {X: 2.23, Y: 2.335} | ||
lensDistort: {rows: 0.0, cols: 0.0} | ||
affineMat: | ||
- [1.0, -0.011, 0.0] | ||
- [0.0, 1.0, 0.0] | ||
- [0.0, 0.0, 1.0] | ||
scannerSettingsIndex: 3.0 | ||
NumTiles: {X: 7.0, Y: 11.0} | ||
Tile: {nRows: 562.0, nColumns: 562.0} | ||
TileStepSize: {X: 1.15198, Y: 1.15198} | ||
VoxelSize: {X: 2.278, Y: 2.278, Z: 6.3} | ||
ScannerSettings: | ||
pixelsPerLine: 562.0 | ||
linesPerFrame: 562.0 | ||
micronsBetweenOpticalPlanes: 6.3 | ||
numOpticalSlices: 8.0 | ||
zoomFactor: 1.0 | ||
objectiveResolution: 54.7 | ||
scannerType: RG | ||
pixEqLinCheckBox: true | ||
scanAngleShiftFast: 0.0 | ||
scanAngleShiftSlow: 0.0 | ||
slowMult: 1.0 | ||
fastMult: 1.0 | ||
bidirectionalScan: true | ||
pixelBinFactor: 1.0 | ||
sampleRate: 1.2E8 | ||
fillFractionSpatial: 0.9000000000000001 | ||
FOV_alongColsinMicrons: 1279.98 | ||
FOV_alongRowsinMicrons: 1279.98 | ||
micronsPerPixel_cols: 2.278 | ||
micronsPerPixel_rows: 2.278 | ||
framePeriodInSeconds: 0.036 | ||
activeChannels: [2.0, 3.0] | ||
averageEveryNframes: 1.0 | ||
beamPower: 30.0 | ||
powerZAdjust: true | ||
beamPowerLengthConstant: 500.0 | ||
powerZAdjustType: | ||
- [] | ||
scanMode: resonant | ||
scannerID: ScanImage via SIBT | ||
version: ScanImage(R) Basic 2020.1.4 619cfaf81f on MATLAB 9.7.0.1434023 (R2019b) Update 6 | ||
SYSTEM: | ||
ID: brainsaw | ||
xySpeed: 35.0 | ||
cutterSide: 1.0 | ||
defaultFrontLeft: [12.5, 10.0] | ||
homeZjackOnZeroMove: 1.0 | ||
type: bakingtray | ||
version: branch=dev commit=cb5caae318258027f4a41ee123c60aa66413b07a | ||
SLICER: {approachSpeed: 25.0, vibrateRate: 9.0, postCutDelay: 6.0, postCutVibrate: 3.0} | ||
SLACK: {user: '@BrainSaw', hook: 'https://hooks.slack.com/services/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'} |
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