"Please input a file path." #128
Description
Upgraded to the new version of CIATAH and now I get "Please input a file path." during preprocess movie. Everything is the same as how I have done it in other versions....
Running: obj.modelPreprocessMovie
Loading MIJI + ImageJ.
Adding to Java path: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\_external_programs\imagej\mij.jar
Warning: Invalid file or directory 'C:\Users\HomePC\OneDrive - Northwestern
University\Documents\ciatah-master\_external_programs\imagej\mij.jar'.
> In javaclasspath>local_validate_dynamic_path (line 271)
In javaclasspath>local_javapath (line 187)
In javaclasspath (line 124)
In javaaddpath (line 71)
In ciapkg.io.manageMiji (line 122)
In ciapkg.api.manageMiji (line 10)
In ciapkg.io.modelAddOutsideDependencies (line 43)
In ciapkg.api.modelAddOutsideDependencies (line 10)
In ciatah/modelPreprocessMovie (line 21)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
Loading MIJI + ImageJ.
Adding to Java path: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\_external_programs\imagej\ij.jar
Warning: Invalid file or directory 'C:\Users\HomePC\OneDrive - Northwestern
University\Documents\ciatah-master\_external_programs\imagej\ij.jar'.
> In javaclasspath>local_validate_dynamic_path (line 271)
In javaclasspath>local_javapath (line 187)
In javaclasspath (line 124)
In javaaddpath (line 71)
In ciapkg.io.manageMiji (line 122)
In ciapkg.api.manageMiji (line 10)
In ciapkg.io.modelAddOutsideDependencies (line 43)
In ciapkg.api.modelAddOutsideDependencies (line 10)
In ciatah/modelPreprocessMovie (line 21)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
matfilePath: ''
matfileVarname: 'thisMovie'
runMatfile: 0
showFigures: 1
folderListPath: {'C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope'}
checkConcurrentAnalysis: 1
concurrentAnalysisFilename: '_currentlyAnalyzingFolderCheck.mat'
processMoviesSeparately: 0
processMovies: 1
loadOptionsFromFile: 0
turboregNumFramesSubset: 3000
turboregType: 'preselect'
turboreg: [1×1 struct]
dfofMovie: 1
dfofType: 'dfof'
downsampleFactor: 4
pxToCrop: 14
fileFilterRegexp: 'concat_.*.h5'
inputPCAICA: 0
askForPCICs: 0
frameList: []
datasetName: '/1'
outputDatasetName: '/1'
refCropFrame: 1
deflateLevel: 1
supportedTypes: {'.h5' '.hdf5' '.tif' '.tiff' '.avi' '.isxd'}
calcDroppedFramesFromMovie: []
minType: 'soft'
minSoftPct: 1.0000e-03
saveMovies: 0
saveDfofMovie: 0
turboregMovie: 1
normalizeMovie: 0
downsampleMovie: 1
logFileRegexp: '(recording.*.(txt|xml)|.*_metadata.mat)'
nwbSettingsDatasetname: '/general/optophysiology/imaging_plane/description'
h5SettingsDatasetname: '/movie/preprocessingSettingsAll'
saveFilePrefix: ''
saveFileSuffix: ''
videoPlayer: 'matlab'
ans =
1
Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead.
> In inputdlg (line 258)
In ciatah/modelPreprocessMovieFunction (line 487)
In ciatah/modelPreprocessMovie (line 42)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
{0×0 char}
{'raw' }
{'/1' }
{'/1' }
{'1' }
{'0' }
{0×0 char}
{0×0 char}
{'matlab'}
{0×0 char}
ans =
struct with fields:
MAIN______________: [1×1 struct]
checkConcurrentAnalysis: [1×1 struct]
resetParallelPool: [1×1 struct]
analyzeFromDisk: [1×1 struct]
calcDroppedFramesFromMovie: [1×1 struct]
REGISTRATION______________: [1×1 struct]
parallel: [1×1 struct]
registrationFxn: [1×1 struct]
turboregRotation: [1×1 struct]
RegisType: [1×1 struct]
numTurboregIterations: [1×1 struct]
turboregNumFramesSubset: [1×1 struct]
pxToCrop: [1×1 struct]
motionCorrectionRefFrame: [1×1 struct]
REGISTRATION_NORMALIZATION______________: [1×1 struct]
normalizeMeanSubtract: [1×1 struct]
normalizeMeanSubtractNormalize: [1×1 struct]
normalizeComplementMatrix: [1×1 struct]
normalizeType: [1×1 struct]
normalizeFreqLow: [1×1 struct]
normalizeFreqHigh: [1×1 struct]
normalizeBandpassType: [1×1 struct]
normalizeBandpassMask: [1×1 struct]
SmoothX: [1×1 struct]
SmoothY: [1×1 struct]
zapMean: [1×1 struct]
MOVIE_NORMALIZATION______________: [1×1 struct]
filterBeforeRegister: [1×1 struct]
saveBeforeFilterRegister: [1×1 struct]
saveFilterBeforeRegister: [1×1 struct]
filterBeforeRegFreqLow: [1×1 struct]
filterBeforeRegFreqHigh: [1×1 struct]
filterBeforeRegImagejFFTLarge: [1×1 struct]
filterBeforeRegImagejFFTSmall: [1×1 struct]
medianFilterSize: [1×1 struct]
MOVIE_DOWNSAMPLING______________: [1×1 struct]
downsampleFactorTime: [1×1 struct]
downsampleFactorSpace: [1×1 struct]
IO_and_MOVIE_IDENTIFICATION______________: [1×1 struct]
inputDatasetName: [1×1 struct]
outputDatasetName: [1×1 struct]
fileFilterRegexp: [1×1 struct]
processMoviesSeparately: [1×1 struct]
loadMoviesFrameByFrame: [1×1 struct]
treatMoviesAsContinuousSwitch: [1×1 struct]
loadMovieInEqualParts: [1×1 struct]
useParallel: [1×1 struct]
nParallelWorkers: [1×1 struct]
STRIPE_REMOVAL______________: [1×1 struct]
stripOrientationRemove: [1×1 struct]
stripSize: [1×1 struct]
stripfreqLowExclude: [1×1 struct]
stripfreqHighExclude: [1×1 struct]
stripfreqBandpassType: [1×1 struct]
ans =
1
:
MAIN______________: {'====================='}
checkConcurrentAnalysis: 0
resetParallelPool: 0
analyzeFromDisk: 0
calcDroppedFramesFromMovie: []
REGISTRATION______________: {'====================='}
mcMethod: 'turboreg'
parallel: 1
registrationFxn: 'transfturboreg'
turboregRotation: 0
RegisType: 1
numTurboregIterations: 1
turboregNumFramesSubset: 5000
pxToCrop: 14
motionCorrectionRefFrame: 100
regRegionUseBtwnSessions: 1
REGISTRATION_NORMALIZATION______________: {'====================='}
normalizeMeanSubtract: 1
normalizeMeanSubtractNormalize: 1
normalizeComplementMatrix: 1
normalizeType: 'bandpass'
normalizeFreqLow: 70
normalizeFreqHigh: 100
normalizeBandpassType: 'bandpass'
normalizeBandpassMask: 'gaussian'
SmoothX: 10
SmoothY: 10
zapMean: 0
MOVIE_NORMALIZATION______________: {'====================='}
filterBeforeRegister: []
saveBeforeFilterRegister: 0
saveFilterBeforeRegister: []
filterBeforeRegFreqLow: 0
filterBeforeRegFreqHigh: 10
filterBeforeRegImagejFFTLarge: 10000
filterBeforeRegImagejFFTSmall: 80
medianFilterSize: 3
MOVIE_DETREND______________: {'====================='}
detrendDegree: 1
MOVIE_DOWNSAMPLING______________: {'====================='}
downsampleFactorTime: 2
downsampleFactorSpace: 3
IO_and_MOVIE_IDENTIFICATION______________: {'====================='}
inputDatasetName: '/1'
outputDatasetName: '/1'
fileFilterRegexp: 'raw'
processMoviesSeparately: 0
loadMoviesFrameByFrame: 0
treatMoviesAsContinuousSwitch: 1
loadMovieInEqualParts: 0
useParallel: 1
nParallelWorkers: 11
largeMovieLoad: 0
STRIPE_REMOVAL______________: {'====================='}
stripOrientationRemove: 'none'
stripSize: 7
stripfreqLowExclude: 20
stripfreqHighExclude: 20
stripfreqBandpassType: 'highpass'
refCropFrame: 100
Saving settings to: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\private\settings\20230419_004031_modelPreprocessMovieFunction_settings.mat.
folderListMinusComments class: double
1/1: C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope
options.fileFilterRegexp: raw
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(1).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(2).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(3).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(4).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(5).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(6).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(7).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(8).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(9).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(10).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(11).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(12).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(13).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(14).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(15).avi
Please input a file path.
>> `