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pelkmanslab / CellProfilerPelkmans

A fork of CellProfiler1.0 developed by members of Pelkmans Lab https://www.pelkmanslab.org
GNU General Public License v2.0
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LoadImages "the number of images identified for each image type is not equal" #9

Closed ewiger closed 9 years ago

ewiger commented 9 years ago

Can we fix the dataset? i.e. Do we miss any tiff/png files?

Now there is a problem with the amount of images (which indeed gets triggered later in the code). Counting files with "C01." and "C02." and "C03." (the input of LoadImages) yields (also outside of CP) a different amount of files for "C01." and "C02." and "C03."

>> check_missing_images_in_folder: checking /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Prisca/240215_siRNA_SM_TfRecycling_Simple/TIFF/
check_missing_images_in_folder: number of images per well (and timepoint) is as follows:

  Columns 1 through 13

     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0   168   168   168   168   168   168   168   168     0   168
     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0     0     0

  Columns 14 through 24

     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
   168   168     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0
     0     0     0     0     0     0     0     0     0     0     0

check_missing_images_in_folder: dataset looks complete
>> 
filepathsep =

/

Ignoring custom project code support. Path does not exist: /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Prisca/240215_siRNA_SM_TfRecycling_Simple/LIB/MATLAB
PreCluster file contains pipeline only
- loading template handles file
- loading pipeline
  - Loading setting for module 1: LoadImages
  - Loading setting for module 2: IlluminationCorrectionZScoring
  - Loading setting for module 3: IlluminationCorrectionZScoring
  - Loading setting for module 4: IlluminationCorrectionZScoring
  - Loading setting for module 5: IlluminationCorrectionZScoring
  - Loading setting for module 6: Smooth
  - Loading setting for module 7: IdentifyPrimaryIterative
  - Loading setting for module 8: DiscardSinglePixelObjects
  - Loading setting for module 9: Smooth
  - Loading setting for module 10: ExpandOrShrink
  - Loading setting for module 11: IdentifySecondaryIterative
  - Loading setting for module 12: IdentifyTertiarySubregion
  - Loading setting for module 13: ExpandOrShrink
  - Loading setting for module 14: IdentifyTertiarySubregion
  - Loading setting for module 15: SaveSegmentedCells
  - Loading setting for module 16: SaveSegmentedCells
  - Loading setting for module 17: SaveSegmentedCells
  - Loading setting for module 18: MeasureObjectAreaShape
  - Loading setting for module 19: MeasureObjectIntensity
  - Loading setting for module 20: MeasureObjectNeighbors
  - Loading setting for module 21: MeasureTexture
  - Loading setting for module 22: MeasureTexture
  - Loading setting for module 23: MeasureObjectIntensity
  - Loading setting for module 24: CreateBatchFiles
- faking figure number for modules
PreCluster_with_pipeline: searching for .png or .tif images
PreCluster_with_pipeline: 16632 .png images detected, checking handles.Settings.VariableValues

Starting PreCluster analysis
- Running  module 01: LoadImages (t=0s)
Batch Error: LoadImages Error using LoadImages (line 741)
Image processing was canceled in the LoadImages module because the number of images identified for each image type is not equal.  In the window under this box you will see how many images have been found for each image type.
{Error using LoadImages (line 741)
Image processing was canceled in the LoadImages module because the number of
images identified for each image type is not equal.  In the window under this
box you will see how many images have been found for each image type.

Error in LoadImages (line 741)
            error(['Image processing was canceled in the ', ModuleName, '
            module because the number of images identified for each image type
            is not equal.  In the window under this box you will see h
Error in PreCluster_with_pipeline (line 137)
            handles = feval(ModuleName,handles);
} 
>>
ewiger commented 9 years ago

Was a wrong number of images. Indeed