demo2D04

[needonature]

in jupyter:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-1-4bdb62cb9c47> in <module>()
     15 filenames = ['/home/murphylab/cellorganizer/demos/2D/demo2D01/lamp2.mat']
     16 
---> 17 img2slml(filenames, options)

TypeError: img2slml() missing 3 required positional arguments: 'cell', 'protein', and 'options'
___
2D04: in jupyter cmd
Warning: Name is nonexistent or not a directory: /home/jovyan/.mcrCache9.2/img2sl0/home/bteo/cellorganizer3/utilities/3D/LDDMM_fast/imrender/vgg
> In path (line 109)
  In addpath (line 88)
  In startup (line 3)
Warning: Name is nonexistent or not a directory: /home/jovyan/.mcrCache9.2/img2sl0/home/bteo/cellorganizer3/utilities/3D/LDDMM_fast/imrender/ojw
> In path (line 109)
  In addpath (line 88)
  In startup (line 4)
Running deployed version of slml2img
Attempting to read input file input.txt
Evaluating lines from input file
Checking selection of nuclear model class/type
Checking selection of cell membrane model class/type
Checking the existence of temporary folder
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell1.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell1.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell1.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell1.tif
Warning: Unable to extract parameters for cell 1: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell2.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell2.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell2.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell2.tif
Warning: Unable to extract parameters for cell 2: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell3.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell3.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell3.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell3.tif
Warning: Unable to extract parameters for cell 3: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell4.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell4.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell4.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell4.tif
Warning: Unable to extract parameters for cell 4: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell5.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell5.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell5.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell5.tif
Warning: Unable to extract parameters for cell 5: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell6.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell6.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell6.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell6.tif
Warning: Unable to extract parameters for cell 6: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell7.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell7.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell7.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell7.tif
Warning: Unable to extract parameters for cell 7: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell8.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell8.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell8.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell8.tif
Warning: Unable to extract parameters for cell 8: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgdna/cell9.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgcell/cell9.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/orgprot/cell9.tif
Reading file /home/murphylab/cellorganizer/images/HeLa/2D/LAM/crop/cell9.tif
Warning: Unable to extract parameters for cell 9: it will be ignored.
> In img2model (line 163)
  In img2slml (line 475)

ans =

    'Error using img2param_2D (line 175)
     Unrecognized protein model type vesicle

     Error in img2param (line 57)

     Error in img2model (line 155)

     Error in img2slml (line 475)'

Check the images exist or that you are using the correct options.
Index exceeds matrix dimensions.

Error in param2model_2D (line 51)

Error in param2model (line 39)

Error in img2model (line 171)

Error in img2slml (line 475)

MATLAB:badsubscript

[needonature]

@icaoberg fixed at branch: 8-demo2D04

[RuijiaChen]

This issue is similar to error of demo2D05, maybe I should check the mallab demo, I also need access to cellorganizer.

[needonature]

@RuijiaChen I have fixed it, see the comment of mine

[icaoberg]

@RuijiaChen check the latest version of the demo on

• http://repositories.compbio.cs.cmu.edu/cellorganizer/cellorganizer3

and update Jupyter notebook.