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murphygroup / docker-cellorganizer-jupyter-notebook

CellOrganizer on Jupyter Notebook
http://www.cellorganizer.org
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Issue with demo2D06 #39

Closed icaoberg closed 5 years ago

icaoberg commented 5 years ago

I will remove this demo from this distribution. Please fix in next release

[I 02:10:46.717 NotebookApp](B Saving file at /demos/2D/demo2D06/demo2D06.ipynb
Running deployed version of slml2img
Attempting to read input file input.txt
Evaluating lines from input file
Setting synthesis option
Checking existence of log folder
Checking the validity of input files
Parsing SLML instancesChecking existence of temporary folder
Temporary folder found in /home/murphylab/cellorganizer/demos/2D/demo2D06/temp. Removing all temporary files.
Setting target directory to /home/murphylab/cellorganizer/demos/2D/demo2D06
Setting prefix to: img
Setting number of synthesized images to 1
Setting compression to lzw
Checking all models have the same dimensionality
Setting protein model resolution
Protein model object(s) resolution set to   
Synthesizing image 1. Please wait, this might take several minutes.
Setting model dimensionality to 2D
Checking all models have the same dimensionality
Reference to non-existent field 'pca_synthesis_method'.
Error in model2framework (line 183)
Error in model2img (line 300)
Error in slml2img (line 483)
MATLAB:nonExistentField

However it works on Matlab

>> demo2D06;
demo2D06
The estimated running time is 1 minute. Please wait.
Setting synthesis option
Checking existence of log folder
Checking the validity of input files
Parsing SLML instancesChecking existence of temporary folder
Creating temporary folder in /Users/icaoberg/code/cellorganizer3/demos/2D/demo2D06/temp
Setting target directory to /Users/icaoberg/code/cellorganizer3/demos/2D/demo2D06
Setting prefix to: img
Setting number of synthesized images to 1
Setting compression to lzw
Checking all models have the same dimensionality
Setting protein model resolution
Protein model object(s) resolution set to   
Synthesizing image 1. Please wait, this might take several minutes.
Setting model dimensionality to 2D
Checking all models have the same dimensionality
Loading /Users/icaoberg/code/cellorganizer3/demos/2D/demo2D06/temp/channel1.tif
Image size is 618  679
Loading /Users/icaoberg/code/cellorganizer3/demos/2D/demo2D06/temp/channel2.tif
Image size is 618  679
PhysicalSizeZ not set. Assuming you are attempting to create a 2D image
Removing temporary folder
Removing temporary files
Closing log file
Finished synthesis
icaoberg commented 5 years ago

The issue was related to demo2D05 not running properly.