Add support for storing PK maps from OncoQuant

[fedorov]

The idea is to organize results of OncoQuant in the same hierarchy for different options of PK analysis as below:

└── RESOURCES
    ├── 1
    │   └── Reconstructions
    │       ├── 1.nrrd
    │       └── 1.xml
    ├── 100 (where type is SUB)
    │   ├── Reconstructions
    │   │   ├── 100.nrrd
    │   │   └── 100.xml
    │   └── Segmentations
    │        └── readerId-StructureName-datetime.nrrd
    │   ├── OncoQuant
    │       └── version-selectionofaif-MapName-datetime.nrrd

where selectionofaif is one of the following: Auto, ManualLeftArteryROI, ManualRightArteryROI, Model. DCE series should be used to run the analysis, but the results should be saved under SUB series in OncoQuant folder.

The result should be a bash or python script that takes on input the locaiton of PCampReview-style dataset, and adds OncoQuant directory with the maps. The following maps should be saved: Ktrans, ve, BAT, Rsqr, Auc, MaxSlope

[mehrtash]

@fedorov Where is the best place to store the OncoQunt nrrd reconsecration files (nrrd image and dce MR parameters text file)? In the same reconstruction folder(A) or in a separate folder (B)? or probably out of the studies tree?

A:

└── RESOURCES
    ├── 1
    │   └── Reconstructions
    │       ├── 1.nrrd
    │       └── 1.xml
    │       ├── 1_DCE.nrrd
    │       └── 1_DCE_MR_Parameters.txt

B:

└── RESOURCES
    ├── 1
    │   └── Reconstructions
    │       ├── 1.nrrd
    │       └── 1.xml
    │   └── Reconstructions_OncoQuant    
    │       ├── 1.nrrd
    │       └── 1_MR_Parameters.txt

Please also comment on file naming for oncoquant reconstructions. There is also a chance that the new hierarchy structure breaks the rest of PcampReview functionality. E.g. here and other places in utils and so on.

[fedorov]

I think we should keep these reconstructions in OncoQuant folder, side by side with the PK maps. For naming, let's use <series_number>.nrrd and <series_number>_parameters.txt. This should also have less chances of breaking the code, if it is all in OncoQuant folder.

[rweiss42]

+1 Existing code is looking for an OncoQuant dir and I like that there's more of a difference in the dir name. https://github.com/fedorov/PCampReview/blob/master/PCampReview.py#L1151

[fedorov]

apparently, github formatting garbled some of the content.

I meant to say let's use begin quote series number end quote underscore .nrrd for the reconstruction saved in OncoQuant folder, and begin quote series number end quote underscore begin quote parameters end quote .nrrd