saving of hidden files that are not updated with changes to heuristic

[nipy]

saving of hidden files that are not updated with changes to heuristic

[satra]

noted - we did a big merge with a large number of changes. time to clean up the changes from this.

[yarikoptic]

This I think bitten me as well a few times. But I just found peace of mind with it as a feature ;-)

[satra]

@poldrack - as we move forward with this codebase, we will be bringing in a few more things.

• change in heuristic | heudiconv | environment will trigger a regeneration. at present there are two primary sources of difference: heuristic, dcm2niix but changes could come from heudiconv itself as well.
• integration of dcmstack into nibabel and/or extraction of features via other means

i think the biggest drawback from a testing standpoint is the absence of sufficient varied dicom datasets.

[yarikoptic]

I think that the problem is also due to trying to address two target use-cases:

• original two stage:
  1. generate .edit.txt with mapping to be adjusted if needed
  2. run actual conversion
• single stage:
  1. convert what is given without giving even a chance to adjust anything

The "single stage" is kinda my use-case which I added later, while "original two stage" is what Satra+Michael envisioned/implemented originally. And ATM it is not clear when heudiconv performs in two stage or a single stage scenario.
In my case, I am trying to avoid silent 're-conversion' since it could lead to spurious files laying around left from previous attempts with previous heuristic and inconsistent conversion altogether. That is why added explicit --overwrite flag to instruct when I explicitly want to overwrite previous results of the conversion, and otherwise to crash if any files tries to override any previous present file (be it a converted or a heuristic file).

I think we should sit down (during code rodeo) and outline major use-cases/workflows we would like to see supported, and make them clear(er) presented in API/documentation.

[satra]

@yarikoptic - sounds like a good discussion topic for code rodeo.