Devin OKelly (3c5509ba) at 13 Sep 14:43
Added RAFT_README and example spectra
... and 10 more commits
Devin OKelly (312f0108) at 27 Apr 13:45
Fix single quotes for other parse path
Devin OKelly (312f0108) at 27 Apr 13:37
Fix single quotes for other parse path
Devin OKelly (f217e54d) at 27 Apr 13:22
Remove single quotes in endmember strings
Once again this is a case where moving to Python would be a good idea, since pandas
and xarray
both offer dimensionally-labeled arrays that would be helpful here.
Xarray would be needed for anything larger than 2 dimensions.
Multi-indexing is also supported, which helps for things like kroneckerized representations of tensors.
Must be aware of the possible applications:
We want to be able to describe coordinate systems and then abstractly use those for making abstract mappings. A specific algorithm is then an implementation of that mapping. A direct mapping may require certain parameters (e.g. speed of sound for backprojection), while an inverse mapping requires a forward model as well as distinct parameters for the solver itself.
We want to be able to relate different coordinate systems for e.g. transformations. For example, being able to calculate the distance between two coordinate systems which are just Z-slices of a 3-D object. Similarly, if we have a target coordinate system which is 3-D and axis-aligned, and a source which is a 2-D slice but skewed, we may want to splat the 2-D slice to the 3-D system with minimal loss of info.
This is something we'd want to be able to do automatically and efficiently (e.g. calling FFT on a dataframe should give the FFT of that data frame as well as transforming the units and domain of the coordinate system).
-There must be a way to describe scale-space representations, especially wavelet transformations.
Need a container for describing bulk data. Looking at the XDR and related standards may be particularly helpful.
A coordinate system should be an abstract thing which is associated with a dataframe.
There are many considerations: Explicit coordinates (e.g. every single element is treated as independent, so for NxM (y,x) frame you have NM x coordinates and NM y coordinates). This is effectively identical to the point cloud representation. Implicit rectilinear coordinates (e.g. the coordinates are stored elsewhere and per-element coordinates derived based on indices of elements).
Global/absolute coordinate systems vs. object coordinate systems.
Different coordinate systems, conversion between representations. e.g. if I have a cartesian coordinate system, what if I want all of the elements converted into a polar coordinate system? What about cylindrical/spherical?
Element pitch - size of each element (e.g. pixel size)
Differential domain (e.g. is the pixel representing point-sampled data? Is it showing integrated densities? Is it representing gradients?)
Units - of coordinates (e.g. time (s) or time (us)) and of data elements (e.g. pressure, microvolts)
Domain (e.g. R, R^+, Complex numbers)
Gauge/metric (given two elements, how close are they in space. Separate but related, given two elements, how similar are they?)
Interpolation - To a specific set of coordinates, or to a specific number of elements (e.g. 256 sample points, interpolate to 350 over the same span).
Devin OKelly (986fe0c8) at 12 Jan 16:15
Fix escaped slashes in sed output for params.json
Devin OKelly (f33b25b5) at 12 Jan 12:02
Add inline sed to fix parsing of double quotes in params.json
Devin OKelly (662c2274) at 18 Dec 12:10
Included minimum_astrocyte_version in astrocyte_pkg.yml
Devin OKelly (5d024034) at 18 Dec 11:57
Included nextflow_version in astrocyte_pkg.yml
Devin OKelly (ae99a0f8) at 18 Dec 11:19
Force gitlab to add matlab module
Devin OKelly (a22490d9) at 18 Dec 11:14
Change nextflow endmember list management to accommodate astrocyte ...
Devin OKelly (6aca9666) at 07 Dec 12:41
Modifications to test for astrocyte 0.4.0
Devin OKelly (e6ba292e) at 07 Dec 11:44
Cleaned up gitignore to reject Nextflow stuff
... and 2 more commits
Devin OKelly (dbbca437) at 02 Dec 17:14
Switch to double quotes in astrocyte_pkg unmixing endmembers.
Devin OKelly (9f5aa456) at 02 Dec 13:14
Modified gitlab CI to no longer pull to handle new gitlab version