Skip to content
Snippets Groups Projects
Santiago Ospina's avatar
[!3] Resolve "Include more options to initializate stetes"
Santiago Ospina De Los Ríos authored
Merge branch '2-include-more-options-to-initializate-stetes' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

Implements TIFF input data for the solver.

The section model.data is read if defined. It should contain a key assigned to
a path of a valid gayscale tiff of 16 bits. e.g.

    [model.data]
    tiff_data = data/tiff/flower-minisblack-16.tif

The key can be latter used in the initial condition of a compartment as a
function of the **grid** \$x\$ and \$y\$ coordinates. If arguments are out of
bound of the tiff image the function will return 0.

    [model.<compartment>.initial]
    u_0 = tiff_data(x,y)

The arguments of the function may be anything defined on muparser. This is
useful to shift and scale the data. Additionaly, data is interpreted between 0
and 1 depending on the photometric information (*zero_is_white* or
*zero_is_black*). In case data has another scale, its result may be scaled as
any other function in muparser. e.g.

    [model.<compartment>.initial]
    u_0 = 1.3+5.1*tiff_data(2*x, y+0.25)

### Is there something that needs to be double checked?

<!-- Is there something a reviewer should look out for _especially_? -->

No

### Can this MR be accepted?

-   [x] Implemented \...
    -   [x] Generic tiff reader
    -   [x] muParser function for tiff data
-   [x] Added/Updated tests:
    -   [x] Unit test for tiff reader
    -   [x] System test for initial condition
-   [ ] Pipelines passing <!-- please check for new warnings -->
     <!-- change all occurences of <branch> for your branch name -->

    -   [x] [![Build Status]]
    -   [x] [![Build Status][1]]
    -   [ ] [![Build status][2]]

-   [x] Delete branch option set <!-- unless there's a good reason -->

### Related issues

Closes [#2]

<!-- For automatic closing, do not forget the commas between issue numbers-->

<!--
PLEASE READ THIS!

A Merge Request should be associated to a certain task or issue.
Its changes are supposed to be merged into the master branch.

Briefly explain __how__ you achieved the proposal of the task.

IMPORTANT: Make sure to set the merge request WIP if you are not finished yet.
-->

See merge request [!3]

  [Build Status]: https://gitlab.dune-project.org/copasi/dune-copasi/badges/2-include-more-options-to-initializate-stetes/pipeline.svg
  [![Build Status]]: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
  [1]: https://travis-ci.org/SoilRos/dune-copasi.svg?branch=2-include-more-options-to-initializate-stetes
  [![Build Status][1]]: https://travis-ci.org/SoilRos/dune-copasi
  [2]: https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/2-include-more-options-to-initializate-stetes?svg=true
  [![Build status][2]]: https://ci.appveyor.com/project/SoilRos/dune-copasi/history
  [#2]: gitlab.dune-project.org/NoneNone/issues/2
  [!3]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/3


Closes #2
30680ce1
History
Name Last commit Last update
..