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Base64 I/O for Paraview and XML #634

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Base64 I/O for Paraview and XML #634

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jzwar
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@jzwar jzwar commented Aug 31, 2023 •
edited by filiatra

Motivation

Although I was aware of the gismo-PR #236, I saw that there has not been an update since 2018 and it also relies on an external library. Further, it only acted on the XML-files without support for Paraview exports.

The need to redo the implementation of this feature originated as we had fields with very small magnitudes, which is very tedious with fixed-point string conversion.

Implementation

The implementation is based on this, which I implemented as an interface to @j042's python library splinepy. It relied on c++17 features, so adaptations were required, and further overloads for gsMatrix were added. The ToVTK-function was updated accordingly.

Details

  • Moved functions related to GoTools into a separate file, although it seems to be used nowhere (?)
  • Added a new class of static functions only for base64 encoding and decoding
  • Added base64 option to Paraview collection and added argument to toVTK
  • Updated some variable names to make code clearer, formatted modified sections
  • XML I/O

Complementary

I would add the following, should there be a demand for it:

  • Support KnotVectors in XML input
  • Tests for De/Encoding (they already exist, but I did not know where to put them)

@jzwar jzwar requested a review from a team as a code owner August 31, 2023 16:04
@mmoelle1
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mmoelle1 commented Sep 1, 2023

I think that adding base64 support for the knot vectors would be very good. We are planning to implement something similar to the Geometry tag to write solutions as native spline objects in XML. These solutions will often have many coefficients and hence benefit largely from base64 support.

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jzwar commented Sep 12, 2023

I think that adding base64 support for the knot vectors would be very good. We are planning to implement something similar to the Geometry tag to write solutions as native spline objects in XML. These solutions will often have many coefficients and hence benefit largely from base64 support.

Done and rebased

@jzwar
Create new Base64 class in gsIOUtils
a37f0d8 
- create new file
- rename old gsIOUtils to gsGoTools
- move actual utils into gsIOUtils
@jzwar
Update deprecated paths and file header
3fcc582
@jzwar
First working example with b64 export
859df76
@jzwar
Extend export for fields and expressions
9cbf01d
@jzwar
Copy pasting issue
43b148b
@jzwar
Support binary import for Geometry and Matrix data using format flag
cb2922c
@jzwar
Paraview is case insensitive, so flags should be too
a1fe41b
@jzwar
Update Code style on changed lines
5dae090
@jzwar
Added b64 encoded file for poisson example
6452695
@jzwar
Add knot-vector parsing (change layout of gsIOUtils)
fe24793
@jzwar
Bugfix, did not call lambda after definition
d403316
@jzwar
Update Documentation
39bc094
@jzwar
Solve linker issue by placing B64 into a seperate header
ef66e6c
@jzwar
Reformat to gismo style guide (tab 2->tab 4) to minimize changes
dde2c64
@jzwar jzwar mentioned this pull request Feb 9, 2024
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@filiatra
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filiatra commented Mar 6, 2024

Very usefull !
Tests can go in a new file inside /unittests
Please set in cmake GISMO_BUILD_UNITTESTS=ON
to be able to compile (make unitttestss) and run (./bin/unittests) the unittests.

@jzwar
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jzwar commented Mar 10, 2024 •
edited

@filiatra As discussed, I looked into the structure date is currently written to file. Adding a flag to gsFileData will not be sufficient. Streaming a file into gsFileData calls the put function, which is non-member. So, as far as I can see, no trivial way to add format flags to the output of the children without changing the layout of every put function.

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OK then let's go on with this one as it is and let the writing for later.

filiatra
filiatra requested changes Mar 25, 2024
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src/gsIO/gsXml.hpp
base_type_flag_.reserve(base_type_flag.size());
std::transform(base_type_flag.cbegin(), base_type_flag.cend(),
std::back_inserter(base_type_flag_),
[](unsigned char c) { return std::tolower(c); });
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Please use "::tolower" instead of "std::tolower" because some windows compiles like it better.

src/gsNurbs/gsKnotVector.hpp
std::string format_flag = format ? format->value() : "ascii";
std::transform(format_flag.cbegin(), format_flag.cend(),
format_flag.begin(),
[](unsigned char c) { return std::tolower(c); });
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Please use "::tolower" instead of "std::tolower" because some windows compiles like it better.

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@jzwar @mmoelle1 @filiatra